Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures: Research on COVID- 19 (Springer Series in Biophysics, 23) 3031367723, 9783031367724

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Springer Series in Biophysics  23

Jiapu Zhang

Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures Research on COVID- 19

Springer Series in Biophysics Volume 23

Series Editor Boris Martinac, Molecular Cardiology & Biophysics, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia

The “Springer Series in Biophysics” spans all areas of modern biophysics, such as molecular, membrane, cellular or single molecule biophysics. More than that, it is one of the few series of its kind to present biophysical research material from a biological perspective. All postgraduates, researchers and scientists working in biophysical research will benefit from the comprehensive and timely volumes of this well-structured series.

Jiapu Zhang

Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures Research on COVID- 19

Jiapu Zhang Institute of Innovation, Science and Sustainability (IISS), School of IT and Applied Mathematics, Sciences and Engineering Federation University Ballarat, VIC, Australia

ISSN 0932-2353 ISSN 1868-2561 (electronic) Springer Series in Biophysics ISBN 978-3-031-36772-4 ISBN 978-3-031-36773-1 (eBook) https://doi.org/10.1007/978-3-031-36773-1 © The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland AG 2023 This work is subject to copyright. All rights are solely and exclusively licensed by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors, and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, expressed or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. This Springer imprint is published by the registered company Springer Nature Switzerland AG The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland Paper in this product is recyclable.

Dedicate to my mother Xian’ai LIU

Preface

Let us first briefly introduce the three classes of proteins of SARS-CoV-2: the structural proteins (SPs), the non-structural proteins (NSPs), and the accessory proteins (APs). Coronaviruses (CoVs) are viruses with a spherical positive single-stranded RNA envelope assigned to .α, β, γ , and .δ genera. SARS-CoV-2 of COVID-19 belongs to the .β genus. SARS-CoV-2 has a positive viral RNA genome expressing open reading frames (ORFs) that code for 4 SPs, 16 NSPs, and about 7 accessory proteins (ORF1a, ORF1ab, ORF3a, ORF6, ORF7a, ORF7b, ORF8, ORF9b, ORF9c, and ORF10). The four SPs of .β-CoV are envelope protein (E-protein), membrane glycoprotein (M-protein), nucleocapsid phosphoprotein (N-protein), and spike glycoprotein (S-protein), and mediation of coronavirus host infection is established by S-protein, where S-protein has a Receptor-Binding Domain (RBD) S1 that mediates the binding to host cell receptor, the Angiotensin Converting Enzyme 2 (ACE2), while the S2 subunit of S-protein promotes membrane fusion. The SPs are bound to the RNA in the N-protein or to the lipid bilayer membrane of the viral envelope, where the lipid bilayer proteins include the E-protein, Mprotein, and S-protein. The N-protein is composed of a serine-rich linker region sandwiched between N-Terminal Domain (NTD) and C-Terminal Domain (CTD); these terminals play a role in viral entry and its processing post entry. The NTD forms orthorhombic crystals and binds to the viral genome. The linker region contains phosphorylation sites that regulate its functioning. The CTD promotes nucleocapsid formation. The E-protein contains an NTD, hydrophobic domain, and CTD which form viroporins needed for viral assembly. The M-protein possesses hydrophilic C-terminal and amphipathic N-terminal; its long-form promotes spike incorporations and the interaction with E facilitates virion production. SPs are encoded within the 3’ end of the genome. During COVID-19, there appears variants of SPs. Among the SPs, S-protein and N-protein accumulated a larger number of mutations whereas E- and M-proteins are mostly conserved. In terms of mutational changes, E- and M-proteins are relatively more stable than N- and S-proteins. Several co-occurrence substitutions are observed, particularly in S- and N-proteins. Substitution specific to active sub-domains reveals that heptapeptide repeat, fusion peptides, transmembrane in Svii

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protein, and NTD and CTD in N-protein are remarkably mutated. A few deleterious mutations in the above domains are also observed. The NSPs of SARS-CoV-2, the highly conserved components in the life cycle of CoVs, are named as NSP1 to NSP16 and they act as enzymes, coenzymes, and binding proteins to facilitate the replication, transcription, and translation of the virus. The 16 NSPs are the leader protein (NSP1), the NSP2, the papain-like protease (PLpro, NPS3), the NSP4, the 3C-like protease (or called main protease, 3CLpro, Mpro, NSP5), the NSP6, the NSP7, the NSP8, the replicase protein (NSP9), the NSP10, the NSP11, the RNA-directed RNA polymerase (RdRp, NSP12) – RdRp variant P323L, the RNA-helicase (NSP13), the guanine-N7 methyltransferase protein (MTase, NSP14), the uridylate-specific endonuclease/endoribonuclease protein (NSP15), the 2’-O-methyltransferase (NSP16), and their complexes. The APs of SARS-CoV-2 participate in the viral replication, assembly, and virus-host interactions. The SARS-CoV-2 accessory proteins are ORF1a, ORF1ab, ORF3a, ORF4a, ORF6, ORF7a, ORF7b, ORF8, ORF9b, ORF9c, and ORF10. Mutations in ORF1ab, ORF3, ORF6, and ORF8 are observed during the COVID-19. Because APs have too much variation between viruses, APs are not good drug targets. Hence, two types of anti-coronavirus drug targets are: S-, E-, M-, and Nproteins of SPs (especially the S-protein) and NSP1-NSP16 of NSPs (especially the 3CLpro (NSP5), RdRp (NSP12), PLpro (NSP3), and helicase protein (NSP13)). Therefore, the search for drug development targets and repositioning of existing therapeutics is essential for fighting the present COVID-19 pandemic. This book studies the following proteins and their drug bindings: PLpro, 3CLpro, RdRp, RNA-helicase, RNA-helicase binding with NSP12-ADTPMg2, RNA-helicase binding with ADTPMg2, spike, D614G mutant, N501Y mutant, N165A-and-N234A mutant, SARS, MERS, human-ACE2, human-L6, humanL6R, PLpro-monomer binding with 12 drugs, 3CLpro-monomer binding with drugs, 3CLpro-dimer binding with drugs, S-protein binding with 50 drugs, humanACE2 binding with 78 drugs, S-protein and human-ACE2 binding with 100 drugs, E-protein, M-protein, N-protein, RNA genome, NSP7, NSP8, NSP9, NSP10, NSP10-NSP16 complex, NSP16, NSP10-NSP14 complex, NSP14, NSP15, and other-mutants (including alpha-, alpha1-, alpha2-, beta-, delta-, epsilon-, gamma-, kappa-, omicron-variants). Vaccines (such as Pfizer, Moderna, AstraZeneca, Janssen, Sinopharm, Covaxin, Novavax, Icosavax), drugs, antigen rapid test (ART), pandemic mathematical models (including time-delays models), epidemiology and virus origins etc. are also introduced in this book. This book first did local optimization (because of the three-body movement) of each molecular structure. The optimized structure is at a transition state with the best stability and the lowest energy. The hybrid strategy of mathematical optimization’s neighboring different (local search) algorithms is used. The optimization strategy will significantly reduce the scale of data and at the same time get rid of useless bioinformatics. To really understand the stability of molecules and their action mechanism, we should consider not only the static NMR, X-ray, or cryo-EM structures concerned but also the dynamical information obtained by Molecular Dynamics (MD) or Quantum Mechanics/Molecular Mechanics (QM/MM) simu-

Preface

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lating their internal motions or dynamic process. Secondly, for each protein, we will confirm the structural bioinformatics gotten from the optimized structure by analyzing the large-scale MD trajectory databases, where all the MD trajectory databases are the ones that can be openly and freely available on-line. The strong network of hydrogen bonds and hydrophobic interactions along with van der Waals interactions inhibit receptors, which are essential to the entry and replication of the SARS-CoV-2. Basic structural bioinformatics such as hydrogen bonds, salt bridges, .π -interactions, secondary structures, RMSD and RMSF etc. of each SARS-CoV-2 protein are presented in this book. Biological mathematics models are also studied in this book. To understand this book needs some basic knowledge on biochemistry, biophysics, biomedicine, mathematical optimization and statistical analysis, etc.; we list the basic knowledge as the Appendix. The intended audiences of this book are researchers in computational biochemistry, computational biophysics, optimization and molecular dynamics, structural bioinformatics, biological mathematics, statistical analysis, etc. Clearly, structurebased drug designing or discovery research staff will be also benefited from some original results of this book. For students or teachers, they might also quickly know all the molecular structures and their structural dynamics of SARS-CoV-2. As an accessible introduction to these fields, this book is also ideal as a teaching material for students. Acknowledgments This research (with project no. pb04 at Federation University Australia and under NCI) was undertaken with the assistance of resources and services from the National Computational Infrastructure (NCI), which is supported by the Australian Government. I wish to thank all those who have helped me in one way or another. This book systematically united my research results during COVID19 pandemic years but without any research fund support; thus, I am deeply in debt to my wife Grace Xiao-Yan Yuan for her patience and accompany during this research. Last but not least, Springer Nature’s team are gratefully acknowledged; Professors Dzalilov Z, Bagirov AM et al. are also gratefully acknowledged for their kind help, support and encouragement. Ballarat, VIC, Australia April, 2023

Jiapu Zhang

Contents

1

Papain-Like Cysteine Protease (PLpro). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.2 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.3 Structural Bioinformatics Results and Discussions . . . . . . . . . . . . . . . 1.3.1 Monomer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.3.2 Dimer Without Inhibitor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.3.3 The C111S Mutant . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.3.4 Compared with SARS-CoV-1-PLpro . . . . . . . . . . . . . . . . . . . . 1.3.5 Inhibitors S43, GRL0617, XR8-89, JUN9-84-3, and JUN9-72-2 Bindings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.4 Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

1 1 2 3 3 6 8 9 10 11

2

3C-Like Protease (3CLpro) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.2 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.2.1 Monomer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.2.2 Dimer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.3 Results and Discussions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.3.1 Monomer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.3.2 Dimer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.3.3 Comparison with SARS-CoV-1-Mpro . . . . . . . . . . . . . . . . . . . 2.3.4 Comparison with SARS-CoV-1-Mpro-N3 . . . . . . . . . . . . . . . 2.3.5 Variants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.4 Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

33 33 34 34 34 35 35 39 55 56 59 61

3

RNA-Dependent RNA Polymerase (RdRp) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3.2 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3.3 New Results and Discussions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3.4 Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

161 161 162 163 170

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4

RNA Helicase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4.2 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4.3 New Results and Discussions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4.4 Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

195 195 196 196 203

5

RNA Helicase Binding with RdRp, NSP7, NSP8a, NSP8b, pRNA, tRNA, .ADP-Mg2+ , and .ATP-Mg2+ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5.2 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5.3 New Results and Discussions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5.4 Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

227 227 228 228 231

RNA Helicase Binding with ADP-Mg2+ , ATP-Mg2+ , and RNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6.2 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6.3 New Results and Discussions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6.4 Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

243 243 244 244 246

6

7

8

Spike (S) Glycoprotein . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7.2 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7.2.1 Trimeric SARS-CoV-2 S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7.2.2 Human ACE2. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7.2.3 Binding of SARS-CoV-2 S-RBD and Human ACE2 . . . . 7.3 Results and Discussions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7.3.1 The 6VXX (SARS-CoV-2 S Close) Model: Model1 . . . . 7.3.2 The 6VYB (SARS-CoV-2 S with One SB Open) Model: Model2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7.3.3 The 1R4L (ACE2 Close) Model: Model3. . . . . . . . . . . . . . . . 7.3.4 The 1R42 (ACE2 Open) Model: Model4 . . . . . . . . . . . . . . . . 7.3.5 The 6M17 (B0 AT1) Model: Model5 . . . . . . . . . . . . . . . . . . . . . 7.3.6 The 6VW1 (Chimera) Model: Model6 . . . . . . . . . . . . . . . . . . . 7.3.7 Glycans’ Shields . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7.3.8 Spike-Trimer Binding with Nanobody-Nb6c . . . . . . . . . . . . 7.3.9 The RGD Motif of Spike-RBD . . . . . . . . . . . . . . . . . . . . . . . . . . . 7.4 Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

263 264 264 264 265 265 267 267

Spike (S) Glycoprotein D614G Mutant . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8.2 Homology Structures of D614G Mutant . . . . . . . . . . . . . . . . . . . . . . . . . . . 8.3 Structural Bioinformatics of D614G Mutant . . . . . . . . . . . . . . . . . . . . . . 8.3.1 6vxx-Close-D614G-Mutant. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8.3.2 6vyb-Open-D614G-Mutant . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8.4 Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8.4.1 Confirmed from Some MD Datasets . . . . . . . . . . . . . . . . . . . . .

327 327 327 328 328 329 331 332

268 270 271 273 275 281 282 283 283

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9

Spike (S) Glycoprotein N501Y Mutant . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9.2 The Homology Structure of N501Y Mutant . . . . . . . . . . . . . . . . . . . . . . . 9.3 Structural Bioinformatics of N501Y Mutant . . . . . . . . . . . . . . . . . . . . . . 9.3.1 From the optimized-6m17-N501Y-mutant Model . . . . . . . 9.3.2 From MD Simulations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9.4 Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

349 349 350 350 350 354 355

10

Spike (S) Glycoprotein N165A and N234A Mutant . . . . . . . . . . . . . . . . . . . . . 10.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10.2 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10.3 Results and Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10.4 Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

359 360 360 360 364

11

SARS (SARS-CoV-1) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11.2 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11.3 New Structural Bioinformatics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11.3.1 SARS-CoV-1 Spike in Folding@home . . . . . . . . . . . . . . . . . . 11.3.2 HCoV-NL63 Spike in Folding@home . . . . . . . . . . . . . . . . . . . 11.4 Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

393 393 394 394 397 399 401

12

MERS-Coronavirus (MERS) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12.2 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12.3 New Structural Bioinformatics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12.4 Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

417 417 418 418 419

13

Human ACE2, Human IL6, Human IL6R, and Human nAChRs . . . . 13.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13.2 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13.3 New Structural Bioinformatics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13.3.1 Human ACE2 Monomer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13.3.2 Human IL6 Monomer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13.3.3 Human IL6R Monomer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13.3.4 Human α4β2-, α7-, and αβγ δ-nAChR . . . . . . . . . . . . . . . . . . 13.4 Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

423 423 424 424 424 427 431 432 438

14

PLpro Binding with 12 Compounds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14.2 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14.3 Results and Discussions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14.4 Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

445 445 445 446 448

15

3CLpro Binding with N3/Lopinavir/Ritonavir . . . . . . . . . . . . . . . . . . . . . . . . . . 15.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15.2 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15.2.1 N3 at the Binding Pocket of SARS-CoV-2 Mpro . . . . . . . .

457 457 458 458

xiv

Contents

15.2.2

15.3

15.4

Lopinavir at the Binding Pocket of SARS-CoV-2 Mpro . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15.2.3 Ritonavir at the Binding Pocket of SARS-CoV-2 Mpro . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15.2.4 Top 100 Drugs Binding with SARS-CoV-2 Mpro . . . . . . . 15.2.5 X77 Inhibitor Binding with SARS-CoV-2 Mpro . . . . . . . . Results and Discussions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15.3.1 N3 at the Binding Pocket of SARS-CoV-2 Mpro . . . . . . . . 15.3.2 Lopinavir at the Binding Pocket of SARS-CoV-2 Mpro . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15.3.3 Ritonavir at the Binding Pocket of SARS-CoV-2 Mpro . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15.3.4 Top 100 Drugs Binding with SARS-CoV-2 Mpro . . . . . . . 15.3.5 X77 Inhibitor Binding with SARS-CoV-2 Mpro . . . . . . . . Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

458 459 459 459 460 460 461 463 466 467 469

16

3CLpro Dimer Binding with 7 HIV Inhibitors and Others . . . . . . . . . . . . 16.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16.2 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16.2.1 7 HIV Inhibitors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16.2.2 2A5I-Ligand, 2OP9-Ligand, and 6LU7-Indinavir . . . . . . . 16.3 Results and Discussions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16.3.1 7 HIV Inhibitors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16.3.2 2A5I-Ligand, 2OP9-Ligand, and 6LU7-Indinavir . . . . . . . 16.4 Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

479 479 479 479 480 480 480 482 488

17

Spike RBDs Binding with 50 Drugs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17.2 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17.3 Results and Discussions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17.4 Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

511 511 512 512 513

18

Human ACE2 Ectodomain Binding with 78 Drugs . . . . . . . . . . . . . . . . . . . . . 18.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18.2 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18.3 Results and Discussions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18.4 Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

529 529 530 530 531

19

Spike-and-ACE2 Binding with 100 Drugs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19.2 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19.3 Results and Discussions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19.4 Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

545 545 546 546 547

20

Envelope Protein (E-Protein) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 557 20.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 557 20.2 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 559

Contents

20.3

Results and Discussions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20.3.1 7K3G.pdb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20.3.2 7M4R.pdb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20.3.3 MD of “Single E-protein Pentamer in Membrane” . . . . . . 20.3.4 The Optimized “Four E-protein Pentamers in Membrane” Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

560 560 560 561

Membrane Glycoprotein (M-Protein) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21.2 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21.3 Results and Discussions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21.3.1 MD on the “Single M-Protein Dimer in Membrane” . . . . 21.3.2 The Optimized “Three M-Protein Dimers and One E-Protein Pentamer in Membrane” Model. . . . . . . . . . 21.4 Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

573 573 574 574 576

Nucleocapsid Phosphoprotein (N-Protein) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22.2 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22.3 Results and Discussions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22.3.1 The N-Protein’s C-Terminal Tail PRO365-ALA419 Monomer Model . . . . . . . . . . . . . . . . . . . . . 22.3.2 The N-Protein’s C-Terminal Tail PRO365-ALA419 Dimer Model . . . . . . . . . . . . . . . . . . . . . . . . . 22.3.3 The N-Protein’s Full-Length MET1-ALA419 Dimer Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22.3.4 The N-Protein’s Full-Length MET1-ALA419 Dimer with RNA G1-C60 Model . . . . . . . . . . . . . . . . . . . . . . . . 22.3.5 The N-Protein’s Full-Length MET1-ALA419 Octamer with the Four RNAs Model. . . . . . . . . . . . . . . . . . . . . 22.3.6 The N-Protein’s Dimerization-Domain THR247-PRO364 Dimer Model . . . . . . . . . . . . . . . . . . . . . . . . . 22.3.7 The N-Protein’s RBD ALA50-ALA173 Monomer Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22.4 Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

597 597 600 601

20.4 21

22

xv

566 567

585 596

601 603 614 616 620 621 627 629

23

SARS-CoV-2 RNA Genome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 639

24

NSP7, NSP8, NSP9, NSP10, NSP16, and NSP14 . . . . . . . . . . . . . . . . . . . . . . . . 24.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24.2 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24.3 Results and Discussions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24.3.1 NSP7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24.3.2 NSP8 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24.3.3 NSP9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24.3.4 NSP10 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

645 645 655 655 655 656 658 660

xvi

Contents

24.3.5 NSP10-NSP16 Complex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24.3.6 NSP16 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24.3.7 NSP10-NSP14 Complex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24.3.8 NSP14 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

663 665 667 670 675

25

NSP15 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25.2 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25.3 Results and Discussions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25.4 Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

711 711 714 714 716

26

Other Mutants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26.2 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26.3 Results and Discussions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26.3.1 The Alpha-, Beta-, Delta-, and Kappa-variant of [288] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26.3.2 The P.1-Variant (i.e., Gamma-Variant) of [58, 253] . . . . . 26.3.3 The Alpha1-, Alpha2-, Beta-, and Delta-variant and the wt of [68] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26.3.4 The Alpha-, Beta-, Delta-, Epsilon-, Kappa-, and Omicron-variant of [284] Optimized . . . . . . . . . . . . . . . . 26.3.5 Omicron-Variants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26.4 Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

723 723 723 724

27

Vaccines and Drugs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27.2 Pfizer-BioNTech COVID-19 Vaccine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27.2.1 Bivalent Vaccines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27.3 Moderna COVID-19 Vaccine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27.4 Oxford-AstraZeneca COVID-19 Vaccine. . . . . . . . . . . . . . . . . . . . . . . . . . 27.5 Janssen COVID-19 Vaccine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27.6 Sinopharm BIBP COVID-19 Vaccine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27.7 Covaxin COVID-19 Vaccine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27.8 Novavax COVID-19 Vaccine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27.9 Antigen Rapid Test (ART). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27.10 Drugs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27.11 Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

887 887 888 890 890 892 893 893 894 894 894 895 896

28

Pandemic Mathematical Models, Epidemiology, and Virus Origins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28.2 Pandemic Mathematical Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28.3 Epidemiology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28.4 Origins of SARS-CoV-2 Virus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28.5 Concluding Remarks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

897 897 897 905 907 908

24.4

724 729 735 766 771 872

Contents

A

xvii

Mathematical Optimization Algorithms and Free Energy Calculations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 909

References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 915 Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 945

Acronyms

3CLpro 3D aa ACE2 APs BFGS CG chon2 chon4 CoVs CS1 CTD dex2 dex4 DSSP E-protein EPS FMNR GA GO GROMACS h6s2 h6s4 HB hep2 hep4 HYD L-BFGS

3C-like protease three-dimensional amino acid angiotensin converting enzyme 2 accessory proteins Broyden-Fletcher-Goldfarb-Shanno quasi-Newton algorithm conjugate gradient method chondroitin sulfate dimer chondroitin sulfate tetramer Coronaviruses cleavage site S1 C-terminal domain dextran sulfate dimer dextran sulfate tetramer Database/Dictionary of Secondary Structures of a Protein envelope protein electrostatic potential surfaces full matrix Newton Raphson genetic algorithm global optimization Groningen machine for chemical simulations heparan sulfate dimer heparan sulfate tetramer hydrogen bond heparin dimer heparin tetramer hydrophobic interaction limited-memory Broyden-Fletcher-Goldfarb-Shanno quasi-Newton algorithm

xix

xx

lbfgs-TNCG LMOD MC MD MERS Mpro Mpro-dm M-protein MSIR MTase nAChRs NMR N-protein NSPs NTD ORFs OSVM PD PDB PLpro PRCG RBD RdRp RMS RMSD RMSF RTC SA SARS SASA SB SD SEIR SI SIMPLEX SIMPLEX-GENETIC SIR SIRD SIRS SIS S-protein SPs TNCG vdW wt

Acronyms

L-BFGS preconditioned truncated Newton conjugate gradient algorithm low-MOD methods Monte Carlo molecular dynamics Middle East respiratory syndrome main protease Mpro-delP168-and-a173v membrane glycoprotein immunity-susceptible-infected-recovered methyltransferase protein nicotinic acetylcholine receptors nuclear magnetic resonance nucleocapsid phosphoprotein non-structural proteins N-terminal domain open reading frames Oren-Spedicato Variable Metric peptidase domain Protein Data Bank papain-like protease Polak-Ribiere conjugate gradient method receptor-binding domain RNA-directed RNA polymerase root mean square root mean square deviation root mean square fluctuation replication-transcription complex simulated annealing severe acute respiratory syndrome solvent accessible surface area salt bridge steepest descent algorithm susceptible-latent-infected-recovered susceptible-infected the downhill simplex minimizer the hybrid simplex-genetic algorithm susceptible-infected-recovered susceptible-infected-recovered-deceased susceptible-infected-recovered-susceptible susceptible-infected-susceptible spike glycoprotein structural proteins truncated Newton conjugate gradient van der Waals wild-type

Chapter 1

Papain-Like Cysteine Protease (PLpro)

Abstract Viral papain-like cysteine protease (PLpro, NSP3) is essential for SARSCoV-2 replication and represents a promising drug target against SARS-CoV-2 virus. Fortunately, the crystal structure of SARS-CoV-2-PLpro in complex with peptide inhibitor VIR251 was already released into Protein Data Bank (PDB) on May 20, 2020 with PDB entry 6WX4. This chapter is firstly optimizing this structure of the monomer and dimer, with and without the inhibitor. Then, basing from the optimized models, we present some structural bioinformatics for SARS-CoV2-PLpro monomer (with/without the inhibitor) and dimer (without the inhibitor). The structural bioinformatics of this brief chapter might be useful or helpful for developing therapies against the currently fatal SARS-CoV-2 virus. For PLpro, we found some preliminary interesting results such as (1) the polar contacts ASP76ARG82 and ASP286-HIS272 are very important for keeping the monomer structure stable, (2) the broken of salt bridge GLU307-LYS217 might lead to some motion in the C-terminal residues, and (3) for the dimer the polar contacts GLU143ARG138 and hydrogen bonds ARG140.H-TYR137.OH make the two monomers (of a dimer) linking to each other, etc. For the SARS-CoV-2-PLpro C111S mutant, the SB GLU67-HIS17 cannot be maintained during MD simulation because of ion ZN503. Comparisons with SARS-VoV-1-PLpro and the binding sites for inhibitors S43, GRL0617, XR8-89, JUN9-84-3, JUN9-72-2 are also studied in this chapter. Keywords SARS-CoV-2-PLpro · Monomer and dimer and trimer · With/without inhibitor · Structural bioinformatics · Optimization and molecular dynamics

1.1 Introduction Paper [297] provides the structure of inhibitor-bound SARS-CoV-2-PLpro (with PDB entry 6WX4) and recently molecular dynamics (MD) 100-.μs trajectory data for 6WX4 removing the covalent inhibitor was released on July 15, 2020 [321]. Thus, we have data resources to study the static and dynamic structural behaviours of SARS-CoV-2-PLpro. We organize this chapter as two parts: the first part will © The Author(s), under exclusive license to Springer Nature Switzerland AG 2023 J. Zhang, Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures, Springer Series in Biophysics 23, https://doi.org/10.1007/978-3-031-36773-1_1

1

2

1 Papain-Like Cysteine Protease (PLpro)

discuss SARS-CoV-2-PLpro monomer without and with the inhibitor, and the second part is discussing SARS-CoV-2-PLpro dimer models without the inhibitor.

1.2 Materials and Methods The material used in the chapter is 6WX4.pdb. 6WX4.pdb has two chains: D-Chain is the structure of PLpro, and I-Chain is the structure of the inhibitor VIR251. Basing on 6WX4.pdb (i.e. the monomer with the inhibitor), we built four models: (model1) a monomer without the inhibitor (i.e. D-Chain only) and (model2 to model4) three dimers without the inhibitor I-Chain. The methods of this chapter are the optimization computations and MD trajectory data analyses (in this book packages such as VMD [154], SWISS-MODEL and Swiss-PdbViewer [133, 134], Maestro-10.1, Amber, etc. are used to analyse the MD trajectories). We first optimize the above four models (why the models need to optimize can be seen from Page 8 of [411]). Optimized structure in a transition state is much more stable. The hybrid strategy of mathematical optimization’s neighbouring different local search algorithms [405] is used for the optimization computing. For the MD trajectory data analyses, because the noncovalent interactions of hydrogen bonds (HBs), salt bridges (SBs), van der Wales contacts (vdWs), and hydrophobic interactions (HYDs) are driving a protein to be able to perform its biological functions (Page 167 of [411]), in the below we will find out the HBs, SBs, HYDs, and vdWs of the four models and the optimized 6WX4.pdb. The performances of the MD trajectory data are evaluated by the MD analysis methods of [412] (Pages 8–10). In addition, the PLpro C111S mutant is also studied in this chapter. In [332], the supervised MD-trajectories datasets for PLpro in complex with the inhibitors GRL0617, SNYDER495, SNYDER530, and SNYDER441 are presented for the PDB entries 7cmd, 7jit, 7jiw, and 7jn2, respectively. In this chapter, we choose the two files in directory /Data/7JIT-S495/7JIT-Unbinding-rep1/ of [332]: Concat-Unbinding-SuMD-7JIT-rep1-fit-fit-2260.gro and Concat-UnbindingSuMD-7JIT-rep1-fit-fit.xtc. In http://chemcha-gpu0.ucr.edu/software/, there are five sets of PLpro 1.μs MD trajectories for (1) SARS-CoV-2-PLpro-wt (C-chain of 6W9C.pdb: aa THR4-ILE314 without ligand), (2) SARS-CoV-2-PLpro-C111S-mutant (A-chain of 6WRH.pdb: aa THR4-ILE314 without ligand), (3) SARS-CoV-2-PLpro-wt ligand-bound (A-chain of 6W9C.pdb: aa THR4-LYS315 with ligand S88), (4) SARS-CoV-1-PLpro-wt (A-chain of 4OW0.pdb: aa LYS4-THR5-..-ILE315 without ligand), and (5) SARS-CoV-1-PLpro-wt ligand-bound (A-chain of 4OW0.pdb: aa THR5-ILE315 with ligand S88), respectively, where the residue numbers of SARSCoV-2 should be added 1 to agree with the ones of SARS-CoV-1. In this chapter, we also study the optimized structures of these five models and present their MD results.

1.3 Structural Bioinformatics Results and Discussions

3

1.3 Structural Bioinformatics Results and Discussions 1.3.1 Monomer 1.3.1.1

Without Inhibitor

The optimized monomer without the inhibitor (with 0.146302 Å of backbone RMSD from the unoptimized structure) has 4 SBs ASP76-ARG82, ASP286-HIS272, ASP62-ARG65, GLU67-HIS17; 145 HBs; 1 .π-cation LYS.+ 92.NZ-HIS89, 3 .π.π stackings TYR71-TYR72, TYR136-TYR137, and TYR264-TYR273; and lower Solvent Accessible/accessibility Surface Area (SASA) values at PRO129-PRO130ALA131 and SER245-ALA246-PRO247 and larger SASA values at TYR136TYR137-ARG138 and PHE216-LYS217-LYS218. From the 100-.μs MD trajectory data with 100,000 frames of [321], we picked up 1000 frames with a frame interval of 100 ns. From analyses of the 1000 frames, we get 59 SBs and 1112 HBs. Seeing Fig. 1.1, we can confirm the stronger SBs ASP76-ARG82 (ARG82.NH2-ASP76.OD2 (11.29%), ARG82.NH2-ASP76.OD1 (11.19%), ARG82.NH1-ASP76.OD2 (2.40%), and ARG82.NH1-ASP76.OD1 (1.70%)—wherein the brackets are the HB occupancy rates), ASP286-HIS272 (HIS272.NE2-ASP286.OD1 (23.78%), HIS272.NE2-ASP286.OD2 (20.48%)), and the very weaker SBs ASP62-ARG65 and GLU67-HIS17. Thus, we may say the polar contacts ASP76-ARG82 and ASP286-HIS272 are very important for keeping the structure stable.

Other 17 SBs such as GLU263-LYS274 (with HBs GLU263.N-LYS274.O (40.46%), LYS274.NZ-GLU263.OE2 (20.08%), LYS274.N-GLU263.O (19.08%),

Fig. 1.1 The 4 SBs (of the optimized model) ASP76-ARG82, ASP286-HIS272, ASP62-ARG65, and GLU67-HIS17 confirmed by MD trajectory data of [321]

4

1 Papain-Like Cysteine Protease (PLpro)

LYS274.NZ-GLU263.OE1 (18.58%)), GLU167-LYS157, GLU214-LYS217, GLU252-LYS254, GLU295-LYS254, GLU307-LYS217 (first 20 .μs), GLU1ARG3, GLU143-ARG138 (with HBs ARG138.NH2-GLU143.OE1 (10.19%), ARG138.NH2-GLU143.OE2 (9.69%), ARG138.NE-GLU143.OE1 (4.90%), ARG138.NE-GLU143.OE2 (3.90%)), GLU161-LYS157, ASP302-ARG166 (with HB ARG166.NE-ASP302.OD1 (11.29%)), GLU124-ARG140, GLU124-LYS126, GLU214-LYS218 (with HB LYS218.N-GLU214.O (23.18%)), GLU238-LYS182 (with HBs GLU238.N-LYS182.O (28.37%), LYS182.N-GLU238.O (26.77%)), GLU252-LYS297, GLU318-HIS320, and GLU318-LYS315 can be seen from Fig. 1.9. From Fig. 1.9, we may see that the polar contacts GLU263-LYS274, GLU143-ARG138, ASP302-ARG166, GLU214-LYS218, and GLU238-LYS182 are also contributing to the structural stability. We list the HBs with more than 30% occupancy rates during the 100 .μs in Table 1.1. We know residues TYR72, TYR136, and TYR264 are key residues: (i) at residue TYR72 there are one .π-.π stacking TYR72-TYR71 and three strong HBs TYR72.OH-VAL11.O (49.45%), TYR72.N-ALA68.O (35.86%), and TYR72.O-TYR154.OH (55.84%), (ii) at residue TYR136 there is one .π-.π stacking TYR136-TYR137, one HB TYR136.O-ARG140.N (46.55%), and a hydrophilic region TYR136-TYR137-ARG138, and (iii) at residue TYR264 there is one .π -.π stacking TYR264-TYR273 and two strong HBs TYR264.N-ASN267.O (30.37%) and TYR264.N-PRO299.O (36.56%). From Table 1.1, we know the HBs in segments VAL165-MET169-PHE173, LYS94-LYS105-ASN110, PHE79-TYR83LEU87, LEU113-LEU117-GLN121, ASN146-LEU150-TYR154, TYR83-LEU87LYS91, and ALA86-THR90-TYR95 contribute to maintain the structural stability locally. The 100 .μs’ MD RMSD, Secondary Structures, and RMSF performances are illuminated in Fig. 1.2.

From Fig. 1.2, as said in [321], “the overall structure is fairly stable, some motion in the microsecond timescale is observed in the loops and in the (C)terminal residues.” The RMSD values reach equilibrations around 2.1 Å during the first 22 .μs and then around 4.8 Å during 23–100 .μs—during 22–23 .μs there is a jump (for example) because of the broken of SB GLU307-LYS217 (Fig. 1.9) (but HBs GLU307.N-PRO240.O (21.48%), THR311-GLU307 (N-O 14.69%, OG1O 10.09%), and TYR310.N-GLU307.O (5.79%) (Table 1.1 and Fig. 1.10) are

1.3 Structural Bioinformatics Results and Discussions

5

Fig. 1.2 The 100 .μs’ MD RMSD, Secondary Structures, RMSF performances, and SB GLU307LYS217

complementary to the SB GLU307-LYS217)—thus leading to the structure around segment GLU307-SER309 changed from Coil into 3.10 -helix.

1.3.1.2

With the Inhibitor

The optimized monomer with the inhibitor is with 1.093729 Å of backbone RMSD from the unoptimized structure. 6WX4.pdb has 3 .π -cations LYS.+ 92.NZHIS89, LYS274.+ .NZ-HIS272, LYS217.+ .NZ-TYR310 and 4 .π -.π stackings TYR71-TYR72, TYR136-TYR137, TYR264-TYR273, and HIS50-PHE55; after optimization, the .π -interactions LYS274.+ .NZ-HIS272, LYS217.+ .NZ-TYR310, and HIS50-PHE55 were lost. For the 6WX4optimized structure, its Ligand Interaction Diagram can be seen in Fig. 1.3, where there are HBs I:GLY4.HD:GLY163.O (1.85 Å), I:GLY4.O-D:GLY163.H (1.94 Å), I:DPP3.O-D:GLY271.H (2.08 Å), and I:DPP3.O-D:TYR264.H (2.60 Å). For the 6WX4optimized structure, the distances around Zn.2+ are illuminated in Fig. 1.4.

6

1 Papain-Like Cysteine Protease (PLpro)

Fig. 1.3 The Ligand Interaction Diagram and 4 HBs around the inhibitor

Fig. 1.4 The atom distances from the ion Zn.2+ with 2 HBs CYS189.O-CYS192.H (2.03 Å) and CYS224.O-CYS226.H (2.72 Å)

1.3.2 Dimer Without Inhibitor We applied the following mathematical formulas: ⎞ −1 0 0 .C = ⎝ 0 −1 0 ⎠ D, 0 0 1 ⎛

⎞ −1 0 0 C = ⎝ 0 1 0 ⎠ D, 0 0 −1 ⎛

⎞ 1 0 0 C = ⎝ 0 −1 0 ⎠ D 0 0 −1 ⎛

(1.1)

to 6WX4.pdb building three dimers and then optimized the three models of dimer without inhibitor (with backbone RMSD values of 2.171411 Å, 1.848472 Å, and 1.853466 Å, respectively, from the unoptimized ones). We denote the models as dimer-1, dimer-2, and dimer-3. For dimer-1, we get 10 SBs D:GLU143-C:ARG138, C:GLU143-D:ARG138, D:ASP286-D:HIS272, C:ASP286-C:HIS272, C:ASP62-C:ARG65, D:ASP62D:ARG65, D:GLU67-D:HIS17, C:GLU67-C:HIS17, C:ASP76-C:ARG82, and D:ASP76-D:ARG82 and 63 HBs. There are two HBs GLU143.OE2-ARG138.H (2.35 Å) between the two monomers (Fig. 1.5). Thus, the polar contacts GLU143ARG138 make the two monomers linking to each other. Seeing Fig. 1.5, we know the HBs ARG140.H-TYR137.OH (2.40 Å) also make the two monomers linking to each other.

1.3 Structural Bioinformatics Results and Discussions

7

Fig. 1.5 The polar contacts GLU143-ARG138 and the HBs ARG140.H-TYR137.OH (2.40 Å) are between the two monomers of dimer-1

For dimer-2, we found the Poisson–Boltzmann Electrostatic Potential Surfaces and the Hydrophilic Surfaces of the two monomers are touching to each other (Fig. 1.6).

Fig. 1.6 The Poisson–Boltzmann Electrostatic Potential Surfaces and the Hydrophobic/Hydrophilic Surfaces of dimer-2

In dimer-2, there are 2 extra .π -cations LYS.+ 274.NZ-HIS272 and LYS.+ 217.NZTYR310 in each monomer and 1 extra .π -.π stacking PHE55-HIS50 in each monomer. For dimer-3, the results are similar to those of dimer-2 (Fig. 1.7), and there are 2 extra .π -cations LYS.+ 274.NZ-HIS272 and LYS.+ 217.NZ-TYR310 in each monomer and 1 extra .π -.π stacking PHE55-HIS50 in each monomer.

Fig. 1.7 The Poisson–Boltzmann Electrostatic Potential Surfaces, the Hydrophobic/Hydrophilic Surfaces, and the vdW Surfaces (with vdW radius scale 1.0) of dimer-3

8

1 Papain-Like Cysteine Protease (PLpro)

1.3.3 The C111S Mutant In [332], the Concat-Unbinding-SuMD-7JIT-rep1-fit-fit.xtc has 1604 MD-frames, where 7JIT.pdb is the crystal structure of SARS-CoV-2-PLpro C111S mutant in complex with the SNYDER495 inhibitor. The residues in 7JIT.pdb are aa VAL2LYS315, Y95-501, ZN502-503-504-505, CL506-507-508, MES509, and ACT510511. The MD RMSD values are stable, but the RMSF values in segment aa 182–202 around residue 192 are larger, and at residue 92 its RMSF value is also larger. The MD Secondary Structure performance can be seen from Fig. 1.8, where the .α-helix aa THR26-GLY32 has slight changes into Turns or .310 -helix.

Fig. 1.8 The MD Secondary Structure of the SARS-CoV-2-PLpro C111S mutant during 1604 MD-frames

Table 1.2 lists the HBs (with more than 5% occupancy rates) of the SARSCoV-2-PLpro C111S mutant from the analyses of the 1604 frames’ supervised MD trajectory data (Concat-Unbinding-SuMD-7JIT-rep1-fit-fit.xtc) of [332]. The MD finds 662 HBs and 31 SBs as follows: ASP37-LYS91, ASP40-LYS43, GLU51-LYS6, ASP62-ARG65, GLU70-HIS73, ASP76-ARG82, ASP108-HIS89, ASP108-LYS92, GLU124ARG140, GLU124-LYS126, GLU124-LYS306, ASP134-ARG138, GLU143-ARG138, GLU161LYS157, ASP164-ARG166, GLU167-ARG166, GLU167-LYS157, ASP179-LYS200, GLU214LYS217, GLU214-LYS218, GLU238-LYS182, GLU252-LYS254, GLU252-LYS297, GLU263LYS274, GLU280-LYS279, GLU280-LYS292, ASP286-HIS272, ASP286-LYS274, GLU295LYS254, ASP302-ARG166, and GLU307-LYS217.

We optimize 7JIT.pdb (without HOH waters) and get three .π -.π stackings TYR71-TYR72, PHE127-TYR136, and TYR273-TYR264 and two .π -cations LYS217.NZ.+ -TYR310 and LYS279.NZ.+ -TYR283; the ions bindings ZN502CYS189/192/224/226.SG, CL506-HID17.NE2-ZN503-GLU67.OE2, HID89.ND1-

1.3 Structural Bioinformatics Results and Discussions

9

ZN504-ASP108, HID73.ND1-ZN505-CL507/8, the ACT510 binding with PLpro residues SER111, TRP106, ASN109 ASN110, HIS272, GLY271, and the ligand Y95.501 binding with PLpro residues GLU167, ASP164, LEU162, GLN269, THR301, TYR264, TYR273, PRO248, MET208, TYR268, and ACT511. The Poisson–Boltzmann Electrostatic Potential Surfaces seem to be neutral for almost all surfaces. The optimized structure has 16 SBs ASP37-LYS91, GLU51-LYS6, GLU67-HIS17, GLU238-LYS182, GLU252-LYS297, GLU295-LYS254, GLU307LYS217, ASP62-ARG65, ASP76-ARG82, GLU143-ARG138, GLU161-LYS157, GLU167-LYS157, GLU214-LYS218, GLU252-LYS254, GLU280-LYS292, and ASP286-LYS274, where the SB GLU67-HIS17 is not appearing during the supervised MD (but with HBs HIS17.N-THR9.O 31.92% and THR9.OG1-HIS17.O 14.40%) (Figs. 1.9 and 1.10).

1.3.4 Compared with SARS-CoV-1-PLpro In this subsection, we study the five models: (1) SARS-CoV-2-PLpro-wt (C-chain of 6W9C.pdb: aa THR4-ILE314 without ligand), (2) SARS-CoV-2-PLpro-C111Smutant (A-chain of 6WRH.pdb: aa THR4-ILE314 without ligand), (3) SARSCoV-2-PLpro-wt ligand-bound (A-chain of 6W9C.pdb: aa THR4-LYS315 with ligand S88), (4) SARS-CoV-1-PLpro-wt (A-chain of 4OW0.pdb: aa LYS4-THR5..-ILE315 without ligand), and (5) SARS-CoV-1-PLpro-wt ligand-bound (A-chain of 4OW0.pdb: aa THR5-ILE315 with ligand S88) presented in http://chemchagpu0.ucr.edu/software/. The residue numbers of SARS-CoV-2 in 6W9C.pdb and 6WRH.pdb should be added 1 to agree with the ones of SARS-CoV-1 in 4OW0.pdb. For the ligand S88, the following residues LEU162, GLY163, ASP164, ARG166, MET208, PRO247, PRO248, TYR264, ASN267, TYR268, GLN269, TYR273, and THR301 are the common residues binding with S88 not only in SARS-CoV-2PLpro (model 3) but also in SARS-CoV-1-PLpro (model 5); two additional residues LYS158 and GLY267 are also involved to binding the ligand S88 in SARS-CoV-1PLpro (model 5). Table 1.3 lists all the SBs of the five PLpro models optimized, where we can see that all the five models have common SBs GLU238-LYS182, ASP286HIS272 (but during MDs it is replaced by ASP286-LYS274), GLU161-LYS157, and GLU214-LYS217; but the mutation made SBs ASP40-LYS43, ASP164ARG166 lost in the four wt models. During 1 .μs’ MDs, the following SBs are kept for all the five models: ASP37-LYS53, ASP37-LYS91, GLU51-LYS6, ASP76-ARG82, ASP108-LYS92, GLU124-ARG140, GLU124-LYS279, GLU143-ARG138, GLU161-LYS157, GLU167-LYS157, ASP286-LYS274, GLU307-LYS217, ASP40-LYS43, ASP134-ARG138, ASP164-ARG166, GLU280-LYS279,

GLU124-LYS306, GLU143-LYS91, GLU214-LYS217, GLU238-LYS182, ASP62-ARG65, GLU124-LYS126, and GLU295-LYS297 (Table 1.4).

We also can confirm the SBs ASP76-ARG82, ASP286-LYS274, GLU307-LYS217, and GLU143-ARG138 are maintained during 1 .μs’ MDs. Tables 1.5 and 1.6 list all the HBs of the five PLpro models optimized. Tables 1.7, 1.8, and 1.9 list all the HBs (with more than 30% occupancy rates)

10

1 Papain-Like Cysteine Protease (PLpro)

of the five PLpro models maintained during 1 .μs’ MDs. Table 1.10 lists all the π -interactions and ZN316 binding residues of the five PLpro models in chemchagpu0.ucr.edu/software/ optimized, where CYM189 is always binding with ZN316. Figure 1.11 illuminates the Secondary Structures performances of the five PLpro models during 1 .μs’ MDs, where we know for models SARS-CoV-2 wt and SARS-CoV-1 wt with/without ligand S88 the two segments GLY28-THR34 around VAL202 have larger variations; but for the SARS-CoV-2 C111S-mutant, its larger variations are in segments GLY39-THR35 and around VAL203. We also know there are slight differences among the five models from the Secondary Structures of the five models optimized (Fig. 1.11).

.

1.3.5 Inhibitors S43, GRL0617, XR8-89, JUN9-84-3, and JUN9-72-2 Bindings In this subsection, we study the inhibitors S43, GRL0617, and XR8-89 binding to SARS-CoV-2-PLpro-dimer, JUN9-84-3, and JUN9-72-2 binding to SARS-CoV2-PLpro-trimer, respectively. The five models (1) C112S-mutant dimer bound to compound S43 (7E35.pdb), (2) wt dimer in complex with inhibitor GRL0617 (7JRN.pdb), (3) wt dimer in complex with inhibitor XR8-89 (7LBR.pdb), (4) wt trimer in complex with inhibitor JUN9-84-3 (7RZC.pdb), and (5) wt trimer in complex with inhibitor JUN9-72-2 (7SDR.pdb) are based on PDB entries 7E35, 7JRN, 7LBR, 7RZC, 7SDR respectively. We optimized the five models and the optimized models have RMSD values 0.545701, 0.453181, 0.441584, 0.477715, and 0.473589 Å, respectively, from the original models. The .π -interactions of the optimized five models are (1) 7E35-PLpro-C112S-S43-dimer ◦ .π -cations A:LYS218.NZ.+-A:TYR311, B:LYS93.NZ.+-B:HID90, ◦ .π -.π stackings A:TYR72-A:TYR73, A:PHE128-A:TYR137, A:TYR265A:TYR274, B:TYR72-B:TYR73-B:PHE80, B:PHE128-B:TYR137, B:PHE174-B:PHE242

. .

(2) 7JRN-PLpro-wt-GRL0617-dimer ◦ .π -cations A:LYS217.NZ.+-A:TYR310, J:LYS92.NZ.+-J:HID89, J:LYS217. NZ.+-J:TYR310, .◦ .π -.π stackings A:TYR71-A:TYR72, A:TYR264-A:TYR273, J:TYR71J:TYR72-J:PHE79, J:TYR264-J:TYR273, J:TYR207-J:PHE216 .

(3) 7LBR-PLpro-wt-XR8-89-dimer ◦ .π -cations A:LYS92.NZ.+-A:HID89, -A:TYR213, B:LYS92.NZ.+-B:HID89,

.

A:TYR310-A:LYS217.NZ.+

1.4 Concluding Remarks

11

◦ .π -.π stackings A:TYR71-A:TYR72-A:PHE79, A:PHE127-A:TYR136, A:TYR207-A:PHE216, B:TYR71-B:TYR72-B:PHE79, B:TYR207B:PHE216

.

(4) 7RZC-PLpro-wt-Jun9-84-3-trimer ◦ .π -cations A:LYS92.NZ.+-A:HID89, A:LYS217.NZ.+-A:TYR310, B:LYS92.NZ.+-B:HID89, .◦ .π -.π stackings A:TYR71-A:TYR72, A:TYR154-A:HID175, B:TYR71B:TYR72, B:TYR136-B:TYR137, B:TYR264-B:TYR273, C:TYR71C:TYR72, C:TYR207-C:PHE216 .

(5) 7SDR-PLpro-wt-Jun9-72-2-trimer ◦ .π -cations A:LYS217.NZ.+-A:TYR310, B:LYS217.NZ.+-B:TYR310, B:LYS92.NZ.+-B:HID89, C:LYS92.NZ.+-C:HID89, .◦ .π -.π stackings A:TYR71-A:TYR72, B:TYR71-B:TYR72, B:TYR136B:TYR137, C:TYR71-C:TYR72, C:TYR207-C:PHE216 .

where we can see .π -cation LYS92.NZ.+-HID89 and .π -.π stacking TYR71-TYR72 are always there (Fig. 1.12). The SBs and HBs of the five models optimized are listed in Tables 1.11, 1.12, and 1.13. All the residues of the optimized models of (1) 7E35PLpro-C112S-S43-dimer, (2) 7JRN-PLpro-wt-GRL0617-dimer, (3) 7LBR-PLprowt-XR8-89-dimer, (4) 7RZC-PLpro-wt-Jun9-84-3-trimer, and (5) 7SDR-PLpro-wtJun9-72-2-trimer that bind with the ions Zn2.+ and their respective inhibitors are listed in Table 1.14, where we can see the binding sites are almost the same for the five models. We also find for the dimer models (2)–(3) around residues HIS73THR75 and ASN128-PRO129 there is a large area of negative charge EPS, and for the trimer models (4)–(5) their .β-sheets have a large area of positive charge EPS (Fig. 1.13). All the above observations may be confirmed by the three sets of MD databases of each model [283].

1.4 Concluding Remarks In conclusion, for PLpro in this brief chapter, we found some interesting preliminary results such as (1) the polar contacts ASP76-ARG82 and ASP286-HIS272 are very important for keeping the monomer structure stable, (2) the broken of salt bridge GLU307-LYS217 might lead to some motion in the C-terminal residues, and (3) for the dimer, the polar contacts GLU143-ARG138 (in Mpro-dimer the SBs GLU290ARG4 linking its two monomers (Chap. 2)) and HBs ARG140.H-TYR137.OH make the two monomers (of a dimer) linking to each other, etc. For the SARSCoV-2-PLpro C111S mutant, the SB GLU67-HIS17 cannot be maintained during MD simulation because of ion ZN503. Comparisons with SARS-VoV-2-PLpro and the binding sites for inhibitors S43, GRL0617, XR8-89, JUN9-84-3, and JUN9-72-2 are also studied in this chapter.

12

1 Papain-Like Cysteine Protease (PLpro)

Supplementary Information

Fig. 1.9 Other SBs from the analyses of the MD trajectory data of [321]

Supplementary Information

Fig. 1.9 (continued)

13

14

1 Papain-Like Cysteine Protease (PLpro)

Fig. 1.10 HBs GLU307.N-PRO240.O (21.48%), THR311-GLU307 (N-O 14.69%, OG1-O 10.09%), and TYR310.N-GLU307.O (5.79%)

Table 1.1 The HBs with more than 30% occupancy rates from the analyses of the 100 μs’ MD trajectory data of [321]

Donor

Acceptor

Occupancy

PHE173-Main-N

MET169-Main-O

71.53%

MET243-Main-N

VAL205-Main-O

67.13%

LYS105-Main-N

LYS94-Main-O

66.73%

MET244-Main-N

VAL303-Main-O

66.63%

MET169-Main-N

VAL165-Main-O

66.53%

TYR83-Main-N

PHE79-Main-O

64.64%

PHE304-Main-N

CYS260-Main-O

64.54%

LEU117-Main-N

LEU113-Main-O

63.94%

PHE55-Main-N

PHE8-Main-O

63.74%

LEU199-Main-N

ARG183-Main-O

63.54%

ASP22-Main-N

GLN30-Side-OE1

62.24%

ILE285-Main-N

HIS275-Main-O

61.94%

TYR154-Main-N

LEU150-Main-O

61.44%

MET84-Main-N

LEU80-Main-O

61.04%

PHE31-Main-N

TYR27-Main-O

60.44%

VAL7-Main-N

GLN19-Main-O

60.14%

LEU120-Main-N

ALA116-Main-O

59.44%

LYS232-Main-N

VAL220-Main-O

56.04%

TYR154-Side-OH

TYR72-Main-O

55.84%

LEU87-Main-N

TYR83-Main-O

53.85%

TYR95-Side-OH

THR90-Main-O

53.35%

TYR305-Side-OH

LEU211-Main-O

52.75%

ASN128-Main-N

HIS175-Main-O

52.65%

ILE276-Main-N

ALA261-Main-O

52.45%

ILE151-Main-N

PHE147-Main-O

52.05%

GLY209-Main-N

SER245-Main-O

51.95%

ALA230-Main-N

ILE222-Main-O

51.35%

CYS284-Main-N

THR291-Main-O

51.15%

GLN237-Side-NE2

ALA204-Main-O

49.75%

TYR72-Side-OH

VAL11-Main-O

49.45%

ARG183-Side-NE

GLN237-Side-OE1

49.25%

THR34-Side-OG1

GLY32-Main-O

48.95%

GLN121-Side-NE2

LEU117-Main-O

48.55%

(continued)

Supplementary Information Table 1.1 (continued)

15 Donor

Acceptor

Occupancy

VAL188-Main-N

THR231-Main-O

48.25%

THR168-Side-OG1

ASP164-Main-O

48.15%

VAL220-Main-N

LYS232-Main-O

47.65%

ILE222-Main-N

ALA230-Main-O

47.45%

THR102-Main-N

GLN121-Side-OE1

46.65%

ARG140-Main-N

TYR136-Main-O

46.55%

VAL303-Main-N

MET244-Main-O

46.35%

TYR35-Main-N

TYR56-Main-O

46.15%

PHE69-Main-N

ARG65-Main-O

45.65%

SER103-Main-N

PRO96-Main-O

45.55%

ASP134-Main-N

PRO130-Main-O

44.76%

GLN19-Main-N

VAL7-Main-O

44.06%

SER85-Main-N

GLY81-Main-O

43.76%

VAL98-Main-N

LEU101-Main-O

43.66%

ARG65-Side-NE

PRO59-Main-O

43.46%

LEU150-Main-N

ASN146-Main-O

43.26%

THR10-Side-OG1

ASN15-Main-O

43.06%

GLY52-Main-N

LYS6-Main-O

42.86%

GLY219-Main-N

GLN215-Main-O

42.76%

THR119-Side-OG1

THR115-Main-O

42.56%

THR277-Main-N

TYR283-Main-O

42.26%

ALA139-Main-N

ALA135-Main-O

40.96%

THR301-Main-N

SER262-Main-O

40.76%

ASN177-Main-N

LYS126-Main-O

40.66%

GLN121-Side-NE2

THR102-Main-O

40.46%

GLU263-Main-N

LYS274-Main-O

40.46%

VAL184-Main-N

GLN236-Main-O

40.36%

ASP286-Main-N

LEU289-Main-O

40.06%

TYR251-Main-N

GLY298-Main-O

39.16%

CYS148-Main-N

ALA144-Main-O

39.16%

LEU36-Main-N

ALA39-Main-O

38.96%

SER239-Side-OG

PHE241-Main-O

38.56%

TYR233-Main-N

ASN186-Main-O

38.36%

LEU185-Main-N

THR197-Main-O

38.26%

TYR283-Main-N

THR277-Main-O

38.26%

THR90-Main-N

ALA86-Main-O

38.26%

LYS217-Main-N

TYR213-Main-O

37.26%

ASN110-Side-ND2

LYS105-Main-O

36.96%

TYR264-Main-N

PRO299-Main-O

36.56%

TYR72-Main-N

ALA68-Main-O

35.86%

LEU118-Main-N

ALA114-Main-O

35.56%

CYS155-Main-N

ILE151-Main-O

35.46%

THR259-Main-N

PHE304-Main-O

34.57%

THR197-Main-N

LEU185-Main-O

33.97%

GLN215-Main-N

SER212-Side-OG

33.47%

LYS91-Main-N

LEU87-Main-O

33.37%

ALA114-Main-N

ASN110-Main-O

32.77%

GLU70-Main-N

VAL66-Main-O

32.57%

LYS157-Side-NZ

LEU162-Main-O

32.27%

HIS175-Side-ND1

TYR171-Main-O

32.17%

LYS157-Main-N

LEU152-Main-O

32.07%

THR9-Main-N

HIS17-Main-O

31.97%

THR90-Side-OG1

ALA145-Main-O

31.87%

HIS17-Main-N

THR9-Main-O

31.57%

ASN267-Main-N

CYS270-Main-O

31.47%

TYR296-Side-OH

GLU263-Side-OE2

31.27%

ILE123-Main-N

THR119-Main-O

31.27%

VAL21-Main-N

ILE5-Main-O

30.97%

PHE8-Main-N

LYS53-Main-O

30.97%

THR115-Main-N

CYS111-Main-O

30.97%

TYR56-Main-N

TYR35-Main-O

30.67%

TYR305-Main-N

VAL242-Main-O

30.57%

TYR264-Side-OH

ASN267-Main-O

30.37%

TYR171-Main-N

GLU167-Main-O

30.37%

ALA131-Main-N

TYR71-Main-O

30.07%

Table 1.2 The HBs (with more than 5% occupancy rates) of the SARS-CoV-2-PLpro C111S mutant from the analyses of the 1604 frames’ supervised MD trajectory data (Concat-UnbindingSuMD-7JIT-rep1-fit-fit.xtc) of [332] TYR213.OH-GLU307.OE1 82.67%

GLY209.N-SER245.O 41.02%

SER24.N-ASP22.OD1 25.37%

TRP93.NE1-ASP108.OD1 12.16%

HIS272.NE2-ASP286.OD1 74.31%

LEU87.N-TYR83.O 40.84%

THR42.OG1-ASP40.OD1 25.25%

GLU143.N-ARG138.O 11.66%

ASN15.N-ASP12.OD1 72.44%

ARG82.N-SER78.O 40.34%

LEU117.N-LEU113.O 24.88%

GLU70.N-VAL66.O 11.66%

SER245.OG-ASP302.OD1 71.82%

GLN19.N-VAL7.O 39.78%

HIS50.N-HIS47.O 24.69%

THR119.N-THR115.O 11.47%

TYR283.OH-GLU280.OE2 70.32%

LEU118.N-ALA114.O 39.59%

ALA261.N-ILE276.O 24.56%

ARG140.NH1-GLU124.OE1 11.28%

PHE304.N-CYS260.O 64.90%

HIS255.NE2-LYS279.O 39.21%

SER245.N-TYR207.O 24.25%

THR168.N-ASP164.O 11.03%

TYR95.OH-THR90.O 63.72%

LYS105.N-LYS94.O 39.03%

HIS272.N-THR265.O 24.00%

LYS274.N-GLU263.O 10.85%

GLN237.NE2-ALA204.O 62.28%

THR301.N-SER262.O 38.65%

ARG140.NH2-GLU124.OE2 23.75%

ASN88.N-MET84.O 10.66%

TYR296.OH-GLU263.OE2 61.41%

LYS217.NZ-GLU214.OE1 38.40%

CYS155.N-ILE151.O 23.63%

CYS181.N-LEU178.O 10.66%

TYR305.OH-LEU211.O 61.35%

MET169.N-VAL165.O 38.03%

ARG138.NH2-GLU143.OE2 23.50%

ARG138.NH1-ASP134.OD2 10.66%

THR63.OG1-ASP61.OD2 59.73%

TYR83.N-PHE79.O 37.97%

THR291.N-CYS284.O 23.32%

MET206.N-VAL202.O 10.60%

THR168.OG1-ASP164.O 59.10%

LYS279.N-THR281.O 37.22%

GLU167.N-ASP164.OD1 23.07%

ASN60.ND2-LEU58.O 10.41%

VAL188.N-THR231.O 58.85%

HIS275.NE2-GLN122.OE1 36.85%

THR90.N-ALA86.O 22.76%

LYS91.N-LEU87.O 10.35%

LEU253.N-TYR296.O 58.29%

ASP134.N-PRO130.O 36.78%

LYS200.NZ-ASP179.OD1 22.63%

TYR27.N-ILE44.O 10.22%

MET243.N-VAL205.O 57.61%

LYS182.N-GLU238.O 36.41%

ALA116.N-TYR112.O 22.44%

ASN13.N-THR10.OG1 10.16%

VAL98.N-LEU101.O 56.42%

CYS148.N-ALA144.O 36.28%

GLN237.N-TYR310.O 22.38%

TYR296.N-LEU253.O 10.10%

ASN308.N-GLU307.OE2 56.17%

ASP286.N-LEU289.O 36.03%

TYR264.OH-ASN267.O 22.38%

LYS157.NZ-GLU167.OE1 9.98%

GLN121.NE2-LEU117.O 55.92%

SER239.OG-PHE241.O 36.03%

SER293.OG-GLU295.O 22.26%

ARG140.NH1-GLU124.OE2 9.73%

ALA230.N-ILE222.O 55.86%

THR231.N-VAL188.O 35.97%

VAL242.N-TYR305.O 22.19%

LYS157.NZ-LEU162.O 9.60%

TYR72.OH-VAL11.O 55.30%

GLU263.N-LYS274.O 35.85%

GLY227.N-CYS224.O 22.19%

TYR112.OH-GLU161.O 9.60%

ILE285.N-HIS275.O 54.74%

SER85.N-GLY81.O 35.79%

ALA68.N-LEU64.O 22.07%

VAL205.N-VAL202.O 9.29%

TRP93.NE1-ASP108.OD2 54.55%

ARG138.NH2-GLU143.OE1 35.54%

GLN97.NE2-THR102.OG1 21.70%

GLN221.NE2-THR231.OG1 9.29%

MET244.N-VAL303.O 54.49%

SER262.N-ASP302.O 35.54%

ALA139.N-ALA135.O 21.51%

HIS89.NE2-ASP108.OD1 9.23%

LEU36.N-ALA39.O 54.11%

ALA114.N-ASN110.O 35.54%

TYR233.N-ASN186.O 21.45%

GLN122.N-THR119.O 9.16%

TYR35.N-TYR56.O 53.93%

SER78.OG-ASP76.OD1 35.41%

SER78.OG-ASP76.OD2 20.95%

TYR268.N-ASN267.OD1 9.10%

GLY219.N-GLN215.O 53.49%

ASN15.ND2-ASP12.OD2 35.41%

TYR83.OH-ASN146.OD1 20.57%

ARG166.NE-ASP302.OD1 9.10%

TYR305.N-VAL242.O 53.49%

THR197.N-LEU185.O 35.22%

LEU152.N-CYS148.O 20.51%

HIS89.NE2-ASP108.OD2 8.79%

PHE127.N-GLN133.OE1 52.56%

VAL235.N-VAL184.O 34.85%

LEU234.N-PHE216.O 20.32%

LYS92.NZ-ASP108.OD2 8.73%

SER24.OG-ASP22.OD1 52.43%

TYR27.OH-HIS50.ND1 34.79%

THR115.N-SER111.O 20.26%

HIS275.N-ILE285.O 8.60%

GLN237.NE2-SER239.OG 52.37%

VAL220.N-LYS232.O 34.79%

PHE31.N-TYR27.O 19.89%

GLN215.N-SER212.OG 7.86%

LEU199.N-ARG183.O 51.87%

TYR56.OH-TYR72.OH 34.54%

GLY256.N-SER278.OG 19.83%

GLN174.NE2-SER170.O 7.86%

CYS284.N-THR291.O 50.94%

THR34.N-THR42.OG1 33.98%

LYS254.NZ-GLU295.OE1 19.51%

GLY201.N-CYS181.O 7.73%

ILE276.N-ALA261.O 50.87%

GLU238.N-LYS182.O 33.60%

LYS254.NZ-GLU252.OE1 19.45%

LYS91.NZ-ASP37.O 7.67%

TYR56.N-TYR35.O 50.25%

THR257.OG1-LYS254.O 32.42%

THR90.OG1-ALA86.O 19.20%

ALA86.N-ARG82.O 7.42%

THR119.OG1-THR115.O 50.19%

VAL184.N-GLN236.O 32.11%

THR265.OG1-GLU263.OE1 19.14%

HIS47.N-HIS50.ND1 7.36%

TYR154.OH-TYR72.O 49.50%

ARG183.NH1-MET206.O 32.04%

THR312.N-VAL235.O 18.70%

TYR71.OH-ASP134.OD2 7.29%

TYR283.N-THR277.O 49.19%

HIS17.N-THR9.O 31.92%

LYS254.NZ-GLU252.OE2 18.39%

ARG65.N-ASP61.O 7.23%

ASN177.N-LYS126.O 49.19%

SER309.OG-GLU238.OE2 30.74%

ARG138.NE-GLU143.OE1 18.20%

LEU162.N-GLU161.OE2 7.11%

TYR264.N-PRO299.O 48.75%

PHE55.N-PHE8.O 30.67%

ALA149.N-ALA145.O 17.89%

THR63.N-ASP61.OD1 7.04%

GLY193.N-CYS189.O 48.32%

ASN186.N-TYR233.O 30.49%

SER85.OG-GLY81.O 17.64%

GLY81.N-SER78.O 7.04%

VAL7.N-GLN19.O 48.19%

HIS175.ND1-TYR171.O 29.80%

TYR251.N-GLY298.O 17.21%

SER111.OG-ASN109.OD1 7.04%

SER103.N-PRO96.O 48.19%

ALA246.N-THR301.O 29.61%

SER170.N-ARG166.O 17.14%

THR231.OG1-GLN221.OE1 6.98%

THR277.N-TYR283.O 47.69%

LYS254.NZ-GLU295.OE2 29.05%

ILE5.N-VAL21.O 16.96%

ALA249.N-ILE300.O 6.92%

ASN128.N-HIS175.O 46.95%

LEU120.N-ALA116.O 28.99%

THR42.N-ASP40.OD2 16.96%

ARG140.N-TYR136.O 6.61%

TYR154.N-LEU150.O 46.88%

THR277.OG1-GLN122.OE1 28.87%

GLN215.NE2-GLY219.O 16.90%

ASN186.ND2-GLN196.OE1 6.61%

PHE173.N-MET169.O 46.45%

THR259.N-PHE304.O 28.43%

LEU150.N-ASN146.O 16.27%

LEU172.N-THR168.O 6.36%

THR9.N-HIS17.O 46.38%

PHE69.N-ARG65.O 27.93%

SER278.N-THR259.O 16.21%

GLU167.N-ASP164.OD2 6.30%

SER103.OG-GLY287.O 46.38%

LYS200.NZ-ASP179.OD2 27.81%

LYS279.NZ-ASN99.OD1 15.90%

PHE8.N-LYS53.O 6.23%

GLN121.NE2-THR102.O 46.13%

THR34.OG1-GLY32.O 27.81%

THR42.N-ASP40.OD1 15.77%

ASN177.ND2-ASN128.OD1 6.23%

VAL303.N-MET244.O 45.64%

ARG183.N-LEU199.O 27.68%

LYS91.NZ-ASP37.OD2 15.59%

ARG166.NH2-ASP302.OD2 6.23%

ARG183.NE-GLN237.OE1 45.20%

THR42.OG1-ASP40.OD2 27.68%

SER170.OG-ARG166.O 15.52%

LYS53.N-HIS50.O 6.05%

ARG82.NE-SER78.OG 44.70%

CYS224.N-LYS228.O 27.49%

LYS217.NZ-GLU214.OE2 15.27%

LYS157.NZ-GLU161.OE1 5.99%

THR301.OG1-ALA246.O 44.45%

ASN146.ND2-TYR83.OH 27.31%

THR63.OG1-ASP61.OD1 15.15%

ARG65.NH1-ASP62.OD1 5.99%

LYS232.N-VAL220.O 44.26%

THR102.OG1-ALA139.O 27.18%

THR9.OG1-HIS17.O 14.40%

TYR171.N-GLU167.O 5.92%

TYR72.N-ALA68.O 44.01%

THR63.N-ASP61.OD2 27.12%

VAL165.N-TYR273.OH 14.21%

GLN122.NE2-THR277.OG1 5.80%

ASN110.ND2-LYS105.O 43.95%

CYS192.N-CYS189.O 27.12%

ASN186.ND2-GLN194.OE1 14.21%

LYS92.N-HIS89.O 5.74%

THR102.N-GLN121.OE1 43.70%

MET23.N-ARG3.O 27.06%

ASN186.ND2-TYR233.OH 14.21%

LEU101.N-VAL98.O 5.61%

ARG82.NH2-ASP76.OD2 43.52%

SER293.N-LEU282.O 26.87%

TYR136.N-LEU132.O 13.72%

SER78.N-ASP76.OD1 5.49%

LEU185.N-THR197.O 43.27%

ARG140.NH2-GLU124.OE1 26.87%

THR277.OG1-THR259.O 13.65%

HIS89.N-ALA86.O 5.42%

VAL21.N-ILE5.O 43.20%

CYS189.N-GLY193.O 26.81%

THR90.OG1-ALA145.O 13.59%

ASN15.ND2-ASP12.OD1 5.42%

TYR136.OH-LEU120.O 43.08%

ARG138.NE-GLU143.OE2 26.62%

GLU307.N-PRO240.O 13.28%

ARG140.NH2-TYR136.OH 5.42%

ILE222.N-ALA230.O 42.96%

SER24.OG-ASP22.OD2 26.50%

GLN195.N-VAL187.O 13.28%

ALA131.N-TYR71.O 5.30%

TYR310.N-GLN237.O 42.39%

SER309.OG-GLU238.OE1 26.43%

LYS91.NZ-ASP37.OD1 13.28%

SER49.N-HIS47.ND1 5.17%

LYS274.NZ-GLU263.OE1 42.39%

ARG82.NH1-ALA153.O 26.43%

SER24.N-ASP22.OD2 13.28%

CYS270.N-ASN267.O 5.11%

VAL41.N-THR34.O 42.33%

ARG82.NH2-ASP76.OD1 26.18%

LYS279.NZ-GLU280.OE1 13.15%

THR231.OG1-VAL220.O 5.11%

THR115.OG1-SER111.O 42.02%

ILE14.N-ASP12.OD1 26.06%

GLU280.N-GLU280.OE1 12.91%

TYR283.OH-GLU280.OE1 5.05%

VAL187.N-GLN195.O 41.40%

ILE151.N-PHE147.O 26.06%

SER49.OG-HIS47.ND1 12.84%

THR10.OG1-ASN15.O 41.27%

LYS157.N-LEU152.O 25.37%

GLN133.NE2-TYR137.OH 12.28%

Supplementary Information

17

Table 1.3 All the SBs of the five PLpro models in http://chemcha-gpu0.ucr.edu/software/ optimized (1) SARS-CoV-2-wt

(4) SARS-CoV-1-wt

(3) SARS-CoV-2-wt-S88

(5) SARS-CoV-1-wt-S88

(2) SARS-CoV-2-C111S-mutant

ASP37-LYS91 ASP40-LYS43

ASP41-LYS44

ASP40-LYS43

ASP41-LYS44 GLU52-LYS7

GLU51-LYS6

ASP61-HIS17 ASP62-ARG65

ASP62-ARG65 GLU68-HIS18

GLU68-HIS18 ASP76-ARG82

ASP77-ARG83

ASP77-ARG83

ASP76-ARG82

GLU78-ARG66

GLU78-ARG66 ASP108-HIS89 ASP108-LYS92 GLU124-LYS126

GLU124-LYS126 GLU125-LYS307

GLU124-LYS126 GLU125-LYS307 GLU143-ARG138

ASP134-ARG138

GLU135-ARG139

GLU143-ARG138

ASP144-ARG139

ASP134-ARG138

GLU161-LYS157

GLU162-LYS158

GLU161-LYS157

GLU162-LYS158

ASP164-ARG166

ASP165-ARG167

ASP164-ARG166

ASP165-ARG167

ASP144-ARG139 GLU161-LYS157

GLU167-LYS157 GLU167-ARG166 GLU168-ARG167

GLU168-ARG167

GLU180-LYS127

GLU180-LYS127

ASP179-LYS200 GLU214-LYS217

ASP215-LYS218

GLU214-LYS218

ASP215-LYS218

GLU214-LYS217

GLU214-LYS218 ASP230-ARG229 ASP230-LYS191 GLU238-LYS182

GLU239-LYS183

GLU238-LYS182

GLU251-LYS298

GLU239-LYS183

GLU252-LYS254

GLU252-LYS297

GLU252-LYS297

GLU263-LYS274

GLU263-LYS274 GLU264-ARG285

GLU263-LYS274 GLU264-ARG285 GLU281-LYS280

GLU280-LYS279 GLU281-LYS293 ASP286-HIS272

GLU238-LYS182

GLU251-LYS298 GLU252-LYS254

ASP287-HIS273

GLU280-LYS279

GLU281-LYS293 ASP286-HIS272

ASP287-ARG285

ASP287-HIS273

ASP286-HIS272

ASP287-ARG285

GLU296-LYS253 GLU295-LYS254

GLU295-LYS254

ASP302-ARG166 GLU307-LYS217

18

1 Papain-Like Cysteine Protease (PLpro)

Table 1.4 All the SBs of the five PLpro models in http://chemcha-gpu0.ucr.edu/software/ during 1 μs’ MDs (1) SARS-CoV-2-wt

(4) SARS-CoV-1-wt

(3) SARS-CoV-2-wt-S88

(5) SARS-CoV-1-wt-S88

(2) SARS-CoV-2-C111S-mutant

ASP37-LYS53

ASP38-LYS54

ASP37-LYS53

ASP38-LYS54

ASP37-LYS53

ASP37-LYS91

ASP38-LYS92

ASP37-LYS91

ASP38-LYS92

ASP37-LYS91

ASP37-ARG138 ASP40-LYS43

ASP41-LYS44

ASP40-LYS43

ASP41-LYS44

ASP40-LYS43

GLU51-LYS6

GLU52-LYS4

GLU51-LYS6

GLU52-LYS7

GLU51-LYS6

GLU52-LYS7 ASP61-ARG65 ASP62-ARG65

ASP63-ARG66

ASP62-ARG65

ASP63-ARG66

ASP62-ARG65

ASP76-ARG82

ASP77-ARG83

ASP76-ARG82

ASP77-ARG83

ASP76-ARG82

GLU78-ARG66

GLU78-ARG66

ASP108-LYS92

ASP109-LYS93

ASP108-LYS92

ASP109-LYS93

ASP108-LYS92

GLU124-ARG140

GLU125-ARG141

GLU124-ARG140

GLU125-ARG141

GLU124-ARG140

GLU124-LYS126

GLU125-LYS127

GLU124-LYS126

GLU125-LYS127

GLU124-LYS126

GLU124-LYS279

GLU125-LYS280

GLU124-LYS279

GLU125-LYS280

GLU124-LYS279

GLU124-LYS306

GLU125-LYS307

GLU124-LYS306

GLU125-LYS307

GLU124-LYS306

ASP134-ARG138

GLU135-ARG139

ASP134-ARG138

GLU135-ARG139

ASP134-ARG138

GLU143-LYS91

ASP144-LYS92

GLU143-LYS91

ASP144-LYS92

GLU143-LYS91

GLU143-ARG138

ASP144-ARG139

GLU143-ARG138

ASP144-ARG139

GLU143-ARG138

GLU161-LYS157

GLU162-LYS158

GLU161-LYS157

GLU162-LYS158

GLU161-LYS157

ASP164-ARG166

ASP165-ARG167

ASP164-ARG166

ASP165-ARG167

ASP164-ARG166

ASP164-LYS157 GLU167-LYS157

GLU168-LYS158

GLU167-LYS157

GLU168-LYS158

GLU168-ARG167

GLU167-ARG166

GLU168-ARG167

GLU167-LYS157 GLU167-ARG166 ASP179-LYS126

GLU180-LYS127 GLU180-LYS183 ASP179-LYS200 GLU214-LYS217

ASP179-LYS200 ASP215-LYS218

GLU214-LYS218

GLU214-LYS217

ASP179-LYS200 ASP215-LYS218

GLU214-LYS218

GLU214-LYS217 GLU214-LYS218

GLU214-LYS254 GLU214-LYS315

GLU214-LYS315 ASP230-LYS191

ASP230-LYS191

ASP230-ARG229 GLU238-LYS182

GLU239-LYS183

ASP230-ARG229 GLU238-LYS182

GLU239-LYS183

GLU238-LYS182

GLU238-LYS315 GLU251-LYS253 GLU251-LYS298

GLU251-LYS298

GLU252-LYS254

GLU252-LYS254

GLU252-LYS297

GLU252-LYS297

GLU252-LYS297

GLU263-LYS274

GLU263-LYS274

GLU263-LYS274

GLU264-ARG285 GLU280-LYS279

GLU281-LYS280

GLU280-LYS292

GLU281-LYS293

ASP286-LYS274

ASP287-ARG285

GLU252-LYS254

GLU264-ARG285 GLU280-LYS279

GLU281-LYS280

GLU280-LYS279 GLU280-LYS292

GLU281-LYS307 ASP286-LYS274

GLU296-LYS253

ASP287-ARG285

GLU295-LYS254

GLU295-LYS254

ASP286-LYS274

GLU296-LYS253 GLU295-LYS254

GLU295-LYS297

GLU296-LYS298

GLU295-LYS297

ASP302-ARG166

ASP303-ARG167

ASP302-ARG166

GLU307-LYS217

GLU308-LYS218

GLU307-LYS217

GLU308-LYS218

GLU308-LYS307

GLU307-LYS306

GLU308-LYS307

GLU296-LYS298

GLU295-LYS297 ASP302-ARG166 GLU307-LYS217

Supplementary Information

19

Table 1.5 All the HBs of the five PLpro models in http://chemcha-gpu0.ucr.edu/software/ optimized (1) SARS-CoV-2-wt

(4) SARS-CoV-1-wt

(3) SARS-CoV-2-wt-S88

(5) SARS-CoV-1-wt-S88

(2) SARS-CoV-2-C111S-mutant

THR4.N-ASP22.OD1

THR5.OG1-VAL22.O

ILE5.N-VAL21.O

LYS7.N-GLU52.OE1

THR4.N-ASP22.OD1

LYS6.N-GLU51.OE2

LYS7.N-GLU52.OE2

LYS6.N-GLU51.OE1

LYS7.NZ-GLU52.OE2

LYS6.N-GLU51.OE2

VAL7.N-GLN19.O

VAL8.N-GLN20.O

VAL7.N-GLN19.O

PHE9.N-LYS54.O

LYS6.NZ-GLU51.OE1

PHE8.N-LYS53.O

THR10.OG1-HIS18.O

PHE8.N-LYS53.O

THR10.N-HIS18.O

ILE14.N-ASP12.OD1

THR9.N-HIS17.O

THR15.N-ASP13.OD1

THR9.N-HIS17.O

THR10.OG1-HIS18.O

ASN15.ND2-ASP12.OD2

THR9.OG1-HIS17.O

ASN16.N-ASP13.OD1

ILE14.N-ASP12.OD2

THR15.N-ASP13.OD1

GLN19.N-VAL7.O

ILE14.N-ASP12.OD1

ASN16.ND2-ASP13.OD2

ASN15.N-ASP12.OD2

ASN16.ND2-ASP13.OD2

VAL21.N-ILE5.O

ASN15.ND2-ASP12.OD2

HIS18.NE2-GLU68.OE2

ASN15.ND2-ASP12.OD1

HIS18.NE2-GLU68.OE2

ASP22.N-GLN30.OE1

GLN19.N-VAL7.O

GLN20.N-VAL8.O

THR18.OG1-VAL7.O

GLN20.N-VAL8.O

SER24.N-ASP22.OD2

ASP22.N-GLN30.OE1

VAL22.N-ILE6.O

VAL21.N-ILE5.O

VAL22.N-ILE6.O

SER24.OG-ASP22.OD2

SER24.N-ASP22.OD2

ASP23.N-GLN31.OE1

SER24.N-ASP22.OD2

SER25.OG-ASP23.OD2

THR26.N-GLN29.OE1

THR26.N-GLN29.OE1

MET26.N-ASP23.OD2

SER24.OG-ASP22.OD1

MET26.N-ASP23.OD1

TYR27.OH-HIS50.ND1

TYR27.OH-HIS50.ND1

TYR28.N-ILE45.O

THR26.N-GLN29.OE1

TYR28.N-ILE45.O

GLN30.NE2-THR26.O

GLN30.NE2-THR26.O

TYR28.OH-HIS51.ND1

THR26.OG1-GLN29.OE1

TYR28.OH-HIS51.ND1

PHE31.N-TYR27.O

PHE31.N-TYR27.O

GLN31.NE2-ASP23.O

TYR27.N-ILE44.O

GLN31.NE2-ASP23.O

THR34.OG1-GLY32.O

THR34.OG1-GLY32.O

PHE32.N-TYR28.O

TYR27.OH-HIS50.ND1

PHE32.N-TYR28.O

THR34.N-THR42.OG1

THR34.N-THR42.OG1

GLY33.N-TYR28.O

GLN29.N-THR26.O

THR35.OG1-GLY33.O

TYR35.N-TYR56.O

TYR35.N-TYR56.O

THR35.N-THR43.OG1

PHE31.N-TYR27.O

THR35.N-THR43.OG1

THR42.N-ASP40.OD1

LEU36.N-ALA39.O

THR35.OG1-GLY33.O

GLY32.N-TYR27.O

LEU37.N-ALA40.O

LYS45.NZ-SER24.O

ASP40.OD1-LYS43.NZ

TYR36.N-PHE57.O

THR34.OG1-GLY32.O

ASP41.OD2-LYS44.NZ

HIS50.N-HIS47.O

VAL41.N-THR34.O

ALA40.N-LEU37.O

TYR35.N-TYR56.O

VAL42.N-THR35.O

GLU51.OE1-LYS6.NZ

LYS43.NZ-ASP40.OD1

ASP41.OD2-LYS44.NZ

LEU36.N-ALA39.O

LYS44.NZ-ASP41.OD2

LYS53.NZ-SER49.O

SER49.OG-HIS47.ND1

VAL42.N-THR35.O

ASP37.OD1-LYS91.NZ

LYS46.NZ-SER25.O

TYR56.N-TYR35.O

HIS50.N-HIS47.O

THR43.N-ASP41.OD1

ASP40.OD1-LYS43.NZ

GLU52.OE2-LYS7.NZ

ASN60.ND2-PHE31.O

GLY52.N-LYS6.O

LYS44.NZ-ASP41.OD2

VAL41.N-THR34.O

GLY53.N-LYS7.O

ASP62.OD1-ARG65.NH2

LYS53.NZ-SER49.O

LYS46.NZ-SER25.O

THR42.N-ASP40.OD2

LYS54.N-HIS51.O

THR63.OG1-ASP61.OD2

PHE55.N-PHE8.O

GLY53.N-LYS7.O

LYS43.NZ-ASP40.OD1

PHE56.N-PHE9.O

ARG65.NE-ASP62.OD2

THR63.N-ASP61.OD2

PHE56.N-PHE9.O

LYS45.NZ-SER24.O

VAL58.N-THR11.O

ARG65.NH2-ASP62.OD1

LEU64.N-ASP61.OD1

VAL58.N-THR11.O

SER49.OG-HIS47.ND1

THR64.N-ASP62.OD2

GLU70.N-VAL66.O

ARG65.NH1-ASN60.O

THR64.OG1-ASP62.OD1

HIS50.N-HIS47.O

THR64.OG1-ASP62.OD2

TYR72.OH-VAL11.O

GLU67.N-THR63.O

ARG66.NE-SER61.O

GLY52.N-LYS6.O

LEU65.N-ASP62.OD1

TYR72.N-ALA68.O

GLU70.N-VAL66.O

ARG66.NH1-GLU78.OE1

LYS53.NZ-SER49.O

ARG66.NE-SER61.O

ASP76.OD2-ARG82.NH2

TYR71.OH-ASP134.OD1

ARG66.NH2-GLU78.OE2

PHE55.N-PHE8.O

ARG66.NH1-GLU78.OE1

SER78.OG-ASP76.OD1

TYR72.N-ALA68.O

SER67.OG-ASP63.O

TYR56.N-TYR35.O

ARG66.NH2-GLU78.OE2

ARG82.NH2-ASP76.OD2

TYR72.OH-VAL11.O

GLU68.N-THR64.O

TYR56.OH-TYR72.OH

GLU68.OE2-HIS18.NE2

ARG82.NH1-ALA153.O

ASP76.OD2-ARG82.NH1

ALA69.N-LEU65.O

LEU64.N-ASP62.O

TYR72.OH-GLU135.OE1

TYR83.N-PHE79.O

SER78.OG-ASP76.OD1

GLU71.N-SER67.O

ARG65.NH1-PRO59.O

TYR73.OH-VAL12.O

MET84.N-LEU80.O

ARG82.NH1-ASP76.OD2

TYR72.OH-GLU135.OE1

VAL66.N-ASP62.O

TYR73.N-ALA69.O

LEU87.N-TYR83.O

ARG82.NH2-ALA153.O

TYR73.OH-VAL12.O

ALA68.N-LEU64.O

GLU78.OE1-ARG66.NH1

THR90.N-ALA86.O

TYR83.N-PHE79.O

TYR73.N-ALA69.O

TYR71.OH-ASP134.OD2

GLU78.OE2-ARG66.NH2

LYS91.NZ-GLY38.O

MET84.N-LEU80.O

ASP77.OD2-ARG83.NH2

TYR72.OH-VAL11.O

ARG83.NH2-SER79.OG

LYS92.NZ-HIS89.ND1

SER85.N-GLY81.O

GLU78.OE1-ARG66.NH1

TYR72.N-ALA68.O

TYR84.N-PHE80.O

TRP93.NE1-ASP108.OD1

LEU87.N-TYR83.O

GLU78.OE2-ARG66.NH2

SER78.N-ASP76.OD2

MET85.N-LEU81.O

TYR95.OH-THR90.O

THR90.N-ALA86.O

SER79.OG-ASP77.OD1

LEU80.N-ASP76.O

SER86.N-GLY82.O

VAL98.N-LEU101.O

THR90.OG1-ALA145.O

ARG83.NH2-ASP77.OD2

ARG82.NE-ALA153.O

ALA87.N-ARG83.O

THR102.OG1-ALA139.O

LYS91.NZ-ASP37.O

ARG83.NE-SER79.OG

SER85.N-GLY81.O

LEU88.N-TYR84.O

SER103.OG-GLY287.O

LYS92.NZ-ASN88.O

ARG83.NH1-ALA154.O

THR90.N-ALA86.O

THR91.N-ALA87.O

LEU118.N-ALA114.O

LYS92.NZ-HIS89.ND1

TYR84.N-PHE80.O

THR90.OG1-ALA145.O

THR91.OG1-ALA146.O

THR119.N-THR115.O

TRP93.NE1-ASP108.OD2

MET85.N-LEU81.O

LYS91.NZ-ASP37.OD1

LYS92.NZ-ASP38.O

THR119.OG1-THR115.O

GLN97.NE2-GLY100.O

SER86.OG-GLY82.O

LYS92.NZ-ASP108.OD2

LYS93.N-HIS90.O

LEU120.N-ALA116.O

GLN97.NE2-THR102.OG1

LEU88.N-TYR84.O

TRP93.NE1-ASP108.OD2

TRP94.NE1-ASP109.OD2

GLN121.NE2-LEU117.O

TYR95.OH-THR90.O

THR91.N-ALA87.O

LYS94.NZ-TRP93.O

GLN98.NE2-GLY101.O

GLN122.NE2-THR277.OG1

GLY100.N-GLN97.O

THR91.OG1-ALA146.O

TYR95.OH-THR90.O

VAL99.N-LEU102.O

ASN128.N-HIS175.O

THR102.N-GLN121.OE1

TRP94.NE1-ASP109.OD2

VAL98.N-LEU101.O

THR103.N-GLN122.OE1

GLN133.NE2-PHE127.O

THR102.OG1-ALA139.O

THR103.N-GLN122.OE1

THR102.N-GLN121.OE1

SER104.N-PRO97.O

ASP134.N-PRO130.O

SER103.N-PRO96.O

SER104.N-PRO97.O

THR102.OG1-ALA139.O

SER104.OG-GLY288.O

TYR136.OH-LEU120.O

SER103.OG-GLY287.O

SER104.OG-GLY288.O

SER103.N-PRO96.O

LYS106.N-LYS95.O

ARG138.N-ASP134.O

ASP108.OD2-TRP93.NE1

LEU119.N-SER115.O

ASN109.ND2-GLY271.O

ASN110.ND2-GLY161.O

ARG140.NH2-TYR136.OH

TYR112.OH-GLU161.O

LEU121.N-VAL117.O

TYR112.OH-GLU161.O

TYR113.OH-GLU162.O

ASN146.ND2-TYR83.OH

LEU118.N-ALA114.O

GLN122.NE2-LEU118.O

THR115.N-CYM111.O

LEU119.N-SER115.O

CYS148.N-ALA144.O

THR119.OG1-THR115.O

GLN122.NE2-THR103.O

LEU118.N-ALA114.O

LEU121.N-VAL117.O

TYR154.OH-TYR72.O

LEU120.N-ALA116.O

GLN123.NE2-THR278.OG1

GLN121.NE2-THR102.O

GLN122.NE2-THR103.O

TYR154.N-LEU150.O

GLN121.NE2-LEU117.O

LYS127.N-ASN178.OD1

GLN121.NE2-LEU117.O

GLN122.NE2-LEU118.O

LYS157.NZ-GLU161.OE1

GLN122.NE2-LEU118.O

LYS127.NZ-GLU180.OE2

ILE123.N-THR119.O

LYS127.N-ASN178.OD1

LYS157.NZ-LEU162.O

(continued)

20

1 Papain-Like Cysteine Protease (PLpro)

Table 1.5 (continued) (1) SARS-CoV-2-wt

(4) SARS-CoV-1-wt

(3) SARS-CoV-2-wt-S88

(5) SARS-CoV-1-wt-S88

(2) SARS-CoV-2-C111S-mutant

GLU124.OE2-LYS126.NZ

PHE128.N-GLN134.OE1

GLU124.OE2-LYS126.NZ

LYS127.NZ-GLU180.OE2

THR158.OG1-GLU161.OE2

LYS126.NZ-GLU124.OE2

ASN129.ND2-GLU180.OE1

LYS126.NZ-GLU124.OE2

PHE128.N-GLN134.OE1

GLU161.OE1-LYS157.NZ

PHE127.N-GLN133.OE1

ASN129.N-HIS176.O

PHE127.N-GLN133.OE1

ASN129.N-HIS176.O

ARG166.NE-GLU167.OE2

ASN128.N-HIS175.O

ALA132.N-TYR72.O

ASN128.N-HIS175.O

ASN129.ND2-GLU180.OE1

GLU167.N-ASP164.OD1

ALA131.N-TYR71.O

GLU135.N-PRO131.O

ALA131.N-TYR71.O

ALA132.N-TYR72.O

MET169.N-VAL165.O

ASP134.N-PRO130.O

GLU135.OE2-ARG139.NH1

GLN133.NE2-TYR137.OH

GLU135.N-PRO131.O

LEU172.N-THR168.O

TYR136.OH-LEU120.O

TYR137.OH-LEU121.O

ASP134.N-PRO130.O

TYR137.OH-LEU121.O

PHE173.N-MET169.O

ARG138.NE-GLU143.OE1

ARG139.NH1-GLU135.OE2

ALA135.N-ALA131.O

ARG139.NE-ASP144.OD2

GLN174.NE2-SER170.O

ARG138.NH1-ASP134.OD2

ARG139.NH2-ASN147.OD1

TYR136.OH-LEU120.O

ARG139.NH2-ASP144.OD1

ASN177.N-LYS126.O

ARG138.NH2-GLU143.OE2

ARG141.NE-TYR137.O

ARG138.NE-ASP134.OD1

ASN147.ND2-TYR84.OH

ASN177.ND2-ASN128.OD1

GLU143.OE2-ARG138.NH2

ASN147.ND2-TYR84.OH

ARG138.NH2-ASP134.OD2

CYS149.N-ALA145.O

LYS182.NZ-GLU238.OE2

ASN146.ND2-TYR83.OH

CYS149.N-ALA145.O

CYS148.N-ALA144.O

LEU153.N-CYS149.O

ARG183.N-LEU199.O

CYS148.N-ALA144.O

TYR155.N-LEU151.O

ILE151.N-PHE147.O

TYR155.N-LEU151.O

ARG183.NH1-MET206.O

ILE151.N-PHE147.O

TYR155.OH-TYR73.O

LEU152.N-CYS148.O

LYS158.N-LEU153.O

VAL184.N-GLN236.O

TYR154.OH-TYR72.O

LYS158.NZ-GLU162.OE2

TYR154.OH-TYR72.O

LYS158.NZ-GLU162.OE2

LEU185.N-THR197.O

TYR154.N-LEU150.O

LYS158.NZ-LEU163.O

TYR154.N-LEU150.O

LYS158.NZ-LEU163.O

ASN186.ND2-TYR233.OH

LYS157.NZ-GLU167.OE1

THR159.N-GLU162.OE1

CYS155.N-ILE151.O

THR159.N-GLU162.OE1

ASN186.N-TYR233.O

THR158.OG1-GLU161.OE2

VAL166.N-TYR274.OH

LYS157.NZ-GLU161.OE1

GLU162.OE2-LYS158.NZ

VAL187.N-GLN195.O

ASP164.N-GLU167.OE2

ARG167.NH2-ASP165.OD1

GLU161.OE1-LYS157.NZ

ARG167.NH2-GLU168.OE2

VAL188.N-THR231.O

THR168.N-ASP164.O

GLU168.N-ASP165.OD2

ARG166.NE-ASP302.OD1

THR169.N-ASP165.O

LYS190.NZ-LYS190.O

Table 1.6 All the HBs of the five PLpro models in http://chemcha-gpu0.ucr.edu/software/ optimized (continuation) (1) SARS-CoV-2-wt

(4) SARS-CoV-1-wt

(3) SARS-CoV-2-wt-S88

(5) SARS-CoV-1-wt-S88

(2) SARS-CoV-2-C111S-mutant

THR168.OG1-ASP164.O

THR169.OG1-ASP165.O

ARG166.NH2-ASP302.OD2

THR169.OG1-ASP165.O

LEU199.N-ARG183.O

MET169.N-VAL165.O

THR171.OG1-ARG167.O

SER170.OG-GLU167.O

THR171.OG1-ARG167.O

GLN215.NE2-GLY219.O

ASN177.N-LYS126.O

LEU173.N-THR169.O

TYR171.OH-GLU167.OE2

LYS183.NZ-GLU239.OE1

LYS217.NZ-GLU214.OE1

ASN177.ND2-ASN128.OD1

LEU174.N-MET170.O

LYS182.NZ-SER180.O

ARG184.N-LEU200.O

LYS218.NZ-GLU214.O

LYS182.N-GLU238.O

GLN175.NE2-THR171.O

ARG183.NE-GLN237.OE1

ARG184.NE-GLN238.OE1

GLY219.N-GLN215.O

LYS182.NZ-GLU238.OE2

GLU180.OE2-LYS127.NZ

ARG183.NH1-MET206.O

VAL185.N-GLN237.O

LYS200.NZ-ASP179.OD2

ARG183.NH1-MET206.O

LYS183.N-GLU239.O

VAL184.N-GLN236.O

LEU186.N-THR198.O

TYR213.OH-GLU307.OE1

VAL184.N-GLN236.O

LYS183.NZ-GLU239.OE1

LEU185.N-THR197.O

ASN187.N-TYR234.O

VAL220.N-LYS232.O

LEU185.N-THR197.O

ARG184.NE-GLN238.OE1

ASN186.N-TYR233.O

VAL188.N-LYS196.O

ILE222.N-ALA230.O

ASN186.ND2-GLN194.OE1

ARG184.NH1-MET207.O

VAL187.N-GLN195.O

VAL189.N-THR232.O

LYS228.NZ-GLY227.O

ASN186.ND2-TYR233.OH

VAL185.N-GLN237.O

VAL188.N-THR231.O

CYM190.N-GLY194.O

ALA230.N-ILE222.O

ASN186.N-TYR233.O

LEU186.N-THR198.O

GLN195.N-VAL187.O

LYS191.NZ-ASP230.OD1

THR231.OG1-GLN221.OE1

VAL188.N-THR231.O

ASN187.ND2-GLN195.OE1

THR198.OG1-GLN196.OE1

LYS196.NZ-THR198.OG1

LYS232.N-VAL220.O

THR197.N-LEU185.O

ASN187.ND2-TYR234.OH

LEU199.N-ARG183.O

LEU200.N-ARG184.O

TYR233.N-ASN186.O

LEU199.N-ARG183.O

ASN187.N-TYR234.O

MET206.N-VAL202.O

GLU204.N-GLU204.OE1

VAL235.N-VAL184.O

MET206.N-VAL202.O

VAL189.N-THR232.O

THR210.OG1-GLY209.O

MET207.N-VAL203.O

GLN237.NE2-ALA204.O

VAL205.N-VAL202.O

LYS191.NZ-ASP230.O

TYR213.OH-GLU307.OE1

TYR214.OH-GLU308.OE1

GLN237.NE2-SER239.OG

GLY209.N-SER245.O

THR198.N-LEU186.O

GLN215.NE2-GLY219.O

THR219.OG1-ASP215.O

GLU238.N-LYS182.O

TYR213.OH-GLU307.OE2

LEU200.N-ARG184.O

GLY219.N-GLN215.O

GLY220.N-ASN216.O

MET243.N-VAL205.O

GLN215.NE2-GLY219.O

MET207.N-VAL203.O

VAL220.N-LYS232.O

VAL221.N-GLN233.O

MET244.N-VAL303.O

LYS217.NZ-GLU214.OE1

GLY210.N-SER246.O

ILE222.N-ALA230.O

GLY228.N-CYM225.O

SER245.N-TYR207.O

LYS218.NZ-GLU214.O

TYR214.OH-GLU308.OE1

ALA230.N-GLY227.O

ARG229.NE-ASP230.OD2

SER245.OG-ASP302.OD1

GLY219.N-GLN215.O

THR219.OG1-ASP215.O

THR231.N-VAL188.O

ASP230.OD2-ARG229.NE

ALA246.N-THR301.O

VAL220.N-LYS232.O

GLY220.N-ASN216.O

THR231.OG1-GLN229.O

TYR234.N-ASN187.O

GLU252.OE2-LYS297.NZ

GLN221.NE2-THR231.OG1

VAL221.N-GLN233.O

LYS232.N-VAL220.O

TYR234.OH-ILE315.OXT

LEU253.N-TYR296.O

ILE222.N-ALA230.O

ARG229.NH1-GLY228.O

TYR233.N-ASN186.O

VAL236.N-VAL185.O

LYS254.NZ-GLU252.OE1

LYS228.N-CYM226.O

GLN233.NE2-TYR208.OH

LEU234.N-PHE216.O

GLN238.NE2-ALA205.O

LYS254.NZ-GLU295.OE2

THR231.N-VAL188.O

GLN233.N-VAL221.O

VAL235.N-VAL184.O

GLN238.NE2-SER240.OG

HIS255.NE2-LYS279.O

LYS232.NZ-TYR207.OH

TYR234.N-ASN187.O

GLN236.NE2-THR311.OG1

SER241.OG-GLU125.O

THR259.N-PHE304.O

LYS232.N-VAL220.O

TYR234.OH-ILE315.OXT

GLN237.NE2-ALA204.O

VAL243.N-TYR306.O

ALA261.N-ILE276.O

TYR233.N-ASN186.O

VAL236.N-VAL185.O

GLN237.NE2-SER239.OG

MET244.N-VAL206.O

SER262.OG-THR115.OG1

LEU234.N-PHE216.O

GLN238.NE2-ALA205.O

GLU238.N-LYS182.O

MET245.N-VAL304.O

GLU263.N-LYS274.O

VAL235.N-VAL184.O

GLN238.N-TYR311.O

SER239.OG-PHE241.O

SER246.N-TYR208.O

TYR264.OH-ASN267.O

GLN237.NE2-ALA204.O

GLU239.OE1-LYS183.NZ

VAL242.N-TYR305.O

SER246.OG-ASP303.OD1

TYR264.N-PRO299.O

(continued)

Supplementary Information

21

Table 1.6 (continued) (1) SARS-CoV-2-wt

(4) SARS-CoV-1-wt

(3) SARS-CoV-2-wt-S88

(5) SARS-CoV-1-wt-S88

(2) SARS-CoV-2-C111S-mutant

GLN237.N-TYR310.O

SER240.OG-PHE242.O

MET244.N-VAL303.O

ALA247.N-THR302.O

ASN267.N-CYS270.O

GLU238.N-LYS182.O

VAL243.N-TYR306.O

SER245.N-TYR207.O

TYR252.N-GLY299.O

HIS272.NE2-ASP286.OD1

GLU238.OE2-LYS182.NZ

SER246.N-TYR208.O

SER245.OG-ASP302.OD1

LEU254.N-TYR297.O

LYS274.N-GLU263.O

SER239.OG-PHE241.O

SER246.OG-ASP303.OD1

ALA246.N-THR301.O

GLN256.NE2-SER295.O

LYS274.NZ-GLU263.OE1

VAL242.N-TYR305.O

ALA247.N-THR302.O

GLU252.OE1-LYS254.NZ

THR258.OG1-GLN255.O

HIS275.NE2-GLN122.OE1

MET243.N-VAL205.O

GLU251.OE2-LYS298.NZ

LEU253.N-TYR296.O

ALA262.N-ILE277.O

ILE276.N-ALA261.O

MET244.N-VAL303.O

LYS253.NZ-GLN255.OE1

LYS254.NZ-GLU252.OE1

ASN263.N-ASP303.O

THR277.OG1-THR259.O

SER245.N-TYR207.O

LEU254.N-TYR297.O

LYS254.NZ-GLU295.OE1

ASN263.ND2-ASP303.OD2

LYS279.NZ-GLU280.OE1

SER245.OG-ASP302.OD1

GLN256.NE2-SER295.O

GLY256.N-SER278.OG

TYR265.OH-ASN268.O

LYS279.N-THR281.O

ALA246.N-THR301.O

LEU260.N-PHE305.O

THR257.OG1-LYS254.O

THR266.N-HIS273.O

GLU280.N-GLU280.OE1

LEU253.N-TYR296.O

ASN263.N-ASP303.O

SER262.OG-ASP302.OD2

ASN268.N-CYS271.O

TYR283.N-THR277.O

HIS255.N-SER294.O

ASN263.ND2-ASP303.OD2

TYR264.OH-ASN267.O

HIS273.NE2-ASP287.OD1

TYR283.OH-GLU280.OE2

SER262.OG-ASP302.OD2

GLU264.N-THR275.O

TYR264.N-PRO299.O

HIS276.NE2-GLN123.OE1

ILE285.N-HIS275.O

TYR264.N-PRO299.O

TYR265.N-PRO300.O

ASN267.N-CYS270.O

ILE277.N-ALA262.O

ASP286.OD1-HIS272.NE2

TYR264.OH-TYR268.O

THR266.N-HIS273.O

HIS272.N-THR265.O

LYS280.NZ-GLU281.OE2

ASP286.N-LEU289.O

HIS272.NE2-ASP286.OD1

TYR269.OH-ASP165.OD1

HIS272.NE2-ASP286.OD2

LEU283.N-MET294.O

THR291.N-CYS284.O

LYS274.N-GLU263.O

HIS273.NE2-ASP287.OD1

HIS275.NE2-GLN122.OE1

TYR284.N-THR278.O

SER293.N-LEU282.O

LYS274.NZ-GLU263.OE1

HIS273.N-THR266.O

ILE276.N-ALA261.O

TYR284.OH-GLU281.OE1

SER293.OG-GLU295.O

HIS275.N-ILE285.O

THR275.OG1-TYR274.O

TYR283.N-THR277.O

ARG285.NE-GLU264.OE1

TYR296.OH-GLU263.OE2

THR277.OG1-GLN122.OE1

ILE277.N-ALA262.O

TYR283.OH-GLU280.OE2

ARG285.NH2-GLU264.OE2

LYS297.NZ-GLU252.OE2

THR277.N-TYR283.O

THR278.OG1-LEU260.O

CYS284.N-THR291.O

ARG285.NH1-ASP287.OD2

THR301.N-SER262.O

LYS279.NZ-GLU280.OE1

THR278.N-TYR284.O

ILE285.N-HIS275.O

ARG285.N-THR292.O

THR301.OG1-ASP302.OD2

GLU280.OE1-LYS279.NZ

MET244.N-VAL206.O

ASP286.OD2-HIS272.NE2

ILE286.N-HIS276.O

PHE304.N-CYS260.O

TYR283.N-THR277.O

MET245.N-VAL304.O

ASP286.N-LEU289.O

ASP287.OD1-HIS273.NE2

TYR305.N-VAL242.O

TYR283.OH-GLU280.OE2

LYS280.N-THR282.O

SER294.OG-GLU295.OE2

ASP287.N-HIS290.O

LYS306.NZ-GLU307.O

CYS284.N-THR291.O

LYS280.NZ-GLY100.O

TYR296.N-LEU253.O

THR292.N-ARG285.O

LYS306.NZ-ASN308.OD1

ILE285.N-HIS275.O

GLU281.OE2-LYS293.NZ

TYR296.OH-GLU263.OE1

SER295.OG-GLU296.OE2

ASN308.N-GLU307.OE2

ASP286.OD1-HIS272.NE2

TYR284.N-THR278.O

THR301.N-SER262.O

TYR297.N-LEU254.O

SER309.OG-GLU238.OE1

ASP286.N-LEU289.O

TYR284.OH-GLU281.OE1

THR301.OG1-ALA246.O

TYR297.OH-GLU264.OE1

LEU289.N-ASP286.O

ARG285.NE-GLU264.OE1

PHE304.N-CYS260.O

LYS298.NZ-GLU251.OE1

SER293.OG-GLU295.O

ARG285.NH1-ASP287.OD2

TYR305.OH-LEU211.O

THR302.N-ASN263.O

SER294.OG-GLU295.OE1

ARG285.NH2-GLU264.OE2

TYR305.N-VAL242.O

THR302.OG1-ALA247.O

TYR296.OH-GLU263.OE2

ARG285.N-THR292.O

GLU307.OE1-TYR213.OH

VAL304.N-MET245.O

LYS297.NZ-GLU252.OE2

ILE286.N-HIS276.O

ASN308.N-GLU307.OE2

PHE305.N-CYS261.O

THR301.OG1-ALA246.O

ASP287.OD1-HIS273.NE2

TYR310.N-GLN237.O

TYR306.OH-LEU212.O

VAL303.N-MET244.O

THR292.N-ARG285.O

TYR306.N-VAL243.O

PHE304.N-CYS260.O

LYS293.NZ-GLU281.OE2

THR309.N-GLU308.OE2

TYR305.N-VAL242.O

TYR297.OH-GLU264.OE1

SER310.OG-GLU239.OE2

ASN308.N-GLU307.OE1

LYS298.NZ-GLU251.OE2

TYR311.N-GLN238.O

SER309.OG-GLU238.OE1

THR302.N-ASN263.O

TYR310.N-GLN237.O

THR302.OG1-ALA247.O

THR312.N-VAL235.O

VAL304.N-MET245.O PHE305.N-CYS261.O TYR306.OH-LEU212.O TYR306.N-VAL243.O LYS307.NZ-GLU308.O GLU308.N-SER241.O THR309.N-GLU308.OE2 TYR311.N-GLN238.O THR314.OG1-THR313.O

22

1 Papain-Like Cysteine Protease (PLpro)

Table 1.7 All the HBs (with more than 30% occupancy rates) of the SARS-CoV-2-wt and SARSCoV-1-wt models with/without ligand S88 bound in http://chemcha-gpu0.ucr.edu/software/ during 1 μs’ MDs (1) SARS-CoV-2-wt

(4) SARS-CoV-1-wt

(3) SARS-CoV-2-wt-S88

(5) SARS-CoV-1-wt-S88

THR168.OG1-ASP164.O 68.43%

SER246.OG-ASP303.OD1 73.35%

SER245.OG-ASP302.OD1 79.12%

SER246.OG-ASP303.OD1 78.62%

TYR72.OH-VAL11.O 65.13%

TYR73.OH-VAL12.O 73.15%

TYR264.OH-ASN267.O 75.22%

THR302.OG1-ALA247.O 74.43%

LYS105.N-LYS94.O 63.14%

THR302.N-ASN263.O 68.46%

THR301.OG1-ALA246.O 73.83%

THR302.N-ASN263.O 73.03%

TYR95.OH-THR90.O 63.04%

THR169.OG1-ASP165.O 63.67%

LYS105.N-LYS94.O 63.44%

TYR265.OH-ASN268.O 73.03%

GLN237.NE2-ALA204.O 61.94%

LYS106.N-LYS95.O 61.28%

GLN237.NE2-ALA204.O 62.04%

TYR73.OH-VAL12.O 69.63%

SER245.OG-ASP302.OD1 61.94%

THR302.OG1-ALA247.O 60.18%

THR301.N-SER262.O 61.94%

THR169.OG1-ASP165.O 68.53%

SER239.OG-PHE241.O 58.14%

THR171.OG1-ARG167.O 59.78%

THR168.OG1-ASP164.O 61.64%

ILE286.N-HIE276.O 62.64%

ASN128.N-HIE175.O 57.24%

TYR155.N-LEU151.O 59.58%

TYR305.OH-LEU211.O 60.04%

SER116.OG-ASN263.OD1 62.64%

TYR305.OH-LEU211.O 56.44%

TYR155.OH-TYR73.O 59.08%

TYR95.OH-THR90.O 59.24%

THR171.OG1-ARG167.O 61.64%

THR115.OG1-CYM111.O 56.34%

LEU200.N-ARG184.O 58.78%

TYR72.OH-VAL11.O 58.04%

ASN263.ND2-ASP303.OD2 60.84%

THR90.N-ALA86.O 54.75%

TYR306.OH-LEU212.O 58.68%

ASN128.N-HIE175.O 56.24%

SER156.OG-ILE152.O 59.54%

LEU199.N-ARG183.O 53.75%

THR219.OG1-ASP215.O 56.99%

THR34.OG1-GLY32.O 55.64%

TYR306.OH-LEU212.O 58.94%

MET244.N-VAL303.O 53.55%

ASN263.ND2-ASP303.OD2 56.99%

SER239.OG-PHE241.O 53.95%

GLN238.NE2-ALA205.O 58.34%

TYR154.N-LEU150.O 52.55%

ILE286.N-HIE276.O 55.59%

LEU199.N-ARG183.O 53.85%

TYR155.N-LEU151.O 56.44%

VAL98.N-LEU101.O 52.55%

GLN238.NE2-ALA205.O 55.19%

PHE173.N-MET169.O 53.75%

TYR155.OH-TYR73.O 55.84%

ILE285.N-HIE275.O 52.25%

SER156.OG-ILE152.O 55.19%

THR115.OG1-CYM111.O 53.65%

LYS106.N-LYS95.O 55.44%

PHE55.N-PHE8.O 51.65%

THR35.OG1-GLY33.O 55.09%

ILE285.N-HIE275.O 53.25%

THR35.OG1-GLY33.O 54.85%

GLN121.NE2-LEU117.O 51.35%

MET244.N-VAL206.O 52.89%

VAL98.N-LEU101.O 50.85%

LEU200.N-ARG184.O 53.55%

TYR213.OH-GLU307.OE2 50.25%

PHE56.N-PHE9.O 52.40%

SER103.OG-GLY287.O 50.25%

MET244.N-VAL206.O 51.55%

LEU253.N-TYR296.O 50.15%

SER116.OG-ASN263.OD1 51.80%

THR90.N-ALA86.O 50.15%

THR219.OG1-ASP215.O 51.25%

MET169.N-VAL165.O 50.05%

VAL189.N-THR232.O 51.10%

MET244.N-VAL303.O 49.75%

PHE56.N-PHE9.O 50.15%

PHE304.N-CYS260.O 49.95%

PHE305.N-CYS261.O 49.70%

LEU253.N-TYR296.O 49.55%

GLN122.NE2-LEU118.O 49.85%

SER103.OG-GLY287.O 48.15%

VAL99.N-LEU102.O 49.20%

VAL7.N-GLN19.O 48.75%

VAL8.N-GLN20.O 49.65%

TYR27.OH-HIE50.ND1 47.65%

LEU186.N-THR198.O 48.80%

THR10.OG1-ASN15.O 48.55%

GLN233.N-VAL221.O 49.65%

THR119.OG1-THR115.O 47.55%

GLN233.N-VAL221.O 47.80%

TYR154.N-LEU150.O 48.35%

PHE305.N-CYS261.O 49.25%

THR301.OG1-ALA246.O 46.35%

MET245.N-VAL304.O 47.70%

GLY209.N-SER245.O 48.25%

LEU37.N-ALA40.O 48.85%

LEU120.N-ALA116.O 45.95%

GLY210.N-SER246.O 47.31%

PHE55.N-PHE8.O 48.05%

MET245.N-VAL304.O 48.35%

PHE31.N-TYR27.O 45.75%

GLY53.N-LYS7.O 46.81%

ASP22.N-GLN30.OE1 48.05%

SER104.OG-GLY288.O 47.75%

CYS284.N-THR291.O 45.55%

VAL8.N-GLN20.O 46.81%

GLN121.NE2-LEU117.O 47.65%

VAL99.N-LEU102.O 47.55%

LEU185.N-THR197.O 45.05%

SER79.OG-ASP77.OD2 45.81%

PHE304.N-CYS260.O 47.35%

GLY53.N-LYS7.O 46.85%

LEU117.N-LEU113.O 44.46%

LEU37.N-ALA40.O 45.61%

THR257.OG1-LYS254.O 46.65%

LEU174.N-MET170.O 46.45%

PHE173.N-MET169.O 44.16%

GLN122.NE2-LEU118.O 44.71%

CYS284.N-THR291.O 46.25%

GLU264.N-THR275.O 46.25%

TYR154.OH-TYR72.O 43.86%

LEU254.N-TYR297.O 43.61%

LEU185.N-THR197.O 45.85%

TYR297.OH-GLU264.OE1 45.85%

THR301.N-SER262.O 43.86%

ASN111.N-ALA108.O 43.61%

PHE31.N-TYR27.O 45.75%

VAL189.N-THR232.O 45.55%

THR10.OG1-ASN15.O 43.66%

PHE128.N-GLN134.OE1 43.61%

TYR305.N-VAL242.O 45.55%

TYR73.N-ALA69.O 45.45%

LEU36.N-ALA39.O 42.46%

TYR297.OH-GLU264.OE1 43.51%

ASN186.N-TYR233.O 45.45%

GLN20.N-VAL8.O 45.15%

TYR83.N-PHE79.O 42.06%

TYR284.N-THR278.O 43.41%

LEU118.N-ALA114.O 45.15%

LEU186.N-THR198.O 44.76%

GLY52.N-LYS6.O 41.56%

LEU174.N-MET170.O 43.31%

LEU36.N-ALA39.O 44.66%

TYR36.N-PHE57.O 44.66%

GLY219.N-GLN215.O 41.46%

TYR306.N-VAL243.O 43.31%

LEU117.N-LEU113.O 43.66%

MET170.N-VAL166.O 44.06%

ASP286.N-LEU289.O 41.16%

LEU119.N-SER115.O 43.11%

LEU120.N-ALA116.O 43.46%

TYR306.N-VAL243.O 43.86%

VAL7.N-GLN19.O 41.06%

PHE32.N-TYR28.O 43.01%

MET169.N-VAL165.O 41.86%

PHE32.N-TYR28.O 43.76%

TYR83.OH-ASN146.OD1 40.96%

THR11.OG1-ASN16.O 42.81%

ASP286.N-LEU289.O 40.46%

VAL304.N-MET245.O 43.56%

THR277.N-TYR283.O 40.76%

TYR234.N-ASN187.O 42.61%

GLN19.N-VAL7.O 39.96%

LEU119.N-SER115.O 43.36%

GLN121.NE2-THR102.O 40.76%

GLN122.NE2-THR103.O 42.51%

CYS148.N-ALA144.O 39.46%

TYR208.OH-GLN233.OE1 43.26%

TYR72.N-ALA68.O 40.66%

MET170.N-VAL166.O 42.51%

GLY219.N-GLN215.O 39.46%

ASP23.N-GLN31.OE1 43.26%

GLY209.N-SER245.O 40.66%

SER240.OG-PHE242.O 41.92%

THR102.N-GLN121.OE1 39.36%

THR11.OG1-ASN16.O 42.76%

VAL303.N-MET244.O 40.56%

TYR73.N-ALA69.O 41.12%

MET243.N-VAL205.O 39.06%

ARG285.N-THR292.O 42.76%

LEU87.N-TYR83.O 40.46%

VAL304.N-MET245.O 40.92%

PHE127.N-GLN133.OE1 38.96%

THR103.OG1-ALA140.O 42.76%

LEU118.N-ALA114.O 40.46%

ARG66.N-ASP62.O 40.82%

TYR27.OH-HIE50.ND1 38.96%

VAL221.N-GLN233.O 42.56%

Supplementary Information

23

Table 1.8 All the HBs (with more than 30% occupancy rates) of the SARS-CoV-2-wt and SARS-CoV-1-wt models with/without ligand S88 bound in http://chemcha-gpu0.ucr.edu/ software/ during 1 μs’ MDs (continuation) (1) SARS-CoV-2-wt

(4) SARS-CoV-1-wt

(3) SARS-CoV-2-wt-S88

(5) SARS-CoV-1-wt-S88

ARG183.NE-GLN237.OE1 40.26%

TYR84.N-PHE80.O 40.72%

VAL21.N-ILE5.O 38.56%

LEU254.N-TYR297.O 42.06%

THR102.N-GLN121.OE1 40.26%

TYR28.OH-HIE51.ND1 40.52%

VAL303.N-MET244.O 38.26%

LEU118.N-LEU114.O 41.56%

ILE151.N-PHE147.O 40.16%

GLU264.N-THR275.O 40.02%

GLN121.NE2-THR102.O 38.16%

ASN111.N-ALA108.O 40.76%

TYR305.N-VAL242.O 39.46%

TYR36.N-PHE57.O 39.72%

ASN110.N-ALA107.O 38.16%

THR275.OG1-TYR274.O 40.76%

CYS148.N-ALA144.O 39.26%

TYR214.OH-GLU308.OE1 39.32%

MET84.N-LEU80.O 37.76%

TYR84.N-PHE80.O 40.56%

TYR296.OH-GLU263.OE2 38.96%

ARG285.N-THR292.O 39.02%

SER103.N-PRO96.O 37.56%

GLY210.N-SER246.O 40.26%

ASN110.N-ALA107.O 38.16%

LEU121.N-VAL117.O 38.72%

ASN15.N-ASP12.OD2 37.46%

GLN122.NE2-THR103.O 40.26%

ASN186.N-TYR233.O 37.86%

SER25.OG-ASP23.OD1 38.02%

LEU87.N-TYR83.O 37.46%

SER240.OG-PHE242.O 40.06%

SER103.N-PRO96.O 37.26%

MET85.N-LEU81.O 37.92%

ALA131.N-TYR71.O 37.26%

TYR234.N-ASN187.O 39.86%

PHE8.N-LYS53.O 37.06%

THR258.OG1-GLN255.O 37.62%

GLY52.N-LYS6.O 36.96%

ASN187.N-TYR234.O 38.96%

PHE127.N-GLN133.OE1 37.06%

SER25.OG-ASP23.OD2 37.52%

SER262.OG-ASP302.OD2 36.86%

SER104.N-PRO97.O 38.16%

SER85.OG-GLY81.O 36.86%

LEU118.N-LEU114.O 37.43%

TRP93.NE1-ASP108.OD1 36.56%

THR91.N-ALA87.O 38.16%

ASN15.N-ASP12.OD2 36.16%

ASN129.N-HIE176.O 37.13%

TYR296.OH-GLU263.OE2 36.06%

TYR28.OH-HIE51.ND1 37.76%

VAL184.N-GLN236.O 36.06%

GLN20.N-VAL8.O 36.83%

MET206.N-VAL202.O 35.46%

MET85.N-LEU81.O 37.26%

TYR310.N-GLN237.O 35.66%

SER104.OG-GLY288.O 36.73%

TYR56.N-TYR35.O 35.46%

LEU88.N-TYR84.O 36.76%

TYR56.N-TYR35.O 35.36%

LEU88.N-TYR84.O 36.53%

ALA246.N-THR301.O 35.26%

THR258.OG1-GLN255.O 36.66%

THR42.OG1-ASP40.OD2 35.36%

TYR265.OH-ASN268.O 36.23%

SER24.OG-ASP22.OD1 35.16%

VAL22.N-ILE6.O 36.46%

LEU234.N-PHE216.O 34.87%

VAL221.N-GLN233.O 36.03%

THR34.N-THR42.OG1 34.97%

ARG66.N-ASP62.O 36.36%

MET84.N-LEU80.O 34.77%

ASN178.N-LYS127.O 35.93%

GLN237.N-TYR310.O 34.97%

TYR284.N-THR278.O 35.96%

THR257.OG1-LYS254.O 34.67%

PHE57.N-TYR36.O 35.83%

ILE151.N-PHE147.O 34.77%

ASN178.N-LYS127.O 34.77%

SER78.OG-ASP76.OD1 34.27%

TYR208.OH-GLN233.OE1 35.23%

TYR35.N-TYR56.O 34.57%

ASN129.N-HIE176.O 34.67%

THR9.N-HIE17.O 34.17%

TYR297.N-LEU254.O 35.13%

TYR83.N-PHE79.O 34.17%

THR103.N-GLN122.OE1 34.67%

VAL220.N-LYS232.O 33.57%

THR198.N-LEU186.O 34.23%

ASP134.N-PRO130.O 34.17%

PHE128.N-GLN134.OE1 34.57%

SER24.OG-ASP22.OD2 33.47%

VAL22.N-ILE6.O 34.03%

TYR83.OH-ASN146.OD1 34.07%

THR266.N-HIP273.O 34.27%

ALA246.N-THR301.O 33.37%

SER104.N-PRO97.O 33.73%

THR277.N-TYR283.O 33.87%

ALA247.N-THR302.O 34.27%

TYR296.OH-GLU263.OE1 33.17%

ASN187.N-TYR234.O 33.63%

TYR72.N-ALA68.O 33.57%

ASN263.N-ASP303.O 34.17%

VAL188.N-THR231.O 33.07%

ALA247.N-THR302.O 33.53%

SER262.N-ASP302.O 33.57%

TYR214.OH-GLU308.OE1 33.97%

ALA131.N-TYR71.O 32.67%

THR103.OG1-ALA140.O 33.53%

SER24.OG-ASP22.OD2 33.27%

PHE57.N-TYR36.O 33.97%

MET206.N-VAL202.O 32.67%

SER67.OG-ASP63.O 33.53%

LEU234.N-PHE216.O 32.87%

SER25.OG-ASP23.OD1 33.57%

SER24.OG-ASP22.OD1 32.27%

ASP23.N-GLN31.OE1 33.33%

VAL220.N-LYS232.O 32.87%

TYR137.OH-LEU121.O 33.47%

THR42.OG1-ASP40.OD1 32.27%

TYR297.OH-GLU264.OE2 33.03%

THR42.OG1-ASP40.OD2 32.77%

TYR297.N-LEU254.O 33.07%

VAL21.N-ILE5.O 32.17%

MET207.N-VAL203.O 32.34%

ASN15.ND2-ASP12.OD1 31.67%

THR198.N-LEU186.O 32.97%

ASN308.N-GLU307.OE1 31.57%

THR43.OG1-ASP41.OD2 32.24%

TYR136.OH-LEU120.O 31.47%

THR91.OG1-ALA146.O 32.77%

ASN15.ND2-ASP12.OD1 31.57%

THR43.OG1-ASP41.OD1 32.24%

VAL242.N-TYR305.O 31.37%

ALA140.N-ALA136.O 32.67%

TYR35.N-TYR56.O 31.07%

ILE6.N-VAL22.O 32.24%

VAL184.N-GLN236.O 31.17%

SER86.N-GLY82.O 32.47%

SER170.OG-ARG166.O 31.07%

VAL58.N-THR11.O 32.14%

ARG183.NE-GLN237.OE1 30.97%

CYS149.N-ALA145.O 32.37%

SER262.N-ASP302.O 30.67%

VAL185.N-GLN237.O 31.84%

VAL187.N-GLN195.O 30.47%

SER79.OG-ASP77.OD2 32.17%

SER85.N-GLY81.O 30.47%

THR91.N-ALA87.O 31.64%

THR42.OG1-ASP40.OD1 30.47%

THR43.OG1-ASP41.OD1 32.07%

THR115.N-CYM111.O 30.17%

TYR137.OH-LEU121.O 31.54%

VAL57.N-THR10.O 30.27%

PHE70.N-ARG66.O 31.87%

GLN237.N-TYR310.O 30.07%

LEU151.N-ASN147.O 31.54%

PHE8.N-LYS53.O 29.57%

TYR252.N-GLY299.O 31.77%

TYR213.OH-GLU307.OE1 29.97%

ASP287.N-HIE290.O 31.34%

SER49.OG-HIE47.ND1 29.47%

ILE223.N-ALA231.O 31.77%

ASP134.N-PRO130.O 29.87%

THR275.OG1-TYR274.O 30.84%

ALA114.N-ASN110.O 29.47%

SER25.OG-ASP23.OD2 31.57%

ALA114.N-ASN110.O 29.57%

ASN16.N-ASP13.OD2 30.84%

LYS232.N-VAL220.O 29.27%

ALA262.N-ILE277.O 30.87%

THR90.OG1-ALA145.O 29.07%

TYR252.N-GLY299.O 30.54%

VAL41.N-THR34.O 28.97%

TYR297.OH-GLU264.OE2 30.77%

THR102.OG1-ALA139.O 28.87%

ASN263.N-ASP303.O 30.34%

LYS182.N-GLU238.O 28.67%

HIP273.N-THR266.O 30.67%

VAL57.N-THR10.O 28.57%

PHE9.N-LYS54.O 30.34%

THR102.OG1-ALA139.O 28.57%

PHE9.N-LYS54.O 30.47%

TYR136.OH-LEU120.O 28.17%

ASN16.ND2-ASP13.OD1 29.94%

SER85.OG-GLY81.O 28.57%

ALA120.N-SER116.O 30.47%

ASN177.N-LYS126.O 28.07%

PHE70.N-ARG66.O 29.74%

PHE69.N-ARG65.O 28.57%

THR43.OG1-ASP41.OD2 30.37%

LYS157.N-LEU152.O 27.97%

MET24.N-LYS4.O 29.74%

THR115.N-CYM111.O 28.57%

SER67.OG-ASP63.O 30.27%

VAL187.N-GLN195.O 27.87%

GLU239.N-LYS183.O 29.54%

TYR296.OH-GLU263.OE1 28.47%

LYS183.N-GLU239.O 30.07%

24

1 Papain-Like Cysteine Protease (PLpro)

Fig. 1.11 The Secondary Structure performances of the five PLpro models: (1) SARS-CoV-2-wt, (4) SARS-CoV-1-wt, (3) SARS-CoV-2-wt-S88, (5) SARS-CoV-1-wt-S88, and (2) SARS-CoV-2C111S-mutant during 1 μs’ MDs of http://chemcha-gpu0.ucr.edu/software/

Table 1.9 All the HBs (with more than 30% occupancy rates) of the SARS-CoV-2-C111S-mutant model in http://chemchagpu0.ucr.edu/software/ during the 1 μs’ MD

(2) SARS-CoV-2-C111S-mutant SER245.OG-ASP302.OD1 72.93%

GLU238.N-LYS182.O 34.87%

TYR72.OH-VAL11.O 65.83%

SER24.OG-ASP22.OD1 34.87%

THR168.OG1-ASP164.O 63.74%

GLN121.NE2-THR102.O 34.67%

LYS105.N-LYS94.O 62.04%

SER78.OG-ASP76.OD2 33.97%

TYR95.OH-THR90.O 61.34%

GLN237.N-TYR310.O 33.47%

ASN128.N-HIE175.O 59.54%

PHE8.N-LYS53.O 33.17%

TYR154.OH-TYR72.O 57.94%

TYR233.N-ASN186.O 32.97%

THR34.OG1-GLY32.O 57.04%

ILE222.N-ALA230.O 32.97%

ILE285.N-HIE275.O 56.04%

THR9.N-HIE17.O 32.77%

TYR154.N-LEU150.O 55.84%

THR90.OG1-ALA145.O 32.47%

PHE304.N-CYS260.O 55.24%

THR42.OG1-ASP40.OD1 31.67%

GLN237.NE2-ALA204.O 54.75%

PHE127.N-GLN133.OE1 31.67%

VAL98.N-LEU101.O 54.25%

THR102.N-GLN121.OE1 31.37%

MET84.N-LEU80.O 53.95%

SER24.OG-ASP22.OD2 30.97%

LEU199.N-ARG183.O 53.65%

LEU150.N-ASN146.O 30.77%

THR119.OG1-THR115.O 53.45%

LYS157.N-LEU152.O 30.77%

THR301.N-SER262.O 51.65%

TYR296.OH-GLU263.OE1 30.57%

VAL7.N-GLN19.O 49.85%

TYR56.N-TYR35.O 30.47%

GLN121.NE2-LEU117.O 49.15%

MET206.N-VAL202.O 30.37%

LEU253.N-TYR296.O 48.55%

ASN186.N-TYR233.O 30.27%

PHE31.N-TYR27.O 48.15%

VAL184.N-GLN236.O 29.67%

TYR305.OH-LEU211.O 47.95%

LEU234.N-PHE216.O 29.37%

SER103.OG-GLY287.O 47.95%

TRP93.NE1-ASP108.OD2 29.17%

LYS232.N-VAL220.O 47.65%

VAL242.N-TYR305.O 29.17%

PHE55.N-PHE8.O 47.25%

THR34.N-THR42.OG1 28.97%

LEU185.N-THR197.O 47.05%

THR42.OG1-ASP40.OD2 28.97%

SER239.OG-PHE241.O 46.65%

LYS182.N-GLU238.O 28.77%

LEU120.N-ALA116.O 46.45%

THR301.OG1-ALA246.O 28.77%

MET169.N-VAL165.O 46.35%

SER85.N-GLY81.O 28.67%

PHE173.N-MET169.O 46.25%

HIP272.N-THR265.O 28.27%

THR10.OG1-ASN15.O 46.15%

TYR264.OH-ASN267.O 28.17%

LEU117.N-LEU113.O 46.05%

TYR296.OH-GLU263.OE2 27.97%

THR277.N-TYR283.O 45.95%

ASN15.ND2-ASP12.OD2 27.87%

GLY52.N-LYS6.O 45.75%

THR259.N-PHE304.O 27.77%

MET243.N-VAL205.O 45.65%

VAL41.N-THR34.O 27.37%

LEU36.N-ALA39.O 45.05%

ARG82.NE-SER78.OG 26.57%

TYR83.N-PHE79.O 44.46%

THR277.OG1-GLN122.OE1 26.57%

ASP286.N-LEU289.O 43.86%

VAL57.N-THR10.O 26.37%

THR90.N-ALA86.O 43.86%

GLU263.N-LYS274.O 26.27%

MET244.N-VAL303.O 43.76%

SER49.OG-HIE47.ND1 26.27%

LEU87.N-TYR83.O 43.56%

ILE276.N-ALA261.O 26.17%

THR115.OG1-CYM111.O 43.06%

TYR83.OH-ASN146.OD1 26.17%

CYS284.N-THR291.O 42.96%

CYM189.N-GLY193.O 26.07%

GLY209.N-SER245.O 42.96%

TRP93.NE1-ASP108.OD1 26.07%

TYR72.N-ALA68.O 42.76%

ASN308.N-GLU307.OE1 25.87%

TYR35.N-TYR56.O 42.56%

THR257.OG1-LYS254.O 25.57%

VAL303.N-MET244.O 41.86%

ASP134.N-PRO130.O 24.98%

LEU118.N-ALA114.O 41.26%

LYS274.N-GLU263.O 24.78%

TYR283.N-THR277.O 41.06%

THR63.OG1-ASP61.OD1 24.78%

THR301.OG1-ASP302.OD2 41.06%

THR115.N-CYM111.O 24.78%

TYR213.OH-GLU307.OE1 40.76%

ARG140.N-TYR136.O 24.58%

VAL220.N-LYS232.O 40.76%

THR63.OG1-ASP61.OD2 24.48%

ASN110.N-ALA107.O 40.46%

TYR264.N-PRO299.O 24.48%

TYR27.OH-HIE50.ND1 40.36%

ARG65.N-ASP61.O 24.48%

TYR305.N-VAL242.O 39.76%

VAL188.N-THR231.O 24.28%

ASN177.N-LYS126.O 39.36%

ILE123.N-THR119.O 23.98%

THR102.OG1-ALA139.O 39.06%

ASN308.N-GLU307.OE2 23.78%

TYR213.OH-GLU307.OE2 38.76%

SER170.OG-ARG166.O 23.68%

VAL21.N-ILE5.O 38.26%

ARG82.N-SER78.O 23.58%

CYS148.N-ALA144.O 37.96%

TYR136.OH-LEU120.O 23.08%

ALA246.N-THR301.O 37.76%

GLN196.NE2-ASN186.OD1 22.88%

GLN19.N-VAL7.O 37.66%

ALA139.N-ALA135.O 22.78%

ASN15.N-ASP12.OD1 37.06%

GLU70.N-VAL66.O 22.78%

SER85.OG-GLY81.O 36.76%

ALA114.N-ASN110.O 22.78%

SER262.N-ASP302.O 36.16%

THR197.N-LEU185.O 22.58%

SER78.OG-ASP76.OD1 36.06%

VAL187.N-GLN195.O 22.28%

TYR310.N-GLN237.O 36.06%

HIE17.N-THR9.O 21.98%

SER103.N-PRO96.O 36.06%

CYS155.N-ILE151.O 21.98%

ILE151.N-PHE147.O 35.76%

TYR251.N-GLY298.O 20.68%

ASP22.N-GLN30.OE1 35.56%

ASN110.ND2-LYS105.O 20.58%

GLY219.N-GLN215.O 35.56%

HIE50.N-HIE47.O 20.48% ASN88.N-MET84.O 20.38%

26

1 Papain-Like Cysteine Protease (PLpro)

Table 1.10 All the π -interactions and ZN316 binding residues of the five PLpro models in http:// chemcha-gpu0.ucr.edu/software/ optimized (1) SARS-CoV-2-wt

(4) SARS-CoV-1-wt

(3) SARS-CoV-2-wt-S88

π -π stackings

(5) SARS-CoV-1-wt-S88

(2) SARS-CoV-2-C111S-mutant

HIS48-HIS51 HIS50-PHE55

HIS51-PHE56

HIS51-PHE56

TYR71-TYR72

TYR72-TYR73

TYR72-TYR73

TYR71-TYR72

PHE80-TYR155 TYR93-HIS89-TYR93 TRP107-HIS273-TRP107

TRP106-HIS272-TRP106

TRP106-HIS272-TRP106

PHE128-TYR137 PHE173-PHE241

PHE173-PHE241 TYR207-PHE216

TYR207-PHE216 TYR265-TYR274

π -cations

LYS217.NZ+-TYR310

HIS272.ND1+-TRP106

HIS273.ND1+-TRP107

HIS272.ND1+-TRP106

LYS217.NZ+-TYR310

LYS218.NZ+-TYR311

CYM189

CYM190

CYM189

CYM190

LYS279.NZ+-TYR283

ZN316

LYS218.NZ+-TYR311

HIS272.ND1+ = TRP106 CYM189 THR191 CYS192

PRO224 CYS224

CYM225

CYM226

CYS224

CYM225

CYM226

CYS227

CYM226

LYS228 GLN229 ALA230

GLY228 ALA231

ALA230

Fig. 1.12 The Secondary Structures of the five PLpro models: (1) SARS-CoV-2-wt, (4) SARSCoV-1-wt, (3) SARS-CoV-2-wt-S88, (5) SARS-CoV-1-wt-S88, and (2) SARS-CoV-2-C111Smutant of http://chemcha-gpu0.ucr.edu/software/ optimized

Supplementary Information

27

Table 1.11 All the SBs of the optimized models of (1) 7E35-PLpro-C112S-S43-dimer, (2) 7JRNPLpro-wt-GRL0617-dimer, (3) 7LBR-PLpro-wt-XR8-89-dimer, (4) 7RZC-PLpro-wt-Jun9-84-3trimer, and (5) 7SDR-PLpro-wt-Jun9-72-2-trimer (where “X” denotes the same SB appears in the both/all chains of the dimer/trimer) (3) wt-XR8-89-dimer

(4) wt-Jun9-84-3-trimer

(5) wt-Jun9-72-2-trimer

A:GLU168-B:ARG167

A:ASP134-B:LYS6

A:ASP179-C:LYS228

A:ASP179-C:LYS228

B:GLU168-A:ARG167

B:ASP134-A:LYS6

(1) C112S-S43-dimer

(2) wt-GRL0617-dimer

B:GLU161-C:LYS232

B:GLU161-C:LYS232

B:GLU167-C:ARG166

B:GLU167-C:ARG166

A:GLU2-A:ARG4

A:GLU1-A:ARG3

A:GLU1-A:ARG3

B:GLU203-C:LYS157

B:GLU203-C:LYS157

A:ASP63-A:ARG66

A:ASP40-A:LYS43

A:ASP37-A:LYS91

C:GLU161-B:LYS232

C:GLU161-B:LYS232

A:ASP77-A:ARG83

A:GLU51-A:LYS6

A:ASP62-A:ARG65

C:GLU167-B:ARG166

A:GLU168-A:ARG167

A:ASP76-A:ARG82

A:ASP76-A:ARG82

C:GLU203-B:LYS157

A:GLU253-A:LYS298

A:ASP108-A:HIS89

A:GLU143-A:ARG138

A:ASP40-A:LYS43 A:ASP62-A:ARG65

A:ASP287-A:LYS275

A:GLU124-A:LYS306

A:GLU167-A:LYS157

A:GLU51-A:LYS6

A:ASP76-A:ARG82

A:GLU308-A:LYS218

A:GLU143-A:ARG138

A:GLU214-A:LYS217

A:ASP62-A:ARG65

A:GLU124-A:LYS306

A:GLU161-A:LYS157

A:GLU214-A:LYS218

A:ASP76-A:ARG82

A:GLU143-A:ARG138

A:GLU214-A:LYS218

A:GLU238-A:LYS182

A:GLU124-A:LYS306

A:GLU161-A:LYS157

A:GLU252-A:LYS254

A:GLU252-A:LYS254

A:GLU143-A:ARG138

A:ASP164-A:ARG166

A:GLU252-A:LYS297

A:GLU252-A:LYS297

A:GLU161-A:LYS157

A:GLU214-A:LYS217

A:GLU263-A:LYS274

A:GLU280-A:LYS292

A:ASP164-A:ARG166

A:GLU214-A:LYS218

A:GLU280-A:LYS292

A:ASP286-A:HIS272

A:GLU214-A:LYS217

A:GLU238-A:LYS182

A:GLU295-A:LYS297

A:ASP286-A:LYS274

A:GLU252-A:LYS254

A:GLU252-A:LYS254

A:GLU307-A:LYS217

A:GLU295-A:LYS297

A:GLU252-A:LYS297

A:GLU252-A:LYS297

A:GLU280-A:LYS292

A:GLU280-A:LYS292

B:ASP77-B:ARG83 X

J:GLU1-J:ARG3 X

B:GLU1-B:ARG3 X

A:ASP286-A:LYS274

A:ASP286-A:LYS274

B:ASP165-B:ARG167

J:ASP40-J:LYS43 X

B:ASP40-B:LYS43

A:GLU295-A:LYS254

A:GLU295-A:LYS254

B:GLU168-B:LYS158

J:ASP62-J:ARG65

B:ASP62-B:ARG65 X

J:ASP76-J:ARG82 X

B:ASP76-B:ARG82 X

J:GLU143-J:ARG138 X

B:GLU124-B:LYS306

B:GLU51-B:LYS6

B:ASP62-B:ARG65 X

J:GLU161-J:LYS157 X

B:GLU143-B:ARG138 X

B:ASP62-B:ARG65 X

B:ASP40-B:LYS43

B:ASP76-B:ARG82 X

B:ASP40-B:LYS43 X

J:ASP164-J:ARG166

B:GLU167-B:LYS157 X

B:ASP76-B:ARG82 X

B:ASP108-B:HIS89

J:GLU167-J:LYS157

B:ASP179-B:LYS200

B:GLU124-B:LYS306 X

B:GLU124-B:LYS306 X

J:GLU214-J:LYS218 X

B:GLU214-B:LYS218 X

B:GLU143-B:ARG138 X

B:GLU143-B:ARG138 X

J:GLU252-J:LYS254 X

B:GLU252-B:LYS254 X

B:ASP164-B:ARG166 X

B:GLU161-B:LYS157

J:GLU252-J:LYS297 X

B:GLU252-B:LYS297 X

B:GLU214-B:LYS218

B:ASP164-B:ARG166 X

J:GLU280-J:LYS292 X

B:GLU280-B:LYS292 X

B:GLU238-B:LYS182

B:GLU167-B:ARG166

J:ASP286-J:LYS274

B:ASP286-B:LYS274 X

B:GLU252-B:LYS254 X

B:GLU214-B:LYS217

J:GLU295-J:LYS254

B:GLU295-B:LYS297 X

B:GLU252-B:LYS297 X

B:GLU214-B:LYS218 X

J:GLU307-J:LYS217 X

B:GLU307-B:LYS217

B:GLU280-B:LYS292 X

B:GLU252-B:LYS254 X

B:ASP286-B:LYS274

B:GLU252-B:LYS297 X

B:GLU295-B:LYS254 X

B:GLU280-B:LYS292 X

B:GLU307-B:LYS217

B:ASP286-B:LYS274 B:GLU295-B:LYS254 X

C:ASP37-C:LYS91 C:ASP40-C:LYS43

C:ASP37-C:LYS53

C:ASP62-C:ARG65 X

C:ASP40-C:LYS43 X

C:ASP76-C:ARG82 X

C:GLU51-C:LYS6

C:ASP108-C:HIS89

C:ASP62-C:ARG65 X

C:GLU124-C:LYS306 X

C:ASP76-C:ARG82 X

C:GLU143-C:ARG138 X

C:GLU124-C:LYS306 X

C:ASP164-C:ARG166 X

C:GLU143-C:ARG138 X

C:GLU167-C:ARG166

C:ASP164-C:ARG166 X

C:GLU214-C:LYS218

C:GLU214-C:LYS218 X

C:GLU238-C:LYS182

C:GLU238-C:LYS182

C:GLU252-C:LYS254 X

C:GLU252-C:LYS254 X

C:GLU252-C:LYS297 X

C:GLU252-C:LYS297 X

C:GLU263-C:LYS274

C:GLU263-C:LYS274

C:GLU280-C:LYS292 X

C:GLU280-C:LYS292 X

C:GLU295-C:LYS254 X

C:GLU295-C:LYS254 X

C:GLU307-C:LYS217

C:GLU307-C:LYS217

28

1 Papain-Like Cysteine Protease (PLpro)

Fig. 1.13 The Poisson–Boltzmann Electrostatic Potential Surface (EPS) of the models (2) 7JRNPLpro-wt-GRL0617-dimer, (3) 7LBR-PLpro-wt-XR8-89-dimer, (4) 7RZC-PLpro-wt-Jun9-84-3trimer, and (5) 7SDR-PLpro-wt-Jun9-72-2-trimer optimized. For the dimer models (2)–(3) around residues HIS73-THR75 and ASN128-PRO129, there is a large area of negative charge EPS, and for the trimer models (4)–(5) their β-sheets have a large area of positive charge EPS

Table 1.12 All the HBs of the optimized models of (1) 7E35-PLpro-C112S-S43-dimer, (2) 7JRN-PLpro-wt-GRL0617-dimer, (3) 7LBR-PLpro-wt-XR8-89-dimer, (4) 7RZC-PLpro-wtJun9-84-3-trimer, and (5) 7SDR-PLpro-wt-Jun9-72-2-trimer (1) C112S-S43-dimer

(2) wt-GRL0617-dimer

(3) wt-XR8-89-dimer

(4) wt-Jun9-84-3-trimer

(5) wt-Jun9-72-2-trimer

PHE9.N-LYS54.O

LYS6.N-GLU51.OE1

ARG3.NE-GLU1.OE1

LYS6.N-GLU51.OE1

ARG3.NH2-ASN48.OD1

THR10.N-GLN20.OE1

VAL7.N-GLN19.O

PHE8.N-LYS53.O

LYS6.NZ-GLU51.OE2

LYS6.N-GLU51.OE1

ASP13.N-THR11.OG1

PHE8.N-LYS53.O

ASP12.N-THR10.OG1

PHE8.N-LYS53.O

LYS6.N-GLU51.OE2

ASN16.N-ASP13.OD1

ASN13.N-THR10.OG1

ASN13.N-THR10.OG1

ILE14.N-ASP12.OD1

PHE8.N-LYS53.O

ASN16.ND2-GLU68.OE2

ILE14.N-ASP12.OD1

ILE14.N-ASP12.OD1

ASN15.ND2-ASP12.OD2

ILE14.N-ASP12.OD1

HIS18.N-THR10.O

ASN15.N-ASP12.OD1

ASN15.N-ASP12.OD1

HIS17.N-THR9.O

ASN15.ND2-ASP12.OD2

GLN20.N-VAL8.O

LEU16.N-LEU16.O

LEU16.N-LEU16.O

GLN19.N-VAL7.O

HIS17.N-THR9.O

VAL22.N-ILE6.O

HIS17.N-THR9.O

HIS17.N-THR9.O

GLN19.NE2-THR9.OG1

GLN19.N-VAL7.O

MET24.N-ARG4.O

HIS17.ND1-ASN15.OD1

THR18.N-ILE14.O

VAL21.N-ILE5.O

GLN19.NE2-THR9.OG1

GLN31.N-TYR28.O

GLN19.N-VAL7.O

GLN19.N-VAL7.O

SER24.N-ASP22.OD2

VAL21.N-ILE5.O

PHE32.N-TYR28.O

GLN19.NE2-THR9.OG1

MET23.N-ARG3.O

GLN29.N-THR26.O

SER24.N-ASP22.OD1

TYR36.N-TYR57.O

MET23.N-ARG3.O

SER24.N-ASP22.OD1

GLN30.NE2-THR26.O

GLN30.NE2-THR26.O

ALA40.N-LEU37.O

SER24.N-ASP22.OD1

GLN29.N-THR26.O

GLN30.N-TYR27.O

PHE31.N-TYR27.O

VAL42.N-THR35.O

GLN30.NE2-THR26.O

GLN30.N-TYR27.O

PHE31.N-TYR27.O

TYR35.N-TYR56.O

HIS48.ND1-SER50.OG

PHE31.N-TYR27.O

PHE31.N-TYR27.O

TYR35.N-TYR56.O

VAL41.N-THR34.O

HIS51.N-HIS48.O

TYR35.N-TYR56.O

THR34.N-THR42.OG1

VAL41.N-THR34.O

THR42.N-ASP40.OD1

GLY53.N-LYS7.O

VAL41.N-THR34.O

TYR35.N-TYR56.O

THR42.N-ASP40.OD1

LYS43.NZ-ASP40.OD2

LYS54.N-HIS51.O

THR42.N-ASP40.OD1

VAL41.N-THR34.O

LYS43.NZ-ASP40.OD2

LYS45.NZ-SER24.O

PHE56.N-PHE9.O

LYS43.NZ-ASP40.OD2

THR42.N-ASP40.OD1

LYS45.NZ-SER24.O

HIS50.ND1-TYR27.OH

VAL58.N-THR11.O

LYS45.NZ-SER24.O

LYS43.NZ-ASP40.OD2

HIS47.ND1-SER49.OG

HIS50.N-HIS47.O

ALA69.N-LEU65.O

HIS47.ND1-SER49.OG

LYS45.NZ-SER24.O

HIS50.ND1-TYR27.OH

GLY52.N-LYS6.O

GLU68.N-THR64.O

HIS50.ND1-TYR27.OH

HIS50.ND1-TYR27.OH

HIS50.N-HIS47.O

LYS53.N-HIS50.O

VAL67.N-ASP63.O

GLY52.N-LYS6.O

LYS53.N-HIS50.O

GLY52.N-LYS6.O

THR63.N-ASP61.OD1

GLU71.N-VAL67.O

LYS53.N-HIS50.O

LEU64.N-ASP61.OD1

PHE55.N-PHE8.O

LEU64.N-ASP61.OD2

TYR72.OH-ASP135.OD1

LEU64.N-ASP61.OD1

ARG65.NE-ASP62.OD2

ASN60.ND2-LEU58.O

GLU70.N-VAL66.O

TYR84.N-PHE80.O

ALA68.N-LEU64.O

GLU67.N-THR63.O

THR63.N-ASP61.OD2

TYR71.N-GLU67.O

ALA87.N-ARG83.O

GLU70.N-VAL66.O

ALA68.N-LEU64.O

LEU64.N-ASP61.OD1

TYR72.OH-VAL11.O

LEU88.N-TYR84.O

TYR71.OH-ASP134.OD2

GLU70.N-VAL66.O

VAL66.N-THR63.O

HIS73.N-PHE69.O

HIS90.N-ALA87.O

TYR72.N-ALA68.O

TYR72.N-ALA68.O

GLU70.N-VAL66.O

ARG82.NH2-ASP76.OD2

THR91.N-ALA87.O

ARG82.NH2-ASP76.OD2

ARG82.NH2-ASP76.OD2

TYR71.OH-ASP134.OD2

ARG82.NE-SER78.OG

LYS92.NZ-ASP38.O

ARG82.NE-SER78.OG

ARG82.NE-SER78.OG

HIS73.N-PHE69.O

TYR83.N-PHE79.O

LYS93.N-HIS90.O

TYR83.N-PHE79.O

ARG82.NH1-ALA153.O

ARG82.NH2-ASP76.OD2

MET84.N-LEU80.O

TRP94.NE1-ASP109.OD2

MET84.N-LEU80.O

TYR83.N-PHE79.O

ARG82.NE-SER78.OG

ALA86.N-ARG82.O

TYR96.OH-THR91.O

SER85.N-GLY81.O

MET84.N-LEU80.O

ARG82.NH1-ALA153.O

LEU87.N-TYR83.O

VAL99.N-LEU102.O

ALA86.N-ARG82.O

SER85.N-GLY81.O

TYR83.N-PHE79.O

HIS89.ND1-SER85.O

THR103.OG1-ALA140.O

LEU87.N-TYR83.O

ALA86.N-ARG82.O

MET84.N-LEU80.O

HIS89.N-ALA86.O

SER104.N-PRO97.O

TRP93.NE1-ASP108.OD2

LEU87.N-TYR83.O

SER85.N-GLY81.O

HIS89.ND1-ASP108.OD2

LYS106.N-LYS95.O

TYR95.OH-THR90.O

LYS91.NZ-ASP37.O

LEU87.N-TYR83.O

LYS92.NZ-ASN88.O

ASN111.N-ALA108.O

GLN97.NE2-THR102.OG1

LYS91.NZ-ASP37.OD2

HIS89.N-ALA86.O

TRP93.NE1-ASP108.OD2

ASN111.ND2-LYS106.O

THR102.N-GLN121.OE1

TRP93.NE1-ASP108.OD2

LYS91.NZ-ASP37.OD2

VAL98.N-LEU101.O

GLN122.NE2-THR103.O

THR102.OG1-ALA139.O

TYR95.OH-THR90.O

LYS92.NZ-ASN88.O

THR102.OG1-ALA139.O

GLN122.NE2-LEU118.O

SER103.N-PRO96.O

GLN97.NE2-THR102.OG1

TRP93.NE1-ASP108.OD2

SER103.N-PRO96.O

ASN129.N-HIS176.O

LYS105.N-LYS94.O

THR102.OG1-ALA139.O

THR102.N-GLN121.OE1

LYS105.N-LYS94.O

ALA132.N-TYR72.O

ASN109.ND2-GLY160.O

SER103.N-PRO96.O

THR102.OG1-ALA139.O

ASN109.ND2-GLY160.O

ASP135.N-PRO131.O

ASN110.ND2-LYS105.O

LYS105.N-LYS94.O

SER103.N-PRO96.O

ASN110.ND2-LYS105.O

TYR138.N-GLN134.O

ASN110.N-ALA107.O

ASN109.ND2-GLY160.O

LYS105.N-LYS94.O

ASN110.N-ALA107.O

ASN147.ND2-TYR84.OH

LEU117.N-LEU113.O

ASN110.N-ALA107.O

ASN109.ND2-GLY160.O

THR115.N-CYS111.O

CYS149.N-ALA145.O

GLN121.NE2-THR102.O

THR115.N-CYS111.O

ASN110.N-ALA107.O

LEU117.N-LEU113.O

ILE152.N-PHE148.O

GLN121.NE2-LEU117.O

LEU117.N-LEU113.O

ASN110.ND2-LYS105.O

LEU118.N-ALA114.O

TYR155.OH-TYR73.O

GLN122.N-THR119.O

LEU120.N-ALA116.O

THR115.N-CYS111.O

THR119.N-THR115.O

CYS156.N-ILE152.O

ASN128.N-HIS175.O

GLN121.NE2-LEU117.O

LEU117.N-LEU113.O

LEU120.N-ALA116.O

LYS158.N-LEU153.O

ALA131.N-TYR71.O

GLN122.NE2-LEU118.O

LEU118.N-ALA114.O

GLN121.NE2-THR102.O

THR159.N-GLU162.OE1

ASP134.N-PRO130.O

GLN122.N-THR119.O

GLN121.NE2-THR102.O

GLN121.NE2-LEU117.O

VAL166.N-TYR274.OH

GLY142.N-ARG138.O

ILE123.N-THR119.O

GLN121.NE2-LEU117.O

GLN122.N-THR119.O

ARG167.NH1-GLU168.OE1

ASN146.ND2-TYR83.OH

ALA131.N-TYR71.O

GLN122.N-THR119.O

ASN128.N-HIS175.O

GLU168.N-ASP165.OD2

CYS148.N-ALA144.O

TYR136.N-LEU132.O

LYS126.NZ-GLN133.OE1

ALA131.N-TYR71.O

MET170.N-VAL166.O

TYR154.N-LEU150.O

ARG138.NE-GLU143.OE1

ASN128.ND2-HIS175.O

ASP134.N-PRO130.O

SER171.N-ARG167.O

LYS157.NZ-GLU161.OE2

ARG138.NH1-GLU143.OE2

ASN128.N-HIS175.O

ARG138.NH2-ASN146.OD1

ASN178.N-LYS127.O

ASP164.N-GLU167.OE1

ARG138.NH2-GLU143.OE2

ALA131.N-TYR71.O

GLY142.N-ALA139.O

ARG184.N-LEU200.O

THR168.N-ASP164.O

CYS148.N-ALA144.O

ASP134.N-PRO130.O

CYS148.N-ALA144.O

VAL185.N-GLN237.O

MET169.N-VAL165.O

ILE151.N-PHE147.O

ARG138.N-ASP134.O

TYR154.N-LEU150.O

ASN187.ND2-GLN195.OE1

SER170.N-ARG166.O

TYR154.OH-TYR72.O

ARG138.NE-GLU143.OE1

CYS155.N-ILE151.O

GLN196.NE2-CYS193.O

ASN177.N-LYS126.O

TYR154.N-LEU150.O

ARG138.NH1-GLU143.OE1

LYS157.N-LEU152.O

THR198.N-LEU186.O

CYS181.N-LEU178.O

CYS155.N-ILE151.O

ARG138.NH1-GLU143.OE2

LYS157.NZ-GLU161.OE2

ALA205.N-GLY202.O

LYS182.N-GLU238.O

LYS157.NZ-GLU167.OE2

ARG138.NH2-GLU143.OE2

ASP164.N-GLU167.OE2

MET207.N-VAL203.O

ARG183.NE-GLN237.OE1

THR158.N-GLU161.OE1

CYS148.N-ALA144.O

ARG166.NH1-GLU167.OE2

LYS218.NZ-GLU308.OE1

VAL184.N-GLN236.O

THR168.N-ASP164.O

ILE151.N-PHE147.O

ARG166.NH2-GLU167.OE1

GLY220.N-GLN216.O

LEU185.N-THR197.O

MET169.N-VAL165.O

LEU152.N-CYS148.O

THR168.N-ASP164.O

VAL221.N-LYS233.O

ASN186.ND2-GLN194.OE1

CYS181.N-LEU178.O

TYR154.N-LEU150.O

MET169.N-VAL165.O

ILE223.N-ALA231.O

ASN186.ND2-TYR233.OH

LEU185.N-THR197.O

LYS157.N-LEU152.O

GLN174.NE2-SER170.O

VAL236.N-VAL185.O

VAL187.N-GLN195.O

ASN186.ND2-GLN196.OE1

LYS157.NZ-GLU203.OE1

ASN177.N-LYS126.O

Table 1.13 All the HBs of the optimized models of (1) 7E35-PLpro-C112S-S43-dimer, (2) 7JRN-PLpro-wt-GRL0617-dimer, (3) 7LBR-PLpro-wt-XR8-89-dimer, (4) 7RZC-PLpro-wtJun9-84-3-trimer, and (5) 7SDR-PLpro-wt-Jun9-72-2-trimer (continuation) (1) C112S-S43-dimer

(2) wt-GRL0617-dimer

(3) wt-XR8-89-dimer

(4) wt-Jun9-84-3-trimer

(5) wt-Jun9-72-2-trimer

ALA231.N-ILE223.O

GLY193.N-CYS189.O

VAL187.N-GLN195.O

THR158.N-GLU203.OE2

ASN177.ND2-ASP179.OD1

TYR234.N-ASN187.O

GLN195.N-VAL187.O

VAL188.N-THR231.O

ARG166.NE-ASP164.OD2

CYS181.N-LEU178.O

TYR234.CD1-LYS233.C

LEU199.N-ARG183.O

CYS189.N-GLY193.O

THR168.N-ASP164.O

ARG183.NE-GLN237.OE1

LEU235.N-PHE217.O

LYS200.NZ-ASP179.O

THR197.N-LEU185.O

MET169.N-VAL165.O

VAL184.N-GLN236.O

GLN238.N-TYR311.O

GLN215.NE2-GLY219.O

LYS200.N-GLU203.OE1

SER170.N-ARG166.O

LEU185.N-THR197.O

GLU239.N-LYS183.O

LYS217.NZ-GLU307.OE1

MET206.N-VAL202.O

ASN177.N-LYS126.O

ASN186.ND2-GLN194.OE1

MET245.N-VAL304.O

GLU203.N-GLU203.OE1

TYR207.OH-LYS232.NZ

ARG183.NE-GLN237.OE1

ASN186.ND2-TYR233.OH

GLN251.N-GLN251.OE1

MET206.N-VAL202.O

TYR213.OH-GLU307.OE1

VAL184.N-GLN236.O

VAL187.N-GLN195.O

THR260.N-PHE305.O

GLY219.N-GLN215.O

GLN215.NE2-GLY219.O

ASN186.ND2-GLN194.OE1

CYS189.N-GLY193.O

TYR265.OH-ASN268.O

ILE222.N-ALA230.O

LYS217.NZ-GLU307.OE2

ASN186.ND2-TYR233.OH

GLY193.N-CYS189.O

THR266.N-HIS273.O

ALA230.N-ILE222.O

GLY219.N-GLN215.O

VAL187.N-GLN195.O

GLN194.NE2-LYS315.O

ASN268.N-CYS271.O

LYS232.NZ-TYR207.OH

ILE222.N-ALA230.O

CYS189.N-GLY193.O

GLN196.NE2-GLN250.OE1

GLN270.N-ASN268.OD1

VAL235.N-VAL184.O

GLN229.NE2-GLN221.OE1

GLN195.NE2-GLN196.O

THR198.N-GLY266.O

LYS275.N-GLU264.O

GLN236.NE2-GLU238.OE2

ALA230.N-ILE222.O

GLN196.NE2-GLN250.OE1

LEU199.N-ARG183.O

HIS276.N-ILE286.O

GLN237.NE2-ALA204.O

LYS232.NZ-TYR207.OH

THR197.N-LEU185.O

LYS200.N-GLU203.OE1

ILE277.N-ALA262.O

GLU238.N-LYS182.O

VAL235.N-VAL184.O

LEU199.N-ARG183.O

LYS200.NZ-CYS181.O

SER279.N-THR260.O

MET243.N-VAL205.O

GLN236.NE2-THR311.OG1

LYS200.NZ-ASP179.O

LYS200.NZ-SER180.O

LYS280.NZ-ASN100.OD1

MET244.N-VAL303.O

GLN237.NE2-ALA204.O

VAL205.N-VAL202.O

VAL205.N-VAL202.O

LYS280.N-THR282.O

SER245.N-TYR207.O

GLN237.NE2-SER239.OG

MET206.N-VAL202.O

MET206.N-VAL202.O

GLU281.N-GLU281.OE1

TYR251.N-GLY298.O

GLU238.N-LYS182.O

TYR207.OH-LYS232.NZ

GLY209.N-SER245.O

ILE286.N-HIS276.O

THR259.N-PHE304.O

SER239.N-ASN308.O

GLN215.NE2-GLY219.O

TYR213.OH-GLU307.OE1

ASP287.N-LEU290.O

LYS274.NZ-GLU263.OE1

MET243.N-VAL205.O

LYS217.NZ-GLU214.OE2

GLN215.NE2-GLY219.O

LEU290.N-ASP287.O

LYS274.NZ-ASP286.OD2

MET244.N-VAL303.O

LYS217.NZ-GLU307.OE1

LYS217.NZ-GLU214.OE2

THR292.N-CYS285.O

ILE276.N-ALA261.O

SER245.N-TYR207.O

LYS218.N-GLN215.O

LYS217.NZ-GLU307.OE1

TYR297.CE2-GLU264.OE2

LYS279.NZ-ASN99.OD1

THR259.N-PHE304.O

GLY219.N-GLN215.O

LYS218.NZ-GLU214.OE1

THR302.N-SER263.O

LYS279.N-THR281.O

TYR264.N-PRO299.O

VAL220.N-LYS232.O

GLY219.N-GLN215.O

PHE305.N-CYS261.O

TYR283.N-THR277.O

LYS274.NZ-ASP286.OD2

GLN221.NE2-GLN174.OE1

VAL220.N-LYS232.O

TYR306.OH-LEU212.O

TYR283.OH-GLU280.OE1

HIS275.N-ILE285.O

ILE222.N-ALA230.O

GLN221.NE2-GLN229.OE1

TYR306.N-VAL243.O

ASP286.N-LEU289.O

SER278.N-THR259.O

LYS228.NZ-ASN177.OD1

ILE222.N-ALA230.O

LEU289.N-ASP286.O

LYS279.N-THR281.O

LYS228.NZ-THR191.OG1

ALA230.N-ILE222.O

TYR296.OH-GLU263.OE2

TYR283.N-THR277.O

GLN229.N-ASP179.OD1

LYS232.NZ-GLU161.OE1

LYS297.NZ-GLU252.OE2

TYR283.OH-GLU280.OE1

ALA230.N-ILE222.O

LYS232.NZ-TYR207.OH

VAL303.N-MET244.O

ILE285.N-HIS275.O

LYS232.NZ-TYR207.OH

VAL235.N-VAL184.O

PHE304.N-CYS260.O

ASP286.N-LEU289.O

LYS232.NZ-GLN269.OE1

GLN236.NE2-THR311.OG1

TYR305.OH-LEU211.O

LEU289.N-ASP286.O

VAL235.N-VAL184.O

GLN237.NE2-ALA204.O

THR291.N-CYS284.O

GLN237.NE2-ALA204.O

GLN237.NE2-SER239.OG

LYS292.NZ-GLU280.OE2

GLN237.NE2-SER239.OG

GLU238.N-LYS182.O

SER293.N-LEU282.O

GLU238.N-LYS182.O

MET243.N-VAL205.O

TYR296.OH-GLU263.OE2

MET243.N-VAL205.O

MET244.N-VAL303.O

LYS297.NZ-GLU252.OE1

MET244.N-VAL303.O

SER245.N-TYR207.O

THR301.N-SER262.O

SER245.N-TYR207.O

LEU253.N-TYR296.O

PHE304.N-CYS260.O

LEU253.N-TYR296.O

LYS254.NZ-GLU252.OE2

TYR305.N-VAL242.O

LYS254.NZ-GLU252.OE1

LYS254.NZ-GLU295.OE1

THR259.N-PHE304.O

THR259.N-PHE304.O

TYR264.OH-ASN267.O

TYR264.OH-ASN267.O

GLY266.N-THR225.O

GLY266.N-THR225.O

ASN267.N-CYS270.O

ASN267.N-CYS270.O

GLN269.NE2-MET208.O

GLN269.N-ASN267.OD1

GLN269.NE2-GLY209.O

LYS274.NZ-GLU263.OE1

GLN269.N-ASN267.OD1

LYS274.NZ-ASP286.OD2

LYS274.N-GLU263.O

ILE276.N-ALA261.O

LYS274.NZ-GLU263.OE1

LYS279.NZ-ASN99.OD1

LYS274.NZ-ASP286.OD2

LYS279.N-THR281.O

ILE276.N-ALA261.O

TYR283.N-THR277.O

LYS279.NZ-ASN99.OD1

TYR283.OH-GLU280.OE1

LYS279.N-THR281.O

ILE285.N-HIS275.O

TYR283.N-THR277.O

ASP286.N-LEU289.O

TYR283.OH-GLU280.OE1

LEU289.N-ASP286.O

ILE285.N-HIS275.O

THR291.N-CYS284.O

ASP286.N-LEU289.O

LYS292.NZ-TYR283.OH

LEU289.N-ASP286.O

TYR296.OH-GLU263.OE2

THR291.N-CYS284.O

LYS297.NZ-GLU252.OE2

TYR296.OH-GLU263.OE2

THR301.N-SER262.O

LYS297.NZ-GLU252.OE2

VAL303.N-MET244.O

THR301.N-SER262.O

PHE304.N-CYS260.O

VAL303.N-MET244.O

TYR305.N-VAL242.O

PHE304.N-CYS260.O

ASN308.N-GLU307.OE2

TYR305.N-VAL242.O

TYR310.N-GLN237.O

LYS306.NZ-GLU124.OE1

TYR310.OH-LEU234.O

LYS306.NZ-GLU124.OE2 TYR310.N-GLN237.O LYS315.NZ-LYS315.N

Supplementary Information

31

Table 1.14 All the residues of the optimized models of (1) 7E35-PLpro-C112S-S43-dimer, (2) 7JRN-PLpro-wt-GRL0617-dimer, (3) 7LBR-PLpro-wt-XR8-89-dimer, (4) 7RZC-PLpro-wtJun9-84-3-trimer, and (5) 7SDR-PLpro-wt-Jun9-72-2-trimer that bind with the ions Zn2+ and their respective inhibitors (2) wt-GRL0617-dimer

(1) C112S-S43-dimer A:ZN401

A:CYS190, A:THR192, A:CYS193,

A:ZN402

(3) wt-XR8-89-dimer A:ZN401

A:CYS224, A:THR225, A:CYS226.

A:CYS225, A:THR226, A:CYS227. B:ZN401

A:CYS189, A:THR191, A:CYS192,

B:CYS190, B:THR192, B:CYS193,

B:ZN401

A:GLU158,

B:CYS189, B:THR191, B:CYS192, B:CYS224, B:THR225, B:CYS226,

B:CYS225, B:THR226, B:CYS227. A:GYX402

A:CYS189, A:THR191, A:CYS192, A:CYS224, A:CYS226, A:LYS228.

A:TTT401

A:LEU163,

A:LEU162,

B:LYS228.

A:GLY163,

A:ASP165,

A:ASP164,

A:ARG167,

A:MET208,

A:X77-404

A:GLY163,

A:LEU162,

A:PRO248,

A:PRO248,

A:ASP164,

A:PRO249,

A:TYR264,

A:GLU167,

A:TYR265,

A:TYR268,

A:PRO247,

A:ASN268,

A:GLN269,

A:PRO248,

A:TYR269,

A:TYR273,

A:TYR264,

A:TYR274,

A:THR301.

A:GLY266,

A:THR302,

A:TYR268,

B:MET209,

A:GLN269,

B:GLY210,

A:TYR273,

B:ALA247,

A:THR301.

B:PRO248, B:SER246, B:TYR269. B:GYX402

A:TYR208,

B:X77-404

B:LEU162,

A:TYR269,

B:GLY163,

B:GLU162,

B:ASP164,

B:LEU163,

B:GLU167,

B:GLY164,

B:PRO248,

B:ASP165,

B:ALA249,

B:PRO249,

B:TYR264,

B:TYR265,

B:GLY266,

B:ASN268,

B:ASN267,

B:TYR269,

B:TYR268,

B:TYR274,

B:GLN269, B:TYR273,

B:PRO248,

B:THR301.

B:THR302. (4) wt-Jun9-84-3-trimer A:ZN502

A:CYS189, A:THR191, A:CYS192,

B:ZN502

B:CYS189, B:CYS192,

(5) wt-Jun9-72-2-trimer A:ZN502

A:CYS189, A:THR191, A:CYS192,

B:ZN502

B:CYS189, B:THR191, B:CYS192,

A:CYS224, A:CYS226.

A:CYS224, A:CYS226. B:CYS224, C:CYS226, C:LYS228. C:ZN502

C:CYS189, C:CYS192,

B:CYS224, B:CYS226. C:ZN502

C:CYS189, C:THR191, C:CYS192,

A:JW9-501

A:LYS157,

C:CYS224, C:THR225, C:CYS226. A:JWX501

B:LYS157,

A:MET209,

A:LEU162,

C:CYS224, C:CYS226.

A:ASP164,

A:LEU162,

A:GLU167,

A:GLY163,

A:MET208,

A:ASP164,

A:PRO248,

A:GLU167,

A:TYR264,

A:PRO248,

A:ASN267,

A:TYR264,

A:TYR268,

A:ASN267,

A:TYR273.

A:TYR268, A:TYR273.

(continued)

32

1 Papain-Like Cysteine Protease (PLpro)

Table 1.14 (continued) (1) C112S-S43-dimer B:JWX501

A:GLN195,

(2) wt-GRL0617-dimer B:JW9-501

A:GLN195,

B:LEU162,

A:THR197,

B:GLY163,

B:LYS157,

B:ASP164,

B:LEU162,

B:ARG166,

B:GLY163,

B:GLU167,

B:ASP164,

B:MET208,

B:PRO248,

B:PRO247,

B:TYR264,

B:PRO248,

B:ASN267,

B:TYR264,

B:TYR268,

B:ASN267,

B:TYR273,

B:TYR268,

C:TYR268.

B:TYR273, B:THR301, C:TYR268. C:JWX501

A:THR225,

C:JW9-501

B:TYR268,

B:ARG166,

C:LYS157,

B:TYR268,

C:LEU162,

C:LEU162,

C:GLY163,

C:GLY163,

C:ASP164,

C:ASP164,

C:GLU167,

C:GLU167,

C:TYR264,

C:MET208,

C:ASN267,

C:PRO248,

C:TYR268,

C:TYR264,

C:TYR273,

C:ASN267,

C:THR301.

C:TYR268, C:TYR273.

(3) wt-XR8-89-dimer

Chapter 2

3C-Like Protease (3CLpro)

Abstract The 3C-like protease (or called the main protease) of COVID-19 is a critical enzyme for the maturation of viral particles and a potential target for antiviral drugs. This chapter firstly did the work skillfully by locally optimizing the structures of SARS-CoV-2 3C-like protease (3CLpro) in complex with its inhibitor, N3/carmofur (6LU7.pdb & 7BQY.pdb/7BUY.pdb), from COVID-19 virus; then some new structural bioinformatics from the structures optimized for developing therapies of the currently fatal COVID-19 virus are reported. Currently, lots of researchers are using optimization to screen, dock, find, and design new therapies for COVID-19 but it is not used professionally. The hybrid strategy of mathematical optimization’s neighboring different (local search) algorithms is used professionally in this chapter. The X-ray crystallography structure for the COVID-19 3CLpro with unliganded active site was also released into the Protein Data Bank (PDB) with PDB entry 6Y84; this chapter will also study the dimer 3CLpro (with unliganded active site/without the ligand N3) by optimization and molecular dynamics (MD) techniques. The 3CLpro variants delP168, a173v, delP168, and a173v are also studied by optimization and MD techniques. In common, from almost all the models of the 3CLpro dimer, we found that sometimes, there are two strong polar contacts between GLU290 and ARG4 linking the two monomers. In comparison, we also study the SARS-CoV-1-Mpro and SARS-CoV-1-Mpro-N3 in this chapter by optimization and MD techniques. Keywords COVID-19 virus · 3C-Like protease (3CLpro) · Optimizing their structures · Molecular dynamics · Monomer and dimer · Structural bioinformatics

2.1 Introduction The COVID-19 virus 3CLpro is a key coronavirus enzyme that plays a pivotal role in mediating viral replication and transcription, making it an attractive drug (e.g., N3, carmofur) target for this virus [160]. The X-ray crystallography structures for © The Author(s), under exclusive license to Springer Nature Switzerland AG 2023 J. Zhang, Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures, Springer Series in Biophysics 23, https://doi.org/10.1007/978-3-031-36773-1_2

33

34

2 3C-Like Protease (3CLpro)

3CLpro-N3 (with PDB entries 6LU7 and 7BQY) were recently released into the PDB (www.rcsb.org). The dimer of 3CLpro (with unliganded active site) has been reported to be the best option of drug targets against the COVID-19 virus and its Xray structure was also released into the PDB with PDB entry 6Y84 [259]. This brief chapter will also study these (monomeric and dimeric) structures optimized through MD computations in order to seek additional useful structural bioinformatics for developing therapies of the currently fatal COVID-19.

2.2 Materials and Methods 2.2.1 Monomer The materials used in this chapter are the PDB entries 6LU7 and 7BQY. The methods are used to optimize their structures and to confirm the bioinformatics of optimized structures from the analyses of MD trajectory datasets. The hybrid strategy of mathematical optimization’s neighboring different algorithms is completely the same as the one used in [405, 413]. We optimized the structures locally and slightly, looking at the optimization problem as a three-body problem. The decreased energies (KJ/mol) are .−13411.358 (E3), .−13734.746 (E6), and .−13988.698 (E9) for 6LU7.pdb and .−12957.118 (E3), .−13285.783 (E6), and .−13550.220 (E9) for 7BQY.pdb, respectively. The RMSD (Chapter 1 of [412]) values of the optimized structures from the original structures are 1.456041 Å for 6LU7.pdb and 1.286947 Å for 7BQY.pdb, respectively; thus, the optimized 3CLproN3 structures are as good as their original structures. The differences of the 3D structure and secondary structure between each optimized and original structures can be detected by the package MOLMOL [184] and its CalcSecondary output files produced.

2.2.2 Dimer The MD materials and methods for the dimer of COVID-19 3CLpro with unliganded active site can be seen from [321] (with data ID DESRES-ANTON10880334): “This trajectory is from a 100 .μs MD simulation of the apo enzyme started from the apo enzyme structure determined by X-ray crystallography (PDB entry 6Y84). The protein was solvated in a .120 × 120 × 120 Å water box containing 0.15 M NaCl. The simulation was performed on Anton 2 using the DES-Amber force field. The interval between frames is 1 ns. The simulation was conducted at 300 K in the NPT ensemble.” We denote the model as the 6Y84-dimer model. The MD materials and methods of the dimeric SARS-Cov-2 3CLpro without any ligand can be seen from [180]: The starting structure was prepared based on

2.3 Results and Discussions

35

6LU7.pdb with amber99sb-ildn force field; the MD was done using GROMACS under NVT at 310 K, with time-size about 2.5 fs, the MD system composed of 98,694 atoms in 9.98921 nm length cubic box with periodic boundary conditions, and the two sets of 10 .μs MD trajectories were done with different random seeds for the preparation of solvent and the production runs. We denote the model as the 6LU7-dimer model. In [113] we find three sets of 50 ns’ REMD trajectories for the dimeric SARSCoV-2 3CLpro without any ligand. We denote the model as the Evans-dimer model. In [346] the MD trajectories are presented for SARS-CoV-1 and SARS-CoV2 main proteases in monomeric/dimeric and apo/holo states, where the MD simulations are built on the four PDB entries 1q2w (SARS-CoV-1-Mpro), 6y2e (SARS-CoV-2-Mpro), 2hob (SARS-CoV-1-Mpro with ligand N3), and 6lu7 (SARSCoV-2-Mpro with ligand N3, where 6lu7-monomer/dimer without ligand MDdatabases can also be gotten now). The 3CLpro variants delP168, a173v, delP168, and a173v are also 17 studied by optimization (Tables 2.1 and 2.2) and MD techniques.

2.3 Results and Discussions 2.3.1 Monomer We report some new findings from our optimized structures. Let us analyze our optimized structures of 6LU7 and 7BQY. We set the hydrogen bond (HB) donor-acceptor distance cutoff to 3.0 Å and the angle cutoff to 20 degrees. We found the following HBs for both 6LU7optimized and 7BQYoptimized models: C:Val3.O-A:Glu166.H, C:Val3.H-A:Glu166.O, C:Leu4.H-A:Gln189.OE1, C:Ala2.H-A:Thr190.O, and C:010 6.O-A:Gly143.N for 6LU7optimized model and C:PJE101.O7-A:Cys145.H for 7BQYoptimized model. For 6LU7optimized model, we confirm these HBs by the 100 ns’ molecular dynamics (MD) productions of [102]: A:GLU166.N-C:VAL3.O with 30.07% occupancy rate, C:VAL3.NA:GLU166.O with 26.67% occupancy rate, A:HIE41.NE2-C:LEU4.O with 0.10% occupancy rate, C:ALA2.N-A:THR190.O with 3.20% occupancy rate, C:ALA2.NA:GLN192.O with 3.40% occupancy rate, and A:GLN189.NE2-C:ALA2.O with 5.69% occupancy rate . For the A-chain (i.e., 3CLpro), its main HBs with occupancy rates greater than 50% can be seen from Table 2.3. For both 6LU7optimized and 7BQYoptimized 3CLpros, we find that there are four .π -.π stackings HIS163-PHE140-HIS172-HIS163, TYR37-PHE103, and one + .π -cation ARG. 298.NH2-PHE8. We found out the following salt bridges (SBs) (oxygen-nitrogen cutoff: 3.2 Å) for 3CLpro during the 100 ns’ MD production phase of [102]: GLU55-ARG40, ASP295-ARG298, ASP229-LYS269, ASP289-ARG131, ASP197-LYS137, ASP197-ARG131, ASP153-ARG298, GLU47-ARG60, ASP48-LYS61, ASP155-LYS12, ASP176-ARG105, GLU290-LYS137, ASP92-ARG76, GLU14-LYS97, GLU290-LYS5, GLU288-LYS5, GLU270-LYS269, ASP48-ARG60, ASP263-ARG222, GLU290-ARG131,

36

2 3C-Like Protease (3CLpro)

ASP187-ARG40, ASP155-LYS100, ASP34-LYS90, ASP153-LYS102, and GLU288-LYS137.

Among them, (i) GLU290-ARG131, GLU228-LYS137, GLU55-ARG40, GLU47ARG60, GLU14-LYS97, ASP295-ARG298, ASP263-ARG222, ASP176-ARG105, ARG153-ARG298, and ASP155-LYS12 are always broken during the 100 ns of MD; (ii) ARG92-ARG76 exists during 76–100 ns, ASP48-LYS61 exists during 86–100 ns, and ASP229-LYS269 exists during 33–48 ns; (iii) ASP153LYS102, ASP48-ARG60, ARG197-ARG131 (broken during most of the time), and GLU270-LYS269 are weak but last longer during the whole 100 ns of MD; (iv) ARG289-ARG131, ASP187-ARG40, ASP187-ARG40, ASP34-LYS90, ASP197LYS137 (18–40 ns), ASP155-LYS100 (72–82 ns broken), and GLU288-LYS5 (GLU290-LYS95 is weak) are maintained during the 100 ns’ MD production. Some SBs are shown in Fig. 2.17 (where the x-axis is the MD production time, 100 ns, and y-axis is the distance (Å))—for each SB’s two residues, the numbers of residues that spanned are 56, 55, 147, 60, 158, 283, and 285, respectively. The SBs ASP155-LYS100 and ASP187-ARG40 strongly maintain the binding pocket for N3. For the optimized N3-3CLpro, its Ramachandran plots for 6LU7optimized and 7BQYoptimized models are shown in Fig. 2.1, where we can see that there is a slight difference between the 6LU7optimized and BQY7optimized models. The Ramachandran plots with large percentage of residues in most favored regions might reveal that 3CLpro protein structures are suitable for docking studies with the compounds.

Fig. 2.1 The Ramachandran plot for the 6LU7optimized model (left) and the 7BQYoptimized model (right)

For the 6LU7optimized model and 7BQYoptimized model, let us look at their N3-3CLpro interaction diagrams (Figs. 2.2 and 2.3) (there is a slight difference between these two diagrams). The compound N3 consists of the three strictly hydrophobic residues ALA2-VAL3-LEU4, and it is surrounded by the hydrophobic residues LEU27, PHE140, LEU141, MET165, PRO168, and ALA191 (thus forming a small hydrophobic pocket); the polar residues HIS, ASN142, SER144, and THR190, the charged residue GLU166; etc. (thus forming a binding site).

2.3 Results and Discussions

37

Fig. 2.2 The N3-3CLpro interaction diagram for the 6LU7optimized model

Fig. 2.3 The N3-3CLpro interaction diagram for the 7BQYoptimized model

For the 100 ns’ MD productions, from the secondary structure development (with RMSF (Chapter 1 of [412]) values for each residue (Fig. 2.4)), we can see some secondary structural changes in segments 10–16, 46–50, 46–50, 181–200, 235–238, and 285–300 (Fig. 2.18) during the whole 100 ns’ MD, and for the RMSD, we know that during 28–100 ns, the protein equilibrates around an RMSD value of 2.1 Å (Fig. 2.4). Larger RMSF variations (Fig. 2.4) are at N- and C-terminals and segments 218–228, 48–58, and 188–198 (during 54–100 ns).

38

2 3C-Like Protease (3CLpro)

Fig. 2.4 The RMSF and RMSD for the 6LU7optimized model during 100 ns’ MD

Similarly, the newly released 3CLpro-carmofur structure 7BUY.pdb [161] is optimized and studied as follows. The decreasing energies (KJ/mol) of optimizing the 7BUY.pdb structure are .−12014.130 (E3), .−12448.631 (E6), and .−12809.334 (E9). After optimization, the RMSD value between the optimized structure (the 7BUYoptimized model) and the original structure is 0.004811 Å. We find the HBs JRY401.O-A:Gly143.H, JRY401.O-Cys145.H, DMS405.O-Gln192.H, and DMS405-Thr190.H and other residue-pair HBs: ASP216-ALA211, LEU282-ASP216, ILE213-TYR209, TYR209-ILE259, SER284-ILE281, SER254-LEU250, ARG298-PHE294, LYS269-CYS265, ASP153-CYS156, CYS128-PHE112, VAL114-TYR126, SER113-PHE150, VAL157-LYS100, CYS16-VAL13, LYS97-ASN95, ARG131-ASP289, ILE200ASP289, ASN203-GLY109, SER139-TYR126, ASN95-TRP31, LEU242-ASN231, ASN231-LEU242, GLY109-MET130, GLN107-GLN110, CYS160-GLY149, PHE159-LYS102, GLY29-VAL18, ALA70-VAL73, MET235-ASN231, ARG131THR135, HIS163-TYR161, TYR182-CYS160, VAL104-PHE159, VAL20-LEU27, LEU75-VAL68, ASN133-GLY195, PHE134-ARG131, ALA173-MET165, MET162-THR175, GLY146-HIS163, TYR182-GLY174, LEU89-VAL36, ILE78LYS90, ARG105-PHE181, ASN84-GLU178, VAL86-GLN83, LYS88-SER81, PHE66-ASN63, GLN192-VAL186, CYS85-GLY179, ARG40-ASP187, GLN83VAL86, TYR54-ASP187, THR45-ASP48, SER62-ASN65, ASP48-THR45, and LYS61-LEU58. We also find seven residue-pair SBs, SP187-ARG40, ASP176-ARG105, ASP197-ARG131, ASP229-LYS269, GLU166-HIS172, ASP289-ARG131, and GLU290-ARG131, and five .π -.π stackings HIS163PHE140-HIS172-HIS163, TYR37-PHE103, and TRP218-PHE219. We show the Ramachandran plot and the ligand interaction diagram, respectively, for the 7BUYoptimized model in Fig. 2.5 (comparing it with Figs. 2.1, 2.2, and 2.3) for further studies.

2.3 Results and Discussions

39

Fig. 2.5 The Ramachandran plot and the carmofur-3CLpro interaction diagram for the 7BUYoptimized model

2.3.2 Dimer 2.3.2.1

The 3CLpro (with Unliganded Active Site): The 6Y84-Dimer Model

We optimize the original structure with PDB entry 6Y84 [259], and the optimized structure (the 6Y84optimized model) has an RMSD value of 17.814106 Å from its original structure (20.212018 Å for the dimer). For the 6Y84optimized model, we get its following structural bioinformatics—which will be confirmed with our analysis of the MD data (with data ID DESRES-ANTON-10880334) in [321]. With oxygen-nitrogen cutoff of 3.2 Å, the 6Y84optimized model has the following SBs: ASP187-ARG40, ASP155-LYS100, ASP197-ARG131, ASP295-ARG298, GLU290ARG131, ASP289-ARG131, ASP176-ARG105, ASP229-LYS269, and GLU166-HIS172 in each inner monomer and GLU290-ARG4 between the two monomers. We set 3.0 Å as the donor-acceptor cutoff distance and 20 degrees as the cutoff angle for HBs and find 71 HBs (confirmed in Table 2.4 by the MD) for the 6Y84optimized model. We find four .π -.π stackings PHE103-TYR37, HIS172PHE140-HIS163-HIS172 (with HB HIS163.NE2-HIS172.ND1 (19.28%)), and one + .π -cation PHE291-LYS. 5:NZ. The analysis of 100 .μs’ MD trajectory data in [321] can confirm to us the strong inner-monomer SBs: ◦ ASP187-ARG40 (with strong HBs ARG40.NH2-ASP187.OD1 (70.63%) and ARG40.NE-ASP187.OD2 (69.63%): the SB and HBs are broken during 92.6– 100 .μs),

.

40

2 3C-Like Protease (3CLpro)

◦ ASP295-ARG298 (with HBs ARG298.NH1-ASP295.OD1 (15.38%), ARG298. NH1-ASP295.OD2 (12.99%), ARG298.NH2-ASP295.OD2 (8.29%), and ARG298.NH2-ASP295.OD1 (7.59%)), .◦ ASP176-ARG105 (with strong HBs ARG105.NH1-ASP176.OD1 (32.27%) and ARG105.NH1-ASP176.OD2 (30.77%)), .◦ ASP289-ARG131 (with HBs ARG131.NH2-ASP289.OD2 (26.27%), ARG131. NH2-ASP289.OD1 (23.48%), ARG131.NH1-ASP289.OD1 (12.09%), ARG131. NH1-ASP289.OD2 (9.89%), ARG131.NE-ASP289.OD2 (9.39%), and ARG131.NE-ASP289.OD1 (9.29%)), .◦ GLU290-LYS5 (with strong HBs LYS5.NZ-GLU290.OE2 (54.25%) and LYS5.NZ-GLU290.OE1 (52.95%)), .◦ ASP155-LYS100 (with HBs LYS100.NZ-ASP155.OD1 (15.78%) and LYS100.NZ-ASP155.OD2 (14.69%)) (see Fig. 2.19), and .◦ weaker SBs GLU166-HIS172, GLU290-ARG131 (broken after 2.4 .μs), and ASP229-LYS269 (with strong HB LYS269.NZ-ASP229.O (29.07%)) (Fig. 2.19). .

We discuss the performance of the MD. The RMSD values of the MD equilibrates around 2.5 Å and are within 2 Å of variations (Fig. 2.6).

Fig. 2.6 The RMSF and RMSD for dimeric 3CLpro of the 6Y84optimized model during 100 .μs’ MD

During the 100 .μs’ MD, the secondary structural changes (Fig. 2.20, where the frame interval is 0.1 .μs) are mainly in segments 39–53 of both monomers and segments 222–239 and 298–306 of monomer B; and the large RMSF values mainly happen in residue segments 46–51, 136–141, and 303–306 (Fig. 2.6).

2.3.2.2

The 3CLpro (Without Any Ligand): The 6LU7-Dimer Model

For the file 6LU7.pdb, we remove the C-chain (i.e., inhibitor N3) and just keep the A-chain (3CLpro). Then we apply the following mathematical formula to get a

2.3 Results and Discussions

41

dimer (original structure) with AB-chains of 3CLpro: ⎛

⎞ ⎛ ⎞ −1 0 0 −43.04696 ⎠ .B = ⎝ 0 1 0 ⎠ A + ⎝ 0 0 0 −1 94.23992

(2.1)

and we then optimize this dimer (to get an optimized structure) by the decreased energies (KJ/mol) .−36500.988 (E102), .−37390.438 (E204), and .−37605.098 (E248) with an RMSD value of 1.470148 Å from the original dimer structure. For the optimized model, we get 127 HBs which can be confirmed by the analysis of MD data of [180] in Tables 2.5 and 2.6. For the 6LU7-dimer-optimized model, we get the same SBs as that of the 6Y84-dimer-optimized model : ASP187-ARG40, ASP197-ARG131, GLU290-ARG131, ASP289-ARG131, ASP176-ARG105, GLU166-HIS172, ASP92-ARG76, and GLU290-LYS5 in each inner monomer and GLU290-ARG4 between each monomer. We confirm some strong SBs among them in Figs. 2.21 and 2.22 by the analysis of MD data of [180] in both sets of trajectories. The SB ASP155-LYS100 strongly maintains a pocket of 3CLpro. Now, we analyze the reliability of the MD data of [180]. Seeing Fig. 2.7, we know that the RMSD values for Traj1 steadily go up from 6600 ns to 10000 ns but are stable during 0–6600 ns, but on the contrary for Traj2 during 6600–10000 ns, the RMSD values equilibrate around 3.2 Å, but during 0–6600 ns, the RMSD values go up slowly. The whole variations of RMSD values are within 3 Å and 2 Å, respectively, for the Traj1 and Traj2 sects of MD data.

Fig. 2.7 The RMSD-time (Å-ns) graphs for the 10,000 ns’ MD data of [180] for the 6LU7-dimer model (the left graph is for the Traj1-MD data and the right graph is for the Traj2-MD data)

The RMSF graphs in Fig. 2.8 show that (i) from 6600 ns to 10000 ns, the residue segment 226–286 (even the segment 191–286) seems to unfold or has a large change and (ii) the segments 46–56, 271–276, and 301–306 have large RMSF values.

42

2 3C-Like Protease (3CLpro)

Fig. 2.8 The RMSF graphs for the 10,000 ns’ MD data of [180] for the 6LU7-dimer model (the left graph is for the Traj1-MD data and the right graph is for the Traj2-MD data)

The MD secondary structural developments for Traj1 and Traj2 can be seen from Fig. 2.9. In Fig. 2.9, we know that the segment around residue PRO52 will be changed from .α-helix to turn starting from 1520th ns for B-chain and from 1760th ns for A-chain (in Traj2 for both AB-chains starting from 14th and 32th ns, respectively), the segment around residue LYS137 changes between turn and 3.10 -helix structures, for A-chain the .α-helices in segment 290–306 have unfolded into turns, and for the segment around ARG188, the coils changed into turns during Traj2 6940-10000 ns for A-chain. However, we cannot see significant changes of secondary structures of the monomer (Fig. 2.18)—this may be explained by the longer 10,000 ns’ MD here but the MD of the 6LU7-monomer is 100 ns in all.

Fig. 2.9 The secondary structural graphs for the 10,000 ns’ MD data of [180] for the 6LU7-dimer model (the left graph is for the Traj1-MD data and the right graph is for the Traj2-MD data; the frame interval is 10 ns).

For the optimized Evans-dimer model, we find 6 .π -interactions, A:ARG298. NH2+-A:PHE8-A:PHE305, B:ARG298.NH2+-B:PHE8-B:PHE305, A:PHE134A:ARG105.NH2+, and B:PHE134-B:ARG105.NH2+, and 32 SBs (Fig. 2.23): − in rep0: • A:GLU290-B:ARG4/B:GLU290-A:ARG4 (with HBs B:ARG4.NH1-A:GLU 290.OE2 37.56%, B:ARG4.NH2-A:GLU290.OE1 31.77%, B:ARG4.NH1A:GLU290.OE1 24.58%, B:ARG4.NH2-A:GLU290.OE2 19.48%/A:ARG4. NH1-B:GLU290.OE2 33.67%, A:ARG4.NH2-B:GLU290.OE1 22.68%, A:ARG4.NH1-B:GLU290.OE1 14.29%),

.

2.3 Results and Discussions

43

• A:ASP34-A:LYS90/B:ASP34-B:LYS90 (with HBs A:LYS90.NZ-A:ASP34.OD1 27.17%, A:LYS90.NZ-A:ASP34.OD2 21.68%, A:LYS90.N-A:GLY79.O 52.15%, A:ILE78.N-A:LYS90.O 51.95%, A:VAL91.N-A:ASP34.O 47.65%/B: LYS90.NZ-B:ASP34.OD1 27.77%, B:LYS90.NZ-B:ASP34.OD2 22.88%, B:VAL91.N-B:ASP34.O 42.16%, B:LYS90.N-B:GLY79.O 52.45%, B:ILE78.NB:LYS90.O 49.45%), • A:ASP48-A:ARG60/B:ASP48-B:ARG60 (with HBs A:ARG60.NH1-A:ASP4 8.OD1 20.28%, A:ARG60.NH2-A:ASP48.OD2 18.08%, A:THR45.OG1A:ASP48.OD1 27.77%, A:THR45.OG1-A:ASP48.OD2 24.88%, A:THR45.NA:ASP48.OD2 16.68%, A:THR45.N-A:ASP48.OD1 15.68%/B:ARG60.NH1B:ASP48.OD2 10.09%, B:THR45.OG1-B:ASP48.OD2 27.87%, B:THR45.NB:ASP48.OD2 19.18%, B:THR45.OG1-B:ASP48.OD1 18.78%, B:THR45.NB:ASP48.OD1 10.69%, B:ARG60.NH1-B:ASP56.OD2 11.19%), • A:ASP92-A:ARG76/B:ASP92-B:ARG76 (with HBs A:ARG76.NE-A:ASP92. OD1 17.08%, A:ARG76.NH2-A:ASP92.OD1 14.09%, A:ASP92.N-A:ARG76.O 12.19%, A:ARG76.NH2-A:ASP92.OD2 11.99%, A:ARG76.NE-A:ASP92.OD2 10.49%, A:THR93.OG1-A:ASP92.OD2 25.77%/B:ARG76.NE-B:ASP92.OD2 18.88%, B:ARG76.NH2-B:ASP92.OD1 14.89%, B:ARG76.NH2-B:ASP92. OD2 13.59%, B:ARG76.NE-B:ASP92.OD1 13.39%, B:THR93.OG1-B:ASP92. OD1 17.48%, B:THR93.OG1-B:ASP92.OD2 16.58%), • A:ASP153-A:LYS102/B:ASP153-B:LYS102 (with HBs A:LYS102.NZA:ASP153.OD2 15.88%, A:LYS102.NZ-A:ASP153.OD1 14.49%, A:ASP153. N-A:CYS156.O 45.25%, A:CYS156.N-A:ASP153.O 28.67%, A:PHE159.NA:LYS102.O 30.17%, A:LYS102.N-A:VAL157.O 10.09%/ B:LYS102.NZB:ASP153.OD2 21.08%, B:ASP153.N-B:CYS156.O 44.06%, B:CYS156.NB:ASP153.O 33.27%, B:PHE159.N-B:LYS102.O 30.87%), • A:ASP155-A:LYS100/B:ASP155-B:LYS100 (with HBs A:LYS100.NZA:ASP155.OD2 40.36%, A:VAL157.N-A:LYS100.O 49.85%/B:LYS100.NZB:ASP155.OD2 39.06%, B:VAL157.N-B:LYS100.O 47.15%), • A:ASP176-A:ARG105/B:ASP176-B:ARG105 (with HBs A:ARG105.NH1A:ASP176.OD2 44.46%, A:ARG105.NH1-A:ASP176.OD1 13.99%, A:ASN 180.N-A:ASP176.OD1 53.85%, A:ASN180.N-A:ASP176.OD2 17.28%, A:ASP 176. N-A:ASN180.O 13.59%, A:THR175.OG1-A:ASP176.O 33.37%, A:ARG 105.NH2-A:PHE181.O 56.74%/B:ARG105.NH1-B:ASP176.OD2 28.77%, B:ARG105.NH1-B:ASP176.OD1 28.47%, B:ASN180.N-B:ASP176.OD1 34.87%, B:ASN180.N-B:ASP176.OD2 34.57%, B:ASP176.N-B:ASN180.O 16.48%, B:THR175.OG1-B:ASP176.O 33.87%, B:ARG105.NH2-B:PHE181.O 52.65%, B:ARG105.NH1-B:ASN180.O 10.09%), • A:ASP187-A:ARG40/B:ASP187-B:ARG40 (with HBs A:ARG40.NE-A:ASP 187.OD2 79.12%, A:ARG40.NH2-A:ASP187.OD1 58.84%, A:TYR54.OHA:ASP187.OD1 27.87%, A:TYR54.OH-A:ASP187.OD2 12.49%/B:ARG40. NE-B:ASP187.OD2 68.23%, B:ARG40.NH2-B:ASP187.OD1 51.65%, B:TYR5 4.OH-B:ASP187.OD2 15.28%, B:TYR54.OH-B:ASP187.OD1 14.59%), • A:ASP197-A:ARG131/B:ASP197-B:ARG131 (with HBs A:ARG131.NEA:ASP197.OD1 23.68%, A:ARG131.NE-A:ASP197.OD2 15.68%, A:LYS137.

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NZ-A:ASP197.OD2 12.89%, A:ARG131.NH2-A:ASP289.OD2 46.45%, A:ARG131.NH1-A:ASP289.OD1 31.27%, A:ARG131.NH1-A:ASP289.OD2 14.59%, A:ARG131.N-A:THR135.O 32.17%, A:PHE134.N-A:ARG131.O 13.49%/B:ARG131.NE-B:ASP197.OD2 20.38%, B:ARG131.NE-B:ASP197. OD1 15.28%, B:LYS137.NZ-B:ASP197.OD1 12.19%, B:ARG131.NH2B:ASP289.OD2 55.84%, B:ARG131.NH1-B:ASP289.OD1 33.77%, B:ARG131. NH1-B:ASP289.OD2 11.09%, B:ARG131.N-B:THR135.O 31.57%, B:PHE134. N-B:ARG131.O 12.79%), A:ASP197-A:LYS137/B:ASP197-B:LYS137 (with HBs A:LYS137.NZ-A:ASP 197.OD2 12.89%, A:ARG131.NE-A:ASP197.OD1 23.68%, A:ARG131.NEA:ASP197.OD2 15.68%/B:ARG131.NE-B:ASP197.OD2 20.38%, B:ARG131. NE-B:ASP197.OD1 15.28%, B:LYS137.NZ-B:ASP197.OD1 12.19%, B:TYR 126.OH-B:LYS137.O 17.18%), A:ASP229-A:LYS269/B:ASP229-B:LYS269 (weak during MD; with HBs A:THR226.OG1-A:ASP229.OD1 10.29%, A:LYS269.N-A:CYS265.O 36.56%, A:GLN273.N-A:LYS269.O 25.17%, A:LYS269.NZ-A:GLU270.OE2 14.69%, A:LYS269.NZ-A:GLU270.OE1 12.69%/B:LYS269.N-B:CYS265.O 40.26%, B:GLN273.N-B:LYS269.O 24.38%, B:LYS269.NZ-B:GLU270.OE1 17.98%), A:ASP289-A:ARG131/B:ASP289-B:ARG131 (with HBs A:ARG131.NH2A:ASP289.OD2 46.45%, A:ARG131.NH1-A:ASP289.OD1 31.27%, A:ARG 131.NH1-A:ASP289.OD2 14.59%, A:ASN203.ND2-A:ASP289.O 36.46%, A:ILE200.N-A:ASP289.OD2 35.86%, A:ARG131.N-A:THR135.O 32.17%, A:ARG131.NE-A:ASP197.OD1 23.68%, A:ARG131.NE-A:ASP197.OD2 15.68%, A:PHE134.N-A:ARG131.O 13.49%/B:ARG131.NH2-B:ASP289.OD2 55.84%, B:ARG131.NH1-B:ASP289.OD1 33.77%, B:ARG131.NH1-B:ASP 289.OD2 11.09%, B:ILE200.N-B:ASP289.OD2 45.75%, B:ASN203.ND2B:ASP289.O 36.06%, B:ARG131.N-B:THR135.O 31.57%, B:ARG131.NEB:ASP197.OD2 20.38%, B:ARG131.NE-B:ASP197.OD1 15.28%, B:PHE134. N-B:ARG131.O 12.79%), A:ASP295-A:ARG298/B:ASP295-B:ARG298 (with HBs A:ARG298.NH2A:ASP295.OD1 41.36%, A:ARG298.NH2-A:ASP295.OD2 15.78%, A:THR 111.OG1-A:ASP295.OD2 41.66%, A:THR111.OG1-A:ASP295.OD1 15.98%, A:THR292.N-A:ASP295.OD2 40.26%, A:THR292.OG1-A:ASP295.OD2 31.87%, A:THR292.N-A:ASP295.OD1 15.18%, A:THR292.OG1-A:ASP295. OD1 14.39%, A:GLN299.N-A:ASP295.O 28.57%, A:ARG298.N-A:PHE294.O 53.75%, A:VAL303.N-A:ARG298.O 11.19%/B:ARG298.NH2-B:ASP295.OD1 40.76%, B:ARG298.NH2-B:ASP295.OD2 16.98%, B:THR111.OG1-B:ASP 295.OD2 47.05%, B:THR111.OG1-B:ASP295.OD1 17.98%, B:GLN299.NB:ASP295.O 39.76%, B:THR292.N-B:ASP295.OD2 39.06%, B:THR292.OG1B:ASP295.OD2 31.87%, B:THR292.N-B:ASP295.OD1 15.88%, B:ARG298.NB:PHE294.O 50.75%, B:ARG298.NH1-B:MET6.O 16.08%), A:GLU55-A:ARG40/B:GLU55-B:ARG40 (not existing during MD; with HBs A:ARG40.NE-A:ASP187.OD2 79.12%, A:ARG40.NH2-A:ASP187.OD1 58.84%/B:ARG40.NE-B:ASP187.OD2 68.23%, B:ARG40.NH2-B:ASP187. OD1 51.65%),

2.3 Results and Discussions

45

• A:GLU288-A:LYS5/B:GLU288-B:LYS5 (with HBs A:LYS5.NZ-A:GLU288. OE2 30.17%, A:LYS5.NZ-A:GLU288.OE1 29.37%, A:LYS5.NZ-A:GLU290. OE1 46.55%, A:LYS5.NZ-A:GLU290.OE2 13.89%/B:LYS5.NZ-B:GLU288. OE2 30.77%, B:LYS5.NZ-B:GLU288.OE1 28.17%, B:LYS5.NZ-B:GLU290. OE1 32.97%, B:LYS5.NZ-B:GLU290.OE2 32.17%), • A:GLU290-A:LYS5/B:GLU290-B:LYS5 (with HBs A:LYS5.NZ-A:GLU290. OE1 46.55%, A:LYS5.NZ-A:GLU290.OE2 13.89%, A:LYS5.NZ-A:GLU288. OE2 30.17%, A:LYS5.NZ-A:GLU288.OE1 29.37%/B:LYS5.NZ-B:GLU290. OE1 32.97%, B:LYS5.NZ-B:GLU290.OE2 32.17%, B:LYS5.NZ-B:GLU288. OE2 30.77%, B:LYS5.NZ-B:GLU288.OE1 28.17%); .− in rep1: • A:GLU290-B:ARG4/B:GLU290-A:ARG4 (with HBs B:ARG4.NH1-A:GLU 290.OE2 39.56%, B:ARG4.NH2-A:GLU290.OE1 32.77%, B:ARG4.NH1A:GLU290.OE1 22.08%, B:ARG4.NH2-A:GLU290.OE2 19.28%/A:ARG4. NH1-B:GLU290.OE2 33.87%, A:ARG4.NH2-B:GLU290.OE1 21.58%, A:ARG4.NH1-B:GLU290.OE1 14.99%, A:ARG4.NH2-B:GLU290.OE2 10.69%), • A:ASP34-A:LYS90/B:ASP34-B:LYS90 (with HBs A:LYS90.NZ-A:ASP34.OD1 26.77%, A:LYS90.NZ-A:ASP34.OD2 21.48%, A:VAL91.N-A:ASP34.O 44.06%, A:ILE78.N-A:LYS90.O 50.65%, A:LYS90.N-A:GLY79.O 50.45%/B: LYS90.NZ-B:ASP34.OD1 25.87%, B:LYS90.NZ-B:ASP34.OD2 20.88%, B:VAL91.N-B:ASP34.O 40.26%, B:ILE78.N-B:LYS90.O 53.15%, B:LYS90.NB:GLY79.O 52.75%), • A:ASP48-A:ARG60/B:ASP48-B:ARG60 (with HBs A:ARG60.NH1-A:ASP48. OD1 15.48%, A:ARG60.NH2-A:ASP48.OD2 12.09%, A:THR45.OG1A:ASP48.OD2 30.07%, A:THR45.OG1-A:ASP48.OD1 20.78%, A:THR45.NA:ASP48.OD2 17.68%, A:THR45.N-A:ASP48.OD1 12.09%/B:THR45.OG1B:ASP48.OD2 28.67%, B:THR45.N-B:ASP48.OD2 18.68%, B:THR45.OG1B:ASP48.OD1 16.18%), • A:ASP92-A:ARG76/B:ASP92-B:ARG76 (with HBs A:ARG76.NE-A:ASP92. OD1 15.48%, A:ARG76.NH2-A:ASP92.OD1 12.19%, A:ASP92.N-A:ARG76.O 11.49%, A:ARG76.NH2-A:ASP92.OD2 10.69%, A:ARG76.NE-A:ASP92.OD2 10.19%, A:THR93.OG1-A:ASP92.OD2 22.18%, A:THR93.OG1-A:ASP92.OD1 11.09%/B:ARG76.NE-B:ASP92.OD2 15.98%, B:ARG76.NH2-B:ASP92.OD2 15.48%, B:ARG76.NE-B:ASP92.OD1 13.99%, B:ARG76.NH2-B:ASP92.OD1 12.69%, B:THR93.OG1-B:ASP92.OD1 17.08%, B:THR93.OG1-B:ASP92.OD2 15.58%), • A:ASP153-A:LYS102/B:ASP153-B:LYS102 (with HBs A:LYS102.NZA:ASP153.OD1 17.48%, A:LYS102.NZ-A:ASP153.OD2 15.78%, A:LYS102.NA:VAL157.O 11.29%, A:PHE159.N-A:LYS102.O 28.07%, A:ASP153.NA:CYS156.O 41.86%, A:CYS156.N-A:ASP153.O 27.37%/B:LYS102.NZB:ASP153.OD2 17.98%, B:ASP153.N-B:CYS156.O 44.16%, B:CYS156.NB:ASP153.O 28.87%, B:PHE159.N-B:LYS102.O 28.67%), • A:ASP155-A:LYS100/B:ASP155-B:LYS100 (with HBs A:LYS100.NZA:ASP155.OD2 35.66%, A:VAL157.N-A:LYS100.O 54.05%/B:LYS100.NZ-

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2 3C-Like Protease (3CLpro)

B:ASP155.OD2 37.76%, B:LYS100.NZ-B:ASP155.OD1 10.89%, B:VAL157.NB:LYS100.O 49.95%), A:ASP176-A:ARG105/B:ASP176-B:ARG105 (with HBs A:ARG105.NH1A:ASP176.OD2 44.06%, A:ARG105.NH1-A:ASP176.OD1 14.59%, A:ASN 180.N-A:ASP176.OD1 52.15%, A:ASN180.N-A:ASP176.OD2 19.68%, A:ASP 176.N-A:ASN180.O 14.19% A:THR175.OG1-A:ASP176.O 33.87%, A:ARG 105.NH2-A:PHE181.O 54.15%, A:ARG105.NH1-A:ASN180.O 10.39%/B: ARG105.NH1-B:ASP176.OD2 28.97%, B:ARG105.NH1-B:ASP176.OD1 25.97%, B:ASN180.N-B:ASP176.OD1 37.66%, B:ASN180.N-B:ASP176.OD2 32.17%, B:ASP176.N-B:ASN180.O 15.38%, B:THR175.OG1-B:ASP176.O 32.87%, B:ARG105.NH2-B:PHE181.O 55.24%), A:ASP187-A:ARG40/B:ASP187-B:ARG40 (with HBs A:ARG40.NE-A:ASP 187.OD2 77.32%, A:ARG40.NH2-A:ASP187.OD1 58.54%, A:TYR54.OHA:ASP187.OD1 25.37%, A:TYR54.OH-A:ASP187.OD2 16.18%/B:ARG40. NE-B:ASP187.OD2 65.23%, B:ARG40.NH2-B:ASP187.OD1 55.54%, B:TYR54.OH-B:ASP187.OD1 14.39%, B:TYR54.OH-B:ASP187.OD2 13.79%, B:TYR182.OH-B:CYS160.O 65.33%), A:ASP197-A:ARG131/B:ASP197-B:ARG131 (with HBs A:ARG131.NEA:ASP197.OD1 21.38%, A:ARG131.NE-A:ASP197.OD2 16.68%, A:LYS137. NZ-A:ASP197.OD2 13.89%, A:ARG131.NH2-A:ASP289.OD2 51.85%, A:ARG131.NH1-A:ASP289.OD1 36.96%, A:ARG131.NH1-A:ASP289.OD2 12.69%, A:ARG131.N-A:THR135.O 31.97%, A:PHE134.N-A:ARG131.O 11.79%/B:ARG131.NE-B:ASP197.OD2 18.98%, B:ARG131.NE-B:ASP197. OD1 16.18%, B:LYS137.NZ-B:ASP197.OD1 12.89%, B:ARG131.NH2B:ASP289.OD2 58.24%, B:ARG131.NH1-B:ASP289.OD1 39.46%, B:ARG 131.N-B:THR135.O 32.37%, B:PHE134.N-B:ARG131.O 12.49%), A:ASP197-A:LYS137/B:ASP197-B:LYS137 (with HBs A:LYS137.NZA:ASP197.OD2 13.89%, A:ARG131.NE-A:ASP197.OD1 21.38%, A:ARG131. NE-A:ASP197.OD2 16.68%/B:LYS137.NZ-B:ASP197.OD1 12.89%, B:ARG 131.NE-B:ASP197.OD2 18.98%, B:ARG131.NE-B:ASP197.OD1 16.18%, B:TYR126.OH-B:LYS137.O 16.78%), A:ASP229-A:LYS269/B:ASP229-B:LYS269 (weak during MD; with HBs A:LYS269.N-A:CYS265.O 33.77%, A:GLN273.N-A:LYS269.O 27.57%, A:LYS269.NZ-A:GLU270.OE1 13.79%, A:LYS269.NZ-A:GLU270.OE2 13.49%/B:LYS269.N-B:CYS265.O 40.26%, B:GLN273.N-B:LYS269.O 22.38%, B:LYS269.NZ-B:GLU270.OE1 18.78%), A:ASP289-A:ARG131/B:ASP289-B:ARG131 (with HBs A:ARG131.NH2A:ASP289.OD2 51.85%, A:ARG131.NH1-A:ASP289.OD1 36.96%, A:ARG 131.NH1-A:ASP289.OD2 12.69%, A:ILE200.N-A:ASP289.OD2 36.06%, A:ASN203.ND2-A:ASP289.O 35.96%, A:ARG131.N-A:THR135.O 31.97%, A:PHE134.N-A:ARG131.O 11.79%, A:ARG131.NE-A:ASP197.OD1 21.38%, A:ARG131.NE-A:ASP197.OD2 16.68%/B:ARG131.NH2-B:ASP289.OD2 58.24%, B:ARG131.NH1-B:ASP289.OD1 39.46%, B:ILE200.N-B:ASP289. OD2 46.45%, B:ASN203.ND2-B:ASP289.O 37.46%, B:ARG131.N-B:THR

2.3 Results and Discussions

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135.O 32.37%, B:ARG131.NE-B:ASP197.OD2 18.98%, B:ARG131.NEB:ASP197.OD1 16.18%, B:PHE134.N-B:ARG131.O 12.49%), A:ASP295-A:ARG298/B:ASP295-B:ARG298 (with HBs A:ARG298.NH2A:ASP295.OD1 42.66%, A:ARG298.NH2-A:ASP295.OD2 14.79%, A:THR 111.OG1-A:ASP295.OD2 43.76%, A:THR111.OG1-A:ASP295.OD1 14.39%, A:THR292.N-A:ASP295.OD2 37.06%, A:THR292.OG1-A:ASP295.OD2 32.07%, A:THR292.N-A:ASP295.OD1 13.59%, A:THR292.OG1-A:ASP295. OD1 12.69%, A:GLN299.N-A:ASP295.O 27.37%, A:ARG298.N-A:PHE294.O 49.25%, A:VAL303.N-A:ARG298.O 13.69%/B:ARG298.NH2-B:ASP295.OD1 39.76%, B:ARG298.NH2-B:ASP295.OD2 13.69%, B:THR111.OG1-B:ASP 295.OD2 50.85%, B:THR111.OG1-B:ASP295.OD1 13.69%, B:THR292.NB:ASP295.OD2 39.46%, B:THR292.OG1-B:ASP295.OD2 30.97%, B:THR292. N-B:ASP295.OD1 13.29%, B:GLN299.N-B:ASP295.O 35.46%, B:ARG298.NB:PHE294.O 52.75%, B:ARG298.NH1-B:MET6.O 13.99%), A:GLU55-A:ARG40/B:GLU55-B:ARG40 (not existing during MD; with HBs A:ARG40.NE-A:ASP187.OD2 77.32%, A:ARG40.NH2-A:ASP187.OD1 58.54%/B:ARG40.NE-B:ASP187.OD2 65.23%, B:ARG40.NH2-B:ASP187. OD1 55.54%), A:GLU288-A:LYS5/B:GLU288-B:LYS5 (with HBs A:LYS5.NZ-A:GLU288. OE1 29.37%, A:LYS5.NZ-A:GLU288.OE2 28.37%, A:LYS5.NZ-A:GLU290. OE1 44.26%, A:LYS5.NZ-A:GLU290.OE2 14.69%/B:LYS5.NZ-B:GLU288. OE1 27.97%, B:LYS5.NZ-B:GLU288.OE2 25.77%, B:LYS5.NZ-B:GLU290. OE1 31.37%, B:LYS5.NZ-B:GLU290.OE2 29.27%), A:GLU290-A:LYS5/B:GLU290-B:LYS5 (with HBs A:LYS5.NZ-A:GLU290. OE1 44.26%, A:LYS5.NZ-A:GLU290.OE2 14.69%, A:LYS5.NZ-A:GLU288. OE1 29.37%, A:LYS5.NZ-A:GLU288.OE2 28.37%/B:LYS5.NZ-B:GLU290. OE1 31.37%, B:LYS5.NZ-B:GLU290.OE2 29.27%, B:LYS5.NZ-B:GLU288. OE1 27.97%, B:LYS5.NZ-B:GLU288.OE2 25.77%); in rep2: A:GLU290-B:ARG4/B:GLU290-A:ARG4 (with HBs B:ARG4.NH1-A:GLU 290.OE2 38.76%, B:ARG4.NH2-A:GLU290.OE1 30.17%, B:ARG4.NH1A:GLU290.OE1 20.68%, B:ARG4.NH2-A:GLU290.OE2 19.28%/A:ARG4. NH1-B:GLU290.OE2 36.06%, A:ARG4.NH2-B:GLU290.OE1 23.78%, A:ARG4.NH1-B:GLU290.OE1 13.99%, A:ARG4.NH2-B:GLU290.OE2 10.69%), A:ASP34-A:LYS90/B:ASP34-B:LYS90 (with HBs A:LYS90.NZ-A:ASP34.OD1 27.17%, A:LYS90.NZ-A:ASP34.OD2 19.58%, A:VAL91.N-A:ASP34.O 40.76%, A:LYS90.N-A:GLY79.O 50.45%, A:ILE78.N-A:LYS90.O 49.35%/B: LYS90.NZ-B:ASP34.OD1 26.17%, B:LYS90.NZ-B:ASP34.OD2 20.88%, B:VAL91.N-B:ASP34.O 40.36%, B:LYS90.N-B:GLY79.O 47.65%, B:ILE78.NB:LYS90.O 53.85%), A:ASP48-A:ARG60/B:ASP48-B:ARG60 (with HBs A:ARG60.NH2-A:ASP48. OD2 10.29%, A:ARG60.NH1-A:ASP48.OD1 10.19%, A:THR45.OG1A:ASP48.OD2 32.37%, A:THR45.OG1-A:ASP48.OD1 20.28%, A:THR45.NA:ASP48.OD2 20.08%, A:THR45.N-A:ASP48.OD1 11.39%/B:THR45.OG1-

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2 3C-Like Protease (3CLpro)

B:ASP48.OD2 25.17%, B:THR45.N-B:ASP48.OD2 16.88%, B:THR45.OG1B:ASP48.OD1 14.79%), A:ASP92-A:ARG76/B:ASP92-B:ARG76 (with HBs A:ASP92.N-A:ARG76.O 13.69%, A:ARG76.NH2-A:ASP92.OD1 12.79%, A:ARG76.NE-A:ASP92.OD2 12.69%, A:ARG76.NE-A:ASP92.OD1 10.69%, A:THR93.OG1-A:ASP92.OD2 18.28%, A:THR93.OG1-A:ASP92.OD1 14.29%/B:ARG76.NE-B:ASP92.OD2 17.28%, B:ARG76.NH2-B:ASP92.OD2 15.38%, B:ARG76.NH2-B:ASP92.OD1 14.39%, B:ARG76.NE-B:ASP92.OD1 12.99%, B:THR93.OG1-B:ASP92.OD1 15.68%), A:ASP153-A:LYS102/B:ASP153-B:LYS102 (with HBs A:LYS102.NZA:ASP153.OD1 15.08%, A:LYS102.NZ-A:ASP153.OD2 13.99%, A:ASP153. N-A:CYS156.O 46.15%, A:CYS156.N-A:ASP153.O 28.67%, A:PHE159.NA:LYS102.O 32.17%, A:LYS102.N-A:VAL157.O 10.99%/B:LYS102.NZB:ASP153.OD2 18.58%, B:LYS102.NZ-B:ASP153.OD1 10.09%, B:ASP153.NB:CYS156.O 44.06%, B:CYS156.N-B:ASP153.O 28.27%, B:PHE159.NB:LYS102.O 29.77%), A:ASP155-A:LYS100/B:ASP155-B:LYS100 (with HBs A:LYS100.NZA:ASP155.OD2 32.37%, A:LYS100.NZ-A:ASP155.OD1 11.19%, A:VAL157. N-A:LYS100.O 49.25%/B:LYS100.NZ-B:ASP155.OD2 37.56%, B:LYS100. NZ-B:ASP155.OD1 11.49%, B:VAL157.N-B:LYS100.O 49.25%), A:ASP176-A:ARG105/B:ASP176-B:ARG105 (with HBs A:ARG105.NH1A:ASP176.OD2 38.26%, A:ARG105.NH1-A:ASP176.OD1 18.78%, A:ASN 180.N-A:ASP176.OD1 47.05%, A:ASN180.N-A:ASP176.OD2 24.08%, A:ASP176.N-A:ASN180.O 12.79%, A:THR175.OG1-A:ASP176.O 32.37%, A:ARG105.NH2-A:PHE181.O 56.24%/B:ARG105.NH1-B:ASP176.OD2 30.67%, B:ARG105.NH1-B:ASP176.OD1 27.27%, B:ASN180.N-B:ASP176. OD2 36.56%, B:ASN180.N-B:ASP176.OD1 36.36%, B:ASP176.N-B:ASN 180.O 17.68%, B:THR175.OG1-B:ASP176.O 31.37%, B:ARG105.NH2B:PHE181.O 53.35%), A:ASP187-A:ARG40/B:ASP187-B:ARG40 (with HBs A:ARG40.NE-A:ASP 187.OD2 73.63%, A:ARG40.NH2-A:ASP187.OD1 52.45%, A:TYR54.OHA:ASP187.OD1 25.37%, A:TYR54.OH-A:ASP187.OD2 13.79%/B:ARG40. NE-B:ASP187.OD2 68.33%, B:ARG40.NH2-B:ASP187.OD1 54.25%, B:TYR 54.OH-B:ASP187.OD1 13.69%, B:TYR54.OH-B:ASP187.OD2 12.09%), A:ASP197-A:ARG131/B:ASP197-B:ARG131 (with HBs A:ARG131.NEA:ASP197.OD1 20.28%, A:ARG131.NE-A:ASP197.OD2 17.78%, A:LYS137. NZ-A:ASP197.OD2 12.79%, A:ARG131.NH2-A:ASP289.OD2 52.15%, A:ARG131.NH1-A:ASP289.OD1 36.46%, A:ARG131.N-A:THR135.O 33.57%, A:PHE134.N-A:ARG131.O 13.19%/B:ARG131.NE-B:ASP197.OD2 18.28%, B:ARG131.NE-B:ASP197.OD1 15.88%, B:LYS137.NZ-B:ASP197. OD1 12.79%, B:ARG131.NH2-B:ASP289.OD2 57.04%, B:ARG131.NH1B:ASP289.OD1 36.36%, B:ARG131.N-B:THR135.O 31.17%, B:PHE134.NB:ARG131.O 12.69%), A:ASP197-A:LYS137/B:ASP197-B:LYS137 (with HBs A:LYS137.NZA:ASP197.OD2 12.79%, A:ARG131.NE-A:ASP197.OD1 20.28%, A:ARG131.

2.3 Results and Discussions

•

•

•

•

•

•

49

NE-A:ASP197.OD2 17.78%/B:LYS137.NZ-B:ASP197.OD1 12.79%, B:ARG 131.NE-B:ASP197.OD2 18.28%, B:ARG131.NE-B:ASP197.OD1 15.88%, B:TYR126.OH-B:LYS137.O 16.08%), A:ASP229-A:LYS269/B:ASP229-B:LYS269 (weak during MD; with HBs A:LYS269.N-A:CYS265.O 34.67%, A:GLN273.N-A:LYS269.O 23.48%, A:LYS269.NZ-A:GLU270.OE2 11.79%, A:LYS269.NZ-A:GLU270.OE1 10.39%/B:LYS269.N-B:CYS265.O 35.06%, B:GLN273.N-B:LYS269.O 21.78%, B:LYS269.NZ-B:GLU270.OE1 16.98%), A:ASP289-A:ARG131/B:ASP289-B:ARG131 (with HBs A:ARG131.NH2A:ASP289.OD2 52.15%, A:ARG131.NH1-A:ASP289.OD1 36.46%, A:ASN 203.ND2-A:ASP289.O 36.26%, A:ILE200.N-A:ASP289.OD2 35.76%, A:ARG131.N-A:THR135.O 33.57%, A:PHE134.N-A:ARG131.O 13.19%, A:ARG131.NE-A:ASP197.OD1 20.28%, A:ARG131.NE-A:ASP197.OD2 17.78%/B:ARG131.NH2-B:ASP289.OD2 57.04%, B:ARG131.NH1-B:ASP 289.OD1 36.36%, B:ILE200.N-B:ASP289.OD2 40.96%, B:ASN203.ND2B:ASP289.O 36.66%, B:ARG131.N-B:THR135.O 31.17%, B:PHE134.NB:ARG131.O 12.69%, B:ARG131.NE-B:ASP197.OD2 18.28%, B:ARG131. NE-B:ASP197.OD1 15.88%), A:ASP295-A:ARG298/B:ASP295-B:ARG298 (with HBs A:ARG298.NH2A:ASP295.OD1 39.86%, A:ARG298.NH2-A:ASP295.OD2 14.89%, A:THR 111.OG1-A:ASP295.OD2 41.46%, A:THR111.OG1-A:ASP295.OD1 18.08%, A:THR292.N-A:ASP295.OD2 38.76%, A:THR292.OG1-A:ASP295.OD2 31.07%, A:THR292.N-A:ASP295.OD1 16.68%, A:THR292.OG1-A:ASP295. OD1 12.19%, A:GLN299.N-A:ASP295.O 29.17%, A:ARG298.N-A:PHE294.O 48.05%, A:VAL303.N-A:ARG298.O 12.29%/B:ARG298.NH2-B:ASP295.OD1 39.36%, B:ARG298.NH2-B:ASP295.OD2 12.39%, B:THR292.OG1-B:ASP 295.OD2 30.77%, B:THR111.OG1-B:ASP295.OD2 47.25%, B:THR111.OG1B:ASP295.OD1 14.99%, B:THR292.N-B:ASP295.OD2 38.26%, B:THR292.NB:ASP295.OD1 12.19%, B:GLN299.N-B:ASP295.O 33.27%, B:ARG298.NB:PHE294.O 49.75%, B:ARG298.NH1-B:MET6.O 15.48%), A:GLU55-A:ARG40/B:GLU55-B:ARG40 (not existing during MD; with HBs A:ARG40.NE-A:ASP187.OD2 73.63%, A:ARG40.NH2-A:ASP187.OD1 52.45%/B:ARG40.NE-B:ASP187.OD2 68.33%, B:ARG40.NH2-B:ASP187. OD1 54.25%), A:GLU288-A:LYS5/B:GLU288-B:LYS5 (with HBs A:LYS5.NZ-A:GLU288. OE2 29.37%, A:LYS5.NZ-A:GLU288.OE1 28.07%, A:LYS5.NZ-A:GLU290. OE1 43.96%, A:LYS5.NZ-A:GLU290.OE2 14.49%/B:LYS5.NZ-B:GLU288. OE1 26.17%, B:LYS5.NZ-B:GLU288.OE2 24.68%, B:LYS5.NZ-B:GLU290. OE1 36.46%, B:LYS5.NZ-B:GLU290.OE2 25.17%), A:GLU290-A:LYS5/B:GLU290-B:LYS5 (with HBs A:LYS5.NZ-A:GLU290. OE1 43.96%, A:LYS5.NZ-A:GLU290.OE2 14.49%, A:LYS5.NZ-A:GLU288. OE2 29.37%, A:LYS5.NZ-A:GLU288.OE1 28.07%/B:LYS5.NZ-B:GLU290. OE1 36.46%, B:LYS5.NZ-B:GLU290.OE2 25.17%, B:LYS5.NZ-B:GLU288. OE1 26.17%, B:LYS5.NZ-B:GLU288.OE2 24.68%);

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2 3C-Like Protease (3CLpro)

where in each monomer, the polar contacts ASP34-LYS90, ASP48-ARG60, ASP92ARG76, ASP153-LYS102, ASP155-LYS100, ASP176-ARG105, ASP187-ARG40, ASP197-ARG131, ASP197-LYS137, ASP289-ARG131, ASP295-ARG298, GLU288-LYS5, and GLU290-LYS5 are strong and stable during the three sets of REMDs: rep0, rep1, and rep2. Table 2.7 lists the HBs with more than 50% occupancy rates during the three sets of 50 .μs’ REMD rep0-rep1-rep3 for the Evans-dimer model, where the HBs linking the two monomers (A-chain and B-chain) are the following: − 1. 2. 3.

.

4. 5. 6. 7.

8. 9. 10. .− 11. 12.

13. 14. 15. 16. 17.

in rep0: A:SER123.OG-B:VAL303.O 53.65%/B:SER123.OG-A:VAL303.O 53.35%, A:PHE305.N-B:PRO122.O 38.16%/B:PHE305.N-A:PRO122.O 31.27%, A:ARG4.NH1-B:GLU290.OE2 33.67%, A:ARG4.NH2-B:GLU290.OE1 22.68%, A:ARG4.NH1-B:GLU290.OE1 14.29%/B:ARG4.NH1-A:GLU290. OE2 37.56%, B:ARG4.NH2-A:GLU290.OE1 31.77%, B:ARG4.NH1-A:GLU 290.OE1 24.58%, B:ARG4.NH2-A:GLU290.OE2 19.48%, A:PHE140.N-B:SER1.O 29.57%/B:PHE140.N-A:SER1.O 17.58%, A:ALA7.N-B:VAL125.O 29.17%, B:VAL125.N-A:ALA7.O 20.58%/B:ALA7. N-A:VAL125.O 23.68%, A:GLY11.N-B:GLU14.OE2 22.78%/B:GLY11.N-A:GLU14.OE2 18.48%, A:SER1.N-B:GLU166.OE2 18.38%, A:SER1.N-B:GLU166.OE1 18.18%, A:SER1.OG-B:GLU166.OE2 10.49%, A:SER1.N-B:HSD172.NE2 17.18%, A:SER1.N-B:PHE140.O 12.59%/B:SER1.N-A:GLU166.OE2 24.68%, B:SER1.N-A:GLU166.OE1 22.18%, B:SER1.OG-A:GLU166.OE2 14.39%, B:SER1.OG-A:GLU166.OE1 10.79%, B:SER1.N-A:HSD172.NE2 37.86%, B:SER1.N-A:PHE140.O 21.68%, A:VAL125.N-B:ALA7.O 16.48%, A:SER139.OG-B:GLY2.O 15.58%, A:SER10.N-B:SER10.OG 10.79%; in rep1: A:SER123.OG-B:VAL303.O 55.44%/B:SER123.OG-A:VAL303.O 54.25%, A:ARG4.NH1-B:GLU290.OE2 33.87%, A:ARG4.NH2-B:GLU290.OE1 21.58%, A:ARG4.NH1-B:GLU290.OE1 14.99%, A:ARG4.NH2-B:GLU290. OE2 10.69%/B:ARG4.NH1-A:GLU290.OE2 39.56%, B:ARG4.NH2A:GLU290.OE1 32.77%, B:ARG4.NH1-A:GLU290.OE1 22.08%, B:ARG4. NH2-A:GLU290.OE2 19.28%, A:PHE305.N-B:PRO122.O 33.17%/B:PHE305.N-A:PRO122.O 29.37%, A:ALA7.N-B:VAL125.O 31.77%/B:ALA7.N-A:VAL125.O 26.57%, A:PHE140.N-B:SER1.O 28.57%, A:GLY11.N-B:GLU14.OE2 23.68%/B:GLY11.N-A:GLU14.OE2 21.68%, A:SER1.N-B:GLU166.OE1 19.18%, A:SER1.N-B:GLU166.OE2 17.18%, A:SER1.N-B:HSD172.NE2 16.28%, A:SER1.N-B:PHE140.O 10.39%/B:SER 1.N-A:GLU166.OE2 24.48%, B:SER1.OG-A:GLU166.OE1 13.39%, B:SER 1.OG-A:GLU166.OE2 13.09%, B:SER1.N-A:HSD172.NE2 34.17%, B:SER1.

2.3 Results and Discussions

18. .− 19. 20.

21. 22. 23. 24. 25.

26. 27. 28.

51

N-A:PHE140.O 21.18%, B:PHE140.N-A:SER1.O 16.98%, A:SER139.OGB:GLY2.O 18.58%, A:VAL125.N-B:ALA7.O 17.98%/B:VAL125.N-A:ALA7.O 20.48%, in rep2: A:SER123.OG-B:VAL303.O 49.45%/B:SER123.OG-A:VAL303.O 55.74%, A:ARG4.NH1-B:GLU290.OE2 36.06%, A:ARG4.NH2-B:GLU290.OE1 23.78%, A:ARG4.NH1-B:GLU290.OE1 13.99%, A:ARG4.NH2-B:GLU290. OE2 10.69%/B:ARG4.NH1-A:GLU290.OE2 38.76%, B:ARG4.NH2A:GLU290.OE1 30.17%, B:ARG4.NH1-A:GLU290.OE1 20.68%, B:ARG4. NH2-A:GLU290.OE2 19.28%, A:PHE305.N-B:PRO122.O 33.07%/B:PHE305.N-A:PRO122.O 26.37%, A:ALA7.N-B:VAL125.O 29.07%/B:ALA7.N-A:VAL125.O 28.37% / B:VAL 125.N-A:ALA7.O 21.38%, A:PHE140.N-B:SER1.O 24.88%/B:PHE140.N-A:SER1.O 17.38%, A:GLY11.N-B:GLU14.OE2 22.78%/B:GLY11.N-A:GLU14.OE2 21.08%, A:SER1.N-B:GLU166.OE2 20.68%, A:SER1.N-B:GLU166.OE1 17.78%, A:SER1.N-B:HSD172.NE2 17.68%, A:SER1.N-B:PHE140.O 11.99%/B:SER 1.N-A:GLU166.OE2 23.88%, B:SER1.N-A:GLU166.OE1 22.18%, B:SER1. OG-A:GLU166.OE2 12.19%, B:SER1.OG-A:GLU166.OE1 10.49%, B:SER 1.N-A:HSD172.NE2 33.47%, B:SER1.N-A:PHE140.O 22.58%, A:SER139.OG-B:GLY2.O 16.18%, A:VAL125.N-B:ALA7.O 15.98%, A:SER10.N-B:SER10.OG 10.19%.

The REMD secondary structural developments for rep0-rep2 can be seen from Fig. 2.10, where we know that segments A:TYR37-A:LYS61 and B:ILE43B:LEU67 and residues A:PHE181 and B:ASP187 have unstable secondary structures during 50 ns’ MD rep0-rep2.

Fig. 2.10 The secondary structural graphs for the three sets of 50 ns’ REMD data in [113] for the 3CLpro-dimer (where from left to right are for rep0, rep1, and rep2, respectively, and 1 ns has 20 frames)

For the Evans-dimer model, Fig. 2.11 shows an important SB between GLU290 and ARG4 linking the two monomers and the RMSD performance of the three sets of REMD data in [113]. The polar contact between GLU290 and ARG4 linking the two monomers are strong.

52

2 3C-Like Protease (3CLpro)

Fig. 2.11 The SBs A:GLU290-B:ARG4 and B:GLU290-A:ARG4 linking the two monomers of the Evans-dimer model during the three sets of 50 ns’ REMD production phase and the RMSDs of the three sets of REMDs

In [340], six 6LU7-3CLpro models monomer_apo (aa 1–306, 4682 atoms), monomer_N3 (aa 1–306 + N3I 307, 4780 atoms), dimer_apo (aa 1–306 + aa 307– 612, 9364 atoms), dimer_N3 (aa 1–306 + aa 307–612 + N3I 613, 9642 atoms), dimer_2N3 (aa 1–306 + N3I 307 + aa 308–613 + N3I 614, 9560 atoms), and dimer_2N3_covalent (aa 1–306 + N3I 145 + aa 307–612 + N3I 451, 9562 atoms) are presented. We optimized the six models and list all their SBs in Table 2.8, where all the above SBs can be confirmed. HBs of the optimized six models of [340] are listed in Tables 2.9, 2.10, and 2.11. The .π -cations and .π -.π stackings of each model optimized are the following: ◦ 6LU7_monomer_apo: PHE8-ARG298.NH2+-PHE294; PHE103-TYR37, PHE3-PHE291, PHE219-TYR218; .◦ 6LU7_monomer_N3: TYR54-ARG40.NH2+, TYR101-LYS100.NZ+; HIS164HIS41, PHE103-TYR37, TRP207-PHE291; .◦ 6LU7_dimer_apo: TYR360-ARG494.NH2+; PHE409-TYR343, HIS469PHE446-HIS478-HIS469, HIS163-PHE140-HIS172-HIS163, PHE291-PHE3TRP207, PHE597-PHE309-TRP513, PHE219-TRP218, PHE525-TRP524; .◦ 6LU7_dimer_N3: PHE314-ARG604.NH2+, TYR237-LYS236.NZ+; TYR343PHE409, HIS469-HIS478-PHE446-HIS469, HIS163-PHE140, PHE103TYR37, TRP207-PHE3-TRP207-PHE291; .◦ 6LU7_dimer_2N3: TRP525-ARG586.NH2+, PHE315-ARG605.NH2+; HIS 163-PHE140-HIS172-HIS163, TYR37-PHE103, PHE3-TRP207, HIS470PHE447-HIS479, HIS387-PHE373, HIS348-HIS471; .◦ 6LU7_dimer_2N3_covalent: PHE305-LYS12.NZ+; TYR37-PHE103, TYR54HIS41-HIS164-PHE181, HIS163-HIS172-PHE140-HIS163, TRP524-PHE525TRP524, TYR360-HIS347, HIS478-HIS469-PHE446-HIS478. .

For the optimized models, the residues binding with the ligand N3 are the following: ◦ 6LU7_monomer_N3: THR25, LEU27, HIS41, SER46, MET49, LEU50, PHE140, LEU141, ASN142, GLY143, SER144, CYS145, 164, 165, 168, GLU166, GLN189, THR190, ALA191;

.

2.3 Results and Discussions

53

◦ 6LU7_dimer_2N3-N3I307: THR25, LEU27, HIS41, MET49, TYR54, PHE140, LEU141, ASN142, GLY143, SER144, CYS145, HIS163, HIS164, MET165, GLU166, LEU167, PRO168, HIS172, PHE181, VAL186, ASP187, ARG188, GLN189, THR190, ALA191, GLN192, ALA193, SER308; .◦ 6LU7_dimer_2N3-N3I614: SER1, THR331, THR333, HIS348, MET356, GLY450, SER451, CYS452, HIS470, HIS471, MET472, GLU473, LEU474, PRO475, PHE488, VAL493, ASP494, ARG495, GLN496, THR497, ALA498, GLN499; .◦ 6LU7_dimer_2N3_covalent-N3I145: THR25, THR26, LEU27, ASN28, PRO39, HIS41, MET49, TYR54, TYR118, LEU141, ASN142, GLY143, SER144, GLY146, SER147, HIS163, HIS164, MET165, GLU166, LEU167, PRO168, PHE181, ASP187, GLN189, THR190, ALA191, GLN192; .◦ 6LU7_dimer_2N3_covalent-N3I451: THR331, THR332, LEU333, ASN334, PRO345, HIS347, VAL348, CYS350, MET355, TYR360, ASN448, GLY449, SER450, GLY452, SER453, HIS469, HIS470, MET471, GLU472, LEU473, PHE487, VAL492, ASP493, GLN495, THR496, ALA497, GLN498 .

and they are shown in Fig. 2.12.

Fig. 2.12 The ligand interaction diagrams for the optimized 6LU7_monomer_N3, 6LU7_dimer_2N3-N3I307, 6LU7_dimer_2N3-N3I614, 6LU7_dimer_2N3_covalent-N3I145, and 6LU7_dimer_2N3_covalent-N3I451 models of [340], respectively (from left to right in turns)

For the six optimized models of [340], we also find some differences among them in secondary structures and Ramachandran plot distributions (Fig. 2.13).

54

2 3C-Like Protease (3CLpro)

Fig. 2.13 The secondary structures and Ramachandran plot diagrams of the optimized six models of [340]

Tables 2.12, 2.13, 2.14, 2.15, 2.16, 2.17, 2.18, 2.19, 2.20, 2.21, 2.22, and 2.23 list all the SBs and HBs of MDs of the six models of [340], where each MD has five sets

2.3 Results and Discussions

55

of simulations, i.e., rep1-rep5, and all the above SBs and HBs of 3CLpro should be able to be confirmed from these Tables. Figures 2.24 and 2.25 show the secondary structures and RMSF performances of the MDs of [340].

2.3.3 Comparison with SARS-CoV-1-Mpro The PDB entry 1q2w is the X-ray crystal structure of the SARS-CoV-1 Mpro; it has AB-chains; A-chain has aa PHE3-SER301, MPD307, and aa HOH308-541; and Bchain has aa [SER-1-LEU0-]SER1-SER301 and aa HOH307-528, and the monomer has aa SER1-GLY306. The PDB entry 6y2e is the X-ray structure unliganded SARS-CoV-2-Mpro; it has A-chain aa SER1-GLN306, aa HOH401-713. In [346] the dimeric and monomeric MD trajectories for SARS-CoV-1-Mpro and SARSCoV-2-Mpro are without any ligand; for each model, there are three MD replicates. We denote the models as follows: ◦ ◦ .◦ .◦ . .

SARS-CoV-1-Mpro-1q2w-monomer-rep1, -rep2, -rep3, SARS-CoV-2-Mpro-6y2e-monomer-rep1, -rep2, -rep3, SARS-CoV-1-Mpro-1q2w-dimer-rep1, -rep2, -rep3, SARS-CoV-2-Mpro-6y2e-dimer-rep1, -rep2, -rep3.

The MD secondary structural developments during the 12 sets of MD simulations are shown in Fig. 2.14, where we can see the following: ◦ for the “SARS1 monomer” and “SARS2 monomer,” their .α-helices at Nand C-terminal segments aa ALA7-VAL13, TRP37-ILE43, MET49-LYS61, and ASP295-GLY304 are unstable and sometimes unfold, .◦ for the “SARS1 dimer,” the .α -helices in A-chain aa VAL36-LEU58, B-chain aa TYR54-SER65, and TER285-SER301 are unstable, and .◦ for the “SARS2 dimer,” the N-terminals’ .α-helices aa TYR37-LYS41 of A-chain and aa IL43-GLU55 of B-chain are unstable. .

The MD RMSD values are generally leveling off. The RMSF performances of the 12 sets of MD show that the segment aa 41–51 and residue 221 have larger RMSF values. The SBs and HBs (with occupancy rates .≥20%) of the 12 sets of MD can be seen in Tables 2.24 (MD-SBs of monomer of SARS-CoV-1/2-Mpro), Table 2.25 (MD-SBs of dimer of SARS-CoV-1/2-Mpro), Tables 2.26 and 2.27 (MD-HBs of monomer of SARS-CoV-1/2-Mpro), Tables 2.28, 2.29, and 2.30 (MD-HBs of dimer of SARS-CoV-1-Mpro), Tables 2.31, 2.32, and 2.33 (MD-HBs of dimer of SARSCoV-2-Mpro).

56

2 3C-Like Protease (3CLpro)

Fig. 2.14 The MD secondary structural developments during 500 frames (with frame stride = 10) of the four models: SARS-CoV-1-Mpro-1q2w-monomer (denoted as “SARS1 monomer”), SARSCoV-2-Mpro-6y2e-monomer (denoted as “SARS2 monomer”), SARS-CoV-1-Mpro-1q2w-dimer (denoted as “SARS1 dimer”), and SARS-CoV-2-Mpro-6y2e-dimer (denoted as “SARS2 dimer”) (from up to down in turns)—each model has three sets of MD simulations, rep1-rep3 (from left to right in turns)

2.3.4 Comparison with SARS-CoV-1-Mpro-N3 The PDB entry 2hob is the X-ray crystal structure of the SARS-CoV-1 Mpro in complex with the inhibitor N3; it has AB-chains, A-chain has aa SER1-GLN306 and aa HOH401-707, and B-chain has aa 02J1-ALA2-VAL3-LEU4-PJE5-010-6 and HOH101; in the MD datasets of [346], the SARS-CoV-1-Mpro-N3 monomer has aa SER1-GLN306 and ligand LIG307, and its dimer has LIG307 and LIG308, A-chain has aa SER1-GLN306, and B-chain has aa SER1-GLN306. The PDB entry 6lu7 is the X-ray structure unliganded SARS-CoV-2-Mpro in complex with the inhibitor N3; A-chain has aa SER1-GLN306 and aa HOH401-484 and C-chain has 02J1ALA2-VAL3-LEU4-PJE5-010-6; in the MD datasets of [346], the SARS-CoV-2Mpro-N3 monomer has aa SER1-GLN306 and ligand LIG307, and its dimer has LIG307 and LIG308, A-chain has aa SER1-GLN306, and B-chain has aa SER1GLN306. In the dimeric and monomeric MD trajectories of SARS-CoV-1-Mpro-N3

2.3 Results and Discussions

57

and SARS-CoV-2-Mpro-N3, each model has three MD replicates. We denote the models as: ◦ ◦ .◦ .◦ . .

SARS-CoV-1-Mpro-N3-2hob-monomer-rep1, -rep2, -rep3, SARS-CoV-2-Mpro-N3-6lu7-monomer-rep1, -rep2, -rep3, SARS-CoV-1-Mpro-N3-2hob-dimer-rep1, -rep2, -rep3, SARS-CoV-2-Mpro-N3-6lu7-dimer-rep1, -rep2, -rep3.

The MD secondary structural developments during the 12 sets of MD simulations are shown in Fig. 2.15, where we can see the following: ◦ For “SARS1-N3 monomer,” the .α -helices aa ALA7-VAL13 and ILE43-LYS61 unfold. .◦ For “SARS2-N3 monomer,” the .α -helices aa ALA7-VAL13, ILE43-LYS61, and ASP295-GLN306 (rep1 and rep3) unfold. .◦ For “SARS1-N3 dimer,” the .α -helix aa A:TYR37-A:LYS61, around B:ASP295, unfolds. .◦ For “SARS2-N3 dimer,” the .α -helices A:TYR37-A:LYS61 and B:ILE43B:LEU67, around B:295 (rep1), unfold. .

The MD RMSD values are generally leveling off. The SBs and HBs (with occupancy rates .≥20%) of the 12 sets of MD can be seen in Table 2.34 (MDSBs of monomer of SARS-CoV-1/2-Mpro-N3), Table 2.35 (MD-SBs of dimer of SARS-CoV-1/2-Mpro-N3), Table 2.36 (MD-HBs linking the monomer of SARSCoV-1/2-Mpro and the ligand LIG307), Tables 2.37 and 2.38 (MD-HBs of monomer of SARS-CoV-1/2-Mpro), Table 2.39 (MD-HBs linking the dimer of SARS-CoV-1Mpro and the two ligands LIG307 and LIG308, where for rep3 the ligand LIG307 has not been binding any residue of the dimer ARS-CoV-1 during the MD of rep3), Tables 2.40, 2.41, and 2.42 (MD-HBs of dimer of SARS-CoV-1-Mpro-N3), Table 2.43 (MD-HBs linking the dimer of SARS-CoV-2-Mpro and the two ligands LIG307 and LIG308), and Tables 2.44, 2.45, and 2.46 (MD-HBs of dimer of SARSCoV-2-Mpro-N3). The MD-HBs between the ligands and the dimer the SARS-CoV-1-MproN3-2hob model (denoted as “SARS-CoV-1-N3 dimer”) and the SARS-CoV-2Mpro-N3-6lu7 model (denoted as “SARS-CoV-2-N3 dimer”) can be seen in Tables 2.39, 2.40, 2.41, 2.42, and 2.43. The MD-SBs-HBs between the two monomers (denoted as A-chain and B-chain) of dimer the SARS-CoV-1-Mpro-N32hob model (denoted as “SARS-CoV-1-N3 dimer”) and the SARS-CoV-2-MproN3-6lu7 model (denoted as “SARS-CoV-2-N3 dimer”) can be seen in Table 2.48. Similarly, the MD-SBs-HBs polar contacts between the two monomers (denoted as A-chain and B-chain) of dimer the SARS-CoV-1-Mpro-1q2w model (denoted as “SARS-CoV-1 dimer”) and the SARS-CoV-2-Mpro-6y2e model (denoted as “SARS-CoV-2 dimer”) can be seen in Table 2.47. From these tables, we can easily know that the strong polar contact GLU290-ARG4 linking the two monomers of SARS-CoV-1-Mpro/SARS-CoV-2-Mpro/SARS-CoV-1-Mpro-N3/SARS-CoV-2Mpro-N3 dimer (Table 2.48).

58

2 3C-Like Protease (3CLpro)

Fig. 2.15 The MD secondary structural developments during 500 frames (with frame stride = 10) of the four models: SARS-CoV-1-Mpro-N3-2hob-monomer (denoted as “SARS1-N3 monomer”), SARS-CoV-2-Mpro-N3-6lu7-monomer (denoted as “SARS2-N3 monomer”), SARSCoV-1-Mpro-N3-2hob-dimer (denoted as “SARS1-N3 dimer”), and SARS-CoV-2-Mpro-N3-6lu7dimer (denoted as “SARS2-N3 dimer”) (from up to down in turns)—each model has three sets of MD simulations, rep1-rep3 (from left to right in turns). In the dimers, we denote the two monomers CD as A-chain and B-chain, respectively

We optimized the A-chain aa PHE3-SER301 of 1q2w.pdb (SARS-CoV1-Mpro) and the A-chain aa SER1-GLN306 with B-chain aa 02J1-ALA2VAL3-LEU4-PJE5-010-6 of 2hob.pdb (SARS-CoV-1-Mpro-N3). The 2hobmodel (SARS-CoV-1-Mpro-N3) has 4 .π -.π stackings, TRP218-PHE219, HID172-PHE140-HID163, PHE181-HID164-HID41, and PHE103-TYR37; 2 + + .π -cations, ARG298.NH2. -PHE8 and ARG105.NH2. -TYR182; and 14 SBs ASP34-LYS90, ASP56-ARG60, ASP92-ARG76, ASP153-LYS102, ASP155LYS12, ASP176-ARG105, ASP187-ARG40, ASP197-ARG131, ASP197LYS137, ASP229-LYS269, ASP289-ARG131, GLU288-LYS5, GLU290LYS5, and GLU290-ARG131;the SARS-CoV-1-Mpro residues (Fig. 2.16) bind with: ◦ 02J1: GLN192, THR190, ALA191, PRO168, B:ALA2, B:VAL3,

.

2.3 Results and Discussions

59

◦ ALA2-VAL3-LEU4: LEU167, GLN192, GLN189, THR190, ARG188, MET49, HID41, HID164, GLU166, MET165, .◦ PJE5: THR26, HID41, SER144, HID163, CYS145, PHE140, HID172, GLU166, LEU141, B:VAL3, B:LEU4, ASN142, HID164, LEU27, GLY143, MET49, .◦ 02J1-ALA2-VAL3-LEU4-PJE5-010-6: GLN189, LEU167, GLN192, THR190, PRO168, ALA191, HID41, MET49, HID164, ARG188, THR26, GLY143, LEU27, GLU166, PHE140, HID172, LEU141, CYS145, HID163, ASN142, SER144, MET165. .

The 1q2w-model (SARS-CoV-1-Mpro) has 2 .π -.π stackings, PHE103-TYR37 and HID172-PHE140-HID163, 1 .π -cation LYS236.NZ.+ -TYR237, and 14 SBs ASP34-LYS90, GLU55-ARG40, ASP56-ARG60, ASP92-ARG76, ASP153-LYS102, ASP155-LYS12, ASP176-ARG105, GLU178-LYS180, ASP187-ARG40, ASP197-ARG131, GLU288-LYS5, ASP289-ARG131, GLU290-LYS5, and ASP295-ARG298. Both the 2hob-

model (SARS-CoV-1-Mpro-N3) and the 1q2w-model (SARS-CoV-1-Mpro) have the same segment, i.e., ALA193-ALA194-GLY195, with low SASA values. Detailed MD-results of all these Mpro-wt monomer/dimer with/without ligand can be seen from Figs. 2.17, 2.18, 2.19, 2.20, 2.21, 2.22, 2.23, 2.24, and 2.25.

Fig. 2.16 The SARS-CoV-1-Mpro residues binding with the ligand N3 in the optimized 2hobmodel (SARS-CoV-1-Mpro-N3)

2.3.5 Variants 7BB2.pdb is the X-ray diffraction crystal structure of the main protease (3CLpro/Mpro) of SARS-COV-2 at 1.6 Å resolution (spacegroup P2(1)2(1)2(1)) [77], binding the model of MG-132 both to the Mpro of SARS-CoV-2 and to the human cathepsin L. MG-132 fits well into the Mpro active site, forming a covalent bond with Cys145 independently from reducing agents and crystallization conditions; docking of MG-132 into cathepsin L matches well with a covalent binding to the catalytic cysteine; and MG-132 inhibits cathepsin L with nanomolar potency and reversibly inhibits Mpro with micromolar potency [77]. 7BB2.pdb is the structure of Mpro-dimer with A-chain aa SER1-GLN306 and B-chain aa SER1-SER301. In [238], it is reported that the transmissible SARS-CoV-2 variants Mpro-delP168, Mpro-a173v, and Mpro-delP168-and-

60

2 3C-Like Protease (3CLpro)

a173v (Mpro-dm) have resistance to clinical protease inhibitors. Mpro-variants T45I, S46F, E47K, D48Y, M49I/L/T/V, S144A, M165I, P168S, .ΔP168, T169I, V171I, A173V/T/S, .ΔP168/A173V, T45I/M49L, T45I/A173V, T45I/.ΔP168, D48Y/.ΔP168, M49I/.ΔP168, and M49L/.ΔP168 are listed in Tables 1–3 of [238]. In the website amarolab.ucsd.edu/covid19.php, an openly accessible database “TRAJECTORIES_INPUTS_DATA_mpro_wt_variants_amarolab.tar.gz,” is listed, presenting the MD trajectories of the two monomers—in fact, we prefer the MD trajectories of the dimer. As follows we first build the three Mpro-variants by the use of 7BB2.pdb and then present some basic structural bioinformatics of the variants and the wild type (wt), confirmed by the analyses of the tar.gz file (Figs. 2.26, 2.27, 2.28, 2.29, 2.30, 2.31, 2.32, 2.33 and 2.34). We built the dimers of the three models, Mpro-dm, Mpro-delP168, and Mpro-a173v, from 7BB2.pdb and then we optimized the four Mpro-wt, Mprodm, Mpro-delP168, and Mpro-a173v models with RMSD values 0.383307, 4.387699, 4.388842, and 4.382586 Å, respectively, from the unoptimized ones. For the optimized four models, it seems that they all have the same Na.+ ion binding residues, B:ASN221, B:PHE223, and B:ASP263 (B:ASN221.O, B:ASN221.OD1, B:PHE223.O, B:ASP263.O, B:ASP263.OD2 (salt bridge)), the same two .π -cations A:ARG222.NH2+-A:PHE223 and A:ARG298.NH2+A:PHE8, and the same 12 .π -.π stackings, B:TRP218-B:PHE219-B:TRP218, B:HIS163-B:HIS172-B:PHE140-B:HIS163, B:PHE181-B:HIS164, B:PHE103B:TYR37, A:HIS163-A:HIS172-A:PHE140-A:HIS163, A:PHE181-A:HIS164, and A:PHE103-A:TYR37. In addition, the optimized Mpro-wt model has one additional .π -.π stacking, A:PHE219-A:TRP218, and the optimized Mpro-a173v model has two additional .π -.π stackings, A:TRP218-A:PHE219-A:TRP218. All the four models have the low-SASA-value residues A:ALA193-A:ALA194-A:GLY195. All the four optimized models have the SBs A:GLU14-B:LYS12, A:GLU290B:ARG4, and B:GLU290-A:ARG4 linking the two monomers (Table 2.1) and there exist SBs ASP155-LYS100, ASP176-ARG105, ASP187-ARG40, ASP197ARG131, ASP197-LYS137, ASP289-ARG131, ASP34-LYS90, ASP56-ARG60, ASP92-ARG76, GLU166-HIS172, GLU288-LYS5, and GLU290-LYS5 within each monomer (Table 2.1). Besides the SBs A:GLU14-B:LYS12, A:GLU290-B:ARG4, and B:GLU290A:ARG4 linking the two monomers (Table 2.1), there are some HBs linking the two monomers (Table 2.2); we may easily see that the polar contacts between residues GLU290 and ARG4 contribute to the linkage of the two monomers. For the optimized models of the three variants and its wild type, Mpro-dm has an .α-helix aa A:GLY11-A:GLU14 around residue A:LYS12, but the .α-helix of the wt, delP168, a173v models seems to be turn-and-.310 -helix structures (Fig. 2.26). To confirm all the above structural bioinformatics of the wt and its three variants, we analyze the MD trajectories of the A-chain and B-chain. The 550 ns MDSB and MD-HB results can be seen in Tables 2.49, 2.50, 2.51, 2.52, 2.53, 2.54, 2.55, and 2.56. The SBs ASP155-LYS100, ASP176-ARG105, ASP187-ARG40, ASP197-ARG131, ASP197-LYS137, ASP289-ARG131, ASP34-LYS90, ASP56ARG60, ASP92-ARG76, GLU166-HIS172, GLU288-LYS5, and GLU290-LYS5

2.4 Concluding Remarks

61

within each monomer can be confirmed from Tables 2.49, 2.50, 2.51, and 2.52. The 550 ns MD secondary structures and MD-RMSF results are shown in Figs. 2.27, 2.28, 2.29, 2.30, 2.31, 2.32, 2.33, and 2.34. We know that for both the A-chain and B-chain, the segment aa TYR37-LYS61 is unstable during the 550 ns MDs, where aa TYR37-LYS61 consists of two .310 -helices, aa TYR37-ILE43 and aa ASP48-LEU50, and one .α-helix, aa ASP56-ILE59. The loop aa TYR182-ARG188 is also unstable for both monomers. In Fig. 2.29 for rep2, the B-chain C-terminal .α-helix aa 290-VAL296 sometimes unfolds into turns or .310 -helix during 0–303 ns. The MD-RMSF values are larger around residues ASN51, ALA191, and the C-terminals (Figs. 2.31, 2.32, 2.33, and 2.34); this agrees with the observations from Fig. 4A of [238]. For the SARS-CoV-2-Mpro 6lu7-monomer/dimer models without ligand, three sets (sim1-sim3) of 1ms MD databases are presented by the same first author of [353]. From the MD secondary structure performances, we may know the unstable segments are ILE43-LYS61 (sim1-sim3), SER139-CYS145 (sim2), ASP295-GLN306 (sim1, sim3) for the monomer-models, TYR37-LYS61 for the dimer A-chain, and ILE43-LEU67 and C-terminal around ASP295 for the dimer Bchain. The SBs GLU290-ARG4 (very strong) and GLU14-LYS12 (weak) link the two monomers. The linkage GLU290-ARG4 is a strong polar contact; between GLU290 and ARG4 there are HBs A:ARG4.NH2-B:GLU290.OE2 41.16%, A:ARG4.NH1-B:GLU290.OE1 37.46%, B:ARG4.NH1-A:GLU290.OE2 31.47%, B:ARG4.NH2-A:GLU290.OE1 27.57%, B:ARG4.NH1-A:GLU290.OE1 14.39%, A:ARG4.NH1-B:GLU290.OE2 13.49%, B:ARG4.NH2-A:GLU290.OE2 11.19%, A:ARG4.NH2-B:GLU290.OE1 10.99% in sim1; A:ARG4.NH2-B:GLU290.OE1 39.72%, A:ARG4.NH1-B:GLU290.OE2 35.33%, B:ARG4.NH1-A:GLU290.OE1 29.64%, B:ARG4.NH2-A:GLU290.OE2 29.14%, B:ARG4.NH1-A:GLU290.OE2 19.36%, B:ARG4.NH2-A:GLU290.OE1 16.57%,A:ARG4.NH1-B:GLU290.OE1 12.28% in sim2; and B:ARG4.NH1-A:GLU290.OE1 40.82%, B:ARG4.NH2A:GLU290.OE2 36.03%, A:ARG4.NH2-B:GLU290.OE2 22.75%, A:ARG4.NH1B:GLU290.OE1 22.36%, A:ARG4.NH1-B:GLU290.OE2 17.37%, A:ARG4.NH2B:GLU290.OE1 11.58% in sim3. It is also worth keeping an eye on all the HBs linking the two monomers.

2.4 Concluding Remarks This chapter studied the Mpro molecular structures with pdb entries 6LU7, 7BQY, 7BUY, 6Y84, and 7BB2 by optimization and MD strategies. In common, from almost all the models of the 3CLpro dimer, we found that sometimes, there are two polar contacts between GLU290 and ARG4 linking the two monomers. In comparison, in this chapter, we also studies the SARS-CoV-1-Mpro and SARSCoV-1-Mpro-N3 by optimization and MD strategies.

62

2 3C-Like Protease (3CLpro)

Supplementary Information

Fig. 2.17 Some SBs of the monomer 6LU7optimized model during the 100 ns MD production phase (where in all there are 1000 frames and the frame interval is 0.1 ns)

2.4 Concluding Remarks

63

Fig. 2.18 The secondary structural developments for the 6LU7optimized model during 100 ns MD

B:GLU290-A:ARG4

B:GLU290-A:ARG4

B:GLU290-A:ARG4

B:ASP229-B:LYS269

B:GLU166-B:HIS172

B:GLU288-B:LYS5

B:GLU290-B:LYS5

A:GLU166-A:HIS172

A:GLU288-A:LYS5

A:GLU290-A:LYS5

B:ASP56-B:ARG60

B:ASP92-B:ARG76

A:ASP56-A:ARG60

B:ASP48-B:ARG60

B:ASP34-B:LYS90

B:ASP295-B:ARG298

B:ASP289-B:ARG131

A:ASP92-A:ARG76

A:ASP34-A:LYS90

A:ASP289-A:ARG131

B:ASP197-B:ARG131

B:ASP197-B:LYS137

A:ASP197-A:ARG131

A:ASP197-A:LYS137 B:ASP229-B:LYS269

B:GLU290-B:LYS5

B:GLU166-B:HIS172 B:GLU288-B:LYS5

A:GLU166-A:HIS172

A:GLU288-A:LYS5

A:GLU290-A:LYS5

B:ASP92-B:ARG76

B:ASP56-B:ARG60

B:ASP48-B:ARG60

B:ASP34-B:LYS90

B:ASP295-B:ARG298

B:ASP289-B:ARG131

A:ASP92-A:ARG76

A:ASP56-A:ARG60

A:ASP34-A:LYS90

A:ASP289-A:ARG131

B:ASP197-B:ARG131 B:ASP197-B:LYS137

A:ASP197-A:ARG131

A:ASP197-A:LYS137

A:GLU290-A:LYS5

A:GLU288-A:LYS5

A:GLU166-A:HIS172

A:ASP92-A:ARG76

A:ASP56-A:ARG60

A:ASP34-A:LYS90

A:ASP289-A:ARG131

A:ASP197-A:LYS137

A:ASP197-A:ARG131

A:ASP187-A:ARG40

B:ASP187-B:ARG40

A:ASP187-A:ARG40

B:ASP187-B:ARG40

A:ASP187-A:ARG40

A:ASP155-A:LYS12 A:ASP176-A:ARG105

B:ASP176-B:ARG105

A:ASP155-A:LYS12

A:ASP176-A:ARG105

A:ASP155-A:LYS12

A:ASP176-A:ARG105

B:ASP176-B:ARG105

B:ASP155-B:LYS100

B:ASP155-B:LYS100

A:ASP155-A:LYS100

A:ASP155-A:LYS100

A:ASP155-A:LYS100

A:GLU290-B:ARG4

A:GLU290-B:ARG4

A:GLU290-B:ARG4

B:ASP153-B:LYS102

A:GLU14-B:LYS12

A:GLU14-B:LYS12

A:GLU14-B:LYS12

B:ASP153-B:LYS102

delP168-Mpro-7bb2

dm-Mpro-7bb2

wt-Mpro-7bb2

B:GLU290-B:LYS5

B:GLU288-B:LYS5

B:GLU166-B:HIS172

B:ASP92-B:ARG76

B:ASP56-B:ARG60

B:ASP48-B:ARG60

B:ASP34-B:LYS90

B:ASP295-B:ARG298

B:ASP289-B:ARG131

B:ASP229-B:LYS269

B:ASP197-B:LYS137

B:ASP197-B:ARG131

B:ASP187-B:ARG40

B:ASP176-B:ARG105

B:ASP155-B:LYS100

B:ASP153-B:LYS102

A:GLU290-A:LYS5

A:GLU288-A:LYS5

A:GLU166-A:HIS172

A:ASP92-A:ARG76

A:ASP56-A:ARG60

A:ASP34-A:LYS90

A:ASP289-A:ARG131

A:ASP197-A:LYS137

A:ASP197-A:ARG131

A:ASP187-A:ARG40

A:ASP176-A:ARG105

A:ASP155-A:LYS12

A:ASP155-A:LYS100

B:GLU290-A:ARG4

A:GLU290-B:ARG4

A:GLU14-B:LYS12

a173v-Mpro-7bb2

Table 2.1 All the SBs in the Mpro-wt, Mpro-delP168-and-a173v, Mpro-delP168, and Mpro-a173v dimer models are optimized

B:ASP153-B:LYS102

B:GLU290-B:LYS5

B:GLU288-B:LYS5

B:GLU166-B:HIS172

B:ASP92-B:ARG76

B:ASP56-B:ARG60

B:ASP48-B:ARG60

B:ASP34-B:LYS90

B:ASP295-B:ARG298

B:ASP289-B:ARG131

B:ASP229-B:LYS269

B:ASP197-B:LYS137

B:ASP197-B:ARG131

B:ASP187-B:ARG40

B:ASP176-B:ARG105

B:ASP155-B:LYS100

64 2 3C-Like Protease (3CLpro)

2.4 Concluding Remarks

65

Table 2.2 All the HBs linking the two monomers in the optimized Mpro-wt, Mpro-delP168-anda173v, Mpro-delP168, and Mpro-a173v dimer models wt-Mpro-7bb2

dm-Mpro-7bb2

delP168-Mpro-7bb2

a173v-Mpro-7bb2

A:ARG298.NH2-B:SER123.O

A:ARG298.NH2-B:SER123.O

A:ARG4.NH1-B:GLU290.OE2

A:ARG298.NH2-B:SER123.O

A:ARG4.NH1-B:GLU290.OE2

A:ARG4.NH1-B:GLU290.OE2

A:ARG4.NH2-B:GLU290.OE1

A:ARG4.NH1-B:GLU290.OE2

A:ARG4.NH2-B:GLU290.OE1

A:ARG4.NH2-B:GLU290.OE1

A:GLU290.OE1-B:ARG4.NH2

A:ARG4.NH2-B:GLU290.OE1

A:GLU290.OE1-B:ARG4.NH2

A:GLU290.OE1-B:ARG4.NH2

A:GLU290.OE2-B:ARG4.NH1

A:GLU290.OE1-B:ARG4.NH2

A:GLU290.OE2-B:ARG4.NH1

A:GLU290.OE2-B:ARG4.NH1

A:GLY11.N-B:GLU14.OE2

A:GLU290.OE2-B:ARG4.NH1

A:GLY11.N-B:GLU14.OE2

A:GLY11.N-B:GLU14.OE2

A:SER1.N-B:PHE140.O

A:GLY11.N-B:GLU14.OE2

A:SER1.N-B:PHE140.O

A:SER1.N-B:PHE140.O

A:SER1.OG-B:GLU166.OE2

A:SER1.N-B:PHE140.O

A:SER1.OG-B:GLU166.OE2

A:SER1.OG-B:GLU166.OE2

A:SER10.N-B:SER10.OG

A:SER1.OG-B:GLU166.OE2

A:SER10.N-B:SER10.OG

A:SER10.N-B:SER10.OG

A:SER139.OG-B:GLN299.OE1

A:SER10.N-B:SER10.OG

A:SER139.OG-B:GLN299.OE1

A:SER139.OG-B:GLN299.OE1

A:VAL125.N-B:ALA7.O

A:VAL125.N-B:ALA7.O

B:ALA7.N-A:VAL125.O

B:ALA7.N-A:VAL125.O

A:VAL125.N-B:ALA7.O

A:SER139.OG-B:GLN299.OE1

B:ALA7.N-A:VAL125.O

B:ALA7.N-A:VAL125.O

A:VAL125.N-B:ALA7.O

B:ARG4.NH1-A:GLU290.OE2

B:ARG4.NH1-A:GLU290.OE2

B:ARG4.NH1-A:GLU290.OE2

B:ARG4.NH1-A:GLU290.OE2

B:ARG4.NH2-A:GLU290.OE1

B:ARG4.NH2-A:GLU290.OE1

B:ARG4.NH2-A:GLU290.OE1

B:ARG4.NH2-A:GLU290.OE1

B:GLU290.OE1-A:ARG4.NH2

B:GLU290.OE1-A:ARG4.NH2

B:GLU290.OE1-A:ARG4.NH2

B:GLU290.OE1-A:ARG4.NH2

B:GLY11.N-A:GLU14.OE2

B:PHE140.N-A:SER1.O

B:GLY11.N-A:GLU14.OE2

B:PHE140.N-A:SER1.O

B:PHE140.N-A:SER1.O

B:SER1.N-A:PHE140.O

B:PHE140.N-A:SER1.O

B:SER1.N-A:PHE140.O

B:SER1.N-A:PHE140.O

B:SER1.OG-A:GLU166.OE2

B:SER1.N-A:PHE140.O

B:SER1.OG-A:GLU166.OE2

B:SER1.OG-A:GLU166.OE2

B:SER139.OG-A:GLN299.OE1

B:SER1.OG-A:GLU166.OE2

B:SER139.OG-A:GLN299.OE1

B:SER139.OG-A:GLN299.OE1

B:SER139.OG-A:GLN299.OE1

Fig. 2.19 Some SBs of the dimer 6Y84optimized model during the 100 μs MD production phase

66

Fig. 2.19 (continued)

2 3C-Like Protease (3CLpro)

2.4 Concluding Remarks

67

Fig. 2.20 The secondary structural developments for dimeric 3CLpro of the 6Y84optimized model during 100 μs MD

68

2 3C-Like Protease (3CLpro)

Fig. 2.21 Some SBs of the dimer 6LU7optimized model during the 10,000 ns MD-Traj1 production phase

2.4 Concluding Remarks

69

Fig. 2.22 Some SBs of the dimer 6LU7optimized model during the 10,000 ns MD-Traj2 production phase

70

2 3C-Like Protease (3CLpro)

Fig. 2.23 Some SBs of the Evans-dimer model during the three sets of 50 ns REMD production phase

2.4 Concluding Remarks

Fig. 2.23 (continued)

71

72 Table 2.3 The HBs with occupancy rate greater than 50% of the MD of [102] for the 6LU7optimized model

Table 2.4 The HBs with more than 50% occupancy rates during the 100 μs MD simulations for the 6Y84-dimer model

2 3C-Like Protease (3CLpro) Occupancy

Donor-acceptor

85.91%

A:ARG131@NH2-A:ASP289.OD2

80.62%

A:ARG40.NH2-A:ASP187.OD1

80.22%

A:ARG131.NH1-A:ASP289.OD1

68.63%

A:TRP31.N-A:CYS16.O

66.73%

A:VAL36.N-A:LEU89.O

65.53%

A:ILE78.N-A:LYS90.O

64.24%

A:ASN95.N-A:ASP33.O

60.84%

A:THR201.OG1-A:GLU240.O

60.84%

A:LEU87.N-A:CYS38.O

59.04%

A:VAL114.N-A:TYR126.O

58.34%

A:HIP164.NE2-A:ASP187.OD2

58.24%

A:PHE8.N-A:SER113.OG

58.04%

A:ARG131.N-A:THR135.O

57.54%

A:ARG40.NE-A:ASP187.OD2

56.54%

A:ALA70.N-A:VAL73.O

56.24%

A:GLN256.NE2-A:VAL303.O

55.94%

A:LYS88.N-A:SER81.O

54.65%

A:TYR182.OH-A:CYS160.O

54.15%

A:GLN83.N-A:VAL86.O

53.15%

A:LEU89.N-A:VAL36.O

53.15%

A:VAL20.N-A:LEU27.O

51.35%

A:LYS5.NZ-A:GLU288.OE2

51.05%

A:ASN221.N-A:SER267.OG

50.95%

A:ASN231.N-A:LEU227.O

50.55%

A:ARG105.NH2-A:PHE181.O

50.35%

A:ALA116.N-A:GLY124.O

50.25%

A:HIS163.N-A:SER147.O

50.15%

A:SER267.OG-A:ASP263.O

49.75%

A:ASN28.ND2-A:CYS145.O

49.05%

A:TYR209.OH-A:ILE259.O

Donor

Acceptor

Occupancy

TRP31.N

CYS16.O

93.41%

GLY149.N

TYR161.O

91.91%

LYS88.N

SER81.O

88.71%

TYR182.OH

CYS160.O

87.31%

GLY109.N

MET130.O

86.81%

VAL36.N

LEU89.O

86.61%

VAL114.N

TYR126.O

85.91%

LEU89.N

VAL36.O

84.72%

PHE8.N

SER113.OG

84.42%

VAL157.N

LYS100.O

84.12%

THR201.OG1

GLU240.O

83.12%

LEU167.N

VAL171.O

81.22%

SER123.N

ALA116.O

80.82%

LEU87.N

CYS38.O

80.82%

LEU75.N

VAL68.O

80.72%

ALA210.N

ALA206.O

80.12%

GLN299.NE2

ARG4.O

79.72%

MET130.N

GLN110.O

78.82%

LEU30.N

TYR37.O

76.92%

GLN256.N

PRO252.O

76.82%

TYR37.N

LEU30.O

76.52%

GLN83.N

VAL86.O

76.12%

ASN231.N

LEU227.O

75.32%

TYR182.N

GLY174.O

74.63%

LYS269.N

CYS265.O

73.73%

HIS163.N

SER147.O

73.53%

TYR209.OH

ILE259.O

73.43%

LEU268.N

MET264.O

73.03%

(continued)

2.4 Concluding Remarks Table 2.4 (continued)

73

Donor

Acceptor

Occupancy

TYR54.OH

ASP187.O

72.83%

TYR118.N

SER121.O

71.83%

LEU115.N

VAL148.O

71.83%

VAL91.N

ASP34.O

71.53%

ASN95.N

ASP33.O

71.33%

ALA255.N

GLY251.O

71.03%

VAL20.N

LEU27.O

70.73%

ALA234.N

PHE230.O

70.73%

ARG40.NH2

ASP187.OD1

70.63%

LEU242.N

ASN231.OD1

70.43%

TYR239.N

ALA234.O

70.23%

THR21.N

LEU67.O

69.83%

ALA70.N

VAL73.O

69.73%

ARG40.NE

ASP187.OD2

69.63%

LEU27.N

VAL20.O

69.53%

ARG298.N

PHE294.O

69.23%

ILE78.N

LYS90.O

69.03%

GLY29.N

VAL18.O

67.53%

SER113.N

PHE150.O

67.33%

ASN95.ND2

TRP31.O

67.23%

ALA173.N

MET165.O

67.03%

SER254.OG

ILE259.O

67.03%

SER10.OG

GLU14.OE1

66.93%

GLN19.N

GLN69.O

66.03%

ARG105.NH2

PHE181.O

65.83%

CYS265.N

VAL261.O

65.03%

CYS22.N

THR25.O

64.64%

LYS90.N

GLY79.O

64.44%

PHE150.N

SER113.O

63.84%

CYS128.N

PHE112.O

63.54%

ASP153.N

CYS156.O

62.84%

GLN273.N

LYS269.O

62.04%

VAL18.N

GLY29.O

61.04%

ALA206.N

VAL202.O

61.04%

LEU205.N

THR201.O

59.74%

HIS80.ND1

ASN63.OD1

59.24%

SER254.N

LEU250.O

58.74%

ILE213.N

TYR209.O

58.44%

ARG4.N

GLN299.OE1

58.24%

HIS41.NE2

HIS164.O

58.04%

VAL297.N

PRO293.O

57.54%

ILE281.N

SER284.O

57.34%

LEU57.N

ASN53.O

57.14%

GLY11.N

GLU14.OE1

56.44%

TYR209.N

LEU205.O

56.14%

ASP248.N

GLN244.O

55.14%

SER158.N

ASN151.O

54.85%

LYS5.NZ

GLU290.OE2

54.25%

THR199.N

ASN238.O

53.75%

LEU67.N

THR21.O

53.65%

LEU272.N

LEU268.O

53.45%

ASN221.N

SER267.OG

53.25%

ASN274.N

GLU270.O

53.15%

LYS5.NZ

GLU290.OE1

52.95%

LEU32.N

VAL35.O

52.65%

GLN107.N

GLN110.OE1

52.25%

MET235.N

ASN231.O

51.75%

THR257.OG1

LEU253.O

51.25%

ASN214.N

ALA210.O

51.15%

CYS160.N

GLY149.O

50.85%

GLY120.N

ASN28.OD1

50.55%

GLN192.NE2

VAL186.O

50.35%

CYS300.N

VAL296.O

50.25%

LYS102.N

VAL157.O

50.15%

PHE134.N

ARG131.O

50.15%

74 Table 2.5 The HBs with more than 50% occupancy rates during the 10 μs Traj1-MD simulations for the 6LU7-dimer model

2 3C-Like Protease (3CLpro) Donor

Acceptor

Occupancy

SER10.OG

GLU14.OE2

89.81%

TYR209.OH

ILE259.O

87.51%

SER267.OG

ASP263.O

87.31%

TYR182.OH

CYS160.O

84.22%

ILE78.N

LYS90.O

82.72%

TRP31.N

CYS16.O

82.42%

THR201.OG1

GLU240.O

81.32%

SER147.OG

SER144.O

80.32%

HIS163.N

SER147.O

79.72%

THR257.OG1

LEU253.O

78.42%

VAL36.N

LEU89.O

77.02%

VAL114.N

TYR126.O

75.62%

LYS88.N

SER81.O

73.93%

LEU87.N

CYS38.O

73.43%

LEU27.N

VAL20.O

72.93%

TYR37.N

LEU30.O

72.83%

VAL157.N

LYS100.O

72.53%

LEU115.N

VAL148.O

72.23%

LEU89.N

VAL36.O

71.33%

GLY149.N

TYR161.O

70.13%

GLN19.N

GLN69.O

69.93%

PHE150.N

SER113.O

69.53%

ASP153.N

CYS156.O

69.33%

LYS90.N

GLY79.O

68.53%

LEU242.N

ASN231.OD1

68.33%

ASN95.N

ASP33.O

67.73%

ALA70.N

VAL73.O

67.63%

CYS128.N

PHE112.O

67.33%

LEU75.N

VAL68.O

66.93%

VAL20.N

LEU27.O

66.33%

SER123.N

ALA116.O

66.13%

THR175.OG1

ASP176.O

65.93%

HIS172.N

ILE136.O

65.93%

THR135.OG1

ASN133.OD1

65.43%

ILE281.N

SER284.O

65.13%

TYR118.N

SER121.O

64.94%

ASN203.ND2

ASP289.O

64.64%

ALA173.N

MET165.O

64.44%

LEU167.N

VAL171.O

63.94%

VAL18.N

GLY29.O

63.44%

THR199.N

ASN238.O

62.94%

GLN83.N

VAL86.O

62.64%

LEU30.N

TYR37.O

62.24%

GLY146.N

HIS163.O

61.94%

ASN28.ND2

CYS145.O

61.54%

VAL91.N

ASP34.O

60.84%

GLY109.N

MET130.O

60.34%

TYR182.N

GLY174.O

59.94%

LEU205.N

THR201.O

59.74%

GLN192.NE2

VAL186.O

58.54%

TYR239.N

ALA234.O

58.54%

ARG131.N

THR135.O

58.34%

LEU32.N

VAL35.O

57.64%

ASN203.ND2

GLY109.O

57.34%

PHE8.N

SER113.OG

57.14%

PHE112.N

CYS128.O

56.94%

ASN95.ND2

TRP31.O

56.54%

GLU14.N

SER10.O

55.24%

THR45.OG1

ASP48.OD2

53.55%

SER158.N

ASN151.O

53.15%

ASN231.N

LEU227.O

53.05%

THR21.N

LEU67.O

51.95%

CYS160.N

GLY149.O

50.15%

2.4 Concluding Remarks Table 2.6 The HBs with more than 50% occupancy rates during the 10 μs Traj2-MD simulations for the 6LU7-dimer model

75 Donor

Acceptor

Occupancy

SER10.OG

GLU14.OE1

88.91%

TYR209.OH

ILE259.O

88.71%

SER267.OG

ASP263.O

87.51%

TRP31.N

CYS16.O

86.11%

THR201.OG1

GLU240.O

85.21%

TYR182.OH

CYS160.O

83.82%

ILE78.N

LYS90.O

80.42%

THR257.OG1

LEU253.O

78.72%

VAL114.N

TYR126.O

76.92%

VAL36.N

LEU89.O

76.52%

HIS163.N

SER147.O

75.62%

SER123.N

ALA116.O

75.12%

SER147.OG

SER144.O

74.43%

LEU89.N

VAL36.O

73.73%

TYR37.N

LEU30.O

73.03%

LYS88.N

SER81.O

71.43%

LEU167.N

VAL171.O

71.03%

PHE150.N

SER113.O

70.63%

LEU87.N

CYS38.O

70.43%

LEU27.N

VAL20.O

70.43%

GLY149.N

TYR161.O

69.23%

ASN95.N

ASP33.O

69.03%

LEU115.N

VAL148.O

68.43%

GLN19.N

GLN69.O

68.13%

LYS90.N

GLY79.O

68.03%

GLY109.N

MET130.O

67.93%

VAL20.N

LEU27.O

67.43%

LEU75.N

VAL68.O

66.93%

ALA70.N

VAL73.O

66.73%

VAL157.N

LYS100.O

66.43%

THR175.OG1

ASP176.O

66.03%

TYR118.N

SER121.O

65.53%

HIS172.N

ILE136.O

65.33%

CYS128.N

PHE112.O

65.13%

PHE8.N

SER113.OG

64.14%

GLY146.N

HIS163.O

64.04%

ASP153.N

CYS156.O

64.04%

ASN28.ND2

CYS145.O

63.74%

TYR182.N

GLY174.O

63.64%

PHE112.N

CYS128.O

62.94%

ASN203.ND2

ASP289.O

61.54%

GLN83.N

VAL86.O

61.34%

ALA173.N

MET165.O

61.34%

LEU30.N

TYR37.O

61.04%

ASN95.ND2

TRP31.O

60.94%

LEU32.N

VAL35.O

60.14%

THR199.N

ASN238.O

59.84%

VAL18.N

GLY29.O

59.54%

ILE281.N

SER284.O

59.34%

ARG105.NH2

PHE181.O

58.14%

VAL91.N

ASP34.O

57.54%

THR135.OG1

ASN133.OD1

56.34%

LEU205.N

THR201.O

56.34%

GLU14.N

SER10.O

55.54%

THR21.N

LEU67.O

54.65%

SER158.N

ASN151.O

54.35%

LEU242.N

ASN231.OD1

53.35%

ASN231.N

LEU227.O

50.75%

THR292.OG1

ASP295.OD1

50.15%

76

2 3C-Like Protease (3CLpro)

Table 2.7 The HBs with more than 50% occupancy rates during the three sets of 50 μs REMD rep0-rep1-rep3 for the Evans-dimer model rep0

rep1

rep2

A:ARG40.NE-A:ASP187.OD2 79.12%

A:ARG40.NE-A:ASP187.OD2 77.32%

A:TRP31.N-A:CYS16.O 75.02%

A:TRP31.N-A:CYS16.O 73.83%

A:TRP31.N-A:CYS16.O 77.02%

A:ARG40.NE-A:ASP187.OD2 73.63%

A:HSD163.N-A:SER147.O 69.33%

A:HSD163.N-A:SER147.O 69.43%

A:HSD163.N-A:SER147.O 68.53%

A:VAL36.N-A:LEU89.O 68.83%

A:VAL36.N-A:LEU89.O 69.43%

A:VAL36.N-A:LEU89.O 67.23%

A:TYR182.OH-A:CYS160.O 67.23%

A:TYR182.OH-A:CYS160.O 68.93%

A:TYR182.OH-A:CYS160.O 66.63%

A:GLY149.N-A:TYR161.O 65.73%

A:VAL20.N-A:LEU27.O 63.04%

A:TYR37.N-A:LEU30.O 61.64%

A:LEU89.N-A:VAL36.O 64.54%

A:GLY149.N-A:TYR161.O 61.94%

A:LEU89.N-A:VAL36.O 60.64%

A:SER267.OG-A:ASP263.O 61.84%

A:TYR37.N-A:LEU30.O 61.04%

A:VAL20.N-A:LEU27.O 60.64%

A:ASN95.N-A:ASP33.O 61.24%

A:SER267.OG-A:ASP263.O 60.94%

A:SER254.OG-A:ILE259.O 58.14%

A:VAL20.N-A:LEU27.O 61.24%

A:ASN95.N-A:ASP33.O 59.64%

A:SER267.OG-A:ASP263.O 57.44%

A:SER254.OG-A:ILE259.O 61.14%

A:LEU89.N-A:VAL36.O 58.74%

A:ASN95.N-A:ASP33.O 57.04%

A:TYR37.N-A:LEU30.O 59.94%

A:ARG40.NH2-A:ASP187.OD1 58.54%

A:GLY146.N-A:HSD163.O 56.84%

A:ARG40.NH2-A:ASP187.OD1 58.84%

A:SER254.OG-A:ILE259.O 58.14%

A:GLY149.N-A:TYR161.O 56.84%

A:GLY146.N-A:HSD163.O 57.34%

A:THR21.N-A:LEU67.O 56.04%

A:LYS88.N-A:SER81.O 56.44%

A:LEU167.N-A:VAL171.O 57.34%

A:SER123.OG-B:VAL303.O 55.44%

A:ARG105.NH2-A:PHE181.O 56.24%

A:ALA173.N-A:MET165.O 56.94%

A:GLY146.N-A:HSD163.O 55.04%

A:THR257.OG1-A:LEU253.O 55.24%

A:ARG105.NH2-A:PHE181.O 56.74%

A:LYS88.N-A:SER81.O 54.95%

A:ALA173.N-A:MET165.O 55.04%

A:LYS88.N-A:SER81.O 54.95%

A:LEU167.N-A:VAL171.O 54.75%

A:LEU167.N-A:VAL171.O 53.35%

A:THR257.OG1-A:LEU253.O 54.85%

A:ARG105.NH2-A:PHE181.O 54.15%

A:ARG40.NH2-A:ASP187.OD1 52.45%

A:VAL114.N-A:TYR126.O 54.25%

A:VAL157.N-A:LYS100.O 54.05%

A:ARG131.NH2-A:ASP289.OD2 52.15%

A:ASN180.N-A:ASP176.OD1 53.85%

A:ALA173.N-A:MET165.O 52.95%

A:SER10.OG-A:GLU14.OE2 51.45%

A:ARG298.N-A:PHE294.O 53.75%

A:THR257.OG1-A:LEU253.O 52.45%

A:SER144.OG-A:LEU141.O 51.45%

A:SER123.OG-B:VAL303.O 53.65%

A:VAL114.N-A:TYR126.O 52.35%

A:THR21.N-A:LEU67.O 51.15%

A:SER144.OG-A:LEU141.O 53.65%

A:ASN180.N-A:ASP176.OD1 52.15%

A:LYS90.N-A:GLY79.O 50.45%

A:LYS90.N-A:GLY79.O 52.15%

A:ASN231.N-A:LEU227.O 51.95%

A:VAL114.N-A:TYR126.O 50.15%

A:ILE78.N-A:LYS90.O 51.95%

A:ARG131.NH2-A:ASP289.OD2 51.85%

A:ASN231.N-A:LEU227.O 51.85%

A:SER144.OG-A:LEU141.O 51.65%

A:THR21.N-A:LEU67.O 51.55%

A:ILE78.N-A:LYS90.O 50.65%

A:SER301.OG-A:VAL297.O 50.05%

A:LYS90.N-A:GLY79.O 50.45%

B:TRP31.N-B:CYS16.O 74.23%

B:TRP31.N-B:CYS16.O 73.63%

B:TRP31.N-B:CYS16.O 73.43%

B:VAL36.N-B:LEU89.O 71.13%

B:VAL36.N-B:LEU89.O 70.53%

B:VAL36.N-B:LEU89.O 70.83%

B:ARG40.NE-B:ASP187.OD2 68.23%

B:HSD163.N-B:SER147.O 68.23%

B:ARG40.NE-B:ASP187.OD2 68.33%

B:HSD163.N-B:SER147.O 68.13%

B:TYR182.OH-B:CYS160.O 65.33%

B:HSD163.N-B:SER147.O 66.43%

B:SER267.OG-B:ASP263.O 64.34%

B:ARG40.NE-B:ASP187.OD2 65.23%

B:TYR182.OH-B:CYS160.O 64.64%

B:TYR182.OH-B:CYS160.O 63.44%

B:SER267.OG-B:ASP263.O 61.94%

B:TYR37.N-B:LEU30.O 60.14%

B:TYR37.N-B:LEU30.O 62.84%

B:TYR37.N-B:LEU30.O 61.34%

B:GLY146.N-B:HSD163.O 59.04%

B:SER254.OG-B:ILE259.O 62.44%

B:SER10.OG-B:GLU14.OE2 61.04%

B:ASN95.N-B:ASP33.O 58.64%

B:SER10.OG-B:GLU14.OE2 60.54%

B:ASN95.N-B:ASP33.O 60.84%

B:LEU89.N-B:VAL36.O 58.14%

B:ASN95.N-B:ASP33.O 59.54%

B:GLY146.N-B:HSD163.O 60.34%

B:SER267.OG-B:ASP263.O 57.44%

B:LEU89.N-B:VAL36.O 58.94%

B:LEU89.N-B:VAL36.O 59.74%

B:GLY149.N-B:TYR161.O 57.14%

B:VAL20.N-B:LEU27.O 58.44%

B:GLY149.N-B:TYR161.O 58.44%

B:ARG131.NH2-B:ASP289.OD2 57.04%

B:GLY146.N-B:HSD163.O 57.24%

B:ARG131.NH2-B:ASP289.OD2 58.24%

B:SER254.OG-B:ILE259.O 56.04%

B:GLY149.N-B:TYR161.O 57.14%

B:VAL20.N-B:LEU27.O 56.94%

B:SER123.OG-A:VAL303.O 55.74%

B:SER301.OG-B:VAL297.O 57.14%

B:LEU167.N-B:VAL171.O 56.84%

B:LEU167.N-B:VAL171.O 55.24%

B:LEU167.N-B:VAL171.O 56.44%

B:SER254.OG-B:ILE259.O 56.74%

B:SER10.OG-B:GLU14.OE2 55.04%

B:ARG131.NH2-B:ASP289.OD2 55.84%

B:ARG40.NH2-B:ASP187.OD1 55.54%

B:ALA173.N-B:MET165.O 54.95%

B:LEU87.N-B:CYS38.O 55.74%

B:LEU87.N-B:CYS38.O 55.34%

B:VAL20.N-B:LEU27.O 54.65%

B:LYS88.N-B:SER81.O 55.14%

B:ARG105.NH2-B:PHE181.O 55.24%

B:LEU87.N-B:CYS38.O 54.45%

B:ALA173.N-B:MET165.O 54.15%

B:SER301.OG-B:VAL297.O 54.95%

B:ARG40.NH2-B:ASP187.OD1 54.25%

B:SER123.OG-A:VAL303.O 53.35%

B:VAL114.N-B:TYR126.O 54.35%

B:ILE78.N-B:LYS90.O 53.85%

B:VAL114.N-B:TYR126.O 52.75%

B:SER123.OG-A:VAL303.O 54.25%

B:ARG105.NH2-B:PHE181.O 53.35%

B:ARG105.NH2-B:PHE181.O 52.65%

B:ALA173.N-B:MET165.O 53.85%

B:SER301.OG-B:VAL297.O 52.05%

B:LYS90.N-B:GLY79.O 52.45%

B:ILE78.N-B:LYS90.O 53.15%

B:VAL114.N-B:TYR126.O 52.05%

B:ASN231.N-B:LEU227.O 51.85%

B:ARG298.N-B:PHE294.O 52.75%

B:THR257.OG1-B:LEU253.O 51.05%

B:SER144.OG-B:LEU141.O 51.75%

B:LYS90.N-B:GLY79.O 52.75%

B:ARG40.NH2-B:ASP187.OD1 51.65%

B:SER144.OG-B:LEU141.O 51.45%

B:LEU75.N-B:VAL68.O 51.55%

B:ASN231.N-B:LEU227.O 51.05%

B:THR257.OG1-B:LEU253.O 51.25%

B:THR111.OG1-B:ASP295.OD2 50.85%

B:ARG298.N-B:PHE294.O 50.75%

B:THR257.OG1-B:LEU253.O 50.65%

B:THR201.OG1-B:GLU240.O 50.75%

B:THR201.OG1-B:GLU240.O 50.45% B:LYS88.N-B:SER81.O 50.15%

2.4 Concluding Remarks

77

Table 2.8 SBs of the optimized six models of [340] Monomer-apo

Monomer-N3

Dimer-apo

Dimer-N3

Dimer-2N3

Dimer-2N3-covalent

ASP153-LYS102

ASP155-LYS12

A-B-chains

A-B-chains

A-B-chains

A-B-chains

ASP155-LYS100

ASP187-ARG188

GLU14-LYS318

GLU290-ARG310

GLU14-LYS319

GLU290-ARG310

ASP176-ARG105

ASP187-ARG40

GLU596-ARG4

GLU320-LYS12

GLU290-ARG311

In A-chain

ASP187-ARG40

ASP187-HIS41

In A-chain

GLU596-ARG4

GLU597-ARG4

ASP34-LYS90

ASP197-ARG131

ASP197-ARG131

ASP34-LYS90

In A-chain

In A-chain

ASP48-LYS61

ASP197-LYS137

ASP197-LYS137

ASP48-LYS61

ASP34-LYS90

ASP34-LYS90

GLU55-ARG188

ASP229-LYS269

ASP229-LYS269

ASP56-ARG60

ASP48-ARG60

GLU55-ARG40

ASP56-ARG60

ASP289-ARG131

ASP263-ARG222

ASP92-ARG76

ASP48-LYS61

ASP56-ARG60

ASP92-ARG76

ASP295-ARG298

ASP289-ARG131

ASP153-LYS102

GLU55-ARG188

ASP92-ARG76

ASP153-LYS102

ASP34-LYS90

ASP295-ARG298

ASP155-LYS100

ASP92-ARG76

ASP153-LYS102

ASP155-LYS100

ASP56-ARG60

ASP34-LYS90

GLU166-HIS172

ASP153-LYS102

ASP155-LYS12

GLU166-HIS172

ASP92-ARG76

ASP56-ARG60

ASP176-ARG105

ASP155-LYS100

ASP155-LYS100

ASP176-ARG105

GLU290-ARG131

ASP92-ARG76

ASP187-ARG40

GLU166-HIS172

GLU166-HIS172

GLU178-LYS88

GLU166-HIS172

ASP197-ARG131

ASP176-ARG105

ASP176-ARG105

ASP187-ARG40

GLU178-LYS88

ASP229-LYS269

ASP187-ARG40

GLU178-LYS88

ASP187-ARG188

GLU288-LYS5

GLU270-ARG222

ASP197-ARG131

ASP187-ARG40

ASP197-ARG131

GLU290-ARG131 GLU290-LYS5

GLU288-LYS5

ASP245-HIS246

ASP197-ARG131

ASP263-ARG222

ASP289-ARG131

ASP263-ARG222

ASP197-LYS137

GLU270-LYS269

GLU290-LYS5

GLU270-LYS269

GLU270-LYS269

GLU288-LYS5

GLU290-ARG310

GLU288-LYS5

GLU288-LYS5

GLU288-LYS137

ASP295-ARG298

ASP289-ARG131

ASP289-ARG131

ASP289-ARG131

In B-chain

GLU290-LYS5

GLU290-LYS5

GLU290-LYS5

GLU320-LYS12

ASP295-ARG298

In B-chain

ASP295-ARG298

ASP362-ARG366

In B-chain

ASP341-LYS397

In B-Chain

ASP340-LYS396

GLU361-ARG346

ASP355-ARG367

ASP340-LYS396

ASP398-ARG382

GLU361-ARG494

ASP363-ARG367

ASP354-LYS367

ASP461-LYS406

ASP340-LYS396

ASP399-ARG383

GLU361-ARG346

GLU472-HIS469

ASP362-ARG366

ASP460-LYS409

ASP362-ARG366

ASP482-ARG411

ASP398-ARG382

ASP462-LYS407

ASP398-ARG382

GLU484-LYS408

ASP459-LYS408

GLU473-HIS479

ASP459-LYS408

ASP493-ARG346

ASP461-LYS318

ASP483-ARG412

ASP461-LYS318

ASP503-ARG437

ASP461-LYS406

GLU485-LYS395

GLU472-HIS478

ASP503-LYS443

GLU472-HIS478

ASP494-ARG347

ASP482-ARG411

ASP569-ARG528

ASP482-ARG411

ASP504-ARG438

GLU484-LYS394

GLU594-LYS311

GLU484-ARG411

ASP504-LYS444

ASP493-ARG346

ASP595-ARG437

ASP493-ARG346

GLU577-LYS576

ASP493-HIS347

GLU596-LYS311

ASP503-ARG437

GLU595-LYS312

ASP503-ARG437

ASP601-ARG604

ASP535-LYS575

ASP596-ARG438

ASP503-LYS443

ASP595-ARG437

GLU597-LYS312

ASP535-LYS575

GLU594-LYS311

ASP602-ARG605

ASP569-ARG528

GLU596-LYS311

GLU594-LYS311 ASP595-ARG437 GLU596-ARG4 GLU596-LYS311 ASP601-ARG604

ARG105.NH2-PHE181.O ARG131.NH2-ASP289.OD1 ARG131.N-THR135.O ARG298.NH2-ASP295.OD1 ARG310.N-GLN605.OE1 ARG310.NH1-GLU290.OE1 ARG310.NH2-GLU290.OE2

ALA210.N-ALA206.O ALA211.N-TRP207.O ALA234.N-PHE230.O ALA255.N-GLY251.O ALA313.N-VAL125.O ALA512.N-VAL508.O ALA516.N-ALA512.O

ARG131.NH1-ASP289.OD1

ARG131.NH2-ASP289.OD2

ARG188.NE-ASN51.OD1

ARG298.NH2-ASP295.OD2

ARG76.NH1-ASP92.OD1

ASN119.ND2-GLN19.OE1

ASN133.ND2-GLY195.O

ALA211.N-TRP207.O

ALA234.N-PHE230.O

ALA255.N-GLY251.O

ALA266.N-LEU262.O

ALA70.N-VAL73.O

ARG105.NH1-ASP176.OD2

GLY283.N-THR280.O

CYS128.N-PHE112.O

HIS172.N-ILE136.O

GLY146.N-HIS163.O

CYS117.N-SER147.OG

CYS300.N-VAL296.O

ASN274.ND2-GLU270.O ASN274.N-GLU270.O

ASN221.ND2-PHE223.O ASN231.ND2-LEU242.O

GLY120.N-ASN28.OD1

ASP92.N-ARG76.O

GLY29.N-VAL18.O

GLY109.N-MET130.O

ASN95.ND2-TRP31.O

HIS163.N-SER147.O

GLU290.N-GLU288.OE2

ASN95.ND2-GLY15.O

CYS22.N-THR25.O

GLU240.N-THR199.O

ASN95.N-ASP33.O

CYS265.N-VAL261.O

ASN238.ND2-ASP197.O

ASN214.ND2-ASP216.OD1

GLU178.N-ASP176.OD2

ASN65.N-SER62.O

ASN277.ND2-ASN274.O

ASN231.N-LEU227.O

ASN214.N-ALA210.O

ASN231.N-LEU227.O

ASN231.ND2-LEU242.O

ASN203.ND2-GLY109.O

ASN214.ND2-ASP216.OD2

ASN142.ND2-GLY608.O

ASN221.N-SER267.OG

ASN180.ND2-ASP176.OD1

ASN133.ND2-GLY195.O ASN203.ND2-ASP289.O

ASN151.ND2-THR111.O

ARG76.NH1-GLN74.OE1

ASN133.ND2-GLY195.O

ARG604.N-PHE600.O

GLN83.N-VAL86.O

ASN119.N-GLY143.O

ASN28.N-CYS145.O

ASN119.ND2-THR26.OG1

ARG604.NH1-ASP601.OD1

GLN69.N-GLN19.O

GLN83.NE2-GLU178.OE1

ASN231.N-LEU227.O

ASN274.N-GLU270.O

ARG60.NH2-ASP56.OD2

ARG585.NE-ASN583.O ARG604.NH1-MET312.O ARG604.NH2-SER123.O

ARG4.NH1-GLU596.OE1 ARG40.NH2-ASP187.OD1 ARG494.NH2-ASP354.O

ASP229.N-THR226.OG1

CYS16.N-VAL13.O

GLN189.N-MET49.O

ASN214.ND2-ALA210.O

ASN221.N-SER267.OG

ARG523.NH1-GLN612.O ARG523.NH2-GLN612.OXT

ARG366.N-ASP362.O ARG382.NH1-ASP398.OD1

ARG437.N-THR441.O ARG494.NH1-GLU361.OE2

ARG310.NH1-GLU290.OE2 ARG346.NH2-ASP493.OD1

ARG40.NH2-ASP187.OD1 ARG437.NH1-ASP595.OD1

ARG222.NE-GLU270.OE2 ARG298.NH2-MET6.O

ARG40.N-CYS85.O ARG40.NE-ASP187.OD2

ARG131.NE-ASP197.OD2 ARG188.NE-MET49.O

ASN231.ND2-LEU242.O

ASN65.N-SER62.O

ASP216.N-ALA211.O

ASN180.N-ASP176.OD1

ASN277.ND2-LEU272.O

ASN53.ND2-ASP56.OD1

ASN133.ND2-GLY195.O

ASN151.N-SER158.O

ASN203.ND2-GLY109.O

ASN231.N-LEU227.O

ASN274.N-GLU270.O

ARG40.NH2-ASP187.OD1

ARG60.NH2-ASP56.OD2

ASN214.ND2-ALA210.O

ASN231.ND2-LEU242.O

ARG40.N-CYS85.O

ARG366.NH1-ASP362.OD2 ARG382.NH2-ASP398.OD2

ALA70.N-VAL73.O ARG105.NH2-PHE181.O

ASN180.ND2-ASP176.OD1

ASN203.ND2-GLY109.O

ARG298.NH2-MET6.O

ARG298.N-PHE294.O

ARG40.NE-ASP187.OD2

ARG346.NE-ASP493.OD1 ARG346.NH2-ASP493.OD2 ARG366.NE-ASP362.OD1

ALA540.N-ASN537.O ALA572.N-LEU568.O ALA7.N-VAL431.O

ASN151.ND2-THR111.O

ASN151.N-SER158.O

ASN180.N-ASP176.OD1

ARG131.N-THR135.O

ARG217.NH2-GLN306.OXT

ARG105.NH2-PHE181.O

ALA479.N-MET471.O

ALA206.N-VAL202.O

ALA194.N-THR169.OG1

ALA210.N-ALA206.O

Dimer-N3 ALA173.N-MET165.O

ALA173.N-MET165.O

Dimer-apo ALA173.N-MET165.O

Monomer-N3

ALA173.N-MET165.O

Monomer-apo

ALA129.N-GLU290.OE1

Table 2.9 HBs of the optimized six models of [340] Dimer-2N3

ASN581.ND2-GLU577.O

ASN538.N-LEU534.O

ASN538.ND2-LEU549.O

ASN510.ND2-GLY416.O

ASN458.ND2-THR418.O

ASN440.ND2-GLY502.O

ASN370.ND2-VAL384.O

ASN335.ND2-CYS452.O

ASN335.N-CYS452.O

ASN274.N-GLU270.O

ASN238.ND2-ASP197.O

ASN231.ND2-LEU242.O

ASN221.ND2-ALA266.O

ASN214.ND2-ASP216.OD2

ASN180.ND2-GLY179.O

ARG524.NH1-GLN613.OE1

ARG438.N-THR442.O

ARG438.NH1-ASP596.OD1

ARG438.NE-ASP504.OD1

ARG412.NH2-PHE488.O

ARG4.NH2-GLU597.OE2

ARG4.NH1-GLU597.OE1

ARG4.N-GLN299.OE1

ARG383.NE-ASP399.OD1

ARG367.NH2-ASP363.OD1

ARG367.NH1-ASP355.OD2

ARG367.NE-ASP363.OD2

ARG347.NH2-ASP494.OD1

ARG311.NH2-GLU290.OE2

ARG311.NH1-GLU290.OE1

ARG311.N-GLN606.OE1

ARG279.NH1-ASN277.O

ARG131.N-THR135.O

ARG131.NH2-ASP289.OD2

ARG131.NH1-ASP289.OD1

ALA480.N-MET472.O

ALA255.N-GLY251.O

ALA234.N-PHE230.O

Dimer-2N3-covalent

LYS443.NZ-ASP503.OD2

ASN214.ND2-ALA210.O

ALA255.N-GLY251.O

MET541.N-ASN537.O

ASN221.N-SER267.OG

PHE223.N-ASN221.OD1

LEU381.N-VAL374.O

TYR343.OH-GLU484.OE2

LYS394.NZ-GLU484.OE2

LEU336.N-TYR343.O

GLY335.N-VAL324.O

GLU484.N-ASP482.OD1

ASN425.ND2-GLN306.OE1

HIS469.N-SER453.O

PHE446.N-SER1.O

GLN256.NE2-CYS300.O

ARG222.NE-ASP263.OD2

LEU395.N-VAL342.O

TYR424.OH-ASN448.O

SER450.N-LEU447.O

HIS478.N-ILE442.O

ASN439.ND2-GLY501.O

ILE384.N-LYS396.O

LYS394.N-SER387.OG

LEU373.N-THR327.O

LEU473.N-VAL477.O

MET388.N-GLN389.OE1

ARG346.N-CYS391.O

ASN371.N-SER368.O

THR331.OG1-CYS350.O

ARG346.NH2-ASP493.OD1

GLN498.NE2-VAL492.O

GLU361.N-GLU361.OE2

ASN359.ND2-GLU361.OE2

THR351.N-ASP354.OD1

ASN359.N-ASN357.OD1

ARG366.NE-ASP362.OD1

ASN357.ND2-ASP362.OD2

78 2 3C-Like Protease (3CLpro)

TRP207.NE1-PHE3.O

TRP218.N-ASP216.OD1

TYR209.OH-ILE259.O

TYR237.N-ALA234.O

VAL18.N-GLY29.O

VAL20.N-LEU27.O

VAL35.N-LEU32.O

VAL91.N-ASP34.O

LEU268.N-MET264.O

LEU272.N-LEU268.O

LEU30.N-TYR37.O

LEU57.N-ASN53.O

LEU58.N-TYR54.O

LEU67.N-THR21.O

LEU75.N-VAL68.O

LEU87.N-CYS38.O

GLY149.N-TYR161.O GLY29.N-VAL18.O

GLN192.NE2-ALA193.O

GLY146.N-HIS163.O

CYS606.N-VAL602.O GLN19.N-GLN69.O

GLY11.N-GLU320.OE1

CYS571.N-VAL567.O

GLU546.N-THR505.O

CYS423.N-SER453.OG

GLY109.N-MET130.O

GLU353.N-GLU353.OE1

CYS38.N-LEU87.O CYS434.N-PHE418.O

GLU290.N-GLU288.OE1

CYS350.N-HIS347.O

GLU240.N-THR199.O

THR45.N-ASP48.OD2

LEU242.N-ASN231.OD1

CYS344.N-LEU393.O

THR292.N-ASP295.OD1

LEU208.N-VAL204.O GLN83.N-VAL86.O

GLN74.NE2-GLN69.OE1

CYS322.N-VAL319.O

THR25.OG1-CYS44.O

LEU205.N-THR201.O CYS328.N-THR331.O

GLN416.NE2-THR417.O GLN562.NE2-VAL609.O

CYS265.N-VAL261.O CYS300.N-VAL296.O

THR111.OG1-ASP295.OD1

THR21.N-LEU67.O

LEU141.N-TYR118.OH

LEU167.N-VAL171.O

GLN19.NE2-ASN119.O GLN244.NE2-ASP248.OD1 GLN389.N-VAL392.O

CYS117.N-SER147.OG CYS128.N-PHE112.O CYS156.N-ASP153.O

MET235.N-ASN231.O

SER254.N-LEU250.O

SER62.N-ASN65.OD1

ILE136.N-HIS172.O

LEU115.N-VAL148.O

ILE106.N-TYR182.OH

CYS434.N-PHE418.O GLN107.NE2-GLN110.OE1

ASP56.N-ASN53.OD1 ASP92.N-ARG76.O

MET162.N-THR175.O

MET165.N-ALA173.O

HIS164.N-ALA173.O

HIS80.ND1-ASN63.OD1

CYS322.N-VAL319.O CYS423.N-SER453.OG

ASN95.ND2-GLY15.O ASN95.ND2-TRP31.O

LYS5.NZ-GLU288.OE2

LYS90.NZ-ASP34.CG

GLY29.N-VAL18.O

HIS163.N-SER147.O

CYS156.N-ASP153.O CYS16.N-VAL13.O

ASN580.N-GLU576.O ASN95.N-ASP33.O

LYS12.NZ-ASP155.OD1

LYS269.NZ-THR225.OG1

GLY149.N-TYR161.O

GLY15.N-GLY11.O

ASP354.N-THR351.O CYS128.N-PHE112.O

ASN537.N-LEU533.O ASN580.ND2-GLY581.O

LYS102.N-VAL157.O

LYS102.NZ-PHE103.O

GLY120.N-ASN28.OD1

ASN65.N-SER62.O ASP153.N-CYS156.O

ASN520.ND2-ALA516.O ASN537.ND2-LEU548.O

GLY146.N-HIS163.O

LYS100.N-ASP155.OD2

LYS100.NZ-TYR101.O

GLU290.N-GLU288.OE2

GLY109.N-MET130.O

HIS172.N-ILE136.O

GLY565.N-SER561.O

GLY486.N-ASP483.OD1

GLY456.N-TYR468.O

GLY416.N-MET437.O

GLY336.N-VAL325.O

GLY318.N-GLU14.OE1

GLY29.N-VAL18.O

GLY215.N-ALA211.O

GLY149.N-TYR161.O

GLY146.N-HIS163.O

GLY120.N-ASN28.OD1

GLY109.N-MET130.O

GLU547.N-THR506.O

GLU290.N-GLU288.OE1

GLN83.N-VAL86.O

GLN69.N-GLN19.O

GLN613.NE2-THR564.O

GLN563.NE2-VAL610.O

GLN563.NE2-CYS607.O

GLN551.NE2-ASP555.OD1

GLN499.NE2-VAL493.O

GLN496.N-MET356.O

GLN417.NE2-THR418.O

GLN376.NE2-GLY378.O

GLN299.NE2-ASP295.O

GLN19.NE2-THR26.OG1

GLN189.N-MET49.O

GLN107.N-GLN110.OE1

ASN53.ND2-ASP56.OD1 ASN537.ND2-LEU548.O ASN63.ND2-ILE78.O

ASN457.N-SER464.O ASN509.ND2-ASP595.O ASN509.ND2-GLY415.O

LEU32.N-VAL35.O

LEU87.N-CYS38.O

LEU89.N-VAL36.O

GLU14.N-SER10.O

GLU240.N-THR199.O

GLN273.N-LYS269.O

CYS435.N-PHE419.O CYS607.N-VAL603.O

ASN509.ND2-GLY415.O

CYS424.N-SER454.OG

CYS160.N-GLY149.O

ASP460.N-CYS463.O

ASN95.ND2-TRP31.O

ASN95.ND2-GLY15.O

ASN65.N-SER62.O

ASN527.N-SER573.OG

ASN401.ND2-TRP337.O ASN439.ND2-GLY501.O

LEU27.N-VAL20.O

LEU30.N-TYR37.O

GLN192.NE2-VAL186.O

ASN486.ND2-ARG411.NH2

GLN256.NE2-VAL303.O

ASN457.N-SER464.O

ASN390.ND2-GLY485.O ASN401.ND2-GLY321.O

LEU141.N-TYR118.OH

LEU167.N-VAL171.O

GLN189.N-MET49.O

ASN439.ND2-GLY501.O

ASN371.N-SER368.O

ILE78.N-LYS90.O

GLN127.NE2-ASP295.OD1

GLN19.N-GLN69.O

ASN390.ND2-GLY485.O

ASN334.ND2-CYS451.O

ILE43.N-ARG40.O

GLN107.N-GLN110.OE1

ASN334.ND2-CYS451.O

ASN28.ND2-CYS145.O

ILE213.N-TYR209.O

ASN28.ND2-CYS145.O

ASN274.ND2-GLU270.O

ILE136.N-HIS172.O

CYS44.N-HIS41.O

CYS85.N-GLY179.O

PHE8.N-SER113.OG

(continued)

THR598.N-ASP601.OD1

TRP513.N-ASN509.O

LYS5.NZ-GLU288.OE1

LYS575.N-CYS571.O

ASN231.N-LEU227.O

ARG585.NH2-ASN580.OD1

VAL233.N-PHE230.O

LYS408.NZ-ASP459.OD2

ARG298.NH2-ASP295.OD1

GLN550.NE2-ASP551.OD1

ASP295.N-THR292.O

GLU596.N-GLU594.OE1

THR532.N-ASP535.OD2

GLY584.N-ALA285.O

ASN228.ND2-ASP229.OD1

ARG298.NH1-SER429.O

GLN299.NE2-ARG4.O

LEU593.N-GLY283.O

LEU268.N-MET264.O

THR226.N-ASP229.OD2

ASN401.ND2-TRP337.O

SER427.OG-PHE305.O

CYS466.N-GLY455.O

SER429.N-ALA422.O

GLY415.N-MET436.O

ARG4.NH2-GLU596.OE2

SER445.OG-GLN299.OE1

ARG437.NH1-ASP595.OD2

ASN537.ND2-LEU548.O

ALA376.N-VAL379.O

TRP337.N-CYS322.O

GLY426.N-ASN334.OD1

GLY455.N-TYR467.O

TYR424.N-SER427.O

SER445.N-TYR432.OH

CYS300.N-VAL296.O

2.4 Concluding Remarks 79

GLN299.NE2-ARG4.O GLN325.N-GLN375.O GLN375.NE2-ASN378.O GLN375.N-GLN325.O GLN389.NE2-LEU483.O GLN413.N-GLN416.OE1

LYS102.N-VAL157.O

LYS236.N-LEU232.O

LYS88.N-SER81.O

MET165.N-ALA173.O

MET17.N-GLU14.O

MET235.N-ASN231.O

Dimer-apo GLN256.N-PRO252.O

Monomer-N3

LEU89.N-VAL36.O

Monomer-apo

Table 2.9 (continued)

HIS172.N-ILE136.O

HIS164.ND1-MET162.O

HIS163.N-SER147.O

GLY455.N-TYR467.O

GLY452.N-HIS469.O

GLY415.N-MET436.O

GLY335.N-VAL324.O

Dimer-N3

LEU242.N-ASN231.OD1

ILE78.N-LYS90.O

ILE556.N-ASP552.O

ILE507.N-ASP596.OD2

ILE200.N-ASP289.OD2

HIS80.ND1-ASN63.OD1

HIS371.ND1-SER369.OG

Dimer-2N3

ARG131.NH1-ASP289.OD1

VAL463.N-LYS406.O

LYS100.NZ-ASP155.OD2

SER316.N-SER10.OG

LYS12.NZ-ASP155.O

CYS156.N-ASP153.O

PHE314.N-SER419.OG

Dimer-2N3-covalent

80 2 3C-Like Protease (3CLpro)

LYS88.N-SER81.O LYS90.N-GLY79.O MET165.N-ALA173.O MET471.N-ALA479.O PHE223.N-ASN221.OD1 PHE305.N-GLY302.O PHE440.N-ARG437.O PHE529.N-ASN527.OD1 PHE611.N-GLN562.O PHE66.N-ASN63.O SER284.N-ILE281.O SER368.N-ASN371.OD1

HIS163.N-SER147.O HIS469.N-SER453.O HIS478.N-ILE442.O HIS80.ND1-ASN63.OD1 ILE136.N-HIS172.O ILE249.N-ASP245.O ILE384.N-LYS396.O ILE412.N-TYR488.OH ILE442.N-HIS478.O ILE78.N-LYS90.O LEU115.N-VAL148.O LEU167.N-VAL171.O

TYR126.OH-LYS137.O

TYR161.OH-PHE134.O

TYR182.N-GLY174.O

TYR182.OH-CYS160.O

TYR209.N-LEU205.O

TYR209.OH-ILE259.O

TYR239.N-ALA234.O

TYR37.N-LEU30.O

VAL104.N-PHE159.O

VAL114.N-TYR126.O

VAL157.N-LYS100.O

LYS102.NZ-ASP153.OD2

GLY415.N-MET436.O

THR25.N-CYS22.O

TYR118.N-SER121.O

LEU89.N-VAL36.O

GLY335.N-VAL324.O

THR21.OG1-THR26.OG1

LYS575.NZ-ASP535.OD2

LEU574.N-MET570.O

GLY29.N-VAL18.O

THR21.N-LEU67.O

GLY608.N-GLN605.O

LEU473.N-VAL477.O

GLY275.N-LEU271.O

THR111.OG1-ASP295.OD2

TYR101.OH-ASP33.OD2

LEU395.N-VAL342.O

GLY149.N-TYR161.O

SER81.N-LYS88.O

LYS443.NZ-GLY283.O

LEU381.N-VAL374.O

GLY146.N-HIS163.O

SER62.N-ASN65.OD1

GLY521.N-VAL518.O

LEU363.N-ASN359.O

GLY120.N-ASN28.OD1

SER267.N-ASP263.O

TRP31.N-CYS16.O

LEU32.N-VAL35.O

GLY11.N-GLU320.OE1

SER254.N-LEU250.O

LYS406.NZ-ASP461.OD1

LEU282.N-ASP216.OD1

GLU596.N-GLU594.OE1

SER158.N-ASN151.O

GLY455.N-TYR467.O

LEU27.N-VAL20.O

GLU320.N-SER316.O

SER147.OG-SER144.O

TRP218.NE1-THR280.O

LEU268.N-MET264.O

GLU290.N-GLU288.OE2

SER123.N-ALA116.O

LYS269.NZ-GLU270.OE2

LEU167.N-VAL171.O

GLU270.N-ALA266.O

LYS394.N-SER387.O

ILE506.N-ASP595.OD2

GLU240.N-THR199.O

PHE8.N-SER113.OG

SER113.OG-GLN127.OE1

GLY426.N-ASN334.OD1

ILE384.N-LYS396.O

GLU14.N-SER10.O

PHE230.N-THR226.O

GLY452.N-HIS469.O

ILE249.N-ASP245.O

GLN83.N-VAL86.O

PHE223.N-ASN221.OD1

TRP207.N-ASN203.O

HIS478.N-ILE442.O

GLN69.N-GLN19.O

THR25.OG1-CYS44.O

HIS470.N-ALA479.O

GLN579.NE2-GLU576.OE1

PHE150.N-SER113.O

HIS386.ND1-ASN369.OD1

Dimer-N3

PHE112.N-CYS128.O

Dimer-apo GLN498.NE2-VAL492.O

Monomer-N3

MET264.N-ALA260.O

Monomer-apo

Table 2.10 HBs of the optimized six models of [340] (continuation 1)

SER1.OG-GLU473.OE2

PHE530.N-ASN528.OD1

PHE466.N-LYS409.O

PHE441.N-ARG438.O

PHE230.N-THR226.O

PHE140.N-SER308.O

PHE134.N-ARG131.O

MET437.N-GLN417.O

MET235.N-ASN231.O

LYS90.NZ-ASP34.OD1

LYS90.N-GLY79.O

LYS88.NZ-GLU178.OE1

LYS88.N-SER81.O

LYS576.N-CYS572.O

LYS543.N-VAL540.O

LYS5.NZ-GLU290.OE1

LYS444.NZ-ASP504.OD2

LYS395.NZ-GLN390.OE1

LYS395.N-SER388.O

LYS236.NZ-LEU232.O

LYS137.NZ-ASP197.OD1

LYS102.NZ-ASP153.OD2

LYS100.NZ-ASP155.OD1

LEU75.N-VAL68.O

LEU589.N-ASP523.OD2

LEU578.N-SER574.O

LEU575.N-MET571.O

LEU512.N-THR508.O

LEU396.N-VAL343.O

LEU394.N-CYS345.O

LEU365.N-TYR361.O

LEU337.N-TYR344.O

LEU334.N-VAL327.O

LEU282.N-ASP216.OD1

LEU268.N-MET264.O

Dimer-2N3

Dimer-2N3-covalent

GLY179.N-ASP176.O

ASN180.N-ASP176.OD2

TYR182.N-GLY174.O

ARG105.NH2-PHE181.O

ALA173.N-MET165.O

LEU167.N-VAL171.O

SER121.N-TYR118.O

GLY120.N-ASN28.OD1

HIS163.N-SER147.O

ASN133.ND2-GLY195.O

(continued)

TYR101.OH-ASP33.OD1

ILE106.N-TYR182.OH

ARG131.N-THR135.O

PHE134.N-ARG131.O

GLY521.N-ALA517.O

SER123.N-ALA116.O

CYS160.N-GLY149.O

GLN107.N-GLN110.OE1

GLY109.N-MET130.O

ARG131.NE-ASP197.OD2

ASN238.ND2-ASP197.O

CYS128.N-PHE112.O

ALA516.N-ALA512.O

ARG310.NH2-GLU290.OE2

TYR515.OH-ILE565.O

LYS137.NZ-GLY589.O

LEU588.N-ASP522.OD1

ARG131.NH2-ASP197.OD1

TRP524.NE1-THR586.O

GLU240.N-THR199.O

THR199.N-ASN238.O

SER158.N-ASN151.O

ASN151.ND2-THR111.O

ASN203.ND2-ASP289.O

ASN203.ND2-GLY109.O

2.4 Concluding Remarks 81

THR21.N-LEU67.O THR332.OG1-CYS351.O THR352.N-ASP355.OD1 THR405.OG1-ASP340.OD1 THR45.N-ASP48.OD1 THR533.N-ASP536.OD1 THR98.OG1-ASP33.OD1 TRP218.NE1-THR280.O TRP338.N-CYS323.O TRP514.N-ASN510.O TYR101.OH-ASP33.OD2 TYR182.N-GLY174.O TYR209.OH-ILE259.O TYR344.N-LEU337.O TYR489.N-GLY481.O TYR54.OH-ASP187.O

THR98.OG1-ASP33.OD2 TRP31.N-CYS16.O TRP337.N-CYS322.O TRP524.NE1-THR586.O TYR118.N-SER121.O TYR118.OH-ARG604.O TYR182.N-GLY174.O TYR209.OH-ILE259.O TYR239.N-ALA234.O TYR488.N-GLY480.O TYR488.OH-CYS466.O VAL18.N-GLY29.O VAL20.N-LEU27.O VAL324.N-GLY335.O VAL342.N-LEU395.O VAL36.N-LEU89.O

LEU250.N-HIS246.O

LEU268.N-MET264.O

LEU27.N-VAL20.O

LEU272.N-LEU268.O

LEU282.N-ASP216.OD2

LEU30.N-TYR37.O

LEU32.N-VAL35.O

LEU333.N-VAL326.O

LEU336.N-TYR343.O

LEU338.N-VAL341.O

LEU364.N-TYR360.O

LEU373.N-THR327.O

LEU381.N-VAL374.O

LEU393.N-CYS344.O

LEU395.N-VAL342.O

LEU421.N-VAL454.O

LEU447.N-SER450.OG

LEU511.N-THR507.O

LEU514.N-VAL510.O

VAL297.N-PRO293.O

VAL35.N-LEU32.O

VAL36.N-LEU89.O

VAL91.N-ASP34.O

THR598.N-ASP601.OD2

THR531.N-LEU568.O

THR404.OG1-ASP339.OD1

THR292.N-ASP295.OD2

THR199.N-ASN238.O

SER446.N-TYR433.OH

SER420.OG-GLN434.OE1

SER301.N-GLN306.OXT

SER284.N-ILE281.O

LEU232.N-ASN228.O

THR25.OG1-CYS44.O

VAL212.N-LEU208.O

SER139.OG-GLN606.OE1

THR199.N-ASN238.O

LEU208.N-VAL204.O

Dimer-2N3

Dimer-N3

VAL20.N-LEU27.O

Dimer-apo

LEU205.N-THR201.O

Monomer-N3

VAL18.N-GLY29.O

Monomer-apo

Table 2.10 (continued)

ARG60.NH2-ASP56.OD1

ASN51.N-ASP48.O

ASN65.N-SER62.O

THR45.N-ASP48.OD1

ARG188.NH1-GLU55.OE1

GLN189.NE2-MET49.O

GLN189.NE2-TYR54.OH

TYR54.OH-ASP187.O

ARG188.NH1-ASP187.OD2

ARG40.NH2-ASP187.OD1

ASN63.ND2-VAL77.O

GLN192.NE2-THR190.O

GLN192.NE2-VAL186.O

LYS88.N-SER81.O

GLN83.N-VAL86.O

CYS85.N-GLY179.O

VAL91.N-ASP34.O

GLN19.NE2-THR26.OG1

LEU27.N-VAL20.O

VAL20.N-LEU27.O

GLY29.N-VAL18.O

GLN83.NE2-GLU178.OE2

Dimer-2N3-covalent

82 2 3C-Like Protease (3CLpro)

VAL20.N-LEU27.O

VAL68.N-LEU75.O

VAL411.N-PHE466.O VAL464.N-LYS407.O

LEU592.N-SER590.OG

LEU67.N-THR21.O

LYS90.N-GLY79.O

LYS88.N-SER81.O

LYS61.N-LEU58.O

LYS575.N-CYS571.O

LYS5.NZ-GLU290.OE2

LYS443.NZ-ASP503.OD2

LYS406.NZ-ASP461.OD2

LYS403.N-ASN401.OD1

LYS396.N-GLY385.O

LYS394.NZ-GLN389.OE1

LYS394.N-SER387.O

LYS269.NZ-THR225.OG1

LYS269.N-CYS265.O

LYS102.N-VAL157.O

LEU89.N-VAL36.O

LEU75.N-VAL68.O

VAL327.N-LEU334.O VAL398.N-ASP341.O

LEU578.N-LEU574.O

LEU588.N-ASP522.OD2

VAL247.N-GLN244.O VAL320.N-SER317.O

LEU57.N-ASN53.O

LEU574.N-MET570.O

LEU577.N-SER573.O

VAL104.N-PHE159.O VAL18.N-GLY29.O

VAL397.N-ASP340.O VAL603.N-PRO599.O

LEU538.N-ASN534.O

LEU548.N-ASN537.OD1

ARG60.NE-ASP56.OD2

2.4 Concluding Remarks 83

84

2 3C-Like Protease (3CLpro)

Table 2.11 HBs of the optimized six models of [340] (continuation 2) Monomer-apo

Monomer-N3

Dimer-apo

Dimer-N3

Dimer-2N3

Dimer-2N3-covalent

LYS97.N-ASN95.OD1 LYS97.NZ-ASN95.OD1 MET162.N-THR175.O MET165.N-ALA173.O MET235.N-ASN231.O MET264.N-ALA260.O MET355.N-THR351.O MET468.N-THR481.O PHE112.N-CYS128.O PHE150.N-SER113.O PHE309.N-LEU588.O PHE314.N-SER419.OG PHE418.N-CYS434.O PHE456.N-SER419.O PHE536.N-THR532.O PHE8.N-SER113.OG SER10.OG-GLU14.OE1 SER113.OG-GLN127.OE1 SER139.N-TYR126.OH SER147.N-SER144.O SER158.N-ASN151.O SER254.N-LEU250.O SER254.OG-ILE259.O SER267.N-ASP263.O SER307.OG-GLU166.OE1 SER387.N-LYS394.O SER387.OG-HIS386.O SER419.OG-GLN433.OE1 SER445.N-TYR432.OH SER450.N-LEU447.O SER573.N-ASP569.O SER607.N-VAL603.O THR111.OG1-ASP295.OD2 THR175.N-MET162.O THR190.OG1-GLN189.O THR21.N-LEU67.O THR257.OG1-LEU253.O THR327.N-LEU373.O THR331.N-CYS328.O THR404.OG1-ASN401.O THR481.N-MET468.O THR481.OG1-ASN486.O THR507.OG1-GLU546.O THR532.N-ASP535.OD1 TRP207.N-ASN203.O TRP218.NE1-THR280.O TRP31.N-CYS16.O TRP513.N-ASN509.O TRP524.NE1-THR586.O TYR118.N-SER121.O TYR182.N-GLY174.O TYR182.OH-CYS160.O TYR209.N-LEU205.O TYR209.OH-ILE259.O TYR239.N-ALA234.O TYR343.N-LEU336.O TYR37.N-LEU30.O TYR407.OH-ASP339.OD2 TYR424.N-SER427.O

(continued)

2.4 Concluding Remarks

85

Table 2.11 (continued) Monomer-apo

Monomer-N3

Dimer-apo

Dimer-N3

Dimer-2N3

Dimer-2N3-covalent

TYR432.N-VAL420.O TYR488.N-GLY480.O TYR488.OH-CYS466.O TYR515.N-LEU511.O TYR515.OH-ILE565.O VAL114.N-TYR126.O VAL125.N-ALA313.O VAL157.N-LYS100.O VAL18.N-GLY29.O VAL20.N-LEU27.O VAL204.N-ILE200.O VAL324.N-GLY335.O VAL326.N-LEU333.O VAL341.N-LEU338.O VAL342.N-LEU395.O VAL36.N-LEU89.O VAL392.N-GLN389.O VAL397.N-ASP340.O VAL410.N-PHE465.O VAL420.N-TYR432.O VAL431.N-ALA7.O VAL463.N-LYS406.O VAL492.N-GLN498.OE1 VAL91.N-ASP34.O

Table 2.12 SBs of MDs of the monomer-apo model of [340] rep1

rep2

rep3

rep4

ASP153-ARG298

ASP153-ARG298

ASP153-ARG298

ASP153-ARG298

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

ASP155-LYS100

rep5

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS12

ASP155-LYS12

ASP155-LYS102

ASP155-LYS12

ASP155-LYS12

ASP176-ARG105

ASP176-ARG105

ASP155-LYS12

ASP176-ARG105

ASP176-ARG105

ASP187-ARG188

ASP187-ARG188

ASP176-ARG105

ASP187-ARG188

ASP187-ARG188

ASP187-ARG40

ASP187-ARG40

ASP187-ARG188

ASP187-ARG40

ASP187-ARG40

ASP197-ARG131

ASP197-ARG131

ASP187-ARG40

ASP197-ARG131

ASP197-ARG131

ASP197-LYS137

ASP197-LYS137

ASP197-ARG131

ASP197-LYS137

ASP197-LYS137

ASP216-ARG279

ASP216-ARG279

ASP197-LYS137

ASP216-ARG279

ASP216-ARG279

ASP229-LYS269

ASP229-LYS269

ASP216-ARG279

ASP229-LYS269

ASP229-ARG222

ASP263-ARG222

ASP263-ARG222

ASP229-LYS269

ASP263-ARG222

ASP229-LYS269

ASP289-ARG131

ASP289-ARG131

ASP263-ARG222

ASP289-ARG131

ASP263-ARG222

ASP289-LYS137

ASP289-LYS137

ASP289-ARG131

ASP289-LYS137

ASP289-ARG131

ASP295-ARG298

ASP295-ARG298

ASP289-LYS137

ASP295-ARG298

ASP289-LYS137

ASP34-LYS90

ASP295-ARG4

ASP295-ARG298

ASP34-LYS90

ASP295-ARG298

ASP48-ARG60

ASP34-LYS90

ASP34-LYS90

ASP48-ARG60

ASP34-LYS90

ASP48-LYS61

ASP48-ARG60

ASP48-ARG60

ASP48-LYS61

ASP48-ARG60

ASP56-ARG60

ASP48-LYS61

ASP48-LYS61

ASP56-ARG60

ASP48-LYS61

ASP92-ARG76

ASP56-ARG60

ASP56-ARG60

ASP92-ARG76

ASP56-ARG60

GLU14-LYS97

ASP92-ARG76

ASP92-ARG76

GLU178-ARG105

ASP92-ARG76

GLU178-ARG105

GLU14-LYS97

GLU178-ARG105

GLU178-LYS88

GLU178-ARG105

GLU178-LYS88

GLU178-ARG105

GLU178-LYS88

GLU270-ARG222

GLU270-ARG222

GLU270-LYS269

GLU178-LYS88

GLU270-ARG279

GLU270-LYS269

GLU270-LYS269

GLU288-LYS137

GLU270-ARG222

GLU270-LYS269

GLU288-LYS137

GLU288-LYS137

GLU288-LYS5

GLU270-LYS269

GLU288-LYS137

GLU288-LYS5

GLU288-LYS5

GLU290-ARG131

GLU288-ARG4

GLU288-LYS5

GLU290-ARG131

GLU290-ARG131

GLU290-LYS137

GLU288-LYS137

GLU290-ARG131

GLU290-LYS137

GLU290-LYS137

GLU290-LYS5

GLU288-LYS5

GLU290-LYS137

GLU290-LYS5

GLU290-LYS5

GLU55-ARG40

GLU290-ARG131

GLU290-LYS5

GLU47-LYS61

GLU290-LYS137

GLU47-ARG188

GLU55-ARG188

GLU290-LYS5

GLU55-ARG188

GLU55-ARG40

GLU55-ARG188

GLU55-ARG40

GLU55-ARG40

86

2 3C-Like Protease (3CLpro)

Table 2.13 SBs of MDs of the monomer-N3 model of [340] rep1

rep2

rep3

rep4

ASP153-LYS102

ASP153-ARG298

ASP153-ARG298

ASP153-ARG298

ASP153-ARG298

ASP155-LYS100

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

rep5

ASP155-LYS102

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS12

ASP155-LYS102

ASP155-LYS102

ASP155-LYS102

ASP155-LYS12

ASP176-ARG105

ASP155-LYS12

ASP155-LYS12

ASP155-LYS12

ASP176-ARG105

ASP187-ARG188

ASP176-ARG105

ASP176-ARG105

ASP176-ARG105

ASP187-ARG188

ASP187-ARG40

ASP187-ARG188

ASP187-ARG188

ASP187-ARG188

ASP187-ARG40

ASP197-ARG131

ASP187-ARG40

ASP187-ARG40

ASP187-ARG40

ASP197-ARG131

ASP197-LYS137

ASP197-ARG131

ASP197-ARG131

ASP197-ARG131

ASP197-LYS137

ASP216-ARG279

ASP197-LYS137

ASP197-LYS137

ASP197-LYS137

ASP216-ARG279

ASP229-LYS269

ASP216-ARG279

ASP216-ARG279

ASP216-ARG279

ASP229-LYS269

ASP263-ARG222

ASP229-LYS269

ASP229-LYS269

ASP229-LYS269

ASP263-ARG222

ASP289-ARG131

ASP263-ARG222

ASP263-ARG222

ASP263-ARG222

ASP289-ARG131

ASP295-ARG298

ASP289-ARG131

ASP289-ARG131

ASP289-ARG131

ASP289-LYS137

ASP34-LYS90

ASP295-ARG298

ASP289-LYS137

ASP289-LYS137

ASP295-ARG298

ASP48-ARG60

ASP34-LYS90

ASP295-ARG298

ASP295-ARG298

ASP34-LYS90

ASP295-ARG4

ASP48-ARG60

ASP48-LYS61

ASP48-ARG60

ASP295-LYS5

ASP56-ARG60

ASP48-LYS61

ASP34-LYS90

ASP34-LYS90

ASP48-LYS61

ASP92-ARG76

ASP56-ARG60

ASP48-ARG60

ASP48-ARG60

ASP56-ARG60

GLU178-ARG105

ASP92-ARG76

ASP48-LYS61

ASP48-LYS61

ASP92-ARG76

GLU178-LYS88

GLU178-ARG105

ASP56-ARG60

ASP56-ARG60

GLU178-ARG105

GLU270-ARG222

GLU270-ARG222

ASP92-ARG76

ASP92-ARG76

GLU178-LYS88

GLU270-LYS269

GLU270-LYS269

GLU178-ARG105

GLU14-LYS97

GLU270-ARG279

GLU288-ARG4

GLU288-LYS5

GLU178-LYS88

GLU178-ARG105

GLU270-LYS269

GLU288-LYS137

GLU290-ARG131

GLU270-ARG222

GLU178-LYS88

GLU288-ARG4 GLU288-LYS137

GLU288-LYS5

GLU290-LYS137

GLU270-LYS269

GLU270-ARG222

GLU290-ARG131

GLU290-LYS5

GLU288-ARG4

GLU270-LYS269

GLU288-LYS5

GLU290-LYS137

GLU55-ARG40

GLU288-LYS137

GLU288-LYS137

GLU290-ARG131

GLU288-LYS5

GLU288-LYS5

GLU290-LYS5

GLU290-LYS137

GLU55-ARG188

GLU290-ARG131

GLU290-ARG131

GLU290-LYS5

GLU55-ARG40

GLU290-ARG4

GLU290-LYS137

GLU55-ARG40

GLU290-LYS137

GLU290-LYS5

GLU290-LYS5

GLU55-ARG40

GLU55-ARG40

2.4 Concluding Remarks

87

Table 2.14 SBs of MDs of the dimer-apo model of [340] rep1

rep2

rep3

rep4

rep5

ASP153-LYS102

ASP153-LYS102

ASP153-ARG298

ASP153-ARG298

ASP153-LYS102

ASP155-LYS100

ASP155-LYS100

ASP153-LYS102

ASP153-LYS102

ASP155-LYS100

ASP155-LYS12

ASP155-LYS12

ASP155-LYS100

ASP155-LYS100

ASP155-LYS12

ASP176-ARG105

ASP176-ARG105

ASP155-LYS12

ASP155-LYS12

ASP176-ARG105

ASP187-ARG188

ASP187-ARG188

ASP176-ARG105

ASP176-ARG105

ASP187-ARG188

ASP187-ARG40

ASP187-ARG40

ASP187-ARG188

ASP187-ARG188

ASP187-ARG40

ASP197-ARG131

ASP197-ARG131

ASP187-ARG40

ASP187-ARG40

ASP197-ARG131

ASP197-LYS137

ASP197-LYS137

ASP197-ARG131

ASP197-ARG131

ASP197-LYS137

ASP216-ARG217

ASP216-ARG279

ASP197-LYS137

ASP197-LYS137

ASP216-ARG279

ASP216-ARG279

ASP229-LYS269

ASP216-ARG279

ASP216-ARG279

ASP229-LYS269

ASP229-LYS269

ASP263-ARG222

ASP229-LYS269

ASP229-LYS269

ASP263-ARG222

ASP263-ARG222

ASP289-ARG131

ASP263-ARG222

ASP263-ARG222

ASP289-ARG131

ASP289-ARG131

ASP295-ARG298

ASP289-ARG131

ASP289-ARG131

ASP295-ARG298

ASP295-ARG298

ASP340-LYS396

ASP289-LYS137

ASP295-ARG298

ASP340-LYS396

ASP340-LYS396

ASP34-LYS90

ASP295-ARG298

ASP340-LYS396

ASP34-LYS90

ASP34-LYS90

ASP354-ARG366

ASP295-LYS5

ASP34-LYS90

ASP354-ARG366

ASP354-ARG366

ASP354-LYS367

ASP340-LYS396

ASP354-ARG366

ASP354-LYS367

ASP354-LYS367

ASP362-ARG366

ASP34-LYS90

ASP354-LYS367

ASP362-ARG366

ASP362-ARG366

ASP398-ARG382

ASP354-ARG366

ASP362-ARG366

ASP398-ARG382

ASP398-ARG382

ASP459-LYS408

ASP354-LYS367

ASP362-LYS367

ASP459-LYS408

ASP459-LYS408

ASP461-LYS318

ASP362-ARG366

ASP398-ARG382

ASP461-LYS318

ASP461-LYS318

ASP461-LYS406

ASP398-ARG382

ASP459-ARG604

ASP461-LYS406

ASP461-LYS406

ASP482-ARG411

ASP459-LYS408

ASP459-LYS408

ASP482-ARG411

ASP482-ARG411

ASP48-ARG60

ASP461-LYS318

ASP461-LYS318

ASP48-ARG60

ASP48-ARG60

ASP48-LYS61

ASP461-LYS406

ASP461-LYS406

ASP493-ARG346

ASP48-LYS61

ASP493-ARG346

ASP482-ARG411

ASP461-LYS408

ASP493-ARG494

ASP493-ARG346

ASP493-ARG494

ASP48-ARG60

ASP482-ARG411

ASP503-ARG437

ASP493-ARG494

ASP503-ARG437

ASP48-LYS61

ASP48-ARG60

ASP503-LYS443

ASP503-ARG437

ASP503-LYS443

ASP493-ARG346

ASP48-LYS61

ASP522-ARG585

ASP503-LYS443

ASP522-ARG585

ASP493-ARG494

ASP493-ARG346

ASP535-LYS575

ASP522-ARG585

ASP535-LYS575

ASP503-ARG437

ASP493-ARG494

ASP569-ARG528

ASP535-LYS575

ASP569-ARG528

ASP503-LYS443

ASP503-ARG437

ASP56-ARG60

ASP569-ARG528

ASP56-ARG60

ASP522-ARG585

ASP503-LYS443

ASP595-ARG437

ASP56-ARG60

ASP595-ARG437

ASP535-LYS575

ASP522-ARG585

ASP601-ARG604

ASP595-ARG437

ASP601-ARG604

ASP569-ARG528

ASP535-LYS575

ASP92-ARG76

ASP601-ARG604

ASP601-LYS311

ASP56-ARG60

ASP569-ARG528

GLU178-ARG105

ASP92-ARG76

ASP92-ARG76

ASP595-ARG437

ASP56-ARG60

GLU178-LYS88

GLU178-ARG105

GLU14-LYS318

ASP601-ARG604

ASP595-ARG437

GLU270-ARG222

GLU178-LYS88

GLU178-ARG105

ASP92-ARG76

ASP601-ARG604

GLU270-LYS269

GLU270-ARG222

GLU178-LYS88

GLU178-ARG105

ASP92-ARG76

GLU288-LYS5

GLU270-LYS269

GLU270-LYS269

GLU178-LYS88

GLU178-ARG105

GLU290-ARG131

GLU288-LYS5

GLU288-LYS5

GLU270-ARG222

GLU178-LYS88

GLU290-ARG310

GLU290-ARG131

GLU290-ARG131

GLU270-ARG279

GLU270-ARG222

GLU290-LYS137

GLU290-ARG310

GLU290-ARG310

GLU270-LYS269

GLU270-ARG279

GLU290-LYS5

GLU290-LYS5

GLU290-LYS5

GLU288-LYS137

GLU270-LYS269

GLU353-LYS367

GLU361-ARG346

GLU320-LYS12

GLU288-LYS5

GLU288-LYS5

GLU361-ARG346

GLU484-ARG411

GLU353-ARG366

GLU290-ARG310

GLU290-ARG131

GLU484-ARG411

GLU576-ARG528

GLU353-LYS367

GLU290-LYS137

GLU290-ARG310

GLU484-LYS394

GLU576-LYS575

GLU361-ARG346

GLU290-LYS5

GLU290-LYS5

GLU55-ARG188

GLU594-LYS311

GLU361-ARG494

GLU320-LYS12

GLU320-LYS12

GLU55-ARG40

GLU594-LYS443

GLU47-ARG60

GLU353-LYS367

GLU353-ARG366

GLU576-ARG528

GLU596-ARG4

GLU47-LYS61

GLU361-ARG346

GLU361-ARG346

GLU576-ARG585

GLU596-ARG437

GLU484-ARG411

GLU47-LYS61

GLU361-ARG366

GLU576-LYS575

GLU596-LYS311

GLU484-LYS394

GLU484-ARG411

GLU47-LYS61

GLU594-LYS311

GLU55-ARG188

GLU484-LYS394

GLU484-ARG411

GLU596-ARG4

GLU576-ARG528

GLU576-ARG528

GLU484-LYS394

GLU596-ARG437

GLU576-LYS575

GLU576-LYS575

GLU55-ARG188

GLU596-LYS311

GLU594-LYS311

GLU594-ARG4

GLU576-ARG528

GLU596-LYS443

GLU594-LYS443

GLU594-LYS311

GLU576-LYS575

GLU596-ARG4

GLU594-LYS443

GLU594-LYS311

GLU596-ARG437

GLU594-LYS5

GLU596-ARG4

GLU596-LYS311

GLU596-ARG4

GLU596-ARG437

GLU596-LYS443

GLU596-ARG437

GLU596-LYS311

GLU596-LYS311

GLU596-LYS443

88

2 3C-Like Protease (3CLpro)

Table 2.15 SBs of MDs of the dimer-N3 model of [340] rep1

rep2

rep3

rep4

rep5

ASP153-ARG298

ASP153-ARG298

ASP153-ARG298

ASP153-LYS102

ASP153-ARG298

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

ASP155-LYS100

ASP153-LYS102

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS102

ASP155-LYS100

ASP155-LYS12

ASP155-LYS102

ASP155-LYS12

ASP155-LYS12

ASP155-LYS12

ASP176-ARG105

ASP155-LYS12

ASP176-ARG105

ASP176-ARG105

ASP176-ARG105

ASP187-ARG188

ASP176-ARG105

ASP187-ARG188

ASP187-ARG188

ASP187-ARG188

ASP187-ARG40

ASP187-ARG188

ASP187-ARG40

ASP187-ARG40

ASP187-ARG40

ASP197-ARG131

ASP187-ARG40

ASP197-ARG131

ASP197-ARG131

ASP197-ARG131

ASP197-LYS137

ASP197-ARG131

ASP197-LYS137

ASP197-LYS137

ASP197-LYS137

ASP216-ARG279

ASP197-LYS137

ASP216-ARG279

ASP216-ARG279

ASP216-ARG279

ASP229-LYS269

ASP216-ARG279

ASP229-LYS269

ASP229-LYS269

ASP229-LYS269

ASP263-ARG222

ASP229-LYS269

ASP263-ARG222

ASP263-ARG222

ASP263-ARG222

ASP289-ARG131

ASP263-ARG222

ASP289-ARG131

ASP289-ARG131

ASP289-ARG131

ASP295-ARG298

ASP289-ARG131

ASP289-LYS137

ASP295-ARG298

ASP295-ARG298

ASP340-LYS396

ASP295-ARG298

ASP295-ARG298

ASP340-LYS396

ASP340-LYS396

ASP34-LYS90

ASP340-LYS396

ASP340-LYS396

ASP34-LYS90

ASP34-LYS90

ASP354-ARG366

ASP34-LYS90

ASP34-LYS90

ASP354-ARG366

ASP354-ARG366

ASP354-LYS367

ASP354-ARG366

ASP354-ARG366

ASP354-LYS367

ASP354-LYS367

ASP362-ARG366

ASP354-LYS367

ASP354-LYS367

ASP362-ARG366

ASP362-ARG366

ASP398-ARG382

ASP362-ARG366

ASP362-ARG366

ASP398-ARG382

ASP398-ARG382

ASP459-LYS408

ASP398-ARG382

ASP398-ARG382

ASP459-LYS408

ASP459-ARG604

ASP461-LYS318

ASP459-LYS408

ASP459-ARG604

ASP461-LYS318

ASP459-LYS408

ASP461-LYS406

ASP461-LYS318

ASP459-LYS408

ASP461-LYS406

ASP461-LYS318

ASP482-ARG411

ASP461-LYS406

ASP461-LYS318

ASP482-ARG411

ASP461-LYS406

ASP48-ARG60

ASP461-LYS408

ASP461-LYS406

ASP48-ARG60

ASP461-LYS408

ASP48-LYS61

ASP482-ARG411

ASP482-ARG411

ASP48-LYS61

ASP482-ARG411

ASP493-ARG346

ASP48-ARG60

ASP48-ARG60

ASP493-ARG346

ASP48-ARG60

ASP493-ARG494

ASP48-LYS61

ASP48-LYS61

ASP493-ARG494

ASP48-LYS61

ASP503-ARG437

ASP493-ARG346

ASP493-ARG346

ASP503-ARG437

ASP493-ARG346

ASP503-LYS443

ASP493-ARG494

ASP493-ARG494

ASP503-LYS443

ASP493-ARG494

ASP522-ARG585

ASP503-ARG437

ASP503-ARG437

ASP522-ARG585

ASP503-ARG437

ASP535-LYS575

ASP503-LYS443

ASP503-LYS443

ASP535-LYS575

ASP503-LYS443

ASP569-ARG528

ASP522-ARG585

ASP522-ARG585

ASP569-ARG528

ASP522-ARG585

ASP56-ARG60

ASP535-LYS575

ASP535-LYS575

ASP56-ARG60

ASP535-LYS575

ASP56-LYS61

ASP569-ARG528

ASP569-ARG528

ASP595-ARG437

ASP569-ARG528

ASP595-ARG437

ASP56-ARG60

ASP56-ARG60

ASP601-ARG604

ASP56-ARG60

ASP601-ARG604

ASP595-ARG437

ASP595-ARG437

ASP92-ARG76

ASP595-ARG437

ASP92-ARG76

ASP601-ARG604

ASP601-ARG604

GLU14-LYS318

ASP601-ARG604

GLU14-LYS318

ASP92-ARG76

ASP92-ARG76

GLU178-ARG105

ASP92-ARG76

GLU178-LYS88

GLU178-ARG105

GLU178-ARG105

GLU178-LYS88

GLU178-ARG105

GLU270-LYS269

GLU178-LYS88

GLU178-LYS88

GLU270-ARG222

GLU178-LYS88

GLU288-ARG310

GLU270-ARG222

GLU270-LYS269

GLU270-LYS269

GLU270-ARG222

GLU288-LYS5

GLU270-ARG279

GLU288-LYS137

GLU288-LYS5

GLU270-LYS269

GLU290-ARG131

GLU270-LYS269

GLU288-LYS5

GLU290-ARG131

GLU288-LYS137

GLU290-ARG310

GLU288-LYS5

GLU290-ARG131

GLU290-ARG310

GLU288-LYS5

GLU290-LYS5

GLU290-ARG131

GLU290-ARG310

GLU290-LYS5

GLU290-ARG131

GLU361-ARG346

GLU290-ARG310

GLU290-LYS137

GLU361-ARG346

GLU290-ARG310

GLU361-ARG494

GLU290-LYS5

GLU290-LYS5

GLU484-ARG411

GLU290-LYS137

GLU47-LYS61

GLU320-LYS12

GLU361-ARG346

GLU484-LYS394

GLU290-LYS5

GLU484-ARG411

GLU361-ARG346

GLU47-ARG60

GLU55-ARG188

GLU320-LYS12

GLU484-LYS394

GLU484-ARG411

GLU47-LYS61

GLU55-ARG40

GLU361-ARG346

GLU55-ARG188

GLU484-LYS394

GLU484-ARG411

GLU576-ARG585

GLU361-ARG494

GLU55-ARG40

GLU55-ARG40

GLU484-LYS394

GLU576-LYS575

GLU47-ARG60

GLU55-ARG60

GLU576-LYS575

GLU55-ARG188

GLU594-LYS311

GLU47-LYS61

GLU576-ARG528

GLU594-LYS311

GLU55-ARG40

GLU596-ARG4

GLU484-ARG411

GLU576-ARG585

GLU596-ARG4

GLU576-ARG528

GLU596-LYS311

GLU484-LYS394

GLU576-LYS575

GLU596-ARG437

GLU576-LYS575

GLU55-ARG188

GLU594-LYS311

GLU596-LYS311

GLU594-LYS311

GLU55-ARG40

GLU596-ARG4

GLU596-ARG4

GLU576-ARG528

GLU596-ARG437

GLU596-ARG437

GLU576-LYS575

GLU596-LYS311

GLU596-LYS311

GLU594-ARG4

GLU596-LYS443

GLU596-LYS443

GLU594-LYS311 GLU596-ARG4 GLU596-ARG437 GLU596-LYS311

2.4 Concluding Remarks

89

Table 2.16 SBs of MDs of the dimer-2N3 model of [340] rep1

rep2

rep3

rep4

rep5

ASP153-LYS102

ASP153-ARG298

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

ASP155-LYS100

ASP153-LYS102

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS12

ASP155-LYS100

ASP155-LYS102

ASP155-LYS12

ASP155-LYS102

ASP176-ARG105

ASP155-LYS102

ASP155-LYS12

ASP176-ARG105

ASP155-LYS12

ASP187-ARG188

ASP155-LYS12

ASP176-ARG105

ASP187-ARG188

ASP176-ARG105

ASP187-ARG40

ASP176-ARG105

ASP187-ARG188

ASP187-ARG40

ASP187-ARG188

ASP197-ARG131

ASP187-ARG188

ASP187-ARG40

ASP197-ARG131

ASP187-ARG40

ASP197-LYS137

ASP187-ARG40

ASP197-ARG131

ASP197-LYS137

ASP197-ARG131

ASP216-ARG279

ASP197-ARG131

ASP197-LYS137

ASP216-ARG279

ASP197-LYS137

ASP229-LYS269

ASP197-LYS137

ASP216-ARG279

ASP229-LYS269

ASP216-ARG217

ASP263-ARG222

ASP216-ARG279

ASP229-LYS269

ASP263-ARG222

ASP216-ARG279

ASP289-ARG131

ASP229-LYS269

ASP263-ARG222

ASP289-ARG131

ASP229-LYS269

ASP295-ARG298

ASP263-ARG222

ASP289-ARG131

ASP295-ARG298

ASP263-ARG222

ASP341-LYS397

ASP289-ARG131

ASP295-ARG298

ASP341-LYS397

ASP289-ARG131

ASP34-LYS90

ASP295-ARG298

ASP341-LYS397

ASP34-LYS90

ASP289-LYS137

ASP355-ARG367

ASP341-LYS397

ASP34-LYS90

ASP355-ARG367

ASP295-ARG298

ASP355-LYS368

ASP34-LYS90

ASP355-ARG367

ASP355-LYS368

ASP341-LYS397

ASP363-ARG367

ASP355-ARG367

ASP355-LYS368

ASP363-ARG367

ASP34-LYS90

ASP399-ARG383

ASP355-LYS368

ASP363-ARG367

ASP399-ARG383

ASP355-ARG367

ASP460-LYS409

ASP363-ARG367

ASP399-ARG383

ASP460-ARG605

ASP355-LYS368

ASP462-LYS319

ASP399-ARG383

ASP460-ARG605

ASP460-LYS409

ASP363-ARG367

ASP462-LYS407

ASP460-LYS409

ASP460-LYS409

ASP462-LYS319

ASP399-ARG383

ASP483-ARG412

ASP462-LYS319

ASP462-LYS319

ASP462-LYS407

ASP460-LYS409

ASP48-ARG60

ASP462-LYS407

ASP462-LYS407

ASP462-LYS409

ASP462-LYS319

ASP48-LYS61

ASP483-ARG412

ASP462-LYS409

ASP483-ARG412

ASP462-LYS407

ASP494-ARG347

ASP48-ARG60

ASP483-ARG412

ASP48-ARG60

ASP483-ARG412

ASP494-ARG495

ASP48-LYS61

ASP48-ARG60

ASP48-LYS61

ASP48-ARG60

ASP504-ARG438

ASP494-ARG347

ASP48-LYS61

ASP494-ARG347

ASP48-LYS61

ASP504-LYS444

ASP494-ARG495

ASP494-ARG347

ASP494-ARG495

ASP494-ARG347

ASP523-ARG524

ASP504-ARG438

ASP494-ARG495

ASP504-ARG438

ASP494-ARG495

ASP523-ARG586

ASP504-LYS444

ASP504-ARG438

ASP504-LYS444

ASP504-ARG438

ASP536-LYS576

ASP536-LYS576

ASP504-LYS444

ASP523-ARG586

ASP504-LYS444

ASP56-ARG60

ASP56-ARG60

ASP523-ARG586

ASP536-LYS576

ASP523-ARG586

ASP570-ARG529

ASP570-ARG529

ASP536-LYS576

ASP56-ARG60

ASP536-LYS576

ASP596-ARG438

ASP596-ARG438

ASP56-ARG60

ASP570-ARG529

ASP56-ARG60

ASP602-ARG605

ASP602-ARG605

ASP570-ARG529

ASP596-ARG438

ASP570-ARG529

ASP92-ARG76

ASP92-ARG76

ASP596-ARG438

ASP602-ARG605

ASP596-ARG438

GLU178-ARG105

GLU14-LYS319

ASP602-ARG605

ASP92-ARG76

ASP596-LYS444

GLU178-LYS88

GLU178-ARG105

ASP92-ARG76

GLU14-LYS319

ASP602-ARG605

GLU270-LYS269

GLU178-LYS88

GLU14-LYS319

GLU178-ARG105

ASP92-ARG76

GLU288-LYS5

GLU270-ARG222

GLU178-ARG105

GLU178-LYS88

GLU14-LYS319

GLU290-ARG131

GLU270-LYS269

GLU178-LYS88

GLU270-ARG222

GLU178-ARG105

GLU290-ARG311

GLU288-LYS5

GLU270-ARG222

GLU270-LYS269

GLU178-LYS88

GLU290-LYS5

GLU290-ARG131

GLU270-LYS269

GLU288-LYS5

GLU270-ARG279

GLU354-LYS368

GLU290-ARG311

GLU288-LYS5

GLU290-ARG131

GLU270-LYS269

GLU362-ARG347

GLU290-LYS5

GLU290-ARG131

GLU290-ARG311

GLU288-LYS137

GLU362-ARG495

GLU321-LYS12

GLU290-ARG311

GLU290-LYS5

GLU288-LYS5

GLU485-ARG412

GLU362-ARG347

GLU290-LYS137

GLU321-LYS12

GLU290-ARG131

GLU485-LYS395

GLU47-ARG60

GLU290-LYS5

GLU362-ARG347

GLU290-ARG311

GLU55-ARG188

GLU47-LYS61

GLU321-LYS12

GLU485-ARG412

GLU290-LYS137

GLU55-ARG40

GLU485-ARG412

GLU362-ARG347

GLU485-LYS395

GLU290-LYS5

GLU577-ARG529

GLU485-LYS395

GLU47-ARG60

GLU55-ARG188

GLU321-LYS12

GLU577-LYS576

GLU55-ARG188

GLU485-ARG412

GLU55-ARG40

GLU362-ARG347

GLU595-LYS312

GLU55-ARG40

GLU485-LYS395

GLU577-ARG586

GLU362-ARG495

GLU597-ARG4

GLU577-ARG529

GLU55-ARG188

GLU577-LYS576

GLU485-ARG412

GLU597-ARG438

GLU577-LYS576

GLU55-ARG40

GLU595-ARG4

GLU485-LYS395

GLU597-LYS312

GLU595-ARG4

GLU577-LYS576

GLU595-LYS312

GLU55-ARG188

GLU595-LYS312

GLU595-LYS312

GLU597-ARG4

GLU55-ARG40

GLU597-ARG4

GLU595-LYS444

GLU597-ARG438

GLU577-ARG529

GLU597-ARG438

GLU597-ARG4

GLU597-LYS312

GLU577-LYS576

GLU597-LYS312

GLU597-ARG438

GLU595-LYS312

GLU597-LYS312

GLU595-LYS444 GLU597-ARG4 GLU597-ARG438 GLU597-LYS312 GLU597-LYS444

90

2 3C-Like Protease (3CLpro)

Table 2.17 SBs of MDs of the dimer-2N3-covalent model of [340] rep1

rep2

rep3

rep4

rep5

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

ASP153-ARG298

ASP153-LYS102

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP153-LYS102

ASP155-LYS100

ASP155-LYS12

ASP155-LYS102

ASP155-LYS12

ASP155-LYS100

ASP155-LYS12

ASP176-ARG105

ASP155-LYS12

ASP176-ARG105

ASP155-LYS12

ASP176-ARG105

ASP187-ARG188

ASP176-ARG105

ASP187-ARG188

ASP176-ARG105

ASP187-ARG188

ASP187-ARG40

ASP187-ARG188

ASP187-ARG40

ASP187-ARG188

ASP187-ARG40

ASP197-ARG131

ASP187-ARG40

ASP197-ARG131

ASP187-ARG40

ASP197-ARG131

ASP197-LYS137

ASP197-ARG131

ASP197-LYS137

ASP197-ARG131

ASP197-LYS137

ASP216-ARG279

ASP197-LYS137

ASP216-ARG279

ASP197-LYS137

ASP216-ARG279

ASP229-LYS269

ASP216-ARG279

ASP229-LYS269

ASP216-ARG279

ASP229-LYS269

ASP263-ARG222

ASP229-LYS269

ASP263-ARG222

ASP229-LYS269

ASP263-ARG222

ASP289-ARG131

ASP263-ARG222

ASP289-ARG131

ASP263-ARG222

ASP289-ARG131

ASP295-ARG298

ASP289-ARG131

ASP289-LYS137

ASP289-ARG131

ASP295-ARG298

ASP340-LYS396

ASP295-ARG298

ASP295-ARG298

ASP295-ARG298

ASP340-LYS396

ASP34-LYS90

ASP340-LYS396

ASP340-LYS396

ASP340-LYS396

ASP34-LYS90

ASP354-ARG366

ASP34-LYS90

ASP34-LYS90

ASP34-LYS90

ASP354-ARG366

ASP354-LYS367

ASP354-ARG366

ASP354-ARG366

ASP354-ARG366

ASP354-LYS367

ASP362-ARG366

ASP354-LYS367

ASP354-LYS367

ASP354-LYS367

ASP362-ARG366

ASP398-ARG382

ASP362-ARG366

ASP362-ARG366

ASP362-ARG366

ASP398-ARG382

ASP459-ARG604

ASP398-ARG382

ASP398-ARG382

ASP362-LYS367

ASP459-ARG604

ASP459-LYS408

ASP459-ARG604

ASP459-ARG604

ASP398-ARG382

ASP459-LYS408

ASP461-LYS318

ASP459-LYS408

ASP459-LYS408

ASP459-LYS408

ASP461-LYS318

ASP461-LYS406

ASP461-LYS318

ASP461-LYS318

ASP461-LYS318

ASP461-LYS406

ASP461-LYS408

ASP461-LYS406

ASP461-LYS406

ASP461-LYS406

ASP461-LYS408

ASP482-ARG411

ASP482-ARG411

ASP461-LYS408

ASP482-ARG411

ASP482-ARG411

ASP48-ARG60

ASP48-ARG60

ASP482-ARG411

ASP48-ARG60

ASP48-ARG60

ASP48-LYS61

ASP48-LYS61

ASP48-ARG60

ASP48-LYS61

ASP48-LYS61

ASP493-ARG346

ASP493-ARG346

ASP48-LYS61

ASP493-ARG346

ASP493-ARG346

ASP493-ARG494

ASP493-ARG494

ASP493-ARG346

ASP493-ARG494

ASP493-ARG494

ASP503-ARG437

ASP503-ARG437

ASP493-ARG494

ASP503-ARG437

ASP503-ARG437

ASP503-LYS443

ASP503-LYS443

ASP503-ARG437

ASP503-LYS443

ASP503-LYS443

ASP535-LYS575

ASP522-ARG585

ASP503-LYS443

ASP522-ARG585

ASP522-ARG585

ASP569-ARG528

ASP535-LYS575

ASP522-ARG585

ASP535-LYS575

ASP535-LYS575

ASP56-ARG60

ASP569-ARG528

ASP535-LYS575

ASP569-ARG528

ASP569-ARG528

ASP595-ARG437

ASP56-ARG60

ASP569-ARG528

ASP56-ARG60

ASP56-ARG60

ASP601-ARG604

ASP595-ARG437

ASP56-ARG60

ASP595-ARG437

ASP595-ARG437

ASP92-ARG76

ASP601-ARG604

ASP595-ARG437

ASP601-ARG604

ASP595-LYS443

GLU14-LYS318

ASP92-ARG76

ASP601-ARG604

ASP92-ARG76

ASP601-ARG604

GLU178-ARG105

GLU14-LYS318

ASP92-ARG76

GLU14-LYS318

ASP92-ARG76

GLU178-LYS88

GLU178-ARG105

GLU14-LYS318

GLU178-ARG105

GLU178-ARG105

GLU270-ARG222

GLU178-LYS88

GLU178-ARG105

GLU178-LYS88

GLU178-LYS88

GLU270-LYS269

GLU270-LYS269

GLU178-LYS88

GLU270-ARG222

GLU270-LYS269

GLU288-LYS137

GLU288-LYS137

GLU270-LYS269

GLU270-LYS269

GLU288-LYS5

GLU288-LYS5

GLU288-LYS5

GLU288-LYS5

GLU288-LYS5

GLU290-ARG310

GLU290-ARG131

GLU290-ARG131

GLU290-ARG131

GLU290-ARG131

GLU290-LYS5

GLU290-ARG310

GLU290-ARG310

GLU290-ARG310

GLU290-ARG310

GLU353-LYS367

GLU290-LYS5

GLU290-LYS137

GLU290-LYS137

GLU290-LYS5

GLU361-ARG346

GLU320-LYS12

GLU290-LYS5

GLU290-LYS5

GLU353-LYS367

GLU361-ARG494

GLU353-LYS367

GLU361-ARG346

GLU320-LYS12

GLU361-ARG346

GLU484-ARG411

GLU361-ARG346

GLU361-ARG494

GLU361-ARG346

GLU361-ARG366

GLU484-LYS394

GLU361-ARG494

GLU484-ARG411

GLU361-ARG494

GLU47-LYS61

GLU55-ARG188

GLU47-ARG60

GLU484-LYS394

GLU484-ARG411

GLU484-ARG411

GLU55-ARG40

GLU484-ARG411

GLU55-ARG188

GLU484-LYS394

GLU484-LYS394

GLU576-LYS575

GLU484-LYS394

GLU55-ARG40

GLU55-ARG188

GLU55-ARG188

GLU594-LYS311

GLU55-ARG188

GLU576-ARG528

GLU55-ARG40

GLU55-ARG40

GLU596-ARG4

GLU55-ARG40

GLU576-ARG585

GLU576-ARG528

GLU576-ARG528

GLU596-ARG437 GLU596-LYS311

GLU576-ARG585

GLU576-LYS575

GLU576-ARG585

GLU576-ARG585

GLU576-LYS575

GLU594-LYS311

GLU576-LYS575

GLU576-LYS575

GLU594-LYS311

GLU594-LYS443

GLU594-LYS311

GLU594-LYS311

GLU596-ARG4

GLU596-ARG4

GLU596-ARG4

GLU596-ARG4

GLU596-ARG437

GLU596-ARG437

GLU596-LYS311

GLU596-LYS311

GLU596-LYS311 GLU596-LYS443

GLU596-LYS311 GLU596-LYS443

THR201.OG1-GLU240.O 59.0 TRP31.N-CYS16.O 57.5

THR201.OG1-GLU240.O 61.0 SER267.OG-ASP263.O 59.5 VAL36.N-LEU89.O 57.5 SER147.OG-SER144.O 56.0

TYR182.OH-CYS160.O 60.0

SER267.OG-ASP263.O 57.0

TRP31.N-CYS16.O 52.0

TRP31.N-CYS16.O 60.0

TYR182.OH-CYS160.O 58.5

GLY149.N-TYR161.O 47.0

VAL91.N-ASP34.O 38.5

CYS22.N-THR25.O 37.0 ASN151.N-SER158.O 36.5 HIE172.N-ILE136.O 36.5

GLY109.N-MET130.O 39.5 ASN28.ND2-CYS145.O 39.0 ARG131.N-THR135.O 39.0

LEU167.N-VAL171.O 37.0

ASN133.ND2-GLY195.O 36.5

ASN95.ND2-TRP31.O 36.5

GLY146.N-HIE163.O 38.0

ASN203.ND2-ASP289.O 38.0 GLY109.N-MET130.O 38.0

LEU115.N-VAL148.O 39.5 SER254.OG-ILE259.O 39.5

GLY109.N-MET130.O 39.0

ARG131.N-THR135.O 38.0

LEU268.N-MET264.O 38.0

TYR209.OH-ILE259.O 38.0

ARG40.NH2-ASP187.OD2 37.5

ASP176.N-ASN180.O 40.0 ALA70.N-VAL73.O 39.5

VAL157.N-LYS100.O 40.0 GLY146.N-HIE163.O 40.0

VAL18.N-GLY29.O 39.5

SER144.OG-LEU141.O 39.0

LEU208.N-VAL204.O 38.5

ALA234.N-PHE230.O 38.5

THR175.OG1-ASP176.O 37.5

LEU32.N-VAL35.O 38.5

ILE78.N-LYS90.O 40.0 PHE112.N-CYS128.O 40.0

GLU240.N-THR199.O 41.0 ASN95.ND2-TRP31.O 40.5

ASN231.N-LEU227.O 40.5

VAL91.N-ASP34.O 40.0

LEU89.N-VAL36.O 40.0

VAL18.N-GLY29.O 41.0

TYR126.N-VAL114.O 38.5

ILE200.N-ASP289.OD2 38.5

GLN19.N-GLN69.O 39.5

SER254.OG-ILE259.O 39.5

LEU30.N-TYR37.O 40.0

LYS269.N-CYS265.O 40.5

LEU115.N-VAL148.O 40.5

GLY149.N-TYR161.O 40.5

LYS88.N-SER81.O 39.5

LYS88.N-SER81.O 41.0 LEU30.N-TYR37.O 40.5

ILE78.N-LYS90.O 42.0

ASN28.ND2-CYS145.O 41.0

ASN231.N-LEU227.O 42.0

VAL20.N-LEU27.O 41.0

LEU75.N-VAL68.O 41.5

ALA255.N-GLY251.O 41.5

TYR37.N-LEU30.O 41.5

VAL20.N-LEU27.O 42.0

ASN95.N-ASP33.O 42.0

LEU205.N-THR201.O 42.5

ASP176.N-ASN180.O 44.0

GLY146.N-HIE163.O 44.0

LYS88.N-SER81.O 44.0

HIE163.N-SER147.O 44.5

LEU167.N-VAL171.O 46.5

LEU89.N-VAL36.O 46.5

LEU27.N-VAL20.O 47.0

TYR209.OH-ILE259.O 47.0

HIE172.N-ILE136.O 47.5

THR175.OG1-ASP176.O 49.0

TRP31.N-CYS16.O 50.5

VAL114.N-TYR126.O 51.0

ILE78.N-LYS90.O 51.0

SER267.OG-ASP263.O 52.5

THR257.OG1-LEU253.O 52.5

THR201.OG1-GLU240.O 59.5

VAL36.N-LEU89.O 60.0

TYR182.OH-CYS160.O 66.5

rep5

LEU75.N-VAL68.O 41.5

TYR209.OH-ILE259.O 41.0

LEU89.N-VAL36.O 41.5 LEU115.N-VAL148.O 41.5 ASN95.N-ASP33.O 41.0

LEU89.N-VAL36.O 42.5 LEU205.N-THR201.O 41.5 LEU75.N-VAL68.O 41.0

GLU14.N-SER10.O 42.5

LEU75.N-VAL68.O 42.0

VAL20.N-LEU27.O 43.0

GLY146.N-HIE163.O 42.0

LEU27.N-VAL20.O 43.5 VAL157.N-LYS100.O 43.0

LYS88.N-SER81.O 43.0 CYS128.N-PHE112.O 42.5

LEU30.N-TYR37.O 42.5

GLY149.N-TYR161.O 42.5

LEU27.N-VAL20.O 44.5

PHE150.N-SER113.O 43.5

ARG131.N-THR135.O 42.5

THR257.OG1-LEU253.O 44.0 LEU32.N-VAL35.O 43.5

LEU30.N-TYR37.O 44.5 HIE163.N-SER147.O 44.5

LEU27.N-VAL20.O 43.0

CYS128.N-PHE112.O 42.5

LEU30.N-TYR37.O 45.5

SER254.OG-ILE259.O 45.0

ASN203.ND2-ASP289.O 42.0

LEU205.N-THR201.O 45.0 VAL114.N-TYR126.O 44.5

TYR37.N-LEU30.O 45.0 LEU27.N-VAL20.O 45.0

PHE150.N-SER113.O 44.0

LEU115.N-VAL148.O 43.0

LEU205.N-THR201.O 46.5

ILE78.N-LYS90.O 46.0

ASN231.N-LEU227.O 45.5 ASN203.ND2-GLY109.O 45.5

THR135.OG1-ASN133.OD1 46.5

SER254.OG-ILE259.O 44.5

ASN95.N-ASP33.O 44.0

TYR182.N-GLY174.O 46.5 VAL114.N-TYR126.O 45.5

TYR37.N-LEU30.O 45.5 VAL20.N-LEU27.O 45.5

ILE78.N-LYS90.O 48.0 PHE150.N-SER113.O 48.0

ASN95.N-ASP33.O 46.5

TYR209.OH-ILE259.O 45.5

VAL157.N-LYS100.O 45.0

THR257.OG1-LEU253.O 48.0

VAL157.N-LYS100.O 46.5

TYR209.OH-ILE259.O 46.0 SER254.OG-ILE259.O 46.0

ASN95.N-ASP33.O 51.0 THR175.OG1-ASP176.O 50.5 LEU167.N-VAL171.O 49.0

LEU205.N-THR201.O 47.0

VAL114.N-TYR126.O 47.0

SER147.OG-SER144.O 46.0

TYR37.N-LEU30.O 50.0

SER147.OG-SER144.O 48.5

HIE163.N-SER147.O 48.5

HIE163.N-SER147.O 49.5 PHE150.N-SER113.O 47.5

THR257.OG1-LEU253.O 54.5 GLY149.N-TYR161.O 51.5

HIE163.N-SER147.O 49.0

THR257.OG1-LEU253.O 47.0

GLY149.N-TYR161.O 54.5

VAL114.N-TYR126.O 52.5

VAL36.N-LEU89.O 51.0 SER147.OG-SER144.O 50.0

TRP31.N-CYS16.O 55.5

THR135.OG1-ASN133.OD1 51.0

VAL36.N-LEU89.O 50.0

VAL36.N-LEU89.O 58.0

THR135.OG1-ASN133.OD1 57.5

TYR182.OH-CYS160.O 56.0

THR135.OG1-ASN133.OD1 59.5

SER267.OG-ASP263.O 63.0

rep4

THR201.OG1-GLU240.O 65.0

THR201.OG1-GLU240.O 67.5 TYR182.OH-CYS160.O 63.0

rep2

rep1

rep3

Table 2.18 HBs with more than 30% occupancy rates during the five sets (each set runs for 200 ns) of MDs of the monomer-apo model of [340]

(continued)

2.4 Concluding Remarks 91

ALA234.N-PHE230.O 35.0

ALA173.N-MET165.O 37.0

LEU75.N-VAL68.O 36.0

ASN231.N-LEU227.O 34.5

ASN133.ND2-GLY195.O 32.0

CYS265.N-VAL261.O 33.5

SER10.OG-GLU14.OE2 30.0 ILE281.N-SER284.O 30.0 ALA173.N-MET165.O 30.0 LYS90.N-GLY79.O 30.0

LEU67.N-THR21.O 32.0 PHE159.N-LYS102.O 32.0 PHE112.N-CYS128.O 31.5 TYR54.OH-ASP187.OD2 31.0

PHE112.N-CYS128.O 31.0

CYS160.N-GLY149.O 31.0

LEU272.N-LEU268.O 31.0

ALA173.N-MET165.O 31.0

LEU242.N-ASN231.OD1 30.5

TYR239.N-ALA234.O 30.0

ASN133.ND2-GLY195.O 30.0

GLN19.N-GLN69.O 29.5

ASN133.ND2-GLY195.O 30.0

TRP207.N-ASN203.O 29.5

TYR182.N-GLY174.O 29.0

TYR239.N-ALA234.O 29.0

GLY120.N-ASN28.OD1 27.5

ILE200.N-ASP289.OD2 27.5

SER123.N-ALA116.O 27.5

THR21.N-LEU67.O 30.0

ALA210.N-ALA206.O 29.5

LEU57.N-ASN53.O 28.0

ASN151.N-SER158.O 28.0

TYR118.N-SER121.O 30.0

TYR239.N-ALA234.O 30.0

SER113.N-PHE150.O 30.0

LYS102.N-VAL157.O 30.0

LYS269.N-CYS265.O 29.5

TRP207.N-ASN203.O 29.5

TYR209.N-LEU205.O 29.5

ALA211.N-TRP207.O 29.5

CYS128.N-PHE112.O 30.0 ALA255.N-GLY251.O 29.5

ARG131.NH2-ASP289.OD1 31.0 TYR126.N-VAL114.O 30.5

SER10.OG-GLU14.OE1 30.5

ALA255.N-GLY251.O 30.5

THR175.OG1-ASP176.O 30.5

PHE112.N-CYS128.O 29.0

ALA266.N-LEU262.O 29.0

VAL297.N-PRO293.O 30.5

TYR118.N-SER121.O 28.5

ASN203.ND2-GLY109.O 32.5

GLU14.N-SER10.O 31.0 ARG131.N-THR135.O 31.0

GLN83.N-VAL86.O 30.5

SER123.N-ALA116.O 33.0 GLN83.N-VAL86.O 32.5

TYR118.N-SER121.O 32.0

LEU208.N-VAL204.O 31.5

VAL18.N-GLY29.O 31.0

ASP153.N-CYS156.O 31.5

TYR126.N-VAL114.O 31.5

TYR54.OH-ASP187.OD1 32.0

GLN192.NE2-VAL186.O 33.0

LEU268.N-MET264.O 33.0

ASP176.N-ASN180.O 33.5

GLN127.NE2-GLU290.O 31.0

CYS22.N-THR25.O 32.5

SER10.OG-GLU14.OE2 32.0

ALA210.N-ALA206.O 32.0

CYS22.N-THR25.O 32.0

ASP176.N-ASN180.O 33.0

GLN69.N-GLN19.O 32.5

VAL91.N-ASP34.O 32.5

CYS128.N-PHE112.O 32.5

GLY146.N-HIE163.O 32.5 GLN69.N-GLN19.O 32.5 ASN28.ND2-CYS145.O 32.0

VAL91.N-ASP34.O 34.0 CYS22.N-THR25.O 34.0 PHE8.N-SER113.OG 33.5

ALA234.N-PHE230.O 34.0

GLU240.N-THR199.O 33.5

LEU32.N-VAL35.O 33.0

GLN19.N-GLN69.O 33.5

VAL91.N-ASP34.O 33.0

LEU167.N-VAL171.O 33.0

GLN83.N-VAL86.O 33.5

ALA210.N-ALA206.O 34.0

VAL18.N-GLY29.O 33.5

THR21.N-LEU67.O 34.0

VAL18.N-GLY29.O 35.5

LEU32.N-VAL35.O 33.5

ASN151.N-SER158.O 34.5

LEU89.N-VAL36.O 34.0

ALA255.N-GLY251.O 34.5

ASN95.ND2-TRP31.O 34.0

LEU87.N-CYS38.O 35.0 LEU32.N-VAL35.O 34.5

SER113.OG-GLN127.OE1 35.0

ASN203.ND2-ASP289.O 35.0

LYS269.N-CYS265.O 35.5

ASP153.N-CYS156.O 35.0

ASN95.ND2-TRP31.O 34.5

THR175.OG1-ASP176.O 34.0

TRP207.N-ASN203.O 35.0

THR111.OG1-ASP295.OD1 35.5

VAL20.N-LEU27.O 35.5

SER144.OG-LEU141.O 36.0

TYR239.N-ALA234.O 34.5

ALA173.N-MET165.O 35.5

ALA234.N-PHE230.O 36.0

LEU268.N-MET264.O 36.0

SER123.N-ALA116.O 36.0

THR21.N-LEU67.O 36.0

LEU115.N-VAL148.O 36.0

TYR182.N-GLY174.O 36.0 LEU87.N-CYS38.O 35.5

GLU14.N-SER10.O 38.0 TYR182.N-GLY174.O 37.5 ASN203.ND2-ASP289.O 37.5

LYS269.N-CYS265.O 36.0

PHE8.N-SER113.OG 36.0

CYS265.N-VAL261.O 36.0

TYR37.N-LEU30.O 36.0

ALA70.N-VAL73.O 38.5

ILE200.N-ASP289.OD2 36.0

GLN19.N-GLN69.O 38.5

ARG40.NE-ASP187.OD1 36.5

LEU87.N-CYS38.O 36.5

ASN28.ND2-CYS145.O 37.0

rep4

rep3

ALA70.N-VAL73.O 36.5

LYS88.N-SER81.O 36.5

LEU167.N-VAL171.O 37.0

LEU87.N-CYS38.O 36.0

rep2

rep1

Table 2.18 (continued)

MET235.N-ASN231.O 29.5

CYS265.N-VAL261.O 29.5

ASN28.ND2-CYS145.O 29.5

SER113.N-PHE150.O 30.0

GLN83.N-VAL86.O 30.5

THR21.N-LEU67.O 30.5

ASN95.ND2-TRP31.O 30.5

LEU268.N-MET264.O 30.5

ASN203.ND2-ASP289.O 30.5

THR135.OG1-ASN133.OD1 31.0

HID164.ND1-ASP187.O 31.5

TYR209.N-LEU205.O 31.5

TYR154.OH-PRO9.O 32.0

THR292.OG1-ASP295.OD1 32.0

ALA70.N-VAL73.O 32.0

CYS160.N-GLY149.O 32.0

TYR239.N-ALA234.O 32.5

SER147.OG-SER144.O 33.0

LEU272.N-LEU268.O 33.0

PHE112.N-CYS128.O 33.5

ARG131.N-THR135.O 33.5

ALA116.N-GLY124.O 33.5

ALA173.N-MET165.O 34.5

ASN151.N-SER158.O 34.5

TYR182.N-GLY174.O 35.0

GLU14.N-SER10.O 35.0

ALA234.N-PHE230.O 35.5

PHE150.N-SER113.O 35.5

ASN231.N-LEU227.O 36.0

ALA210.N-ALA206.O 36.0

GLY120.N-ASN28.OD1 36.0

VAL157.N-LYS100.O 36.0

THR111.OG1-ASP295.OD2 37.0

LEU87.N-CYS38.O 37.5

rep5

92 2 3C-Like Protease (3CLpro)

rep3

rep4

LEU32.N-VAL35.O 38.0

LEU205.N-THR201.O 37.5

VAL20.N-LEU27.O 37.0

GLN189.N-MET49.O 37.0

GLY109.N-MET130.O 37.0

LEU242.N-ASN231.OD1 38.5

ILE200.N-ASP289.OD1 38.0

SER113.OG-GLN127.OE1 37.5

LEU75.N-VAL68.O 37.5

ALA234.N-PHE230.O 34.0 LYS269.N-CYS265.O 33.5

LEU268.N-MET264.O 34.0

TYR37.N-LEU30.O 37.0 THR175.OG1-ASP176.O 37.0

TYR54.OH-ASP187.OD1 35.0

SER144.OG-LEU141.O 38.5

THR292.OG1-ASP295.OD1 36.5

LEU87.N-CYS38.O 36.0

ASN95.N-ASP33.O 38.5

VAL91.N-ASP34.O 36.5

LEU89.N-VAL36.O 39.0

LYS102.N-VAL157.O 36.5

SER113.OG-GLN127.OE1 38.0

ASN231.N-LEU227.O 39.5

ASN95.ND2-TRP31.O 39.0

ASN203.ND2-ASP289.O 38.5

LEU27.N-VAL20.O 39.5

ALA70.N-VAL73.O 39.0

CYS128.N-PHE112.O 39.0

CYS160.N-GLY149.O 36.5

SER147.OG-SER144.O 37.0

LYS88.N-SER81.O 40.0

GLY146.N-HIE163.O 39.0

LEU32.N-VAL35.O 40.5

TYR54.OH-ASP187.OD2 40.0 VAL18.N-GLY29.O 39.5

LEU89.N-VAL36.O 37.5 VAL157.N-LYS100.O 37.5

VAL20.N-LEU27.O 40.5 ALA234.N-PHE230.O 40.0

LEU89.N-VAL36.O 40.0

LEU75.N-VAL68.O 40.0

LEU115.N-VAL148.O 41.5

GLY146.N-HIE163.O 41.0

ASP176.N-ASN180.O 38.5 GLY149.N-TYR161.O 38.0

ALA173.N-MET165.O 41.0

LEU30.N-TYR37.O 40.5

GLU14.N-SER10.O 40.0

ILE78.N-LYS90.O 42.0

GLN19.N-GLN69.O 42.0

LEU115.N-VAL148.O 40.5

LEU205.N-THR201.O 42.5

ILE136.N-HIE172.O 38.5

SER254.OG-ILE259.O 40.5

THR25.OG1-CYS44.O 43.0

PHE150.N-SER113.O 39.0

THR257.OG1-LEU253.O 42.0

LEU89.N-VAL36.O 41.0

ASN95.ND2-TRP31.O 41.0

LEU87.N-CYS38.O 43.5

LYS88.N-SER81.O 39.0

CYS128.N-PHE112.O 42.0

ILE78.N-LYS90.O 40.5

ASN95.N-ASP33.O 41.5

SER254.OG-ILE259.O 43.5

LEU205.N-THR201.O 39.0

ASN203.ND2-ASP289.O 43.0

PHE112.N-CYS128.O 38.5

LYS88.N-SER81.O 41.5

TYR37.N-LEU30.O 43.5

TYR182.N-GLY174.O 40.5

LEU27.N-VAL20.O 43.0

LEU75.N-VAL68.O 41.5

LEU87.N-CYS38.O 43.0

ASN95.N-ASP33.O 43.5

SER254.OG-ILE259.O 42.0

GLY146.N-HIE163.O 43.5

LEU75.N-VAL68.O 38.5

ASN28.ND2-CYS145.O 44.0

ASN95.N-ASP33.O 42.0

LEU115.N-VAL148.O 43.5

VAL157.N-LYS100.O 46.0

LEU30.N-TYR37.O 43.5

LEU27.N-VAL20.O 44.5

VAL114.N-TYR126.O 47.0

LEU205.N-THR201.O 41.5

THR175.OG1-ASP176.O 44.5

THR175.OG1-ASP176.O 45.5

SER144.OG-LEU141.O 44.5

ASN28.ND2-GLY146.O 42.5

GLU14.N-SER10.O 44.0

HIE163.N-SER147.O 45.0

VAL114.N-TYR126.O 46.5

TYR37.N-LEU30.O 45.0

VAL114.N-TYR126.O 46.0

LEU167.N-VAL171.O 46.0

LEU115.N-VAL148.O 45.0

LEU27.N-VAL20.O 46.5

VAL157.N-LYS100.O 47.0

HIE163.N-SER147.O 45.5

LEU167.N-VAL171.O 46.5

LYS88.N-SER81.O 47.0

CYS128.N-PHE112.O 45.5

ILE78.N-LYS90.O 43.0 VAL20.N-LEU27.O 43.0

ILE78.N-LYS90.O 45.5 ARG131.N-THR135.O 45.0

TYR209.OH-ILE259.O 47.5

TYR209.OH-ILE259.O 47.5

LEU30.N-TYR37.O 45.0

THR135.OG1-ASN133.OD1 47.5

LEU30.N-TYR37.O 48.0 TYR209.OH-ILE259.O 48.0

PHE150.N-SER113.O 48.0 THR175.OG1-ASP176.O 46.0

THR257.OG1-LEU253.O 49.5

GLY149.N-TYR161.O 52.5

SER147.OG-SER144.O 48.5

THR135.OG1-ASN133.OD1 48.5 ASP176.N-ASN180.O 50.0

TRP31.N-CYS16.O 50.5

SER267.OG-ASP263.O 54.0

THR257.OG1-LEU253.O 49.5

GLY149.N-TYR161.O 49.0

THR257.OG1-LEU253.O 48.5 TYR37.N-LEU30.O 46.5

HIE163.N-SER147.O 52.0 VAL114.N-TYR126.O 51.5

TRP31.N-CYS16.O 57.0 VAL36.N-LEU89.O 56.0

GLY149.N-TYR161.O 50.0

VAL157.N-LYS100.O 49.5

VAL36.N-LEU89.O 53.5

VAL20.N-LEU27.O 52.5

SER113.OG-GLN127.OE1 50.5

SER267.OG-ASP263.O 54.0 TYR209.OH-ILE259.O 53.5

TYR182.OH-CYS160.O 58.0 SER147.OG-SER144.O 58.0

VAL36.N-LEU89.O 56.0

SER267.OG-ASP263.O 55.0

SER147.OG-SER144.O 55.0

TRP31.N-CYS16.O 54.5

THR201.OG1-GLU240.O 60.0 VAL36.N-LEU89.O 55.5

HIE163.N-SER147.O 59.0 THR135.OG1-ASN133.OD1 59.0

TRP31.N-CYS16.O 60.0

TYR182.OH-CYS160.O 60.0

TYR182.OH-CYS160.O 62.5

SER267.OG-ASP263.O 60.5

THR201.OG1-GLU240.O 61.5

THR201.OG1-GLU240.O 61.0

rep2

THR201.OG1-GLU240.O 62.5

rep1

TYR182.OH-CYS160.O 63.0

VAL18.N-GLY29.O 39.0

GLN83.N-VAL86.O 39.0

GLY146.N-HIE163.O 39.0

ALA234.N-PHE230.O 39.0

GLU14.N-SER10.O 39.5

ASN95.N-ASP33.O 39.5

LEU205.N-THR201.O 39.5

ASN95.ND2-TRP31.O 40.0

LEU89.N-VAL36.O 40.5

PHE150.N-SER113.O 40.5

HIE163.N-SER147.O 40.5

THR175.N-MET162.O 41.0

SER144.OG-LEU141.O 42.0

SER254.OG-ILE259.O 42.0

LEU75.N-VAL68.O 43.0

VAL157.N-LYS100.O 43.0

LYS88.N-SER81.O 43.5

ILE78.N-LYS90.O 43.5

LEU27.N-VAL20.O 44.0

TYR37.N-LEU30.O 44.0

(continued)

SER113.OG-GLN127.OE1 46.0

CYS128.N-PHE112.O 46.0

LEU167.N-VAL171.O 46.5

VAL114.N-TYR126.O 46.5

LEU30.N-TYR37.O 47.0

LEU115.N-VAL148.O 47.0

GLY149.N-TYR161.O 47.0

TYR209.OH-ILE259.O 48.0

THR175.OG1-ASP176.O 48.5

SER267.OG-ASP263.O 48.5

ASP176.N-ASN180.O 48.5

VAL36.N-LEU89.O 51.5

SER147.OG-SER144.O 52.0

THR257.OG1-LEU253.O 52.5

LEU87.N-CYS38.O 53.0

TYR182.OH-CYS160.O 55.0

THR135.OG1-ASN133.OD1 57.0

TRP31.N-CYS16.O 59.0

THR201.OG1-GLU240.O 65.0

rep5

Table 2.19 HBs with more than three occupancy rates during the five sets (each set runs for 200 ns) of MDs of monomer-N3 model of [340]

2.4 Concluding Remarks 93

SER254.OG-ILE259.O 36.0

LEU167.N-VAL171.O 30.5 LEU67.N-THR21.O 30.5

LEU32.N-VAL35.O 33.0 TYR118.N-SER121.O 33.0

TYR182.N-GLY174.O 35.0

LEU67.N-THR21.O 35.0

THR111.OG1-ASP295.OD2 35.0

LYS269.N-CYS265.O 34.5

TYR182.N-GLY174.O 36.0

ASN95.ND2-TRP31.O 35.0

ASN28.ND2-CYS145.O 34.0

LYS90.N-GLY79.O 27.0

ALA255.N-GLY251.O 31.0

ASP176.N-ASN180.O 32.0

LYS90.N-GLY79.O 31.5

GLU240.N-THR199.O 31.5

GLY109.N-MET130.O 31.5

GLN189.N-MET49.O 30.0 THR111.OG1-ASP295.OD2 29.5

ALA173.N-MET165.O 30.5

LEU208.N-VAL204.O 30.0

ILE136.N-HIE172.O 30.0

TRP207.N-ASN203.O 29.0

GLN299.N-ASP295.O 28.5

LEU242.N-ASN231.OD1 28.0

SER10.OG-GLU14.OE2 30.0

VAL91.N-ASP34.O 30.0

ASN214.N-ALA210.O 30.0

ALA255.N-GLY251.O 29.5

THR21.N-LEU67.O 29.5

ALA210.N-ALA206.O 29.5

LYS102.N-VAL157.O 31.0

LEU67.N-THR21.O 29.5

MET235.N-ASN231.O 30.0

THR25.OG1-CYS44.O 30.0

GLY109.N-MET130.O 30.5

GLU240.N-THR199.O 30.5

TYR126.N-VAL114.O 31.0

THR25.OG1-CYS44.O 31.0

MET235.N-ASN231.O 30.5

LEU272.N-LEU268.O 31.0

LYS269.N-CYS265.O 32.0

LEU268.N-MET264.O 32.0

LEU67.N-THR21.O 30.5

ASN231.N-LEU227.O 31.5

ASN133.ND2-GLY195.O 32.0

ALA70.N-VAL73.O 31.5

LEU268.N-MET264.O 31.5

TYR126.N-VAL114.O 28.0 GLY29.N-VAL18.O 27.5

ASN28.ND2-CYS145.O 31.5 GLN192.NE2-VAL186.O 31.5

ALA70.N-VAL73.O 32.5

PHE8.N-SER113.OG 31.5

CYS22.N-THR25.O 31.0

VAL104.N-PHE159.O 28.0

ASN214.N-ALA210.O 32.0

GLN83.N-VAL86.O 33.0

ARG131.NH2-ASP289.OD1 32.0

CYS265.N-VAL261.O 31.0

THR21.N-LEU67.O 29.5 LEU272.N-LEU268.O 29.5

ASN151.N-SER158.O 25.5

GLN192.NE2-VAL186.O 26.0

CYS128.N-PHE112.O 26.0

ARG131.N-THR135.O 26.0

THR111.OG1-THR292.OG1 26.5

GLN299.N-ASP295.O 26.5

ASN231.N-LEU227.O 26.5

SER123.N-ALA116.O 26.5

THR199.N-ASN238.O 27.0

ASN203.ND2-ASP289.O 28.5

GLU14.N-SER10.O 29.0

LEU32.N-VAL35.O 29.5

PHE8.N-SER113.OG 32.0 GLN19.N-GLN69.O 32.0 LYS90.N-GLY79.O 32.0

TYR118.N-SER121.O 34.0

THR21.N-LEU67.O 34.0

SER113.N-PHE150.O 33.0

GLY146.N-HIE163.O 30.0

TYR239.N-ALA234.O 33.0

TYR182.N-GLY174.O 32.5

ARG40.NH2-ASP187.OD1 32.5

ARG40.NE-ASP187.OD2 33.0

LEU57.N-ASN53.O 29.5

GLN83.N-VAL86.O 32.5

VAL91.N-ASP34.O 34.5

ALA234.N-PHE230.O 34.0

ASN203.ND2-ASP289.O 33.5

ARG40.NH2-ASP187.OD2 30.0

GLY120.N-ASN28.OD1 33.0

THR21.N-LEU67.O 33.0

VAL18.N-GLY29.O 34.5

SER123.N-ALA116.O 34.5

GLU14.N-SER10.O 33.5

THR175.N-MET162.O 31.0

THR45.OG1-ASP48.OD1 31.0

ALA255.N-GLY251.O 31.0

ALA173.N-MET165.O 33.5

PHE112.N-CYS128.O 33.5

ASN231.N-LEU227.O 34.0

VAL91.N-ASP34.O 34.0

GLN189.N-MET49.O 32.0 GLN83.N-VAL86.O 32.0

ASN95.ND2-TRP31.O 32.0

LYS269.N-CYS265.O 36.0

HIE172.N-ILE136.O 34.5

LEU87.N-CYS38.O 35.5

SER144.OG-LEU141.O 35.5

ARG131.NH2-ASP289.OD2 35.5

GLN19.N-GLN69.O 35.0

ARG131.N-THR135.O 36.5 ALA210.N-ALA206.O 35.5

CYS300.N-VAL296.O 33.0 CYS265.N-VAL261.O 32.5

LEU268.N-MET264.O 36.0

PHE150.N-SER113.O 36.0

ASP176.N-ASN180.O 36.0

LEU272.N-LEU268.O 36.0

ASN203.ND2-GLY109.O 36.0

ALA234.N-PHE230.O 37.0

VAL18.N-GLY29.O 36.5

rep4 ARG40.NE-ASP187.OD1 33.5

rep3 LEU167.N-VAL171.O 36.0

rep2

ARG131.N-THR135.O 36.5

rep1

PHE150.N-SER113.O 37.0

Table 2.19 (continued) rep5

LYS90.N-GLY79.O 30.0

GLY120.N-ASN28.OD1 30.0

ALA210.N-ALA206.O 30.5

TYR209.N-LEU205.O 30.5

MET235.N-ASN231.O 32.0

ALA255.N-GLY251.O 32.0

PHE8.N-SER113.OG 32.5

ASN28.ND2-CYS145.O 32.5

ASN221.N-SER267.OG 33.0

GLN19.N-GLN69.O 33.0

THR25.OG1-CYS44.O 33.0

ASN151.N-SER158.O 33.0

CYS22.N-THR25.O 33.5

LEU32.N-VAL35.O 33.5

GLU240.N-THR199.O 34.0

LEU242.N-ASN231.OD1 34.5

ASN203.ND2-ASP289.O 34.5

SER113.N-PHE150.O 35.0

HIE172.N-ILE136.O 35.0

THR111.OG1-ASP295.OD1 35.0

TRP207.N-ASN203.O 35.0

ARG40.N-CYS85.O 35.5

TYR118.N-SER121.O 35.5

TYR126.N-VAL114.O 35.5

LYS269.N-CYS265.O 36.0

VAL20.N-LEU27.O 36.5

ALA70.N-VAL73.O 37.0

ALA173.N-MET165.O 37.5

VAL91.N-ASP34.O 38.5

ARG131.N-THR135.O 38.5

ASN231.N-LEU227.O 38.5

GLY109.N-MET130.O 38.5

94 2 3C-Like Protease (3CLpro)

SER147.OG-SER144.O 48.5

LEU421.N-VAL454.O 45.5 LEU75.N-VAL68.O 45.5

SER560.OG-ILE565.O 47.5 GLY146.N-HIE163.O 47.5

ASP153.N-CYS156.O 46.5

PHE150.N-SER113.O 46.0

LEU338.N-VAL341.O 46.0

THR257.OG1-LEU253.O 45.5

ASN401.ND2-TRP337.O 46.0

SER560.OG-ILE565.O 46.0

LEU115.N-VAL148.O 46.0

PHE456.N-SER419.O 46.0

GLY455.N-TYR467.O 47.0

VAL114.N-TYR126.O 47.0

GLY452.N-HIE469.O 46.5

VAL326.N-LEU333.O 47.5

THR563.OG1-LEU559.O 47.5

VAL157.N-LYS100.O 47.5

LEU473.N-VAL477.O 44.0 LEU167.N-VAL171.O 44.0

TYR37.N-LEU30.O 47.0

TYR515.OH-ILE565.O 44.5 VAL463.N-LYS406.O 44.5

ARG4.NH2-GLU596.OE2 47.0 LEU115.N-VAL148.O 47.0 VAL114.N-TYR126.O 46.5

PHE150.N-SER113.O 45.0

THR481.OG1-ASP482.O 47.0

VAL157.N-LYS100.O 46.5 VAL326.N-LEU333.O 45.5

ILE78.N-LYS90.O 48.0 TYR209.OH-ILE259.O 47.5

VAL420.N-TYR432.O 47.5

LEU30.N-TYR37.O 47.5

THR257.OG1-LEU253.O 48.5

GLY146.N-HIE163.O 46.5

THR481.OG1-ASP482.O 48.0

SER560.OG-ILE565.O 46.5

LEU167.N-VAL171.O 48.5 HIE469.N-SER453.O 48.0

SER147.OG-SER144.O 48.5

TYR343.N-LEU336.O 48.5

THR175.OG1-ASP176.O 49.0

VAL420.N-TYR432.O 47.0 TYR209.OH-ILE259.O 46.5

LEU333.N-VAL326.O 49.0 THR441.OG1-ASN439.OD1 48.5

LEU381.N-VAL374.O 49.0

LYS88.N-SER81.O 49.5

LEU393.N-CYS344.O 48.5

VAL420.N-TYR432.O 49.5

GLY452.N-HIE469.O 47.5 SER254.OG-ILE259.O 47.0

PHE112.N-CYS128.O 49.0 LYS394.N-SER387.O 49.0

GLY149.N-TYR161.O 49.5

TRP31.N-CYS16.O 49.5

THR441.OG1-ASN439.OD1 51.0

LEU421.N-VAL454.O 49.5

TYR343.N-LEU336.O 49.0

LEU395.N-VAL342.O 48.0 ILE78.N-LYS90.O 48.0

GLY149.N-TYR161.O 51.0 VAL420.N-TYR432.O 49.5

LEU473.N-VAL477.O 51.0

TYR209.OH-ILE259.O 50.0

VAL342.N-LEU395.O 51.5

GLN299.NE2-ARG4.O 51.0

TYR37.N-LEU30.O 48.5 HIE469.N-SER453.O 48.5

LEU30.N-TYR37.O 52.0 THR257.OG1-LEU253.O 51.0

ILE78.N-LYS90.O 53.0

THR563.OG1-LEU559.O 52.0

GLY146.N-HIE163.O 51.5

TYR182.OH-CYS160.O 53.0

VAL114.N-TYR126.O 52.5

HIE163.N-SER147.O 52.0

VAL114.N-TYR126.O 50.0 THR257.OG1-LEU253.O 48.5

PHE150.N-SER113.O 52.5 ARG437.N-THR441.O 52.5

GLY455.N-TYR467.O 52.0 THR563.OG1-LEU559.O 51.0

HIE163.N-SER147.O 52.0

PHE456.N-SER419.O 53.5

THR175.OG1-ASP176.O 53.5

SER147.OG-SER144.O 53.5

GLY455.N-TYR467.O 53.0

VAL342.N-LEU395.O 55.5

SER453.OG-SER450.O 53.5

TYR515.OH-ILE565.O 54.0

HIE469.N-SER453.O 53.5

SER453.OG-SER450.O 53.5

SER453.OG-SER450.O 53.0 THR135.OG1-ASN133.OD1 53.0

TRP31.N-CYS16.O 55.0 VAL342.N-LEU395.O 55.0

THR441.OG1-ASN439.OD1 56.5

TRP337.N-CYS322.O 56.5

VAL36.N-LEU89.O 56.0

GLY149.N-TYR161.O 55.0 THR563.OG1-LEU559.O 53.5

TRP31.N-CYS16.O 53.5 VAL36.N-LEU89.O 53.5

ARG131.N-THR135.O 56.0 SER267.OG-ASP263.O 55.5

VAL36.N-LEU89.O 58.5

HIE469.N-SER453.O 57.0

THR507.OG1-GLU546.O 57.5

THR135.OG1-ASN133.OD1 56.5

THR507.OG1-GLU546.O 57.0 TRP337.N-CYS322.O 54.5 SER573.OG-ASP569.O 53.5

TYR182.OH-CYS160.O 60.0 SER573.OG-ASP569.O 60.0 VAL36.N-LEU89.O 56.5

TYR488.OH-CYS466.O 59.0

SER267.OG-ASP263.O 59.0

TYR182.OH-CYS160.O 58.5

TRP337.N-CYS322.O 58.0

SER254.OG-ILE259.O 58.0

TYR182.OH-CYS160.O 60.0 VAL342.N-LEU395.O 57.5

TRP337.N-CYS322.O 61.0 THR201.OG1-GLU240.O 60.5

HIE163.N-SER147.O 61.0

THR135.OG1-ASN133.OD1 60.0

SER445.OG-GLN299.OE1 60.0

TRP31.N-CYS16.O 60.0

SER573.OG-ASP569.O 58.0

SER267.OG-ASP263.O 62.5 THR441.OG1-ASN439.OD1 60.5

THR135.OG1-ASN133.OD1 62.5 THR507.OG1-GLU546.O 62.0

SER573.OG-ASP569.O 63.0

THR201.OG1-GLU240.O 62.0

TYR488.OH-CYS466.O 62.5

TYR488.OH-CYS466.O 63.5 THR201.OG1-GLU240.O 63.5

SER10.OG-GLU14.OE1 77.0 TYR488.OH-CYS466.O 63.5

rep4 SER316.OG-GLU320.OE1 75.0

rep3 SER316.OG-GLU320.OE1 79.5

SER267.OG-ASP263.O 62.0

SER10.OG-GLU14.OE1 78.0

THR507.OG1-GLU546.O 71.0

SER316.OG-GLU320.OE1 79.0

THR201.OG1-GLU240.O 69.5

rep2

SER316.OG-GLU320.OE1 80.0

rep1

SER10.OG-GLU14.OE1 80.5

VAL463.N-LYS406.O 46.0

LEU393.N-CYS344.O 46.0

LEU473.N-VAL477.O 46.5

ILE384.N-LYS396.O 46.5

ASN401.N-ASP339.O 47.5

PHE314.N-SER419.OG 48.0

GLY455.N-TYR467.O 48.0

THR257.OG1-LEU253.O 48.5

PHE150.N-SER113.O 49.0

SER453.OG-SER450.O 49.0

GLY452.N-HIE469.O 49.0

ILE78.N-LYS90.O 49.5

LEU167.N-VAL171.O 49.5

LEU115.N-VAL148.O 49.5

HIE469.N-SER453.O 49.5

TYR515.OH-ILE565.O 50.5

SER254.OG-ILE259.O 51.0

TRP31.N-CYS16.O 51.5

SER267.OG-ASP263.O 52.5

VAL114.N-TYR126.O 53.0

HIE163.N-SER147.O 53.0

PHE112.N-CYS128.O 53.0

VAL342.N-LEU395.O 53.5

VAL420.N-TYR432.O 54.0

(continued)

THR135.OG1-ASN133.OD1 54.0

THR507.OG1-GLU546.O 54.5

SER573.OG-ASP569.O 55.0

VAL36.N-LEU89.O 56.0

SER147.OG-SER144.O 56.5

TYR182.OH-CYS160.O 57.0

TRP337.N-CYS322.O 57.5

THR175.OG1-ASP176.O 57.5

THR563.OG1-LEU559.O 57.5

SER445.OG-GLN299.OE1 59.5

THR441.OG1-ASN439.OD1 60.5

THR201.OG1-GLU240.O 61.0

TYR488.OH-CYS466.O 62.0

SER316.OG-GLU320.OE1 80.0

rep5

Table 2.20 HBs with more than 40% occupancy rates during the five sets (each set runs for 200 ns) of MDs of the dimer-apo model of [340]

2.4 Concluding Remarks 95

THR175.OG1-ASP176.O 45.5

LEU167.N-VAL171.O 44.0

ILE78.N-LYS90.O 44.5

SER445.OG-GLN299.OE1 39.5

LYS5.NZ-GLU290.OE2 39.5

SER450.OG-LEU447.O 39.0

ILE506.N-ASP595.OD2 39.0

LEU27.N-VAL20.O 39.0

ASN203.ND2-GLY109.O 38.5

PHE112.N-CYS128.O 40.0

TYR488.N-GLY480.O 39.5

VAL397.N-ASP340.O 39.5

ASN95.ND2-TRP31.O 40.0

LYS394.N-SER387.O 40.0

ARG437.N-THR441.O 40.0

ASN401.ND2-TRP337.O 40.5

GLY146.N-HIE163.O 40.0

ASN231.N-LEU227.O 39.5

SER254.OG-ILE259.O 40.5

PHE314.N-SER419.OG 40.5

ASP176.N-ASN180.O 39.5

TYR515.OH-ILE565.O 40.5

LEU511.N-THR507.O 41.5

LEU381.N-VAL374.O 41.5

LEU473.N-VAL477.O 42.5

ASN203.ND2-ASP289.O 42.0

ASP459.N-CYS462.O 41.5

LEU115.N-VAL148.O 41.5

LEU336.N-TYR343.O 42.5

LEU336.N-TYR343.O 40.5

PHE314.N-SER419.OG 41.5

ASN95.ND2-TRP31.O 43.0

LEU89.N-VAL36.O 41.5

TYR360.OH-ASP493.OD2 40.0

ASN334.ND2-CYS451.O 42.0

SER429.N-ALA422.O 41.5

TYR209.OH-ILE259.O 43.0

LYS575.N-CYS571.O 41.0

ASN401.N-ASP339.O 42.0

VAL20.N-LEU27.O 43.0

ARG437.N-THR441.O 41.0

VAL463.N-LYS406.O 42.5

ASN95.N-ASP33.O 43.0

PHE112.N-CYS128.O 42.0

ALA479.N-MET471.O 42.5 LEU336.N-TYR343.O 42.5

VAL157.N-LYS100.O 42.5

ASN509.ND2-ASP595.O 41.5

HIE163.N-SER147.O 40.0

ASN95.N-ASP33.O 42.5

SER560.OG-ILE565.O 42.5

ILE384.N-LYS396.O 43.0

HIE172.N-ILE136.O 40.5

LEU393.N-CYS344.O 40.5

LEU87.N-CYS38.O 40.5

VAL20.N-LEU27.O 40.5

ALA210.N-ALA206.O 40.5

ALA540.N-PHE536.O 41.0

ASN401.N-ASP339.O 41.0

PHE8.N-SER113.OG 41.5

LEU421.N-VAL454.O 41.5

LEU32.N-VAL35.O 42.0

ILE136.N-HIE172.O 42.0

PHE418.N-CYS434.O 42.0

ALA70.N-VAL73.O 42.5

CYS434.N-PHE418.O 43.0

VAL157.N-LYS100.O 43.0

ASN509.ND2-ASP595.O 43.0

LEU89.N-VAL36.O 44.0

VAL326.N-LEU333.O 44.5

LEU115.N-VAL148.O 42.5

ASN203.ND2-ASP289.O 37.5

ASN509.ND2-ASP595.O 37.5

CYS328.N-THR331.O 37.5

LYS575.N-CYS571.O 38.0

VAL397.N-ASP340.O 38.5

LEU27.N-VAL20.O 38.5

LEU32.N-VAL35.O 38.5

PHE8.N-SER113.OG 38.5

LYS394.N-SER387.O 39.0

SER10.OG-GLU14.OE2 39.5

ASN401.N-ASP339.O 39.5

PHE314.N-SER419.OG 40.0

GLN299.NE2-ARG4.O 40.0

ARG437.N-THR441.O 40.0

GLY149.N-TYR161.O 40.5

THR481.OG1-ASP482.O 40.5

ALA70.N-VAL73.O 40.5

LEU381.N-VAL374.O 40.5

ASN95.N-ASP33.O 41.5

ILE384.N-LYS396.O 41.5

LEU336.N-TYR343.O 42.0

LEU167.N-VAL171.O 43.5

LEU511.N-THR507.O 45.0 VAL463.N-LYS406.O 45.0

ASN95.N-ASP33.O 43.5

LEU421.N-VAL454.O 42.5

VAL20.N-LEU27.O 43.0

PHE456.N-SER419.O 43.0

VAL91.N-ASP34.O 43.5

LEU30.N-TYR37.O 43.5

LEU333.N-VAL326.O 43.5

LYS88.N-SER81.O 44.0

ASP153.N-CYS156.O 43.5

SER147.OG-SER144.O 45.0

TYR515.OH-ILE565.O 46.0

GLY455.N-TYR467.O 46.0

LEU89.N-VAL36.O 44.0

rep4

LYS88.N-SER81.O 43.5

ILE384.N-LYS396.O 43.5

PHE8.N-SER113.OG 44.5

LEU205.N-THR201.O 44.5

LEU75.N-VAL68.O 43.5

ILE200.N-ASP289.OD2 45.0

ASN401.N-ASP339.O 44.5

GLY452.N-HIE469.O 44.0

PHE456.N-SER419.O 46.0

VAL20.N-LEU27.O 45.0

SER453.OG-SER450.O 45.0

PHE150.N-SER113.O 44.0

TYR343.N-LEU336.O 46.0 GLN605.NE2-ARG310.O 46.0

rep3

rep2

LEU87.N-CYS38.O 45.5

rep1

LEU75.N-VAL68.O 45.5

Table 2.20 (continued)

LEU395.N-VAL342.O 38.0

LEU268.N-MET264.O 38.5

VAL326.N-LEU333.O 38.5

THR327.N-LEU373.O 38.5

ASP176.N-ASN180.O 39.0

SER429.N-ALA422.O 39.0

VAL91.N-ASP34.O 39.0

LEU87.N-CYS38.O 39.5

GLN299.NE2-ARG4.O 40.5

CYS328.N-THR331.O 40.5

TYR182.N-GLY174.O 40.5

ASN95.N-ASP33.O 41.0

CYS128.N-PHE112.O 41.0

LEU30.N-TYR37.O 41.5

LYS394.N-SER387.O 41.5

TYR209.OH-ILE259.O 41.5

PHE456.N-SER419.O 42.0

LEU75.N-VAL68.O 43.0

VAL157.N-LYS100.O 43.0

LYS88.N-SER81.O 43.5

GLY146.N-HIE163.O 43.5

ARG437.N-THR441.O 44.0

GLY149.N-TYR161.O 44.0

ASN537.N-LEU533.O 44.0

SER10.OG-GLU14.OE1 44.5

ASN203.ND2-GLY109.O 44.5

LEU421.N-VAL454.O 44.5

TYR343.N-LEU336.O 44.5

LEU27.N-VAL20.O 45.5

VAL20.N-LEU27.O 45.5

TYR37.N-LEU30.O 45.5

rep5

96 2 3C-Like Protease (3CLpro)

SER267.OG-ASP263.O 65.5 TYR488.OH-CYS466.O 65.0

TYR488.OH-CYS466.O 63.5 TYR182.OH-CYS160.O 62.5

THR507.OG1-GLU546.O 66.5

TYR488.OH-CYS466.O 64.5

TYR488.OH-CYS466.O 69.5

THR507.OG1-GLU546.O 63.0

LEU27.N-VAL20.O 49.5

GLY149.N-TYR161.O 49.5

VAL420.N-TYR432.O 51.0

SER267.OG-ASP263.O 50.5

PHE314.N-SER419.OG 49.5 LEU473.N-VAL477.O 49.0

LEU473.N-VAL477.O 49.0 VAL114.N-TYR126.O 48.5

ARG437.N-THR441.O 46.5

VAL420.N-TYR432.O 46.5

ILE506.N-ASP595.OD2 47.5

ARG310.NH2-GLU290.OE2 47.5

GLY149.N-TYR161.O 47.5

PHE456.N-SER419.O 45.5

TYR209.OH-ILE259.O 45.0

GLY455.N-TYR467.O 45.0

TYR209.OH-ILE259.O 44.5

SER453.OG-SER450.O 44.0

LEU75.N-VAL68.O 44.0

PHE8.N-SER113.OG 46.5 VAL463.N-LYS406.O 46.5 TYR343.N-LEU336.O 46.5

THR481.OG1-ASP482.O 47.0 SER254.OG-ILE259.O 46.5 TYR37.N-LEU30.O 46.0

HIE469.N-SER453.O 47.5 LEU381.N-VAL374.O 47.0

GLY452.N-HIE469.O 47.0 LEU333.N-VAL326.O 47.0 HIE469.N-SER453.O 47.0

LYS88.N-SER81.O 46.0

TYR515.OH-ILE565.O 46.0

SER254.OG-ILE259.O 45.5

ARG310.NH1-GLU290.OE1 46.5

ASN401.N-ASP339.O 45.0

PHE150.N-SER113.O 49.0 TYR209.OH-ILE259.O 48.5

ASN509.ND2-ASP595.O 47.0 ARG131.N-THR135.O 47.0

GLY452.N-HIE469.O 44.5

TYR343.N-LEU336.O 46.5

VAL114.N-TYR126.O 46.0

LYS88.N-SER81.O 47.5

TYR515.OH-ILE565.O 46.5

THR481.OG1-ASP482.O 50.5 GLY452.N-HIE469.O 50.0

THR563.OG1-LEU559.O 50.5 ILE384.N-LYS396.O 49.0

ILE78.N-LYS90.O 47.5

GLY146.N-HIE163.O 47.0

GLY149.N-TYR161.O 48.0

ASN203.ND2-ASP289.O 48.0

TYR515.OH-ILE565.O 51.0 LEU115.N-VAL148.O 51.0

TRP31.N-CYS16.O 51.0 SER453.OG-SER450.O 51.0

HIE478.N-ILE442.O 48.0

LYS394.N-SER387.O 47.5

THR563.OG1-LEU559.O 48.5

PHE456.N-SER419.O 48.5

VAL36.N-LEU89.O 52.5 SER573.OG-ASP569.O 51.5 SER147.OG-SER144.O 51.5

SER573.OG-ASP569.O 52.5 TRP337.N-CYS322.O 51.5 THR441.OG1-ASN439.OD1 51.0

ILE384.N-LYS396.O 48.5

HIE469.N-SER453.O 48.5

LEU421.N-VAL454.O 48.0

THR257.OG1-LEU253.O 50.0

VAL114.N-TYR126.O 54.5 TRP31.N-CYS16.O 54.0

PHE456.N-SER419.O 52.5 SER267.OG-ASP263.O 52.5

THR441.OG1-ASN439.OD1 48.5

LEU167.N-VAL171.O 50.0

THR563.OG1-LEU559.O 54.5 SER139.OG-GLN605.OE1 54.5

PHE150.N-SER113.O 53.0 GLY455.N-TYR467.O 52.5

VAL342.N-LEU395.O 52.0

HIE163.N-SER147.O 49.5

ILE78.N-LYS90.O 52.0

VAL342.N-LEU395.O 51.5

VAL342.N-LEU395.O 54.5 THR441.OG1-ASN439.OD1 54.5

THR257.OG1-LEU253.O 53.5 SER445.OG-GLN299.OE1 53.0

THR135.OG1-ASN133.OD1 54.0

THR441.OG1-ASN439.OD1 53.5

SER450.OG-LEU447.O 53.0

GLY455.N-TYR467.O 52.5

TYR182.OH-CYS160.O 57.5 TRP337.N-CYS322.O 57.0

GLY149.N-TYR161.O 55.0 VAL342.N-LEU395.O 55.0

TRP31.N-CYS16.O 56.0

SER573.OG-ASP569.O 54.5

TRP337.N-CYS322.O 53.5

THR135.OG1-ASN133.OD1 58.0 SER453.OG-SER450.O 57.5

THR507.OG1-GLU546.O 56.5 VAL420.N-TYR432.O 55.5

HIE469.N-SER453.O 53.5

TYR182.OH-CYS160.O 59.0

TRP337.N-CYS322.O 56.0

SER573.OG-ASP569.O 55.0

VAL36.N-LEU89.O 53.5

THR507.OG1-GLU546.O 63.0 THR201.OG1-GLU240.O 62.0 THR257.OG1-LEU253.O 58.0

THR201.OG1-GLU240.O 57.5 VAL36.N-LEU89.O 57.5 THR135.OG1-ASN133.OD1 57.0

THR201.OG1-GLU240.O 64.0

VAL36.N-LEU89.O 60.0

SER267.OG-ASP263.O 59.0

TRP31.N-CYS16.O 59.0

THR201.OG1-GLU240.O 58.5

TYR182.OH-CYS160.O 60.5

SER316.OG-GLU320.OE1 77.5

SER10.OG-GLU14.OE1 72.5

SER10.OG-GLU14.OE1 78.5

SER10.OG-GLU14.OE1 81.0

SER10.OG-GLU14.OE1 78.0

rep4

SER316.OG-GLU320.OE1 78.5

SER316.OG-GLU320.OE1 80.0 SER316.OG-GLU320.OE1 74.5

rep2

rep1

rep3

SER453.OG-SER450.O 45.5

THR481.OG1-ASP482.O 46.0

LEU75.N-VAL68.O 46.0

(continued)

THR135.OG1-ASN133.OD1 46.0

ASP482.N-ASN486.O 46.5

THR257.OG1-LEU253.O 47.0

LEU473.N-VAL477.O 47.5

ILE384.N-LYS396.O 48.0

SER147.OG-SER144.O 49.0

HIE163.N-SER147.O 49.5

LEU115.N-VAL148.O 49.5

THR441.OG1-ASN439.OD1 50.0

GLY149.N-TYR161.O 50.0

TYR209.OH-ILE259.O 50.0

GLY452.N-HIE469.O 50.5

ILE78.N-LYS90.O 50.5

VAL36.N-LEU89.O 51.5

TRP337.N-CYS322.O 51.5

VAL420.N-TYR432.O 52.0

TYR515.OH-ILE565.O 52.5

THR563.OG1-LEU559.O 53.0

HIE469.N-SER453.O 53.0

VAL114.N-TYR126.O 53.5

GLY455.N-TYR467.O 55.0

SER267.OG-ASP263.O 55.5

TYR488.OH-CYS466.O 55.5

VAL342.N-LEU395.O 56.0

THR507.OG1-GLU546.O 59.0

TYR182.OH-CYS160.O 59.5

TRP31.N-CYS16.O 60.0

THR201.OG1-GLU240.O 61.0

SER573.OG-ASP569.O 63.0

SER316.OG-GLU320.OE1 75.5

SER10.OG-GLU14.OE1 81.5

rep5

Table 2.21 HBs with more than 40% occupancy rates during the five sets (each set runs for 200 ns) of MDs of the dimer-N3 model of [340]

2.4 Concluding Remarks 97

ASN95.N-ASP33.O 43.5

ARG310.NH2-GLU290.OE1 44.0 HIE172.N-ILE136.O 43.5

LYS394.N-SER387.O 42.0

LYS88.N-SER81.O 42.5 LEU421.N-VAL454.O 42.5

TYR182.N-GLY174.O 42.5

LEU338.N-VAL341.O 42.5

LEU381.N-VAL374.O 41.5

PHE314.N-SER419.OG 41.0 LEU336.N-TYR343.O 42.5 VAL463.N-LYS406.O 42.5

ASN95.ND2-TRP31.O 41.0 GLN69.N-GLN19.O 40.5 VAL326.N-LEU333.O 40.5 CYS434.N-PHE418.O 40.0 ARG437.N-THR441.O 40.0 THR21.N-LEU67.O 40.0

HIE172.N-ILE136.O 41.0 ASN401.ND2-TRP337.O 40.5 SER560.OG-ILE565.O 40.5 LEU511.N-THR507.O 40.5 PHE8.N-SER113.OG 40.0 GLY146.N-HIE163.O 40.0 VAL157.N-LYS100.O 40.0 LEU30.N-TYR37.O 39.5

LEU511.N-THR507.O 41.5

PHE150.N-SER113.O 41.5

LEU205.N-THR201.O 41.5

VAL18.N-GLY29.O 41.5

PHE8.N-SER113.OG 41.0

VAL157.N-LYS100.O 41.0

LYS311.NZ-GLU596.OE1 40.5

LEU336.N-TYR343.O 40.5

LEU89.N-VAL36.O 39.5

GLY415.N-MET436.O 39.0

LEU205.N-THR201.O 40.5

LEU338.N-VAL341.O 40.5

ARG131.N-THR135.O 40.0

LEU30.N-TYR37.O 40.0

ALA70.N-VAL73.O 40.0

LEU27.N-VAL20.O 40.0

GLY146.N-HIE163.O 40.0

HIE478.N-ILE442.O 39.5

SER123.N-ALA116.O 39.5

ARG40.NH2-ASP187.OD2 39.5

LEU381.N-VAL374.O 41.0

GLN299.NE2-ARG4.O 41.5

LYS269.N-CYS265.O 40.0

SER254.OG-ILE259.O 41.0

TYR488.N-GLY480.O 41.0

LYS5.NZ-GLU290.OE2 41.5

ILE506.N-ASP595.OD1 41.5

HIE163.N-SER147.O 40.5

ASN401.N-ASP339.O 41.5 GLN325.N-GLN375.O 41.5

SER139.OG-GLN605.OE1 42.0

VAL397.N-ASP340.O 41.5

GLN605.NE2-ARG310.O 41.0

ASN95.N-ASP33.O 41.5

PHE456.N-SER419.O 41.5

VAL397.N-ASP340.O 42.0

VAL157.N-LYS100.O 42.0

VAL20.N-LEU27.O 42.5

LEU115.N-VAL148.O 41.0

GLN605.NE2-ARG310.O 42.0

ARG310.NH2-GLU290.OE2 42.5

VAL463.N-LYS406.O 42.0

SER560.OG-ILE565.O 42.0

VAL20.N-LEU27.O 41.0

LEU75.N-VAL68.O 42.5

LEU333.N-VAL326.O 41.0

VAL157.N-LYS100.O 41.0

LEU395.N-VAL342.O 42.5

ILE78.N-LYS90.O 42.5

SER147.OG-SER144.O 42.5

LEU167.N-VAL171.O 42.5

LEU511.N-THR507.O 41.5

TYR37.N-LEU30.O 43.0 LEU393.N-CYS344.O 42.5

VAL326.N-LEU333.O 41.5

HIE163.N-SER147.O 42.5

LEU75.N-VAL68.O 43.0

ASN28.ND2-CYS145.O 43.5

ILE78.N-LYS90.O 43.5

HIE163.N-SER147.O 43.5

SER453.OG-SER450.O 43.0

THR331.OG1-CYS350.O 43.5

ARG40.N-CYS85.O 44.5 ARG310.NH1-GLU290.OE2 44.5

ASN95.ND2-TRP31.O 42.0

VAL20.N-LEU27.O 43.5

ILE384.N-LYS396.O 45.0 VAL420.N-TYR432.O 44.5

TYR37.N-LEU30.O 42.0

LEU30.N-TYR37.O 43.5

THR563.OG1-LEU559.O 43.0

TYR343.N-LEU336.O 42.5

LEU421.N-VAL454.O 42.0

LEU167.N-VAL171.O 45.0 TYR209.OH-ILE259.O 44.5 ARG437.N-THR441.O 44.5

GLY452.N-HIE469.O 44.0

GLN495.N-MET355.O 43.5

ASN95.ND2-TRP31.O 43.5

LYS394.N-SER387.O 42.5

SER147.OG-SER144.O 43.0

LYS394.N-SER387.O 45.0 VAL326.N-LEU333.O 45.0

VAL324.N-GLY335.O 42.5

THR481.OG1-ASP482.O 44.0

ALA234.N-PHE230.O 44.0

LYS5.NZ-GLU290.OE1 43.0

ASN95.N-ASP33.O 43.0

TYR515.OH-ILE565.O 45.0

LEU87.N-CYS38.O 45.5

VAL20.N-LEU27.O 44.5

ASN401.N-ASP339.O 44.0

LEU336.N-TYR343.O 43.5

THR135.OG1-ASN133.OD1 43.5

ILE587.N-SER590.O 45.5

TYR343.N-LEU336.O 45.5 LEU89.N-VAL36.O 45.5

LEU473.N-VAL477.O 44.5

THR257.OG1-LEU253.O 44.5

ILE384.N-LYS396.O 44.0

LEU473.N-VAL477.O 44.0 LEU421.N-VAL454.O 45.5

rep4 ASN401.N-ASP339.O 45.5

rep3 TYR488.N-GLY480.O 46.0

rep2

LEU87.N-CYS38.O 45.0

rep1

SER560.OG-ILE565.O 44.0

Table 2.21 (continued) rep5

ASN509.ND2-ASP595.O 38.5

VAL18.N-GLY29.O 39.0

PHE150.N-SER113.O 39.0

CYS434.N-PHE418.O 39.5

ASN509.ND2-GLY415.O 40.0

SER560.OG-ILE565.O 40.5

ARG131.NH2-ASP289.OD1 41.0

VAL463.N-LYS406.O 41.0

LEU87.N-CYS38.O 41.0

LEU333.N-VAL326.O 41.5

LYS311.NZ-GLU596.OE1 41.5

PHE456.N-SER419.O 41.5

TYR37.N-LEU30.O 41.5

SER139.OG-GLN605.OE1 41.5

VAL397.N-ASP340.O 42.0

LEU27.N-VAL20.O 42.0

GLY146.N-HIE163.O 42.0

ALA70.N-VAL73.O 42.5

ASN95.N-ASP33.O 42.5

LEU511.N-THR507.O 42.5

LEU395.N-VAL342.O 42.5

ASN439.ND2-GLY501.O 43.0

ARG4.NH2-GLU596.OE2 43.5

ASN28.ND2-CYS145.O 43.5

LEU393.N-CYS344.O 43.5

VAL157.N-LYS100.O 44.0

LEU421.N-VAL454.O 44.0

ARG4.NH1-GLU596.OE1 44.5

TYR343.N-LEU336.O 44.5

LYS394.N-SER387.O 44.5

LEU167.N-VAL171.O 45.0

SER254.OG-ILE259.O 45.0

LYS88.N-SER81.O 45.5

98 2 3C-Like Protease (3CLpro)

ARG438.N-THR442.O 46.0

TYR516.OH-ILE566.O 48.0

LEU512.N-THR508.O 47.5

GLY456.N-TYR468.O 47.5

LEU337.N-TYR344.O 47.0

ASN95.ND2-TRP31.O 47.0

LEU75.N-VAL68.O 47.0

LEU337.N-TYR344.O 46.0

VAL327.N-LEU334.O 46.0

LYS88.N-SER81.O 44.5 LYS395.N-SER388.O 44.5

VAL36.N-LEU89.O 46.5 LEU396.N-VAL343.O 46.0

ASN402.N-ASP340.O 45.0 GLY453.N-HIE470.O 45.0

SER254.OG-ILE259.O 46.5 HIE163.N-SER147.O 46.5

GLY146.N-HIE163.O 45.5 ILE385.N-LYS397.O 45.0

HIE172.N-ILE136.O 48.0 THR257.OG1-LEU253.O 47.0 SER147.OG-SER144.O 47.0

GLY146.N-HIE163.O 48.0

HIE172.N-ILE136.O 48.0

THR175.OG1-ASP176.O 48.0

TYR516.OH-ILE566.O 47.5

GLY456.N-TYR468.O 47.0

SER139.OG-GLN606.OE1 47.0

SER446.OG-GLN299.OE1 47.0 THR482.OG1-ASP483.O 46.5

GLY149.N-TYR161.O 48.0 TRP31.N-CYS16.O 48.0

ILE385.N-LYS397.O 48.5

TYR37.N-LEU30.O 48.0

THR175.OG1-ASP176.O 48.0

ARG131.N-THR135.O 47.5

TYR37.N-LEU30.O 48.0 TYR516.OH-ILE566.O 48.0

VAL114.N-TYR126.O 49.0 GLY146.N-HIE163.O 49.0

LYS5.NZ-GLU290.OE1 48.5

LEU422.N-VAL455.O 48.5

LEU167.N-VAL171.O 48.0

VAL421.N-TYR433.O 48.0

SER147.OG-SER144.O 49.0 LEU27.N-VAL20.O 48.5

ILE385.N-LYS397.O 49.5 LEU337.N-TYR344.O 49.5

THR482.OG1-ASP483.O 49.0

VAL421.N-TYR433.O 49.0

LYS5.NZ-GLU290.OE1 48.5

SER454.OG-SER451.O 48.5

PHE457.N-SER420.O 50.0 HIE470.N-SER454.O 49.5

TYR209.OH-ILE259.O 49.5 LYS88.N-SER81.O 49.5

VAL464.N-LYS407.O 50.0

VAL114.N-TYR126.O 49.5

SER446.OG-GLN299.OE1 49.5

TYR209.OH-ILE259.O 51.5 VAL421.N-TYR433.O 50.5 SER454.OG-SER451.O 50.0

THR135.OG1-ASN133.OD1 51.5 THR564.OG1-LEU560.O 50.5 THR175.OG1-ASP176.O 50.0

THR257.OG1-LEU253.O 48.5

SER561.OG-ILE566.O 52.0

TRP338.N-CYS323.O 50.5

GLY149.N-TYR161.O 50.5

HIE172.N-ILE136.O 51.5

ASN402.N-ASP340.O 50.0

THR135.OG1-ASN133.OD1 50.0

TRP31.N-CYS16.O 52.0 THR257.OG1-LEU253.O 51.5

LEU115.N-VAL148.O 52.0 HIE470.N-SER454.O 51.5

THR257.OG1-LEU253.O 53.5

SER139.OG-GLN606.OE1 52.5

VAL114.N-TYR126.O 51.5

LEU115.N-VAL148.O 51.5

VAL343.N-LEU396.O 52.5 GLY149.N-TYR161.O 52.5

TRP338.N-CYS323.O 53.5

THR442.OG1-ASN440.OD1 55.0

TRP31.N-CYS16.O 54.5

VAL343.N-LEU396.O 54.0 LEU167.N-VAL171.O 52.0

THR442.OG1-ASN440.OD1 53.5 THR564.OG1-LEU560.O 53.0

THR482.OG1-ASP483.O 54.5 GLY456.N-TYR468.O 54.0

TRP338.N-CYS323.O 55.5 TYR182.OH-CYS160.O 55.5

THR442.OG1-ASN440.OD1 56.0

HIE470.N-SER454.O 51.5

VAL36.N-LEU89.O 56.0

HIE470.N-SER454.O 55.5

SER267.OG-ASP263.O 56.0

TYR209.OH-ILE259.O 54.0

GLN606.NE2-ARG311.O 57.5

SER574.OG-ASP570.O 57.0

VAL36.N-LEU89.O 57.5

TRP31.N-CYS16.O 57.0

VAL421.N-TYR433.O 55.5

SER574.OG-ASP570.O 57.0 GLY456.N-TYR468.O 56.0

THR508.OG1-GLU547.O 59.0 VAL343.N-LEU396.O 58.5

THR201.OG1-GLU240.O 61.0

LEU167.N-VAL171.O 60.0

GLY149.N-TYR161.O 58.0

THR442.OG1-ASN440.OD1 57.5

THR508.OG1-GLU547.O 60.0 THR201.OG1-GLU240.O 59.0 TYR489.OH-CYS467.O 58.5

SER267.OG-ASP263.O 61.0 SER454.OG-SER451.O 60.0 TYR489.OH-CYS467.O 59.0

TYR489.OH-CYS467.O 61.5

THR135.OG1-ASN133.OD1 61.5

THR508.OG1-GLU547.O 61.5

TRP338.N-CYS323.O 59.5

TYR182.OH-CYS160.O 59.0

THR508.OG1-GLU547.O 61.0

SER267.OG-ASP263.O 61.5 THR135.OG1-ASN133.OD1 60.5

SER574.OG-ASP570.O 64.5

VAL343.N-LEU396.O 62.0

TYR182.OH-CYS160.O 62.0

THR201.OG1-GLU240.O 63.0

SER574.OG-ASP570.O 62.0

TYR182.OH-CYS160.O 63.0

SER10.OG-GLU14.OE1 73.5 VAL36.N-LEU89.O 61.5

SER317.OG-GLU321.OE1 79.5 THR201.OG1-GLU240.O 65.5

SER10.OG-GLU14.OE1 79.5

SER267.OG-ASP263.O 62.5

SER10.OG-GLU14.OE1 77.5

TYR489.OH-CYS467.O 63.5

rep4 SER317.OG-GLU321.OE1 76.5

rep3 SER10.OG-GLU14.OE1 80.5

rep2

SER317.OG-GLU321.OE1 80.0

rep1

SER317.OG-GLU321.OE1 81.0

LEU167.N-VAL171.O 47.5

(continued)

SER139.OG-GLN606.OE1 47.5

ILE385.N-LYS397.O 47.5

GLN606.NE2-ARG311.O 48.0

THR257.OG1-LEU253.O 48.0

HIE470.N-SER454.O 48.0

LEU30.N-TYR37.O 48.5

GLY149.N-TYR161.O 48.5

PHE112.N-CYS128.O 48.5

TYR516.OH-ILE566.O 48.5

TYR209.OH-ILE259.O 48.5

PHE457.N-SER420.O 49.0

ILE78.N-LYS90.O 49.5

HIE163.N-SER147.O 49.5

GLY453.N-HIE470.O 49.5

PHE150.N-SER113.O 50.5

ARG438.N-THR442.O 50.5

HIE172.N-ILE136.O 50.5

VAL114.N-TYR126.O 51.0

VAL343.N-LEU396.O 53.0

SER267.OG-ASP263.O 53.5

GLY456.N-TYR468.O 53.5

THR482.OG1-ASP483.O 53.5

VAL36.N-LEU89.O 53.5

THR442.OG1-ASN440.OD1 53.5

SER574.OG-ASP570.O 55.0

SER10.OG-GLU14.OE1 57.5

THR135.OG1-ASN133.OD1 58.5

TRP31.N-CYS16.O 59.0

TRP338.N-CYS323.O 59.5

TYR489.OH-CYS467.O 59.5

SER446.OG-GLN299.OE1 62.0

TYR182.OH-CYS160.O 63.0

THR201.OG1-GLU240.O 63.5

THR508.OG1-GLU547.O 66.5

SER317.OG-GLU321.OE1 82.0

rep5

Table 2.22 HBs with more than 40% occupancy rates during the five sets (each set runs for 200 ns) of MDs of the dimer-2N3 model of [340]

2.4 Concluding Remarks 99

LEU30.N-TYR37.O 43.5

VAL325.N-GLY336.O 45.0 ILE200.N-ASP289.OD2 44.0

TYR489.N-GLY481.O 42.5 LEU89.N-VAL36.O 42.5

LEU87.N-CYS38.O 43.0 PHE457.N-SER420.O 43.0

LEU115.N-VAL148.O 45.0

ASN95.N-ASP33.O 45.0

ASN28.ND2-CYS145.O 43.5

LEU205.N-THR201.O 42.0

HIE479.N-ILE443.O 42.5

LEU339.N-VAL342.O 41.0

GLU240.N-THR199.O 41.5

LEU30.N-TYR37.O 40.5 SER446.OG-GLN299.OE1 40.5

LEU30.N-TYR37.O 42.5

ASP483.N-ASN487.O 42.5

SER147.OG-SER144.O 41.5

LEU512.N-THR508.O 41.0

ALA480.N-MET472.O 41.0

ASN510.ND2-ASP596.O 40.5

LEU89.N-VAL36.O 40.5

LEU394.N-CYS345.O 40.0

LEU382.N-VAL375.O 39.5

LYS395.N-SER388.O 39.0

PHE315.N-SER420.OG 39.0

ASP176.N-ASN180.O 39.0

LEU382.N-VAL375.O 41.0

LYS88.N-SER81.O 41.0

ASN133.ND2-GLY195.O 40.0

GLN83.N-VAL86.O 40.0

TYR54.OH-ASP187.OD2 40.0 ARG131.N-THR135.O 39.5

GLY416.N-MET437.O 39.0

ASP483.N-ASN487.O 38.5

LYS576.N-CYS572.O 38.5

ASN510.ND2-GLY416.O 38.5

LEU422.N-VAL455.O 39.0

ARG311.NH1-GLU290.OE1 39.0

ARG4.NH2-GLU597.OE2 38.0

ASP483.N-ASN487.O 38.0

ALA480.N-MET472.O 38.0

ASN203.ND2-ASP289.O 38.5

LEU115.N-VAL148.O 38.5

VAL327.N-LEU334.O 39.0

PHE8.N-SER113.OG 39.0

LEU474.N-VAL478.O 39.5 LEU382.N-VAL375.O 39.0 ARG438.NH2-ASP596.OD2 39.0

ALA234.N-PHE230.O 41.5

LYS395.N-SER388.O 41.5

GLN496.N-MET356.O 41.5

ALA541.N-PHE537.O 40.0

ARG4.NH2-GLU597.OE1 40.5

ASP460.N-CYS463.O 40.0

THR418.OG1-ASP602.OD2 40.0

THR482.OG1-ASP483.O 40.5

VAL114.N-TYR126.O 40.0

VAL327.N-LEU334.O 39.5

LEU75.N-VAL68.O 42.0

ASN538.N-LEU534.O 41.5

GLN606.NE2-ARG311.O 41.0

PHE150.N-SER113.O 40.5 GLN326.N-GLN376.O 40.0

PHE150.N-SER113.O 40.5

ARG438.N-THR442.O 40.0

ARG438.N-THR442.O 42.0

ASN203.ND2-GLY109.O 42.0

GLY146.N-HIE163.O 41.0

ASN95.ND2-TRP31.O 40.5

PHE315.N-SER420.OG 40.5

ASN538.N-LEU534.O 40.5

LEU422.N-VAL455.O 41.0

ASN203.ND2-ASP289.O 40.5

ASN402.N-ASP340.O 40.5

VAL157.N-LYS100.O 43.0

TYR489.N-GLY481.O 42.5

LEU339.N-VAL342.O 42.0

ASN402.ND2-TRP338.O 41.5

ARG4.NH1-GLU597.OE1 41.5 GLY416.N-MET437.O 41.0 LEU75.N-VAL68.O 41.0

GLN83.N-VAL86.O 42.0 GLY453.N-HIE470.O 41.5 ASN231.N-LEU227.O 41.5

ARG311.NH2-GLU290.OE1 43.5

ASN203.ND2-ASP289.O 43.0

LEU474.N-VAL478.O 43.0

THR564.OG1-LEU560.O 42.0

ILE78.N-LYS90.O 42.0

HIE163.N-SER147.O 42.5

LEU334.N-VAL327.O 42.0

SER144.OG-LEU141.O 42.0

THR332.OG1-CYS351.O 43.0

TYR37.N-LEU30.O 42.0

ASN402.N-ASP340.O 44.0

PHE457.N-SER420.O 43.5

CYS22.N-THR25.O 42.5

ILE385.N-LYS397.O 42.0

ASP176.N-ASN180.O 42.5

PHE150.N-SER113.O 42.5

SER144.OG-LEU141.O 44.0

LEU334.N-VAL327.O 44.0

LEU87.N-CYS38.O 42.5

ASN510.ND2-ASP596.O 42.5

ILE78.N-LYS90.O 42.5

VAL157.N-LYS100.O 43.0

ASP176.N-ASN180.O 45.0

THR564.OG1-LEU560.O 44.5

PHE8.N-SER113.OG 43.0

LEU334.N-VAL327.O 42.5

VAL464.N-LYS407.O 42.5

ILE78.N-LYS90.O 43.5

ASN95.N-ASP33.O 43.0 VAL20.N-LEU27.O 43.0

SER254.OG-ILE259.O 43.0

ASN95.ND2-TRP31.O 44.0 LEU334.N-VAL327.O 43.5

ASP460.N-CYS463.O 45.5

PHE150.N-SER113.O 45.0

ARG438.N-THR442.O 43.5

LEU382.N-VAL375.O 43.0

LEU167.N-VAL171.O 43.0

VAL157.N-LYS100.O 44.0

SER561.OG-ILE566.O 43.5

PHE8.N-SER113.OG 44.0

TYR344.N-LEU337.O 46.0

LEU396.N-VAL343.O 45.5

LEU87.N-CYS38.O 45.5

LEU30.N-TYR37.O 44.0

TYR516.OH-ILE566.O 45.5

GLY453.N-HIE470.O 43.5

LYS88.N-SER81.O 44.5

VAL464.N-LYS407.O 44.0

TYR344.N-LEU337.O 45.0

ILE78.N-LYS90.O 46.5

SER454.OG-SER451.O 46.5

TYR344.N-LEU337.O 44.5

LEU396.N-VAL343.O 44.0

VAL20.N-LEU27.O 44.5

TYR344.N-LEU337.O 44.5

LYS395.N-SER388.O 45.5 VAL464.N-LYS407.O 45.5

TYR209.OH-ILE259.O 47.0

ARG131.N-THR135.O 46.5

PHE457.N-SER420.O 45.0

LEU396.N-VAL343.O 44.5

rep4 LEU422.N-VAL455.O 44.5

rep3 LEU75.N-VAL68.O 45.5

rep2

HIE163.N-SER147.O 47.0

rep1

ARG311.NH1-GLU290.OE1 46.0

Table 2.22 (continued) rep5

LEU75.N-VAL68.O 39.0

LEU115.N-VAL148.O 40.0

SER254.OG-ILE259.O 40.5

LYS395.N-SER388.O 40.5

ASP460.N-CYS463.O 41.0

SER147.OG-SER144.O 41.0

HIE41.NE2-ASP187.OD1 41.5

VAL91.N-ASP34.O 41.5

LEU89.N-VAL36.O 41.5

LEU422.N-VAL455.O 41.5

THR25.OG1-CYS44.O 42.0

PHE419.N-CYS435.O 42.0

ASN203.ND2-GLY109.O 42.0

ASP483.N-ASN487.O 42.5

LEU337.N-TYR344.O 42.5

LEU27.N-VAL20.O 43.0

LEU474.N-VAL478.O 43.0

GLY146.N-HIE163.O 43.0

TYR37.N-LEU30.O 43.0

LYS88.N-SER81.O 43.0

VAL464.N-LYS407.O 43.0

ASN402.N-ASP340.O 43.5

PHE8.N-SER113.OG 43.5

ASN95.N-ASP33.O 43.5

PHE315.N-SER420.OG 43.5

TYR344.N-LEU337.O 44.5

GLN299.NE2-ARG4.O 45.5

LEU87.N-CYS38.O 45.5

ASN95.ND2-TRP31.O 45.5

ILE507.N-ASP596.OD2 45.5

ASN538.N-LEU534.O 45.5

VAL157.N-LYS100.O 46.0

TYR489.N-GLY481.O 46.0

SER561.OG-ILE566.O 47.0

LEU334.N-VAL327.O 47.0

THR564.OG1-LEU560.O 47.0

VAL421.N-TYR433.O 47.0

SER454.OG-SER451.O 47.0

100 2 3C-Like Protease (3CLpro)

SER10.OG-GLU14.OE1 79.0

SER316.OG-GLU320.OE1 74.0

THR507.OG1-GLU546.O 66.0

THR563.OG1-LEU559.O 51.5

SER147.OG-SER144.O 52.0

GLY149.N-TYR161.O 48.5 GLY455.N-TYR467.O 48.0 LEU421.N-VAL454.O 47.5

LEU30.N-TYR37.O 49.0 PHE150.N-SER113.O 49.0 THR257.OG1-LEU253.O 48.5

HIE163.N-SER147.O 47.5

ILE78.N-LYS90.O 47.5

HIE469.N-SER453.O 47.0

VAL114.N-TYR126.O 47.0

VAL36.N-LEU89.O 48.5

ASN95.N-ASP33.O 47.5

LEU27.N-VAL20.O 47.5

LEU336.N-TYR343.O 47.5

SER445.OG-GLN299.OE1 47.0 TYR515.OH-ILE565.O 47.0 SER453.OG-SER450.O 46.5 TYR37.N-LEU30.O 46.0 TYR343.N-LEU336.O 46.0

CYS328.N-THR331.O 47.5 LEU115.N-VAL148.O 47.5 ARG310.NH1-GLU290.OE1 47.0 GLY149.N-TYR161.O 47.0 LEU167.N-VAL171.O 46.0

LEU115.N-VAL148.O 47.0

THR563.OG1-LEU559.O 47.0

LEU167.N-VAL171.O 47.0

TYR37.N-LEU30.O 46.5

THR257.OG1-LEU253.O 46.0

SER254.OG-ILE259.O 45.5

TYR360.OH-ASP493.O 45.0

GLY455.N-TYR467.O 47.5

VAL463.N-LYS406.O 46.0

TYR209.OH-ILE259.O 45.5

PHE456.N-SER419.O 47.5

ASN401.N-ASP339.O 48.0

VAL114.N-TYR126.O 49.0 HIE163.N-SER147.O 49.0

VAL114.N-TYR126.O 49.5 ARG131.N-THR135.O 49.0

LEU336.N-TYR343.O 48.0

SER450.OG-LEU447.O 48.0

VAL114.N-TYR126.O 49.0

ASN95.N-ASP33.O 49.5 HIE469.N-SER453.O 49.0

ASN95.N-ASP33.O 50.0 TYR37.N-LEU30.O 49.5

VAL157.N-LYS100.O 50.5 LEU473.N-VAL477.O 50.0

HIE469.N-SER453.O 50.5 THR135.OG1-ASN133.OD1 50.0

LEU87.N-CYS38.O 51.0 LYS88.N-SER81.O 50.5

LEU473.N-VAL477.O 51.5 THR563.OG1-LEU559.O 51.0

LEU333.N-VAL326.O 48.5

LEU473.N-VAL477.O 49.5

GLY455.N-TYR467.O 49.0

SER453.OG-SER450.O 50.0

VAL420.N-TYR432.O 49.0

TYR209.OH-ILE259.O 50.0

PHE456.N-SER419.O 50.0

THR441.OG1-ASN439.OD1 50.0

HIE469.N-SER453.O 50.0

SER573.OG-ASP569.O 52.0

VAL420.N-TYR432.O 51.5

TRP31.N-CYS16.O 51.0

LEU167.N-VAL171.O 54.0

THR257.OG1-LEU253.O 52.5

HIE163.N-SER147.O 51.0

THR135.OG1-ASN133.OD1 52.5 VAL420.N-TYR432.O 52.0

THR441.OG1-ASN439.OD1 52.0 LYS311.NZ-GLU596.OE1 52.0

THR481.OG1-ASP482.O 52.5

GLY452.N-HIE469.O 52.5

HIE172.N-ILE136.O 54.5

SER573.OG-ASP569.O 54.0

THR257.OG1-LEU253.O 54.0 SER254.OG-ILE259.O 53.0

SER453.OG-SER450.O 52.5 GLY455.N-TYR467.O 52.5

THR135.OG1-ASN133.OD1 54.5

SER453.OG-SER450.O 53.0

SER147.OG-SER144.O 55.0

TRP337.N-CYS322.O 54.5

TRP31.N-CYS16.O 57.0 SER267.OG-ASP263.O 55.0

SER573.OG-ASP569.O 53.5

GLY149.N-TYR161.O 56.5

TRP337.N-CYS322.O 55.0

THR563.OG1-LEU559.O 55.5

TRP337.N-CYS322.O 54.5

THR441.OG1-ASN439.OD1 58.0 VAL342.N-LEU395.O 57.0

SER445.OG-GLN299.OE1 55.5 VAL342.N-LEU395.O 55.0

THR201.OG1-GLU240.O 58.5 TRP337.N-CYS322.O 58.0

TYR488.OH-CYS466.O 60.0 TRP31.N-CYS16.O 55.5

THR481.OG1-ASP482.O 55.0

VAL36.N-LEU89.O 58.5

SER267.OG-ASP263.O 58.5

THR135.OG1-ASN133.OD1 57.5

LEU87.N-CYS38.O 56.0

VAL342.N-LEU395.O 59.5

SER445.OG-GLN299.OE1 58.5

SER267.OG-ASP263.O 59.5

SER316.OG-GLU320.OE1 59.5

THR507.OG1-GLU546.O 62.0 SER573.OG-ASP569.O 58.5 VAL36.N-LEU89.O 58.5

TYR182.OH-CYS160.O 62.5 VAL36.N-LEU89.O 61.0 SER267.OG-ASP263.O 60.0

TYR488.OH-CYS466.O 61.0

THR175.OG1-ASP176.O 60.0

THR441.OG1-ASN439.OD1 59.5

THR201.OG1-GLU240.O 60.5

THR507.OG1-GLU546.O 60.5

VAL342.N-LEU395.O 59.5

TYR488.OH-CYS466.O 65.0 TYR182.OH-CYS160.O 62.5

THR507.OG1-GLU546.O 66.0 THR201.OG1-GLU240.O 66.0

TYR182.OH-CYS160.O 64.0

THR201.OG1-GLU240.O 61.5

TYR182.OH-CYS160.O 62.0

TYR488.OH-CYS466.O 61.0

SER316.OG-GLU320.OE1 79.0

TRP31.N-CYS16.O 64.0

rep4

SER316.OG-GLU320.OE1 78.5

SER10.OG-GLU14.OE1 81.0 SER10.OG-GLU14.OE1 80.0

rep2

rep1

rep3

ILE200.N-ASP289.OD2 47.0

SER450.OG-LEU447.O 47.5

THR257.OG1-LEU253.O 48.0

ARG131.N-THR135.O 48.5

VAL420.N-TYR432.O 48.5

PHE456.N-SER419.O 49.5

(continued)

HIE347.NE2-ASP493.OD2 50.0

LEU473.N-VAL477.O 50.0

VAL114.N-TYR126.O 50.0

LEU167.N-VAL171.O 51.0

GLY455.N-TYR467.O 51.0

TRP337.N-CYS322.O 51.5

TRP31.N-CYS16.O 52.5

VAL36.N-LEU89.O 52.5

PHE150.N-SER113.O 53.0

VAL342.N-LEU395.O 53.0

THR135.OG1-ASN133.OD1 53.5

SER10.OG-GLU14.OE1 53.5

TYR360.OH-ASP493.O 53.5

SER445.OG-GLN299.OE1 54.0

HIE469.N-SER453.O 54.0

ILE78.N-LYS90.O 55.0

SER573.OG-ASP569.O 55.5

THR563.OG1-LEU559.O 55.5

SER453.OG-SER450.O 56.5

LEU87.N-CYS38.O 57.5

THR201.OG1-GLU240.O 58.0

SER267.OG-ASP263.O 58.0

SER147.OG-SER144.O 59.5

THR441.OG1-ASN439.OD1 59.5

HIE163.N-SER147.O 59.5

THR507.OG1-GLU546.O 60.5

TYR488.OH-CYS466.O 66.0

TYR182.OH-CYS160.O 73.0

SER316.OG-GLU320.OE1 79.5

rep5

Table 2.23 HBs with more than 40% occupancy rates during the five sets (each set runs for 200 ns) of MDs of the dimer-2N3-covalent model of [340]

2.4 Concluding Remarks 101

rep2

HIE478.N-ILE442.O 45.5

HIE172.N-ILE136.O 45.5

LEU30.N-TYR37.O 45.5

VAL326.N-LEU333.O 45.5

CYS328.N-THR331.O 45.5

ILE200.N-ASP289.OD2 45.0

LYS88.N-SER81.O 45.0

LEU393.N-CYS344.O 45.0

ASN95.N-ASP33.O 44.5

LYS394.N-SER387.O 44.5

ARG131.N-THR135.O 44.5

LEU421.N-VAL454.O 44.0

ASN95.ND2-TRP31.O 44.0

SER10.OG-GLU14.OE2 44.0

ASP482.N-ASN486.O 43.5

PHE314.N-SER419.OG 43.5

SER254.OG-ILE259.O 43.0

TYR515.OH-ILE565.O 43.0

LEU89.N-VAL36.O 43.0

ILE384.N-LYS396.O 42.5

SER147.OG-SER144.O 42.5

ASN509.ND2-ASP595.O 42.0

GLN83.N-VAL86.O 42.0

TYR343.N-LEU336.O 42.0

ASN401.ND2-TRP337.O 41.5

ASN203.ND2-ASP289.O 41.5

VAL91.N-ASP34.O 41.0

LEU511.N-THR507.O 40.5

VAL463.N-LYS406.O 40.5

VAL157.N-LYS100.O 40.5

LEU75.N-VAL68.O 40.5

THR331.OG1-CYS350.O 40.5

ARG437.N-THR441.O 39.5

LEU338.N-VAL341.O 39.5

SER560.OG-ILE565.O 39.5

rep1

LEU421.N-VAL454.O 45.0

SER560.OG-ILE565.O 45.0

HIE478.N-ILE442.O 44.5

LEU75.N-VAL68.O 44.0

LYS88.N-SER81.O 44.0

VAL324.N-GLY335.O 43.5

PHE456.N-SER419.O 43.5

LEU89.N-VAL36.O 43.5

LEU205.N-THR201.O 43.5

ILE384.N-LYS396.O 43.0

VAL157.N-LYS100.O 43.0

ILE78.N-LYS90.O 43.0

ASN509.ND2-ASP595.O 43.0

LEU115.N-VAL148.O 43.0

ASN401.ND2-TRP337.O 42.5

GLN83.N-VAL86.O 42.5

ARG437.NH2-ASP595.OD2 42.5

TYR515.OH-ILE565.O 42.5

LEU473.N-VAL477.O 42.0

SER445.OG-GLN299.OE1 42.0

PHE314.N-SER419.OG 41.5

PHE150.N-SER113.O 41.5

ILE506.N-ASP595.OD2 41.5

ARG131.N-THR135.O 41.5

LYS394.N-SER387.O 41.5

ASP482.N-ASN486.O 41.5

TYR343.N-LEU336.O 41.0

LEU511.N-THR507.O 41.0

TYR37.N-LEU30.O 41.0

LEU32.N-VAL35.O 40.5

VAL20.N-LEU27.O 40.5

THR331.OG1-CYS350.O 40.0

TYR424.N-SER427.O 40.0

GLY149.N-TYR161.O 40.0

ASN537.N-LEU533.O 40.0

Table 2.23 (continued) rep3

LEU333.N-VAL326.O 39.5

MET471.N-ALA479.O 40.0

LEU574.N-MET570.O 40.5

CYS22.N-THR25.O 40.5

LEU32.N-VAL35.O 40.5

PHE314.N-SER419.OG 40.5

LEU336.N-TYR343.O 40.5

ILE78.N-LYS90.O 40.5

LYS394.N-SER387.O 40.5

ASN203.ND2-ASP289.O 41.0

ARG437.N-THR441.O 41.0

PHE8.N-SER113.OG 41.0

SER254.OG-ILE259.O 41.0

LEU75.N-VAL68.O 41.5

LEU381.N-VAL374.O 41.5

LEU393.N-CYS344.O 42.0

ASN509.ND2-GLY415.O 42.5

THR175.OG1-ASP176.O 42.5

GLY415.N-MET436.O 42.5

SER560.OG-ILE565.O 43.0

VAL420.N-TYR432.O 43.0

LYS88.N-SER81.O 43.0

ASN401.ND2-TRP337.O 43.0

TYR209.OH-ILE259.O 43.5

GLY452.N-HIE469.O 43.5

TYR343.N-LEU336.O 43.5

LEU395.N-VAL342.O 44.0

THR25.OG1-CYS44.O 44.5

LEU89.N-VAL36.O 44.5

LEU87.N-CYS38.O 44.5

HIE163.N-SER147.O 44.5

PHE456.N-SER419.O 44.5

LEU421.N-VAL454.O 44.5

TYR515.OH-ILE565.O 45.5

LYS5.NZ-GLU290.OE1 46.0

rep4

ALA255.N-GLY251.O 39.0

ASN509.ND2-ASP595.O 39.5

SER123.N-ALA116.O 39.5

LEU511.N-THR507.O 40.0

ASN133.ND2-GLY195.O 40.0

GLN83.N-VAL86.O 40.5

PHE150.N-SER113.O 40.5

ARG310.NH2-GLU290.OE2 40.5

LYS5.NZ-GLU290.OE1 40.5

HIE172.N-ILE136.O 41.0

LYS394.N-SER387.O 41.0

VAL324.N-GLY335.O 41.5

ASN95.ND2-TRP31.O 41.5

ASN401.ND2-TRP337.O 41.5

ARG131.N-THR135.O 42.0

VAL463.N-LYS406.O 42.0

HIE478.N-ILE442.O 42.5

LEU30.N-TYR37.O 42.5

GLN299.NE2-ARG4.O 42.5

ILE384.N-LYS396.O 42.5

ILE78.N-LYS90.O 43.0

ASN401.N-ASP339.O 43.0

SER560.OG-ILE565.O 43.0

LEU395.N-VAL342.O 43.0

SER144.OG-LEU141.O 43.5

VAL91.N-ASP34.O 44.0

LEU115.N-VAL148.O 44.0

ARG437.N-THR441.O 44.5

LEU393.N-CYS344.O 44.5

LEU89.N-VAL36.O 45.0

SER450.OG-LEU447.O 45.0

TYR209.OH-ILE259.O 45.0

LEU167.N-VAL171.O 45.5

ASN439.ND2-GLY501.O 45.5

SER147.OG-SER144.O 46.0

rep5

LEU333.N-VAL326.O 39.5

VAL20.N-LEU27.O 39.5

SER144.OG-LEU141.O 39.5

SER139.OG-GLN605.OE1 40.0

CYS128.N-PHE112.O 40.5

TYR209.OH-ILE259.O 41.0

ARG346.N-CYS391.O 41.0

PHE112.N-CYS128.O 41.0

GLN299.NE2-ARG4.O 41.0

LEU381.N-VAL374.O 41.5

LYS311.NZ-GLU596.OE1 41.5

ARG310.NH1-GLU290.OE1 41.5

LEU30.N-TYR37.O 41.5

TYR515.OH-ILE565.O 41.5

ARG437.N-THR441.O 41.5

ASN401.N-ASP339.O 42.0

SER254.OG-ILE259.O 42.0

TYR343.N-LEU336.O 42.0

LYS88.N-SER81.O 42.5

ASN203.ND2-GLY109.O 43.0

VAL91.N-ASP34.O 43.0

TYR37.N-LEU30.O 43.0

HIE172.N-ILE136.O 43.0

GLN605.NE2-ARG310.O 43.0

SER560.OG-ILE565.O 43.5

TYR54.OH-ASP187.O 43.5

GLY149.N-TYR161.O 43.5

LEU115.N-VAL148.O 44.0

GLY452.N-HIE469.O 44.0

ILE384.N-LYS396.O 44.0

HIE478.N-ILE442.O 44.5

ASN439.ND2-GLY501.O 45.0

CYS434.N-PHE418.O 45.5

LYS5.NZ-GLU290.OE1 45.5

ASN95.N-ASP33.O 46.5

102 2 3C-Like Protease (3CLpro)

2.4 Concluding Remarks

103

Fig. 2.24 The secondary structural graphs for the five sets (each set runs for 200 ns) of MDs of the six models of monomer-apo, monomer-N3, dimer-apo, dimer-N3, dimer-2N3, and dimer-2N3covalent in [340], where from left to right is the six models in turns and from up to down is the five sets of the MDs

Fig. 2.25 The RMSF graphs for the five sets (each set runs for 200 ns) of MDs of the six models of monomer-apo, monomer-N3, dimer-apo, dimer-N3, dimer-2N3, and dimer-2N3-covalent in [340]. The first two columns are for the monomer-apo and monomer-N3, respectively (where from up to down is the five sets of MDs). Then the second five columns (i.e., the five sets of MDs rep1rep5) are for the dimer-apo and dimer-N3 where the five columns up are for dimer-apo and the five columns down are for dimer-N3. And then the last five columns (i.e., the five sets of MDs rep1rep5) are for the dimer-2N3 and dimer-2N3-covalent where the five columns up are for dimer-2N3 and the five columns down are for dimer-2N3-covalent

104

2 3C-Like Protease (3CLpro)

Table 2.24 The MD-SBs of monomeric the SARS-CoV-1-Mpro-1q2w model (denoted as “SARS-CoV-1 monomer”) and the SARS-CoV-2-Mpro-6y2e model (denoted as “SARS-CoV-2 monomer”), where each model has three sets of MD simulations [346] SARS-CoV-1 rep1

rep2

rep3

SARS-CoV-2 rep1

ASP153-ARG298

ASP153-ARG298

ASP153-ARG298

ASP153-ARG298

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

rep2

rep3

ASP153-LYS102

ASP153-LYS102

ASP153-ARG298

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS12

ASP155-LYS12

ASP155-LYS12

ASP155-LYS12

ASP155-LYS12

ASP155-LYS12

ASP176-ARG105

ASP176-ARG105

ASP176-ARG105

ASP176-LYS180

ASP176-LYS180

ASP176-LYS180

ASP187-ARG188

ASP187-ARG188

ASP187-ARG188

ASP187-ARG40

ASP187-ARG40

ASP187-ARG40 ASP187-HIS41

ASP176-ARG105

ASP176-ARG105

ASP176-ARG105

ASP187-ARG188

ASP187-ARG188

ASP187-ARG188

ASP187-ARG40

ASP187-ARG40

ASP187-ARG40

ASP187-HIS41

ASP187-HIS41

ASP197-ARG131

ASP197-ARG131

ASP197-ARG131

ASP197-ARG131

ASP197-ARG131

ASP197-ARG131

ASP197-LYS137

ASP197-LYS137

ASP197-LYS137

ASP197-LYS137

ASP197-LYS137

ASP197-LYS137

ASP229-LYS269

ASP229-LYS269

ASP229-LYS269

ASP216-ARG279

ASP216-ARG279

ASP229-LYS269

ASP229-LYS269

ASP229-LYS269 ASP245-HIS246

ASP245-HIS246

ASP245-HIS246

ASP263-ARG222

ASP263-ARG222

ASP263-ARG222

ASP263-ARG222

ASP263-ARG222

ASP263-ARG222

ASP289-ARG131

ASP289-ARG131

ASP289-ARG131

ASP289-ARG131

ASP289-ARG131

ASP289-ARG131

ASP289-LYS137

ASP289-LYS137

ASP289-LYS137

ASP289-LYS137

ASP289-LYS137

ASP295-ARG298

ASP295-ARG298

ASP295-ARG298

ASP295-ARG298

ASP295-ARG298

ASP295-ARG298

ASP245-HIS246

ASP216-ARG279

ASP295-LYS5 ASP34-LYS90

ASP34-LYS90

ASP34-LYS90

ASP34-LYS90

ASP34-LYS90

ASP34-LYS90

ASP48-ARG60

ASP48-ARG60

ASP48-ARG60

ASP48-ARG60

ASP48-ARG60

ASP48-ARG60

ASP48-LYS61

ASP48-LYS61

ASP48-LYS61

ASP48-LYS61

ASP48-LYS61

ASP48-LYS61

ASP56-ARG60

ASP56-ARG60

ASP56-ARG60

ASP56-ARG60

ASP56-ARG60

ASP56-ARG60

ASP92-ARG76

ASP92-ARG76

ASP92-ARG76

ASP92-ARG76

ASP92-ARG76

ASP92-ARG76

GLU14-LYS97

GLU14-LYS97

GLU166-HIS163

GLU166-HIS163

GLU166-HIS172

GLU166-HIS172

GLU166-HIS172

GLU166-HIS172

GLU166-HIS172

GLU166-HIS172

GLU178-ARG105

GLU178-ARG105

GLU178-ARG105

GLU178-LYS180

GLU178-LYS180

GLU178-LYS88

GLU240-HIS246

GLU240-HIS246

GLU240-HIS246

GLU240-HIS246

GLU240-HIS246

GLU270-ARG222

GLU270-ARG222

GLU270-ARG222

GLU270-ARG222

GLU270-ARG222

GLU270-LYS269

GLU270-LYS269

GLU270-LYS269

GLU288-ARG4

GLU288-ARG4

GLU14-LYS97

GLU178-ARG105 GLU178-LYS180 GLU270-ARG222

GLU288-LYS5

GLU288-LYS5

GLU288-LYS5

GLU270-LYS269

GLU270-LYS269

GLU270-LYS269

GLU288-ARG4

GLU288-ARG4

GLU288-ARG4

GLU288-LYS5

GLU288-LYS5

GLU288-LYS5

GLU288-ARG131 GLU288-LYS137 GLU290-ARG4

GLU290-ARG4

GLU290-LYS5

GLU290-LYS5

GLU288-LYS137 GLU290-LYS5

GLU288-LYS137

GLU288-LYS137

GLU290-ARG4

GLU290-ARG4

GLU290-ARG4

GLU290-LYS5

GLU290-LYS5

GLU290-LYS5

GLU290-ARG131

GLU290-ARG131

GLU290-ARG131

GLU290-ARG131

GLU290-ARG131

GLU290-ARG131

GLU290-LYS137

GLU290-LYS137

GLU290-LYS137

GLU290-LYS137

GLU290-LYS137

GLU290-LYS137

GLU305-ARG4

GLU305-ARG4

GLU305-ARG4

GLU55-ARG188

GLU55-ARG188

GLU55-ARG40

GLU55-ARG40

GLU55-ARG40

GLU305-LYS5 GLU305-ARG217

GLU305-ARG217

GLU305-ARG298

GLU305-ARG298

GLU55-ARG40

GLU55-ARG40

GLU55-ARG188 GLU47-ARG60 GLU47-LYS61

GLU55-ARG40

2.4 Concluding Remarks

105

Table 2.25 The MD-SBs of dimer the SARS-CoV-1-Mpro-1q2w model (denoted as “SARS-CoV1 dimer”) and the SARS-CoV-2-Mpro-6y2e model (denoted as “SARS-CoV-2 dimer”), where each model has three sets of MD simulations [346] SARS-CoV-1 rep1

rep2

A:GLU14-B:LYS12

B:GLU14-A:LYS12

B:GLU14-A:LYS12

A:GLU290-B:ARG4

B:GLU290-A:ARG4

A:GLU290-B:ARG4

B:GLU290-A:ARG4

A:GLU290-B:ARG4

B:GLU290-A:ARG4

B:ASP153-B:ARG298

A:ASP153-A:ARG298

rep3

B:ASP153-B:ARG298

A:ASP153-A:LYS102

B:ASP153-B:LYS102

A:ASP153-A:LYS102

B:ASP153-B:LYS102

A:ASP153-A:LYS102

B:ASP153-B:LYS102

A:ASP155-A:LYS100

B:ASP155-B:LYS100

A:ASP155-A:LYS100

B:ASP155-B:LYS100

A:ASP155-A:LYS100

B:ASP155-B:LYS100

A:ASP155-A:LYS12

B:ASP155-B:LYS12

A:ASP155-A:LYS12

B:ASP155-B:LYS12

A:ASP155-A:LYS12

B:ASP155-B:LYS12

A:ASP176-A:ARG105

B:ASP176-B:ARG105

A:ASP176-A:ARG105

B:ASP176-B:ARG105

A:ASP176-A:ARG105

B:ASP176-B:ARG105

B:ASP176-B:LYS180

A:ASP176-A:LYS180

B:ASP176-B:LYS180

A:ASP176-A:LYS180

B:ASP176-B:LYS180

A:ASP176-A:LYS180

A:ASP187-A:ARG188

B:ASP187-B:ARG188

A:ASP187-A:ARG188

A:ASP187-A:ARG40

B:ASP187-B:ARG40

A:ASP187-A:HIS41

A:ASP187-A:ARG188

A:ASP187-A:ARG40

B:ASP187-B:ARG40

A:ASP187-A:ARG40

B:ASP187-B:ARG40

A:ASP197-A:ARG131

B:ASP197-B:ARG131

A:ASP197-A:ARG131

B:ASP197-B:ARG131

A:ASP197-A:ARG131

B:ASP197-B:ARG131

A:ASP197-A:LYS137

B:ASP197-B:LYS137

A:ASP197-A:LYS137

B:ASP197-B:LYS137

A:ASP197-A:LYS137

B:ASP197-B:LYS137

A:ASP216-A:ARG279

B:ASP216-B:ARG279

A:ASP216-A:ARG279

B:ASP216-B:ARG279

A:ASP229-A:LYS269

B:ASP229-B:LYS269

A:ASP229-A:LYS269

A:ASP263-A:ARG222

B:ASP263-B:ARG222

A:ASP263-A:ARG222

B:ASP263-B:ARG222

A:ASP263-A:ARG222

B:ASP263-B:ARG222

A:ASP289-A:ARG131

B:ASP289-B:ARG131

A:ASP289-A:ARG131

B:ASP289-B:ARG131

A:ASP289-A:ARG131

B:ASP289-B:ARG131

A:ASP295-A:ARG298

B:ASP295-B:ARG298

A:ASP295-A:ARG298

B:ASP295-B:ARG298

A:ASP295-A:ARG298

B:ASP295-B:ARG298

A:ASP34-A:LYS90

B:ASP34-B:LYS90

A:ASP34-A:LYS90

B:ASP34-B:LYS90

A:ASP34-A:LYS90

B:ASP34-B:LYS90

A:ASP289-A:LYS137

A:ASP48-A:ARG60 A:ASP56-A:ARG60

A:GLU166-A:HIS172 A:GLU178-A:LYS180

B:ASP229-B:LYS269

A:ASP48-A:ARG188

A:ASP48-A:ARG188 A:ASP56-A:ARG60

B:ASP56-B:ARG60

A:ASP92-A:ARG76

B:ASP92-B:ARG76

A:ASP56-A:ARG60

B:ASP56-B:ARG60

A:ASP92-A:ARG76

B:ASP92-B:ARG76

B:ASP92-B:ARG76

A:GLU166-A:HIS163

A:GLU166-A:HIS163

A:ASP229-A:LYS269

A:ASP48-A:ARG60 B:ASP56-B:ARG60

A:ASP56-A:LYS61 A:ASP92-A:ARG76

B:ASP229-B:LYS269

A:GLU166-A:HIS172

A:GLU166-A:HIS163 A:GLU166-A:HIS172

B:GLU166-B:HIS172

A:GLU178-A:ARG88

B:GLU166-B:HIS172

B:GLU166-B:HIS172

A:GLU178-A:ARG88

B:GLU178-B:ARG88

A:GLU178-A:LYS180

B:GLU178-B:LYS180

B:GLU178-B:ARG88

A:GLU178-A:LYS180

B:GLU178-B:LYS180

A:GLU240-A:HIS246

B:GLU240-B:HIS246

B:GLU178-B:LYS180

A:GLU240-A:HIS246

A:GLU240-A:HIS246

B:GLU240-B:HIS246

A:GLU270-A:ARG222

B:GLU270-B:ARG222

A:GLU270-A:LYS269

B:GLU270-B:LYS269

A:GLU270-A:ARG222

B:GLU270-B:ARG222

A:GLU270-A:LYS269

B:GLU270-B:LYS269

A:GLU288-A:LYS5

B:GLU288-B:LYS5

A:GLU270-A:LYS269

B:GLU270-B:LYS269

B:GLU290-B:ARG131

A:GLU288-A:LYS137

B:GLU240-B:HIS246

A:GLU270-A:ARG222

A:GLU288-A:LYS5

B:GLU288-B:LYS5

A:GLU290-A:ARG131

A:GLU290-A:ARG131

B:GLU290-B:ARG131

A:GLU290-A:LYS137

B:GLU290-B:LYS5

A:GLU288-A:LYS5

B:GLU288-B:LYS5

A:GLU290-A:LYS5

A:GLU290-A:ARG131

B:GLU290-B:ARG131

A:GLU47-A:ARG60

A:GLU290-A:LYS137

B:GLU290-B:LYS137

A:GLU47-A:LYS61

A:GLU290-A:LYS5

B:GLU290-B:LYS5

A:GLU290-A:LYS5

B:GLU270-B:ARG222

B:GLU290-B:LYS5

A:GLU47-A:ARG188 B:GLU290-B:LYS137

A:GLU47-A:ARG60 A:GLU47-A:HIS41

B:GLU47-B:HIS41 A:GLU47-A:ARG60 A:GLU47-A:LYS61 A:GLU55-A:ARG40

B:GLU55-B:ARG40

B:GLU55-B:ARG40

B:GLU55-B:ARG188

B:GLU55-B:ARG188

A:GLU55-A:ARG40

B:GLU55-B:ARG40

A:GLU55-A:ARG60 B:GLU55-B:ARG188

B:ASP187-B:HIS164

B:ASP187-B:HIS164

B:ASP187-B:HIS41

B:ASP187-B:HIS41

B:ASP216-B:ARG217

B:GLU178-B:ARG105

B:ASP56-B:ARG188 B:GLU288-B:ARG131

(continued)

106

2 3C-Like Protease (3CLpro)

Table 2.25 (continued) SARS-CoV-2 rep1

rep2

rep3

A:GLU14-B:LYS12

A:GLU14-B:LYS12

A:GLU14-B:LYS12

B:GLU14-A:LYS12

A:GLU290-B:ARG4

A:GLU290-B:ARG4

A:GLU290-B:ARG4

B:GLU290-A:ARG4

B:GLU290-A:ARG4 A:ASP216-B:LYS137

B:GLU290-A:ARG4 A:ASP153-A:ARG298

B:ASP153-B:ARG298

A:ASP153-A:LYS102

B:ASP153-B:LYS102

A:ASP153-A:LYS102

B:ASP153-B:LYS102

A:ASP153-A:LYS102

B:ASP153-B:LYS102

A:ASP155-A:LYS100

B:ASP155-B:LYS100

A:ASP155-A:LYS100

B:ASP155-B:LYS100

A:ASP155-A:LYS100

B:ASP155-B:LYS100

A:ASP155-A:LYS12

B:ASP155-B:LYS12

B:ASP176-B:ARG105

A:ASP176-A:ARG105

B:ASP176-B:ARG105

A:ASP155-A:LYS12

B:ASP155-B:LYS12

A:ASP155-A:LYS12

A:ASP176-A:ARG105

B:ASP176-B:ARG105

A:ASP176-A:ARG105

A:ASP187-A:ARG188

B:ASP187-B:ARG188

A:ASP187-A:ARG188

B:ASP187-B:ARG188

A:ASP187-A:ARG188

B:ASP187-B:ARG188

A:ASP187-A:ARG40

B:ASP187-B:ARG40

A:ASP187-A:ARG40

B:ASP187-B:ARG40

A:ASP187-A:ARG40

B:ASP187-B:ARG40

A:ASP197-A:ARG131

B:ASP197-B:ARG131

A:ASP187-A:HIS41

B:ASP187-B:HIS41

A:ASP197-A:ARG131

B:ASP197-B:ARG131

A:ASP197-A:LYS137

B:ASP197-B:LYS137

A:ASP197-A:ARG131

B:ASP197-B:ARG131

A:ASP197-A:LYS137

B:ASP197-B:LYS137

B:ASP229-B:LYS269

A:ASP197-A:LYS137

A:ASP229-A:LYS269

B:ASP197-B:LYS137

A:ASP216-A:ARG279

A:ASP263-A:ARG222

B:ASP263-B:ARG222

A:ASP216-A:ARG217

A:ASP289-A:ARG131

B:ASP289-B:ARG131

A:ASP216-A:ARG279

B:ASP216-B:ARG279

A:ASP229-A:LYS269

B:ASP229-B:LYS269

A:ASP289-A:ARG131

B:ASP289-B:ARG131

B:ASP295-B:ARG298

A:ASP263-A:ARG222

B:ASP263-B:ARG222

A:ASP289-A:LYS137

B:ASP289-B:LYS137

A:ASP289-A:LYS137 A:ASP295-A:ARG298

A:ASP229-A:LYS269

B:ASP229-B:LYS269

A:ASP263-A:ARG222

B:ASP263-B:ARG222

A:ASP34-A:LYS90

B:ASP34-B:LYS90

A:ASP289-A:ARG131

B:ASP289-B:ARG131

A:ASP295-A:ARG298

B:ASP295-B:ARG298

A:ASP48-A:ARG60

B:ASP48-B:ARG60

A:ASP295-A:ARG298

B:ASP295-B:ARG298

A:ASP34-A:LYS90

B:ASP34-B:LYS90

A:ASP48-A:LYS61

B:ASP48-B:LYS61

A:ASP34-A:LYS90

B:ASP34-B:LYS90

A:ASP48-A:ARG60

B:ASP48-B:ARG60

A:ASP56-A:ARG60

B:ASP56-B:ARG60

A:ASP48-A:ARG60

B:ASP48-B:ARG60

A:ASP48-A:LYS61

B:ASP48-B:LYS61

A:ASP92-A:ARG76

B:ASP92-B:ARG76

A:ASP48-A:LYS61

B:ASP48-B:LYS61

A:ASP56-A:ARG60

B:ASP56-B:ARG60

A:GLU166-A:HIS172

B:GLU166-B:HIS172

A:ASP56-A:ARG60

B:ASP56-B:ARG60

A:ASP92-A:ARG76

B:ASP92-B:ARG76

A:GLU178-A:ARG105

A:ASP92-A:ARG76

A:GLU178-A:LYS88 A:GLU240-A:HIS246

B:GLU240-B:HIS246

B:ASP92-B:ARG76

A:GLU166-A:HIS172

B:GLU166-B:HIS172

A:GLU240-A:HIS246

B:GLU240-B:HIS246

A:GLU178-A:ARG105

B:GLU178-B:LYS88

A:GLU270-A:ARG222

B:GLU270-B:ARG222 B:GLU270-B:LYS269

A:GLU270-A:ARG222

B:GLU270-B:ARG222

A:GLU240-A:HIS246

B:GLU240-B:HIS246

A:GLU270-A:LYS269

A:GLU270-A:LYS269

B:GLU270-B:LYS269

A:GLU270-A:ARG222

B:GLU270-B:ARG222

A:GLU288-A:LYS137

A:GLU270-A:LYS269

B:GLU270-B:LYS269

B:GLU288-B:LYS5

A:GLU288-A:LYS137

B:GLU290-B:LYS137

A:GLU290-A:ARG131

A:GLU288-A:LYS137 A:GLU288-A:LYS5 A:GLU290-A:ARG131 A:GLU290-A:LYS137

B:GLU166-B:HIS172

A:GLU166-A:HIS172

A:GLU288-A:LYS5

A:GLU290-A:LYS5

B:GLU290-B:LYS5

A:GLU290-A:LYS137

A:GLU55-A:ARG40

B:GLU55-B:ARG40

A:GLU290-A:LYS5

B:GLU288-B:LYS5

A:GLU288-A:LYS5

B:GLU288-B:LYS5

A:GLU290-A:LYS5

B:GLU290-B:LYS5

A:GLU55-A:ARG40

B:GLU55-B:ARG40 B:ASP187-B:HIS41 B:GLU178-B:ARG105

B:GLU290-B:LYS5

B:GLU290-B:ARG131

B:ASP155-B:LYS102

A:GLU47-A:ARG60

B:GLU290-B:LYS137

B:ASP216-B:ARG217

A:GLU47-A:LYS61

B:GLU55-B:ARG188

B:ASP216-B:ARG279

A:GLU55-A:ARG40

B:GLU55-B:ARG40

THR201.OG1-GLU240.O 60.08

LEU89.N-VAL36.O 51.50

ARG131.N-THR135.O 47.70 THR175.OG1-ASP176.O 47.50 GLY149.N-TYR161.O 46.71 ASP153.N-CYS156.O 46.51 LEU75.N-VAL68.O 46.11

LEU27.N-VAL20.O 45.71 ASN95.N-ASP33.O 45.31 LEU242.N-ASN231.OD1 45.31 VAL18.N-GLY29.O 44.51 GLN83.N-LEU86.O 43.51 TYR37.N-LEU30.O 42.51

ALA173.N-MET165.O 48.10

THR45.OG1-ASP48.OD2 47.70

VAL114.N-TYR126.O 47.50

LEU242.N-ASN231.OD1 47.50

LYS90.N-GLY79.O 45.71

ALA70.N-VAL73.O 45.51

ARG105.NH2-PHE181.O 44.91

SER147.OG-SER144.O 44.71

VAL114.N-TYR126.O 49.70

ARG88.N-SER81.O 48.50

LEU75.N-VAL68.O 48.10

LEU242.N-ASN231.OD1 47.31

GLN189.N-MET49.O 47.11

VAL157.N-LYS100.O 46.91

SER113.N-PHE150.O 46.31

LEU167.N-VAL171.O 45.51

LEU167.N-VAL171.O 50.90

SER144.OG-LEU141.O 48.10 HIS172.N-ILE136.O 47.90

LEU75.N-VAL68.O 46.11 SER123.N-ALA116.O 46.11

ALA70.N-VAL73.O 46.11

ASN95.N-ASP33.O 49.70

LEU167.N-VAL171.O 46.51

GLN19.N-GLN69.O 49.90

ARG88.N-SER81.O 46.91 LYS90.N-GLY79.O 46.51

ARG88.N-SER81.O 49.90

GLN19.N-GLN69.O 49.10

PHE150.N-SER113.O 49.10

ASN203.ND2-ASP289.O 50.70

GLY149.N-TYR161.O 50.30

THR21.N-LEU67.O 50.30

LEU87.N-CYS38.O 51.30

VAL20.N-LEU27.O 48.50 ARG105.NH2-PHE181.O 47.70

VAL157.N-LYS100.O 51.10

VAL20.N-LEU27.O 50.50

LEU89.N-VAL36.O 51.70

SER147.OG-LEU115.O 51.10

TYR37.N-LEU30.O 52.30 LYS88.N-SER81.O 52.10

PHE150.N-SER113.O 49.30 ALA70.N-VAL73.O 48.70

LEU89.N-VAL36.O 52.50

LEU27.N-VAL20.O 52.30

GLN69.N-GLN19.O 52.10

GLN19.N-GLN69.O 50.30

ASN95.N-ASP33.O 51.90

HIS163.N-SER147.O 53.49 VAL36.N-LEU89.O 52.89

VAL157.N-LYS100.O 51.10

GLY146.N-HIS163.O 52.69

LEU87.N-CYS38.O 52.50

VAL36.N-LEU89.O 52.89

THR257.OG1-LEU253.O 54.49 VAL157.N-LYS100.O 53.49

LEU89.N-VAL36.O 54.29 VAL114.N-TYR126.O 51.90

VAL114.N-TYR126.O 56.49 THR135.OG1-ASN133.OD1 55.29

THR257.OG1-LEU253.O 56.89 HIS163.N-SER147.O 54.69

LYS90.N-GLY79.O 52.69

VAL36.N-LEU89.O 55.69

LEU167.N-VAL171.O 55.29

THR257.OG1-LEU253.O 56.69

TYR182.OH-CYS160.O 55.09

THR257.OG1-LEU253.O 60.28

HIS172.N-ILE136.O 56.09

ARG131.N-THR135.O 58.28

ILE136.N-HIS172.O 57.49

TYR182.OH-CYS160.O 58.68 TRP31.N-CYS16.O 56.49

ILE78.N-LYS90.O 60.88 VAL36.N-LEU89.O 58.48 TYR182.OH-CYS160.O 58.08

ILE78.N-LYS90.O 61.88

THR201.OG1-GLU240.O 61.28

SER267.OG-ASP263.O 63.47

TRP31.N-CYS16.O 62.28

HIS163.N-SER147.O 61.88

TRP31.N-CYS16.O 61.88

ILE78.N-LYS90.O 63.47

ILE78.N-LYS90.O 64.67

THR201.OG1-GLU240.O 65.87

TYR182.OH-CYS160.O 61.08

TYR209.OH-ILE259.O 64.27

THR135.OG1-ASN133.OD1 65.87

TYR209.OH-ILE259.O 69.06

SARS-CoV-2 rep1

TYR209.OH-ILE259.O 69.06

rep3

VAL20.N-LEU27.O 59.48

THR201.OG1-GLU240.O 64.27

TRP31.N-CYS16.O 66.07

TYR209.OH-ILE259.O 59.28

rep2

SARS-CoV-1 rep1

LEU75.N-VAL68.O 43.91

HIS163.N-SER147.O 44.51

LEU242.N-ASN231.OD1 45.11

LEU167.N-VAL171.O 45.11

GLN69.N-GLN19.O 47.50

VAL114.N-TYR126.O 47.50

VAL36.N-LEU89.O 47.70

TYR37.N-LEU30.O 48.10

THR21.N-LEU67.O 48.10

ASN95.N-ASP33.O 48.50

LEU89.N-VAL36.O 49.70

TYR118.N-SER121.O 51.30

LEU87.N-CYS38.O 51.90

ASP153.N-CYS156.O 52.10

LYS88.N-SER81.O 53.49

TYR182.OH-CYS160.O 55.89

ILE136.N-HIS172.O 56.69

THR257.OG1-LEU253.O 57.09

GLY149.N-TYR161.O 59.88

ILE78.N-LYS90.O 59.88

TRP31.N-CYS16.O 60.48

THR201.OG1-GLU240.O 62.28

VAL20.N-LEU27.O 63.07

THR135.OG1-ASN133.OD1 64.07

ARG131.N-THR135.O 64.67

SER267.OG-ASP263.O 68.06

TYR209.OH-ILE259.O 69.46

rep2

(continued)

THR199.N-ASN238.O 44.11

LYS90.N-GLY79.O 44.51

VAL20.N-LEU27.O 44.71

GLY109.N-MET130.O 44.91

ALA70.N-VAL73.O 45.51

GLY149.N-TYR161.O 45.71

TYR182.N-GLY174.O 45.71

ASN95.N-ASP33.O 48.30

GLN19.N-GLN69.O 49.50

LEU89.N-VAL36.O 49.50

LEU167.N-VAL171.O 49.90

LEU27.N-VAL20.O 50.50

THR135.OG1-ASN133.OD1 51.30

ASP153.N-CYS156.O 52.30

TYR37.N-LEU30.O 53.69

VAL114.N-TYR126.O 53.89

VAL36.N-LEU89.O 54.09

LEU87.N-CYS38.O 55.69

VAL157.N-LYS100.O 56.49

THR257.OG1-LEU253.O 58.68

HIS163.N-SER147.O 59.48

ILE78.N-LYS90.O 59.48

TRP31.N-CYS16.O 62.67

THR201.OG1-GLU240.O 63.07

TYR182.OH-CYS160.O 63.67

TYR209.OH-ILE259.O 65.67

SER267.OG-ASP263.O 65.67

rep3

Table 2.26 The MD-HBs (with occupancy rates ≥20%) of monomeric the SARS-CoV-1-Mpro-1q2w model (denoted as “SARS-CoV-1 monomer”) and the SARS-CoV-2-Mpro-6y2e model (denoted as “SARS-CoV-2 monomer”), where each model has three sets of MD simulations [346]

2.4 Concluding Remarks 107

GLN192.NE2-VAL186.O 42.12 CYS128.N-PHE112.O 42.12

THR199.N-ASN238.O 39.32 LEU115.N-VAL148.O 39.32

VAL18.N-GLY29.O 44.51

SER123.N-ALA116.O 44.31

TYR37.N-LEU30.O 43.91

LEU75.N-VAL68.O 43.91

THR135.OG1-ASN133.OD1 43.51

CYS22.N-THR25.O 43.31

LEU32.N-THR35.O 42.12

LEU115.N-VAL148.O 41.92

GLN83.N-LEU86.O 41.12

GLN83.N-LEU86.O 44.11

PHE112.N-CYS128.O 44.11

GLN299.N-ASP295.O 44.11

LEU87.N-CYS38.O 43.91

CYS128.N-PHE112.O 43.71

ASN231.N-LEU227.O 43.31

LYS137.N-ALA129.O 43.31

SER123.N-ALA116.O 42.71

LEU27.N-VAL20.O 41.32

LEU205.N-THR201.O 37.52 ILE200.N-ASP289.OD2 37.52

GLY149.N-TYR161.O 40.52

GLN189.N-MET49.O 38.72

THR292.OG1-ASP295.OD1 40.32

TYR37.N-LEU30.O 40.12

GLU14.N-SER10.O 35.73

VAL91.N-ASP34.O 35.53

THR175.OG1-ASP176.O 35.33

LEU30.N-TYR37.O 34.73

THR292.OG1-ASP295.OD2 34.13

THR25.OG1-CYS44.O 34.13

TYR239.N-ALA234.O 33.93

ASN84.ND2-GLU178.O 33.53

ASN95.ND2-TRP31.O 33.33

HIS41.NE2-HIS164.O 32.93

CYS160.N-GLY149.O 32.73

ARG40.NH2-ASP187.OD2 32.53

ASN203.ND2-ASP289.O 32.14

ARG105.NH2-PHE181.O 36.33

ALA70.N-VAL73.O 35.93

TYR182.N-GLY174.O 35.93

LEU268.N-MET264.O 35.73

THR175.OG1-ASP176.O 35.53

THR199.N-ASN238.O 35.13

ALA116.N-GLY124.O 34.33

TYR239.N-ALA234.O 34.13

ALA129.N-LYS137.O 33.93

HIS163.N-SER147.O 33.73

ASN95.ND2-GLY15.O 33.33

CYS160.N-GLY149.O 32.93

ASN84.ND2-GLU178.O 32.93

LEU30.N-TYR37.O 36.53

THR21.N-LEU67.O 36.73

TYR182.N-GLY174.O 36.33

GLY109.N-MET130.O 37.13

GLN192.NE2-VAL186.O 36.53

THR135.OG1-ASN133.OD1 36.73

TYR118.N-SER121.O 36.93

CYS128.N-PHE112.O 36.93

TYR126.N-VAL114.O 38.12

PHE150.N-SER113.O 37.52

CYS160.N-GLY149.O 31.74

ASN95.ND2-TRP31.O 32.14

SER113.OG-GLN127.OE1 32.53

CYS22.N-THR25.O 32.53

THR21.N-LEU67.O 32.93

GLN189.N-MET49.O 32.93

GLY109.N-MET130.O 33.13

TYR182.N-GLY174.O 33.33

HIS80.ND1-ASN63.OD1 33.73

TYR239.N-ALA234.O 34.93

THR45.OG1-ASP48.OD2 35.13

ALA173.N-MET165.O 35.13

TYR54.OH-ASP187.O 35.53

LEU87.N-CYS38.O 36.13

THR175.OG1-ASP176.O 36.73

ASN28.ND2-CYS145.O 37.33

HIS172.N-ILE136.O 37.33

THR199.N-ASN238.O 37.72

ARG131.N-THR135.O 37.52

PHE112.N-CYS128.O 37.33

LEU205.N-THR201.O 38.72

THR198.OG1-GLU240.OE1 38.32

TYR54.OH-ASP187.O 38.12

LEU32.N-THR35.O 38.72

ARG131.NH1-ASP289.OD2 39.12

ASN231.N-LEU227.O 40.72

LEU205.N-THR201.O 40.72

LEU32.N-THR35.O 40.72

TYR118.N-SER121.O 40.32

TYR118.N-SER121.O 39.32

GLY149.N-TYR161.O 39.72

PHE8.N-SER113.OG 39.72

ASN203.ND2-ASP289.O 39.92

GLU14.N-SER10.O 40.12

GLN192.NE2-VAL186.O 40.72

SER147.OG-SER144.O 41.12

ASN231.N-LEU227.O 41.32

TYR126.N-VAL114.O 32.73

LEU67.N-THR21.O 33.13

SER10.OG-GLU14.OE2 33.13

THR292.OG1-ASP295.OD2 33.13

ASN28.ND2-CYS145.O 33.93

THR111.OG1-ASP295.OD2 33.93

ASN95.ND2-TRP31.O 34.73

PHE8.N-SER113.OG 35.53

TYR239.N-ALA234.O 35.93

SER113.OG-GLN127.OE1 37.33

ASN84.ND2-GLU178.O 37.92

GLY109.N-MET130.O 38.12

TYR182.N-GLY174.O 38.12

ILE136.N-HIS172.O 38.52

LEU32.N-VAL35.O 38.92

LEU242.N-ASN231.OD1 39.12

LEU115.N-VAL148.O 39.12

ASN203.ND2-ASP289.O 40.12

GLN83.N-VAL86.O 40.52

PHE150.N-SER113.O 41.12

LYS90.N-GLY79.O 41.52

SER147.OG-SER144.O 41.52

LEU30.N-TYR37.O 41.72

VAL20.N-LEU27.O 42.12

VAL18.N-GLY29.O 42.71

GLN189.N-MET49.O 42.91

ASN231.N-LEU227.O 42.91

VAL91.N-ASP34.O 43.11

GLU14.N-SER10.O 43.31

GLY146.N-HIS163.O 43.51

THR45.OG1-ASP48.OD2 43.71

SARS-CoV-2 rep1 LEU27.N-VAL20.O 44.31

rep3 GLY146.N-HIS163.O 42.32

rep2

ASN95.N-ASP33.O 44.71

SARS-CoV-1 rep1

SER144.OG-LEU141.O 44.31

Table 2.26 (continued) rep2

VAL86.N-GLN83.O 29.94

LEU268.N-MET264.O 30.54

TYR126.N-VAL114.O 31.34

SER158.N-ASN151.O 31.54

SER81.N-LYS88.O 31.74

THR243.OG1-HIS246.ND1 32.14

LYS269.N-CYS265.O 32.14

ALA210.N-ALA206.O 32.34

PHE8.N-SER113.OG 33.53

ILE281.N-SER284.O 33.73

ALA70.N-VAL73.O 33.93

GLN299.NE2-ASP295.O 34.13

SER123.N-ALA116.O 35.13

THR199.N-ASN238.O 35.33

CYS128.N-PHE112.O 35.73

VAL91.N-ASP34.O 35.73

SER147.OG-SER144.O 37.13

LEU32.N-VAL35.O 37.33

ASN203.ND2-ASP289.O 37.52

TYR239.N-ALA234.O 37.92

LYS137.N-ALA129.O 38.52

GLN83.N-VAL86.O 38.72

THR45.OG1-ASP48.OD1 38.92

GLN192.NE2-VAL186.O 39.32

LEU205.N-THR201.O 39.32

ASN231.N-LEU227.O 40.32

PHE112.N-CYS128.O 40.72

GLY109.N-MET130.O 41.12

LEU27.N-VAL20.O 41.52

TYR182.N-GLY174.O 43.11

VAL157.N-LYS100.O 43.11

LYS90.N-GLY79.O 43.51

PHE150.N-SER113.O 43.91

THR175.OG1-ASP176.O 43.91

rep3

THR25.OG1-CYS44.O 32.14

PHE112.N-CYS128.O 32.73

ASN28.ND2-CYS145.O 33.13

THR21.N-LEU67.O 33.53

LEU115.N-VAL148.O 34.13

ALA116.N-GLY124.O 34.13

CYS22.N-THR25.O 34.13

ILE281.N-SER284.O 34.33

LEU30.N-TYR37.O 35.33

THR45.OG1-ASP48.OD2 35.93

ARG131.N-THR135.O 36.53

ASN203.ND2-ASP289.O 37.13

ARG105.NH2-PHE181.O 37.13

GLY146.N-HIS163.O 37.13

ASN95.ND2-TRP31.O 37.52

SER144.OG-LEU141.O 37.52

SER113.OG-GLN127.OE1 38.32

ASN231.N-LEU227.O 38.32

LEU205.N-THR201.O 38.32

PHE8.N-SER113.OG 38.52

LEU32.N-VAL35.O 38.92

GLU14.N-SER10.O 39.52

PHE150.N-SER113.O 40.52

VAL91.N-ASP34.O 40.92

TYR239.N-ALA234.O 40.92

VAL18.N-GLY29.O 41.12

HIS172.N-ILE136.O 41.72

LEU242.N-ASN231.OD1 42.32

GLN83.N-VAL86.O 42.32

THR175.OG1-ASP176.O 42.71

ASN133.ND2-GLY195.O 42.91

LEU75.N-VAL68.O 43.31

CYS128.N-PHE112.O 43.51

LYS88.N-SER81.O 43.91

108 2 3C-Like Protease (3CLpro)

SER62.N-ASN65.OD1 27.15 TRP218.NE1-THR280.O 27.15

ARG131.N-THR135.O 25.55 ARG105.NH1-ASP176.OD1 25.35

SER10.OG-GLU14.OE2 24.35

GLN107.N-GLN110.OE1 24.15

ILE200.N-ASP289.OD1 25.35

VAL91.N-ASP34.O 25.15

ILE200.N-ASP289.OD2 27.15 ALA210.N-ALA206.O 27.15

HIS41.NE2-HIS164.O 25.75 ASN151.N-SER158.O 25.55

GLN192.NE2-VAL186.O 24.95

ASN151.N-SER158.O 24.55

THR292.OG1-ASP295.OD2 25.35

THR198.OG1-GLU240.OE2 25.35

VAL104.N-PHE159.O 27.54 THR198.OG1-GLU240.OE1 27.35

THR292.OG1-ASP295.OD2 26.55 SER254.OG-ILE259.O 25.75

TRP218.NE1-THR280.O 26.35

ILE281.N-SER284.O 25.35

ALA116.N-GLY124.O 25.15

THR198.OG1-GLU240.OE1 25.35

ARG4.NH2-GLU288.OE1 26.55

LYS180.N-ASP176.OD1 25.15

ILE281.N-SER284.O 25.35

GLN19.NE2-ASN28.OD1 26.95 SER113.N-PHE150.O 28.14

ARG105.NH2-PHE181.O 28.94

SER81.N-ARG88.O 27.54

LEU67.N-THR21.O 25.95

ASN151.ND2-THR111.O 26.95 THR198.OG1-GLU240.OE2 26.95

SER10.OG-GLU14.OE1 29.14

LYS180.N-ASP176.OD2 27.74

GLY120.N-ASN28.OD1 26.15

LYS180.N-ASP176.OD2 27.15 ALA173.N-MET165.O 28.94

ARG40.NH2-ASP187.OD2 29.34

LEU67.N-THR21.O 27.74

SER158.N-ASN151.O 26.35

LYS269.N-CYS265.O 27.15

ASN84.ND2-GLU178.O 26.95

THR25.OG1-CYS44.O 29.94

THR98.OG1-ASP33.OD2 27.35

LEU205.N-THR201.O 30.74

ALA116.N-GLY124.O 28.54 SER158.N-ASN151.O 27.94

TYR209.N-LEU205.O 26.55

THR98.OG1-ASP33.OD1 27.74

TYR118.N-SER121.O 30.94

LEU86.N-GLN83.O 28.74

THR292.OG1-ASP295.OD1 26.55

LYS269.N-CYS265.O 26.75

ASN28.ND2-GLY143.O 28.34

SER123.N-ALA116.O 30.94

SER10.OG-GLU14.OE2 28.74

ASN151.N-SER158.O 30.14

TYR126.N-VAL114.O 27.35

SER81.N-ARG88.O 28.74 THR198.OG1-GLU240.OE1 27.94

TYR54.OH-ASP187.O 28.34

ARG131.NH1-ASP289.OD1 29.14

THR199.N-ASN238.O 31.54 CYS160.N-GLY149.O 31.34

ASN231.ND2-LEU242.O 29.94 ILE281.N-SER284.O 29.34

VAL104.N-PHE159.O 28.74

LYS102.N-VAL157.O 28.54

CYS22.N-THR25.O 30.74

ASN231.ND2-LEU242.O 30.14

LEU268.N-MET264.O 31.74 VAL86.N-GLN83.O 31.54

TRP218.NE1-THR280.O 30.74 PHE112.N-CYS128.O 29.94

ARG40.NE-ASP187.OD1 29.54

HIS80.ND1-ASN63.OD1 28.94

ASN133.ND2-GLY195.O 31.14

SER158.N-ASN151.O 31.14

LYS269.N-CYS265.O 32.34 PHE112.N-CYS128.O 32.34 SER158.N-ASN151.O 31.94

VAL91.N-ASP34.O 31.34 LEU268.N-MET264.O 31.34 THR292.OG1-ASP295.OD1 30.74

LEU268.N-MET264.O 30.74

ASN231.ND2-LEU242.O 30.54

ASN28.ND2-CYS145.O 29.94

THR198.OG1-GLU240.OE2 32.34

CYS128.N-PHE112.O 31.54

ILE281.N-SER284.O 32.53

LYS102.N-VAL157.O 31.74

LYS102.N-VAL157.O 32.34

GLY109.N-MET130.O 31.74

CYS300.N-ASP295.O 32.73

SARS-CoV-2 rep1

rep3

PHE8.N-SER113.OG 32.14

PHE8.N-SER113.OG 31.94

GLN19.N-GLN69.O 32.73

HIS172.N-ILE136.O 31.34

rep2

SARS-CoV-1 rep1

ASN84.ND2-GLU178.O 25.55

CYS22.N-THR25.O 25.95

THR292.OG1-ASP295.OD1 26.35

ASN151.N-SER158.O 26.55

SER113.N-PHE150.O 26.55

LYS102.N-VAL157.O 27.15

LEU67.N-THR21.O 27.15

THR21.OG1-THR26.OG1 27.35

ARG105.NH2-PHE181.O 27.74

ALA255.N-GLY251.O 27.74

GLN299.NE2-ARG4.O 27.74

ARG40.NE-ASP187.OD1 27.94

ALA173.N-MET165.O 27.94

TYR209.N-LEU205.O 27.94

ARG60.NH2-ASP48.OD1 28.14

HIS80.ND1-ASN63.OD1 28.34

THR98.OG1-ASP33.OD1 28.34

CYS160.N-GLY149.O 28.54

ARG40.NE-ASP187.OD2 28.74

ASN133.ND2-GLY195.O 28.94

VAL104.N-PHE159.O 28.94

ARG60.NH1-ASP48.OD2 29.14

SER254.OG-ILE259.O 29.14

VAL18.N-GLY29.O 29.34

ALA129.N-LYS137.O 29.74

rep2

(continued)

ARG40.NH2-ASP187.OD2 25.75

SER113.N-PHE150.O 26.15

ASN221.N-SER267.OG 26.55

LEU67.N-THR21.O 28.34

ASN231.ND2-LEU242.O 28.34

GLN299.NE2-ARG4.O 28.34

ARG298.N-PHE294.O 28.94

SER147.OG-SER144.O 29.54

CYS160.N-GLY149.O 30.14

LYS102.N-VAL157.O 30.34

SER123.N-ALA116.O 30.34

TYR54.OH-ASP187.O 30.74

VAL86.N-GLN83.O 30.74

ASN203.ND2-GLY109.O 30.74

TYR118.N-SER121.O 30.74

LYS269.N-CYS265.O 30.94

SER10.OG-GLU14.OE2 30.94

ALA173.N-MET165.O 31.14

THR198.OG1-GLU240.OE2 31.14

LEU268.N-MET264.O 31.34

THR292.OG1-ASP295.OD2 31.34

ILE136.N-HIS172.O 31.54

SER10.OG-GLU14.OE1 31.74

GLN192.NE2-VAL186.O 31.74

TYR126.N-VAL114.O 31.74

rep3

Table 2.27 The MD-HBs (with occupancy rates ≥20%) of monomeric the SARS-CoV-1-Mpro-1q2w model (denoted as “SARS-CoV-1 monomer”) and the SARS-CoV-2-Mpro-6y2e model (denoted as “SARS-CoV-2 monomer”), where each model has three sets of MD simulations [346] (continuation)

2.4 Concluding Remarks 109

THR26.OG1-THR21.OG1 21.36

ARG131.NH2-ASP289.OD1 21.36

LEU208.N-VAL204.O 21.36

ASN28.N-CYS145.O 21.36

ARG105.NH1-ASP176.OD2 20.96

ARG40.NH2-ASP187.OD1 21.56

GLY120.N-GLN19.OE1 21.76

ALA255.N-GLY251.O 20.36

SER254.OG-ILE259.O 21.56

SER301.N-GLY2.O 21.76

GLN83.NE2-GLU178.O 20.96

ARG40.NE-ASP187.OD2 21.76

ARG131.NH2-ASP289.OD2 21.96

SER113.N-PHE150.O 20.96

ASP216.N-ALA211.O 21.76

ALA210.N-ALA206.O 21.96

HIS80.ND1-ASN63.OD1 20.96

THR21.OG1-THR26.OG1 21.96

SER254.OG-ILE259.O 22.36

ARG4.NH1-GLU288.OE2 20.76

ARG217.NH1-ASP216.O 22.75

ASN133.ND2-GLY195.O 22.36

ALA173.N-MET165.O 22.75

LEU30.N-TYR37.O 22.55

TRP218.NE1-THR280.O 23.35

ARG105.NH1-LYS180.O 22.75

ASN95.ND2-TRP31.O 23.15

TYR209.N-LEU205.O 22.95

SER81.N-ARG88.O 23.55

ALA210.N-ALA206.O 23.35

ASN28.ND2-SER147.OG 24.35

LYS5.NZ-ASP295.OD1 24.35

THR292.N-ASP295.OD2 25.75 ASN133.ND2-GLY195.O 25.55

THR21.OG1-THR26.OG1 23.95

HIS164.N-ALA173.O 21.36

MET130.N-GLN110.O 21.96

THR25.OG1-CYS44.O 21.96

ARG131.NH2-ASP289.OD1 22.16

VAL104.N-PHE159.O 22.36

GLN107.N-GLN110.OE1 22.95

VAL186.N-GLN192.OE1 23.15

TYR101.OH-ASP33.OD2 23.15

ALA255.N-GLY251.O 23.35

GLN69.N-GLN19.O 23.35

GLY120.N-ASN28.OD1 23.55

ILE136.N-HIS172.O 23.95

GLN69.N-GLN19.O 21.76 GLN273.N-LYS269.O 21.56

THR292.N-ASP295.OD1 21.96 ASN180.N-ASP176.OD1 21.76

VAL186.N-GLN192.OE1 20.16

ARG131.NH2-ASP289.OD2 21.96

LEU272.N-LEU268.O 20.56 CYS265.N-VAL261.O 20.56 ASN180.N-ASP176.OD1 20.56 SER254.N-LEU250.O 20.36

THR26.OG1-THR21.OG1 20.56 ASN180.N-ASP176.OD2 20.56 LEU272.N-LEU268.O 20.36 ASP216.N-ALA211.O 20.36

ASN28.N-CYS145.O 20.36

ARG131.NH2-ASP289.OD1 20.96 ASN180.N-ASP176.OD2 20.56

ARG298.N-PHE294.O 21.76 TYR54.OH-ASP187.O 21.76 LEU115.N-VAL148.O 21.56

THR21.OG1-THR26.OG1 21.96

GLY120.N-GLN19.OE1 22.55 THR226.OG1-ASP229.OD2 22.36

TYR101.OH-ASP33.OD1 21.36

HIS164.N-ALA173.O 22.16

TRP218.NE1-THR280.O 22.16

TYR209.N-LEU205.O 22.36

MET130.N-GLN110.O 22.75

SER62.N-ASN65.OD1 22.75

SER121.N-TYR118.O 22.75

HIS41.NE2-HIS164.O 23.15

THR243.OG1-HIS246.ND1 23.15

CYS156.N-ASP153.O 23.35

LEU208.N-VAL204.O 23.55

THR292.OG1-ASP295.OD1 23.55

ALA255.N-GLY251.O 23.75

THR111.OG1-ASP295.OD1 24.15

GLY120.N-ASN28.OD1 24.15

SER158.N-ASN151.O 24.35

ASN151.N-SER158.O 24.55

HIS80.ND1-ASN63.OD1 24.55

THR45.OG1-ASP48.OD1 24.75

GLN107.N-GLN110.OE1 24.75

SER254.OG-ILE259.O 24.95

VAL104.N-PHE159.O 25.15

THR198.OG1-GLU240.OE1 25.35

SER81.N-LYS88.O 25.35

GLN189.N-MET49.O 25.55

rep3

ASN180.N-ASP176.OD1 20.16

THR45.OG1-ASP48.OD2 22.75 ARG40.NH2-ASP187.OD1 22.55

ASN274.ND2-GLU270.O 21.36 ALA255.N-GLY251.O 21.36

THR111.OG1-ASP295.OD2 22.95 TYR161.OH-HIS172.ND1 22.95

THR21.N-LEU67.O 21.56

GLN19.NE2-ASN28.OD1 23.35

SER10.OG-GLU14.OE1 23.35

THR198.OG1-GLU240.OE1 23.75

THR98.OG1-ASP33.OD2 23.75

ALA116.N-GLY124.O 23.95

GLY146.N-HIS163.O 23.95

ASN95.ND2-TRP31.O 24.15

ARG40.NH2-ASP187.OD2 24.35

HIS172.N-ILE136.O 24.55

ASN221.N-SER267.OG 24.55

ASN151.ND2-THR111.O 24.55

ILE200.N-ASP289.OD1 24.95

GLU14.N-SER10.O 24.95

ASN231.ND2-LEU242.O 25.15

GLN19.N-GLN69.O 25.15

LEU30.N-TYR37.O 25.15

SER113.OG-GLN127.OE1 25.35

TRP218.NE1-THR280.O 25.55

SER10.OG-GLU14.OE2 25.55

THR198.OG1-GLU240.OE2 25.55

rep2

ARG40.NE-ASP187.OD2 21.36

ARG40.NH2-ASP187.OD1 21.56

ASN231.ND2-LEU242.O 21.56

ASP216.N-ALA211.O 21.76

TYR101.OH-ASP33.OD2 21.96

TYR209.N-LEU205.O 21.96

GLN273.N-LYS269.O 22.55

GLN69.N-GLN19.O 23.55

THR243.OG1-HIS246.ND1 23.75

ALA116.N-GLY124.O 23.75

ASN221.N-SER267.OG 24.15

ASN180.N-ASP176.OD2 24.35

GLN107.N-GLN110.OE1 24.35

LYS102.N-VAL157.O 24.55

SER254.OG-ILE259.O 24.95

ASN203.ND2-GLY109.O 25.15

HIS80.ND1-ASN63.OD1 25.15

SER10.OG-GLU14.OE1 24.35 ALA210.N-ALA206.O 24.15 ALA234.N-PHE230.O 24.15

ALA255.N-GLY251.O 23.55

LEU208.N-VAL204.O 23.55

ALA234.N-PHE230.O 23.55

ALA234.N-PHE230.O 24.35

THR21.OG1-THR26.OG1 24.35

LEU67.N-THR21.O 24.35

ARG131.NE-ASP197.OD2 25.95

LYS269.N-CYS265.O 24.95

SER10.OG-GLU14.OE1 23.75

THR292.N-ASP295.OD1 24.75

SARS-CoV-2 rep1 ARG40.NE-ASP187.OD1 27.15

TYR126.N-VAL114.O 24.95

CYS117.N-GLY143.O 24.95

rep3

rep2

LEU86.N-GLN83.O 24.15

SARS-CoV-1 rep1

Table 2.27 (continued)

110 2 3C-Like Protease (3CLpro)

2.4 Concluding Remarks

111

Table 2.28 The MD-HBs (with occupancy rates ≥20%) of dimer the SARS-CoV-1-Mpro-1q2w model (denoted as “SARS-CoV-1 dimer”) —the model has three sets of MD simulations [346] SARS-CoV-1 rep1

rep2

rep3

A:TYR118.OH-B:ARG298.O 35.86%

A:SER139.OG-B:GLN299.OE1 54.38%

B:GLN299.NE2-A:SER139.O 47.61%

A:SER139.OG-B:GLY2.O 32.67%

B:VAL125.N-A:ALA7.O 34.46%

B:ARG4.NH1-A:GLU290.OE2 40.84%

A:ALA7.N-B:VAL125.O 28.69%

A:GLY11.N-B:GLU14.OE2 31.47%

A:ARG4.NH2-B:GLU290.OE2 39.04%

A:GLY11.N-B:GLU14.OE2 28.49%

A:VAL125.N-B:ALA7.O 31.27%

A:GLY11.N-B:GLU14.OE2 37.25%

B:ARG4.NH2-A:GLU290.OE1 30.08%

B:ALA7.N-A:VAL125.O 30.88%

A:ALA7.N-B:VAL125.O 32.27%

B:VAL125.N-A:ALA7.O 25.30%

B:ARG4.NH1-A:GLU290.OE1 29.88%

B:ARG4.NH2-A:GLU290.OE1 35.46%

B:ARG4.NH1-A:GLU290.OE2 24.30%

B:ARG4.NH2-A:GLU290.OE2 29.48%

A:TYR118.OH-B:ARG298.O 29.48%

B:GLY11.N-A:GLU14.OE2 23.71%

B:GLY11.N-A:GLU14.OE2 28.49%

A:ARG4.NH1-B:GLU290.OE1 28.29%

B:ARG4.NH2-A:GLU290.OE2 21.31%

A:ARG4.NH1-B:GLU290.OE1 22.51%

A:ARG4.NH2-B:GLU290.OE1 25.10%

A:ARG4.N-B:SER139.OG 20.32%

A:ARG4.NH2-B:GLU290.OE2 21.51%

A:VAL125.N-B:ALA7.O 20.12%

B:GLY11.N-A:GLU14.OE2 23.71% A:VAL125.N-B:ALA7.O 21.12%

A:SER10.OG-A:GLU14.OE2 82.47%

A:SER10.OG-A:GLU14.OE2 85.46%

A:SER10.OG-A:GLU14.OE2 84.46%

A:TYR209.OH-A:ILE259.O 65.94%

A:TRP31.N-A:CYS16.O 66.93%

A:TYR209.OH-A:ILE259.O 69.92%

A:TYR182.OH-A:CYS160.O 64.74%

A:THR201.OG1-A:GLU240.O 65.54%

A:THR201.OG1-A:GLU240.O 66.73%

A:TRP31.N-A:CYS16.O 62.95%

A:TYR182.OH-A:CYS160.O 63.75%

A:TYR182.OH-A:CYS160.O 63.55%

A:THR201.OG1-A:GLU240.O 62.55%

A:TYR209.OH-A:ILE259.O 62.15%

A:ILE78.N-A:LYS90.O 63.35%

A:VAL36.N-A:LEU89.O 60.36%

A:THR257.OG1-A:LEU253.O 59.96%

A:TRP31.N-A:CYS16.O 62.35%

A:HIS163.N-A:SER147.O 59.16%

A:HIS163.N-A:SER147.O 59.96%

A:SER147.OG-A:SER144.O 60.76%

A:SER147.OG-A:SER144.O 59.16%

A:ILE78.N-A:LYS90.O 59.56%

A:HIS163.N-A:SER147.O 60.56%

A:ILE78.N-A:LYS90.O 58.76%

A:VAL36.N-A:LEU89.O 58.37%

A:GLY149.N-A:TYR161.O 60.36%

A:THR257.OG1-A:LEU253.O 56.77%

A:VAL20.N-A:LEU27.O 56.18%

A:LEU115.N-A:VAL148.O 56.77%

A:GLY149.N-A:TYR161.O 56.37%

A:LEU87.N-A:CYS38.O 53.78%

A:VAL36.N-A:LEU89.O 55.18%

A:LEU167.N-A:VAL171.O 53.78%

A:VAL114.N-A:TYR126.O 53.19%

A:PHE150.N-A:SER113.O 53.59%

A:PHE150.N-A:SER113.O 52.99%

A:LEU167.N-A:VAL171.O 52.99%

A:THR257.OG1-A:LEU253.O 53.59%

A:VAL157.N-A:LYS100.O 52.99%

A:LYS90.N-A:GLY79.O 51.59%

A:VAL114.N-A:TYR126.O 51.79%

A:HIS172.N-A:ILE136.O 52.59%

A:GLY146.N-A:HIS163.O 50.80%

A:LEU167.N-A:VAL171.O 51.59%

A:ARG131.N-A:THR135.O 52.59%

A:VAL157.N-A:LYS100.O 49.80%

A:ARG131.N-A:THR135.O 51.59%

A:LEU89.N-A:VAL36.O 51.79%

A:GLN19.N-A:GLN69.O 49.40%

A:LEU89.N-A:VAL36.O 51.20%

A:VAL114.N-A:TYR126.O 51.79%

A:LEU115.N-A:VAL148.O 49.20%

A:LYS90.N-A:GLY79.O 50.60%

A:ASN203.ND2-A:GLY109.O 50.60%

A:SER147.OG-A:SER144.O 48.41%

A:THR135.OG1-A:ASN133.OD1 50.60%

A:GLN192.NE2-A:VAL186.O 50.60%

A:TYR37.N-A:LEU30.O 48.21%

A:LEU87.N-A:CYS38.O 50.40%

A:SER123.N-A:ALA116.O 49.80%

A:ASN203.ND2-A:GLY109.O 48.01%

A:VAL157.N-A:LYS100.O 50.20%

A:THR135.OG1-A:ASN133.OD1 49.80%

A:LEU89.N-A:VAL36.O 47.81%

A:LEU30.N-A:TYR37.O 49.60%

A:LEU115.N-A:VAL148.O 49.20%

A:ARG88.N-A:SER81.O 47.61%

A:GLN19.N-A:GLN69.O 49.00%

A:GLN19.N-A:GLN69.O 48.80%

A:THR135.OG1-A:ASN133.OD1 47.01%

A:SER123.N-A:ALA116.O 47.61%

A:ARG88.N-A:SER81.O 47.81%

A:HIS172.N-A:ILE136.O 46.81%

A:HIS172.N-A:ILE136.O 47.01%

A:LYS90.N-A:GLY79.O 47.61%

A:ASN203.ND2-A:ASP289.O 46.81%

A:TYR37.N-A:LEU30.O 47.01%

A:LEU87.N-A:CYS38.O 47.21%

A:GLY149.N-A:TYR161.O 46.61%

A:ASN95.N-A:ASP33.O 44.42%

A:LEU27.N-A:VAL20.O 47.21%

A:ASN95.N-A:ASP33.O 45.82%

A:PHE8.N-A:SER113.OG 44.22%

A:TYR37.N-A:LEU30.O 46.61%

A:LEU242.N-A:ASN231.OD1 45.22%

A:ASN28.ND2-A:CYS145.O 43.23%

A:LEU242.N-A:ASN231.OD1 46.22%

A:ARG105.NH2-A:PHE181.O 45.02%

A:VAL18.N-A:GLY29.O 43.23%

A:ARG105.NH2-A:PHE181.O 45.22%

A:LEU75.N-A:VAL68.O 44.02%

A:ARG88.N-A:SER81.O 43.23%

A:PHE8.N-A:SER113.OG 45.22%

A:LEU27.N-A:VAL20.O 44.02%

A:SER113.OG-A:GLN127.OE1 42.43%

A:ALA70.N-A:VAL73.O 44.62%

A:ALA70.N-A:VAL73.O 43.82%

A:ALA70.N-A:VAL73.O 42.43%

A:ASN95.N-A:ASP33.O 44.02%

A:GLY109.N-A:MET130.O 43.82%

A:LEU242.N-A:ASN231.OD1 42.03%

A:LEU75.N-A:VAL68.O 43.63%

A:PHE8.N-A:SER113.OG 43.82%

A:GLY146.N-A:HIS163.O 41.83%

A:LEU30.N-A:TYR37.O 42.23%

A:SER123.N-A:ALA116.O 43.43%

A:LEU27.N-A:VAL20.O 41.63%

A:CYS128.N-A:PHE112.O 42.03%

A:PHE150.N-A:SER113.O 42.63%

A:LEU75.N-A:VAL68.O 40.84%

A:ASN231.N-A:LEU227.O 41.83%

A:PHE112.N-A:CYS128.O 41.83%

A:SER144.OG-A:LEU141.O 40.64%

A:GLY146.N-A:HIS163.O 41.24%

A:ARG131.N-A:THR135.O 41.63%

A:SER158.N-A:ASN151.O 40.64%

A:VAL20.N-A:LEU27.O 40.64%

A:VAL18.N-A:GLY29.O 41.63%

A:ARG105.NH2-A:PHE181.O 40.44%

A:VAL18.N-A:GLY29.O 40.64%

A:THR199.N-A:ASN238.O 40.64%

A:ASN203.ND2-A:ASP289.O 40.24%

A:ASN28.ND2-A:CYS145.O 39.84%

A:SER144.OG-A:LEU141.O 39.84%

A:ASN203.ND2-A:GLY109.O 39.84%

A:THR175.OG1-A:ASP176.O 39.44%

A:LEU32.N-A:THR35.O 38.84%

A:LEU205.N-A:THR201.O 39.24%

A:LEU32.N-A:THR35.O 38.84%

A:ASN231.N-A:LEU227.O 38.84%

A:THR199.N-A:ASN238.O 39.04%

A:GLN83.N-A:LEU86.O 38.84%

A:LEU30.N-A:TYR37.O 38.65%

A:LEU32.N-A:THR35.O 38.25%

A:ASN203.ND2-A:ASP289.O 36.25%

A:TYR118.N-A:SER121.O 37.85%

A:ASN231.N-A:LEU227.O 37.85%

A:SER113.OG-A:GLN127.OE1 36.06%

A:ASN95.ND2-A:TRP31.O 37.45%

A:THR175.OG1-A:ASP176.O 37.65%

A:THR198.OG1-A:GLU240.OE2 35.46%

A:ILE281.N-A:SER284.O 37.05%

A:LYS5.NZ-A:GLU290.OE2 36.65%

A:ASN133.ND2-A:GLY195.O 34.86%

A:THR45.OG1-A:HIS41.O 36.45%

A:GLN192.NE2-A:VAL186.O 36.25%

A:ASN95.ND2-A:TRP31.O 34.86%

A:ILE136.N-A:HIS172.O 36.06%

A:TYR239.N-A:ALA234.O 36.06%

A:THR21.N-A:LEU67.O 34.66%

A:ALA7.N-B:VAL125.O 35.86%

A:VAL91.N-A:ASP34.O 35.46%

A:CYS22.N-A:THR25.O 34.46%

A:GLU14.N-A:SER10.O 35.66%

A:LEU268.N-A:MET264.O 35.46%

A:ASN231.ND2-A:LEU242.O 34.06%

A:ARG40.NH2-A:ASP187.OD2 34.86%

A:CYS128.N-A:PHE112.O 35.46%

(continued)

112

2 3C-Like Protease (3CLpro)

Table 2.28 (continued) SARS-CoV-1 rep1

rep2

rep3

A:TYR182.N-A:GLY174.O 33.47%

A:CYS128.N-A:PHE112.O 34.66%

A:PHE112.N-A:CYS128.O 34.26%

A:SER158.N-A:ASN151.O 33.07%

A:THR175.OG1-A:ASP176.O 33.86%

A:ASN95.ND2-A:TRP31.O 34.26%

A:VAL91.N-A:ASP34.O 32.87%

A:ASN28.ND2-A:CYS145.O 33.67%

A:THR292.OG1-A:ASP295.OD2 33.47%

A:GLU14.N-A:SER10.O 32.67%

A:THR21.N-A:LEU67.O 33.67%

A:THR26.OG1-A:THR21.OG1 32.87%

A:ILE281.N-A:SER284.O 32.67%

A:LEU205.N-A:THR201.O 33.47%

A:GLN83.N-A:LEU86.O 32.07%

A:PHE112.N-A:CYS128.O 32.67%

A:GLN83.N-A:LEU86.O 33.47%

A:ASN119.N-A:GLY143.O 32.07%

A:TYR118.N-A:SER121.O 32.27%

A:VAL91.N-A:ASP34.O 33.27%

A:ASN84.ND2-A:GLU178.O 30.68%

A:THR198.OG1-A:GLU240.OE1 31.87%

A:ALA116.N-A:GLY124.O 33.07%

A:THR198.OG1-A:GLU240.OE2 30.48%

A:GLN299.NE2-A:ARG4.O 31.67%

A:SER158.N-A:ASN151.O 32.47%

A:ASN119.ND2-A:THR26.O 30.48%

A:TYR239.N-A:ALA234.O 31.47%

A:THR198.OG1-A:GLU240.OE1 32.07%

A:LEU67.N-A:THR21.O 30.08%

A:LEU268.N-A:MET264.O 31.27%

A:ARG60.NH2-A:GLU47.OE2 31.87%

A:TYR118.N-A:SER121.O 29.68%

A:LEU67.N-A:THR21.O 31.27%

A:ASN84.ND2-A:GLU178.O 31.67%

A:ILE281.N-A:SER284.O 29.68%

A:THR199.N-A:ASN238.O 31.08%

A:ASN231.ND2-A:LEU242.O 31.67%

A:TRP218.NE1-A:THR280.O 29.68%

A:ALA173.N-A:MET165.O 30.08%

A:CYS22.N-A:THR25.O 31.27%

A:ASN133.ND2-A:GLY195.O 29.68%

Table 2.29 The MD-HBs (with occupancy rates ≥20%) of dimer the SARS-CoV-1-Mpro-1q2w model (denoted as “SARS-CoV-1 dimer”) —the model has three sets of MD simulations [346] (continuation-1) A:SER144.OG-A:LEU141.O 29.68%

A:TYR182.N-A:GLY174.O 30.88%

A:TYR182.N-A:GLY174.O 29.48%

A:ASN214.ND2-A:ALA210.O 29.48%

A:TYR239.N-A:ALA234.O 30.68%

A:GLY109.N-A:MET130.O 29.28%

A:TRP218.NE1-A:THR280.O 29.08%

A:ARG60.NH1-A:GLU47.OE1 30.48%

A:VAL20.N-A:LEU27.O 29.28%

A:SER81.N-A:ARG88.O 28.88%

A:TRP218.NE1-A:THR280.O 30.08%

A:PHE159.N-A:LYS102.O 28.69%

A:THR111.OG1-A:ASP295.OD2 28.29%

A:ARG40.NE-A:ASP187.OD1 29.68%

A:HIS80.ND1-A:ASN63.OD1 28.29%

A:ARG298.NH1-A:MET6.O 28.09%

A:CYS44.N-A:ARG40.O 29.48%

A:ASN231.ND2-A:LEU242.O 28.09%

A:LEU208.N-A:VAL204.O 27.49%

A:SER113.N-A:PHE150.O 29.08%

A:SER81.N-A:ARG88.O 28.09%

A:VAL104.N-A:PHE159.O 27.29%

A:ILE43.N-A:ARG40.O 29.08%

A:ARG40.NH2-A:ASP187.OD1 27.89%

A:GLY109.N-A:MET130.O 27.29%

A:SER81.N-A:ARG88.O 28.88%

A:HIS164.N-A:ALA173.O 27.49%

A:LEU205.N-A:THR201.O 27.09%

A:LYS102.N-A:VAL157.O 28.29%

A:ALA173.N-A:MET165.O 27.49%

A:ASN95.ND2-A:GLY15.O 26.69%

A:ASN133.ND2-A:GLY195.O 28.09%

A:GLU14.N-A:SER10.O 27.09%

A:ALA234.N-A:PHE230.O 26.29%

A:ASN151.ND2-A:THR111.O 28.09%

A:THR21.N-A:LEU67.O 27.09%

A:LYS269.N-A:CYS265.O 26.10%

A:ALA173.N-A:MET165.O 27.89%

A:TYR161.OH-A:HIS172.ND1 26.89%

A:CYS160.N-A:GLY149.O 26.10%

A:LEU268.N-A:MET264.O 27.69%

A:LYS269.N-A:CYS265.O 26.10%

A:ILE136.N-A:HIS172.O 25.70%

A:THR292.OG1-A:ASP295.OD2 26.69%

A:CYS160.N-A:GLY149.O 25.90%

A:HIS164.N-A:ALA173.O 25.70%

A:SER254.OG-A:ILE259.O 26.49%

A:SER113.N-A:PHE150.O 25.50%

A:LYS102.N-A:VAL157.O 25.30%

A:ARG105.NH1-A:ASP176.OD2 26.29%

A:ILE136.N-A:HIS172.O 25.30%

A:LYS5.NZ-A:GLU288.OE2 25.30%

A:LEU67.N-A:THR21.O 25.70%

A:ALA234.N-A:PHE230.O 25.10%

A:LEU86.N-A:GLN83.O 25.10%

A:THR198.OG1-A:GLU240.OE2 25.70%

A:GLN299.NE2-A:VAL296.O 24.50%

A:TYR54.OH-A:ASP187.O 24.90%

A:GLN69.N-A:GLN19.O 24.90%

A:LYS102.N-A:VAL157.O 24.30%

A:SER254.OG-A:ILE259.O 24.90%

A:ARG131.NH2-A:ASP289.OD1 24.90%

A:LYS180.N-A:ASP176.OD1 24.10%

A:THR111.OG1-A:ASP295.OD1 24.90%

A:LYS269.N-A:CYS265.O 24.70%

A:THR198.OG1-A:GLU240.OE1 24.10%

A:PHE159.N-A:LYS102.O 23.90%

A:SER113.OG-A:GLN127.OE1 24.50%

A:ARG40.NH2-A:ASP187.OD2 23.90%

A:LYS180.N-A:ASP176.OD1 23.90%

A:LYS180.N-A:ASP176.OD1 24.50%

A:ARG105.NH1-A:ASP176.OD1 23.11%

A:ASN84.ND2-A:GLU178.O 23.31%

A:LEU208.N-A:VAL204.O 24.50%

A:LEU208.N-A:VAL204.O 22.91%

A:SER113.N-A:PHE150.O 22.71%

A:ALA234.N-A:PHE230.O 24.30%

A:VAL104.N-A:PHE159.O 22.31%

A:LYS5.NZ-A:GLU290.OE1 22.11%

A:ALA255.N-A:GLY251.O 24.30%

A:LYS180.N-A:ASP176.OD2 22.31%

A:ARG105.NH1-A:ASP176.OD2 21.51%

A:GLN192.NE2-A:VAL186.O 23.90%

A:SER254.OG-A:ILE259.O 21.51%

A:ASN151.N-A:SER158.O 21.31%

A:ASN214.ND2-A:ALA210.O 23.71%

A:LEU86.N-A:GLN83.O 21.51%

A:HIS80.ND1-A:ASN63.OD1 20.92%

A:ARG40.NH2-A:ASP187.OD1 22.91%

A:GLN273.N-A:LYS269.O 21.91%

A:ASN151.ND2-A:THR111.O 20.92%

A:LYS5.NZ-A:GLU290.OE1 22.71%

A:ARG105.NH1-A:ASP176.OD2 21.31%

A:ASN274.N-A:GLU270.O 20.52%

A:SER254.N-A:LEU250.O 22.71%

A:ARG131.NH2-A:ASP289.OD1 21.31%

A:TYR209.N-A:LEU205.O 20.52%

A:THR26.OG1-A:THR21.OG1 22.51%

A:TYR101.OH-A:ASP33.OD2 21.31%

A:LYS5.NZ-A:GLU290.OE2 20.52%

A:GLN107.N-A:GLN110.OE1 22.51%

A:GLN83.NE2-A:GLU178.O 20.92%

A:ALA255.N-A:GLY251.O 20.32%

A:THR292.OG1-A:ASP295.OD1 22.31%

A:ALA116.N-A:GLY124.O 20.72%

A:THR292.OG1-A:ASP295.OD2 20.32%

A:LEU86.N-A:GLN83.O 22.31%

A:TYR209.N-A:LEU205.O 20.72%

A:GLN273.N-A:LYS269.O 20.32%

A:VAL104.N-A:PHE159.O 22.11%

A:ARG40.NE-A:ASP187.OD1 20.72%

A:LYS180.N-A:ASP176.OD2 20.32%

A:GLY120.N-A:ASN28.OD1 21.51%

A:ASN221.ND2-A:PHE223.O 20.52%

A:GLN83.NE2-A:GLU178.O 20.12%

A:ARG131.NH2-A:ASP289.OD2 21.31%

A:LYS5.NZ-A:GLU288.OE2 20.32%

A:ASN95.ND2-A:GLY15.O 21.31%

A:ASP92.N-A:ARG76.O 20.32%

B:SER10.OG-B:GLU14.OE2 82.87%

A:CYS160.N-A:GLY149.O 21.31%

A:THR45.OG1-A:HIS41.O 20.12%

B:TYR209.OH-B:ILE259.O 67.53%

A:THR111.OG1-A:ASP295.OD1 21.31%

(continued)

2.4 Concluding Remarks

113

Table 2.29 (continued) B:TYR54.OH-B:ASP187.O 66.33%

A:ILE213.N-A:TYR209.O 21.31%

B:SER10.OG-B:GLU14.OE2 85.26%

B:HIS163.N-B:SER147.O 64.94%

A:PHE159.N-A:LYS102.O 20.92%

B:TYR54.OH-B:ASP187.O 73.90%

B:THR201.OG1-B:GLU240.O 64.34%

A:THR21.OG1-A:THR26.OG1 20.92%

B:TYR209.OH-B:ILE259.O 68.33%

B:TYR182.OH-B:CYS160.O 63.94%

A:THR98.OG1-A:ASN95.O 20.72%

B:ARG40.NH2-B:ASP187.OD1 67.33%

B:TRP31.N-B:CYS16.O 63.75%

A:TYR101.OH-A:ASP33.OD2 20.72%

B:THR201.OG1-B:GLU240.O 63.75%

B:SER147.OG-B:SER144.O 61.55%

A:ARG40.NE-A:ASP187.OD2 20.52%

B:SER147.OG-B:SER144.O 63.15%

B:VAL36.N-B:LEU89.O 60.76%

A:TRP207.N-A:ASN203.O 20.32%

B:TRP31.N-B:CYS16.O 62.55%

B:ILE78.N-B:LYS90.O 58.76%

A:ARG4.NH2-B:GLU290.OE1 20.12%

B:ILE78.N-B:LYS90.O 60.76%

B:THR257.OG1-B:LEU253.O 57.97%

A:LYS5.NZ-A:GLU288.OE1 20.12%

B:TYR182.OH-B:CYS160.O 59.16%

B:LEU89.N-B:VAL36.O 55.58%

B:THR135.OG1-B:ASN133.OD1 58.96%

B:LEU115.N-B:VAL148.O 53.59%

B:SER10.OG-B:GLU14.OE2 84.46%

B:HIS163.N-B:SER147.O 58.76%

B:LEU87.N-B:CYS38.O 52.59%

B:TYR209.OH-B:ILE259.O 66.33%

B:VAL114.N-B:TYR126.O 57.97%

B:VAL157.N-B:LYS100.O 52.59%

B:SER147.OG-B:SER144.O 65.14%

B:THR257.OG1-B:LEU253.O 56.77%

B:LEU167.N-B:VAL171.O 51.99%

B:TRP31.N-B:CYS16.O 63.75%

B:ARG131.N-B:THR135.O 53.98%

B:THR135.OG1-B:ASN133.OD1 50.80%

B:ILE78.N-B:LYS90.O 63.35%

B:GLY149.N-B:TYR161.O 53.98%

B:VAL114.N-B:TYR126.O 50.00%

B:THR201.OG1-B:GLU240.O 62.95%

B:THR25.OG1-B:CYS44.O 53.78%

B:GLN19.N-B:GLN69.O 49.40%

B:THR257.OG1-B:LEU253.O 58.17%

B:LEU87.N-B:CYS38.O 53.39%

B:VAL20.N-B:LEU27.O 49.00%

B:HIS163.N-B:SER147.O 57.37%

B:ARG40.NE-B:ASP187.OD2 53.39%

B:GLY146.N-B:HIS163.O 48.41%

B:LEU167.N-B:VAL171.O 56.97%

B:LEU167.N-B:VAL171.O 53.39%

B:TYR37.N-B:LEU30.O 48.01%

B:TYR54.OH-B:ASP187.O 56.77%

B:PHE112.N-B:CYS128.O 51.59%

B:ARG88.N-B:SER81.O 48.01%

B:LEU115.N-B:VAL148.O 56.57%

B:VAL36.N-B:LEU89.O 51.39%

B:PHE150.N-B:SER113.O 47.61%

B:TYR182.OH-B:CYS160.O 55.38%

B:PHE150.N-B:SER113.O 50.40%

B:LEU75.N-B:VAL68.O 46.22%

B:THR25.OG1-B:CYS44.O 53.78%

B:GLN19.N-B:GLN69.O 50.20%

B:LYS90.N-B:GLY79.O 46.22%

B:VAL36.N-B:LEU89.O 53.78%

B:ASN95.N-B:ASP33.O 49.80%

B:ASN95.N-B:ASP33.O 46.22%

B:GLY109.N-B:MET130.O 53.59%

B:VAL20.N-B:LEU27.O 49.60%

B:ALA70.N-B:VAL73.O 45.82%

B:LEU87.N-B:CYS38.O 52.99%

B:ASN203.ND2-B:GLY109.O 48.61%

B:PHE112.N-B:CYS128.O 45.42%

B:VAL157.N-B:LYS100.O 52.59%

B:PHE8.N-B:SER113.OG 48.41%

B:GLY109.N-B:MET130.O 44.62%

B:LEU27.N-B:VAL20.O 51.99%

B:LEU242.N-B:ASN231.OD1 47.81%

B:HIS172.N-B:ILE136.O 44.62%

B:VAL20.N-B:LEU27.O 51.59%

B:LEU75.N-B:VAL68.O 47.21%

B:LEU27.N-B:VAL20.O 44.42%

B:ARG40.NH2-B:ASP187.OD1 51.39%

B:CYS22.N-B:THR25.O 47.21%

B:GLY149.N-B:TYR161.O 42.43%

B:GLY146.N-B:HIS163.O 49.80%

B:ASN203.ND2-B:ASP289.O 46.61%

B:LEU32.N-B:THR35.O 42.03%

B:GLY149.N-B:TYR161.O 49.80%

B:ASN133.ND2-B:GLY195.O 46.41%

B:SER123.N-B:ALA116.O 41.43%

B:GLN299.NE2-B:ARG4.O 48.21%

B:VAL157.N-B:LYS100.O 45.62%

B:PHE8.N-B:SER113.OG 41.04%

B:GLN19.N-B:GLN69.O 47.81%

B:LYS90.N-B:GLY79.O 45.22%

B:VAL18.N-B:GLY29.O 40.64%

B:VAL114.N-B:TYR126.O 47.41%

B:SER123.N-B:ALA116.O 44.62%

B:LEU242.N-B:ASN231.OD1 40.44%

B:ALA70.N-B:VAL73.O 47.41%

B:LEU27.N-B:VAL20.O 44.22%

B:TYR182.N-B:GLY174.O 40.24%

B:LYS90.N-B:GLY79.O 47.21%

B:ALA70.N-B:VAL73.O 44.22%

B:CYS128.N-B:PHE112.O 39.64%

B:HIS172.N-B:ILE136.O 46.22%

B:ASN231.N-B:LEU227.O 44.02%

114

2 3C-Like Protease (3CLpro)

Table 2.30 The MD-HBs (with occupancy rates ≥20%) of dimer the SARS-CoV-1-Mpro-1q2w model (denoted as “SARS-CoV-1 dimer”) —the model has three sets of MD simulations [346] (continuation-2) B:ASN133.ND2-B:GLY195.O 39.44%

B:SER123.N-B:ALA116.O 46.02%

B:VAL18.N-B:GLY29.O 43.82%

B:TYR118.N-B:SER121.O 39.44%

B:ASN95.N-B:ASP33.O 44.82%

B:LEU205.N-B:THR201.O 43.43%

B:GLN299.NE2-B:ARG4.O 39.44%

B:LEU75.N-B:VAL68.O 44.02%

B:LEU32.N-B:THR35.O 43.03%

B:ARG131.N-B:THR135.O 39.24%

B:ARG88.N-B:SER81.O 44.02%

B:LEU115.N-B:VAL148.O 42.03%

B:ARG105.NH2-B:PHE181.O 38.84%

B:PHE150.N-B:SER113.O 43.63%

B:TYR118.N-B:SER121.O 41.83%

B:ASN84.ND2-B:GLU178.O 38.84%

B:ARG105.NH2-B:PHE181.O 43.43%

B:ARG88.N-B:SER81.O 41.43%

B:ASN28.ND2-B:CYS145.O 38.65%

B:LEU89.N-B:VAL36.O 42.43%

B:ASN28.ND2-B:CYS145.O 41.43%

B:THR199.N-B:ASN238.O 37.85%

B:TYR118.N-B:SER121.O 42.23%

B:ASN51.ND2-B:ASN53.O 40.24%

B:ALA173.N-B:MET165.O 37.25%

B:PHE8.N-B:SER113.OG 41.43%

B:LEU89.N-B:VAL36.O 39.84%

B:ASN231.N-B:LEU227.O 37.05%

B:ASN203.ND2-B:ASP289.O 41.24%

B:TYR37.N-B:LEU30.O 39.64%

B:LEU30.N-B:TYR37.O 36.65%

B:LEU205.N-B:THR201.O 40.84%

B:ALA173.N-B:MET165.O 38.84%

B:THR292.OG1-B:ASP295.OD2 36.06%

B:ARG40.NE-B:ASP187.OD2 40.44%

B:THR111.OG1-B:ASP295.OD1 37.65%

B:ASN203.ND2-B:ASP289.O 36.06%

B:CYS22.N-B:THR25.O 40.04%

B:THR199.N-B:ASN238.O 37.45%

B:ASN203.ND2-B:GLY109.O 35.86%

B:CYS128.N-B:PHE112.O 39.64%

B:SER113.OG-B:GLN127.OE1 36.85%

B:ILE200.N-B:ASP289.OD1 35.46%

B:TYR37.N-B:LEU30.O 39.24%

B:GLY146.N-B:HIS163.O 36.85%

B:SER158.N-B:ASN151.O 35.26%

B:ALA173.N-B:MET165.O 39.24%

B:LEU30.N-B:TYR37.O 36.65%

B:LEU205.N-B:THR201.O 34.66%

B:THR21.N-B:LEU67.O 38.65%

B:ASN214.ND2-B:ALA210.O 36.65%

B:THR175.OG1-B:ASP176.O 33.47%

B:LEU32.N-B:THR35.O 38.45%

B:SER158.N-B:ASN151.O 36.06%

B:TYR239.N-B:ALA234.O 32.47%

B:ASN28.ND2-B:CYS145.O 38.05%

B:THR292.OG1-B:ASP295.OD1 35.06%

B:LEU268.N-B:MET264.O 32.27%

B:SER113.OG-B:GLN127.OE1 36.65%

B:TYR239.N-B:ALA234.O 34.66%

B:GLN83.N-B:LEU86.O 32.07%

B:PHE112.N-B:CYS128.O 36.45%

B:THR21.N-B:LEU67.O 34.46%

B:ILE281.N-B:SER284.O 31.67%

B:SER144.OG-B:LEU141.O 35.66%

B:THR198.OG1-B:GLU240.OE2 33.86%

B:ARG40.NH2-B:ASP187.OD1 31.47%

B:ASP153.N-B:CYS156.O 35.06%

B:HIS80.ND1-B:ASN63.OD1 33.47%

B:ASN95.ND2-B:TRP31.O 31.27%

B:ALA116.N-B:GLY124.O 35.06%

B:ASN95.ND2-B:TRP31.O 33.07%

B:THR292.OG1-B:ASP295.OD1 31.08%

B:GLN83.N-B:LEU86.O 34.06%

B:LYS5.NZ-B:GLU290.OE1 32.67%

B:THR198.OG1-B:GLU240.OE2 30.88%

B:ILE281.N-B:SER284.O 33.86%

B:ILE136.N-B:HIS172.O 31.67%

B:THR21.N-B:LEU67.O 30.88%

B:ILE136.N-B:HIS172.O 33.86%

B:GLY109.N-B:MET130.O 31.27%

B:ASN231.ND2-B:LEU242.O 30.28%

B:THR199.N-B:ASN238.O 33.67%

B:GLN83.N-B:LEU86.O 31.08%

B:VAL91.N-B:ASP34.O 29.88%

B:GLU14.N-B:SER10.O 33.47%

B:GLU14.N-B:SER10.O 30.88%

B:CYS22.N-B:THR25.O 29.88%

B:GLN192.NE2-B:GLY183.O 33.27%

B:CYS160.N-B:GLY149.O 30.68%

B:GLU14.N-B:SER10.O 29.88%

B:VAL18.N-B:GLY29.O 32.87%

B:HIS172.N-B:ILE136.O 30.68%

B:LEU67.N-B:THR21.O 29.68%

B:ARG131.NH2-B:ASP289.OD2 32.67%

B:VAL91.N-B:ASP34.O 30.48%

B:ALA116.N-B:GLY124.O 29.28%

B:LEU30.N-B:TYR37.O 32.27%

B:LEU268.N-B:MET264.O 29.48%

B:THR111.OG1-B:ASP295.OD2 28.49%

B:TYR182.N-B:GLY174.O 32.07%

B:TRP218.NE1-B:THR280.O 29.48%

B:TRP218.NE1-B:THR280.O 27.89%

B:ASN95.ND2-B:TRP31.O 32.07%

B:ASN231.ND2-B:LEU242.O 29.48%

B:LYS102.N-B:VAL157.O 27.29%

B:LEU268.N-B:MET264.O 31.27%

B:ALA116.N-B:GLY124.O 29.28%

B:GLN69.N-B:GLN19.O 26.49%

B:SER158.N-B:ASN151.O 30.88%

B:CYS128.N-B:PHE112.O 29.28%

B:HIS80.ND1-B:ASN63.OD1 26.29%

B:ASN84.ND2-B:GLU178.O 30.28%

B:SER81.N-B:ARG88.O 29.08%

B:GLN192.NE2-B:VAL186.O 25.90%

B:THR111.OG1-B:ASP295.OD1 30.08%

B:ILE281.N-B:SER284.O 28.69%

B:LEU208.N-B:VAL204.O 25.90%

B:THR111.OG1-B:ASP295.OD2 29.88%

B:LYS269.N-B:CYS265.O 28.09%

B:SER254.OG-B:ILE259.O 25.70%

B:ILE106.N-B:TYR182.OH 29.68%

B:THR175.OG1-B:ASP176.O 27.89%

B:GLY120.N-B:ASN28.OD1 25.50%

B:TYR239.N-B:ALA234.O 29.68%

B:SER1.OG-B:ASP216.OD2 27.49%

B:VAL104.N-B:PHE159.O 25.10%

B:ASN214.ND2-B:ALA210.O 29.48%

B:THR198.OG1-B:GLU240.OE1 27.29%

B:LYS269.N-B:CYS265.O 24.70%

B:CYS160.N-B:GLY149.O 28.49%

B:ASN84.ND2-B:GLU178.O 26.89%

B:SER81.N-B:ARG88.O 24.30%

B:ALA234.N-B:PHE230.O 28.49%

B:ASN95.ND2-B:GLY15.O 26.69%

B:CYS160.N-B:GLY149.O 24.30%

B:SER81.N-B:ARG88.O 28.09%

B:THR292.N-B:ASP295.OD1 26.69%

B:SER144.OG-B:CYS117.O 24.30%

B:SER254.OG-B:ILE259.O 28.09%

B:LEU208.N-B:VAL204.O 25.70%

B:ARG40.NE-B:ASP187.OD2 23.71%

B:LYS269.N-B:CYS265.O 27.89%

B:GLN83.NE2-B:GLU178.O 25.30%

B:VAL186.N-B:GLN192.OE1 23.31%

B:ASN231.N-B:LEU227.O 27.69%

B:GLN69.N-B:GLN19.O 24.90%

B:ARG40.NH2-B:ASP187.OD2 22.91%

B:ASN151.ND2-B:THR111.O 27.69%

B:TYR182.N-B:GLY174.O 24.50%

B:LEU141.O-B:SER144.OG 22.71%

B:LYS180.N-B:ASP176.OD2 27.69%

B:LYS102.N-B:VAL157.O 24.10%

B:SER144.OG-B:LEU141.O 22.71%

B:ASN51.ND2-B:ASN53.O 27.69%

B:GLN189.NE2-B:LEU50.O 23.71%

B:ALA234.N-B:PHE230.O 22.71%

B:LEU242.N-B:ASN231.OD1 27.29%

B:ALA234.N-B:PHE230.O 23.51%

B:CYS300.N-B:VAL296.O 22.71%

B:HIS80.ND1-B:ASN63.OD1 27.29%

B:VAL104.N-B:PHE159.O 23.31%

B:ALA255.N-B:GLY251.O 22.51%

B:ASN203.ND2-B:GLY109.O 26.49%

B:PHE159.N-B:LYS102.O 23.11%

B:TYR209.N-B:LEU205.O 22.31%

B:VAL91.N-B:ASP34.O 26.10%

B:LEU86.N-B:GLN83.O 22.91%

B:THR198.OG1-B:GLU240.OE1 22.31%

B:THR175.OG1-B:ASP176.O 25.70%

B:SER1.OG-B:ASP216.OD1 22.91%

B:ALA210.N-B:ALA206.O 22.11%

B:ARG131.NE-B:ASP289.OD1 25.70%

B:GLN107.N-B:GLN110.OE1 22.31%

B:THR25.OG1-B:CYS44.O 22.11%

B:GLN69.N-B:GLN19.O 25.30%

B:LEU67.N-B:THR21.O 22.31%

B:ARG131.NH2-B:ASP289.OD1 22.11%

B:THR21.OG1-B:THR26.OG1 25.30%

B:SER254.OG-B:ILE259.O 21.91%

B:GLN107.N-B:GLN110.OE1 21.91%

B:ASN95.ND2-B:GLY15.O 24.10%

B:HIS41.NE2-B:HIS164.O 21.91%

B:ARG105.NH1-B:LYS180.O 21.91%

B:ARG4.N-B:GLN299.OE1 24.10%

B:VAL186.N-B:GLN192.OE1 21.71%

B:LYS180.N-B:ASP176.OD2 21.71%

B:GLN192.N-B:PRO184.O 24.10%

B:LYS180.N-B:ASP176.OD2 21.31%

(continued)

2.4 Concluding Remarks

115

Table 2.30 (continued) B:LEU58.N-B:TYR54.O 21.71%

B:LYS102.N-B:VAL157.O 23.71%

B:ASP216.N-B:ALA211.O 21.12%

B:TYR101.OH-B:ASP33.OD2 21.51%

B:ARG105.NH1-B:ASP176.OD1 23.71%

B:ARG298.NH2-B:ASP295.OD2 20.92%

B:GLN299.NE2-B:ASP295.O 21.51%

B:ALA255.N-B:GLY251.O 23.51%

B:THR21.OG1-B:THR26.OG1 20.72%

B:THR98.OG1-B:ASN95.O 21.31%

B:LEU67.N-B:THR21.O 22.91%

B:THR98.OG1-B:ASN95.O 20.52%

B:ASN95.ND2-B:GLY15.O 21.31%

B:HIS134.N-B:ARG131.O 22.91%

B:SER113.N-B:PHE150.O 20.52%

B:THR111.OG1-B:ASP295.OD1 21.12%

B:LEU86.N-B:GLN83.O 22.11%

B:GLN192.NE2-B:VAL186.O 20.52%

B:ASP92.N-B:ARG76.O 20.92%

B:SER113.N-B:PHE150.O 22.11%

B:ASN51.N-B:TYR54.OH 20.52%

B:ARG105.NH1-B:ASP176.OD1 20.72%

B:ILE200.N-B:ASP289.OD1 21.91%

B:ASN151.N-B:SER158.O 20.32%

B:ARG131.NH1-B:ASP289.OD1 20.52%

B:ASN151.N-B:SER158.O 21.71%

B:LYS5.NZ-B:GLU288.OE1 20.12%

B:THR45.N-B:ASN51.OD1 20.52%

B:GLN273.N-B:LYS269.O 21.71%

B:SER113.N-B:PHE150.O 20.52%

B:SER139.N-B:TYR126.OH 21.31%

B:MET130.N-B:GLN110.O 20.32%

B:PHE159.N-B:LYS102.O 20.92%

B:ARG40.NE-B:ASP187.OD1 20.12%

B:TYR101.OH-B:ASP33.OD1 20.52% B:THR196.OG1-B:THR198.OG1 20.52% B:LYS5.NZ-B:GLU288.OE2 20.32% B:SER254.N-B:LEU250.O 20.12%

Table 2.31 The MD-HBs (with occupancy rates ≥20%) of dimer the SARS-CoV-2-Mpro-6y2e model (denoted as “SARS-CoV-2 dimer”) —the model has three sets of MD simulations [346] SARS-CoV-2 rep1

rep2

rep3

A:SER10.OG-A:GLU14.OE2 82.87%

B:SER139.OG-A:GLN299.OE1 64.34%

B:SER139.OG-A:GLN299.OE1 60.76%

A:SER267.OG-A:ASP263.O 65.94%

A:SER139.OG-B:GLN299.OE1 54.58%

A:SER139.OG-B:GLN299.OE1 48.80%

A:SER139.OG-B:GLN299.OE1 52.79%

B:ARG4.NH1-A:GLU290.OE2 50.00%

B:ARG4.NH1-A:GLU290.OE2 43.03%

B:SER139.OG-A:GLN299.OE1 46.02%

B:ARG4.NH2-A:GLU290.OE1 41.24%

B:ARG4.NH2-A:GLU290.OE1 33.67%

A:SER123.OG-B:VAL303.O 26.49%

B:VAL125.N-A:ALA7.O 34.06%

B:GLY11.N-A:GLU14.OE2 30.28%

B:SER1.OG-A:GLU166.OE2 29.08%

B:GLY11.N-A:GLU14.OE2 28.09%

A:GLY11.N-B:GLU14.OE2 30.08%

B:GLY11.N-A:GLU14.OE2 24.50%

B:SER1.OG-A:GLU166.OE1 23.90%

A:ARG4.NH2-B:GLU290.OE1 27.89%

B:SER1.OG-A:GLU166.OE1 24.10%

B:ASN119.ND2-A:PHE305.O 23.90%

A:VAL125.N-B:ALA7.O 26.10%

B:ARG4.NH1-A:GLU290.OE2 20.92%

A:ARG4.NH2-B:GLU290.OE1 22.51%

B:SER1.OG-A:GLU166.OE2 22.51%

B:SER1.N-A:PHE140.O 20.12%

B:SER1.OG-A:GLU166.OE2 21.71%

A:SER1.OG-B:GLU166.OE1 21.12%

B:PHE305.N-A:PRO122.O 21.12% A:TYR54.OH-A:ASP187.O 65.74%

A:ALA7.N-B:VAL125.O 20.92%

A:SER10.OG-A:GLU14.OE2 84.66%

A:TYR182.OH-A:CYS160.O 64.14%

A:PHE140.N-B:SER1.O 20.32%

A:SER267.OG-A:ASP263.O 66.33%

A:TYR209.OH-A:ILE259.O 63.94%

A:ARG4.NH1-B:GLU290.OE2 20.12%

A:TRP31.N-A:CYS16.O 60.96%

A:TRP31.N-A:CYS16.O 63.94% A:ILE78.N-A:LYS90.O 63.75%

A:ILE78.N-A:LYS90.O 59.96%

A:SER10.OG-A:GLU14.OE2 85.06%

A:THR201.OG1-A:GLU240.O 63.55%

A:THR201.OG1-A:GLU240.O 57.57%

A:SER267.OG-A:ASP263.O 69.12%

A:THR135.OG1-A:ASN133.OD1 60.76%

A:SER123.N-A:ALA116.O 57.17%

A:TYR182.OH-A:CYS160.O 66.14%

A:VAL114.N-A:TYR126.O 60.36%

A:HIS163.N-A:SER147.O 55.98%

A:ILE78.N-A:LYS90.O 64.14%

A:SER147.OG-A:SER144.O 60.16%

A:VAL36.N-A:LEU89.O 55.18%

A:TRP31.N-A:CYS16.O 63.35%

A:TYR182.OH-A:CYS160.O 59.96%

A:GLY146.N-A:HIS163.O 54.18%

A:TYR209.OH-A:ILE259.O 61.75%

A:LEU89.N-A:VAL36.O 57.37%

A:VAL114.N-A:TYR126.O 54.18%

A:THR135.OG1-A:ASN133.OD1 56.57%

A:THR257.OG1-A:LEU253.O 56.77%

A:VAL20.N-A:LEU27.O 53.59%

A:THR201.OG1-A:GLU240.O 56.37%

A:LEU27.N-A:VAL20.O 55.58%

A:THR257.OG1-A:LEU253.O 53.39%

A:GLY149.N-A:TYR161.O 55.78%

A:TYR209.OH-A:ILE259.O 54.98%

A:LEU87.N-A:CYS38.O 52.79%

A:GLY146.N-A:HIS163.O 55.18%

A:GLN19.N-A:GLN69.O 53.59%

A:TYR37.N-A:LEU30.O 51.99%

A:VAL36.N-A:LEU89.O 53.78%

A:GLY146.N-A:HIS163.O 52.59%

A:ASP153.N-A:CYS156.O 51.00%

A:LYS88.N-A:SER81.O 52.99%

A:HIS163.N-A:SER147.O 52.39%

A:GLY149.N-A:TYR161.O 50.80%

A:LEU167.N-A:VAL171.O 51.99%

A:TYR182.N-A:GLY174.O 51.59%

A:GLN299.NE2-A:ARG4.O 50.80%

A:LEU89.N-A:VAL36.O 51.79%

A:VAL36.N-A:LEU89.O 51.59%

A:ALA70.N-A:VAL73.O 50.20%

A:GLY109.N-A:MET130.O 51.59%

A:LEU87.N-A:CYS38.O 51.20%

A:SER147.OG-A:SER144.O 49.80%

A:HIS163.N-A:SER147.O 51.39%

A:TYR37.N-A:LEU30.O 50.60%

A:LEU27.N-A:VAL20.O 49.40%

A:VAL20.N-A:LEU27.O 50.20%

A:ASN95.N-A:ASP33.O 49.20%

A:LEU242.N-A:ASN231.OD1 48.80%

A:LEU27.N-A:VAL20.O 50.00%

A:GLY109.N-A:MET130.O 48.01%

A:GLN19.N-A:GLN69.O 48.41%

A:SER123.N-A:ALA116.O 50.00%

A:GLN299.NE2-A:ARG4.O 47.81%

A:ASN95.N-A:ASP33.O 48.21%

A:VAL114.N-A:TYR126.O 49.20%

A:PHE8.N-A:SER113.OG 46.61%

A:LYS88.N-A:SER81.O 48.01%

A:TYR37.N-A:LEU30.O 48.80%

A:ASP153.N-A:CYS156.O 46.02%

A:LEU89.N-A:VAL36.O 47.81%

A:THR257.OG1-A:LEU253.O 48.80%

A:VAL20.N-A:LEU27.O 45.82%

A:GLN189.N-A:MET49.O 47.81%

A:ALA70.N-A:VAL73.O 48.41%

A:GLY149.N-A:TYR161.O 45.62%

A:THR175.OG1-A:ASP176.O 47.61%

A:ASN95.N-A:ASP33.O 48.21%

A:GLN189.N-A:MET49.O 45.62%

A:LEU75.N-A:VAL68.O 47.41%

A:LEU87.N-A:CYS38.O 47.61%

A:LEU167.N-A:VAL171.O 45.42%

A:ASN231.N-A:LEU227.O 47.01%

A:ASN203.ND2-A:ASP289.O 46.61%

A:ASN203.ND2-A:ASP289.O 45.22%

(continued)

116

2 3C-Like Protease (3CLpro)

Table 2.31 (continued) SARS-CoV-2 rep1

rep2

rep3

A:GLN83.N-A:VAL86.O 46.61%

A:HIS172.N-A:ILE136.O 46.02%

A:LEU75.N-A:VAL68.O 45.02%

A:LEU167.N-A:VAL171.O 45.82%

A:VAL157.N-A:LYS100.O 45.82%

A:TYR54.OH-A:ASP187.O 44.82%

A:GLY109.N-A:MET130.O 45.82%

A:VAL18.N-A:GLY29.O 45.62%

A:LYS90.N-A:GLY79.O 44.82%

A:VAL157.N-A:LYS100.O 44.62%

A:SER144.OG-A:LEU141.O 45.22%

A:HIS172.N-A:ILE136.O 44.42%

A:ARG105.NH2-A:PHE181.O 44.42%

A:GLN19.N-A:GLN69.O 45.22%

A:THR45.OG1-A:ASP48.OD2 44.22%

A:HIS172.N-A:ILE136.O 44.22%

A:PHE150.N-A:SER113.O 45.02%

A:LEU115.N-A:VAL148.O 43.82%

A:SER144.OG-A:LEU141.O 44.22%

A:LYS5.NZ-A:GLU290.OE1 44.82%

A:VAL157.N-A:LYS100.O 43.63%

A:ARG40.NE-A:ASP187.OD1 44.02%

A:GLN299.NE2-A:ARG4.O 44.62%

A:ALA173.N-A:MET165.O 43.03%

A:VAL91.N-A:ASP34.O 43.43%

A:LEU75.N-A:VAL68.O 44.42%

A:ASN95.ND2-A:TRP31.O 42.83%

A:LYS90.N-A:GLY79.O 43.43%

A:LYS90.N-A:GLY79.O 44.22%

A:LYS5.NZ-A:GLU290.OE1 41.63%

A:TYR182.N-A:GLY174.O 43.03%

A:VAL91.N-A:ASP34.O 43.63%

A:ARG105.NH2-A:PHE181.O 41.43%

A:PHE112.N-A:CYS128.O 42.63%

A:TYR182.N-A:GLY174.O 43.23%

A:ALA70.N-A:VAL73.O 41.24%

A:CYS128.N-A:PHE112.O 42.43%

A:SER147.OG-A:SER144.O 43.23%

A:LEU205.N-A:THR201.O 41.24%

A:ARG40.NH2-A:ASP187.OD2 41.24%

A:PHE8.N-A:SER113.OG 42.83%

A:GLN192.NE2-A:VAL186.O 41.24%

A:ASN203.ND2-A:ASP289.O 41.24%

A:PHE112.N-A:CYS128.O 42.23%

A:VAL91.N-A:ASP34.O 40.64%

A:LEU30.N-A:TYR37.O 40.44%

A:TYR118.N-A:SER121.O 42.03%

A:GLN83.N-A:VAL86.O 40.44%

A:THR199.N-A:ASN238.O 39.84%

A:ASN95.ND2-A:TRP31.O 41.63%

A:THR175.OG1-A:ASP176.O 40.44%

A:PHE8.N-A:SER113.OG 39.64%

A:ILE281.N-A:SER284.O 41.43%

A:PHE150.N-A:SER113.O 40.24%

A:ASN95.ND2-A:TRP31.O 42.83%

A:ASN231.N-A:LEU227.O 41.24%

A:PHE112.N-A:CYS128.O 39.44%

A:ALA173.N-A:MET165.O 38.84%

A:LEU205.N-A:THR201.O 41.04%

A:SER123.N-A:ALA116.O 39.04%

A:ILE281.N-A:SER284.O 38.65%

A:LEU242.N-A:ASN231.OD1 40.24%

A:LYS88.N-A:SER81.O 38.84%

A:VAL18.N-A:GLY29.O 38.65%

A:GLN83.N-A:VAL86.O 39.64%

A:ASN133.ND2-A:GLY195.O 38.84%

A:CYS22.N-A:THR25.O 37.45%

A:ASN133.ND2-A:GLY195.O 39.64%

A:LEU32.N-A:VAL35.O 38.05%

A:TYR239.N-A:ALA234.O 37.45%

A:THR45.OG1-A:ASP48.OD1 39.64%

A:ILE281.N-A:SER284.O 37.85%

A:THR25.OG1-A:CYS44.O 37.25%

A:GLN189.N-A:MET49.O 39.04%

A:VAL18.N-A:GLY29.O 37.45%

A:ASN203.ND2-A:GLY109.O 37.25%

A:GLU14.N-A:SER10.O 38.45%

A:SER254.OG-A:ILE259.O 36.85%

A:GLU14.N-A:SER10.O 36.85%

A:ARG105.NH2-A:PHE181.O 37.85%

A:THR199.N-A:ASN238.O 36.85%

A:LEU205.N-A:THR201.O 36.85%

A:TYR239.N-A:ALA234.O 37.85%

A:LEU30.N-A:TYR37.O 36.45%

A:PHE150.N-A:SER113.O 36.45%

A:GLN192.NE2-A:VAL186.O 36.85%

A:LEU242.N-A:ASN231.OD1 36.45%

A:LEU32.N-A:VAL35.O 36.25%

A:ARG40.NE-A:ASP187.OD2 36.65%

A:CYS22.N-A:THR25.O 35.86%

A:TYR118.N-A:SER121.O 35.06%

A:LEU30.N-A:TYR37.O 36.45%

A:TYR118.N-A:SER121.O 35.06%

A:TRP218.NE1-A:THR280.O 34.86%

A:THR175.OG1-A:ASP176.O 35.86%

A:THR25.OG1-A:CYS44.O 34.86%

A:SER158.N-A:ASN151.O 34.66%

A:ARG131.N-A:THR135.O 35.66%

A:GLU14.N-A:SER10.O 34.86%

A:SER254.OG-A:ILE259.O 34.46%

A:CYS22.N-A:THR25.O 35.46%

A:CYS128.N-A:PHE112.O 34.66%

A:THR135.OG1-A:ASN133.OD1 34.06%

A:SER158.N-A:ASN151.O 35.26%

A:ASN203.ND2-A:GLY109.O 34.26%

A:THR45.OG1-A:ASP48.OD1 34.06%

A:LEU32.N-A:VAL35.O 35.06%

A:SER158.N-A:ASN151.O 33.67%

A:SER113.N-A:PHE150.O 32.27%

A:ASP153.N-A:CYS156.O 34.06%

A:TYR239.N-A:ALA234.O 33.07%

A:HIS41.NE2-A:HIS164.O 32.27%

A:SER113.N-A:PHE150.O 33.86%

A:LYS269.N-A:CYS265.O 32.67%

Table 2.32 The MD-HBs (with occupancy rates ≥20%) of dimer the SARS-CoV-2-Mpro-6y2e model (denoted as “SARS-CoV-2 dimer”) —the model has three sets of MD simulations [346] (continuation-1) A:VAL86.N-A:GLN83.O 31.87%

A:THR199.N-A:ASN238.O 33.67%

A:ASN28.ND2-A:CYS145.O 32.47%

A:ALA210.N-A:ALA206.O 30.88%

A:ILE200.N-A:ASP289.OD2 33.47%

A:THR21.N-A:LEU67.O 32.27%

A:ASN151.ND2-A:THR111.O 30.88%

A:SER254.OG-A:ILE259.O 32.87%

A:LEU268.N-A:MET264.O 32.07%

A:LEU268.N-A:MET264.O 30.48%

A:TYR54.OH-A:ASP187.O 32.87%

A:ASN231.N-A:LEU227.O 31.27%

A:THR45.OG1-A:ASP48.OD2 30.28%

A:ARG40.NH2-A:ASP187.OD1 32.27%

A:CYS160.N-A:GLY149.O 30.28%

A:ASN84.ND2-A:GLU178.O 30.28%

A:ALA116.N-A:GLY124.O 31.08%

A:ARG131.N-A:THR135.O 29.68%

A:GLN107.N-A:GLN110.OE1 29.88%

A:LEU268.N-A:MET264.O 31.08%

A:ARG4.NH1-B:GLU290.OE2 29.08%

A:CYS160.N-A:GLY149.O 29.48%

A:ALA173.N-A:MET165.O 30.68%

A:MET130.N-A:GLN110.O 28.88%

A:LYS269.N-A:CYS265.O 29.28%

A:CYS128.N-A:PHE112.O 30.68%

A:THR111.OG1-A:ASP295.OD2 28.88%

A:THR243.OG1-A:HIS246.ND1 29.28%

A:THR111.OG1-A:ASP295.OD2 30.68%

A:ASN95.ND2-A:GLY15.O 28.49%

A:THR21.N-A:LEU67.O 29.08%

A:ASN151.ND2-A:THR111.O 30.68%

A:ASN214.ND2-A:ALA210.O 28.29%

A:GLY120.N-A:ASN28.OD1 28.88%

A:ASN214.ND2-A:ALA210.O 30.28%

A:ALA255.N-A:GLY251.O 28.29%

A:ALA116.N-A:GLY124.O 28.88%

A:ASN203.ND2-A:GLY109.O 29.68%

A:SER81.N-A:LYS88.O 27.09%

(continued)

2.4 Concluding Remarks

117

Table 2.32 (continued) A:HIS80.ND1-A:ASN63.OD1 27.89%

A:THR21.N-A:LEU67.O 29.68%

A:LEU208.N-A:VAL204.O 27.09%

A:GLN192.NE2-A:VAL186.O 27.89%

A:ASN95.ND2-A:GLY15.O 29.28%

A:ALA234.N-A:PHE230.O 26.69%

A:TYR126.N-A:VAL114.O 27.09%

A:GLY11.N-B:GLU14.OE2 29.08%

A:CYS38.N-A:LEU87.O 26.69%

A:ASN221.N-A:SER267.OG 26.89%

A:LYS269.N-A:CYS265.O 29.08%

A:THR21.OG1-A:THR26.OG1 25.70%

A:ASN95.ND2-A:GLY15.O 26.10%

A:THR243.OG1-A:HIS246.ND1 28.49%

A:SER113.N-A:PHE150.O 25.70%

A:ILE136.N-A:HIS172.O 25.50%

A:VAL86.N-A:GLN83.O 28.09%

A:GLY302.N-A:VAL297.O 25.70%

A:ALA255.N-A:GLY251.O 25.30%

A:LEU208.N-A:VAL204.O 27.89%

A:TRP218.NE1-A:THR280.O 24.90%

A:THR198.OG1-A:GLU240.OE2 25.10%

A:ILE136.N-A:HIS172.O 27.89%

A:VAL186.N-A:GLN192.OE1 24.70%

A:SER81.N-A:LYS88.O 24.90%

A:GLY120.N-A:ASN28.OD1 27.09%

A:ILE200.N-A:ASP289.OD2 24.50%

A:LEU67.N-A:THR21.O 24.70%

A:LEU67.N-A:THR21.O 27.09%

A:LEU67.N-A:THR21.O 24.50%

A:THR21.OG1-A:THR26.OG1 24.50%

A:VAL104.N-A:PHE159.O 26.29%

A:THR243.OG1-A:HIS246.ND1 24.50%

A:ASN231.ND2-A:LEU242.O 24.30%

A:THR21.OG1-A:THR26.OG1 26.10%

A:GLN273.N-A:LYS269.O 23.71%

A:ARG105.NH1-A:ASP176.OD2 23.90%

A:ASN221.N-A:SER267.OG 26.10%

A:ASN221.N-A:SER267.OG 23.31%

A:VAL104.N-A:PHE159.O 23.90%

A:SER81.N-A:LYS88.O 26.10%

A:ASP92.N-A:ARG76.O 23.11%

A:ASP216.N-A:ALA211.O 23.90%

A:ALA255.N-A:GLY251.O 25.70%

A:ALA210.N-A:ALA206.O 22.71%

A:SER62.N-A:ASN65.OD1 23.31%

A:TRP218.NE1-A:THR280.O 25.30%

A:LYS102.N-A:VAL157.O 22.31%

A:ASN180.N-A:ASP176.OD1 23.31%

A:LYS102.N-A:VAL157.O 25.30%

A:ASN151.N-A:SER158.O 22.31%

A:THR198.OG1-A:GLU240.OE1 22.71%

A:GLN107.N-A:GLN110.OE1 25.10%

A:VAL86.N-A:GLN83.O 22.31%

A:LYS102.N-A:VAL157.O 22.51%

A:ARG4.N-A:GLN299.OE1 25.10%

A:ASN180.N-A:ASP176.OD1 22.11%

A:CYS38.N-A:LEU87.O 22.51%

A:ASN231.ND2-A:LEU242.O 24.90%

A:THR45.N-A:ASP48.OD2 21.71%

A:THR111.OG1-A:GLU290.O 22.51%

A:ASN28.ND2-A:CYS145.O 24.70%

A:VAL104.N-A:PHE159.O 21.71%

A:LYS97.N-A:ASN95.OD1 22.31%

A:ALA234.N-A:PHE230.O 24.50%

A:ASN65.N-A:SER62.O 21.51%

A:THR225.OG1-A:PHE223.O 22.31%

A:CYS160.N-A:GLY149.O 24.30%

A:ASN238.ND2-A:ASP197.O 21.51%

A:CYS156.N-A:ASP153.O 22.11%

A:ARG131.NH2-A:ASP289.OD2 24.10%

A:THR45.OG1-A:ASP48.OD1 21.31%

A:ASN151.N-A:SER158.O 21.91%

A:THR292.OG1-A:ASP295.OD2 24.10%

A:ASN151.ND2-A:THR111.O 21.12%

A:VAL186.N-A:GLN192.OE1 21.71%

A:THR45.OG1-A:ASP48.OD2 23.71%

A:THR98.OG1-A:ASP33.OD2 21.12%

A:THR226.OG1-A:ASP229.OD1 21.71%

A:GLY302.N-A:VAL297.O 22.91%

A:LYS5.NZ-A:GLU288.OE2 20.92%

A:ASN119.ND2-A:GLN19.OE1 21.51%

A:THR198.OG1-A:GLU240.OE1 22.71%

A:ALA116.N-A:GLY124.O 20.92%

A:CYS300.N-A:VAL296.O 21.31%

A:GLN69.N-A:GLN19.O 22.51%

A:THR98.OG1-A:ASP33.OD1 20.32%

A:THR226.OG1-A:ASP229.OD2 21.31%

A:THR111.OG1-A:ASP295.OD1 22.51%

A:GLY120.N-A:ASN28.OD1 20.12%

A:PHE134.N-A:ARG131.O 21.31%

A:LYS5.NZ-A:GLU288.OE1 22.11%

A:HIS41.NE2-A:HIS164.O 20.12%

A:LYS100.NZ-A:ASP155.OD1 20.92%

A:ARG40.NH2-A:ASP187.OD2 22.11%

A:ARG105.NH1-A:ASP176.OD2 20.12%

A:PHE159.N-A:LYS102.O 20.72%

A:THR25.OG1-A:CYS44.O 21.91%

A:CYS156.N-A:ASP153.O 20.12%

A:ALA7.N-B:VAL125.O 20.52%

A:ASN151.N-A:SER158.O 21.91%

A:ASN180.N-A:ASP176.OD2 20.12%

A:THR198.OG1-A:GLU240.OE2 21.71%

B:SER10.OG-B:GLU14.OE2 83.27%

A:VAL186.N-A:GLN192.OE1 21.31%

B:TYR209.OH-B:ILE259.O 71.91%

B:SER267.OG-B:ASP263.O 67.13%

A:ALA210.N-A:ALA206.O 20.92%

B:SER267.OG-B:ASP263.O 71.51%

B:TYR209.OH-B:ILE259.O 66.93%

A:THR98.OG1-A:ASN95.O 20.92%

B:ILE78.N-B:LYS90.O 64.94%

B:TYR182.OH-B:CYS160.O 65.14%

A:HIS80.ND1-A:ASN63.OD1 20.72%

B:THR201.OG1-B:GLU240.O 60.36%

B:TRP31.N-B:CYS16.O 64.54%

A:CYS38.N-A:LEU87.O 20.72%

B:TRP31.N-B:CYS16.O 59.76%

B:SER10.OG-B:GLU14.OE2 63.94%

A:MET130.N-A:GLN110.O 20.72%

B:HIS163.N-B:SER147.O 59.76%

B:ILE78.N-B:LYS90.O 63.75%

A:SER62.N-A:ASN65.OD1 20.52%

B:TYR182.OH-B:CYS160.O 58.57%

B:THR201.OG1-B:GLU240.O 61.75%

A:SER301.OG-A:GLN256.OE1 20.52%

B:VAL20.N-B:LEU27.O 56.77%

B:SER147.OG-B:SER144.O 59.76%

A:PHE159.N-A:LYS102.O 20.12%

B:VAL36.N-B:LEU89.O 54.18%

B:ALA173.N-B:MET165.O 57.57%

A:TYR126.N-A:VAL114.O 20.12%

B:THR257.OG1-B:LEU253.O 53.39%

B:THR135.OG1-B:ASN133.OD1 55.98%

B:GLN19.N-B:GLN69.O 52.59%

B:LEU87.N-B:CYS38.O 55.18%

B:SER10.OG-B:GLU14.OE2 84.86%

B:VAL157.N-B:LYS100.O 51.59%

B:VAL114.N-B:TYR126.O 53.98%

B:TRP31.N-B:CYS16.O 70.52%

B:ASN95.N-B:ASP33.O 51.59%

B:THR257.OG1-B:LEU253.O 52.99%

B:SER267.OG-B:ASP263.O 68.33%

B:LYS88.N-B:SER81.O 51.00%

B:VAL36.N-B:LEU89.O 51.99%

B:HIS163.N-B:SER147.O 62.15%

B:LEU27.N-B:VAL20.O 51.00%

B:TYR182.N-B:GLY174.O 51.79%

B:TYR209.OH-B:ILE259.O 61.35%

B:SER147.OG-B:SER144.O 50.80%

B:TYR37.N-B:LEU30.O 51.79%

B:ILE78.N-B:LYS90.O 60.36%

B:GLY149.N-B:TYR161.O 50.40%

B:HIS163.N-B:SER147.O 51.20%

B:THR201.OG1-B:GLU240.O 60.16%

B:TYR37.N-B:LEU30.O 50.20%

B:TYR54.OH-B:ASP187.O 51.00%

B:VAL114.N-B:TYR126.O 58.76%

B:TYR118.N-B:SER121.O 50.00%

B:GLN19.N-B:GLN69.O 51.00%

B:TYR182.OH-B:CYS160.O 57.57%

B:ASP153.N-B:CYS156.O 49.60%

B:LEU27.N-B:VAL20.O 50.00%

B:LEU27.N-B:VAL20.O 54.78%

B:LEU87.N-B:CYS38.O 49.00%

B:ALA70.N-B:VAL73.O 49.60%

B:GLY109.N-B:MET130.O 54.38%

B:VAL114.N-B:TYR126.O 48.80%

B:LYS88.N-B:SER81.O 49.00%

B:GLY146.N-B:HIS163.O 53.39%

B:THR135.OG1-B:ASN133.OD1 47.81%

B:ARG105.NH2-B:PHE181.O 47.81%

B:TYR37.N-B:LEU30.O 52.19%

B:PHE8.N-B:SER113.OG 47.01%

B:VAL157.N-B:LYS100.O 47.81%

B:THR257.OG1-B:LEU253.O 51.99%

B:CYS22.N-B:THR25.O 45.82%

B:LEU89.N-B:VAL36.O 47.41%

B:VAL36.N-B:LEU89.O 51.59%

B:PHE150.N-B:SER113.O 45.62%

B:THR175.OG1-B:ASP176.O 45.82%

B:PHE112.N-B:CYS128.O 51.39%

B:LEU89.N-B:VAL36.O 45.02%

B:ASN95.N-B:ASP33.O 45.42%

B:LEU89.N-B:VAL36.O 50.40%

B:ASN203.ND2-B:ASP289.O 44.82%

B:GLN299.NE2-B:ARG4.O 45.22%

B:VAL20.N-B:LEU27.O 50.20%

B:PHE112.N-B:CYS128.O 44.82%

B:PHE150.N-B:SER113.O 45.02%

B:VAL157.N-B:LYS100.O 50.00%

B:LYS90.N-B:GLY79.O 44.42%

B:LEU30.N-B:TYR37.O 43.82%

B:GLN19.N-B:GLN69.O 49.80%

B:ALA70.N-B:VAL73.O 43.82%

B:GLY146.N-B:HIS163.O 43.82%

B:SER147.OG-B:SER144.O 49.00%

B:GLN299.NE2-B:ASP295.O 43.82%

118

2 3C-Like Protease (3CLpro)

Table 2.33 The MD-HBs (with occupancy rates ≥20%) of dimer the SARS-CoV-2-Mpro-6y2e model (denoted as “SARS-CoV-2 dimer”) —the model has three sets of MD simulations [346] (continuation-2) B:ASN133.ND2-B:GLY195.O 43.63%

B:LEU242.N-B:ASN231.OD1 47.81%

B:ALA173.N-B:MET165.O 43.43%

B:ASN203.ND2-B:ASP289.O 43.63%

B:LYS88.N-B:SER81.O 47.81%

B:GLN192.NE2-B:VAL186.O 43.23%

B:GLN189.N-B:MET49.O 43.03%

B:ASP153.N-B:CYS156.O 47.41%

B:TYR239.N-B:ALA234.O 42.63%

B:PHE8.N-B:SER113.OG 43.03%

B:ASN203.ND2-B:GLY109.O 46.81%

B:THR199.N-B:ASN238.O 42.23%

B:GLN83.N-B:VAL86.O 42.63%

B:ASN95.N-B:ASP33.O 46.22%

B:ASN133.ND2-B:GLY195.O 42.23%

B:GLY109.N-B:MET130.O 42.63%

B:LEU75.N-B:VAL68.O 46.02%

B:LEU75.N-B:VAL68.O 42.03%

B:LEU167.N-B:VAL171.O 42.43%

B:VAL18.N-B:GLY29.O 45.82%

B:SER123.N-B:ALA116.O 42.03%

B:GLY149.N-B:TYR161.O 42.43%

B:LEU167.N-B:VAL171.O 45.82%

B:THR175.OG1-B:ASP176.O 41.63%

B:HIS172.N-B:ILE136.O 42.03%

B:PHE8.N-B:SER113.OG 45.82%

B:LEU167.N-B:VAL171.O 40.84%

B:VAL91.N-B:ASP34.O 42.03%

B:LEU87.N-B:CYS38.O 45.62%

B:GLN83.N-B:VAL86.O 40.44%

B:LYS90.N-B:GLY79.O 41.43%

B:ARG105.NH2-B:PHE181.O 45.62%

B:VAL91.N-B:ASP34.O 40.44%

B:LEU242.N-B:ASN231.OD1 41.43%

B:SER144.OG-B:LEU141.O 45.42%

B:TYR182.N-B:GLY174.O 40.04%

B:VAL18.N-B:GLY29.O 40.84%

B:THR135.OG1-B:ASN133.OD1 44.82%

B:THR292.OG1-B:ASP295.OD1 39.64%

B:VAL20.N-B:LEU27.O 40.84%

B:ASN203.ND2-B:ASP289.O 44.82%

B:THR21.N-B:LEU67.O 39.64%

B:ILE281.N-B:SER284.O 40.44%

B:ALA70.N-B:VAL73.O 44.42%

B:LEU205.N-B:THR201.O 39.44%

B:ASN231.N-B:LEU227.O 40.44%

B:THR175.OG1-B:ASP176.O 43.63%

B:GLY109.N-B:MET130.O 38.84%

B:THR199.N-B:ASN238.O 40.24%

B:SER123.N-B:ALA116.O 43.43%

B:ARG40.NH2-B:ASP187.OD2 38.25%

B:LEU75.N-B:VAL68.O 39.84%

B:LYS90.N-B:GLY79.O 43.03%

B:THR45.OG1-B:ASP48.OD2 38.25%

B:ASN28.ND2-B:CYS145.O 39.64%

B:GLN299.NE2-B:ARG4.O 41.63%

B:ARG131.N-B:THR135.O 37.65%

B:THR45.OG1-B:ASP48.OD1 39.64%

B:LEU115.N-B:VAL148.O 41.43%

B:ARG40.NE-B:ASP187.OD1 37.45%

B:TYR239.N-B:ALA234.O 39.44%

B:TYR182.N-B:GLY174.O 41.24%

B:ASN84.ND2-B:GLU178.O 37.05%

B:SER158.N-B:ASN151.O 37.65%

B:ASN231.N-B:LEU227.O 41.04%

B:LEU32.N-B:VAL35.O 37.05%

B:LEU205.N-B:THR201.O 37.45%

B:THR111.OG1-B:GLU290.O 40.04%

B:GLU14.N-B:SER10.O 36.45%

B:THR111.OG1-B:ASP295.OD2 37.05%

B:GLN83.N-B:VAL86.O 39.44%

B:THR25.OG1-B:CYS44.O 36.25%

B:SER113.N-B:PHE150.O 36.85%

B:ALA173.N-B:MET165.O 39.44%

B:ASN95.ND2-B:TRP31.O 35.86%

B:LEU32.N-B:VAL35.O 36.65%

B:LEU30.N-B:TYR37.O 39.24%

B:SER158.N-B:ASN151.O 35.46%

B:ASN95.ND2-B:TRP31.O 36.45%

B:ASN95.ND2-B:TRP31.O 39.04%

B:GLY146.N-B:HIS163.O 35.06%

B:TYR118.N-B:SER121.O 36.06%

B:TYR54.OH-B:ASP187.O 38.84%

B:SER113.OG-B:GLN127.OE1 34.66%

B:ASN151.ND2-B:THR111.O 35.66%

B:THR45.OG1-B:ASP48.OD1 38.65%

B:ARG298.NH2-B:ASP295.OD2 34.46%

B:GLN192.NE2-B:VAL186.O 35.66%

B:TYR239.N-B:ALA234.O 38.25%

B:LYS269.N-B:CYS265.O 34.06%

B:SER254.OG-B:ILE259.O 35.06%

B:ILE281.N-B:SER284.O 38.05%

B:LEU242.N-B:ASN231.OD1 33.86%

B:SER123.N-B:ALA116.O 34.86%

B:THR199.N-B:ASN238.O 38.05%

B:LEU115.N-B:VAL148.O 33.47%

B:ARG40.NE-B:ASP187.OD2 34.26%

B:GLN189.N-B:MET49.O 37.85%

B:ASN231.N-B:LEU227.O 32.67%

B:ARG40.NH2-B:ASP187.OD1 34.26%

B:LEU205.N-B:THR201.O 37.65%

B:CYS128.N-B:PHE112.O 32.07%

B:GLU14.N-B:SER10.O 34.06%

B:PHE150.N-B:SER113.O 37.45%

B:ARG298.N-B:PHE294.O 32.07%

B:LEU115.N-B:VAL148.O 32.87%

B:ASN133.ND2-B:GLY195.O 36.85%

B:LEU30.N-B:TYR37.O 31.47%

B:GLN107.N-B:GLN110.OE1 32.07%

B:HIS172.N-B:ILE136.O 36.65%

B:ARG105.NH2-B:PHE181.O 31.47%

B:THR111.OG1-B:ASP295.OD1 31.87%

B:VAL91.N-B:ASP34.O 36.25%

B:VAL86.N-B:GLN83.O 31.47%

B:ILE200.N-B:ASP289.OD1 31.87%

B:LEU32.N-B:VAL35.O 35.86%

B:ARG4.N-B:GLN299.OE1 31.47%

B:THR292.OG1-B:ASP295.OD2 31.47%

B:CYS22.N-B:THR25.O 35.86%

B:SER144.OG-B:CYS117.O 30.68%

B:MET130.N-B:GLN110.O 30.88%

B:GLY149.N-B:TYR161.O 35.66%

B:VAL18.N-B:GLY29.O 30.48%

B:ALA255.N-B:GLY251.O 30.68%

B:SER254.OG-B:ILE259.O 35.26%

B:ALA116.N-B:GLY124.O 30.08%

B:THR21.N-B:LEU67.O 30.48%

B:ARG298.NH2-B:MET6.O 34.06%

B:LEU268.N-B:MET264.O 30.08%

B:THR292.OG1-B:ASP295.OD1 30.28%

B:THR21.N-B:LEU67.O 33.07%

B:ASN95.ND2-B:GLY15.O 29.68%

B:LEU268.N-B:MET264.O 29.68%

B:CYS128.N-B:PHE112.O 32.07%

B:GLN69.N-B:GLN19.O 29.48%

B:LEU67.N-B:THR21.O 29.48%

B:TYR118.N-B:SER121.O 32.07%

B:ILE281.N-B:SER284.O 28.88%

B:PHE112.N-B:CYS128.O 28.88%

B:SER113.N-B:PHE150.O 31.47%

B:LYS102.N-B:VAL157.O 28.29%

B:VAL86.N-B:GLN83.O 28.29%

B:LEU268.N-B:MET264.O 31.08%

B:MET130.N-B:GLN110.O 27.69%

B:LYS269.N-B:CYS265.O 28.09%

B:GLU14.N-B:SER10.O 30.88%

B:GLN107.N-B:GLN110.OE1 26.89%

B:LEU208.N-B:VAL204.O 27.49%

B:ALA255.N-B:GLY251.O 30.88%

B:THR45.OG1-B:ASP48.OD1 26.49%

B:ASN151.N-B:SER158.O 27.29%

B:THR25.OG1-B:CYS44.O 30.88%

B:SER81.N-B:LYS88.O 26.10%

B:CYS22.N-B:THR25.O 27.09%

B:ARG40.NH2-B:ASP187.OD1 30.48%

B:LYS5.NZ-B:GLU290.OE1 25.90%

B:ARG4.N-B:GLN299.OE1 26.69%

B:THR45.OG1-B:ASP48.OD2 29.88%

B:TYR126.N-B:VAL114.O 25.90%

B:THR45.OG1-B:ASP48.OD2 26.29%

B:LYS269.N-B:CYS265.O 29.48%

B:CYS160.N-B:GLY149.O 25.30%

B:CYS38.N-B:LEU87.O 25.90%

B:ARG40.NE-B:ASP187.OD2 28.88%

B:LEU67.N-B:THR21.O 25.30%

B:SER121.OG-B:TYR118.O 25.50%

B:SER158.N-B:ASN151.O 28.49%

B:LYS5.NZ-B:GLU288.OE1 25.10%

(continued)

2.4 Concluding Remarks

119

Table 2.33 (continued) B:SER62.N-B:ASN65.OD1 25.50%

B:LYS102.N-B:VAL157.O 28.49%

B:TRP218.NE1-B:THR280.O 24.90%

B:HIS80.ND1-B:ASN63.OD1 25.30%

B:THR243.OG1-B:HIS246.ND1 28.29%

B:HIS172.N-B:ILE136.O 24.90%

B:ASP153.N-B:CYS156.O 24.90%

B:ASN231.ND2-B:LEU242.O 28.09%

B:THR198.OG1-B:GLU240.OE1 24.90%

B:LYS5.NZ-B:GLU290.OE2 24.90%

B:ARG131.N-B:THR135.O 28.09%

B:GLY302.N-B:VAL297.O 24.90%

B:ASN221.N-B:SER267.OG 24.70%

B:GLN192.NE2-B:VAL186.O 28.09%

B:VAL104.N-B:PHE159.O 24.50%

B:THR25.OG1-B:CYS44.O 24.70%

B:LEU208.N-B:VAL204.O 27.69%

B:ALA255.N-B:GLY251.O 24.50%

B:ASN231.ND2-B:LEU242.O 24.50%

B:ARG4.N-B:GLN299.OE1 27.29%

B:ASN180.N-B:ASP176.OD2 24.30%

B:TRP218.NE1-B:THR280.O 24.30%

B:TRP218.NE1-B:THR280.O 26.89%

B:GLN299.NE2-B:ARG4.O 23.90%

B:CYS128.N-B:PHE112.O 24.10%

B:GLN107.N-B:GLN110.OE1 26.69%

B:VAL186.N-B:GLN192.OE1 23.71%

B:ASN180.N-B:ASP176.OD2 24.10%

B:ASN214.ND2-B:ALA210.O 26.49%

B:LEU272.N-B:LEU268.O 23.71%

B:ASN84.ND2-B:GLU178.O 23.71%

B:ALA116.N-B:GLY124.O 26.49%

B:LYS5.NZ-B:GLU290.OE2 23.71%

B:CYS300.N-B:VAL296.O 23.51%

B:SER81.N-B:LYS88.O 26.10%

B:TYR54.OH-B:ASP187.O 23.31%

B:LYS102.N-B:VAL157.O 23.31%

B:ASN221.N-B:SER267.OG 25.90%

B:LEU208.N-B:VAL204.O 23.11%

B:ARG131.N-B:THR135.O 23.31%

B:THR198.OG1-B:GLU240.OE2 25.70%

B:GLN189.N-B:MET49.O 23.11%

B:SER81.N-B:LYS88.O 23.11%

B:ASN28.ND2-B:CYS145.O 25.70%

B:SER139.N-B:TYR126.OH 23.11%

B:PHE159.N-B:LYS102.O 23.11%

B:THR21.OG1-B:THR26.OG1 25.10%

B:SER62.N-B:ASN65.OD1 22.91%

B:ASN203.ND2-B:GLY109.O 22.91%

B:ASN180.N-B:ASP176.OD1 24.50%

B:SER284.N-B:ILE281.O 22.91%

B:ARG105.NH1-B:ASP176.OD1 22.71%

B:LEU67.N-B:THR21.O 24.50%

B:ASN221.N-B:SER267.OG 22.91%

B:THR93.OG1-B:ASP92.OD2 22.51%

B:VAL86.N-B:GLN83.O 24.50%

B:HIS164.N-B:ALA173.O 22.71%

B:CYS160.N-B:GLY149.O 22.31%

B:ASN151.N-B:SER158.O 24.50%

B:SER254.OG-B:ILE259.O 22.31%

B:LYS5.NZ-B:GLU290.OE1 22.11%

B:VAL104.N-B:PHE159.O 24.30%

B:ASN231.ND2-B:LEU242.O 21.91%

B:ASN95.ND2-B:GLY15.O 21.91%

B:HIS80.ND1-B:ASN63.OD1 23.71%

B:THR21.OG1-B:THR26.OG1 21.51%

B:ALA116.N-B:GLY124.O 21.51%

B:LYS5.NZ-B:GLU290.OE2 23.51%

B:CYS156.N-B:ASP153.O 21.31%

B:HIS41.NE2-B:HIS164.O 21.51%

B:CYS265.N-B:VAL261.O 23.11%

B:SER113.N-B:PHE150.O 21.12%

B:ARG131.NH2-B:ASP289.OD1 21.51%

B:ILE200.N-B:ASP289.OD1 22.71%

B:ASP92.N-B:ARG76.O 20.92%

B:THR243.OG1-B:HIS246.ND1 21.31%

B:ARG105.NH1-B:ASP176.OD2 22.71%

B:CYS265.N-B:VAL261.O 20.52%

B:THR198.OG1-B:GLU240.OE2 21.12%

B:ASN95.ND2-B:GLY15.O 22.31%

B:THR26.OG1-B:THR21.OG1 20.52%

B:GLY120.N-B:ASN28.OD1 21.12%

B:CYS300.N-B:VAL296.O 21.91%

B:ASN180.N-B:ASP176.OD1 20.32%

B:VAL186.N-B:GLN192.OE1 20.92%

B:SER62.N-B:ASN65.OD1 21.51%

B:ASN203.ND2-B:GLY109.O 20.12%

B:THR292.N-B:ASP295.OD2 20.92%

B:ASN151.ND2-B:THR111.O 21.51%

B:CYS265.N-B:VAL261.O 20.72%

B:SER139.N-B:TYR126.OH 21.12%

B:THR21.OG1-B:THR26.OG1 20.12%

B:LYS5.NZ-B:GLU290.OE1 20.72% B:SER121.N-B:TYR118.O 20.72% B:CYS38.N-B:LEU87.O 20.52%

120

2 3C-Like Protease (3CLpro)

Table 2.34 The MD-SBs of monomeric the SARS-CoV-1-Mpro-N3-2hob model (denoted as “SARS-CoV-1-N3 monomer”) and the SARS-CoV-2-Mpro-N3-6lu7 model (denoted as “SARSCoV-2-N3 monomer”), where each model has three sets of MD simulations [346] SARS-CoV-1-N3 rep1

rep2

rep3

SARS-CoV-2-N3 rep1

ASP153-ARG298

rep2

rep3

ASP153-ARG298

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS12

ASP155-LYS12

ASP155-LYS12 ASP155-LYS102

ASP155-LYS102

ASP155-LYS102

ASP176-ARG105

ASP176-ARG105

ASP176-ARG105

ASP176-ARG105

ASP176-ARG105

ASP176-LYS180

ASP176-LYS180

ASP187-ARG188

ASP155-LYS12

ASP155-LYS12

ASP155-LYS12 ASP176-ARG105

ASP176-LYS180 ASP187-ARG188

ASP187-ARG188

ASP187-ARG188

ASP187-ARG188

ASP187-ARG40

ASP187-ARG40

ASP187-ARG40

ASP187-ARG40

ASP187-ARG40

ASP197-ARG131

ASP197-ARG131

ASP197-ARG131

ASP197-ARG131

ASP197-ARG131

ASP197-ARG131

ASP197-LYS137

ASP197-LYS137

ASP197-LYS137

ASP197-LYS137

ASP197-LYS137

ASP197-LYS137

ASP187-ARG40 ASP187-HIS41

ASP187-HIS41

ASP216-ARG217 ASP229-LYS269

ASP229-LYS269

ASP229-LYS269

ASP229-LYS269

ASP216-ARG279

ASP216-ARG279

ASP229-LYS269

ASP229-LYS269

ASP245-HIS246 ASP263-ARG222

ASP263-ARG222

ASP263-ARG222

ASP289-ARG131

ASP289-ARG131

ASP289-ARG131

ASP289-ARG131

ASP289-ARG131

ASP289-ARG131

ASP289-LYS137

ASP289-LYS137

ASP289-LYS137

ASP289-LYS137

ASP263-ARG222

ASP289-LYS137

ASP263-ARG222

ASP289-LYS137

ASP263-ARG222

ASP295-ARG298

ASP295-ARG298

ASP295-ARG298

ASP295-ARG298

ASP295-ARG298

ASP295-ARG298

ASP295-LYS5 ASP34-LYS90

ASP34-LYS90

ASP34-LYS90

ASP34-LYS90

ASP34-LYS90

ASP34-LYS90

ASP48-ARG60

ASP48-ARG60

ASP48-ARG60

ASP48-ARG60

ASP48-ARG60

ASP48-ARG60

ASP48-LYS61

ASP48-LYS61

ASP56-ARG60

ASP56-ARG60

ASP56-ARG60

ASP56-ARG60

ASP56-ARG60

ASP56-ARG60

ASP92-ARG76

ASP92-ARG76

ASP92-ARG76

ASP92-ARG76

ASP92-ARG76

ASP92-ARG76

GLU14-LYS97

GLU14-LYS97

GLU166-HIS172

GLU166-HIS172

GLU166-HIS172

GLU166-HIS172

GLU166-HIS172

GLU166-HIS172

GLU178-LYS180

GLU178-LYS180 GLU240-HIS246

GLU14-LYS97 GLU178-ARG88

GLU178-ARG88 GLU178-ARG105

GLU178-ARG105 GLU178-LYS180 GLU240-HIS246

GLU240-HIS246

GLU270-ARG222

GLU270-ARG222

GLU270-LYS269

GLU270-LYS269

GLU270-LYS269

GLU178-LYS88 GLU178-ARG105

GLU178-ARG105

GLU178-ARG105

GLU240-HIS246

GLU240-HIS246

GLU240-HIS246

GLU270-ARG222

GLU270-ARG222

GLU270-ARG222

GLU270-LYS269

GLU270-LYS269

GLU270-LYS269

GLU288-LYS5

GLU288-LYS5

GLU270-ARG279 GLU288-ARG4

GLU288-ARG4

GLU288-LYS5

GLU288-ARG4 GLU288-LYS5

GLU288-LYS5

GLU288-LYS5

GLU288-LYS137

GLU288-LYS137

GLU288-LYS137

GLU288-LYS137

GLU290-ARG4

GLU290-ARG4

GLU288-ARG4

GLU288-ARG131 GLU290-ARG4 GLU290-LYS5

GLU290-LYS5

GLU290-LYS5

GLU290-LYS5

GLU288-LYS137 GLU290-LYS5

GLU290-ARG131

GLU290-ARG131

GLU290-ARG131

GLU290-ARG131

GLU290-ARG131

GLU290-LYS137

GLU290-LYS137

GLU290-LYS137

GLU290-LYS137

GLU290-LYS137

GLU47-ARG60

GLU47-ARG60

GLU47-ARG60

GLU55-ARG40

GLU55-ARG40

GLU55-ARG40

GLU55-ARG40

GLU55-ARG40

GLU55-ARG188

GLU288-LYS137 GLU290-ARG4 GLU290-LYS5 GLU290-LYS137 GLU55-ARG40

2.4 Concluding Remarks

121

Table 2.35 The MD-SBs of dimer the SARS-CoV-1-Mpro-N3-2hob model (denoted as “SARSCoV-1-N3 dimer”) and the SARS-CoV-2-Mpro-N3-6lu7 model (denoted as “SARS-CoV-2-N3 dimer”), where each model has three sets of MD simulations [346] SARS-CoV-1-N3 rep1

rep2

A:GLU14-B:LYS12

B:GLU14-A:LYS12

A:GLU14-B:LYS12

A:GLU290-B:ARG4

A:GLU290-B:ARG4

A:GLU290-B:ARG4

B:GLU290-A:ARG4

B:GLU290-A:ARG4

B:GLU290-A:ARG4

rep3

A:ASP153-A:ARG298 A:ASP153-A:LYS102

B:ASP153-B:LYS102

A:ASP153-A:LYS102

B:ASP153-B:LYS102

A:ASP153-A:LYS102

B:ASP153-B:LYS102

A:ASP155-A:LYS100

B:ASP155-B:LYS100

A:ASP155-A:LYS100

B:ASP155-B:LYS100

A:ASP155-A:LYS100

B:ASP155-B:LYS100

B:ASP155-B:LYS102

A:ASP155-A:LYS102

B:ASP155-B:LYS102

B:ASP155-B:LYS12

A:ASP155-A:LYS12

B:ASP155-B:LYS12

A:ASP155-A:LYS12

B:ASP155-B:LYS12

A:ASP155-A:LYS102 A:ASP155-A:LYS12 A:ASP176-A:ARG105

B:ASP176-B:ARG105

A:ASP176-A:ARG105

B:ASP176-B:ARG105

A:ASP176-A:ARG105

B:ASP176-B:ARG105

A:ASP176-A:LYS180

B:ASP176-B:LYS180

A:ASP176-A:LYS180

B:ASP176-B:LYS180

A:ASP176-A:LYS180

B:ASP176-B:LYS180

A:ASP187-A:ARG188

B:ASP187-B:ARG188

A:ASP187-A:ARG188

A:ASP187-A:ARG188

B:ASP187-B:ARG188

A:ASP187-A:ARG40

B:ASP187-B:ARG40

A:ASP187-A:ARG40

A:ASP187-A:ARG40

B:ASP187-B:ARG40

A:ASP197-A:ARG131

B:ASP197-B:ARG131

A:ASP197-A:ARG131

B:ASP197-B:ARG131

A:ASP197-A:LYS137

B:ASP197-B:LYS137

A:ASP197-A:LYS137

B:ASP197-B:LYS137

A:ASP197-A:ARG131

A:ASP216-A:ARG279

B:ASP216-B:ARG279

A:ASP197-A:LYS137

A:ASP216-A:ARG217

A:ASP187-A:HIS41

A:ASP216-A:ARG279

B:ASP216-B:ARG279

A:ASP229-A:LYS269

B:ASP229-B:LYS269

A:ASP216-A:ARG279

A:ASP229-A:LYS269

B:ASP229-B:LYS269

A:ASP263-A:ARG222

B:ASP263-B:ARG222

A:ASP229-A:LYS269

B:ASP197-B:ARG131 B:ASP197-B:LYS137 B:ASP229-B:LYS269

A:ASP263-A:ARG222

B:ASP263-B:ARG222

A:ASP289-A:ARG131

B:ASP289-B:ARG131

A:ASP263-A:ARG222

B:ASP263-B:ARG222

A:ASP289-A:ARG131

B:ASP289-B:ARG131

A:ASP289-A:LYS137

B:ASP289-B:LYS137

A:ASP289-A:ARG131

B:ASP289-B:ARG131

A:ASP295-A:ARG298

B:ASP295-B:ARG298

A:ASP295-A:ARG298

B:ASP295-B:ARG298

A:ASP295-A:ARG298

B:ASP295-B:ARG298

A:ASP34-A:LYS90

B:ASP34-B:LYS90

A:ASP34-A:LYS90

B:ASP34-B:LYS90

A:ASP34-A:LYS90

B:ASP34-B:LYS90

A:ASP48-A:ARG60

B:ASP48-B:ARG60

A:ASP48-A:ARG60

B:ASP48-B:ARG60

A:ASP48-A:ARG60

B:ASP48-B:ARG60

A:ASP48-A:LYS61

B:ASP48-B:LYS61

A:ASP56-A:ARG60

B:ASP56-B:ARG60

A:ASP48-A:LYS61

B:ASP48-B:LYS61

A:ASP56-A:ARG60

B:ASP56-B:ARG60

A:ASP92-A:ARG76

B:ASP92-B:ARG76

A:ASP56-A:ARG60

B:ASP56-B:ARG60

A:ASP92-A:ARG76

B:ASP92-B:ARG76

A:GLU166-A:HIS172

B:GLU166-B:HIS172

A:ASP92-A:ARG76

B:ASP92-B:ARG76

A:GLU166-A:HIS172

B:GLU166-B:HIS172

A:GLU178-A:ARG88

B:GLU178-B:ARG88

A:GLU166-A:HIS172

B:GLU166-B:HIS172

A:GLU178-A:ARG105

B:GLU178-B:ARG105

A:GLU178-A:LYS180

B:GLU178-B:LYS180

A:GLU178-A:ARG88

A:GLU178-A:ARG88

B:GLU178-B:ARG88

A:GLU178-A:LYS180

B:GLU178-B:LYS180

A:GLU270-A:ARG222

B:GLU270-B:ARG222

A:GLU240-A:HIS246

B:GLU240-B:HIS246

A:GLU240-A:HIS246

B:GLU240-B:HIS246

A:GLU270-A:LYS269

B:GLU270-B:LYS269

A:GLU270-A:ARG222

B:GLU270-B:ARG222 B:GLU270-B:LYS269

A:GLU240-A:HIS246

B:GLU240-B:HIS246

A:GLU178-A:LYS180

A:GLU270-A:ARG222

B:GLU270-B:ARG222

A:GLU288-A:LYS5

B:GLU288-B:LYS5

A:GLU270-A:LYS269

A:GLU270-A:LYS269

B:GLU270-B:LYS269

A:GLU290-A:ARG131

B:GLU290-B:ARG131

A:GLU288-A:LYS137

A:GLU290-A:LYS137

B:GLU290-B:LYS137

A:GLU288-A:LYS5

B:GLU288-B:LYS5

A:GLU290-A:LYS5

B:GLU290-B:LYS5

A:GLU290-A:ARG131

A:GLU288-A:LYS137 A:GLU288-A:LYS5

B:GLU178-B:LYS180

B:GLU288-B:LYS5

A:GLU290-A:ARG131

B:GLU290-B:ARG131

A:GLU290-A:LYS137

B:GLU290-B:LYS137

A:GLU290-A:LYS137

B:GLU290-B:LYS137

A:GLU290-A:LYS5

B:GLU290-B:LYS5

A:GLU290-A:LYS5

B:GLU290-B:LYS5

A:GLU55-A:ARG40

B:GLU55-B:ARG40

A:GLU47-A:LYS61 A:GLU55-A:ARG40

B:ASP48-B:LYS61 B:GLU55-B:ARG40

B:GLU55-B:ARG40

B:ASP289-B:LYS137

B:GLU288-B:LYS137 B:GLU178-B:ARG105

B:GLU178-B:ARG105

B:ASP187-B:ARG40 B:GLU288-B:ARG131 SARS-CoV-2-N3 rep1

rep2

A:GLU288-B:ARG4

A:GLU14-B:LYS12

A:GLU14-B:LYS12

A:GLU290-B:ARG4

B:GLU14-A:LYS12

A:GLU290-B:ARG4

A:GLU290-B:ARG4

B:GLU290-A:ARG4

B:GLU290-A:ARG4

rep3

B:GLU290-A:ARG4 A:ASP153-A:ARG298

A:ASP153-A:ARG298 A:ASP153-A:LYS102

B:ASP153-B:LYS102

A:ASP153-A:LYS102

A:ASP153-A:ARG298 B:ASP153-B:LYS102

A:ASP153-A:LYS102

B:ASP153-B:LYS102

(continued)

122

2 3C-Like Protease (3CLpro)

Table 2.35 (continued) SARS-CoV-1-N3 rep1

rep2

rep3

A:ASP155-A:LYS100

B:ASP155-B:LYS100

A:ASP155-A:LYS100

B:ASP155-B:LYS100

A:ASP155-A:LYS100

A:ASP155-A:LYS12

B:ASP155-B:LYS12

A:ASP155-A:LYS12

B:ASP155-B:LYS12

A:ASP155-A:LYS102

B:ASP155-B:LYS100

A:ASP176-A:ARG105

B:ASP176-B:ARG105

A:ASP176-A:ARG105

B:ASP176-B:ARG105

A:ASP155-A:LYS12

B:ASP155-B:LYS12

A:ASP187-A:ARG188

B:ASP187-B:ARG188

A:ASP187-A:ARG188

B:ASP187-B:ARG188

A:ASP176-A:ARG105

B:ASP176-B:ARG105

A:ASP187-A:ARG40

B:ASP187-B:ARG40

A:ASP187-A:ARG40

B:ASP187-B:ARG40

A:ASP187-A:ARG188

B:ASP187-B:ARG188

A:ASP197-A:ARG131

B:ASP197-B:ARG131

A:ASP197-A:ARG131

B:ASP197-B:ARG131

A:ASP187-A:ARG40

B:ASP187-B:ARG40

A:ASP197-A:LYS137

B:ASP197-B:LYS137

A:ASP197-A:LYS137

B:ASP197-B:LYS137

A:ASP197-A:ARG131

B:ASP197-B:ARG131

A:ASP216-A:ARG279

B:ASP216-B:ARG279

A:ASP216-A:ARG279

A:ASP197-A:LYS137

B:ASP197-B:LYS137

A:ASP229-A:LYS269

B:ASP229-B:LYS269

A:ASP229-A:LYS269

B:ASP229-B:LYS269

A:ASP229-A:LYS269

B:ASP229-B:LYS269

A:ASP263-A:ARG222

B:ASP263-B:ARG222

A:ASP263-A:ARG222

B:ASP263-B:ARG222

A:ASP263-A:ARG222

B:ASP263-B:ARG222

A:ASP289-A:ARG131

B:ASP289-B:ARG131

A:ASP289-A:ARG131

B:ASP289-B:ARG131

A:ASP289-A:ARG131

B:ASP289-B:ARG131

A:ASP295-A:ARG298

B:ASP295-B:ARG298

A:ASP295-A:ARG298

B:ASP295-B:ARG298

A:ASP34-A:LYS90

B:ASP34-B:LYS90

A:ASP34-A:LYS90

B:ASP34-B:LYS90

B:ASP48-B:ARG60

A:ASP289-A:LYS137 A:ASP295-A:ARG298

B:ASP295-B:ARG298

A:ASP34-A:LYS90

B:ASP34-B:LYS90

A:ASP48-A:ARG60

A:ASP48-A:ARG60

B:ASP48-B:ARG60

A:ASP48-A:LYS61

A:ASP48-A:LYS61

A:ASP56-A:ARG60

B:ASP48-B:ARG60 B:ASP56-B:ARG60

A:ASP92-A:ARG76

B:ASP92-B:ARG76

A:ASP56-A:ARG60

B:ASP56-B:ARG60

A:ASP92-A:ARG76

B:ASP92-B:ARG76

A:GLU166-A:HIS172

B:GLU166-B:HIS172

A:ASP92-A:ARG76

B:ASP92-B:ARG76

A:GLU166-A:HIS172

B:GLU166-B:HIS172

A:GLU178-A:ARG105

B:GLU178-B:ARG105

A:GLU166-A:HIS172

B:GLU166-B:HIS172

A:GLU178-A:ARG105

A:GLU178-A:ARG105

B:GLU178-B:ARG105

A:GLU178-A:LYS88

B:ASP56-B:ARG60

A:ASP48-A:ARG60 A:ASP56-A:ARG60

A:GLU178-A:LYS88

B:GLU178-B:LYS88

A:GLU240-A:HIS246

B:GLU240-B:HIS246

A:GLU240-A:HIS246

B:GLU240-B:HIS246

A:GLU240-A:HIS246

B:GLU240-B:HIS246

A:GLU270-A:ARG222

B:GLU270-B:ARG222

A:GLU270-A:ARG222

B:GLU270-B:ARG222

A:GLU270-A:ARG222

B:GLU270-B:ARG222

A:GLU270-A:LYS269

B:GLU270-B:LYS269

A:GLU270-A:LYS269

B:GLU270-B:LYS269

A:GLU270-A:LYS269

B:GLU270-B:LYS269

A:GLU288-A:LYS5

B:GLU288-B:LYS5

A:GLU288-A:LYS137

B:GLU288-B:LYS137

A:GLU288-A:LYS5

B:GLU288-B:LYS5

A:GLU290-A:ARG131

B:GLU290-B:ARG131

A:GLU288-A:LYS5

B:GLU288-B:LYS5

A:GLU290-A:ARG131

B:GLU290-B:ARG131

A:GLU290-A:LYS5

B:GLU290-B:LYS5

A:GLU290-A:ARG131

B:GLU290-B:ARG131

A:GLU290-A:LYS5

B:GLU290-B:LYS5

A:GLU290-A:LYS5

B:GLU290-B:LYS5

A:GLU55-A:ARG40

B:GLU55-B:ARG40

B:GLU55-B:ARG40

A:GLU47-A:ARG60

B:GLU47-B:ARG60

B:GLU47-B:ARG60

B:ASP48-B:LYS61

A:GLU55-A:ARG40

B:GLU55-B:ARG40 B:ASP187-B:HIS41

B:ASP48-B:ARG188

B:GLU178-B:LYS88 B:GLU290-B:LYS137

B:GLU290-B:LYS137

B:GLU290-B:LYS137

B:GLU47-B:HIS41 B:ASP289-B:LYS137

B:GLU288-B:LYS137 B:ASP216-B:ARG279 B:GLU288-B:ARG131

HIS41.NE2-LIG307.O 0.20 ASN142.ND2-LIG307.O8 0.20 SER46.OG-LIG307.O 0.20

LIG307.N6-GLN189.OE1 1.60 THR26.N-LIG307.O7 1.20 TYR118.OH-LIG307.O7 1.20 LIG307.N5-HIS164.O 0.80 HIS41.NE2-LIG307.O 0.80 LIG307.N6-ASN142.OD1 0.60 ASN142.ND2-LIG307.O8 0.60 LIG307.N5-LIG307.O 0.40 GLN189.NE2-LIG307.O8 0.40 LIG307.N6-GLN189.NE2 0.40 HIS163.NE2-LIG307.O8 0.20 LIG307.N6-ASN142.ND2 0.20

GLN192.N-LIG307.O 3.39 GLN192.N-LIG307.O42 2.20 ASN142.ND2-LIG307.O7 1.00 GLN192.N-LIG307.N2 0.60 HIS41.NE2-LIG307.O7 0.60 LIG307.N5-LIG307.O 0.40 GLY143.N-LIG307.O7 0.40 ASN142.ND2-LIG307.C6 0.20 LIG307.N6-ASN142.O 0.20

SER144.OG-LIG307.O8 0.43

ASN142.ND2-LIG307.O8 0.43

LIG307.N6-GLU166.OE1 0.28

CYS145.SG-LIG307.O7 0.14

LIG307.N6-ASN142.ND2 0.14

GLN192.N-LIG307.O42 0.20

GLN189.NE2-LIG307.O 3.59

ASN142.ND2-LIG307.O 0.20

rep3

ASN142.ND2-LIG307.O8 0.20

LIG307.N6-GLN189.OE1 0.20

LIG307.N6-SER46.OG 0.20

LIG307.N6-THR26.O 0.20

GLY143.N-LIG307.O 0.20

SER144.N-LIG307.O7 0.20

LIG307.N6-SER144.OG 0.20

ASN119.ND2-LIG307.O7 0.20

HIS41.NE2-LIG307.O7 0.20

LIG307.N5-HIS164.O 0.20

LIG307.N-GLN189.O 0.40

GLY143.N-LIG307.O7 0.40

HIS41.NE2-LIG307.O 0.40

HIS163.NE2-LIG307.O8 0.40

LIG307.N5-LIG307.O8 0.60

CYS145.SG-LIG307.O 0.60

GLY143.N-LIG307.O8 0.60

ASN142.ND2-LIG307.O 0.80

CYS145.N-LIG307.O7 0.80

LIG307.N5-LIG307.O 0.80

GLN192.N-LIG307.N2 1.00

LIG307.N-GLN192.O 2.20

GLN189.NE2-LIG307.O8 2.59

LIG307.N-GLN189.OE1 5.19

LIG307.N-THR190.O 5.39

GLN189.NE2-LIG307.O 5.99

LIG307.N6-CYS44.O 14.57

SER46.OG-LIG307.O8 17.56

GLU166.N-LIG307.O 42.71

LIG307.N-GLU166.O 51.30

SER46.OG-LIG307.O7 0.20

HIS41.NE2-LIG307.O7 0.20

HIS163.NE2-LIG307.N6 0.40

THR25.OG1-LIG307.O7 0.40

LIG307.N5-HIS164.O 0.40

GLN192.N-LIG307.O1 0.80

LIG307.N-GLN192.O 0.80

GLN192.N-LIG307.N2 1.20

LIG307.N6-LEU141.O 2.00

THR26.N-LIG307.O7 3.19

GLN189.NE2-LIG307.O 3.59

GLN192.N-LIG307.N2 0.57

SER144.N-LIG307.O8 2.56

GLN192.N-LIG307.N2 0.20

GLY143.N-LIG307.O8 4.59

LIG307.N5-LIG307.O 4.99

CYS145.N-LIG307.O8 1.14

HIS41.NE2-LIG307.O7 4.84

LIG307.N-THR190.O 1.80

LIG307.N-GLN189.OE1 2.20

LIG307.N6-GLU166.OE1 5.79

SER144.N-LIG307.O8 5.59

GLY143.N-LIG307.O8 1.80

LIG307.N6-ASN142.OD1 5.12

LIG307.N6-PHE140.O 3.59

LIG307.N5-LIG307.O8 3.59

LIG307.N6-GLU166.OE2 7.39

CYS145.N-LIG307.O8 5.79

LIG307.N-THR190.O 7.78

LIG307.N6-SER144.OG 13.17

LIG307.N-GLN189.OE1 3.79

GLN189.NE2-LIG307.O 11.81

GLN189.NE2-LIG307.O 5.99

SER46.OG-LIG307.O8 4.19

GLN192.NE2-LIG307.O 9.58

LIG307.N-THR190.O 8.58

GLU166.N-LIG307.O 31.74 LIG307.N-GLN189.OE1 13.77

LIG307.N-LIG307.O 2.00

GLY143.N-LIG307.O8 15.50

LIG307.N-GLN192.O 7.39

LIG307.N6-CYS44.O 12.18

ASN142.ND2-LIG307.O8 9.58

rep2 LIG307.N-GLU166.O 45.11

CYS145.N-LIG307.O7 3.79

LIG307.N-GLN189.OE1 32.43

LIG307.N-GLN192.O 17.92

HIS163.ND1-LIG307.O8 29.54

LIG307.N-GLN189.OE1 21.16

LIG307.N-GLN192.O 9.98

GLU166.N-LIG307.O 36.73 GLN189.NE2-LIG307.O 17.17

LIG307.N-ARG188.O 26.35

LIG307.N-GLU166.O 30.54

GLU166.N-LIG307.O 45.23

LIG307.N5-HIS164.O 37.70

LIG307.N5-HIS164.O 44.71

LIG307.N-GLU166.O 40.92

SARS-CoV-2-N3 rep1 LIG307.N-GLU166.O 55.69

rep3 LIG307.N5-HIS164.O 46.31

rep2

LIG307.N-GLU166.O 55.33

SARS-CoV-1-N3 rep1

GLU166.N-LIG307.O 54.09

Table 2.36 The MD-HBs linking the ligand LIG307 of monomeric the SARS-CoV-1-Mpro-N3-2hob model (denoted as “SARS-CoV-1-N3 monomer”) and the SARS-CoV-2-Mpro-N3-6lu7 model (denoted as “SARS-CoV-2-N3 monomer”), where each model has three sets of MD simulations [346]

2.4 Concluding Remarks 123

HIS163.N-SER147.O 60.68 TYR54.OH-ASP187.O 58.08 LEU167.N-VAL171.O 56.09 THR257.OG1-LEU253.O 55.89 LEU87.N-CYS38.O 55.69

VAL36.N-LEU89.O 58.28 VAL20.N-LEU27.O 55.09 TRP31.N-CYS16.O 54.49 LEU87.N-CYS38.O 54.09 VAL114.N-TYR126.O 53.09 HIS163.N-SER147.O 53.09

TRP31.N-CYS16.O 59.46

VAL36.N-LEU89.O 59.46

VAL20.N-LEU27.O 58.75

ILE136.N-HIS172.O 57.75

TYR182.OH-CYS160.O 57.75

HIS163.N-SER147.O 57.61

THR257.OG1-LEU253.O 57.04

VAL114.N-TYR126.O 55.48

ARG131.N-THR135.O 55.48

LEU87.N-CYS38.O 55.05

TRP31.N-CYS16.O 57.09

VAL36.N-LEU89.O 56.89

THR257.OG1-LEU253.O 56.29

LEU167.N-VAL171.O 55.69

ASP153.N-CYS156.O 54.29

THR135.OG1-ASN133.OD1 54.09

ARG88.N-SER81.O 54.09

LEU89.N-VAL36.O 53.49

TYR37.N-LEU30.O 52.50

VAL114.N-TYR126.O 52.10

LEU167.N-VAL171.O 49.93

VAL157.N-LYS100.O 49.79

ASN95.N-ASP33.O 48.10

LYS90.N-GLY79.O 47.31

GLN192.NE2-VAL186.O 47.31

VAL18.N-GLY29.O 47.50 ALA173.N-MET165.O 47.31 TYR182.N-GLY174.O 47.31

THR21.N-LEU67.O 44.71 CYS128.N-PHE112.O 44.11 ALA70.N-VAL73.O 43.71

SER113.OG-GLN127.OE1 48.36

GLY149.N-TYR161.O 48.08

LEU242.N-ASN231.OD1 47.94

ASN231.N-LEU227.O 47.80

LEU75.N-VAL68.O 47.11

PHE150.N-SER113.O 46.51

CYS22.N-THR25.O 46.11

ALA70.N-VAL73.O 45.91

GLN83.N-VAL86.O 46.91

ASP153.N-CYS156.O 47.70

GLY149.N-TYR161.O 44.71

ALA70.N-VAL73.O 49.36

PHE150.N-SER113.O 43.31

GLN192.NE2-VAL186.O 48.30

LEU27.N-VAL20.O 45.31

VAL20.N-LEU27.O 48.30

ARG88.N-SER81.O 50.50

ASN84.ND2-GLU178.O 48.50

LEU115.N-VAL148.O 50.70

LYS90.N-GLY79.O 50.64

LEU242.N-ASN231.OD1 48.90 GLN192.NE2-VAL186.O 45.31

THR135.OG1-ASN133.OD1 51.90

TYR37.N-LEU30.O 47.90

THR25.OG1-CYS44.O 51.64

HIS172.N-ILE136.O 48.90 LEU75.N-VAL68.O 46.51

VAL114.N-TYR126.O 52.10

PHE112.N-CYS128.O 48.90

HIS172.N-ILE136.O 53.20

VAL157.N-LYS100.O 51.70 TYR37.N-LEU30.O 50.90

LYS88.N-SER81.O 52.50

ARG131.N-THR135.O 51.30

LEU89.N-VAL36.O 53.34

LEU87.N-CYS38.O 51.90

TYR54.OH-ASP187.O 47.31

GLY146.N-HIS163.O 53.29

LYS90.N-GLY79.O 51.50

GLN19.N-GLN69.O 53.49

VAL36.N-LEU89.O 54.69

ARG88.N-SER81.O 52.30 VAL157.N-LYS100.O 53.49

LEU27.N-VAL20.O 55.29

ALA173.N-MET165.O 52.30 HIS172.N-ILE136.O 52.10

SER147.OG-SER144.O 55.69

LEU89.N-VAL36.O 52.89

ILE78.N-LYS90.O 56.69

TYR182.OH-CYS160.O 62.48

VAL20.N-LEU27.O 59.28

THR201.OG1-GLU240.O 62.48

THR257.OG1-LEU253.O 60.28

THR135.OG1-ASN133.OD1 60.74

THR201.OG1-GLU240.O 61.68

THR201.OG1-GLU240.O 62.59

ILE78.N-LYS90.O 61.68

THR201.OG1-GLU240.O 61.08

TYR209.OH-ILE259.O 63.67 SER267.OG-ASP263.O 63.07

TYR182.OH-ILE106.O 66.27 ILE78.N-LYS90.O 64.87

TYR54.OH-ASP187.O 66.00

TYR209.OH-ILE259.O 63.87

TYR182.OH-CYS160.O 62.87

TYR54.OH-ASP187.O 62.48

SARS-CoV-2-N3 rep1 TRP31.N-CYS16.O 65.27

TYR209.OH-ILE259.O 66.67

rep2

ILE78.N-LYS90.O 67.43

SARS-CoV-1-N3 rep1

TYR209.OH-ILE259.O 66.47

rep3

VAL157.N-LYS100.O 46.31

THR175.OG1-ASP176.O 47.11

LEU115.N-VAL148.O 47.31

VAL20.N-LEU27.O 47.70

THR135.OG1-ASN133.OD1 47.70

LEU75.N-VAL68.O 47.90

GLN19.N-GLN69.O 48.30

LEU89.N-VAL36.O 48.90

ASN95.N-ASP33.O 48.90

ALA70.N-VAL73.O 49.10

ARG131.N-THR135.O 49.10

TYR37.N-LEU30.O 49.70

LYS88.N-SER81.O 50.70

VAL36.N-LEU89.O 52.69

VAL114.N-TYR126.O 53.69

THR201.OG1-GLU240.O 54.89

ASN203.ND2-ASP289.O 55.69

THR257.OG1-LEU253.O 56.29

TRP31.N-CYS16.O 56.49

SER144.OG-LEU141.O 56.89

LEU87.N-CYS38.O 57.09

LEU167.N-VAL171.O 58.08

GLY146.N-HIS163.O 59.08

HIS163.N-SER147.O 62.28

ILE78.N-LYS90.O 63.27

TYR182.OH-CYS160.O 63.67

SER267.OG-ASP263.O 65.87

TYR209.OH-ILE259.O 70.66

rep2

LYS90.N-GLY79.O 45.11

ASN95.N-ASP33.O 45.11

VAL36.N-LEU89.O 45.31

VAL157.N-LYS100.O 45.31

GLY146.N-HIS163.O 45.51

GLN189.N-MET49.O 45.91

TYR37.N-LEU30.O 46.11

CYS128.N-PHE112.O 46.11

THR21.N-LEU67.O 46.51

ASP153.N-CYS156.O 46.71

LYS88.N-SER81.O 47.50

GLN192.NE2-VAL186.O 48.70

GLN83.N-VAL86.O 48.70

SER144.OG-LEU141.O 48.70

HIS163.N-SER147.O 49.70

LEU87.N-CYS38.O 50.90

LEU167.N-VAL171.O 51.90

TYR182.OH-CYS160.O 55.09

THR257.OG1-LEU253.O 56.89

THR135.OG1-ASN133.OD1 57.09

ARG131.N-THR135.O 57.09

VAL20.N-LEU27.O 58.28

TYR54.OH-ASP187.O 59.68

THR201.OG1-GLU240.O 61.68

TRP31.N-CYS16.O 61.88

TYR209.OH-ILE259.O 67.27

ILE78.N-LYS90.O 68.06

SER267.OG-ASP263.O 70.66

rep3

Table 2.37 The MD-HBs (with occupancy rates ≥20%) of monomeric the SARS-CoV-1-Mpro-N3-2hob model (denoted as “SARS-CoV-1-N3 monomer”) and the SARS-CoV-2-Mpro-N3-6lu7 model (denoted as “SARS-CoV-2-N3 monomer”), where each model has three sets of MD simulations [346]

124 2 3C-Like Protease (3CLpro)

SER123.N-ALA116.O 43.51

VAL297.N-PRO293.O 32.86

ASN231.ND2-LEU242.O 32.72

ASN95.ND2-TRP31.O 33.93

ALA173.N-MET165.O 33.53

TYR118.N-SER121.O 33.73 ARG105.NH2-PHE181.O 33.73

LYS269.N-CYS265.O 30.94 THR45.OG1-ASP48.OD1 30.74

ASN95.ND2-TRP31.O 33.93

TYR239.N-ALA234.O 30.94

LEU27.N-VAL20.O 34.14

GLY149.N-TYR161.O 34.13

CYS22.N-THR25.O 31.54

GLN83.N-LEU86.O 34.53

ARG40.NH2-ASP187.OD1 34.93

VAL91.N-ASP34.O 31.74

TYR239.N-ALA234.O 35.28

LEU30.N-TYR37.O 34.28

CYS22.N-THR25.O 35.93 LEU32.N-VAL35.O 35.73

HIS80.ND1-ASN63.OD1 32.93 TRP218.NE1-THR280.O 31.94

THR292.OG1-ASP295.OD1 36.42

THR199.N-ASN238.O 36.27

TYR239.N-ALA234.O 35.93

THR45.OG1-ASP48.OD1 34.93

PHE8.N-SER113.OG 34.73

THR292.OG1-ASP295.OD2 36.73 TYR239.N-ALA234.O 36.73

ILE136.N-HIS172.O 34.53 ASN95.ND2-TRP31.O 33.13

LYS137.N-ALA129.O 37.98

THR45.OG1-ASP48.OD1 36.56

HIS164.N-ALA173.O 37.52

GLU14.N-SER10.O 37.33

GLY149.N-TYR161.O 34.53

CYS128.N-PHE112.O 39.32 LEU242.N-ASN231.OD1 39.12 PHE150.N-SER113.O 37.52

ASN231.N-LEU227.O 36.13 SER123.N-ALA116.O 35.73 GLN69.N-GLN19.O 35.33

CYS128.N-PHE112.O 38.41

THR21.N-LEU67.O 38.26

PHE8.N-SER113.OG 37.98

LEU27.N-VAL20.O 38.52

VAL18.N-GLY29.O 38.12

LEU30.N-TYR37.O 38.72

ASN231.N-LEU227.O 39.52 THR199.N-ASN238.O 39.52

ASP153.N-CYS156.O 36.93 LEU242.N-ASN231.OD1 36.53

LEU32.N-THR35.O 39.69

LEU205.N-THR201.O 38.83

GLY109.N-MET130.O 39.12

GLN189.N-MET49.O 39.72 ALA70.N-VAL73.O 39.52

LEU30.N-TYR37.O 37.52 LEU268.N-MET264.O 37.13

TYR182.N-GLY174.O 39.12

ASN203.ND2-ASP289.O 41.54

SER147.OG-SER144.O 40.68

LEU32.N-THR35.O 39.12

ASN133.ND2-GLY195.O 39.12

LEU205.N-THR201.O 40.52

THR199.N-ASN238.O 39.72

SER147.OG-SER144.O 37.92

CYS22.N-THR25.O 42.25

THR175.OG1-ASP176.O 39.72

GLU14.N-SER10.O 41.12

THR199.N-ASN238.O 38.32

TYR182.N-GLY174.O 41.68

GLN192.NE2-VAL186.O 42.39

TYR118.N-SER121.O 41.12

VAL91.N-ASP34.O 41.32

TYR118.N-SER121.O 38.92 THR25.OG1-CYS44.O 41.12

ASN95.N-ASP33.O 42.96

THR21.N-LEU67.O 41.72

LEU30.N-TYR37.O 41.92

LYS90.N-GLY79.O 42.91

ASN84.ND2-GLU178.O 39.92

THR135.OG1-ASN133.OD1 40.52

ASN151.N-SER158.O 38.12

ARG105.NH2-PHE181.O 43.39

SER144.OG-LEU141.O 43.39

ARG105.NH2-PHE181.O 42.32

GLN19.N-GLN69.O 42.12

ASN203.ND2-ASP289.O 43.31 HIS172.N-ILE136.O 42.91

LEU205.N-THR201.O 41.12 LEU115.N-VAL148.O 40.72 LEU32.N-THR35.O 40.52

GLN189.N-MET49.O 45.38

LEU75.N-VAL68.O 44.38

GLN299.NE2-ARG4.O 43.39

THR292.OG1-ASP295.OD1 43.71

LEU205.N-THR201.O 43.51

SER123.N-ALA116.O 42.91

ASN95.N-ASP33.O 45.71 GLN19.N-GLN69.O 45.51

GLN83.N-LEU86.O 41.32 GLN19.N-GLN69.O 41.12

GLN299.NE2-ASP295.O 46.37

ASN133.ND2-GLY195.O 46.23

ARG131.N-THR135.O 44.31

ASN231.N-LEU227.O 44.11

LEU89.N-VAL36.O 46.11 PHE112.N-CYS128.O 45.91

VAL157.N-LYS100.O 42.51 ASN95.N-ASP33.O 41.72

TYR37.N-LEU30.O 46.66

ASP153.N-CYS156.O 46.37

CYS128.N-PHE112.O 45.31

THR175.OG1-ASP176.O 46.51 LEU75.N-VAL68.O 46.11

GLY109.N-MET130.O 43.11 ASN203.ND2-ASP289.O 43.11

THR25.OG1-CYS44.O 44.31

PHE150.N-SER113.O 47.80

ASN84.ND2-GLU178.O 47.08

LEU115.N-VAL148.O 45.71

SER147.OG-SER144.O 45.71

VAL91.N-ASP34.O 45.31

ASN84.ND2-GLU178.O 32.73

TYR182.N-GLY174.O 33.13

SER113.OG-GLN127.OE1 33.13

TYR118.N-SER121.O 33.53

PHE150.N-SER113.O 34.53

TYR239.N-ALA234.O 35.13

ASN95.ND2-TRP31.O 35.13

SER10.OG-GLU14.OE1 35.33

ALA173.N-MET165.O 35.93

LEU67.N-THR21.O 36.33

SER147.OG-SER144.O 36.53

ASN231.N-LEU227.O 36.73

ASN151.N-SER158.O 36.73

ASN28.ND2-CYS145.O 37.52

LEU268.N-MET264.O 37.52

THR199.N-ASN238.O 37.92

ASN203.ND2-GLY109.O 38.32

ASP153.N-CYS156.O 38.52

GLY149.N-TYR161.O 38.72

VAL18.N-GLY29.O 38.92

CYS128.N-PHE112.O 39.72

LEU32.N-VAL35.O 39.92

LEU30.N-TYR37.O 39.92

LEU242.N-ASN231.OD1 40.12

GLN83.N-VAL86.O 40.32

PHE8.N-SER113.OG 40.52

LYS90.N-GLY79.O 42.71

PHE112.N-CYS128.O 42.91

GLU14.N-SER10.O 43.31

GLN192.NE2-VAL186.O 44.71

LEU75.N-VAL68.O 44.91

SER113.N-PHE150.O 34.33

HIS80.ND1-ASN63.OD1 34.93

ASN203.ND2-ASP289.O 35.33

LYS137.N-ALA129.O 36.13

ASN133.ND2-GLY195.O 37.33

TYR118.N-SER121.O 37.92

ASN84.ND2-GLU178.O 38.12

LEU242.N-ASN231.OD1 38.52

ALA116.N-GLY124.O 38.72

THR25.OG1-CYS44.O 39.32

LEU32.N-VAL35.O 39.32

LEU89.N-VAL36.O 39.92

VAL91.N-ASP34.O 39.92

SER123.N-ALA116.O 39.92

TYR182.N-GLY174.O 40.52

GLN19.N-GLN69.O 40.52

ARG40.NH2-ASP187.OD2 40.72

TYR239.N-ALA234.O 40.72

SER147.OG-SER144.O 40.92

GLN69.N-GLN19.O 41.12

CYS22.N-THR25.O 41.72

ALA70.N-VAL73.O 41.72

PHE150.N-SER113.O 42.32

THR175.OG1-ASP176.O 42.71

LEU205.N-THR201.O 43.31

GLY149.N-TYR161.O 43.71

LEU27.N-VAL20.O 43.71

ARG40.NE-ASP187.OD1 44.31

VAL114.N-TYR126.O 44.31

ILE136.N-HIS172.O 44.51

2.4 Concluding Remarks 125

ARG40.NE-ASP187.OD2 31.54 LYS269.N-CYS265.O 31.34 LEU268.N-MET264.O 30.94

THR292.OG1-ASP295.OD1 29.14 LYS180.N-ASP176.OD1 28.94 THR25.OG1-CYS44.O 28.74

ILE281.N-SER284.O 32.01

LEU57.N-ASN53.O 31.58

LYS102.N-VAL157.O 31.44

LEU67.N-THR21.O 31.44

VAL91.N-ASP34.O 31.29

HIS80.ND1-ASN63.OD1 31.01

ALA210.N-ALA206.O 30.58

SER254.OG-ILE259.O 30.58

SER158.N-ASN151.O 30.44

ALA116.N-GLY124.O 30.44

PHE112.N-CYS128.O 30.16

TYR101.OH-ASP33.OD1 30.01

ASN151.N-SER158.O 32.53

PHE112.N-CYS128.O 31.34

LEU268.N-MET264.O 30.54

ILE200.N-ASP289.OD2 29.94

THR111.OG1-ASP295.OD1 29.54

SER81.N-ARG88.O 29.54

ILE281.N-SER284.O 29.54

ASN231.ND2-LEU242.O 29.34

TRP218.NE1-THR280.O 29.34

MET130.N-GLN110.O 28.94

CYS160.N-GLY149.O 28.34

HIS80.ND1-ASN63.OD1 28.14

ASN28.ND2-CYS145.O 33.33

LYS102.N-VAL157.O 29.34 CYS160.N-GLY149.O 28.74 LEU67.N-THR21.O 28.14 ASN151.N-SER158.O 27.94 SER144.OG-LEU141.O 27.94 GLY109.N-MET130.O 27.74 LEU57.N-ASN53.O 27.35 VAL86.N-GLN83.O 27.15 SER254.OG-ILE259.O 27.15 SER10.OG-GLU14.OE2 26.95 SER301.N-GLY2.O 26.95 VAL104.N-PHE159.O 26.35 SER62.N-ASN65.OD1 26.15 SER113.N-PHE150.O 25.95

SER81.N-ARG88.O 27.74 TYR126.N-VAL114.O 27.74 THR198.OG1-GLU240.OE1 27.35 ALA255.N-GLY251.O 26.35 THR198.OG1-GLU240.OE2 26.15 MET162.N-THR175.O 24.55 ALA234.N-PHE230.O 24.55 THR21.OG1-THR26.OG1 24.35 ARG105.NH1-ASP176.OD2 23.95 ASN231.ND2-LEU242.O 23.35 ASN28.ND2-CYS145.O 23.35 VAL104.N-PHE159.O 22.95 CYS160.N-GLY149.O 22.75 LEU167.N-VAL171.O 22.75 ASP216.N-ALA211.O 22.55

THR175.OG1-ASP176.O 29.73

ILE200.N-ASP289.OD2 29.73

TRP218.NE1-THR280.O 29.73

SER123.N-ALA116.O 29.16

ASN95.ND2-TRP31.O 29.16

LEU268.N-MET264.O 28.31

GLN83.N-LEU86.O 28.17

THR21.OG1-THR26.OG1 28.17

LYS180.N-ASP176.OD1 28.02

ALA255.N-GLY251.O 28.02

LEU115.N-VAL148.O 28.02

SER81.N-ARG88.O 27.45

THR292.OG1-ASP295.OD2 27.45

ASN151.N-SER158.O 27.03

VAL104.N-PHE159.O 26.74

GLY109.N-MET130.O 26.74

GLY146.N-HIS163.O 26.46

ARG40.NE-ASP187.OD2 25.32

LYS269.N-CYS265.O 25.32

GLN107.N-GLN110.OE1 25.18

ALA173.N-MET165.O 24.89

VAL91.N-ASP34.O 27.94

THR45.OG1-ASP48.OD2 27.54

LYS269.N-CYS265.O 27.15

SER158.N-ASN151.O 26.95

SER113.OG-GLN127.OE1 26.75

SER10.OG-GLU14.OE2 26.75

THR175.N-MET162.O 26.55

LYS102.N-VAL157.O 26.15

LEU67.N-THR21.O 25.75

ASN28.ND2-CYS145.O 25.75

ASN203.ND2-GLY109.O 25.55

THR292.N-ASP295.OD1 25.55

PHE305.N-TYR154.O 25.15

SER113.N-PHE150.O 24.75

SER10.OG-GLU14.OE1 24.55

ILE136.N-HIS172.O 24.15

LYS180.N-ASP176.OD2 23.95

GLN273.N-LYS269.O 22.75

THR21.OG1-THR26.OG1 21.96

GLY29.N-VAL18.O 21.76

TYR209.N-LEU205.O 24.35 THR45.OG1-ASP48.OD2 24.15

TYR101.OH-ASP33.OD1 21.56 ARG40.NE-ASP187.OD1 21.56

GLN273.N-LYS269.O 24.95

THR292.N-ASP295.OD1 22.16

ASN65.N-SER62.O 24.55

ALA210.N-ALA206.O 24.95

ALA210.N-ALA206.O 22.55 VAL303.N-GLN256.OE1 21.76

ASN221.N-SER267.OG 25.55

THR175.N-MET162.O 22.55

ARG40.NH2-ASP187.OD2 27.54

SER10.OG-GLU14.OE1 30.14

THR292.OG1-ASP295.OD1 30.54

SER113.N-PHE150.O 27.94 LEU67.N-THR21.O 27.94

THR243.OG1-HIS246.ND1 30.54

ARG105.NH2-PHE181.O 28.14

ARG131.N-THR135.O 32.34

ASN133.ND2-GLY195.O 30.94

ASN84.ND2-GLU178.O 32.73

GLY146.N-HIS163.O 29.74 THR45.OG1-ASP48.OD2 29.54

SER158.N-ASN151.O 28.54

THR45.OG1-ASP48.OD1 32.93

ILE281.N-SER284.O 32.93

GLN256.NE2-PRO252.O 29.94

GLN299.N-ASP295.O 30.54

ILE281.N-SER284.O 30.54

SARS-CoV-2-N3 rep1 THR21.N-LEU67.O 33.53

GLN69.N-GLN19.O 33.13

rep3 VAL18.N-GLY29.O 30.54

rep2

CYS160.N-GLY149.O 32.43

SARS-CoV-1-N3 rep1

ASN203.ND2-ASP289.O 33.53

LEU208.N-VAL204.O 23.55

ALA234.N-PHE230.O 23.95

GLY23.N-VAL42.O 24.15

THR243.OG1-HIS246.ND1 24.15

ASN214.N-ALA210.O 24.35

VAL86.N-GLN83.O 24.75

SER62.N-ASN65.OD1 24.95

LYS137.N-ALA129.O 25.35

SER81.N-LYS88.O 25.35

THR198.OG1-GLU240.OE1 25.95

ARG105.NH2-PHE181.O 25.95

ASN180.N-ASP176.OD2 26.15

LYS102.N-VAL157.O 26.95

ALA116.N-GLY124.O 27.15

THR198.OG1-GLU240.OE2 27.54

THR21.OG1-THR25.O 27.74

SER10.OG-GLU14.OE2 27.74

GLU290.N-GLU288.OE1 28.34

SER158.N-ASN151.O 28.34

ALA255.N-GLY251.O 28.54

LYS269.N-CYS265.O 28.74

SER113.N-PHE150.O 28.94

ASN231.ND2-LEU242.O 29.14

SER123.N-ALA116.O 29.14

CYS160.N-GLY149.O 29.54

GLN256.NE2-PRO252.O 30.14

THR292.OG1-ASP295.OD2 30.54

VAL303.N-GLN256.OE1 31.14

ASN133.ND2-GLY195.O 31.54

ARG40.NE-ASP187.OD2 31.74

ARG40.NH2-ASP187.OD1 31.74

HIS80.ND1-ASN63.OD1 32.34

LEU27.N-VAL20.O 32.53

ILE281.N-SER284.O 32.53

rep2

SER10.OG-GLU14.OE2 25.55

ALA210.N-ALA206.O 25.55

GLN107.N-GLN110.OE1 25.75

THR98.OG1-ASP33.OD1 25.75

ASN95.ND2-TRP31.O 25.75

TYR209.N-LEU205.O 25.95

ILE281.N-SER284.O 25.95

VAL18.N-GLY29.O 26.15

THR292.OG1-ASP295.OD1 26.15

SER62.N-ASN65.OD1 26.35

ALA173.N-MET165.O 26.55

LEU30.N-TYR37.O 26.75

ASN151.ND2-THR111.O 26.95

ALA255.N-GLY251.O 26.95

THR243.OG1-HIS246.ND1 27.35

CYS160.N-GLY149.O 27.74

LEU268.N-MET264.O 28.14

HIS172.N-ILE136.O 28.34

THR198.OG1-GLU240.OE1 28.54

SER113.OG-GLN127.OE1 28.54

GLU14.N-SER10.O 28.94

GLY109.N-MET130.O 29.14

LYS102.N-VAL157.O 29.34

VAL86.N-GLN83.O 29.74

HIS41.NE2-HIS164.O 30.14

LYS269.N-CYS265.O 30.34

TRP218.NE1-THR280.O 30.74

ARG105.NH2-PHE181.O 30.94

SER158.N-ASN151.O 31.34

PHE112.N-CYS128.O 31.74

TYR126.N-VAL114.O 32.93

THR199.N-ASN238.O 33.93

ASN231.N-LEU227.O 33.93

PHE8.N-SER113.OG 34.33

rep3

Table 2.38 The MD-HBs (with occupancy rates ≥20%) of monomeric the SARS-CoV-1-Mpro-N3-2hob model (denoted as “SARS-CoV-1-N3 monomer”) and the SARS-CoV-2-Mpro-N3-6lu7 model (denoted as “SARS-CoV-2-N3 monomer”), where each model has three sets of MD simulations [346] (continuation)

126 2 3C-Like Protease (3CLpro)

GLY120.N-ASN28.OD1 20.76 GLN107.N-GLN110.OE1 20.76 THR292.N-ASP295.OD2 20.56

ASN180.N-ASP176.OD1 21.56 ARG105.NH1-ASN180.O 21.56 ASN231.ND2-LEU242.O 21.3 SER158.N-ASN151.O 21.36 SER284.N-ILE281.O 21.16

VAL186.N-GLN192.OE1 22.05

SER10.OG-GLU14.OE2 21.91

ASP92.N-ARG76.O 21.76

THR292.N-ASP295.OD1 21.76

THR198.OG1-GLU240.OE1 21.62

ASN180.N-ASP176.OD2 20.76

ASN65.N-SER62.O 20.16

THR224.OG1-ASP263.OD2 20.20

SER121.N-TYR118.O 20.06

LEU208.N-VAL204.O 20.56 ASP216.N-ALA211.O 20.16

MET130.N-GLN110.O 20.63

ASN238.ND2-ASP197.O 20.34

THR226.OG1-ASP229.OD1 20.56

GLN299.NE2-ASP295.O 20.56

LYS90.NZ-THR35.OG1 20.63

TYR209.N-LEU205.O 21.05

THR198.OG1-GLU240.OE2 20.76 ASN151.N-SER158.O 20.76

PHE8.N-SER113.OG 20.56 THR198.OG1-GLU240.OE2 20.56

THR292.OG1-ASP295.OD2 20.76

THR111.OG1-ASP295.OD2 20.96

SER254.OG-ILE259.O 21.16

THR21.OG1-THR26.OG1 23.35

SER81.N-LYS88.O 23.55

THR292.N-ASP295.OD1 23.55

ASN180.N-ASP176.OD1 23.55

ILE200.N-ASP289.OD1 24.15

LEU272.N-LEU268.O 24.35

SER113.N-PHE150.O 21.19

GLN273.N-LYS269.O 20.96

ASN231.ND2-LEU242.O 24.35

VAL104.N-PHE159.O 24.35

THR45.OG1-ASP48.OD1 24.55

LEU57.N-ASN53.O 24.75

THR45.OG1-ASP48.OD2 24.95

THR111.OG1-ASP295.OD1 24.95

THR26.OG1-THR21.OG1 24.95

GLN299.NE2-ASP295.O 25.15

SER10.OG-GLU14.OE1 25.35

SER10.OG-GLU14.OE1 21.19

VAL186.N-GLN192.OE1 20.76

GLN69.N-GLN19.O 20.76

GLN107.N-GLN110.OE1 21.76

THR224.OG1-ASP263.OD1 20.16

LYS180.N-ASP176.OD2 22.19

GLU14.N-SER10.O 21.34

GLN299.N-ASP295.O 20.96

ASN180.N-ASP176.OD2 21.96

SER254.OG-ILE259.O 20.36

ARG105.NH1-ASP176.OD2 22.33

ASP92.N-ARG76.O 20.96

LYS5.NZ-GLU288.OE2 21.36

TRP218.NE1-THR280.O 21.96

ARG105.NH1-ASP176.OD1 20.16

ARG298.N-PHE294.O 21.36

LEU208.N-VAL204.O 20.36

THR45.OG1-ASP48.OD2 23.04

TYR209.N-LEU205.O 20.36

ARG298.NH2-ASP295.OD1 21.96

TYR126.N-VAL114.O 22.48

LEU208.N-VAL204.O 22.75

TYR209.N-LEU205.O 20.56

SER254.N-LEU250.O 23.90

ALA234.N-PHE230.O 20.36

SER254.OG-ILE259.O 21.96

ASN151.ND2-THR111.O 22.55

ARG105.NH1-ASP176.OD1 22.16

ALA116.N-GLY124.O 23.35

ALA116.N-GLY124.O 20.56

ASP216.N-ALA211.O 24.32

ASN51.ND2-ASP48.O 20.76

THR175.OG1-ASP176.O 20.36

ALA255.N-GLY251.O 23.55

ARG60.NH1-ASP48.OD2 20.76

ALA234.N-PHE230.O 24.75

TYR101.OH-ASP33.OD2 20.96

ILE136.N-HIS172.O 22.95

GLN83.NE2-GLU178.O 22.62

ARG40.NE-ASP187.OD1 23.75

MET165.N-ALA173.O 20.96

LEU141.N-TYR118.OH 24.75

THR198.OG1-GLU240.OE2 21.16

VAL104.N-PHE159.O 22.95

SER81.N-LYS88.O 22.75

HIS41.NE2-HIS164.O 23.95

LEU86.N-GLN83.O 21.16

GLN69.N-GLN19.O 24.75

TYR101.OH-ASP33.OD1 21.36

THR111.OG1-ASP295.OD2 23.35

ASN221.N-SER267.OG 23.55

MET6.N-GLN299.OE1 20.56

GLY120.N-ASN28.OD1 23.95

LYS102.N-VAL157.O 21.16

TYR118.N-SER121.O 24.75

TYR126.N-VAL114.O 24.15

MET130.N-GLN110.O 21.36

ASN28.ND2-CYS145.O 24.89

ALA210.N-ALA206.O 21.76

ALA116.N-GLY124.O 21.36

2.4 Concluding Remarks 127

128

2 3C-Like Protease (3CLpro)

Table 2.39 The MD-HBs linking the ligands LIG307 and LIG308 of dimer the SARS-CoV-1Mpro-N3-2hob model (denoted as “SARS-CoV-1-N3 dimer”) —the model has three sets of MD simulations [346] SARS-CoV-1-N3 rep1

rep2

rep3

LIG307.N-B:GLU166.O 45.22%

B:GLU166.N-LIG307.O 53.78%

A:SER144.N-LIG308.O8 27.09%

B:GLU166.N-LIG307.O 29.28%

LIG307.N5-B:HIS164.O 42.43%

LIG308.N-A:ARG188.O 23.90%

LIG307.N-B:GLN189.OE1 25.50%

LIG307.N-B:GLU166.O 40.24%

A:GLN189.NE2-LIG308.O 18.92%

B:SER144.N-LIG307.O8 23.71%

LIG307.N-B:GLN189.OE1 33.86%

A:GLY143.N-LIG308.O8 11.16%

B:GLY143.N-LIG307.O8 14.74%

B:CYS145.N-LIG307.O7 11.95%

LIG308.N-LIG308.O42 9.96%

LIG307.N5-LIG307.O 9.16%

B:ASN142.ND2-LIG307.O8 9.76%

LIG308.N6-A:LEU141.O 5.38%

LIG307.N-B:THR190.O 8.17%

LIG307.N-B:GLN192.O 5.38%

LIG308.N-LIG308.O 5.38%

LIG307.N6-B:LEU141.O 4.98%

B:THR190.N-LIG307.O 4.38%

LIG308.N-A:GLU166.O 4.58%

B:GLN189.NE2-LIG307.O 4.38%

B:GLN189.NE2-LIG307.O 4.18%

A:GLU166.N-LIG308.O 2.79%

B:CYS145.N-LIG307.O7 3.98%

LIG307.N-B:THR190.O 1.59%

A:CYS145.N-LIG308.O7 2.79%

B:SER144.OG-LIG307.O8 3.19%

LIG307.N6-B:GLU166.OE2 1.20%

LIG308.N-A:GLN189.OE1 2.59%

LIG307.N5-B:HIS164.O 1.79%

LIG307.N-LIG307.O 1.00%

A:SER144.OG-LIG308.O8 1.59%

LIG307.N6-B:SER144.OG 1.59%

LIG307.N6-B:PHE140.O 0.60%

LIG308.N-A:THR190.O 1.20%

B:GLN192.N-LIG307.N2 0.80%

B:GLN192.N-LIG307.N2 0.40%

A:HIS41.NE2-LIG308.O7 1.00%

LIG307.N6-B:GLU166.OE1 0.60%

LIG307.N6-B:GLU166.OE1 0.40%

A:HIS41.NE2-LIG308.O 1.00%

LIG307.N-B:GLN192.O 0.40%

B:THR190.OG1-LIG307.O 0.20%

LIG308.N6-A:SER144.OG 0.80%

B:HIS41.NE2-LIG307.O 0.40%

LIG307.N6-B:SER144.OG 0.20%

A:GLN192.NE2-LIG308.N2 0.80%

B:GLN192.N-LIG307.O1 0.20%

LIG308.N6-A:PHE140.O 0.60%

B:ASN119.ND2-LIG307.C2 0.20%

A:GLU166.N-LIG308.O 43.82%

A:GLN189.NE2-LIG308.O42 0.60%

LIG307.N-B:GLN189.O 0.20%

LIG308.N-A:GLU166.O 32.87%

LIG308.N5-A:ASN142.OD1 0.40%

LIG308.N-A:GLN189.OE1 21.51%

A:THR190.N-LIG308.O 0.40%

A:GLU166.N-LIG308.O 51.79%

LIG308.N5-A:HIS164.O 17.73%

A:GLN192.N-LIG308.N2 0.20%

LIG308.N-A:GLU166.O 39.64%

A:CYS145.N-LIG308.O7 13.15%

LIG308.N-A:GLN192.O 0.20%

LIG308.N-A:GLN189.OE1 34.26%

LIG308.N-A:THR190.O 9.36%

A:GLN192.NE2-LIG308.O1 0.20%

LIG308.N5-A:HIS164.O 21.71%

LIG308.N6-A:GLU166.OE2 4.58%

A:ASN119.ND2-LIG308.C2 0.20%

LIG308.N-A:THR190.O 10.56%

LIG308.N6-A:GLU166.OE1 3.78%

A:THR26.OG1-LIG308.C4 0.20%

A:CYS145.N-LIG308.O7 10.16%

A:THR190.N-LIG308.O 3.19%

A:CYS145.N-LIG308.O8 0.20%

A:THR190.N-LIG308.O 3.39%

A:HIS41.NE2-LIG308.O 1.79%

A:GLN189.NE2-LIG308.O 3.19%

A:HIS172.NE2-LIG308.O8 1.59%

LIG308.N6-A:GLU166.OE2 1.59%

A:GLN189.NE2-LIG308.O 1.39%

LIG308.N6-A:GLU166.OE1 1.39%

LIG308.N6-B:SER1.OG 1.20%

A:GLN192.N-LIG308.N2 1.00%

B:SER1.OG-LIG308.O8 1.20%

LIG308.N-A:GLN192.O 0.60%

A:GLN192.N-LIG308.N2 0.80%

LIG308.N6-A:PHE140.O 0.40%

A:ASN142.ND2-LIG308.O8 0.60%

A:GLN192.N-LIG308.O1 0.20%

A:GLN192.N-LIG308.O1 0.40%

A:HIS41.NE2-LIG308.O 0.20%

LIG308.N-A:GLN192.O 0.40%

LIG308.N5-LIG308.O 0.20%

A:THR190.OG1-LIG308.O 0.20% LIG308.N5-LIG308.O 0.20% LIG308.N-LIG308.O 0.20% LIG308.N-LIG308.O8 0.20% LIG308.N5-LIG308.O8 0.20% A:GLN189.NE2-LIG308.O8 0.20% LIG308.N5-A:GLN189.OE1 0.20% LIG308.N-A:GLN189.O 0.20%

2.4 Concluding Remarks

129

Table 2.40 The MD-HBs (with occupancy rates ≥20%) of dimer the SARS-CoV-1-Mpro-N32hob model (denoted as “SARS-CoV-1-N3 dimer”) —the model has three sets of MD simulations [346] SARS-CoV-1-N3 rep1

rep2

rep3

B:ARG4.NH2-A:GLU290.OE2 45.82%

A:SER139.OG-B:GLN299.OE1 59.36%

B:SER139.OG-A:GLN299.OE1 42.83%

B:ARG4.NH1-A:GLU290.OE1 43.23%

B:SER139.OG-A:GLY2.O 32.27%

A:SER1.OG-B:GLU166.OE2 29.88%

B:SER1.OG-A:GLU166.OE2 30.68%

A:VAL125.N-B:ALA7.O 29.08%

A:ALA7.N-B:VAL125.O 28.88%

B:GLY11.N-A:GLU14.OE1 30.28%

B:ARG4.NH2-A:GLU290.OE2 28.69%

A:ARG4.NH1-B:LYS137.O 28.49%

B:SER1.OG-A:GLU166.OE1 29.28%

A:ALA7.N-B:VAL125.O 28.29%

B:ARG4.NH1-A:GLU290.OE2 28.29%

A:SER1.OG-B:GLU166.OE1 27.69%

B:GLY11.N-A:GLU14.OE1 27.69%

B:ARG4.NH2-A:GLU290.OE1 26.49%

A:GLY11.N-B:GLU14.OE1 25.30%

B:ARG4.NH1-A:GLU290.OE1 23.90%

B:VAL125.N-A:ALA7.O 25.10%

A:SER139.OG-B:GLN299.OE1 23.11%

A:SER1.OG-B:GLU166.OE1 23.51%

A:SER1.OG-B:GLU166.OE1 23.31%

A:GLY143.N-B:VAL303.O 22.11%

B:VAL125.N-A:ALA7.O 22.71%

A:GLY11.N-B:GLU14.OE1 21.71%

A:VAL125.N-B:ALA7.O 21.91%

B:SER1.OG-A:GLU166.OE1 22.11%

B:ALA7.N-A:VAL125.O 20.92%

A:SER1.OG-B:GLU166.OE2 21.12%

B:ALA7.N-A:VAL125.O 21.91%

A:VAL125.N-B:ALA7.O 20.92%

A:SER10.OG-A:GLU14.OE1 83.07%

A:SER10.OG-A:GLU14.OE1 82.47%

B:GLY11.N-A:GLU14.OE1 20.72% A:TYR209.OH-A:ILE259.O 64.34%

A:TYR209.OH-A:ILE259.O 67.53%

A:SER10.OG-A:GLU14.OE1 80.68%

A:TRP31.N-A:CYS16.O 64.14%

A:TRP31.N-A:CYS16.O 66.14%

A:GLU14.OE1-A:SER10.OG 80.68%

A:HIS163.N-A:SER147.O 62.95%

A:HIS163.N-A:SER147.O 65.14%

A:TYR209.OH-A:ILE259.O 66.73%

A:SER147.OG-A:SER144.O 60.76%

A:VAL114.N-A:TYR126.O 57.77%

A:THR201.OG1-A:GLU240.O 65.74%

A:THR257.OG1-A:LEU253.O 59.56%

A:ILE78.N-A:LYS90.O 57.77%

A:ILE78.N-A:LYS90.O 65.34%

A:THR201.OG1-A:GLU240.O 58.57%

A:THR257.OG1-A:LEU253.O 56.37%

A:HIS163.N-A:SER147.O 64.94%

A:VAL114.N-A:TYR126.O 57.57%

A:LEU87.N-A:CYS38.O 56.18%

A:THR135.OG1-A:ASN133.OD1 60.76%

A:ILE78.N-A:LYS90.O 57.37%

A:THR201.OG1-A:GLU240.O 54.38%

A:TRP31.N-A:CYS16.O 59.56%

A:LEU87.N-A:CYS38.O 56.18%

A:VAL157.N-A:LYS100.O 53.19%

A:VAL114.N-A:TYR126.O 57.17%

A:LEU115.N-A:VAL148.O 54.38%

A:LEU115.N-A:VAL148.O 52.39%

A:THR257.OG1-A:LEU253.O 55.18%

A:THR135.OG1-A:ASN133.OD1 53.59%

A:THR45.OG1-A:ASP48.OD1 51.00%

A:LEU167.N-A:VAL171.O 54.98%

A:ASN203.ND2-A:GLY109.O 53.39%

A:VAL36.N-A:LEU89.O 50.80%

A:VAL36.N-A:LEU89.O 54.58%

A:LYS5.NZ-A:GLU290.OE1 52.79%

A:SER147.OG-A:SER144.O 50.40%

A:SER123.N-A:ALA116.O 54.38%

A:ALA70.N-A:VAL73.O 52.59%

A:ASP153.N-A:CYS156.O 50.20%

A:TYR182.OH-A:CYS160.O 54.38%

A:LEU167.N-A:VAL171.O 52.39%

A:GLN19.N-A:GLN69.O 49.60%

A:LEU87.N-A:CYS38.O 53.98%

A:VAL36.N-A:LEU89.O 51.39%

A:LEU89.N-A:VAL36.O 49.00%

A:GLN299.NE2-A:ARG4.O 52.79%

A:LEU89.N-A:VAL36.O 51.20%

A:LEU27.N-A:VAL20.O 48.80%

A:LEU89.N-A:VAL36.O 52.19%

A:ASP153.N-A:CYS156.O 50.80%

A:LYS90.N-A:GLY79.O 48.01%

A:ILE136.N-A:HIS172.O 51.59%

A:LEU27.N-A:VAL20.O 50.40%

A:ARG88.N-A:SER81.O 48.01%

A:ASP153.N-A:CYS156.O 51.39%

A:VAL157.N-A:LYS100.O 50.40%

A:LEU167.N-A:VAL171.O 47.41%

A:VAL20.N-A:LEU27.O 51.00%

A:LYS90.N-A:GLY79.O 49.60%

A:VAL20.N-A:LEU27.O 47.21%

A:ARG131.N-A:THR135.O 50.60%

A:ARG131.N-A:THR135.O 49.60%

A:PHE8.N-A:SER113.OG 46.02%

A:GLY149.N-A:TYR161.O 50.20%

A:VAL18.N-A:GLY29.O 49.00%

A:ASN203.ND2-A:GLY109.O 45.82%

A:LEU115.N-A:VAL148.O 49.80%

A:TYR37.N-A:LEU30.O 48.61%

A:ALA173.N-A:MET165.O 45.82%

A:TYR37.N-A:LEU30.O 49.20%

A:ARG88.N-A:SER81.O 48.41%

A:ASN95.N-A:ASP33.O 45.42%

A:HIS172.N-A:ILE136.O 48.80%

A:GLN19.N-A:GLN69.O 46.41%

A:VAL18.N-A:GLY29.O 45.42%

A:THR25.OG1-A:CYS44.O 48.01%

A:SER123.N-A:ALA116.O 46.02%

A:TYR37.N-A:LEU30.O 45.42%

A:VAL157.N-A:LYS100.O 47.41%

A:GLY146.N-A:HIS163.O 45.82%

A:PHE112.N-A:CYS128.O 45.02%

A:PHE150.N-A:SER113.O 47.01%

A:PHE150.N-A:SER113.O 45.62%

A:ALA70.N-A:VAL73.O 43.82%

A:LEU242.N-A:ASN231.OD1 46.81%

A:LEU30.N-A:TYR37.O 45.22%

A:LEU75.N-A:VAL68.O 43.63%

A:ARG88.N-A:SER81.O 46.61%

A:ASN203.ND2-A:ASP289.O 44.82%

A:CYS128.N-A:PHE112.O 43.63%

A:ASN95.N-A:ASP33.O 46.61%

A:LEU75.N-A:VAL68.O 44.62%

A:TYR182.OH-A:CYS160.O 43.23%

A:LEU75.N-A:VAL68.O 46.41%

A:ALA173.N-A:MET165.O 43.82%

A:HIS172.N-A:ILE136.O 43.03%

A:ALA70.N-A:VAL73.O 46.41%

A:ASN95.N-A:ASP33.O 43.43%

A:LEU30.N-A:TYR37.O 42.23%

A:PHE8.N-A:SER113.OG 46.02%

A:LEU242.N-A:ASN231.OD1 43.43%

A:GLY146.N-A:HIS163.O 41.83%

A:LYS90.N-A:GLY79.O 46.02%

A:HIS172.N-A:ILE136.O 42.83%

A:PHE150.N-A:SER113.O 41.63%

A:GLN19.N-A:GLN69.O 45.42%

A:GLY109.N-A:MET130.O 42.83%

A:SER123.N-A:ALA116.O 41.24%

A:GLY146.N-A:HIS163.O 45.42%

A:CYS128.N-A:PHE112.O 42.23%

A:ASN231.N-A:LEU227.O 41.24%

A:ASN203.ND2-A:ASP289.O 44.42%

A:LEU32.N-A:THR35.O 41.63%

A:THR21.N-A:LEU67.O 41.24%

A:LEU32.N-A:THR35.O 44.42%

A:ASN95.ND2-A:TRP31.O 41.43%

A:LEU242.N-A:ASN231.OD1 41.04%

A:LEU27.N-A:VAL20.O 43.43%

A:ASN231.N-A:LEU227.O 41.24%

A:ASN214.ND2-A:ALA210.O 40.44%

A:ILE200.N-A:ASP289.OD2 43.43%

A:ASN133.ND2-A:GLY195.O 40.84%

A:LEU32.N-A:THR35.O 39.64%

A:LEU30.N-A:TYR37.O 43.43%

(continued)

130

2 3C-Like Protease (3CLpro)

Table 2.40 (continued) SARS-CoV-1-N3 rep1

rep2

rep3

A:TYR118.N-A:SER121.O 40.24%

A:LYS5.NZ-A:GLU290.OE1 38.45%

A:ARG105.NH2-A:PHE181.O 42.63%

A:ASN28.ND2-A:CYS145.O 39.04%

A:ALA234.N-A:PHE230.O 38.05%

A:ARG131.NH2-A:ASP289.OD2 42.43%

A:PHE8.N-A:SER113.OG 39.04%

A:ARG60.NH1-A:ASP48.OD1 37.85%

A:LEU205.N-A:THR201.O 41.83%

A:VAL20.N-A:LEU27.O 38.84%

A:ARG60.NH2-A:ASP48.OD2 37.65%

A:VAL18.N-A:GLY29.O 41.63%

A:THR199.N-A:ASN238.O 38.25%

A:ASN28.ND2-A:CYS145.O 37.45%

A:CYS22.N-A:THR25.O 41.63%

A:TYR182.OH-A:ILE106.O 38.05%

A:ASN203.ND2-A:ASP289.O 37.25%

A:CYS128.N-A:PHE112.O 41.63%

A:TYR239.N-A:ALA234.O 37.65%

A:THR135.OG1-A:ASN133.OD1 37.05%

A:ALA116.N-A:GLY124.O 40.84%

A:LEU268.N-A:MET264.O 36.85%

A:ARG105.NH2-A:PHE181.O 37.05%

A:THR111.OG1-A:ASP295.OD1 40.64%

A:THR45.OG1-A:ASP48.OD2 36.45%

A:GLN192.NE2-A:VAL186.O 37.05%

A:GLU14.N-A:SER10.O 40.24%

A:GLY149.N-A:TYR161.O 36.45%

A:ASN84.ND2-A:GLU178.O 36.85%

A:ASN214.ND2-A:ALA210.O 38.25%

A:THR21.N-A:LEU67.O 36.25%

A:GLY109.N-A:MET130.O 36.45%

A:THR21.N-A:LEU67.O 37.85%

A:GLN83.N-A:LEU86.O 36.25%

A:GLY149.N-A:TYR161.O 36.45%

A:PHE112.N-A:CYS128.O 37.65%

A:PHE112.N-A:CYS128.O 35.86%

A:ASN95.ND2-A:TRP31.O 35.46%

A:ASN231.N-A:LEU227.O 37.45%

A:SER144.OG-A:HIS163.NE2 35.86%

A:TYR118.N-A:SER121.O 34.66%

A:ASN95.ND2-A:TRP31.O 37.05%

A:ARG40.NH2-A:ASP187.OD1 35.66%

A:TYR182.N-A:GLY174.O 34.66%

A:THR199.N-A:ASN238.O 36.85%

A:SER113.OG-A:GLN127.OE1 35.26%

A:GLU14.N-A:SER10.O 34.06%

A:ASN28.ND2-A:CYS145.O 36.85%

A:ASN231.ND2-A:LEU242.O 35.06%

A:GLU290.N-A:GLU288.OE1 34.06%

A:LYS5.NZ-A:GLU290.OE2 36.85%

A:GLN189.N-A:MET49.O 32.47%

A:TYR239.N-A:ALA234.O 33.67%

A:ASN133.ND2-A:GLY195.O 36.65%

A:LEU205.N-A:THR201.O 31.87%

A:ILE281.N-A:SER284.O 33.47%

A:GLN192.NE2-A:VAL186.O 36.45%

A:CYS22.N-A:THR25.O 31.87%

A:SER113.OG-A:GLN127.OE1 33.47%

A:ILE281.N-A:SER284.O 36.06%

A:SER158.N-A:ASN151.O 31.08%

A:ARG40.NH2-A:ASP187.OD1 33.47%

A:SER147.OG-A:SER144.O 35.06%

A:GLU14.N-A:SER10.O 30.48%

A:ARG131.N-A:THR135.O 32.87%

A:ALA173.N-A:MET165.O 35.06%

A:GLN256.NE2-A:PRO252.O 29.88%

A:THR175.OG1-A:ASP176.O 31.87%

A:TYR182.N-A:GLY174.O 34.46%

A:VAL91.N-A:ASP34.O 29.68%

A:THR199.N-A:ASN238.O 31.67%

A:ASN203.ND2-A:GLY109.O 34.46%

Table 2.41 The MD-HBs (with occupancy rates ≥20%) of dimer the SARS-CoV-1-MproN3-2hob model (denoted as “SARS-CoV-1-N3 dimer”) —the model has three sets of MD simulations [346] (continuation-1) SARS-CoV-1-N3 rep1

rep2

rep3

A:THR45.OG1-A:ASP48.OD1 28.88%

A:LEU67.N-A:THR21.O 31.47%

A:GLY109.N-A:MET130.O 34.26%

A:GLN192.NE2-A:VAL186.O 28.69%

A:ASN231.ND2-A:LEU242.O 31.27%

A:SER113.OG-A:GLN127.OE1 33.47%

A:ARG40.NE-A:ASP187.OD2 28.49%

A:GLN189.N-A:MET49.O 30.48%

A:GLN83.N-A:LEU86.O 33.47%

A:SER81.N-A:ARG88.O 28.49%

A:GLN83.N-A:LEU86.O 30.28%

A:SER158.N-A:ASN151.O 32.67%

A:THR111.OG1-A:ASP295.OD2 28.29%

A:SER81.N-A:ARG88.O 30.28%

A:VAL91.N-A:ASP34.O 32.47%

A:ILE281.N-A:SER284.O 28.09%

A:THR292.OG1-A:ASP295.OD2 29.88%

A:LEU268.N-A:MET264.O 31.67%

A:THR198.OG1-A:GLU240.OE2 27.89%

A:SER1.OG-B:GLU166.OE2 29.88%

A:ASN84.ND2-A:GLU178.O 31.47%

A:LEU67.N-A:THR21.O 27.49%

A:GLY11.N-B:GLU14.OE1 29.88%

A:ALA255.N-A:GLY251.O 31.27%

A:THR111.OG1-A:ASP295.OD1 27.49%

A:CYS22.N-A:THR25.O 29.68%

A:THR175.OG1-A:ASP176.O 31.27%

A:GLN69.N-A:GLN19.O 27.09%

A:HIS80.ND1-A:ASN63.OD1 29.48%

A:SER81.N-A:ARG88.O 31.27%

A:ASN95.ND2-A:GLY15.O 27.09%

A:GLN69.N-A:GLN19.O 28.88%

A:TYR239.N-A:ALA234.O 31.08%

A:HIS80.ND1-A:ASN63.OD1 27.09%

A:VAL91.N-A:ASP34.O 28.88%

A:CYS160.N-A:GLY149.O 30.48%

A:ARG131.NH2-A:ASP289.OD2 26.89%

A:THR111.OG1-A:ASP295.OD2 28.88%

A:SER254.OG-A:ILE259.O 30.08%

A:ILE136.N-A:HIS172.O 26.29%

A:ARG40.NE-A:ASP187.OD2 28.69%

A:THR45.OG1-A:ASP48.OD1 29.28%

A:LYS102.N-A:VAL157.O 26.29%

A:ILE43.N-A:ARG40.O 28.69%

A:ARG40.NE-A:ASP187.OD2 29.08%

A:LEU208.N-A:VAL204.O 26.29%

A:SER144.OG-A:CYS117.O 28.69%

A:THR45.OG1-A:ASP48.OD2 28.88%

A:TYR182.N-A:GLY174.O 26.29%

A:LYS102.N-A:VAL157.O 28.49%

A:LYS102.N-A:VAL157.O 28.49%

A:GLN256.NE2-A:THR304.O 26.10%

A:THR225.OG1-A:ASP229.OD1 28.49%

A:ASN231.ND2-A:LEU242.O 28.49%

A:THR175.OG1-A:ASP176.O 25.90%

A:THR226.OG1-A:ASP229.OD2 27.69%

A:ASN28.ND2-A:GLY143.O 28.49%

A:TYR54.OH-A:ASP187.O 25.10%

A:SER144.OG-A:HIS163.NE2 27.49%

A:THR111.OG1-A:ASP295.OD2 28.29%

A:ILE43.N-A:ARG40.O 25.10%

A:SER158.N-A:ASN151.O 27.49%

A:TRP218.NE1-A:THR280.O 28.29%

A:GLY275.N-A:GLU270.O 25.10%

A:SER254.OG-A:ILE259.O 26.29%

A:CYS300.N-A:VAL296.O 28.09%

A:ARG105.NH2-A:PHE181.O 24.90%

A:THR198.OG1-A:GLU240.OE1 26.10%

A:ARG40.NH2-A:ASP187.OD1 28.09%

A:PHE159.N-A:LYS102.O 24.70%

A:SER113.N-A:PHE150.O 25.50%

A:SER144.OG-A:LEU141.O 26.89%

A:ALA7.N-B:VAL125.O 24.70%

A:THR98.OG1-A:ASN95.O 25.30%

A:LEU208.N-A:VAL204.O 26.10%

A:VAL104.N-A:PHE159.O 24.50%

A:LEU208.N-A:VAL204.O 24.70%

A:VAL104.N-A:PHE159.O 25.70%

(continued)

2.4 Concluding Remarks

131

Table 2.41 (continued) SARS-CoV-1-N3 rep1

rep2

rep3

A:THR198.OG1-A:GLU240.OE1 23.90%

A:LEU268.N-A:MET264.O 24.50%

A:GLN69.N-A:GLN19.O 25.50%

A:GLN19.NE2-A:ASN119.O 23.71%

A:VAL104.N-A:PHE159.O 24.30%

A:ASN151.N-A:SER158.O 25.50%

A:LYS269.N-A:CYS265.O 23.51%

A:LYS180.N-A:ASP176.OD1 23.71%

A:THR98.OG1-A:ASN95.O 25.30%

A:TYR182.OH-A:CYS160.O 23.51%

A:THR45.N-A:ASP48.OD1 23.71%

A:LEU67.N-A:THR21.O 24.30%

A:ASN274.N-A:GLU270.O 23.31%

A:TRP218.NE1-A:THR280.O 23.31%

A:ALA234.N-A:PHE230.O 23.90%

A:ASN151.N-A:SER158.O 23.31%

A:THR225.OG1-A:ASP229.OD2 23.31%

A:LEU272.N-A:LEU268.O 23.71%

A:GLN299.NE2-A:GLY2.O 23.11%

A:ALA255.N-A:GLY251.O 23.31%

A:ARG40.NE-A:ASP187.OD1 23.31%

A:LYS5.NZ-A:GLU288.OE2 22.91%

A:MET235.N-A:ASN231.O 23.31%

A:MET130.N-A:GLN110.O 23.11%

A:ARG131.NH1-A:ASP289.OD1 22.11%

A:GLN273.N-A:LYS269.O 23.11%

A:THR292.N-A:ASP295.OD1 22.91%

A:THR292.OG1-A:ASP295.OD1 21.71%

A:ASN95.ND2-A:GLY15.O 23.11%

A:THR198.OG1-A:GLU240.OE1 22.91%

A:THR292.OG1-A:ASP295.OD2 21.51%

A:THR111.OG1-A:ASP295.OD1 22.91%

A:GLN273.NE2-A:LYS269.O 22.91%

A:ASN84.ND2-A:GLU178.O 21.31%

A:THR198.OG1-A:GLU240.OE2 22.51%

A:THR21.OG1-A:THR26.OG1 22.51%

A:THR26.OG1-A:THR21.OG1 20.92%

A:GLN83.NE2-A:GLU178.O 22.31%

A:SER254.N-A:LEU250.O 22.11%

A:ALA255.N-A:GLY251.O 20.92%

A:THR292.OG1-A:ASP295.OD1 22.11%

A:SER284.N-A:ILE281.O 21.91%

A:ARG105.NH1-A:ASP176.OD1 20.72%

A:SER284.N-A:ILE281.O 21.51%

A:LYS269.N-A:CYS265.O 21.71%

A:MET162.N-A:THR175.O 20.52%

A:ARG105.NH1-A:ASP176.OD2 21.51%

A:ARG131.NH1-A:ASP289.OD1 21.71%

A:SER254.OG-A:ILE259.O 20.32%

A:ASN221.ND2-A:ALA266.O 21.51%

A:ARG40.NH2-A:ASP187.OD2 21.71%

A:CYS160.N-A:GLY149.O 20.12%

A:GLU240.N-A:THR199.O 21.51%

A:THR198.OG1-A:GLU240.OE2 21.51%

A:TYR182.OH-A:ILE106.O 21.31%

A:ARG105.NH1-A:ASP176.OD1 21.12%

B:SER10.OG-B:GLU14.OE1 84.06%

A:ALA116.N-A:GLY124.O 21.31%

A:ASN95.ND2-A:GLY15.O 21.12%

B:TYR182.OH-B:CYS160.O 70.72%

A:TYR101.OH-A:ASP33.OD2 21.12%

A:ARG105.NH1-A:LYS180.O 20.72%

B:TYR209.OH-B:ILE259.O 69.12%

A:LYS269.N-A:CYS265.O 20.92%

A:GLN107.N-A:GLN110.OE1 20.52%

B:THR201.OG1-B:GLU240.O 63.94%

A:GLN107.N-A:GLN110.OE1 20.92%

A:THR224.OG1-A:ASP263.OD2 20.52%

B:VAL114.N-B:TYR126.O 63.75%

A:ASN151.ND2-A:THR111.O 20.72%

A:TYR118.N-A:SER121.O 20.32%

B:TRP31.N-B:CYS16.O 62.15%

A:ILE136.N-A:HIS172.O 20.72%

A:ARG4.N-A:GLN299.OE1 20.32%

B:HIS163.N-B:SER147.O 61.35%

A:THR26.OG1-A:THR21.OG1 20.52%

A:SER113.N-A:PHE150.O 20.32%

B:ILE78.N-B:LYS90.O 59.36%

A:ARG40.NH2-A:ASP187.OD2 20.52%

B:TYR54.OH-B:ASP187.O 58.96%

A:ASN151.N-A:SER158.O 20.12%

B:SER10.OG-B:GLU14.OE1 85.66%

B:GLY146.N-B:HIS163.O 57.57%

A:GLY120.N-A:ASN28.OD1 20.12%

B:TYR209.OH-B:ILE259.O 76.69%

B:THR257.OG1-B:LEU253.O 55.78%

A:THR226.OG1-A:ASP229.OD1 20.12%

B:ILE78.N-B:LYS90.O 63.75%

B:LEU27.N-B:VAL20.O 54.78%

B:TYR54.OH-B:ASP187.O 62.35%

B:LEU87.N-B:CYS38.O 53.59%

B:SER10.OG-B:GLU14.OE1 84.86%

B:TRP31.N-B:CYS16.O 61.95%

B:VAL36.N-B:LEU89.O 53.19%

B:TYR54.OH-B:ASP187.O 68.33%

B:VAL36.N-B:LEU89.O 60.96%

B:LEU167.N-B:VAL171.O 52.19%

B:TYR209.OH-B:ILE259.O 66.53%

B:THR201.OG1-B:GLU240.O 60.16%

B:VAL157.N-B:LYS100.O 51.99%

B:THR201.OG1-B:GLU240.O 65.74%

B:LEU115.N-B:VAL148.O 59.36%

B:VAL20.N-B:LEU27.O 51.99%

B:ILE78.N-B:LYS90.O 64.14%

B:LEU27.N-B:VAL20.O 56.77%

B:GLY109.N-B:MET130.O 51.59%

B:TRP31.N-B:CYS16.O 63.15%

B:THR257.OG1-B:LEU253.O 55.58%

B:THR135.OG1-B:ASN133.OD1 51.39%

B:VAL36.N-B:LEU89.O 58.37%

B:LEU167.N-B:VAL171.O 55.18%

B:GLN19.N-B:GLN69.O 51.39%

B:VAL114.N-B:TYR126.O 56.77%

B:VAL114.N-B:TYR126.O 54.98%

B:GLN189.N-B:MET49.O 51.20%

B:GLY179.N-B:ASP176.OD1 55.38%

B:SER147.OG-B:SER144.O 52.99%

B:LEU115.N-B:VAL148.O 50.60%

B:LEU87.N-B:CYS38.O 53.78%

B:ASP153.N-B:CYS156.O 52.79%

B:LEU242.N-B:ASN231.OD1 49.20%

B:ALA173.N-B:MET165.O 53.78%

B:HIS172.N-B:ILE136.O 52.79%

B:ARG88.N-B:SER81.O 48.80%

B:THR135.OG1-B:ASN133.OD1 52.99%

B:GLY146.N-B:HIS163.O 52.19%

B:LYS90.N-B:GLY79.O 48.80%

B:THR257.OG1-B:LEU253.O 52.99%

B:ALA173.N-B:MET165.O 51.79%

B:ASP153.N-B:CYS156.O 48.41%

B:GLY109.N-B:MET130.O 52.59%

B:THR135.OG1-B:ASN133.OD1 51.39%

B:LEU89.N-B:VAL36.O 48.21%

B:HIS163.N-B:SER147.O 52.39%

B:ARG88.N-B:SER81.O 51.00%

B:ALA173.N-B:MET165.O 47.61%

B:VAL20.N-B:LEU27.O 52.19%

B:HIS163.N-B:SER147.O 50.60%

B:GLN192.NE2-B:VAL186.O 47.41%

B:LEU115.N-B:VAL148.O 51.59%

B:GLN19.N-B:GLN69.O 50.00%

B:ASN203.ND2-B:GLY109.O 46.81%

B:LEU167.N-B:VAL171.O 51.59%

B:TYR118.N-B:SER121.O 49.40%

B:CYS22.N-B:THR25.O 46.61%

B:GLN19.N-B:GLN69.O 50.20%

B:LEU87.N-B:CYS38.O 49.20%

B:PHE8.N-B:SER113.OG 46.61%

B:LEU89.N-B:VAL36.O 50.20%

B:CYS128.N-B:PHE112.O 49.20%

B:LEU75.N-B:VAL68.O 45.82%

B:ARG105.NH1-B:ASP176.OD2 49.60%

B:VAL157.N-B:LYS100.O 48.80%

B:SER123.N-B:ALA116.O 45.82%

B:LYS90.N-B:GLY79.O 49.00%

B:PHE150.N-B:SER113.O 48.80%

B:TYR37.N-B:LEU30.O 45.62%

B:TYR182.OH-B:ILE106.O 48.61%

B:SER123.N-B:ALA116.O 48.61%

132

2 3C-Like Protease (3CLpro)

Table 2.42 The MD-HBs (with occupancy rates ≥20%) of dimer the SARS-CoV-1-MproN3-2hob model (denoted as “SARS-CoV-1-N3 dimer”) —the model has three sets of MD simulations [346] (continuation-2) SARS-CoV-1-N3 rep1

rep2

rep3

B:GLN83.N-B:LEU86.O 43.63%

B:ASP153.N-B:CYS156.O 48.21%

B:LYS90.N-B:GLY79.O 48.01%

B:THR199.N-B:ASN238.O 43.63%

B:TYR37.N-B:LEU30.O 48.21%

B:VAL20.N-B:LEU27.O 47.41%

B:ASN231.N-B:LEU227.O 43.63%

B:VAL157.N-B:LYS100.O 48.21%

B:LEU89.N-B:VAL36.O 45.82%

B:ASN95.N-B:ASP33.O 43.03%

B:SER147.OG-B:SER144.O 47.81%

B:GLY149.N-B:TYR161.O 45.22%

B:GLY149.N-B:TYR161.O 43.03%

B:LEU27.N-B:VAL20.O 47.41%

B:LEU242.N-B:ASN231.OD1 44.82%

B:LEU30.N-B:TYR37.O 42.03%

B:SER123.N-B:ALA116.O 47.01%

B:TYR182.OH-B:CYS160.O 44.82%

B:ASN133.ND2-B:GLY195.O 41.04%

B:HIS172.N-B:ILE136.O 47.01%

B:ASN133.ND2-B:GLY195.O 44.22%

B:ALA70.N-B:VAL73.O 41.04%

B:LEU242.N-B:ASN231.OD1 46.81%

B:TYR37.N-B:LEU30.O 44.22%

B:TYR118.N-B:SER121.O 40.04%

B:LEU75.N-B:VAL68.O 46.41%

B:LEU32.N-B:THR35.O 43.23%

B:ARG131.N-B:THR135.O 39.84%

B:ALA70.N-B:VAL73.O 45.02%

B:VAL18.N-B:GLY29.O 43.23%

B:SER147.OG-B:SER144.O 39.84%

B:GLN299.NE2-B:ARG4.O 44.22%

B:ARG40.NH2-B:ASP187.OD1 42.83%

B:VAL18.N-B:GLY29.O 39.84%

B:PHE150.N-B:SER113.O 43.43%

B:THR292.OG1-B:ASP295.OD1 42.43%

B:LEU32.N-B:THR35.O 39.64%

B:SER144.OG-B:HIS163.NE2 43.23%

B:LEU30.N-B:TYR37.O 42.23%

B:ASN28.ND2-B:CYS145.O 39.64%

B:ARG88.N-B:SER81.O 42.83%

B:GLN192.NE2-B:VAL186.O 42.23%

B:PHE112.N-B:CYS128.O 39.24%

B:LEU30.N-B:TYR37.O 42.83%

B:ASN95.N-B:ASP33.O 42.23%

B:ASN95.ND2-B:TRP31.O 38.84%

B:GLY146.N-B:HIS163.O 42.63%

B:ASN28.ND2-B:CYS145.O 41.63%

B:ASN203.ND2-B:ASP289.O 38.25%

B:PHE8.N-B:SER113.OG 42.03%

B:LEU75.N-B:VAL68.O 41.63%

B:THR25.OG1-B:CYS44.O 38.05%

B:VAL18.N-B:GLY29.O 42.03%

B:ALA70.N-B:VAL73.O 41.24%

B:THR21.N-B:LEU67.O 38.05%

B:ASN95.N-B:ASP33.O 42.03%

B:PHE8.N-B:SER113.OG 41.04%

B:PHE150.N-B:SER113.O 37.85%

B:ARG40.NE-B:ASP187.OD2 41.83%

B:ARG40.NE-B:ASP187.OD2 40.64%

B:TYR182.N-B:GLY174.O 37.25%

B:GLN189.N-B:MET49.O 41.43%

B:ASN95.ND2-B:TRP31.O 40.64%

B:ARG40.NE-B:ASP187.OD2 37.05%

B:ASN95.ND2-B:TRP31.O 40.44%

B:ASN231.N-B:LEU227.O 40.04%

B:GLN299.NE2-B:ARG4.O 36.85%

B:ASN231.N-B:LEU227.O 40.04%

B:GLU14.N-B:SER10.O 39.04%

B:LEU205.N-B:THR201.O 35.26%

B:LYS180.N-B:ASP176.OD1 39.84%

B:THR21.N-B:LEU67.O 38.84%

B:TYR239.N-B:ALA234.O 34.26%

B:ASN203.ND2-B:ASP289.O 39.64%

B:ASN203.ND2-B:ASP289.O 38.25%

B:ARG131.NH2-B:ASP289.OD2 34.26%

B:ARG40.NH2-B:ASP187.OD1 39.24%

B:PHE112.N-B:CYS128.O 38.05%

B:SER113.OG-B:GLN127.OE1 34.26%

B:CYS128.N-B:PHE112.O 39.24%

B:THR199.N-B:ASN238.O 37.25%

B:ARG40.NH2-B:ASP187.OD1 34.06%

B:LEU32.N-B:THR35.O 39.04%

B:GLY109.N-B:MET130.O 36.85%

B:HIS172.N-B:ILE136.O 33.67%

B:PHE112.N-B:CYS128.O 38.25%

B:LEU205.N-B:THR201.O 36.85%

B:GLU14.N-B:SER10.O 33.07%

B:ILE200.N-B:ASP289.OD2 37.85%

B:ARG105.NH2-B:PHE181.O 36.65%

B:LYS102.N-B:VAL157.O 32.27%

B:GLN83.N-B:LEU86.O 37.05%

B:ILE281.N-B:SER284.O 36.45%

B:ASN231.ND2-B:LEU242.O 31.47%

B:ASN231.ND2-B:LEU242.O 36.65%

B:LEU57.N-B:ASN53.O 36.06%

B:HIS80.ND1-B:ASN63.OD1 31.08%

B:LEU57.N-B:ASN53.O 36.45%

B:TYR182.N-B:GLY174.O 35.26%

B:LEU268.N-B:MET264.O 30.68%

B:GLY149.N-B:TYR161.O 36.06%

B:THR45.OG1-B:ASP48.OD2 34.86%

B:TRP218.NE1-B:THR280.O 30.28%

B:THR199.N-B:ASN238.O 35.86%

B:LEU268.N-B:MET264.O 34.26%

B:ALA116.N-B:GLY124.O 30.08%

B:TYR118.N-B:SER121.O 35.66%

B:ARG131.N-B:THR135.O 33.47%

B:THR45.OG1-B:ASP48.OD2 30.08%

B:ILE281.N-B:SER284.O 35.06%

B:TYR239.N-B:ALA234.O 33.47%

B:ASN214.ND2-B:ALA210.O 29.28%

B:THR175.OG1-B:ASP176.O 34.86%

B:VAL91.N-B:ASP34.O 32.87%

B:ILE281.N-B:SER284.O 29.28%

B:THR45.OG1-B:ASP48.OD2 34.66%

B:CYS22.N-B:THR25.O 32.67%

B:THR175.OG1-B:ASP176.O 28.49%

B:ASN133.ND2-B:GLY195.O 34.46%

B:ASN231.ND2-B:LEU242.O 31.27%

B:VAL91.N-B:ASP34.O 28.49%

B:THR21.N-B:LEU67.O 34.26%

B:TRP218.NE1-B:THR280.O 31.08%

B:THR45.OG1-B:ASP48.OD1 27.69%

B:LEU205.N-B:THR201.O 33.67%

B:GLN189.N-B:MET49.O 30.28%

B:THR292.OG1-B:ASP295.OD2 27.49%

B:THR292.OG1-B:ASP295.OD1 33.07%

B:SER158.N-B:ASN151.O 30.28%

B:ARG131.NH1-B:ASP289.OD1 27.09%

B:THR25.OG1-B:CYS44.O 32.47%

B:THR25.OG1-B:CYS44.O 29.88%

B:SER158.N-B:ASN151.O 27.09%

B:THR175.N-B:MET162.O 32.27%

B:PHE305.N-B:GLN256.O 29.88%

B:HIS164.N-B:ALA173.O 26.69%

B:LEU268.N-B:MET264.O 31.87%

B:ASN203.ND2-B:GLY109.O 29.28%

B:GLN69.N-B:GLN19.O 26.49%

B:ARG131.N-B:THR135.O 31.67%

B:CYS160.N-B:GLY149.O 28.69%

B:THR198.OG1-B:GLU240.OE1 26.49%

B:TRP218.NE1-B:THR280.O 31.47%

B:GLN83.N-B:LEU86.O 28.49%

B:MET130.N-B:GLN110.O 26.29%

B:ASN28.ND2-B:CYS145.O 31.27%

B:LYS269.N-B:CYS265.O 28.49%

B:ASN151.ND2-B:THR111.O 26.10%

B:GLN192.NE2-B:VAL186.O 31.08%

B:THR175.OG1-B:ASP176.O 28.29%

B:SER254.OG-B:ILE259.O 25.90%

B:VAL91.N-B:ASP34.O 30.88%

B:LYS102.N-B:VAL157.O 28.29%

B:LEU208.N-B:VAL204.O 25.70%

B:TYR239.N-B:ALA234.O 30.28%

B:ILE200.N-B:ASP289.OD2 27.49%

B:THR111.OG1-B:ASP295.OD2 25.50%

B:SER158.N-B:ASN151.O 29.88%

B:SER144.OG-B:HIS163.NE2 27.49%

B:SER81.N-B:ARG88.O 25.30%

B:THR292.OG1-B:ASP295.OD2 29.08%

B:LEU67.N-B:THR21.O 27.09%

B:LEU67.N-B:THR21.O 25.10%

B:CYS22.N-B:THR25.O 28.88%

B:GLY120.N-B:ASN28.OD1 26.69%

B:VAL104.N-B:PHE159.O 24.50%

B:LYS102.N-B:VAL157.O 28.69%

B:GLN69.N-B:GLN19.O 26.69%

(continued)

2.4 Concluding Remarks

133

Table 2.42 (continued) SARS-CoV-1-N3 rep1

rep2

rep3

B:CYS128.N-B:PHE112.O 24.50%

B:LEU67.N-B:THR21.O 28.49%

B:GLN256.NE2-B:VAL303.O 26.29%

B:THR21.OG1-B:THR26.OG1 24.30%

B:SER254.N-B:LEU250.O 28.49%

B:HIS80.ND1-B:ASN63.OD1 26.10%

B:ALA234.N-B:PHE230.O 24.10%

B:MET130.N-B:GLN110.O 28.09%

B:THR292.OG1-B:ASP295.OD2 25.90%

B:TRP207.N-B:ASN203.O 23.90%

B:ALA116.N-B:GLY124.O 27.89%

B:TYR101.OH-B:ASP33.OD2 25.70%

B:LEU272.N-B:LEU268.O 23.90%

B:SER81.N-B:ARG88.O 27.89%

B:ASN95.ND2-B:GLY15.O 25.50%

B:SER113.N-B:PHE150.O 23.71%

B:GLN69.N-B:GLN19.O 27.69%

B:LYS180.N-B:ASP176.OD1 25.50%

B:SER144.OG-B:LEU141.O 23.51%

B:GLU14.N-B:SER10.O 27.69%

B:ILE136.N-B:HIS172.O 25.50%

B:GLN107.N-B:GLN110.OE1 23.11%

B:GLN107.N-B:GLN110.OE1 27.29%

B:ARG131.NH2-B:ASP289.OD2 24.70%

B:CYS160.N-B:GLY149.O 23.11%

B:HIS80.ND1-B:ASN63.OD1 27.29%

B:VAL104.N-B:PHE159.O 24.50%

B:LYS269.N-B:CYS265.O 22.91%

B:PHE159.N-B:LYS102.O 26.49%

B:SER81.N-B:ARG88.O 24.50%

B:THR111.OG1-B:ASP295.OD1 22.71%

B:ASN95.ND2-B:GLY15.O 26.49%

B:THR111.OG1-B:ASP295.OD1 23.71%

B:ASN151.N-B:SER158.O 22.51%

B:ASP216.N-B:ALA211.O 26.10%

B:GLN273.N-B:LYS269.O 23.51%

B:LEU86.N-B:GLN83.O 21.91%

B:VAL297.N-B:PRO293.O 26.10%

B:GLN19.NE2-B:ASN119.O 23.51%

B:TYR101.OH-B:ASP33.OD2 21.91%

B:THR98.OG1-B:ASN95.O 25.50%

B:SER113.N-B:PHE150.O 23.31%

B:ASP92.N-B:ARG76.O 21.71%

B:ASN203.ND2-B:GLY109.O 25.30%

B:THR98.OG1-B:ASN95.O 22.91%

B:THR98.OG1-B:ASN95.O 21.71%

B:ASN84.ND2-B:GLY179.O 25.30%

B:GLN107.N-B:GLN110.OE1 22.71%

B:LYS5.NZ-B:GLU288.OE2 21.51%

B:THR111.OG1-B:ASP295.OD1 25.10%

B:THR45.OG1-B:ASP48.OD1 22.11%

B:LYS5.NZ-B:GLU290.OE1 21.12%

B:MET162.N-B:THR175.O 24.30%

B:MET130.N-B:GLN110.O 21.91%

B:HIS41.NE2-B:HIS164.O 21.12%

B:ALA210.N-B:ALA206.O 24.30%

B:HIS164.N-B:ALA173.O 21.91%

B:SER254.N-B:LEU250.O 20.12%

B:VAL104.N-B:PHE159.O 24.10%

B:TYR209.N-B:LEU205.O 21.91%

B:SER113.N-B:PHE150.O 24.10%

B:ARG105.NH1-B:ASP176.OD1 21.71%

B:LYS269.N-B:CYS265.O 23.71%

B:ASP216.N-B:ALA211.O 21.51%

B:THR45.OG1-B:ASP48.OD1 23.71%

B:LEU86.N-B:GLN83.O 21.51%

B:THR111.OG1-B:ASP295.OD2 22.31%

B:ALA116.N-B:GLY124.O 21.51%

B:ALA255.N-B:GLY251.O 22.31%

B:THR26.OG1-B:THR21.OG1 21.31%

B:SER254.OG-B:ILE259.O 21.51%

B:ASN214.ND2-B:ALA210.O 21.31%

B:THR198.OG1-B:GLU240.OE1 21.12%

B:SER254.OG-B:ILE259.O 21.12%

B:ALA234.N-B:PHE230.O 20.92%

B:ARG105.NH1-B:ASP176.OD2 21.12%

B:TYR101.OH-B:ASP33.OD2 20.92%

B:LYS5.NZ-B:GLU290.OE1 21.12%

B:ILE136.N-B:HIS172.O 20.92%

B:LEU208.N-B:VAL204.O 21.12%

B:CYS160.N-B:GLY149.O 20.92%

B:CYS156.N-B:ASP153.O 20.92%

B:ASP176.N-B:LYS180.O 20.92%

B:ALA210.N-B:ALA206.O 20.72%

B:SER139.N-B:TYR126.OH 20.52%

B:LYS180.N-B:ASP176.OD2 20.72% B:GLN127.NE2-B:ASP295.OD2 20.52% B:TYR182.OH-B:ILE106.O 20.32% B:SER254.N-B:LEU250.O 20.32%

134

2 3C-Like Protease (3CLpro)

Table 2.43 The MD-HBs linking the ligands LIG307 and LIG308 of dimer the SARS-CoV-2Mpro-N3-6lu7 model (denoted as “SARS-CoV-2-N3 dimer”) —the model has three sets of MD simulations [346] SARS-CoV-2-N3 rep1

rep2

rep3

B:GLU166.N-LIG307.O 56.77%

B:GLU166.N-LIG307.O 56.18%

B:GLU166.N-LIG307.O 49.00%

LIG307.N-B:GLU166.O 38.05%

LIG307.N-B:GLU166.O 37.85%

LIG307.N-B:GLU166.O 38.65%

LIG307.N-B:GLN189.OE1 27.29%

LIG307.N5-B:HIS164.O 29.28%

LIG307.N5-B:HIS164.O 33.07%

LIG307.N5-B:HIS164.O 20.32%

LIG307.N-B:GLN189.OE1 24.90%

LIG307.N-B:GLN189.OE1 30.08%

B:HIS163.NE2-LIG307.O8 9.76%

B:HIS163.NE2-LIG307.O8 9.56%

B:HIS163.NE2-LIG307.O8 19.32%

B:CYS145.N-LIG307.O7 6.77%

B:CYS145.N-LIG307.O7 9.16%

LIG307.N-B:THR190.O 8.96%

LIG307.N-B:THR190.O 5.98%

LIG307.N-B:THR190.O 5.58%

B:CYS145.N-LIG307.O7 5.98%

B:GLN189.NE2-LIG307.O 3.98%

LIG307.N6-B:GLU166.OE1 1.59%

LIG307.N-B:GLN192.O 2.59%

LIG307.N-B:GLN192.O 2.39%

LIG307.N-B:GLN192.O 1.39%

B:GLN189.NE2-LIG307.O 1.59%

LIG307.N6-B:GLU166.OE1 1.00%

LIG307.N6-B:GLU166.OE2 1.39%

LIG307.N6-B:PHE140.O 1.59%

LIG307.N6-B:PHE140.O 0.80%

B:GLN192.N-LIG307.N2 1.20%

LIG307.N6-B:GLU166.OE2 1.00%

LIG307.N6-B:GLU166.OE2 0.80%

B:GLN189.NE2-LIG307.O 1.00%

B:THR190.N-LIG307.O 0.80%

B:THR190.N-LIG307.O 0.40%

LIG307.N6-B:PHE140.O 0.20%

LIG307.N6-B:GLU166.OE1 0.80%

B:THR26.N-LIG307.C5 0.40%

B:SER144.OG-LIG307.O8 0.20%

B:HIS41.NE2-LIG307.O 0.20%

B:GLN192.N-LIG307.N2 0.40%

B:GLN192.N-LIG307.O1 0.20%

B:SER144.OG-LIG307.O8 0.20% B:GLN192.N-LIG307.N2 0.20%

LIG308.N-A:GLU166.O 57.97%

LIG308.N-A:GLU166.O 49.00%

LIG308.N-LIG308.O8 42.23%

A:GLU166.N-LIG308.O 35.26%

LIG308.N-A:GLU166.O 29.68%

A:GLU166.N-LIG308.O 32.07%

LIG308.N-LIG308.O8 22.51%

A:GLU166.N-LIG308.O 21.91%

A:GLN189.NE2-LIG308.O 9.96%

LIG308.N-A:GLN189.OE1 8.37%

LIG308.N-A:GLN189.OE1 21.12%

LIG308.N-A:THR190.O 9.56%

LIG308.N-A:THR190.O 8.17%

A:GLN189.NE2-LIG308.O 7.17%

LIG308.N5-LIG308.O8 7.57%

LIG308.N5-LIG308.O8 6.57%

LIG308.N5-A:HIS164.O 6.57%

A:THR26.N-LIG308.O7 7.37%

A:GLN189.NE2-LIG308.O 5.98%

A:HIS41.NE2-LIG308.O 5.98%

LIG308.N-A:GLN189.OE1 1.39%

A:GLN189.NE2-LIG308.O8 4.78%

LIG308.N-A:GLN192.O 5.38%

A:ASN142.ND2-LIG308.O8 1.00%

LIG308.N5-A:GLN189.OE1 2.99%

A:GLN189.NE2-LIG308.O8 3.78%

LIG308.N6-A:GLN189.OE1 0.60%

A:THR26.N-LIG308.O7 2.59%

A:GLU166.N-LIG308.O42 3.19%

LIG308.N6-A:GLU166.OE2 0.40%

A:HIS41.NE2-LIG308.O 2.19%

LIG308.N6-A:LEU141.O 2.99%

A:GLN189.NE2-LIG308.O8 0.40%

LIG308.N6-A:GLN189.OE1 1.99%

A:CYS145.N-LIG308.O8 2.59%

A:HIS41.NE2-LIG308.O7 0.20%

A:SER144.N-LIG308.O8 1.79%

A:SER144.N-LIG308.O8 2.19%

LIG308.N5-A:HIS164.O 0.20%

A:SER46.OG-LIG308.O7 1.39%

LIG308.N6-A:SER144.OG 1.99%

LIG308.N-A:GLN192.O 0.20%

A:ASN142.ND2-LIG308.O8 1.39%

LIG308.N5-A:GLN189.OE1 1.59%

LIG308.N6-A:GLN189.NE2 0.20%

A:SER144.OG-LIG308.O8 0.60%

LIG308.N5-LIG308.O 1.20%

A:GLN189.NE2-LIG308.N6 0.20%

A:GLY143.N-LIG308.O8 0.60%

A:GLY143.N-LIG308.O8 1.20%

A:CYS145.N-LIG308.O8 0.60%

A:THR25.OG1-LIG308.O7 1.20%

LIG308.N6-A:SER46.OG 0.60%

LIG308.N-LIG308.O42 1.00%

LIG308.N-A:GLN192.O 0.40%

A:ASN142.ND2-LIG308.O7 0.60%

LIG308.N5-LIG308.O 0.40%

A:GLY143.N-LIG308.O7 0.60%

A:GLN189.NE2-LIG308.O7 0.40%

A:SER46.OG-LIG308.O8 0.40%

LIG308.N6-A:LEU141.O 0.40%

LIG308.N6-A:PHE140.O 0.20%

LIG308.N-A:GLN189.O 0.40%

A:HIS41.NE2-LIG308.C5 0.20%

A:CYS145.SG-LIG308.O 0.40%

A:GLN192.N-LIG308.N2 0.20%

A:HIS163.NE2-LIG308.O8 0.20%

A:ASN142.ND2-LIG308.O8 0.20%

A:GLN192.N-LIG308.N2 0.20%

A:GLU166.N-LIG308.O8 0.20%

LIG308.N6-A:ASN142.OD1 0.20%

A:GLN192.N-LIG308.O 0.20%

A:THR25.OG1-LIG308.O7 0.20%

A:GLN192.NE2-LIG308.O 0.20%

A:GLN189.NE2-LIG308.C4 0.20%

LIG308.N6-A:HIS41.O 0.20%

LIG308.N5-A:ASN142.OD1 0.20%

LIG308.N6-A:CYS44.O 0.20%

A:ASN142.ND2-LIG308.O7 0.20%

LIG308.N5-LIG308.O8 0.20%

A:ASN142.ND2-LIG308.O 0.20%

2.4 Concluding Remarks

135

Table 2.44 The MD-HBs (with occupancy rates ≥20%) of dimer the SARS-CoV-2-Mpro-N36lu7 model (denoted as “SARS-CoV-2-N3 dimer”) —the model has three sets of MD simulations [346] SARS-CoV-2-N3 rep1

rep2

rep3

A:SER139.OG-B:GLN299.OE1 57.57%

A:SER139.OG-B:GLN299.OE1 57.57%

A:SER139.OG-B:GLN299.OE1 58.37%

B:SER139.OG-A:GLN299.OE1 51.00%

B:SER139.OG-A:GLN299.OE1 53.19%

B:SER139.OG-A:GLN299.OE1 49.80%

B:VAL125.N-A:ALA7.O 32.67%

B:VAL125.N-A:ALA7.O 31.87%

B:GLY11.N-A:GLU14.OE1 33.47%

A:VAL125.N-B:ALA7.O 32.07%

B:SER1.OG-A:GLU166.OE1 31.67%

A:ALA7.N-B:VAL125.O 32.27%

B:SER1.OG-A:GLU166.OE2 30.68%

A:VAL125.N-B:ALA7.O 31.08%

A:GLY11.N-B:GLU14.OE1 30.68%

B:GLY11.N-A:GLU14.OE1 29.68%

B:GLY11.N-A:GLU14.OE1 28.88%

B:VAL125.N-A:ALA7.O 29.88%

A:GLY11.N-B:GLU14.OE1 29.28%

B:ARG4.NH1-A:GLU290.OE1 28.49%

B:SER1.OG-A:GLU166.OE2 24.30%

A:ALA7.N-B:VAL125.O 26.49%

A:ALA7.N-B:VAL125.O 27.69%

B:ALA7.N-A:VAL125.O 21.91%

A:SER1.OG-B:GLU166.OE2 26.29%

A:GLY11.N-B:GLU14.OE1 27.69%

B:SER1.OG-A:GLU166.OE1 21.71%

A:SER1.OG-B:GLU166.OE1 26.29%

B:ARG4.NH2-A:GLU290.OE2 25.90%

B:ARG4.NH2-A:GLU290.OE2 20.32%

B:ALA7.N-A:VAL125.O 26.10%

B:ALA7.N-A:VAL125.O 25.10%

B:ARG4.NH2-A:GLU290.OE1 20.12%

A:ARG4.NH2-B:GLU290.OE2 25.70%

B:SER1.OG-A:GLU166.OE2 22.11%

B:ARG4.NH1-A:GLU290.OE1 24.90%

A:ARG4.NH2-B:GLU290.OE2 21.12%

A:SER10.OG-A:GLU14.OE1 81.27%

B:SER1.OG-A:GLU166.OE1 23.31%

A:ARG4.NH1-B:GLU290.OE2 20.92%

A:SER267.OG-A:ASP263.O 69.12%

A:ARG4.NH1-B:GLU290.OE1 22.91%

A:ARG4.NH2-B:GLU290.OE1 20.32%

A:TRP31.N-A:CYS16.O 63.35%

B:ARG4.NH2-A:GLU290.OE2 22.71%

A:SER1.OG-B:GLU166.OE2 20.12%

A:SER10.OG-A:GLU14.OE1 83.27%

A:SER10.OG-A:GLU14.OE1 81.27%

A:TYR209.OH-A:ILE259.O 58.96%

A:TYR209.OH-A:ILE259.O 65.54%

A:SER267.OG-A:ASP263.O 68.53%

A:HIS163.N-A:SER147.O 58.76%

A:TRP31.N-A:CYS16.O 65.54%

A:TYR182.OH-A:CYS160.O 65.34%

A:VAL114.N-A:TYR126.O 58.76%

A:HIS163.N-A:SER147.O 64.14%

A:TRP31.N-A:CYS16.O 64.74%

A:THR201.OG1-A:GLU240.O 58.76%

A:LEU167.N-A:VAL171.O 62.95%

A:HIS163.N-A:SER147.O 62.95%

A:TYR54.OH-A:ASP187.O 58.57%

A:SER267.OG-A:ASP263.O 61.95%

A:THR201.OG1-A:GLU240.O 61.35%

A:SER144.OG-A:LEU141.O 57.77%

A:THR201.OG1-A:GLU240.O 61.55%

A:TYR209.OH-A:ILE259.O 61.16%

A:LEU87.N-A:CYS38.O 56.77%

A:VAL20.N-A:LEU27.O 61.16%

A:GLN299.NE2-A:ARG4.O 59.76%

A:VAL36.N-A:LEU89.O 52.39%

A:TYR182.OH-A:CYS160.O 60.76%

A:VAL20.N-A:LEU27.O 59.16%

A:PHE150.N-A:SER113.O 52.39%

A:ILE78.N-A:LYS90.O 60.56%

A:ILE78.N-A:LYS90.O 58.96%

A:GLY149.N-A:TYR161.O 52.19%

A:GLY146.N-A:HIS163.O 60.36%

A:GLY146.N-A:HIS163.O 57.97%

A:THR135.OG1-A:ASN133.OD1 51.99%

A:VAL114.N-A:TYR126.O 57.37%

A:LEU167.N-A:VAL171.O 56.77%

A:LYS88.N-A:SER81.O 51.79%

A:VAL36.N-A:LEU89.O 56.57%

A:VAL36.N-A:LEU89.O 56.18%

A:THR257.OG1-A:LEU253.O 51.20%

A:LEU27.N-A:VAL20.O 55.58%

A:THR45.OG1-A:ASP48.OD1 55.78%

A:ALA70.N-A:VAL73.O 51.00%

A:TYR54.OH-A:ASP187.O 55.58%

A:THR257.OG1-A:LEU253.O 55.18%

A:VAL20.N-A:LEU27.O 50.60%

A:GLY149.N-A:TYR161.O 54.18%

A:VAL114.N-A:TYR126.O 54.98%

A:THR175.OG1-A:ASP176.O 50.40%

A:LEU87.N-A:CYS38.O 53.98%

A:TYR37.N-A:LEU30.O 53.98%

A:LEU89.N-A:VAL36.O 50.20%

A:GLY109.N-A:MET130.O 53.19%

A:LEU89.N-A:VAL36.O 53.98%

A:GLY109.N-A:MET130.O 50.00%

A:SER147.OG-A:SER144.O 52.19%

A:GLY109.N-A:MET130.O 52.59%

A:GLY146.N-A:HIS163.O 48.61%

A:LYS88.N-A:SER81.O 51.79%

A:GLN256.NE2-A:VAL303.O 52.59%

A:ARG60.NH1-A:ASP48.OD2 48.21%

A:GLN19.N-A:GLN69.O 50.40%

A:GLY149.N-A:TYR161.O 51.79%

A:GLN256.NE2-A:VAL303.O 48.01%

A:TYR37.N-A:LEU30.O 50.20%

A:LEU27.N-A:VAL20.O 51.39%

A:SER123.N-A:ALA116.O 48.01%

A:THR135.OG1-A:ASN133.OD1 49.80%

A:LEU87.N-A:CYS38.O 51.20%

A:PHE8.N-A:SER113.OG 47.61%

A:GLN83.N-A:VAL86.O 49.80%

A:THR135.OG1-A:ASN133.OD1 50.40%

A:ASN95.N-A:ASP33.O 47.01%

A:LEU89.N-A:VAL36.O 49.80%

A:LYS88.N-A:SER81.O 49.60%

A:LEU167.N-A:VAL171.O 46.81%

A:SER144.OG-A:LEU141.O 49.60%

A:GLN192.NE2-A:VAL186.O 49.20%

A:VAL157.N-A:LYS100.O 46.41%

A:GLN299.NE2-A:ARG4.O 49.00%

A:ASP153.N-A:CYS156.O 47.61%

A:SER147.OG-A:SER144.O 46.41%

A:GLN192.NE2-A:VAL186.O 48.61%

A:THR175.OG1-A:ASP176.O 46.61%

A:LEU27.N-A:VAL20.O 46.41%

A:ASN95.N-A:ASP33.O 48.21%

A:ASN95.N-A:ASP33.O 46.22%

A:ASN203.ND2-A:ASP289.O 45.62%

A:THR257.OG1-A:LEU253.O 48.01%

A:GLN19.N-A:GLN69.O 46.02%

A:ARG131.N-A:THR135.O 45.22%

A:PHE150.N-A:SER113.O 47.41%

A:ASN203.ND2-A:ASP289.O 45.82%

A:VAL18.N-A:GLY29.O 45.22%

A:TYR182.N-A:GLY174.O 47.41%

A:SER123.N-A:ALA116.O 45.62%

A:GLN19.N-A:GLN69.O 45.02%

A:ALA70.N-A:VAL73.O 47.21%

A:LEU242.N-A:ASN231.OD1 45.42%

A:TYR37.N-A:LEU30.O 45.02%

A:SER123.N-A:ALA116.O 47.21%

A:ALA70.N-A:VAL73.O 45.22%

A:LYS90.N-A:GLY79.O 44.22%

A:ASN203.ND2-A:ASP289.O 46.61%

A:LEU30.N-A:TYR37.O 44.62%

A:HIS172.N-A:ILE136.O 44.02%

A:THR175.OG1-A:ASP176.O 46.02%

A:TYR182.N-A:GLY174.O 43.82%

A:ILE281.N-A:SER284.O 43.63%

A:ILE281.N-A:SER284.O 44.22%

A:SER144.OG-A:LEU141.O 43.63%

A:MET130.N-A:GLN110.O 43.23%

A:VAL18.N-A:GLY29.O 44.22%

A:SER147.OG-A:SER144.O 43.63%

A:LEU30.N-A:TYR37.O 42.83%

A:TYR182.OH-A:CYS160.O 60.56% A:ILE78.N-A:LYS90.O 60.16%

(continued)

136

2 3C-Like Protease (3CLpro)

Table 2.44 (continued) SARS-CoV-2-N3 rep1

rep2

rep3

A:CYS22.N-A:THR25.O 43.43%

A:VAL157.N-A:LYS100.O 43.43%

A:VAL91.N-A:ASP34.O 42.63%

A:LEU115.N-A:VAL148.O 42.63%

A:PHE150.N-A:SER113.O 42.83%

A:THR45.OG1-A:ASP48.OD2 42.03%

A:THR25.OG1-A:CYS44.O 42.63%

A:ASN231.N-A:LEU227.O 42.63%

A:ASN95.ND2-A:TRP31.O 41.63%

A:THR45.OG1-A:ASP48.OD1 42.23%

A:LEU75.N-A:VAL68.O 41.63%

A:LEU75.N-A:VAL68.O 41.24%

A:ASP153.N-A:CYS156.O 41.43%

A:ILE281.N-A:SER284.O 41.43%

A:ARG60.NH2-A:ASP48.OD1 41.24%

A:LEU75.N-A:VAL68.O 41.24%

A:PHE8.N-A:SER113.OG 41.43%

A:ASN133.ND2-A:GLY195.O 40.24%

A:LYS90.N-A:GLY79.O 40.24%

A:ASN95.ND2-A:TRP31.O 41.43%

A:GLN83.N-A:VAL86.O 39.64%

A:PHE8.N-A:SER113.OG 40.04%

A:VAL18.N-A:GLY29.O 40.44%

A:LEU32.N-A:VAL35.O 39.04%

A:VAL157.N-A:LYS100.O 40.04%

A:ARG105.NH2-A:PHE181.O 40.44%

A:THR199.N-A:ASN238.O 39.04%

A:LEU205.N-A:THR201.O 39.84%

A:GLN83.N-A:VAL86.O 40.44%

A:GLN299.NE2-A:ARG4.O 38.65%

A:VAL91.N-A:ASP34.O 39.04%

A:LEU205.N-A:THR201.O 40.44%

A:ASP153.N-A:CYS156.O 38.65%

A:LEU30.N-A:TYR37.O 38.65%

A:LYS90.N-A:GLY79.O 39.64%

A:ALA173.N-A:MET165.O 38.45%

A:LEU242.N-A:ASN231.OD1 38.25%

A:VAL91.N-A:ASP34.O 39.24%

A:HIS80.ND1-A:ASN63.OD1 38.45%

A:ASN231.N-A:LEU227.O 38.05%

A:HIS172.N-A:ILE136.O 38.45%

A:TYR182.N-A:GLY174.O 38.25%

A:TYR239.N-A:ALA234.O 37.45%

A:PHE112.N-A:CYS128.O 38.05%

A:ASN28.ND2-A:CYS145.O 38.05%

A:PHE112.N-A:CYS128.O 37.45%

A:ASN214.ND2-A:ALA210.O 37.85%

A:LEU205.N-A:THR201.O 37.85%

A:LEU32.N-A:VAL35.O 37.05%

A:GLU14.N-A:SER10.O 37.45%

A:SER301.OG-A:VAL297.O 37.45%

A:ARG105.NH2-A:PHE181.O 36.85%

A:TYR239.N-A:ALA234.O 37.45%

A:CYS300.N-A:VAL296.O 37.05%

A:ARG40.NE-A:ASP187.OD2 36.85%

A:LEU32.N-A:VAL35.O 37.45%

A:THR111.OG1-A:ASP295.OD1 36.85%

A:HIS172.N-A:ILE136.O 36.85%

A:CYS22.N-A:THR25.O 36.85%

A:SER254.OG-A:ILE259.O 35.86%

A:ASN133.ND2-A:GLY195.O 36.45%

A:SER301.OG-A:VAL297.O 36.25%

A:SER113.N-A:PHE150.O 35.86%

A:THR199.N-A:ASN238.O 36.45%

A:TYR118.N-A:SER121.O 35.06%

A:SER158.N-A:ASN151.O 35.66%

A:SER158.N-A:ASN151.O 36.06%

A:ILE136.N-A:HIS172.O 34.86%

A:ASN151.ND2-A:THR111.O 35.46%

A:ASN95.ND2-A:TRP31.O 35.86%

A:ILE200.N-A:ASP289.OD1 34.86%

A:GLU14.N-A:SER10.O 35.06%

Table 2.45 The MD-HBs (with occupancy rates ≥20%) of dimer the SARS-CoV-2-Mpro-N36lu7 model (denoted as “SARS-CoV-2-N3 dimer”) —the model has three sets of MD simulations [346] (continuation-1) SARS-CoV-2-N3 rep1

rep2

rep3

A:ARG40.NH2-A:ASP187.OD1 35.66%

A:THR199.N-A:ASN238.O 34.66%

A:TYR118.N-A:SER121.O 34.06%

A:ALA173.N-A:MET165.O 35.46%

A:ASN133.ND2-A:GLY195.O 34.66%

A:ASN84.ND2-A:GLU178.O 33.86%

A:SER254.OG-A:ILE259.O 35.26%

A:SER254.OG-A:ILE259.O 34.26%

A:ARG105.NH2-A:PHE181.O 33.07%

A:ASN214.ND2-A:ALA210.O 34.26%

A:ALA173.N-A:MET165.O 34.26%

A:LYS269.N-A:CYS265.O 32.87%

A:ALA116.N-A:GLY124.O 34.26%

A:LEU115.N-A:VAL148.O 34.06%

A:LEU115.N-A:VAL148.O 32.67%

A:ILE136.N-A:HIS172.O 33.86%

A:SER113.N-A:PHE150.O 33.47%

A:LEU67.N-A:THR21.O 31.47%

A:THR111.OG1-A:ASP295.OD2 33.07%

A:SER158.N-A:ASN151.O 33.27%

A:TYR239.N-A:ALA234.O 31.08%

A:THR21.N-A:LEU67.O 32.67%

A:THR111.OG1-A:ASP295.OD1 33.27%

A:ASN214.ND2-A:ALA210.O 31.08%

A:SER113.N-A:PHE150.O 32.47%

A:ASN203.ND2-A:GLY109.O 32.67%

A:LEU242.N-A:ASN231.OD1 30.88%

A:MET130.N-A:GLN110.O 31.67%

A:ALA116.N-A:GLY124.O 32.67%

A:THR292.OG1-A:ASP295.OD1 30.88%

A:HIS41.NE2-A:HIS164.O 30.68%

A:ASN151.ND2-A:THR111.O 32.47%

A:LEU268.N-A:MET264.O 30.48%

A:TYR118.N-A:SER121.O 30.48%

A:GLN189.N-A:MET49.O 32.47%

A:THR111.OG1-A:ASP295.OD2 30.28%

A:ASN151.ND2-A:THR111.O 30.28%

A:THR111.OG1-A:ASP295.OD2 32.27%

A:THR243.OG1-A:HIS246.ND1 29.88%

A:LEU67.N-A:THR21.O 30.28%

A:ASN231.ND2-A:LEU242.O 32.07%

A:THR21.N-A:LEU67.O 28.88%

A:TRP218.NE1-A:THR280.O 30.08%

A:THR292.OG1-A:ASP295.OD2 31.87%

A:ALA116.N-A:GLY124.O 28.88%

A:THR111.OG1-A:ASP295.OD1 29.68%

A:HIS80.ND1-A:ASN63.OD1 31.67%

A:VAL125.N-B:ALA7.O 28.69%

A:ASN203.ND2-A:GLY109.O 29.48%

A:THR21.N-A:LEU67.O 31.27%

A:GLN192.NE2-A:VAL186.O 28.29%

A:GLN107.N-A:GLN110.OE1 29.48%

A:ARG60.NH1-A:ASP48.OD1 30.68%

A:VAL86.N-A:GLN83.O 27.09%

A:LYS269.N-A:CYS265.O 29.08%

A:ARG60.NH2-A:ASP48.OD2 30.68%

A:GLN69.N-A:GLN19.O 26.89%

A:CYS128.N-A:PHE112.O 28.49%

A:ARG40.NE-A:ASP187.OD2 28.88%

A:THR292.OG1-A:ASP295.OD2 26.89%

A:ARG40.NH2-A:ASP187.OD2 28.49%

A:LEU67.N-A:THR21.O 28.69%

A:ALA234.N-A:PHE230.O 26.69%

A:ILE200.N-A:ASP289.OD2 28.29%

A:LEU268.N-A:MET264.O 28.49%

A:CYS128.N-A:PHE112.O 26.29%

A:LEU208.N-A:VAL204.O 28.29%

A:SER1.OG-B:GLU166.OE1 28.29%

A:ILE136.N-A:HIS172.O 26.10%

A:THR21.OG1-A:THR26.OG1 27.89%

A:CYS300.N-A:VAL296.O 28.09%

A:SER81.N-A:LYS88.O 26.10%

A:VAL86.N-A:GLN83.O 27.69%

A:MET130.N-A:GLN110.O 28.09%

A:PHE159.N-A:LYS102.O 25.50%

A:HIS80.ND1-A:ASN63.OD1 27.69%

A:ARG40.NH2-A:ASP187.OD1 27.69%

A:ALA255.N-A:GLY251.O 25.30%

A:THR292.OG1-A:ASP295.OD1 27.09%

A:LYS5.NZ-A:GLU290.OE1 27.49%

A:ASN231.N-A:LEU227.O 25.30%

(continued)

2.4 Concluding Remarks

137

Table 2.45 (continued) SARS-CoV-2-N3 rep1

rep2

rep3

A:GLU14.N-A:SER10.O 26.89%

A:ARG131.N-A:THR135.O 27.29%

A:ASN180.N-A:ASP176.OD2 25.10%

A:LEU268.N-A:MET264.O 26.89%

A:ALA255.N-A:GLY251.O 26.89%

A:LEU208.N-A:VAL204.O 24.90%

A:LYS102.N-A:VAL157.O 26.69%

A:ARG40.NH2-A:ASP187.OD2 26.89%

A:ASN95.ND2-A:GLY15.O 24.90%

A:THR292.OG1-A:ASP295.OD2 25.50%

A:VAL86.N-A:GLN83.O 26.69%

A:VAL104.N-A:PHE159.O 24.70%

A:ASN274.ND2-A:GLU270.O 25.50%

A:ASN84.ND2-A:GLU178.O 26.49%

A:ARG4.NE-A:PHE3.O 24.30%

A:THR198.OG1-A:GLU240.OE2 24.90%

A:PHE159.N-A:LYS102.O 26.49%

A:ASN203.ND2-A:GLY109.O 23.71%

A:ASN221.N-A:SER267.OG 24.90%

A:SER62.N-A:ASN65.OD1 26.49%

A:THR98.OG1-A:ASN95.O 23.31%

A:THR243.OG1-A:HIS246.ND1 24.50%

A:GLN107.N-A:GLN110.OE1 26.10%

A:PHE112.N-A:CYS128.O 22.91%

A:ASN95.ND2-A:GLY15.O 24.50%

A:ASN274.ND2-A:GLU270.O 24.90%

A:LYS102.N-A:VAL157.O 22.71%

A:VAL186.N-A:GLN192.OE1 24.50%

A:VAL104.N-A:PHE159.O 24.90%

A:ASN221.N-A:SER267.OG 22.71%

A:PHE159.N-A:LYS102.O 24.30%

A:ASN28.ND2-A:CYS145.O 24.90%

A:GLY120.N-A:ASN28.OD1 22.51%

A:SER62.N-A:ASN65.OD1 24.30%

A:LYS102.N-A:VAL157.O 24.70%

A:TRP218.NE1-A:THR280.O 21.91%

A:VAL104.N-A:PHE159.O 24.10%

A:CYS128.N-A:PHE112.O 24.50%

A:SER284.N-A:ILE281.O 21.71%

A:GLN189.N-A:MET49.O 23.51%

A:THR98.OG1-A:ASN95.O 24.30%

A:GLN107.N-A:GLN110.OE1 21.51%

A:SER81.N-A:LYS88.O 22.91%

A:GLN69.N-A:GLN19.O 24.10%

A:ILE200.N-A:ASP289.OD2 21.31%

A:LYS5.NZ-A:GLU290.OE1 22.91%

A:THR243.OG1-A:HIS246.ND1 23.90%

A:ILE200.N-A:ASP289.OD1 21.31%

A:ALA255.N-A:GLY251.O 22.71%

A:TRP218.NE1-A:THR280.O 23.71%

A:CYS22.N-A:THR25.O 21.12%

A:ASN28.ND2-A:CYS145.O 21.91%

A:ARG131.NH2-A:ASP289.OD1 23.71%

A:THR198.OG1-A:GLU240.OE1 21.12%

A:THR198.OG1-A:GLU240.OE1 21.91%

A:LEU208.N-A:VAL204.O 23.31%

A:ARG4.N-A:GLN299.OE1 21.12%

A:ARG40.NE-A:ASP187.OD1 21.91%

A:ARG40.NE-A:ASP187.OD1 23.31%

A:SER139.N-A:TYR126.OH 21.12%

A:ASN231.ND2-A:LEU242.O 21.71%

A:ARG4.N-A:GLN299.OE1 22.91%

A:GLN273.N-A:LYS269.O 20.92%

A:THR45.OG1-A:ASP48.OD2 21.71%

A:LYS269.N-A:CYS265.O 22.91%

A:CYS38.N-A:LEU87.O 20.52%

A:ASN180.N-A:ASP176.OD1 21.12%

A:ALA234.N-A:PHE230.O 22.91%

A:THR98.OG1-A:ASN95.O 21.12%

A:THR21.OG1-A:THR26.OG1 22.91%

B:SER10.OG-B:GLU14.OE1 85.86%

A:GLY120.N-A:ASN28.OD1 20.92%

A:ASN95.ND2-A:GLY15.O 22.71%

B:SER267.OG-B:ASP263.O 67.33%

A:ARG131.N-A:THR135.O 20.72%

A:THR292.OG1-A:ASP295.OD1 22.71%

B:THR201.OG1-B:GLU240.O 61.75%

A:THR292.N-A:ASP295.OD2 20.72%

A:ASN221.N-A:SER267.OG 22.31%

B:TYR209.OH-B:ILE259.O 61.75%

A:ARG105.NH1-A:ASP176.OD2 20.72%

A:ASN151.N-A:SER158.O 22.11%

B:TRP31.N-B:CYS16.O 61.55%

A:ARG4.N-A:GLN299.OE1 20.52%

A:THR198.OG1-A:GLU240.OE2 22.11%

B:TYR182.OH-B:CYS160.O 59.96%

A:ARG131.NH2-A:ASP289.OD2 20.52%

A:SER81.N-A:LYS88.O 22.11%

B:ILE78.N-B:LYS90.O 59.36%

A:SER139.N-A:TYR126.OH 20.52%

A:HIS41.NE2-A:HIS164.O 21.71%

B:LEU87.N-B:CYS38.O 56.18%

A:LEU272.N-A:LEU268.O 20.32%

A:TYR54.OH-A:ASP187.O 20.72%

B:GLN299.NE2-B:ARG4.O 55.98%

A:GLN69.N-A:GLN19.O 20.12%

A:THR292.N-A:ASP295.OD1 20.52%

B:LEU167.N-B:VAL171.O 55.98%

A:CYS38.N-A:LEU87.O 20.32%

B:GLY109.N-B:MET130.O 55.18%

B:SER10.OG-B:GLU14.OE1 83.86%

B:VAL20.N-B:LEU27.O 54.18%

B:HIS163.N-B:SER147.O 63.94%

B:SER10.OG-B:GLU14.OE1 84.86%

B:VAL114.N-B:TYR126.O 52.59%

B:TRP31.N-B:CYS16.O 63.35%

B:SER267.OG-B:ASP263.O 65.94%

B:SER144.OG-B:LEU141.O 51.79%

B:THR201.OG1-B:GLU240.O 61.95%

B:TRP31.N-B:CYS16.O 65.14%

B:HIS163.N-B:SER147.O 51.59%

B:TYR182.OH-B:CYS160.O 61.95%

B:THR201.OG1-B:GLU240.O 62.35%

B:LYS88.N-B:SER81.O 51.39%

B:SER267.OG-B:ASP263.O 60.76%

B:ARG40.NH2-B:ASP187.OD1 59.96%

B:LEU89.N-B:VAL36.O 51.39%

B:TYR209.OH-B:ILE259.O 58.76%

B:HIS163.N-B:SER147.O 59.36%

B:VAL36.N-B:LEU89.O 50.60%

B:VAL114.N-B:TYR126.O 58.57%

B:VAL114.N-B:TYR126.O 59.36%

B:SER123.N-B:ALA116.O 50.20%

B:ILE78.N-B:LYS90.O 58.17%

B:ILE78.N-B:LYS90.O 58.96%

B:GLN192.NE2-B:VAL186.O 50.20%

B:LEU87.N-B:CYS38.O 57.37%

B:TYR209.OH-B:ILE259.O 58.96%

B:GLN19.N-B:GLN69.O 49.80%

B:GLN299.NE2-B:ARG4.O 57.17%

B:LEU167.N-B:VAL171.O 57.97%

B:LEU115.N-B:VAL148.O 49.40%

B:THR257.OG1-B:LEU253.O 56.57%

B:LEU87.N-B:CYS38.O 57.77%

B:GLY149.N-B:TYR161.O 49.00%

B:VAL36.N-B:LEU89.O 55.18%

B:TYR182.OH-B:CYS160.O 56.37%

B:LEU27.N-B:VAL20.O 48.61%

B:LEU167.N-B:VAL171.O 54.98%

B:LYS88.N-B:SER81.O 54.18%

B:GLN189.N-B:MET49.O 48.41%

B:GLY109.N-B:MET130.O 54.98%

B:HIS172.N-B:ILE136.O 52.99%

B:VAL91.N-B:ASP34.O 47.81%

B:LYS88.N-B:SER81.O 53.39%

B:THR257.OG1-B:LEU253.O 52.99%

B:GLY146.N-B:HIS163.O 47.81%

B:SER144.OG-B:LEU141.O 51.59%

B:ARG40.NE-B:ASP187.OD2 51.99%

B:THR45.OG1-B:ASP48.OD2 47.81%

B:SER147.OG-B:SER144.O 50.60%

B:SER144.OG-B:LEU141.O 51.99%

B:THR257.OG1-B:LEU253.O 47.61%

B:TYR37.N-B:LEU30.O 50.40%

B:GLN299.NE2-B:ARG4.O 51.59%

B:ASN95.N-B:ASP33.O 46.61%

138

2 3C-Like Protease (3CLpro)

Table 2.46 The MD-HBs (with occupancy rates ≥20%) of dimer the SARS-CoV-2-Mpro-N36lu7 model (denoted as “SARS-CoV-2-N3 dimer”) —the model has three sets of MD simulations [346] (continuation-2) SARS-CoV-2-N3 rep1

rep2

rep3

B:GLY149.N-B:TYR161.O 50.20%

B:VAL36.N-B:LEU89.O 50.60%

B:TYR37.N-B:LEU30.O 45.82%

B:LEU89.N-B:VAL36.O 49.20%

B:THR135.OG1-B:ASN133.OD1 50.20%

B:LEU75.N-B:VAL68.O 45.82%

B:LEU115.N-B:VAL148.O 47.81%

B:GLN83.N-B:VAL86.O 50.20%

B:GLN83.N-B:VAL86.O 44.62%

B:LEU75.N-B:VAL68.O 47.61%

B:LEU89.N-B:VAL36.O 50.00%

B:VAL18.N-B:GLY29.O 44.62%

B:PHE150.N-B:SER113.O 46.41%

B:GLY149.N-B:TYR161.O 50.00%

B:ALA70.N-B:VAL73.O 44.22%

B:VAL18.N-B:GLY29.O 46.41%

B:GLN192.NE2-B:VAL186.O 49.60%

B:ASN203.ND2-B:ASP289.O 44.02%

B:ASN203.ND2-B:ASP289.O 46.22%

B:VAL20.N-B:LEU27.O 49.40%

B:PHE8.N-B:SER113.OG 44.02%

B:SER123.N-B:ALA116.O 46.02%

B:LEU27.N-B:VAL20.O 48.61%

B:ASN95.ND2-B:TRP31.O 43.63%

B:GLY146.N-B:HIS163.O 46.02%

B:TYR37.N-B:LEU30.O 48.61%

B:PHE150.N-B:SER113.O 43.43%

B:ASN95.N-B:ASP33.O 46.02%

B:SER147.OG-B:SER144.O 48.01%

B:SER147.OG-B:SER144.O 43.43%

B:ALA70.N-B:VAL73.O 45.82%

B:GLY146.N-B:HIS163.O 48.01%

B:ARG105.NH2-B:PHE181.O 43.23%

B:ALA173.N-B:MET165.O 45.62%

B:LEU115.N-B:VAL148.O 47.81%

B:VAL157.N-B:LYS100.O 43.03%

B:HIS172.N-B:ILE136.O 45.22%

B:GLY109.N-B:MET130.O 47.61%

B:LEU32.N-B:VAL35.O 42.03%

B:GLN19.N-B:GLN69.O 45.02%

B:ALA70.N-B:VAL73.O 47.01%

B:THR111.OG1-B:ASP295.OD1 42.03%

B:PHE8.N-B:SER113.OG 44.62%

B:ARG131.N-B:THR135.O 46.41%

B:LYS90.N-B:GLY79.O 41.83%

B:GLN83.N-B:VAL86.O 44.22%

B:PHE150.N-B:SER113.O 46.22%

B:ILE136.N-B:HIS172.O 41.63%

B:VAL20.N-B:LEU27.O 43.23%

B:LEU242.N-B:ASN231.OD1 44.62%

B:LEU205.N-B:THR201.O 41.63%

B:LEU27.N-B:VAL20.O 42.83%

B:ASN203.ND2-B:ASP289.O 44.62%

B:TYR182.N-B:GLY174.O 41.43%

B:GLN192.NE2-B:VAL186.O 42.23%

B:GLN19.N-B:GLN69.O 44.42%

B:GLU14.N-B:SER10.O 40.84%

B:LYS90.N-B:GLY79.O 41.63%

B:VAL157.N-B:LYS100.O 44.22%

B:ILE281.N-B:SER284.O 40.64%

B:LEU242.N-B:ASN231.OD1 41.43%

B:LEU32.N-B:VAL35.O 44.02%

B:LYS5.NZ-B:GLU290.OE2 40.24%

B:ASN28.ND2-B:CYS145.O 41.43%

B:SER123.N-B:ALA116.O 44.02%

B:SER158.N-B:ASN151.O 39.64%

B:TYR182.N-B:GLY174.O 41.24%

B:VAL18.N-B:GLY29.O 43.63%

B:ARG60.NH1-B:ASP48.OD2 39.24%

B:VAL157.N-B:LYS100.O 41.24%

B:LYS90.N-B:GLY79.O 43.63%

B:LEU30.N-B:TYR37.O 38.65%

B:ILE281.N-B:SER284.O 41.04%

B:ASN95.N-B:ASP33.O 43.43%

B:TYR239.N-B:ALA234.O 38.45%

B:LEU30.N-B:TYR37.O 40.64%

B:GLN189.N-B:MET49.O 43.23%

B:THR199.N-B:ASN238.O 38.25%

B:TYR118.N-B:SER121.O 40.64%

B:LEU75.N-B:VAL68.O 43.23%

B:LEU242.N-B:ASN231.OD1 37.05%

B:THR199.N-B:ASN238.O 40.24%

B:VAL91.N-B:ASP34.O 42.63%

B:ASN214.ND2-B:ALA210.O 37.05%

B:VAL91.N-B:ASP34.O 40.24%

B:PHE8.N-B:SER113.OG 41.83%

B:HIS172.N-B:ILE136.O 36.85%

B:TYR239.N-B:ALA234.O 40.24%

B:TYR182.N-B:GLY174.O 41.63%

B:ASN231.N-B:LEU227.O 36.45%

B:SER158.N-B:ASN151.O 39.64%

B:ASN95.ND2-B:TRP31.O 41.63%

B:HIS80.ND1-B:ASN63.OD1 36.45%

B:LEU32.N-B:VAL35.O 39.04%

B:ILE281.N-B:SER284.O 41.24%

B:ALA116.N-B:GLY124.O 35.66%

B:ASN95.ND2-B:TRP31.O 39.04%

B:ASP153.N-B:CYS156.O 41.04%

B:ASN151.ND2-B:THR111.O 35.26%

B:LEU205.N-B:THR201.O 38.84%

B:ASN231.N-B:LEU227.O 40.84%

B:TYR126.OH-B:LYS137.O 35.06%

B:TYR54.OH-B:ASP187.O 37.85%

B:ASN133.ND2-B:GLY195.O 40.04%

B:THR135.OG1-B:ASN133.OD1 34.46%

B:ASN231.N-B:LEU227.O 37.05%

B:LEU30.N-B:TYR37.O 38.84%

B:ASP153.N-B:CYS156.O 34.06%

B:CYS128.N-B:PHE112.O 35.86%

B:THR199.N-B:ASN238.O 38.05%

B:PHE112.N-B:CYS128.O 33.86%

B:ASP153.N-B:CYS156.O 35.86%

B:TYR239.N-B:ALA234.O 38.05%

B:THR111.OG1-B:ASP295.OD2 33.86%

B:ARG105.NH2-B:PHE181.O 35.26%

B:LEU205.N-B:THR201.O 36.65%

B:THR21.N-B:LEU67.O 33.47%

B:SER254.OG-B:ILE259.O 35.26%

B:ASN28.ND2-B:CYS145.O 35.86%

B:SER254.OG-B:ILE259.O 32.27%

B:THR111.OG1-B:ASP295.OD1 35.06%

B:GLU14.N-B:SER10.O 35.26%

B:TYR118.N-B:SER121.O 31.87%

B:THR111.OG1-B:ASP295.OD2 34.86%

B:TYR118.N-B:SER121.O 34.86%

B:SER113.N-B:PHE150.O 31.87%

B:GLU14.N-B:SER10.O 34.26%

B:ASN214.ND2-B:ALA210.O 34.06%

B:LYS269.N-B:CYS265.O 31.27%

B:THR21.N-B:LEU67.O 33.47%

B:THR21.N-B:LEU67.O 34.06%

B:ASN28.ND2-B:CYS145.O 31.08%

B:THR25.OG1-B:CYS44.O 32.87%

B:THR111.OG1-B:ASP295.OD1 34.06%

B:THR292.OG1-B:ASP295.OD1 30.88%

B:SER113.N-B:PHE150.O 32.47%

B:THR111.OG1-B:ASP295.OD2 33.86%

B:CYS22.N-B:THR25.O 30.28%

B:LEU268.N-B:MET264.O 32.27%

B:SER254.OG-B:ILE259.O 33.86%

B:ILE43.N-B:ARG40.O 29.88%

B:ALA255.N-B:GLY251.O 31.87%

B:PHE112.N-B:CYS128.O 33.47%

B:ARG40.NH2-B:ASP187.OD1 29.68%

B:THR135.OG1-B:ASN133.OD1 31.47%

B:TYR54.OH-B:ASP187.O 33.07%

B:LEU67.N-B:THR21.O 29.28%

B:CYS22.N-B:THR25.O 31.27%

B:SER158.N-B:ASN151.O 32.87%

B:TRP218.NE1-B:THR280.O 28.88%

B:ASN214.ND2-B:ALA210.O 29.88%

B:ALA173.N-B:MET165.O 32.27%

B:ALA173.N-B:MET165.O 28.29%

B:PHE112.N-B:CYS128.O 29.68%

B:ARG105.NH2-B:PHE181.O 31.47%

B:THR175.OG1-B:ASP176.O 28.09%

B:ARG4.N-B:GLN299.OE1 29.08%

B:ASN231.ND2-B:LEU242.O 31.27%

B:ARG60.NH2-B:ASP48.OD1 28.09%

B:THR175.OG1-B:ASP176.O 28.69%

B:ALA116.N-B:GLY124.O 31.27%

B:ARG40.NE-B:ASP187.OD2 27.89%

B:ALA116.N-B:GLY124.O 28.49%

B:ALA255.N-B:GLY251.O 30.68%

B:ALA255.N-B:GLY251.O 27.89%

B:ASN151.ND2-B:THR111.O 28.29%

B:CYS128.N-B:PHE112.O 30.08%

B:LEU208.N-B:VAL204.O 27.69%

B:GLN69.N-B:GLN19.O 27.89%

B:ASN95.ND2-B:GLY15.O 30.08%

B:GLN69.N-B:GLN19.O 27.69%

B:ASN95.ND2-B:GLY15.O 27.09%

B:HIS80.ND1-B:ASN63.OD1 30.08%

B:THR243.OG1-B:HIS246.ND1 27.49%

(continued)

2.4 Concluding Remarks

139

Table 2.46 (continued) SARS-CoV-2-N3 rep1

rep2

rep3

B:HIS80.ND1-B:ASN63.OD1 27.09%

B:ASN203.ND2-B:GLY109.O 29.68%

B:THR45.N-B:ASP48.OD2 27.29%

B:THR243.OG1-B:HIS246.ND1 26.89%

B:ILE136.N-B:HIS172.O 28.88%

B:PHE159.N-B:LYS102.O 27.09%

B:LYS269.N-B:CYS265.O 26.89%

B:SER62.N-B:ASN65.OD1 28.69%

B:VAL86.N-B:GLN83.O 26.49%

B:PHE159.N-B:LYS102.O 26.89%

B:VAL86.N-B:GLN83.O 28.69%

B:ASN221.N-B:SER267.OG 25.70%

B:LEU67.N-B:THR21.O 26.29%

B:CYS22.N-B:THR25.O 28.09%

B:LEU268.N-B:MET264.O 25.30%

B:TRP218.NE1-B:THR280.O 26.29%

B:ASN151.ND2-B:THR111.O 27.29%

B:ASN151.N-B:SER158.O 25.10%

B:ARG40.NH2-B:ASP187.OD1 25.90%

B:ILE200.N-B:ASP289.OD1 27.29%

B:ASN180.N-B:ASP176.OD2 24.90%

B:ASN203.ND2-B:GLY109.O 25.90%

B:LEU268.N-B:MET264.O 27.29%

B:ASN95.ND2-B:GLY15.O 24.50%

B:SER113.OG-B:GLN127.OE1 25.70%

B:SER113.OG-B:GLN127.OE1 26.89%

B:SER81.N-B:LYS88.O 24.30%

B:LEU272.N-B:LEU268.O 24.70%

B:LEU67.N-B:THR21.O 26.89%

B:ARG4.N-B:GLN299.OE1 24.30%

B:ASN231.ND2-B:LEU242.O 24.30%

B:ILE43.N-B:ARG40.O 26.49%

B:SER62.N-B:ASN65.OD1 24.10%

B:VAL104.N-B:PHE159.O 23.71%

B:GLN69.N-B:GLN19.O 26.49%

B:VAL104.N-B:PHE159.O 23.90%

B:ARG131.NH2-B:ASP289.OD1 23.71%

B:MET130.N-B:GLN110.O 26.29%

B:ARG105.NH1-B:ASP176.OD1 23.71%

B:LYS5.NZ-B:GLU290.OE1 23.31%

B:ARG4.N-B:GLN299.OE1 25.90%

B:CYS160.N-B:GLY149.O 23.71%

B:ARG40.NE-B:ASP187.OD2 22.91%

B:PHE159.N-B:LYS102.O 25.50%

B:CYS128.N-B:PHE112.O 22.91%

B:SER62.N-B:ASN65.OD1 22.91%

B:LYS269.N-B:CYS265.O 25.10%

B:MET165.N-B:ALA173.O 22.91%

B:LEU208.N-B:VAL204.O 22.71%

B:THR45.OG1-B:ASP48.OD1 25.10%

B:ARG131.NH2-B:ASP289.OD1 22.71%

B:SER284.N-B:ILE281.O 21.91%

B:THR175.OG1-B:ASP176.O 24.90%

B:ASN203.ND2-B:GLY109.O 22.51%

B:SER81.N-B:LYS88.O 21.91%

B:THR292.OG1-B:ASP295.OD1 24.10%

B:THR26.OG1-B:THR21.OG1 22.31%

B:LYS102.N-B:VAL157.O 21.71%

B:LYS102.N-B:VAL157.O 23.11%

B:THR292.OG1-B:ASP295.OD2 22.31%

B:ILE136.N-B:HIS172.O 21.51%

B:LEU208.N-B:VAL204.O 22.71%

B:CYS38.N-B:LEU87.O 22.11%

B:ALA210.N-B:ALA206.O 21.31%

B:TRP218.NE1-B:THR280.O 22.71%

B:ASN133.ND2-B:GLY195.O 21.91%

B:THR292.OG1-B:ASP295.OD2 21.31%

B:ASN151.N-B:SER158.O 22.31%

B:LYS102.N-B:VAL157.O 21.71%

B:ASN151.N-B:SER158.O 21.12%

B:ASN221.N-B:SER267.OG 22.31%

B:GLN107.N-B:GLN110.OE1 21.51%

B:ARG40.N-B:CYS85.O 21.12%

B:ALA234.N-B:PHE230.O 22.31%

B:THR198.OG1-B:GLU240.OE2 21.31%

B:ASN180.N-B:ASP176.OD2 20.12%

B:THR292.OG1-B:ASP295.OD2 22.31%

B:GLN273.N-B:LYS269.O 21.12%

B:THR292.N-B:ASP295.OD1 20.12%

B:THR45.OG1-B:ASP48.OD2 21.91%

B:THR21.OG1-B:THR26.OG1 20.32%

B:ARG60.NH1-B:ASP48.OD1 21.91%

B:ASN231.ND2-B:LEU242.O 20.32%

B:VAL104.N-B:PHE159.O 21.71%

B:GLN127.NE2-B:GLU290.OE2 20.32%

B:SER113.N-B:PHE150.O 21.51%

B:GLY29.N-B:VAL18.O 20.12%

B:THR292.N-B:ASP295.OD1 21.51%

B:VAL303.N-B:GLN256.O 20.12%

B:THR226.OG1-B:ASP229.OD2 21.51% B:SER284.N-B:ILE281.O 21.12% B:LYS5.NZ-B:GLU290.OE1 20.92% B:CYS160.N-B:GLY149.O 20.52% B:ASN180.N-B:ASP176.OD2 20.52% B:SER81.N-B:LYS88.O 20.52% B:THR98.OG1-B:ASP33.OD1 20.32% B:ASN238.ND2-B:ASP197.O 20.32% B:THR243.OG1-B:ASP245.OD1 20.12%

Table 2.47 The MD-SBs-HBs between the two monomers of dimer the SARS-CoV-1-Mpro1q2w model (denoted as “SARS-CoV-1 dimer”) and the SARS-CoV-2-Mpro-6y2e model (denoted as “SARS-CoV-2 dimer”), where each model has three sets of MD simulations [346] SARS-CoV-1 rep1

rep2

rep3

A:GLU14-B:LYS12

B:GLU14-A:LYS12

B:GLU14-A:LYS12

A:GLU290-B:ARG4

B:GLU290-A:ARG4

A:GLU290-B:ARG4

B:GLU290-A:ARG4

A:GLU290-B:ARG4

B:GLU290-A:ARG4

A:TYR118.OH-B:ARG298.O 35.86%

A:SER139.OG-B:GLN299.OE1 54.38%

B:GLN299.NE2-A:SER139.O 47.61%

A:SER139.OG-B:GLY2.O 32.67%

B:VAL125.N-A:ALA7.O 34.46%

B:ARG4.NH1-A:GLU290.OE2 40.84%

A:ALA7.N-B:VAL125.O 28.69%

A:GLY11.N-B:GLU14.OE2 31.47%

A:ARG4.NH2-B:GLU290.OE2 39.04%

A:GLY11.N-B:GLU14.OE2 28.49%

A:VAL125.N-B:ALA7.O 31.27%

A:GLY11.N-B:GLU14.OE2 37.25%

B:ARG4.NH2-A:GLU290.OE1 30.08%

B:ALA7.N-A:VAL125.O 30.88%

A:ALA7.N-B:VAL125.O 32.27%

B:VAL125.N-A:ALA7.O 25.30%

B:ARG4.NH1-A:GLU290.OE1 29.88%

B:ARG4.NH2-A:GLU290.OE1 35.46%

B:ARG4.NH1-A:GLU290.OE2 24.30%

B:ARG4.NH2-A:GLU290.OE2 29.48%

A:TYR118.OH-B:ARG298.O 29.48%

B:GLY11.N-A:GLU14.OE2 23.71%

B:GLY11.N-A:GLU14.OE2 28.49%

A:ARG4.NH1-B:GLU290.OE1 28.29%

B:ARG4.NH2-A:GLU290.OE2 21.31%

A:ARG4.NH1-B:GLU290.OE1 22.51%

A:ARG4.NH2-B:GLU290.OE1 25.10%

A:ARG4.N-B:SER139.OG 20.32%

A:ARG4.NH2-B:GLU290.OE2 21.51%

A:VAL125.N-B:ALA7.O 20.12%

B:GLY11.N-A:GLU14.OE2 23.71% A:VAL125.N-B:ALA7.O 21.12%

(continued)

140

2 3C-Like Protease (3CLpro)

Table 2.47 (continued) SARS-CoV-2 rep1

rep2

rep3

A:GLU14-B:LYS12

A:GLU14-B:LYS12

A:GLU14-B:LYS12

B:GLU14-A:LYS12

A:GLU290-B:ARG4

A:GLU290-B:ARG4

B:GLU290-A:ARG4

B:GLU290-A:ARG4

A:GLU290-B:ARG4 B:GLU290-A:ARG4 A:ASP216-B:LYS137

A:SER10.OG-A:GLU14.OE2 82.87%

B:SER139.OG-A:GLN299.OE1 64.34%

B:SER139.OG-A:GLN299.OE1 60.76%

A:SER267.OG-A:ASP263.O 65.94%

A:SER139.OG-B:GLN299.OE1 54.58%

A:SER139.OG-B:GLN299.OE1 48.80%

A:SER139.OG-B:GLN299.OE1 52.79%

B:ARG4.NH1-A:GLU290.OE2 50.00%

B:ARG4.NH1-A:GLU290.OE2 43.03%

B:SER139.OG-A:GLN299.OE1 46.02%

B:ARG4.NH2-A:GLU290.OE1 41.24%

B:ARG4.NH2-A:GLU290.OE1 33.67%

A:SER123.OG-B:VAL303.O 26.49%

B:VAL125.N-A:ALA7.O 34.06%

B:GLY11.N-A:GLU14.OE2 30.28%

B:SER1.OG-A:GLU166.OE2 29.08%

B:GLY11.N-A:GLU14.OE2 28.09%

A:GLY11.N-B:GLU14.OE2 30.08%

B:GLY11.N-A:GLU14.OE2 24.50%

B:SER1.OG-A:GLU166.OE1 23.90%

A:ARG4.NH2-B:GLU290.OE1 27.89%

B:SER1.OG-A:GLU166.OE1 24.10%

B:ASN119.ND2-A:PHE305.O 23.90%

A:VAL125.N-B:ALA7.O 26.10%

B:ARG4.NH1-A:GLU290.OE2 20.92%

A:ARG4.NH2-B:GLU290.OE1 22.51%

B:SER1.OG-A:GLU166.OE2 22.51%

B:SER1.N-A:PHE140.O 20.12%

B:SER1.OG-A:GLU166.OE2 21.71%

A:SER1.OG-B:GLU166.OE1 21.12%

B:PHE305.N-A:PRO122.O 21.12% A:ALA7.N-B:VAL125.O 20.92% A:PHE140.N-B:SER1.O 20.32% A:ARG4.NH1-B:GLU290.OE2 20.12%

Table 2.48 The MD-SBs-HBs between the two monomers of dimer the SARS-CoV-1-Mpro-N32hob model (denoted as “SARS-CoV-1-N3 dimer”) and the SARS-CoV-2-Mpro-N3-6lu7 model (denoted as “SARS-CoV-2-N3 dimer”), where each model has three sets of MD simulations [346] SARS-CoV-1-N3 rep1

rep2

rep3

A:GLU14-B:LYS12

B:GLU14-A:LYS12

A:GLU14-B:LYS12

A:GLU290-B:ARG4

A:GLU290-B:ARG4

A:GLU290-B:ARG4

B:GLU290-A:ARG4

B:GLU290-A:ARG4

B:GLU290-A:ARG4

B:ARG4.NH2-A:GLU290.OE2 45.82%

A:SER139.OG-B:GLN299.OE1 59.36%

B:SER139.OG-A:GLN299.OE1 42.83%

B:ARG4.NH1-A:GLU290.OE1 43.23%

B:SER139.OG-A:GLY2.O 32.27%

A:SER1.OG-B:GLU166.OE2 29.88%

B:SER1.OG-A:GLU166.OE2 30.68%

A:VAL125.N-B:ALA7.O 29.08%

A:ALA7.N-B:VAL125.O 28.88%

B:GLY11.N-A:GLU14.OE1 30.28%

B:ARG4.NH2-A:GLU290.OE2 28.69%

A:ARG4.NH1-B:LYS137.O 28.49%

B:SER1.OG-A:GLU166.OE1 29.28%

A:ALA7.N-B:VAL125.O 28.29%

B:ARG4.NH1-A:GLU290.OE2 28.29%

A:SER1.OG-B:GLU166.OE1 27.69%

B:GLY11.N-A:GLU14.OE1 27.69%

B:ARG4.NH2-A:GLU290.OE1 26.49%

A:GLY11.N-B:GLU14.OE1 25.30%

B:ARG4.NH1-A:GLU290.OE1 23.90%

B:VAL125.N-A:ALA7.O 25.10%

A:SER139.OG-B:GLN299.OE1 23.11%

A:SER1.OG-B:GLU166.OE1 23.51%

A:SER1.OG-B:GLU166.OE1 23.31%

A:GLY143.N-B:VAL303.O 22.11%

B:VAL125.N-A:ALA7.O 22.71%

A:GLY11.N-B:GLU14.OE1 21.71%

A:VAL125.N-B:ALA7.O 21.91%

B:SER1.OG-A:GLU166.OE1 22.11%

B:ALA7.N-A:VAL125.O 20.92%

A:SER1.OG-B:GLU166.OE2 21.12%

B:ALA7.N-A:VAL125.O 21.91%

A:VAL125.N-B:ALA7.O 20.92%

SARS-CoV-2-N3 rep1

rep2

rep3

A:GLU288-B:ARG4

A:GLU14-B:LYS12

A:GLU14-B:LYS12

A:GLU290-B:ARG4

B:GLU14-A:LYS12

A:GLU290-B:ARG4

B:GLU290-A:ARG4

A:GLU290-B:ARG4

B:GLU290-A:ARG4

B:GLY11.N-A:GLU14.OE1 20.72%

B:GLU290-A:ARG4 A:SER139.OG-B:GLN299.OE1 57.57%

A:SER139.OG-B:GLN299.OE1 57.57%

A:SER139.OG-B:GLN299.OE1 58.37%

B:SER139.OG-A:GLN299.OE1 51.00%

B:SER139.OG-A:GLN299.OE1 53.19%

B:SER139.OG-A:GLN299.OE1 49.80%

B:VAL125.N-A:ALA7.O 32.67%

B:VAL125.N-A:ALA7.O 31.87%

B:GLY11.N-A:GLU14.OE1 33.47%

A:VAL125.N-B:ALA7.O 32.07%

B:SER1.OG-A:GLU166.OE1 31.67%

A:ALA7.N-B:VAL125.O 32.27%

B:SER1.OG-A:GLU166.OE2 30.68%

A:VAL125.N-B:ALA7.O 31.08%

A:GLY11.N-B:GLU14.OE1 30.68%

B:GLY11.N-A:GLU14.OE1 29.68%

B:GLY11.N-A:GLU14.OE1 28.88%

B:VAL125.N-A:ALA7.O 29.88%

A:GLY11.N-B:GLU14.OE1 29.28%

B:ARG4.NH1-A:GLU290.OE1 28.49%

B:SER1.OG-A:GLU166.OE2 24.30%

A:ALA7.N-B:VAL125.O 26.49%

A:ALA7.N-B:VAL125.O 27.69%

B:ALA7.N-A:VAL125.O 21.91%

A:SER1.OG-B:GLU166.OE2 26.29%

A:GLY11.N-B:GLU14.OE1 27.69%

B:SER1.OG-A:GLU166.OE1 21.71%

A:SER1.OG-B:GLU166.OE1 26.29%

B:ARG4.NH2-A:GLU290.OE2 25.90%

B:ARG4.NH2-A:GLU290.OE2 20.32%

B:ALA7.N-A:VAL125.O 26.10%

B:ALA7.N-A:VAL125.O 25.10%

B:ARG4.NH2-A:GLU290.OE1 20.12%

A:ARG4.NH2-B:GLU290.OE2 25.70%

B:SER1.OG-A:GLU166.OE2 22.11%

B:ARG4.NH1-A:GLU290.OE1 24.90%

A:ARG4.NH2-B:GLU290.OE2 21.12%

B:SER1.OG-A:GLU166.OE1 23.31%

A:ARG4.NH1-B:GLU290.OE2 20.92%

A:ARG4.NH1-B:GLU290.OE1 22.91%

A:ARG4.NH2-B:GLU290.OE1 20.32%

B:ARG4.NH2-A:GLU290.OE2 22.71%

A:SER1.OG-B:GLU166.OE2 20.12%

2.4 Concluding Remarks

141

Table 2.49 MD-SBs of the Mpro-wt-7bb2 model from the 550 ns MD trajectories (amarolab.ucsd.edu/covid19.php) A-chain – rep1

A-chain – rep2

A-chain – rep3

B-chain – rep1

B-chain – rep2

B-chain – rep3

ASP153-ARG298

ASP153-ARG298

ASP153-ARG298

ASP153-ARG298

ASP153-ARG298

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS102

ASP155-LYS12

ASP155-LYS12

ASP155-LYS12

ASP155-LYS102

ASP155-LYS102

ASP155-LYS12

ASP176-ARG105

ASP176-ARG105

ASP176-ARG105

ASP155-LYS12

ASP176-ARG105

ASP176-ARG105

ASP187-ARG188

ASP187-ARG188

ASP187-ARG188

ASP176-ARG105

ASP187-ARG188

ASP187-ARG188

ASP187-ARG40

ASP187-ARG40

ASP187-ARG40

ASP187-ARG188

ASP187-ARG40

ASP187-ARG40

ASP197-ARG131

ASP197-ARG131

ASP197-ARG131

ASP187-ARG40

ASP197-ARG131

ASP197-ARG131

ASP197-LYS137

ASP197-LYS137

ASP197-LYS137

ASP197-ARG131

ASP197-LYS137

ASP197-LYS137

ASP216-ARG279

ASP216-ARG279

ASP216-ARG279

ASP197-LYS137

ASP216-ARG279

ASP216-ARG279

ASP229-LYS269

ASP229-LYS269

ASP229-LYS269

ASP216-ARG279

ASP229-LYS269

ASP229-LYS269

ASP263-ARG222

ASP263-ARG222

ASP263-ARG222

ASP229-LYS269

ASP263-ARG222

ASP263-ARG222

ASP289-ARG131

ASP289-ARG131

ASP289-ARG131

ASP263-ARG222

ASP289-ARG131

ASP289-ARG131

ASP295-ARG298

ASP295-ARG298

ASP295-ARG298

ASP289-ARG131

ASP295-ARG298

ASP295-ARG298

ASP34-LYS90

ASP34-LYS90

ASP34-LYS90

ASP295-ARG298

ASP34-LYS90

ASP34-LYS90

ASP48-LYS61

ASP48-ARG60

ASP48-ARG60

ASP34-LYS90

ASP48-ARG60

ASP48-ARG60

ASP56-ARG60

ASP48-LYS61

ASP48-LYS61

ASP48-ARG60

ASP48-LYS61

ASP56-ARG60

ASP92-ARG76

ASP56-ARG188

ASP56-ARG60

ASP48-LYS61

ASP56-ARG60

ASP92-ARG76

GLU178-LYS88

ASP56-ARG60

ASP92-ARG76

ASP56-ARG60

ASP92-ARG76

GLU270-LYS269

GLU270-LYS269

ASP92-ARG76

GLU270-LYS269

ASP92-ARG76

GLU178-ARG105

GLU288-LYS5

GLU288-LYS5

GLU178-LYS88

GLU288-LYS5

GLU178-ARG105

GLU270-ARG222

GLU290-ARG131

GLU290-ARG131

GLU270-LYS269

GLU270-LYS269

GLU290-LYS137

GLU290-LYS137

GLU288-LYS5

GLU47-ARG60

GLU270-LYS269

GLU288-LYS5

GLU290-LYS5

GLU290-LYS5

GLU290-ARG131

GLU55-ARG188

GLU290-LYS5

GLU288-LYS5

GLU270-ARG222

GLU290-ARG131

GLU55-ARG188

GLU290-LYS137

GLU55-ARG40

GLU290-ARG131

GLU290-LYS137

GLU55-ARG40

GLU290-LYS5

GLU55-ARG60

GLU290-LYS5

GLU290-LYS5 GLU47-ARG188

GLU47-ARG60

GLU47-ARG188

GLU55-ARG40

GLU55-ARG188

GLU55-ARG60

GLU55-ARG40

Table 2.50 MD-SBs of the Mpro-delP168-and-a173v-7bb2 model from the 550 ns MD trajectories (amarolab.ucsd.edu/covid19.php) A-chain – rep1

A-chain – rep2

A-chain – rep3

B-chain – rep1

B-chain – rep2

B-chain – rep3

ASP153-ARG298

ASP153-ARG298

ASP153-ARG298

ASP153-ARG298

ASP153-ARG298

ASP153-ARG298

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS12

ASP155-LYS12

ASP155-LYS12

ASP155-LYS102

ASP155-LYS102

ASP155-LYS12

ASP176-ARG105

ASP176-ARG105

ASP176-ARG105

ASP155-LYS12

ASP155-LYS12

ASP176-ARG105

ASP187-ARG188

ASP187-ARG188

ASP187-ARG188

ASP176-ARG105

ASP176-ARG105

ASP187-ARG188

ASP187-ARG40

ASP187-ARG40

ASP187-ARG40

ASP187-ARG188

ASP187-ARG188

ASP187-ARG40

ASP197-ARG131

ASP197-ARG131

ASP197-ARG131

ASP187-ARG40

ASP187-ARG40

ASP197-ARG131

ASP197-LYS137

ASP197-LYS137

ASP197-LYS137

ASP197-ARG131

ASP197-ARG131

ASP197-LYS137

ASP216-ARG279

ASP229-LYS269

ASP216-ARG279

ASP197-LYS137

ASP197-LYS137

ASP216-ARG279

ASP229-LYS269

ASP263-ARG222

ASP229-LYS269

ASP216-ARG279

ASP216-ARG279

ASP229-LYS269

ASP263-ARG222

ASP289-ARG131

ASP263-ARG222

ASP229-LYS269

ASP229-LYS269

ASP263-ARG222

ASP289-ARG131

ASP295-ARG298

ASP289-ARG131

ASP263-ARG222

ASP263-ARG222

ASP289-ARG131

ASP295-ARG298

ASP33-LYS100

ASP295-ARG298

ASP289-ARG131

ASP289-ARG131

ASP295-ARG298

ASP34-LYS90

ASP34-LYS90

ASP33-LYS100

ASP295-ARG298

ASP295-ARG298

ASP34-LYS90

ASP48-ARG188

ASP48-ARG60

ASP34-LYS90

ASP34-LYS90

ASP34-LYS90

ASP48-ARG60 ASP48-LYS61

ASP48-ARG60

ASP48-LYS61

ASP48-ARG188

ASP48-ARG60

ASP48-ARG60

ASP48-LYS61

ASP56-ARG60

ASP48-ARG60

ASP48-LYS61

ASP48-LYS61

ASP56-ARG60

ASP92-ARG76

ASP48-LYS61

ASP56-ARG60

ASP56-ARG60

ASP92-ARG76

ASP92-ARG76

GLU270-LYS269

ASP56-ARG60

ASP92-ARG76

ASP92-ARG76

GLU178-ARG105

ASP56-ARG60

(continued)

142

2 3C-Like Protease (3CLpro)

Table 2.50 (continued) A-chain – rep1

A-chain – rep2

A-chain – rep3

B-chain – rep1

B-chain – rep2

GLU270-ARG222

GLU288-LYS5

ASP92-ARG76

GLU270-LYS269

GLU270-ARG222

GLU270-ARG222

GLU270-LYS269

GLU290-ARG131

GLU270-ARG279

GLU288-LYS5

GLU270-LYS269

GLU270-LYS269

B-chain – rep3

GLU288-LYS5

GLU290-LYS137

GLU270-LYS269

GLU290-ARG131

GLU288-LYS5

GLU288-LYS5

GLU290-ARG131

GLU290-LYS5

GLU288-LYS5

GLU290-LYS137

GLU290-ARG131

GLU290-ARG131

GLU290-LYS137

GLU55-ARG188

GLU290-LYS5

GLU55-ARG40

GLU47-ARG188

GLU290-ARG131

GLU290-LYS5

GLU290-LYS5

GLU290-LYS5

GLU290-LYS137

GLU55-ARG40

GLU55-ARG188

GLU55-ARG188

GLU290-LYS5

GLU55-ARG60

GLU55-ARG40

GLU55-ARG40

GLU47-ARG60

GLU47-ARG60

GLU47-LYS61

GLU47-LYS61

GLU55-ARG188

GLU55-ARG188

GLU55-ARG40

GLU55-ARG40

Table 2.51 MD-SBs of the Mpro-delP168-7bb2 model from the 550 ns MD trajectories (amarolab.ucsd.edu/covid19.php) A-chain – rep1

A-chain – rep2

A-chain – rep3

B-chain – rep1

B-chain – rep2

B-chain – rep3

ASP153-ARG298

ASP153-ARG298

ASP153-LYS102

ASP153-ARG298

ASP153-ARG298

ASP153-ARG298

ASP153-LYS102

ASP153-LYS102

ASP155-LYS100

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

ASP155-LYS100

ASP155-LYS100

ASP155-LYS102

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS12

ASP155-LYS12

ASP155-LYS12

ASP155-LYS102

ASP155-LYS102

ASP155-LYS102

ASP176-ARG105

ASP176-ARG105

ASP176-ARG105

ASP155-LYS12

ASP155-LYS12

ASP155-LYS12

ASP187-ARG188

ASP187-ARG188

ASP187-ARG188

ASP176-ARG105

ASP176-ARG105

ASP176-ARG105

ASP187-ARG40

ASP187-ARG40

ASP187-ARG40

ASP187-ARG188

ASP187-ARG188

ASP187-ARG188

ASP197-ARG131

ASP197-ARG131

ASP197-ARG131

ASP187-ARG40

ASP187-ARG40

ASP187-ARG40

ASP197-LYS137

ASP197-LYS137

ASP197-LYS137

ASP197-ARG131

ASP197-ARG131

ASP197-ARG131

ASP229-LYS269

ASP229-LYS269

ASP216-ARG279

ASP197-LYS137

ASP197-LYS137

ASP197-LYS137

ASP263-ARG222

ASP263-ARG222

ASP229-LYS269

ASP229-LYS269

ASP216-ARG279

ASP216-ARG279

ASP289-ARG131

ASP289-ARG131

ASP263-ARG222

ASP263-ARG222

ASP229-LYS269

ASP229-LYS269

ASP295-ARG298

ASP295-ARG298

ASP289-ARG131

ASP289-ARG131

ASP263-ARG222

ASP263-ARG222

ASP34-LYS90

ASP33-LYS100

ASP295-ARG298

ASP295-ARG298

ASP289-ARG131

ASP289-ARG131

ASP48-ARG60

ASP34-LYS90

ASP34-LYS90

ASP34-LYS90

ASP295-ARG298

ASP295-ARG298

ASP48-LYS61

ASP48-ARG188

ASP48-ARG60

ASP48-ARG60

ASP34-LYS90

ASP34-LYS90

ASP56-ARG60

ASP48-ARG60

ASP56-ARG60

ASP48-LYS61

ASP48-ARG188

ASP48-ARG60

ASP92-ARG76

ASP48-LYS61

ASP92-ARG76

ASP56-ARG60

ASP48-ARG60

ASP48-LYS61

GLU270-ARG222

ASP56-ARG60

GLU270-LYS269

ASP92-ARG76

ASP48-LYS61

ASP56-ARG60

GLU270-LYS269

ASP92-ARG76

GLU288-LYS5

GLU270-ARG222

ASP56-ARG60

ASP92-ARG76

GLU288-LYS5

GLU270-LYS269

GLU290-ARG131

GLU270-LYS269

ASP92-ARG76

GLU270-LYS269

GLU290-ARG131

GLU288-LYS5

GLU290-LYS137

GLU288-LYS5

GLU270-ARG222

GLU288-LYS5

GLU290-LYS137

GLU290-ARG131

GLU290-LYS5

GLU290-ARG131

GLU270-LYS269

GLU290-ARG131

GLU290-LYS5

GLU290-LYS137

GLU47-LYS61

GLU290-LYS137

GLU288-LYS5

GLU290-LYS137

GLU55-ARG188

GLU290-LYS5

GLU55-ARG40

GLU290-LYS5

GLU290-ARG131

GLU290-LYS5

GLU55-ARG40

GLU47-ARG60

GLU55-ARG188

GLU290-LYS137

GLU47-ARG188

GLU55-ARG40

GLU55-ARG40

GLU290-LYS5

GLU47-ARG60

GLU47-ARG60

GLU47-LYS61

GLU47-LYS61

GLU55-ARG188

GLU55-ARG188

GLU55-ARG40

GLU55-ARG60

GLU55-ARG40

2.4 Concluding Remarks

143

Table 2.52 MD-SBs of the Mpro-a173v-7bb2 model from the 550 ns MD trajectories (amarolab.ucsd.edu/covid19.php) A-chain – rep1

A-chain – rep2

A-chain – rep3

B-chain – rep1

B-chain – rep2

ASP153-ARG298

ASP153-ARG298

ASP153-ARG298

ASP153-ARG298

ASP153-ARG298

ASP153-ARG298

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

ASP153-LYS102

B-chain – rep3

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS100

ASP155-LYS12

ASP155-LYS12

ASP155-LYS12

ASP155-LYS102

ASP155-LYS102

ASP155-LYS102

ASP176-ARG105

ASP176-ARG105

ASP176-ARG105

ASP155-LYS12

ASP155-LYS12

ASP176-ARG105

ASP187-ARG188

ASP187-ARG188

ASP187-ARG188

ASP176-ARG105

ASP176-ARG105

ASP187-ARG188

ASP187-ARG40

ASP187-ARG40

ASP187-ARG40

ASP187-ARG188

ASP187-ARG188

ASP187-ARG40

ASP197-ARG131

ASP197-ARG131

ASP197-ARG131

ASP187-ARG40

ASP187-ARG40

ASP197-ARG131

ASP197-LYS137

ASP197-LYS137

ASP197-LYS137

ASP197-ARG131

ASP197-ARG131

ASP197-LYS137

ASP216-ARG279

ASP216-ARG279

ASP229-LYS269

ASP197-LYS137

ASP197-LYS137

ASP216-ARG279

ASP229-LYS269

ASP229-LYS269

ASP263-ARG222

ASP229-LYS269

ASP216-ARG279

ASP229-LYS269

ASP263-ARG222

ASP263-ARG222

ASP289-ARG131

ASP263-ARG222

ASP229-LYS269

ASP263-ARG222

ASP289-ARG131

ASP289-ARG131

ASP295-ARG298

ASP289-ARG131

ASP263-ARG222

ASP289-ARG131

ASP295-ARG298

ASP295-ARG298

ASP34-LYS90

ASP295-ARG298

ASP289-ARG131

ASP295-ARG298

ASP34-LYS90

ASP34-LYS90

ASP48-ARG60

ASP34-LYS90

ASP295-ARG298

ASP33-LYS100

ASP48-ARG60

ASP48-ARG60

ASP48-LYS61

ASP48-ARG60

ASP34-LYS90

ASP34-LYS90

ASP48-LYS61

ASP48-LYS61

ASP56-ARG60

ASP48-LYS61

ASP48-ARG60

ASP48-ARG60

ASP56-ARG60

ASP56-ARG60

ASP92-ARG76

ASP56-ARG60

ASP48-LYS61

ASP48-LYS61

ASP92-ARG76

ASP92-ARG76

GLU178-LYS88

ASP92-ARG76

ASP56-ARG60

ASP56-ARG60

GLU178-ARG105

GLU270-ARG222

GLU270-LYS269

GLU270-LYS269

ASP92-ARG76

ASP92-ARG76

GLU270-ARG222

GLU270-LYS269

GLU288-LYS5

GLU288-LYS5

GLU270-LYS269

GLU178-ARG105

GLU270-LYS269

GLU288-LYS5

GLU290-ARG131

GLU290-ARG131

GLU288-LYS5

GLU178-LYS88

GLU288-LYS5

GLU290-ARG131

GLU290-LYS137

GLU290-LYS5

GLU290-ARG131

GLU270-LYS269

GLU290-ARG131

GLU290-LYS137

GLU290-LYS5

GLU47-ARG60

GLU290-LYS5

GLU288-LYS5

GLU290-LYS137

GLU290-LYS5

GLU47-ARG60

GLU47-LYS61

GLU47-LYS61

GLU290-ARG131

GLU290-LYS5

GLU47-LYS61

GLU55-ARG188

GLU55-ARG188

GLU290-LYS137

GLU47-ARG188

GLU55-ARG188

GLU55-ARG40

GLU55-ARG40

GLU290-LYS5

GLU47-ARG60

GLU55-ARG40

GLU47-LYS61 GLU55-ARG188 GLU55-ARG40

GLU47-LYS61 GLU55-ARG188

MET162.N-THR175.O 47.01

LYS5.NZ-GLU290.OE2 46.82

ARG40.NH2-ASP187.OD1 46.64

SER144.OG-LEU141.O 45.74

TYR239.N-ALA234.O 48.09

LYS90.N-GLY79.O 46.82

MET162.N-THR175.O 45.92

LEU268.N-MET264.O 45.55

ARG40.NE-ASP187.OD2 47.55

LEU242.N-ASN231.OD1 47.37

LEU242.N-ASN231.OD1 48.46

ASN231.N-LEU227.O 48.28

GLY109.N-MET130.O 48.82

SER123.N-ALA116.O 48.28

LEU75.N-VAL68.O 48.82

SER144.OG-LEU141.O 48.82

LEU268.N-MET264.O 45.01 THR201.OG1-GLU240.O 44.83

ASN231.N-LEU227.O 48.28 LYS5.NZ-GLU290.OE1 47.91

LEU75.N-VAL68.O 46.28 PHE8.N-SER113.OG 45.74

LEU75.N-VAL68.O 49.18 GLY109.N-MET130.O 49.00

TYR239.N-ALA234.O 46.82 LYS88.N-SER81.O 46.28

ARG131.NH1-ASP289.OD1 49.73 THR201.OG1-GLU240.O 49.55

GLY120.N-ASN28.OD1 47.01 LYS90.N-GLY79.O 47.01

VAL157.N-LYS100.O 50.09 LYS88.N-SER81.O 49.73

LEU115.N-VAL148.O 49.91 ARG131.NH2-ASP289.OD1 47.19

ILE78.N-LYS90.O 50.45 SER123.N-ALA116.O 50.09

THR257.OG1-LEU253.O 50.45

LYS90.N-GLY79.O 49.91

ARG131.NH1-ASP289.OD1 49.73

VAL91.N-ASP34.O 49.18

ASN231.N-LEU227.O 50.27 HSE172.N-ILE136.O 50.09

THR257.OG1-LEU253.O 51.00 HSE172.N-ILE136.O 50.45

HSE172.N-ILE136.O 51.18

LEU75.N-VAL68.O 50.45

VAL157.N-LYS100.O 51.54

GLY146.N-HSE163.O 50.27

GLY146.N-HSE163.O 51.72 GLY109.N-MET130.O 51.00 THR257.OG1-LEU253.O 51.00

SER147.OG-SER144.O 52.27 ASN95.N-ASP33.O 52.09 TYR239.N-ALA234.O 51.00

THR21.N-LEU67.O 53.36

VAL157.N-LYS100.O 53.18

ASN231.N-LEU227.O 52.63

HSE172.N-ILE136.O 53.36

THR201.OG1-GLU240.O 53.36

THR21.N-LEU67.O 54.81 ARG40.NH2-ASP187.OD2 52.99

GLY146.N-HSE163.O 53.72 LEU115.N-VAL148.O 52.45

VAL157.N-LYS100.O 56.62 SER123.N-ALA116.O 55.54

TYR37.N-LEU30.O 54.45 LYS90.N-GLY79.O 54.26

VAL20.N-LEU27.O 57.71 ASN95.N-ASP33.O 56.81

VAL20.N-LEU27.O 55.90

SER123.N-ALA116.O 51.91

ARG105.NH2-PHE181.O 55.90

LYS88.N-SER81.O 53.90

VAL20.N-LEU27.O 54.63

LEU89.N-VAL36.O 54.08

SER267.OG-ASP263.O 56.99

GLY146.N-HSE163.O 56.62

ARG105.NH2-PHE181.O 56.99

LEU115.N-VAL148.O 56.62

TYR37.N-LEU30.O 58.26

ASN95.N-ASP33.O 58.08

ARG40.NH2-ASP187.OD2 58.08

ASN95.N-ASP33.O 57.71

ARG105.NH2-PHE181.O 55.17

SER254.OG-ILE259.O 59.71 GLY149.N-TYR161.O 59.53

GLY149.N-TYR161.O 58.98

TYR182.OH-CYS160.O 59.35

GLY149.N-TYR161.O 59.17

SER254.OG-ILE259.O 58.62

THR257.OG1-LEU253.O 58.26 LEU89.N-VAL36.O 58.62

TYR37.N-LEU30.O 61.89 ARG40.NE-ASP187.OD1 61.52 LEU89.N-VAL36.O 60.98

LEU167.N-VAL171.O 62.98 SER267.OG-ASP263.O 60.25 SER254.OG-ILE259.O 60.07

SER254.OG-ILE259.O 59.89

LEU89.N-VAL36.O 59.53

SER267.OG-ASP263.O 62.43

LEU167.N-VAL171.O 59.53

TYR182.OH-CYS160.O 64.43 SER267.OG-ASP263.O 64.07

TYR182.OH-CYS160.O 64.97 VAL114.N-TYR126.O 64.61

SER10.OG-GLU14.OE2 61.52

VAL20.N-LEU27.O 60.44

TYR37.N-LEU30.O 63.88

GLY149.N-TYR161.O 62.61

LEU167.N-VAL171.O 62.25

SER10.OG-GLU14.OE2 65.88 LEU167.N-VAL171.O 65.15

VAL36.N-LEU89.O 69.87 ARG131.NH2-ASP289.OD2 69.33

ARG131.NH2-ASP289.OD2 62.25

LEU115.N-VAL148.O 61.89

VAL114.N-TYR126.O 66.79

HSE163.N-SER147.O 65.15

TYR182.OH-CYS160.O 59.89

VAL36.N-LEU89.O 69.33 VAL114.N-TYR126.O 66.79

ARG40.NH2-ASP187.OD1 73.32 HSE163.N-SER147.O 71.69

VAL114.N-TYR126.O 67.33

VAL36.N-LEU89.O 66.79

TRP31.N-CYS16.O 70.05

VAL36.N-LEU89.O 67.88

HSE163.N-SER147.O 70.05

TRP31.N-CYS16.O 73.50

HSE163.N-SER147.O 72.78

ARG40.NE-ASP187.OD1 75.14

ARG131.NH2-ASP289.OD2 67.51

B-chain – rep1 TRP31.N-CYS16.O 70.42

A-chain – rep3 ARG40.NE-ASP187.OD2 78.04

A-chain – rep2

TRP31.N-CYS16.O 75.14

A-chain – rep1

GLY29.N-VAL18.O 46.10

LEU67.N-THR21.O 46.82

PHE8.N-SER113.OG 47.37

LEU242.N-ASN231.OD1 47.73

SER144.OG-LEU141.O 47.73

TYR239.N-ALA234.O 48.46

LEU115.N-VAL148.O 49.00

LEU87.N-CYS38.O 49.18

GLY120.N-ASN28.OD1 49.18

LYS90.N-GLY79.O 49.36

GLY146.N-HSE163.O 50.09

ASN231.N-LEU227.O 50.09

ILE78.N-LYS90.O 50.82

THR201.OG1-GLU240.O 51.36

LYS88.N-SER81.O 51.72

LEU75.N-VAL68.O 51.91

VAL157.N-LYS100.O 51.91

THR257.OG1-LEU253.O 53.72

LEU89.N-VAL36.O 53.90

SER254.OG-ILE259.O 55.35

HSE172.N-ILE136.O 55.90

SER123.N-ALA116.O 56.26

GLY109.N-MET130.O 56.44

ASN95.N-ASP33.O 58.44

VAL20.N-LEU27.O 58.62

TYR182.OH-CYS160.O 60.07

SER267.OG-ASP263.O 60.44

TYR37.N-LEU30.O 61.16

GLY149.N-TYR161.O 63.70

LEU167.N-VAL171.O 65.52

VAL114.N-TYR126.O 67.15

VAL36.N-LEU89.O 67.51

HSE163.N-SER147.O 70.24

TRP31.N-CYS16.O 72.60

B-chain – rep2

GLY29.N-VAL18.O 46.28

LEU242.N-ASN231.OD1 46.82

TYR182.N-GLY174.O 47.01

LEU205.N-THR201.O 47.55

ASN231.N-LEU227.O 48.64

VAL91.N-ASP34.O 48.64

PHE8.N-SER113.OG 48.64

ILE78.N-LYS90.O 48.82

ARG105.NH2-PHE181.O 49.73

TYR239.N-ALA234.O 51.00

LEU75.N-VAL68.O 51.00

LEU167.N-VAL171.O 51.18

GLY109.N-MET130.O 51.54

VAL157.N-LYS100.O 51.54

ILE136.N-HSE172.O 52.27

THR257.OG1-LEU253.O 53.18

LYS88.N-SER81.O 53.36

ARG40.NE-ASP187.OD1 54.26

THR175.OG1-ASP176.O 54.81

TYR182.OH-CYS160.O 54.81

LEU89.N-VAL36.O 54.81

LYS90.N-GLY79.O 56.08

TYR37.N-LEU30.O 56.99

GLY149.N-TYR161.O 57.89

SER123.N-ALA116.O 57.89

LEU115.N-VAL148.O 58.08

SER254.OG-ILE259.O 58.44

VAL20.N-LEU27.O 59.71

ASN95.N-ASP33.O 59.89

SER267.OG-ASP263.O 60.25

VAL36.N-LEU89.O 68.60

VAL114.N-TYR126.O 70.96

HSE163.N-SER147.O 72.23

TRP31.N-CYS16.O 77.13

B-chain – rep3

Table 2.53 MD-HBs (with occupancy rates ≥30%) of the Mpro-wt-7bb2 model from the 550 ns MD trajectories (amarolab.ucsd.edu/covid19.php)

144 2 3C-Like Protease (3CLpro)

LEU87.N-CYS38.O 43.74 LEU242.N-ASN231.OD1 43.38 GLN83.N-VAL86.O 42.83

SER144.OG-LEU141.O 43.74 ALA70.N-VAL73.O 43.19 LEU87.N-CYS38.O 43.01

ARG131.NH1-ASP289.OD1 43.92

PHE150.N-SER113.O 42.65

GLY29.N-VAL18.O 42.65

LEU205.N-THR201.O 42.47

ASN274.N-GLU270.O 42.47

GLN83.N-VAL86.O 42.47

VAL18.N-GLY29.O 42.11

GLY109.N-MET130.O 44.28

SER147.OG-SER144.O 44.10

LYS5.NZ-GLU290.OE1 44.10

GLN69.N-GLN19.O 43.92

THR21.N-LEU67.O 43.56

LEU27.N-VAL20.O 43.56

GLY120.N-ASN28.OD1 43.56

LEU87.N-CYS38.O 43.38

SER144.OG-LEU141.O 39.20 TYR54.OH-ASP187.OD1 39.02

MET130.N-GLN110.O 39.93 GLN19.N-GLN69.O 39.56

ILE78.N-LYS90.O 41.20

VAL91.N-ASP34.O 40.83

PHE8.N-SER113.OG 40.65

ARG105.NH1-ASP176.OD2 40.47

ALA70.N-VAL73.O 40.11

LEU87.N-CYS38.O 39.75

THR169.OG1-PRO168.O 41.56

ASN274.N-GLU270.O 41.02

LYS88.N-SER81.O 41.02

LEU67.N-THR21.O 40.65

SER254.N-LEU250.O 40.29

GLN19.N-GLN69.O 40.29

ASP153.N-CYS156.O 39.93

LEU27.N-VAL20.O 37.93

MET130.N-GLN110.O 37.57

PHE159.N-LYS102.O 37.57

ILE200.N-ASP289.OD2 37.57

ILE281.N-SER284.O 37.39

ILE78.N-LYS90.O 38.66

ARG105.NH1-ASP176.OD1 38.48

TYR54.OH-ASP187.OD1 38.29

ILE200.N-ASP289.OD2 37.75

CYS128.N-PHE112.O 37.02

LEU205.N-THR201.O 36.30 ARG131.NH1-ASP289.OD2 36.30

SER113.N-PHE150.O 36.12

ARG105.NH2-PHE181.O 36.48

THR21.N-LEU67.O 36.12

CYS160.N-GLY149.O 36.30

LEU272.N-LEU268.O 36.48

LEU67.N-THR21.O 38.29

LEU205.N-THR201.O 38.84 TYR182.N-GLY174.O 36.66

MET130.N-GLN110.O 37.02

LYS269.N-CYS265.O 37.02

CYS160.N-GLY149.O 38.48

LEU272.N-LEU268.O 39.20 ASN180.N-ASP176.OD2 37.02

CYS128.N-PHE112.O 37.39

ALA234.N-PHE230.O 37.21

ALA116.N-GLY124.O 38.84

ALA173.N-MET165.O 39.20

PHE150.N-SER113.O 36.84

VAL91.N-ASP34.O 37.39

ASN221.N-SER267.OG 37.57

SER254.N-LEU250.O 39.20

PHE150.N-SER113.O 39.38

ILE78.N-LYS90.O 37.02

ASN221.N-SER267.OG 37.57

GLN69.N-GLN19.O 37.93

ALA234.N-PHE230.O 39.38

LEU268.N-MET264.O 36.84

LEU67.N-THR21.O 37.93

LEU30.N-TYR37.O 38.48

SER158.N-ASN151.O 38.11

GLN19.N-GLN69.O 39.38

VAL18.N-GLY29.O 40.47

THR243.OG1-HSE246.ND1 41.20

ALA116.N-GLY124.O 41.92

ALA234.N-PHE230.O 38.29

GLN69.N-GLN19.O 39.38

SER254.N-LEU250.O 40.65

GLY120.N-ASN28.OD1 41.38

SER158.N-ASN151.O 42.11

SER10.OG-GLU14.OE1 38.84

PHE150.N-SER113.O 39.75

ASN180.N-ASP176.OD1 40.83

GLN19.N-GLN69.O 41.38

ASN221.N-SER267.OG 42.47

LEU272.N-LEU268.O 39.02

SER254.N-LEU250.O 40.47

GLY29.N-VAL18.O 40.83

LEU272.N-LEU268.O 41.74

MET130.N-GLN110.O 43.01

LEU30.N-TYR37.O 38.66

MET162.N-THR175.O 41.02

ASN274.N-GLU270.O 41.38

ASN180.N-ASP176.OD1 41.74

VAL91.N-ASP34.O 39.38

ALA70.N-VAL73.O 41.02

ALA116.N-GLY124.O 41.38

ALA116.N-GLY124.O 41.38

VAL18.N-GLY29.O 41.56

LEU205.N-THR201.O 42.65 MET162.N-THR175.O 41.74

ASP153.N-CYS156.O 41.56

GLN83.N-VAL86.O 42.83

GLY29.N-VAL18.O 43.92

GLY120.N-ASN28.OD1 45.19

LEU30.N-TYR37.O 43.92

PHE8.N-SER113.OG 44.65

LEU27.N-VAL20.O 44.10

LEU242.N-ASN231.OD1 45.92

TYR239.N-ALA234.O 44.83

SER147.OG-SER144.O 44.28

VAL18.N-GLY29.O 44.65

ASN274.N-GLU270.O 44.46

LEU67.N-THR21.O 46.64

THR201.OG1-GLU240.O 45.55

PHE8.N-SER113.OG 47.91

SER147.OG-SER144.O 45.74

GLY29.N-VAL18.O 44.83

ASN180.N-ASP176.OD2 44.83

SER147.OG-SER144.O 36.48

PHE159.N-LYS102.O 36.48

MET162.N-THR175.O 36.48

SER10.OG-GLU14.OE2 36.48

ALA173.N-MET165.O 36.66

LYS269.N-CYS265.O 37.02

GLN69.N-GLN19.O 37.02

SER254.N-LEU250.O 37.02

THR175.OG1-ASP176.O 37.21

TYR182.N-GLY174.O 37.21

GLN83.N-VAL86.O 37.75

ASP153.N-CYS156.O 37.75

LEU30.N-TYR37.O 37.93

ASN203.ND2-ASP289.O 38.11

CYS128.N-PHE112.O 38.48

ALA234.N-PHE230.O 38.66

THR21.N-LEU67.O 39.20

ILE200.N-ASP289.OD2 39.38

LEU268.N-MET264.O 39.56

GLN19.N-GLN69.O 40.29

SER158.N-ASN151.O 40.65

PHE150.N-SER113.O 41.02

ASN274.N-GLU270.O 41.02

LEU27.N-VAL20.O 41.20

ALA70.N-VAL73.O 41.38

ARG40.NH2-ASP187.OD1 41.74

LEU272.N-LEU268.O 41.74

LEU205.N-THR201.O 43.38

VAL91.N-ASP34.O 43.92

ARG131.NH2-ASP289.OD2 44.46

ARG40.NE-ASP187.OD2 45.01

ALA116.N-GLY124.O 45.74

(continued)

GLN83.N-VAL86.O 35.39

LYS5.NZ-GLU290.OE2 35.57

LYS269.N-CYS265.O 36.12

ALA234.N-PHE230.O 36.30

CYS38.N-LEU87.O 36.48

ASP153.N-CYS156.O 37.57

GLY146.N-HSE163.O 37.75

ALA116.N-GLY124.O 37.93

ARG4.N-GLN299.OE1 39.20

THR21.N-LEU67.O 39.38

ASN221.N-SER267.OG 39.93

THR243.OG1-HSE246.ND1 39.93

MET162.N-THR175.O 40.11

VAL18.N-GLY29.O 40.47

LEU87.N-CYS38.O 40.83

GLN19.N-GLN69.O 41.20

LEU272.N-LEU268.O 41.20

SER147.OG-SER144.O 41.56

SER158.N-ASN151.O 41.56

HSE172.N-ILE136.O 41.92

LEU27.N-VAL20.O 42.29

TYR118.N-SER121.O 42.29

LEU30.N-TYR37.O 42.29

LEU268.N-MET264.O 43.01

CYS128.N-PHE112.O 43.38

THR201.OG1-GLU240.O 43.56

PHE150.N-SER113.O 44.46

THR135.OG1-ASN133.OD1 45.19

ASN274.N-GLU270.O 45.19

GLY120.N-ASN28.OD1 45.19

LEU67.N-THR21.O 45.37

ARG40.NH2-ASP187.OD2 45.74

2.4 Concluding Remarks 145

SER158.N-ASN151.O 35.03

ASN133.ND2-GLY195.O 34.12

LYS269.N-CYS265.O 33.94

SER113.OG-GLN127.OE1 33.94

ASN203.ND2-ASP289.O 33.94

ASN28.ND2-CYS145.O 32.67

ALA255.N-GLY251.O 32.30

THR45.N-ASP48.OD1 32.30

CYS128.N-PHE112.O 32.12

ASN133.ND2-GLY195.O 34.30

TYR209.OH-ILE259.O 34.12

LYS269.N-CYS265.O 33.58

SER10.OG-GLU14.OE1 33.39

CYS265.N-VAL261.O 32.85

SER267.N-ASP263.O 32.85

THR292.OG1-ASP295.OD2 32.67

THR175.OG1-ASP176.O 31.94

PHE112.N-CYS128.O 31.22

B-chain – rep1

THR175.OG1-ASP176.O 30.13 PHE112.N-CYS128.O 30.13

TYR118.N-SER121.O 30.13 CYS128.N-PHE112.O 30.13

TYR209.OH-ILE259.O 30.67

ILE106.N-TYR182.OH 30.49

THR169.OG1-PRO168.O 30.49 ILE136.N-HSE172.O 30.31

PHE112.N-CYS128.O 31.03 LEU32.N-VAL35.O 30.49

THR175.OG1-ASP176.O 30.85

ASN133.ND2-GLY195.O 30.67

ASN214.N-ALA210.O 30.85

GLN256.N-PRO252.O 30.85

ALA255.N-GLY251.O 31.03

ARG131.N-THR135.O 31.22

LYS5.NZ-GLU288.OE1 31.22

LYS5.NZ-GLU290.OE2 31.40

ILE281.N-SER284.O 31.94

ALA266.N-LEU262.O 32.12

CYS38.N-LEU87.O 32.30

TYR209.OH-ILE259.O 33.21

LYS269.N-CYS265.O 33.21

TYR118.N-SER121.O 34.30

SER267.N-ASP263.O 34.30

PHE159.N-LYS102.O 34.48

LYS5.NZ-GLU290.OE1 34.66

TYR182.N-GLY174.O 34.85

THR243.OG1-HSE246.ND1 35.03

CYS160.N-GLY149.O 35.39

ALA173.N-MET165.O 35.39

SER62.OG-LEU58.O 35.57

ASN203.ND2-ASP289.O 35.75

SER113.N-PHE150.O 30.67

ARG105.NH1-ASP176.OD2 31.40

ALA173.N-MET165.O 31.58

THR45.OG1-ASP48.OD2 32.12

PHE159.N-LYS102.O 32.12

GLN256.N-PRO252.O 32.30

SER158.N-ASN151.O 32.30

THR21.OG1-THR25.O 32.67

ILE281.N-SER284.O 32.85

CYS265.N-VAL261.O 33.21

THR169.OG1-PRO168.O 33.58

THR45.OG1-ASP48.OD1 33.58

THR135.OG1-ASN133.OD1 33.94

ILE200.N-ASP289.OD2 33.94

TYR209.OH-ILE259.O 31.22

THR45.OG1-ASP48.OD1 35.21

THR243.OG1-HSE246.ND1 34.85

ILE136.N-HSE172.O 33.94

PHE112.N-CYS128.O 31.03

LEU268.N-MET264.O 35.75

ALA70.N-VAL73.O 35.57

ALA255.N-GLY251.O 34.85

ALA266.N-LEU262.O 31.03

ASN221.N-SER267.OG 35.93

SER113.N-PHE150.O 35.75

THR243.OG1-HSE246.ND1 35.03

ASN203.ND2-GLY109.O 30.67

THR135.OG1-ASN133.OD1 36.30

ALA266.N-LEU262.O 35.75

LEU27.N-VAL20.O 35.21

GLN256.N-PRO252.O 30.49

CYS265.N-VAL261.O 36.48

PHE159.N-LYS102.O 36.12

ASN203.ND2-ASP289.O 35.39

GLN256.N-PRO252.O 31.40

ARG131.N-THR135.O 36.66

ALA255.N-GLY251.O 36.12

THR175.OG1-ASP176.O 35.39

ALA266.N-LEU262.O 35.75

TYR118.N-SER121.O 31.40

ALA173.N-MET165.O 36.84

ALA234.N-PHE230.O 36.30

A-chain – rep3 CYS38.N-LEU87.O 35.93

ASN203.ND2-ASP289.O 31.03

TYR182.N-GLY174.O 37.21

ILE281.N-SER284.O 30.67

A-chain – rep2

GLN69.N-GLN19.O 37.21

A-chain – rep1

ARG131.N-THR135.O 36.66

CYS160.N-GLY149.O 36.48

Table 2.53 (continued) B-chain – rep2

ARG131.NH1-ASP289.OD1 30.49

SER113.N-PHE150.O 30.49

CYS265.N-VAL261.O 30.49

THR169.OG1-PRO168.O 30.67

LYS5.NZ-GLU290.OE2 30.67

THR175.N-MET162.O 30.85

TYR118.N-SER121.O 31.03

PHE112.N-CYS128.O 31.22

ASN180.N-ASP176.OD2 31.40

ILE136.N-HSE172.O 31.40

TYR209.OH-ILE259.O 31.58

THR135.OG1-ASN133.OD1 31.94

ALA266.N-LEU262.O 32.30

LYS5.NZ-GLU290.OE1 32.30

MET130.N-GLN110.O 32.85

ALA255.N-GLY251.O 32.85

ASN221.N-SER267.OG 33.03

CYS160.N-GLY149.O 33.39

ARG131.N-THR135.O 33.94

VAL18.N-GLY29.O 34.48

ASN180.N-ASP176.OD1 34.66

ASN133.ND2-GLY195.O 35.03

THR243.OG1-HSE246.ND1 35.93

B-chain – rep3

CYS265.N-VAL261.O 30.13

GLN256.N-PRO252.O 30.31

THR292.OG1-ASP295.OD1 30.67

ASN214.N-ALA210.O 30.67

LYS5.NZ-GLU288.OE2 31.03

MET130.N-GLN110.O 31.22

ARG131.NH2-ASP289.OD2 31.76

ALA266.N-LEU262.O 32.12

THR175.N-MET162.O 32.49

ASN203.ND2-ASP289.O 32.49

CYS160.N-GLY149.O 32.67

ALA255.N-GLY251.O 32.67

ALA70.N-VAL73.O 32.85

GLN69.N-GLN19.O 32.85

SER139.N-TYR126.OH 33.21

LYS5.NZ-GLU290.OE1 33.76

SER254.N-LEU250.O 33.94

ILE281.N-SER284.O 34.48

ALA173.N-MET165.O 34.48

TYR209.OH-ILE259.O 34.85

PHE112.N-CYS128.O 34.85

PHE159.N-LYS102.O 35.39

ASN180.N-ASP176.OD1 35.39

146 2 3C-Like Protease (3CLpro)

TYR182.OH-CYS160.O 58.80

SER147.OG-SER144.O 52.81

GLY149.N-TYR161.O 53.54 ARG105.NH2-PHE181.O 53.54 SER123.N-ALA116.O 53.54

THR201.OG1-GLU240.O 55.35

VAL20.N-LEU27.O 55.17

GLY146.N-HSE163.O 54.45

LEU115.N-VAL148.O 52.45

TYR239.N-ALA234.O 52.09

THR257.OG1-LEU253.O 52.99

THR201.OG1-GLU240.O 52.27

ARG40.NE-ASP187.OD1 51.54

GLY146.N-HSE163.O 51.00

GLY109.N-MET130.O 51.00

ASN274.N-GLU270.O 45.92

MET162.N-THR175.O 45.55

LEU67.N-THR21.O 45.19

ASN274.N-GLU270.O 44.65

LEU87.N-CYS38.O 48.64

ILE136.N-HSE172.O 46.64

LEU87.N-CYS38.O 47.55

VAL173.N-MET165.O 47.37

GLY29.N-VAL18.O 47.37

GLN83.N-VAL86.O 46.10

LEU242.N-ASN231.OD1 45.74

SER147.OG-SER144.O 45.19

SER10.OG-GLU14.OE2 49.18 ARG131.NH1-ASP289.OD1 49.00

LYS90.N-GLY79.O 47.19 LEU205.N-THR201.O 47.01

LYS88.N-SER81.O 48.82

ILE78.N-LYS90.O 48.64

MET162.N-THR175.O 46.28

GLY120.N-ASN28.OD1 46.10

LEU67.N-THR21.O 47.55

PHE8.N-SER113.OG 45.55

GLY120.N-ASN28.OD1 46.64

MET162.N-THR175.O 47.91

LEU242.N-ASN231.OD1 45.55 THR175.OG1-ASP176.O 45.37

LYS90.N-GLY79.O 48.46

LEU75.N-VAL68.O 46.46

LYS88.N-SER81.O 49.55 VAL157.N-LYS100.O 49.18

THR201.OG1-GLU240.O 49.18 LEU67.N-THR21.O 48.28

LYS90.N-GLY79.O 49.73

ASN231.N-LEU227.O 49.55

ASN231.N-LEU227.O 48.09

LEU75.N-VAL68.O 46.46

THR257.OG1-LEU253.O 51.36 THR201.OG1-GLU240.O 49.91

GLY146.N-HSE163.O 49.36

GLY109.N-MET130.O 50.09

HSE172.N-ILE136.O 49.91

TYR239.N-ALA234.O 49.00

ASN231.N-LEU227.O 49.55

LEU75.N-VAL68.O 51.72

MET162.N-THR175.O 49.91 TYR239.N-ALA234.O 51.54

SER144.OG-LEU141.O 51.72

VAL157.N-LYS100.O 52.45 TYR239.N-ALA234.O 49.91

VAL20.N-LEU27.O 52.45

LEU87.N-CYS38.O 52.63

LEU115.N-VAL148.O 53.90

TYR182.OH-CYS160.O 56.62

HSE172.N-ILE136.O 48.82

SER123.N-ALA116.O 51.00

HSE172.N-ILE136.O 52.81

ASN95.N-ASP33.O 54.45

ARG105.NH2-PHE181.O 55.35

LYS90.N-GLY79.O 53.18

SER147.OG-SER144.O 50.27

ILE78.N-LYS90.O 53.72

LYS88.N-SER81.O 54.81

THR257.OG1-LEU253.O 55.72

ARG105.NH2-PHE181.O 54.08

LYS88.N-SER81.O 49.91

ARG105.NH2-PHE181.O 55.17

ILE78.N-LYS90.O 54.99

ASN95.N-ASP33.O 56.26

ILE78.N-LYS90.O 49.18

LEU89.N-VAL36.O 56.62

GLY109.N-MET130.O 55.72

GLY149.N-TYR161.O 57.17

ARG40.NH2-ASP187.OD2 54.63

LEU167.N-VAL171.O 56.81

LEU115.N-VAL148.O 55.17

GLY146.N-HSE163.O 58.80

LEU115.N-VAL148.O 56.26 THR257.OG1-LEU253.O 56.08

LEU89.N-VAL36.O 59.17

TYR37.N-LEU30.O 58.44

TYR37.N-LEU30.O 57.35

ASN95.N-ASP33.O 59.17

VAL20.N-LEU27.O 56.44

SER254.OG-ILE259.O 59.35

SER123.N-ALA116.O 55.17

GLY149.N-TYR161.O 59.53

SER254.OG-ILE259.O 56.62

SER254.OG-ILE259.O 59.89

SER267.OG-ASP263.O 59.89

ASN95.N-ASP33.O 60.25

SER267.OG-ASP263.O 57.35

VAL157.N-LYS100.O 60.25

LEU89.N-VAL36.O 60.80

VAL114.N-TYR126.O 66.06 TYR37.N-LEU30.O 64.97 SER267.OG-ASP263.O 60.62

LEU89.N-VAL36.O 61.52 TYR37.N-LEU30.O 58.80 HSE172.N-ILE136.O 58.08

ARG131.NH2-ASP289.OD2 64.61

LEU167.N-VAL171.O 62.25

VAL20.N-LEU27.O 61.34

TYR182.OH-CYS160.O 60.80

ARG131.NH2-ASP289.OD2 67.88 ARG40.NH2-ASP187.OD1 66.79

LEU167.N-VAL171.O 64.61 TYR182.OH-CYS160.O 64.07

ARG40.NH2-ASP187.OD1 70.05

VAL36.N-LEU89.O 67.88

SER254.OG-ILE259.O 63.34

SER267.OG-ASP263.O 63.16

LEU167.N-VAL171.O 61.16

HSE163.N-SER147.O 72.60 VAL36.N-LEU89.O 70.42

VAL36.N-LEU89.O 68.42 VAL114.N-TYR126.O 65.88

HSE163.N-SER147.O 71.32

VAL114.N-TYR126.O 71.14

VAL36.N-LEU89.O 70.05

VAL114.N-TYR126.O 65.52

GLY149.N-TYR161.O 60.98

TRP31.N-CYS16.O 73.32

TRP31.N-CYS16.O 71.32

B-chain – rep1

TRP31.N-CYS16.O 74.05

TRP31.N-CYS16.O 74.05

A-chain – rep3 ARG40.NE-ASP187.OD2 78.77

ARG40.NE-ASP187.OD2 77.50

HSE163.N-SER147.O 74.77 HSE163.N-SER147.O 75.50

A-chain – rep2

A-chain – rep1

ARG131.NH1-ASP289.OD1 46.46

SER147.OG-SER144.O 47.73

THR201.OG1-GLU240.O 47.91

LEU67.N-THR21.O 48.28

GLY29.N-VAL18.O 48.64

TYR239.N-ALA234.O 48.82

ILE78.N-LYS90.O 49.36

LYS90.N-GLY79.O 49.91

ASN231.N-LEU227.O 49.91

THR257.OG1-LEU253.O 49.91

VAL157.N-LYS100.O 51.18

GLY146.N-HSE163.O 51.91

LEU87.N-CYS38.O 51.91

GLY109.N-MET130.O 51.91

HSE172.N-ILE136.O 52.27

LEU115.N-VAL148.O 53.72

ARG105.NH2-PHE181.O 54.08

LYS88.N-SER81.O 54.45

SER267.OG-ASP263.O 54.81

ASN95.N-ASP33.O 55.17

SER123.N-ALA116.O 55.54

SER10.OG-GLU14.OE2 56.99

SER254.OG-ILE259.O 56.99

LEU167.N-VAL171.O 58.44

ARG131.NH2-ASP289.OD2 58.62

ARG40.NH2-ASP187.OD1 58.80

LEU89.N-VAL36.O 60.07

TYR37.N-LEU30.O 61.71

VAL20.N-LEU27.O 62.43

TYR182.OH-CYS160.O 62.98

GLY149.N-TYR161.O 63.34

VAL114.N-TYR126.O 67.70

VAL36.N-LEU89.O 69.87

HSE163.N-SER147.O 70.42

TRP31.N-CYS16.O 74.59

ARG40.NE-ASP187.OD2 77.50

B-chain – rep2

(continued)

LEU205.N-THR201.O 45.55

LEU75.N-VAL68.O 45.74

THR45.N-ASP48.OD1 45.92

THR201.OG1-GLU240.O 46.10

ASN231.N-LEU227.O 46.46

VAL157.N-LYS100.O 48.09

ILE78.N-LYS90.O 48.46

THR257.OG1-LEU253.O 49.18

GLY120.N-ASN28.OD1 50.45

TYR239.N-ALA234.O 50.64

LYS90.N-GLY79.O 51.91

GLN83.N-VAL86.O 52.09

GLY146.N-HSE163.O 52.09

THR21.N-LEU67.O 52.45

LEU115.N-VAL148.O 52.81

SER147.OG-SER144.O 53.72

SER254.OG-ILE259.O 55.17

ASN95.N-ASP33.O 55.35

LYS88.N-SER81.O 56.08

HSE172.N-ILE136.O 56.99

SER267.OG-ASP263.O 58.08

TYR37.N-LEU30.O 58.08

GLY109.N-MET130.O 58.62

GLY149.N-TYR161.O 58.80

SER123.N-ALA116.O 59.17

VAL20.N-LEU27.O 62.07

LEU167.N-VAL171.O 62.61

LEU89.N-VAL36.O 63.34

TYR182.OH-CYS160.O 64.61

ARG40.NE-ASP187.OD1 65.15

VAL114.N-TYR126.O 67.70

THR45.OG1-ASP48.OD1 68.24

VAL36.N-LEU89.O 68.78

ARG40.NH2-ASP187.OD2 72.41

HSE163.N-SER147.O 74.59

TRP31.N-CYS16.O 75.68

B-chain – rep3

Table 2.54 MD-HBs (with occupancy rates ≥30%) of the Mpro-delP168-and-a173v-7bb2 model from the 550 ns MD trajectories (amarolab.ucsd.edu/covid19.php)

2.4 Concluding Remarks 147

B-chain – rep1

GLY109.N-MET130.O 41.38

ARG131.NH2-ASP289.OD2 40.11

SER158.N-ASN151.O 37.57

LEU272.N-LEU268.O 37.57

LEU272.N-LEU268.O 37.21

LEU27.N-VAL20.O 37.21

ALA70.N-VAL73.O 35.75

LYS269.N-CYS265.O 35.39

CYS117.N-SER147.OG 35.03

ALA234.N-PHE230.O 36.48

CYS160.N-GLY149.O 36.48

ILE136.N-HSE172.O 36.12

THR292.OG1-ASP295.OD2 34.66 PHE159.N-LYS102.O 34.48

ALA255.N-GLY251.O 34.66

THR199.N-ASN238.O 35.57

ALA116.N-GLY124.O 35.57

ASN221.N-SER267.OG 35.57

THR21.N-LEU67.O 35.57

PHE159.N-LYS102.O 35.75

SER123.N-ALA116.O 38.48

LEU30.N-TYR37.O 36.12 SER158.N-ASN151.O 35.93 SER254.N-LEU250.O 35.57

ALA266.N-LEU262.O 37.02

SER10.OG-GLU14.OE2 36.84

HSD80.ND1-ASN63.OD1 36.12

SER158.N-ASN151.O 37.02

THR135.OG1-ASN133.OD1 38.84

SER158.N-ASN151.O 38.84

VAL18.N-GLY29.O 39.02

LEU272.N-LEU268.O 39.20

LEU27.N-VAL20.O 39.38

GLN83.N-VAL86.O 39.56

ARG105.NH1-ASP176.OD2 39.93

THR243.OG1-HSE246.ND1 40.11

ASN274.N-GLU270.O 40.11

LEU205.N-THR201.O 40.47

ALA234.N-PHE230.O 40.47

PHE150.N-SER113.O 40.47

VAL91.N-ASP34.O 40.65

THR175.OG1-ASP176.O 41.02

CYS160.N-GLY149.O 41.38

ILE200.N-ASP289.OD2 41.92

CYS128.N-PHE112.O 36.84

CYS160.N-GLY149.O 36.84

ALA70.N-VAL73.O 37.02

LYS269.N-CYS265.O 37.02

THR243.OG1-HSE246.ND1 37.75

LEU268.N-MET264.O 38.11

LEU27.N-VAL20.O 38.48

MET130.N-GLN110.O 38.66

ALA116.N-GLY124.O 38.66

ASN203.ND2-ASP289.O 38.84

ALA234.N-PHE230.O 39.02

PHE150.N-SER113.O 39.20

VAL173.N-MET165.O 39.38

ASN274.N-GLU270.O 39.75

ILE281.N-SER284.O 39.93

VAL91.N-ASP34.O 40.65

ASN180.N-ASP176.OD2 36.48

VAL173.N-MET165.O 37.02

THR21.N-LEU67.O 38.84

ALA234.N-PHE230.O 38.29

ALA116.N-GLY124.O 37.93

CYS128.N-PHE112.O 37.75

THR135.OG1-ASN133.OD1 39.02

VAL18.N-GLY29.O 38.84

SER301.OG-VAL297.O 38.66

MET130.N-GLN110.O 38.29

MET130.N-GLN110.O 39.56

TYR54.OH-ASP187.OD2 39.38

ASN203.ND2-ASP289.O 38.84

SER113.N-PHE150.O 38.66

GLN19.N-GLN69.O 40.11

SER144.OG-LEU141.O 39.75

SER254.N-LEU250.O 39.93

LEU87.N-CYS38.O 39.56

LEU268.N-MET264.O 41.02

GLY120.N-ASN28.OD1 40.29

ALA70.N-VAL73.O 40.29

THR21.N-LEU67.O 39.93

ILE136.N-HSE172.O 41.74

LEU75.N-VAL68.O 41.20

PHE150.N-SER113.O 41.38

VAL18.N-GLY29.O 40.29

ILE200.N-ASP289.OD2 42.29

PHE8.N-SER113.OG 42.11

SER144.OG-LEU141.O 41.56

THR175.OG1-ASP176.O 41.38

ALA70.N-VAL73.O 41.74

GLN83.N-VAL86.O 40.29

LEU205.N-THR201.O 42.65

SER254.N-LEU250.O 42.47

ARG131.NH2-ASP289.OD1 41.74

LEU268.N-MET264.O 43.01 GLN19.N-GLN69.O 42.29

PHE8.N-SER113.OG 41.56

VAL18.N-GLY29.O 41.92 LYS5.NZ-GLU290.OE1 41.92

THR175.OG1-ASP176.O 42.83

LEU67.N-THR21.O 42.65

ASN221.N-SER267.OG 42.83

GLN19.N-GLN69.O 42.47

LEU242.N-ASN231.OD1 43.74

PHE8.N-SER113.OG 43.74

LEU272.N-LEU268.O 42.29

GLY29.N-VAL18.O 42.29

ALA116.N-GLY124.O 43.92

LYS5.NZ-GLU290.OE2 43.01

LEU205.N-THR201.O 43.19

SER10.OG-GLU14.OE2 43.01

ILE136.N-HSE172.O 44.65 ASN231.N-LEU227.O 44.46 GLY29.N-VAL18.O 44.10

GLN19.N-GLN69.O 43.01 SER144.OG-LEU141.O 42.65 GLY120.N-ASN28.OD1 42.65

VAL91.N-ASP34.O 45.19

ARG131.NH1-ASP289.OD1 44.10

GLN69.N-GLN19.O 43.92

ASN180.N-ASP176.OD1 44.83

GLY29.N-VAL18.O 44.28

LEU268.N-MET264.O 44.46

A-chain – rep3 SER147.OG-SER144.O 43.38

VAL157.N-LYS100.O 43.56

A-chain – rep2

LEU242.N-ASN231.OD1 45.37

A-chain – rep1

VAL91.N-ASP34.O 44.65

Table 2.54 (continued) B-chain – rep2

ALA116.N-GLY124.O 36.66

SER254.N-LEU250.O 37.21

THR21.N-LEU67.O 37.21

CYS128.N-PHE112.O 37.39

ASN274.N-GLU270.O 37.39

ASN221.N-SER267.OG 37.57

CYS160.N-GLY149.O 37.75

GLN83.N-VAL86.O 37.93

LEU268.N-MET264.O 38.11

SER158.N-ASN151.O 38.29

LEU27.N-VAL20.O 38.48

LYS269.N-CYS265.O 38.66

ALA234.N-PHE230.O 38.84

LEU205.N-THR201.O 38.84

GLN69.N-GLN19.O 39.20

ALA70.N-VAL73.O 39.20

VAL91.N-ASP34.O 39.38

ASP153.N-CYS156.O 39.38

ASN203.ND2-ASP289.O 39.56

LEU272.N-LEU268.O 39.75

GLN19.N-GLN69.O 39.75

THR243.OG1-HSE246.ND1 40.11

VAL18.N-GLY29.O 40.47

GLY120.N-ASN28.OD1 41.38

PHE150.N-SER113.O 42.11

THR135.OG1-ASN133.OD1 42.11

MET162.N-THR175.O 42.29

VAL173.N-MET165.O 43.92

SER144.OG-LEU141.O 44.46

PHE8.N-SER113.OG 44.65

LEU75.N-VAL68.O 44.83

LEU242.N-ASN231.OD1 44.83

B-chain – rep3

CYS128.N-PHE112.O 34.85

LEU27.N-VAL20.O 35.39

ASN180.N-ASP176.OD2 35.75

LEU272.N-LEU268.O 35.75

SER158.N-ASN151.O 35.75

ASN221.N-SER267.OG 35.93

LYS61.NZ-ASP48.OD1 36.48

SER254.N-LEU250.O 36.48

GLN69.N-GLN19.O 36.48

THR243.OG1-HSE246.ND1 36.66

LYS269.N-CYS265.O 36.66

ASP153.N-CYS156.O 37.02

LEU268.N-MET264.O 37.75

CYS160.N-GLY149.O 37.75

MET162.N-THR175.O 38.11

TYR118.N-SER121.O 38.11

LEU67.N-THR21.O 38.29

LEU30.N-TYR37.O 38.84

VAL18.N-GLY29.O 39.02

ALA70.N-VAL73.O 39.20

PHE150.N-SER113.O 39.38

ASN274.N-GLU270.O 40.65

GLN19.N-GLN69.O 40.65

ARG105.NH2-PHE181.O 41.20

ALA116.N-GLY124.O 41.38

LEU242.N-ASN231.OD1 42.47

ALA234.N-PHE230.O 43.01

GLY29.N-VAL18.O 43.38

SER144.OG-LEU141.O 43.38

SER10.OG-GLU14.OE2 43.74

PHE8.N-SER113.OG 44.10

VAL91.N-ASP34.O 45.19

148 2 3C-Like Protease (3CLpro)

LYS269.N-CYS265.O 32.85 THR111.OG1-ASP295.OD2 32.85

GLN69.N-GLN19.O 32.85 THR135.OG1-ASN133.OD1 32.85 ALA266.N-LEU262.O 31.76 ASN180.N-ASP176.OD2 31.58 ILE200.N-ASP289.OD2 31.22 CYS265.N-VAL261.O 30.85

ASN180.N-ASP176.OD1 34.85

PHE159.N-LYS102.O 34.48

ASN203.ND2-ASP289.O 34.48

LEU27.N-VAL20.O 34.30

SER113.N-PHE150.O 34.30

THR243.OG1-HSE246.ND1 34.30

THR199.N-ASN238.O 34.12

SER113.OG-GLN127.OE1 34.12

CYS128.N-PHE112.O 33.76

ALA255.N-GLY251.O 33.39

THR21.OG1-THR25.O 33.03

ARG298.N-PHE294.O 34.85

PHE159.N-LYS102.O 34.48

ARG105.NH1-ASP176.OD1 34.30

ALA255.N-GLY251.O 33.58

GLN299.N-ASP295.O 33.39

LYS269.N-CYS265.O 33.21

ALA266.N-LEU262.O 33.03

CYS38.N-LEU87.O 32.85

GLN69.N-GLN19.O 32.85

GLN256.N-PRO252.O 30.13

ASN221.N-SER267.OG 30.31

SER62.N-ASN65.OD1 30.31

LYS5.NZ-GLU288.OE1 30.31

LYS5.NZ-GLU290.OE1 30.13

ASN180.N-ASP176.OD1 30.13

GLN83.N-VAL86.O 30.85

PHE112.N-CYS128.O 30.67

CYS117.N-SER147.OG 30.67

ASN203.ND2-GLY109.O 30.13

ASN203.ND2-ASP289.O 30.49

TYR209.OH-ILE259.O 32.12

SER81.N-LYS88.O 31.03

LEU57.N-ASN53.O 31.40

TYR209.OH-ILE259.O 31.03

ALA255.N-GLY251.O 32.12

THR292.N-ASP295.OD2 30.31

VAL173.N-MET165.O 30.85 TYR209.OH-ILE259.O 30.49

ASN221.N-SER267.OG 30.85

ILE281.N-SER284.O 32.67

CYS265.N-VAL261.O 32.67

LEU30.N-TYR37.O 32.30

TYR118.N-SER121.O 32.30

ASN133.ND2-GLY195.O 32.12

GLN69.N-GLN19.O 32.12

CYS265.N-VAL261.O 32.49

PHE112.N-CYS128.O 32.49

ARG298.NH2-ASP295.OD1 33.03

CYS128.N-PHE112.O 33.03

THR292.OG1-ASP295.OD2 34.30

ILE281.N-SER284.O 34.30

SER254.N-LEU250.O 34.66

LEU30.N-TYR37.O 34.85

CYS265.N-VAL261.O 31.94

TYR118.N-SER121.O 33.03

PHE112.N-CYS128.O 33.21

TYR209.OH-ILE259.O 33.39

CYS38.N-LEU87.O 33.39

SER10.OG-GLU14.OE1 33.58

THR21.N-LEU67.O 33.76

ALA266.N-LEU262.O 34.85

THR292.OG1-ASP295.OD1 35.03

MET130.N-GLN110.O 35.21

THR135.OG1-ASN133.OD1 35.03

SER113.N-PHE150.O 33.94

CYS160.N-GLY149.O 35.03

ILE200.N-ASP289.OD1 35.39

SER10.OG-GLU14.OE2 34.12

PHE150.N-SER113.O 35.03

THR243.OG1-HSE246.ND1 35.75

ARG105.NH1-ASP176.OD2 30.31

ASN180.N-ASP176.OD1 30.67

CYS38.N-LEU87.O 31.03

PHE159.N-LYS102.O 31.40

PHE112.N-CYS128.O 31.58

LYS5.NZ-GLU290.OE1 31.76

ALA255.N-GLY251.O 31.76

ASN180.N-ASP176.OD2 32.12

VAL104.N-PHE159.O 32.30

TYR209.OH-ILE259.O 32.49

ASN133.ND2-GLY195.O 32.85

GLN256.N-PRO252.O 33.21

THR21.OG1-THR25.O 33.76

CYS265.N-VAL261.O 33.94

LEU30.N-TYR37.O 34.12

MET130.N-GLN110.O 34.30

THR292.OG1-ASP295.OD2 34.66

THR175.OG1-ASP176.O 35.93

ILE200.N-ASP289.OD2 36.66

VAL173.N-MET165.O 30.31

THR292.OG1-ASP295.OD1 30.31

TYR126.N-VAL114.O 30.31

LYS5.NZ-GLU290.OE1 30.49

LEU87.N-CYS38.O 31.22

ALA266.N-LEU262.O 31.40

THR175.OG1-ASP176.O 31.40

ALA255.N-GLY251.O 31.40

CYS38.N-LEU87.O 32.12

LEU208.N-VAL204.O 32.30

ASN203.ND2-ASP289.O 32.67

ILE136.N-HSE172.O 32.85

ILE281.N-SER284.O 33.21

LYS5.NZ-GLU290.OE2 33.39

PHE112.N-CYS128.O 33.76

THR135.OG1-ASN133.OD1 34.12

CYS265.N-VAL261.O 34.66

2.4 Concluding Remarks 149

ARG131.NH2-ASP289.OD2 64.79

LEU167.N-VAL171.O 62.61

SER267.OG-ASP263.O 64.97

TYR182.OH-CYS160.O 62.79

LEU167.N-VAL171.O 61.71

ASN95.N-ASP33.O 60.25

GLY146.N-HSE163.O 59.89

GLY109.N-MET130.O 59.35

TYR37.N-LEU30.O 58.62

GLY149.N-TYR161.O 58.44

VAL20.N-LEU27.O 57.53

LEU89.N-VAL36.O 57.17

LEU115.N-VAL148.O 56.99

SER123.N-ALA116.O 56.26

THR21.N-LEU67.O 55.35

SER254.OG-ILE259.O 54.26

ARG105.NH2-PHE181.O 53.72

TYR37.N-LEU30.O 62.98

VAL36.N-LEU89.O 62.43

TYR182.OH-CYS160.O 62.25

ASN95.N-ASP33.O 61.16

GLY149.N-TYR161.O 59.53

LEU89.N-VAL36.O 59.17

VAL20.N-LEU27.O 59.17

THR257.OG1-LEU253.O 59.17

ARG105.NH2-PHE181.O 58.26

SER254.OG-ILE259.O 58.26

SER147.OG-SER144.O 57.89

GLY146.N-HSE163.O 57.71

SER267.OG-ASP263.O 56.08

LEU87.N-CYS38.O 56.08

ARG131.NH2-ASP289.OD2 55.72

LYS88.N-SER81.O 54.45

LEU75.N-VAL68.O 52.27

VAL157.N-LYS100.O 51.54

TYR239.N-ALA234.O 51.36

VAL91.N-ASP34.O 50.82

GLY120.N-ASN28.OD1 49.00

ARG131.NH2-ASP289.OD2 49.00

ILE78.N-LYS90.O 48.82

GLN83.N-VAL86.O 47.73

LEU242.N-ASN231.OD1 47.19

SER147.OG-SER144.O 45.92

HSE172.N-ILE136.O 45.92

ALA116.N-GLY124.O 45.37

ASN231.N-LEU227.O 45.19

GLY29.N-VAL18.O 45.01

PHE8.N-SER113.OG 44.46

LEU115.N-VAL148.O 52.45

SER10.OG-GLU14.OE2 50.45

LYS90.N-GLY79.O 50.27

LEU75.N-VAL68.O 49.91

GLY109.N-MET130.O 49.55

ASN231.N-LEU227.O 49.55

THR21.N-LEU67.O 48.09

VAL157.N-LYS100.O 48.09

THR201.OG1-GLU240.O 47.55

TYR239.N-ALA234.O 46.64

GLY120.N-ASN28.OD1 46.64

GLY29.N-VAL18.O 46.28

ALA173.N-MET165.O 46.28

THR175.OG1-ASP176.O 46.28

TYR118.N-SER121.O 45.92

LEU242.N-ASN231.OD1 45.37

PHE8.N-SER113.OG 46.64

VAL18.N-GLY29.O 45.37

THR175.OG1-ASP176.O 45.74

ARG40.NE-ASP187.OD1 46.82 CYS160.N-GLY149.O 45.92

SER144.OG-LEU141.O 45.74

LEU67.N-THR21.O 46.10

VAL91.N-ASP34.O 47.01 TYR239.N-ALA234.O 47.01

PHE8.N-SER113.OG 46.46

ARG105.NH1-ASP176.OD1 47.01

LEU75.N-VAL68.O 46.64

THR201.OG1-GLU240.O 47.55

ASN231.N-LEU227.O 46.64

GLY29.N-VAL18.O 46.82

THR175.OG1-ASP176.O 47.73 THR21.N-LEU67.O 47.55

TYR239.N-ALA234.O 47.37

ILE78.N-LYS90.O 48.09

LYS90.N-GLY79.O 50.09 LEU75.N-VAL68.O 49.73

GLY109.N-MET130.O 49.73

ASN180.N-ASP176.OD2 50.09

SER147.OG-SER144.O 50.27

VAL157.N-LYS100.O 51.36

THR257.OG1-LEU253.O 51.91

LYS88.N-SER81.O 52.27

SER123.N-ALA116.O 53.54 LEU115.N-VAL148.O 50.64

SER123.N-ALA116.O 52.27

ARG105.NH2-PHE181.O 53.36

THR257.OG1-LEU253.O 52.45

ARG40.NH2-ASP187.OD2 53.54

LYS88.N-SER81.O 50.64

HSE172.N-ILE136.O 52.81

ARG60.NH2-ASP48.OD1 53.54

LYS90.N-GLY79.O 52.63

VAL157.N-LYS100.O 50.82

THR257.OG1-LEU253.O 53.36

ASN231.N-LEU227.O 53.90

LYS88.N-SER81.O 51.18

ARG105.NH2-PHE181.O 53.90

THR45.N-ASP48.OD2 54.63

GLY109.N-MET130.O 51.72

LEU89.N-VAL36.O 54.99

LEU89.N-VAL36.O 54.99

LYS90.N-GLY79.O 54.99

VAL20.N-LEU27.O 55.90

SER10.OG-GLU14.OE2 57.53

SER254.OG-ILE259.O 58.26 GLY149.N-TYR161.O 56.08

GLY146.N-HSE163.O 57.71

LEU115.N-VAL148.O 58.08

ASN95.N-ASP33.O 59.17

TYR37.N-LEU30.O 60.25

THR45.OG1-ASP48.OD2 59.53 GLY146.N-HSE163.O 59.17

VAL20.N-LEU27.O 61.71

SER147.OG-SER144.O 60.44 SER123.N-ALA116.O 59.35

SER254.OG-ILE259.O 63.16

GLY149.N-TYR161.O 61.16

LEU167.N-VAL171.O 63.88

TYR182.OH-CYS160.O 65.15

TYR182.OH-CYS160.O 64.97

TRP31.N-CYS16.O 71.51

TYR54.OH-ASP187.OD1 63.16

ASN95.N-ASP33.O 61.34

VAL36.N-LEU89.O 68.24

VAL36.N-LEU89.O 66.24

ARG40.NH2-ASP187.OD1 71.51

LEU167.N-VAL171.O 63.88

SER267.OG-ASP263.O 64.43

ARG40.NH2-ASP187.OD2 68.78

HSE163.N-SER147.O 66.61

VAL114.N-TYR126.O 71.69

VAL114.N-TYR126.O 67.15

TYR37.N-LEU30.O 61.52

HSE163.N-SER147.O 70.96

SER267.OG-ASP263.O 67.15

HSE163.N-SER147.O 71.87

TRP31.N-CYS16.O 71.32

VAL114.N-TYR126.O 64.79

TRP31.N-CYS16.O 72.60

VAL114.N-TYR126.O 72.60

VAL36.N-LEU89.O 72.05

HSE163.N-SER147.O 72.96

SER10.OG-GLU14.OE2 62.07

ARG40.NE-ASP187.OD1 81.67

TRP31.N-CYS16.O 73.87

ARG40.NE-ASP187.OD2 74.77

ARG40.NE-ASP187.OD1 77.13

B-chain – rep1

A-chain – rep3

A-chain – rep2

A-chain – rep1

LEU242.N-ASN231.OD1 45.01

PHE8.N-SER113.OG 45.01

ARG131.NH1-ASP289.OD1 45.19

VAL91.N-ASP34.O 45.37

THR257.OG1-LEU253.O 47.01

LEU67.N-THR21.O 47.19

LYS88.N-SER81.O 47.55

SER147.OG-SER144.O 47.91

ARG40.NH2-ASP187.OD1 47.91

ASN180.N-ASP176.OD1 48.82

ASN231.N-LEU227.O 49.55

TYR239.N-ALA234.O 50.82

THR201.OG1-GLU240.O 51.00

ILE78.N-LYS90.O 51.72

LEU75.N-VAL68.O 52.27

SER123.N-ALA116.O 52.81

LYS90.N-GLY79.O 53.18

LEU115.N-VAL148.O 53.36

HSE172.N-ILE136.O 53.72

VAL157.N-LYS100.O 54.26

SER254.OG-ILE259.O 54.45

GLY109.N-MET130.O 54.45

LEU89.N-VAL36.O 55.54

TYR37.N-LEU30.O 56.99

ARG105.NH2-PHE181.O 57.53

ARG40.NE-ASP187.OD2 57.71

GLY146.N-HSE163.O 58.98

VAL20.N-LEU27.O 59.35

SER267.OG-ASP263.O 59.35

TYR182.OH-CYS160.O 59.89

ASN95.N-ASP33.O 60.25

ARG131.NH2-ASP289.OD2 62.25

SER10.OG-GLU14.OE2 63.70

LEU167.N-VAL171.O 66.97

GLY149.N-TYR161.O 67.15

VAL36.N-LEU89.O 67.70

VAL114.N-TYR126.O 68.78

HSE163.N-SER147.O 73.87

TRP31.N-CYS16.O 74.05

B-chain – rep2

ILE136.N-HSE172.O 43.74

ARG40.NE-ASP187.OD2 43.92

ARG40.NH2-ASP187.OD1 44.83

GLY109.N-MET130.O 45.19

LEU242.N-ASN231.OD1 45.37

THR175.OG1-ASP176.O 45.37

HSE172.N-ILE136.O 45.92

PHE150.N-SER113.O 45.92

GLY120.N-ASN28.OD1 46.82

LEU75.N-VAL68.O 46.82

TYR239.N-ALA234.O 47.37

THR21.N-LEU67.O 48.09

ILE78.N-LYS90.O 49.18

THR201.OG1-GLU240.O 49.18

LYS90.N-GLY79.O 49.36

ASN231.N-LEU227.O 49.55

ARG131.NH2-ASP289.OD1 49.91

THR257.OG1-LEU253.O 50.45

PHE8.N-SER113.OG 50.82

VAL157.N-LYS100.O 51.54

LYS88.N-SER81.O 52.63

ARG105.NH2-PHE181.O 53.36

ASN95.N-ASP33.O 55.17

GLY146.N-HSE163.O 56.08

SER147.OG-SER144.O 57.35

SER254.OG-ILE259.O 57.71

LEU115.N-VAL148.O 57.71

TYR37.N-LEU30.O 58.80

SER123.N-ALA116.O 59.17

VAL20.N-LEU27.O 59.71

SER267.OG-ASP263.O 59.71

LEU89.N-VAL36.O 59.89

LEU167.N-VAL171.O 62.07

TYR182.OH-CYS160.O 62.07

GLY149.N-TYR161.O 65.70

HSE163.N-SER147.O 65.88

TRP31.N-CYS16.O 70.24

VAL36.N-LEU89.O 71.69

VAL114.N-TYR126.O 71.69

B-chain – rep3

Table 2.55 MD-HBs (with occupancy rates ≥30%) of the Mpro-delP168-7bb2 model from the 550 ns MD trajectories (amarolab.ucsd.edu/covid19.php)

150 2 3C-Like Protease (3CLpro)

ALA234.N-PHE230.O 44.83

SER144.OG-LEU141.O 41.02

LEU67.N-THR21.O 36.84

CYS38.N-LEU87.O 36.84

ASN274.N-GLU270.O 39.02

LEU205.N-THR201.O 38.66

ALA266.N-LEU262.O 34.48

SER254.N-LEU250.O 34.12

TYR182.N-GLY174.O 33.94

PHE112.N-CYS128.O 36.84

ALA70.N-VAL73.O 35.93

MET130.N-GLN110.O 35.21

SER10.OG-GLU14.OE1 35.03

LEU87.N-CYS38.O 34.85

ARG131.NH1-ASP289.OD1 37.39

GLN83.N-VAL86.O 37.21

ILE136.N-HSE172.O 35.75

LEU87.N-CYS38.O 35.75

TYR209.OH-ILE259.O 36.48 ASN203.ND2-ASP289.O 35.75

ASN221.N-SER267.OG 36.30 ALA234.N-PHE230.O 35.93

ARG105.NH1-ASP176.OD2 36.48 THR21.N-LEU67.O 36.48

ALA266.N-LEU262.O 36.48 ALA255.N-GLY251.O 36.30

LEU27.N-VAL20.O 37.02 ILE200.N-ASP289.OD2 36.66 MET130.N-GLN110.O 36.66

LEU27.N-VAL20.O 37.57 LEU272.N-LEU268.O 37.21 LEU30.N-TYR37.O 36.66

LEU205.N-THR201.O 35.57

TYR209.OH-ILE259.O 35.39

GLN69.N-GLN19.O 35.21

ASN221.N-SER267.OG 37.75

CYS128.N-PHE112.O 37.75

SER144.OG-LEU141.O 37.57

GLN19.N-GLN69.O 37.39 THR243.OG1-HSE246.ND1 37.21

ASN203.ND2-ASP289.O 37.75

LEU272.N-LEU268.O 37.57

ARG60.NH1-ASP56.OD1 38.48

ASN221.N-SER267.OG 35.93

THR243.OG1-HSE246.ND1 38.11 ASP153.N-CYS156.O 37.75

ALA234.N-PHE230.O 37.93

SER254.N-LEU250.O 38.66

MET130.N-GLN110.O 36.30

ASN180.N-ASP176.OD1 38.48

ASN203.ND2-ASP289.O 35.75

CYS160.N-GLY149.O 37.93

TYR118.N-SER121.O 39.20

THR243.OG1-HSE246.ND1 36.30

CYS160.N-GLY149.O 38.66

PHE159.N-LYS102.O 35.57

SER158.N-ASN151.O 37.93

ALA70.N-VAL73.O 39.56

CYS128.N-PHE112.O 36.66

TYR209.OH-ILE259.O 37.93

THR135.OG1-ASN133.OD1 38.11

LEU67.N-THR21.O 39.75

ALA234.N-PHE230.O 37.93

GLN69.N-GLN19.O 38.66

VAL18.N-GLY29.O 40.29

SER254.N-LEU250.O 38.84

SER158.N-ASN151.O 39.02

ASN221.N-SER267.OG 39.20

LEU272.N-LEU268.O 37.93

LEU27.N-VAL20.O 39.20

ILE200.N-ASP289.OD2 41.38

ASN180.N-ASP176.OD1 38.11

LEU272.N-LEU268.O 39.20 ALA173.N-MET165.O 41.92

MET162.N-THR175.O 40.11 CYS128.N-PHE112.O 40.11 LEU87.N-CYS38.O 39.56

ALA116.N-GLY124.O 42.47 ARG40.NH2-ASP187.OD2 42.47 LEU242.N-ASN231.OD1 42.11

ALA70.N-VAL73.O 39.38

ALA173.N-MET165.O 38.84

ALA234.N-PHE230.O 38.66

SER254.N-LEU250.O 39.20

ARG105.NH1-ASP176.OD2 39.20

VAL18.N-GLY29.O 39.38

LEU268.N-MET264.O 41.38

ALA116.N-GLY124.O 40.65 ASN274.N-GLU270.O 40.65

GLN19.N-GLN69.O 42.83 GLY120.N-ASN28.OD1 42.65

THR201.OG1-GLU240.O 39.38

LEU30.N-TYR37.O 39.38

GLN19.N-GLN69.O 40.83

ALA116.N-GLY124.O 39.56

LEU268.N-MET264.O 41.02 GLN83.N-VAL86.O 41.02

CYS128.N-PHE112.O 42.83 ASN274.N-GLU270.O 42.83

GLN19.N-GLN69.O 40.47

LEU27.N-VAL20.O 39.56

LEU268.N-MET264.O 41.56

ILE200.N-ASP289.OD2 41.02

CYS128.N-PHE112.O 42.29

MET130.N-GLN110.O 34.85

GLN69.N-GLN19.O 35.75

ASN203.ND2-ASP289.O 36.30

ARG131.N-THR135.O 36.48

LEU27.N-VAL20.O 36.66

ASP153.N-CYS156.O 36.84

LYS269.N-CYS265.O 37.02

ALA70.N-VAL73.O 37.21

SER254.N-LEU250.O 37.75

SER158.N-ASN151.O 37.93

ILE200.N-ASP289.OD2 38.29

THR135.OG1-ASN133.OD1 38.84

ILE136.N-HSE172.O 39.02

GLN19.N-GLN69.O 39.38

VAL18.N-GLY29.O 39.56

TYR182.N-GLY174.O 40.11

CYS38.N-LEU87.O 40.29

GLN83.N-VAL86.O 40.65

THR175.OG1-ASP176.O 40.83

ASN274.N-GLU270.O 41.02

ALA116.N-GLY124.O 41.92

CYS160.N-GLY149.O 41.92

PHE150.N-SER113.O 42.29

LEU272.N-LEU268.O 42.29

THR45.OG1-ASP48.OD1 41.20 PHE150.N-SER113.O 41.20

ILE78.N-LYS90.O 44.28 LEU205.N-THR201.O 43.38

PHE150.N-SER113.O 42.11

LEU268.N-MET264.O 42.11

LEU67.N-THR21.O 42.11

ILE136.N-HSE172.O 41.56

GLY120.N-ASN28.OD1 43.74 MET162.N-THR175.O 42.83

GLY120.N-ASN28.OD1 42.11 VAL91.N-ASP34.O 41.38

MET162.N-THR175.O 44.83 PHE150.N-SER113.O 44.65

VAL18.N-GLY29.O 43.01

MET162.N-THR175.O 42.83

GLY29.N-VAL18.O 43.74

LEU205.N-THR201.O 44.10

ARG105.NH1-ASP176.OD2 44.46

THR21.N-LEU67.O 44.65

VAL91.N-ASP34.O 43.01

THR201.OG1-GLU240.O 43.56 ASN180.N-ASP176.OD1 43.01 ARG131.NH1-ASP289.OD1 42.65

ARG131.NH2-ASP289.OD2 45.37 LEU268.N-MET264.O 45.37 GLN83.N-VAL86.O 45.19

TYR54.OH-ASP187.O 44.65 LEU205.N-THR201.O 43.56

HSE172.N-ILE136.O 45.74 GLY29.N-VAL18.O 45.55

LEU242.N-ASN231.OD1 42.83

SER144.OG-LEU141.O 43.56

ILE200.N-ASP289.OD2 43.38

ASN274.N-GLU270.O 43.38

PHE8.N-SER113.OG 44.46

MET162.N-THR175.O 43.92

HSE172.N-ILE136.O 44.65

ILE78.N-LYS90.O 43.56

CYS160.N-GLY149.O 44.10

THR175.OG1-ASP176.O 44.10

PHE150.N-SER113.O 45.37

LEU205.N-THR201.O 43.56

(continued)

LYS269.N-CYS265.O 34.12

TYR209.OH-ILE259.O 35.21

ALA255.N-GLY251.O 35.21

MET130.N-GLN110.O 35.57

CYS160.N-GLY149.O 35.93

ALA70.N-VAL73.O 36.12

SER113.N-PHE150.O 36.48

ARG131.NH1-ASP289.OD2 36.66

SER158.N-ASN151.O 36.66

THR243.OG1-HSE246.ND1 37.21

LEU268.N-MET264.O 37.57

ASN221.N-SER267.OG 37.75

GLN69.N-GLN19.O 37.75

LEU30.N-TYR37.O 37.75

THR292.OG1-ASP295.OD1 38.11

ALA234.N-PHE230.O 38.11

THR135.OG1-ASN133.OD1 38.11

LEU27.N-VAL20.O 38.48

TYR118.N-SER121.O 38.84

GLY29.N-VAL18.O 39.02

LEU272.N-LEU268.O 39.02

GLN19.N-GLN69.O 39.38

ASN274.N-GLU270.O 40.29

SER10.OG-GLU14.OE1 40.65

MET162.N-THR175.O 40.65

VAL18.N-GLY29.O 40.65

CYS128.N-PHE112.O 40.83

LEU67.N-THR21.O 40.83

LEU87.N-CYS38.O 41.02

ASP153.N-CYS156.O 41.74

VAL91.N-ASP34.O 41.92

ALA116.N-GLY124.O 42.11

GLN83.N-VAL86.O 43.01

2.4 Concluding Remarks 151

PHE159.N-LYS102.O 34.66

LYS5.NZ-GLU290.OE1 31.22

CYS265.N-VAL261.O 31.22

GLN256.N-PRO252.O 30.85

THR292.OG1-ASP295.OD2 30.85

ALA255.N-GLY251.O 30.67

ASN133.ND2-GLY195.O 30.49

CYS117.N-SER147.OG 30.49

LYS5.NZ-GLU290.OE1 32.49

SER267.N-ASP263.O 32.30

LYS269.N-CYS265.O 31.76

ARG4.N-GLN299.OE1 31.58

VAL104.N-PHE159.O 31.40

ASN133.ND2-GLY195.O 30.49

THR199.N-ASN238.O 30.31

GLN256.N-PRO252.O 30.31

MET235.N-ASN231.O 31.22

ARG188.NH1-GLU55.OE2 30.49 ARG188.NH1-GLU55.OE1 30.49 SER81.N-LYS88.O 30.13

THR292.OG1-ASP295.OD2 31.03 LYS5.NZ-GLU290.OE2 30.49 ALA211.N-TRP207.O 30.49 ILE281.N-SER284.O 30.13

THR21.OG1-THR25.O 30.49

TYR118.N-SER121.O 30.85

ASN133.ND2-GLY195.O 31.03

ALA255.N-GLY251.O 31.22

GLN256.N-PRO252.O 31.58

CYS265.N-VAL261.O 31.94

LYS269.N-CYS265.O 32.12

ILE281.N-SER284.O 32.30

GLN256.N-PRO252.O 31.40

ILE136.N-HSE172.O 31.94

ARG60.NH1-ASP56.OD2 32.30

CYS265.N-VAL261.O 32.49

PHE112.N-CYS128.O 32.49

TYR209.OH-ILE259.O 33.39

SER144.OG-LEU141.O 33.39

THR135.OG1-ASN133.OD1 33.94

ALA266.N-LEU262.O 32.85

ALA173.N-MET165.O 33.76

SER158.N-ASN151.O 34.30

LYS5.NZ-GLU290.OE2 31.40

GLN69.N-GLN19.O 32.85

THR135.OG1-ASN133.OD1 32.49 THR243.OG1-HSE246.ND1 33.94

ASP153.N-CYS156.O 34.30 LYS5.NZ-GLU290.OE1 34.12 PHE112.N-CYS128.O 33.94

ASN133.ND2-GLY195.O 34.85 TYR182.N-GLY174.O 34.66 VAL104.N-PHE159.O 34.48

THR135.OG1-ASN133.OD1 32.85

ILE136.N-HSE172.O 31.58

ASN180.N-ASP176.OD2 31.40

LEU30.N-TYR37.O 34.48

PHE159.N-LYS102.O 33.39

THR292.OG1-ASP295.OD1 33.76

GLN69.N-GLN19.O 35.57 MET130.N-GLN110.O 35.03

B-chain – rep1 ALA70.N-VAL73.O 35.57

ALA266.N-LEU262.O 33.03

PHE112.N-CYS128.O 33.76

TYR118.N-SER121.O 33.03

ALA255.N-GLY251.O 34.66

LEU30.N-TYR37.O 34.48

A-chain – rep3 PHE159.N-LYS102.O 35.75

A-chain – rep2

SER158.N-ASN151.O 33.94

A-chain – rep1

ASN203.ND2-ASP289.O 34.85

Table 2.55 (continued) B-chain – rep2

THR243.OG1-HSE246.ND1 31.03

LEU30.N-TYR37.O 31.40

ALA255.N-GLY251.O 31.76

LYS5.NZ-GLU288.OE1 31.94

PHE112.N-CYS128.O 32.67

LYS5.NZ-GLU290.OE1 33.39

THR199.N-ASN238.O 33.39

ALA173.N-MET165.O 34.12

ILE281.N-SER284.O 34.12

CYS265.N-VAL261.O 34.12

PHE159.N-LYS102.O 34.30

ASN221.N-SER267.OG 34.30

B-chain – rep3

CYS38.N-LEU87.O 30.67

THR199.N-ASN238.O 30.85

ASN180.N-ASP176.OD2 31.22

LYS5.NZ-GLU288.OE1 31.22

ILE200.N-ASP289.OD1 31.76

LYS5.NZ-GLU290.OE2 32.49

ASN180.N-ASP176.OD1 32.49

LYS5.NZ-GLU290.OE1 32.67

SER254.N-LEU250.O 32.67

PHE112.N-CYS128.O 33.03

PHE159.N-LYS102.O 33.39

TYR182.N-GLY174.O 33.58

ALA266.N-LEU262.O 33.76

ASN203.ND2-ASP289.O 33.94

ALA173.N-MET165.O 33.94

152 2 3C-Like Protease (3CLpro)

TYR182.OH-CYS160.O 62.79 SER267.OG-ASP263.O 62.25 GLY149.N-TYR161.O 61.34

VAL20.N-LEU27.O 62.98 TYR37.N-LEU30.O 62.07

VAL20.N-LEU27.O 60.80

SER123.N-ALA116.O 59.35

SER254.OG-ILE259.O 62.07

LEU272.N-LEU268.O 46.64 MET162.N-THR175.O 46.46

MET162.N-THR175.O 45.92

LEU87.N-CYS38.O 47.01 GLY120.N-ASN28.OD1 46.82

THR135.OG1-ASN133.OD1 46.82 LEU242.N-ASN231.OD1 46.82

TYR239.N-ALA234.O 48.28 ILE78.N-LYS90.O 47.73 ASN231.N-LEU227.O 47.55

SER10.OG-GLU14.OE2 47.73 ARG40.NH2-ASP187.OD1 46.82

LEU268.N-MET264.O 46.82

GLY146.N-HSE163.O 45.74

LEU67.N-THR21.O 48.46

THR201.OG1-GLU240.O 48.09

THR201.OG1-GLU240.O 47.01

LYS88.N-SER81.O 49.73

ILE78.N-LYS90.O 48.82

GLY109.N-MET130.O 48.64

LYS90.N-GLY79.O 48.64

PHE8.N-SER113.OG 46.82

ILE78.N-LYS90.O 50.27

VAL157.N-LYS100.O 49.55

LYS90.N-GLY79.O 49.00

ALA116.N-GLY124.O 49.18

HSE172.N-ILE136.O 45.92

VAL157.N-LYS100.O 50.45

LEU67.N-THR21.O 49.91

SER144.OG-LEU141.O 49.18

TYR239.N-ALA234.O 50.09

LEU268.N-MET264.O 45.37

GLY109.N-MET130.O 50.82

LYS90.N-GLY79.O 50.27

ARG105.NH2-PHE181.O 50.82

ILE78.N-LYS90.O 51.00

ARG105.NH2-PHE181.O 47.19

ASN231.N-LEU227.O 51.36

LEU87.N-CYS38.O 51.00

THR257.OG1-LEU253.O 51.36

GLY109.N-MET130.O 51.91

HSE172.N-ILE136.O 47.19

THR257.OG1-LEU253.O 51.72

ASN231.N-LEU227.O 51.54

SER123.N-ALA116.O 52.27

VAL157.N-LYS100.O 51.91

SER147.OG-SER144.O 47.55

GLY120.N-ASN28.OD1 51.91

SER123.N-ALA116.O 51.54

VAL157.N-LYS100.O 52.99

ARG105.NH2-PHE181.O 52.09

THR21.N-LEU67.O 46.46

LYS90.N-GLY79.O 51.91

GLY146.N-HSE163.O 51.54

ARG131.NH1-ASP289.OD1 53.72

THR257.OG1-LEU253.O 52.63

LEU75.N-VAL68.O 48.64

THR21.N-LEU67.O 52.63

THR257.OG1-LEU253.O 52.63

GLY146.N-HSE163.O 54.63

SER147.OG-SER144.O 53.18

LEU242.N-ASN231.OD1 48.46

LEU89.N-VAL36.O 54.63

GLY109.N-MET130.O 52.99

VAL20.N-LEU27.O 54.81

HSE172.N-ILE136.O 55.35

ARG40.NE-ASP187.OD2 53.90

SER123.N-ALA116.O 53.90

TYR239.N-ALA234.O 47.55

GLY146.N-HSE163.O 55.54

LEU115.N-VAL148.O 53.54

THR201.OG1-GLU240.O 48.64

SER10.OG-GLU14.OE2 56.26

LYS88.N-SER81.O 54.81

LYS88.N-SER81.O 56.08

ASN95.N-ASP33.O 54.63

TYR37.N-LEU30.O 58.26

GLY120.N-ASN28.OD1 48.46

ASN95.N-ASP33.O 56.26

VAL20.N-LEU27.O 57.17

LEU115.N-VAL148.O 56.99

TYR239.N-ALA234.O 48.09

TYR37.N-LEU30.O 56.44

ASN95.N-ASP33.O 57.35

LEU89.N-VAL36.O 58.44

SER254.OG-ILE259.O 57.71

LEU115.N-VAL148.O 56.62

ASN95.N-ASP33.O 58.62

LEU167.N-VAL171.O 58.08

TYR182.OH-CYS160.O 58.08

LEU115.N-VAL148.O 58.80

ARG131.NH2-ASP289.OD2 58.62

SER147.OG-SER144.O 58.08

LEU167.N-VAL171.O 57.53

SER10.OG-GLU14.OE1 58.62

LEU89.N-VAL36.O 58.44

SER254.OG-ILE259.O 59.17

SER267.OG-ASP263.O 60.80 LEU89.N-VAL36.O 59.17

TYR182.OH-CYS160.O 58.26

SER254.OG-ILE259.O 58.08

TYR37.N-LEU30.O 60.07

GLY149.N-TYR161.O 59.35

LEU167.N-VAL171.O 65.88

SER267.OG-ASP263.O 60.44

HSE163.N-SER147.O 71.69 VAL114.N-TYR126.O 70.24

VAL114.N-TYR126.O 66.42 GLY149.N-TYR161.O 65.15 TYR182.OH-CYS160.O 63.70

GLY149.N-TYR161.O 64.79

HSE163.N-SER147.O 62.98

SER267.OG-ASP263.O 62.98

VAL114.N-TYR126.O 66.61

ARG131.NH2-ASP289.OD2 64.07

VAL36.N-LEU89.O 73.32 TRP31.N-CYS16.O 72.05

VAL36.N-LEU89.O 70.78 TRP31.N-CYS16.O 67.51

VAL114.N-TYR126.O 67.70

VAL36.N-LEU89.O 66.61

VAL36.N-LEU89.O 71.32

TRP31.N-CYS16.O 71.14

LEU167.N-VAL171.O 62.98

B-chain – rep1 ARG131.NH2-ASP289.OD2 74.05

A-chain – rep3 HSE163.N-SER147.O 72.23

A-chain – rep2

TRP31.N-CYS16.O 74.95

A-chain – rep1

HSE163.N-SER147.O 72.23

ILE78.N-LYS90.O 44.46

MET162.N-THR175.O 45.19

ASN231.N-LEU227.O 46.10

GLN83.N-VAL86.O 47.01

GLY29.N-VAL18.O 47.01

SER123.N-ALA116.O 47.91

ARG105.NH2-PHE181.O 49.73

VAL157.N-LYS100.O 49.73

SER147.OG-SER144.O 50.45

TYR239.N-ALA234.O 50.82

THR257.OG1-LEU253.O 51.00

LYS90.N-GLY79.O 51.54

HSE172.N-ILE136.O 51.54

GLY109.N-MET130.O 51.72

LYS88.N-SER81.O 52.27

LEU115.N-VAL148.O 52.27

PHE8.N-SER113.OG 52.45

ARG40.NE-ASP187.OD2 57.53

ASN95.N-ASP33.O 57.71

GLY146.N-HSE163.O 58.26

LEU167.N-VAL171.O 58.80

ARG40.NH2-ASP187.OD1 58.80

GLY149.N-TYR161.O 58.80

TYR37.N-LEU30.O 59.17

SER254.OG-ILE259.O 60.07

VAL20.N-LEU27.O 60.44

ARG131.NH2-ASP289.OD2 61.34

LEU89.N-VAL36.O 62.25

TYR182.OH-CYS160.O 62.43

SER267.OG-ASP263.O 63.70

VAL114.N-TYR126.O 70.05

HSE163.N-SER147.O 72.41

VAL36.N-LEU89.O 74.05

TRP31.N-CYS16.O 74.23

B-chain – rep2

(continued)

THR257.OG1-LEU253.O 46.28

LEU242.N-ASN231.OD1 46.28

LEU27.N-VAL20.O 47.55

ARG131.NH1-ASP289.OD1 47.55

ASN231.N-LEU227.O 47.55

LEU115.N-VAL148.O 47.91

ARG40.NE-ASP187.OD1 48.46

THR169.OG1-PRO168.O 48.46

ARG40.NH2-ASP187.OD2 48.64

SER147.OG-SER144.O 49.18

TYR239.N-ALA234.O 50.27

THR45.OG1-ASP48.OD2 50.64

THR21.N-LEU67.O 50.64

LEU75.N-VAL68.O 51.00

VAL157.N-LYS100.O 52.09

LYS88.N-SER81.O 52.99

SER123.N-ALA116.O 53.72

ASN95.N-ASP33.O 54.26

GLY109.N-MET130.O 54.63

TYR182.OH-CYS160.O 55.17

HSE172.N-ILE136.O 55.72

GLY146.N-HSE163.O 56.44

SER254.OG-ILE259.O 57.35

LEU89.N-VAL36.O 57.89

VAL20.N-LEU27.O 58.08

GLY149.N-TYR161.O 62.61

LEU167.N-VAL171.O 62.98

TYR37.N-LEU30.O 63.34

ARG131.NH2-ASP289.OD2 63.88

SER267.OG-ASP263.O 64.25

VAL114.N-TYR126.O 67.33

VAL36.N-LEU89.O 70.42

HSE163.N-SER147.O 73.32

TRP31.N-CYS16.O 73.50

B-chain – rep3

Table 2.56 MD-HBs (with occupancy rates ≥30%) of the Mpro-a173v-7bb2 model from the 550 ns MD trajectories (amarolab.ucsd.edu/covid19.php)

2.4 Concluding Remarks 153

B-chain – rep1

LEU268.N-MET264.O 44.28 THR21.N-LEU67.O 43.19

GLY29.N-VAL18.O 43.74 LEU75.N-VAL68.O 43.56

PHE150.N-SER113.O 45.19

VAL173.N-MET165.O 45.01

LEU242.N-ASN231.OD1 43.74

VAL91.N-ASP34.O 41.20

GLY29.N-VAL18.O 42.11 MET130.N-GLN110.O 42.11

ALA116.N-GLY124.O 39.93

ALA234.N-PHE230.O 39.75

ASN274.N-GLU270.O 38.29

ILE136.N-HSE172.O 37.39

ALA234.N-PHE230.O 37.02

ASN180.N-ASP176.OD2 36.48

ASP153.N-CYS156.O 35.39

ASN133.ND2-GLY195.O 35.75

ARG105.NH1-ASP176.OD2 35.57

LEU87.N-CYS38.O 35.21

ASN221.N-SER267.OG 34.48

SER254.N-LEU250.O 34.48

THR243.OG1-HSE246.ND1 34.48

ARG105.NH2-PHE181.O 33.58

CYS128.N-PHE112.O 35.75

ILE200.N-ASP289.OD2 35.75

ALA266.N-LEU262.O 35.93

MET162.N-THR175.O 35.75

TYR209.OH-ILE259.O 34.85

ALA266.N-LEU262.O 35.57

PHE159.N-LYS102.O 35.57

MET130.N-GLN110.O 36.30

TYR209.OH-ILE259.O 36.12

LYS269.N-CYS265.O 34.30

ILE281.N-SER284.O 35.03

PHE150.N-SER113.O 35.75

THR292.OG1-ASP295.OD1 35.93

ILE281.N-SER284.O 34.85

SER158.N-ASN151.O 36.30 ALA70.N-VAL73.O 36.30

ASP153.N-CYS156.O 36.48

LEU272.N-LEU268.O 36.48

LEU205.N-THR201.O 37.02

SER158.N-ASN151.O 37.75

THR292.OG1-ASP295.OD2 35.39

LEU27.N-VAL20.O 36.48

ASN203.ND2-ASP289.O 36.66

LEU75.N-VAL68.O 35.39

ALA234.N-PHE230.O 37.57

ASN274.N-GLU270.O 37.39

GLN19.N-GLN69.O 35.57

THR135.OG1-ASN133.OD1 35.39

LEU242.N-ASN231.OD1 37.57

VAL18.N-GLY29.O 36.48

CYS265.N-VAL261.O 37.75

ASN180.N-ASP176.OD1 37.57

ARG40.NH2-ASP187.OD2 35.93

LEU30.N-TYR37.O 37.75 ASN180.N-ASP176.OD2 37.75

CYS128.N-PHE112.O 35.75

ILE281.N-SER284.O 37.02 PHE150.N-SER113.O 36.84

CYS128.N-PHE112.O 37.93

ASN203.ND2-ASP289.O 37.75

GLN69.N-GLN19.O 37.93

ARG40.NE-ASP187.OD2 38.11

THR201.OG1-GLU240.O 38.48

SER158.N-ASN151.O 36.30

GLN69.N-GLN19.O 37.21

ALA255.N-GLY251.O 37.39

HSE172.N-ILE136.O 38.11

CYS38.N-LEU87.O 36.12

THR243.OG1-HSE246.ND1 39.20

SER158.N-ASN151.O 38.29

TYR118.N-SER121.O 37.93

ILE200.N-ASP289.OD2 37.39

ARG40.NE-ASP187.OD1 37.39

ASN203.ND2-ASP289.O 36.84

LYS5.NZ-GLU290.OE1 38.48

LEU272.N-LEU268.O 37.75

CYS160.N-GLY149.O 39.38

ARG40.NH2-ASP187.OD2 39.20

TYR118.N-SER121.O 37.93

ARG131.N-THR135.O 38.84 GLN19.N-GLN69.O 38.66

GLN69.N-GLN19.O 37.57

THR21.N-LEU67.O 39.38 THR175.OG1-ASP176.O 38.48

VAL91.N-ASP34.O 39.75

LEU27.N-VAL20.O 39.75

ARG40.NH2-ASP187.OD1 39.75

LEU27.N-VAL20.O 40.65

GLN83.N-VAL86.O 38.48

LYS88.N-SER81.O 39.56

THR243.OG1-HSE246.ND1 39.93

LEU30.N-TYR37.O 38.48

LEU30.N-TYR37.O 40.11

MET130.N-GLN110.O 39.93

PHE150.N-SER113.O 39.38

ALA116.N-GLY124.O 38.84

ALA70.N-VAL73.O 40.11

GLN19.N-GLN69.O 39.75

ALA70.N-VAL73.O 40.83

ILE136.N-HSE172.O 40.47

ASN221.N-SER267.OG 40.29

ILE200.N-ASP289.OD2 40.65 THR135.OG1-ASN133.OD1 40.65

LEU27.N-VAL20.O 39.56

ASN274.N-GLU270.O 40.11

ARG131.NH2-ASP289.OD1 41.38

GLN83.N-VAL86.O 41.74

CYS38.N-LEU87.O 41.20

LEU87.N-CYS38.O 40.29

VAL18.N-GLY29.O 42.83 VAL91.N-ASP34.O 42.65

THR169.OG1-PRO168.O 41.20

CYS160.N-GLY149.O 40.65

LEU205.N-THR201.O 41.02

LYS5.NZ-GLU290.OE1 43.01

THR169.OG1-PRO168.O 43.01

PHE8.N-SER113.OG 44.83

ALA234.N-PHE230.O 40.65

VAL18.N-GLY29.O 42.47

SER254.N-LEU250.O 42.47

GLY29.N-VAL18.O 41.92

LEU272.N-LEU268.O 41.74

MET162.N-THR175.O 41.74

LEU205.N-THR201.O 41.20

ARG131.NH1-ASP289.OD1 42.29

LEU205.N-THR201.O 42.83

ALA116.N-GLY124.O 42.83

SER144.OG-LEU141.O 43.19

VAL91.N-ASP34.O 42.47

ASN221.N-SER267.OG 43.19

LEU268.N-MET264.O 43.92

GLN19.N-GLN69.O 42.83

PHE8.N-SER113.OG 43.56

MET130.N-GLN110.O 43.38

PHE8.N-SER113.OG 44.46

SER147.OG-SER144.O 45.55 LEU75.N-VAL68.O 45.01

GLY29.N-VAL18.O 43.56

VAL173.N-MET165.O 44.46

LEU67.N-THR21.O 45.74

THR135.OG1-ASN133.OD1 45.37

ASN274.N-GLU270.O 44.28

SER10.OG-GLU14.OE1 45.74

ARG131.NH1-ASP289.OD1 43.92

ASN231.N-LEU227.O 44.65

A-chain – rep3 LEU67.N-THR21.O 45.37

A-chain – rep2

GLN83.N-VAL86.O 46.46

A-chain – rep1

LYS5.NZ-GLU290.OE1 44.65

Table 2.56 (continued) B-chain – rep2

THR292.OG1-ASP295.OD2 36.12

ALA116.N-GLY124.O 36.12

ASN203.ND2-ASP289.O 36.48

ASN221.N-SER267.OG 36.66

ARG60.NH1-ASP48.OD2 37.02

GLN69.N-GLN19.O 37.02

ARG105.NH1-ASP176.OD2 37.02

THR243.OG1-HSE246.ND1 37.02

CYS128.N-PHE112.O 37.21

LEU27.N-VAL20.O 37.39

LEU242.N-ASN231.OD1 37.39

PHE150.N-SER113.O 37.57

MET130.N-GLN110.O 37.57

LEU87.N-CYS38.O 37.75

LEU272.N-LEU268.O 37.75

LEU67.N-THR21.O 38.11

ALA70.N-VAL73.O 38.29

LYS5.NZ-GLU290.OE1 38.29

ALA234.N-PHE230.O 38.66

ASP153.N-CYS156.O 38.66

VAL18.N-GLY29.O 39.02

THR135.OG1-ASN133.OD1 39.20

ILE136.N-HSE172.O 39.56

ARG131.NH1-ASP289.OD1 39.56

THR201.OG1-GLU240.O 39.93

VAL91.N-ASP34.O 40.11

ASN274.N-GLU270.O 40.11

SER144.OG-LEU141.O 40.29

SER10.OG-GLU14.OE2 41.56

SER158.N-ASN151.O 41.74

LEU75.N-VAL68.O 41.74

LEU30.N-TYR37.O 42.11

THR21.N-LEU67.O 42.47

GLN19.N-GLN69.O 42.47

LEU205.N-THR201.O 42.65

THR45.OG1-ASP48.OD1 43.01

ASN180.N-ASP176.OD1 43.01

LEU268.N-MET264.O 43.38

B-chain – rep3

ARG131.N-THR135.O 35.75

THR243.OG1-HSE246.ND1 36.48

ALA266.N-LEU262.O 36.48

LYS5.NZ-GLU290.OE1 36.48

MET130.N-GLN110.O 36.66

SER158.N-ASN151.O 36.66

ILE200.N-ASP289.OD2 36.84

ASN180.N-ASP176.OD2 37.02

LEU67.N-THR21.O 37.57

ASN221.N-SER267.OG 37.57

ALA70.N-VAL73.O 38.11

ASP153.N-CYS156.O 38.11

MET162.N-THR175.O 38.11

ALA116.N-GLY124.O 39.02

LEU205.N-THR201.O 39.20

THR135.OG1-ASN133.OD1 39.20

THR45.N-ASP48.OD2 39.38

ALA234.N-PHE230.O 39.38

SER254.N-LEU250.O 39.56

VAL18.N-GLY29.O 40.29

CYS128.N-PHE112.O 40.29

LEU272.N-LEU268.O 40.47

LEU87.N-CYS38.O 40.65

VAL91.N-ASP34.O 41.02

SER144.OG-LEU141.O 41.56

LEU268.N-MET264.O 41.92

THR292.OG1-ASP295.OD2 42.83

PHE150.N-SER113.O 42.83

LEU30.N-TYR37.O 43.01

PHE8.N-SER113.OG 43.19

GLY120.N-ASN28.OD1 43.38

GLN19.N-GLN69.O 43.38

ASN274.N-GLU270.O 43.56

ILE78.N-LYS90.O 44.65

GLN83.N-VAL86.O 45.01

GLY29.N-VAL18.O 45.01

THR201.OG1-GLU240.O 45.37

LYS90.N-GLY79.O 45.74

154 2 3C-Like Protease (3CLpro)

SER254.N-LEU250.O 35.57

THR45.N-ASP48.OD1 32.49

ALA266.N-LEU262.O 30.49

ILE200.N-ASP289.OD1 30.13

ILE106.N-TYR182.OH 30.49

TYR237.OH-GLN273.OE1 30.13

PHE159.N-LYS102.O 31.40

ASN180.N-ASP176.OD1 31.40 TYR118.N-SER121.O 30.49

TYR209.OH-ILE259.O 32.49

SER113.N-PHE150.O 30.67 ALA255.N-GLY251.O 30.67

ARG188.NH1-GLU55.OE2 30.67 ARG188.NH1-GLU55.OE1 30.13

LYS5.NZ-GLU290.OE2 30.49

PHE112.N-CYS128.O 30.49

SER267.N-ASP263.O 31.58

LYS5.NZ-GLU288.OE2 31.58

PHE159.N-LYS102.O 33.39

ARG60.NH2-ASP48.OD2 35.39

PHE159.N-LYS102.O 30.49

LYS5.NZ-GLU288.OE1 30.85 SER113.N-PHE150.O 30.67

ARG60.NH1-ASP56.OD1 30.67 PHE112.N-CYS128.O 30.67

LYS90.NZ-ASP34.OD2 31.03 SER267.N-ASP263.O 31.03

TYR209.OH-ILE259.O 31.03 ARG60.NH1-ASP56.OD2 31.03

GLN256.N-PRO252.O 31.58 TYR118.N-SER121.O 31.22

CYS160.N-GLY149.O 31.22

GLN256.N-PRO252.O 31.40

LYS5.NZ-GLU288.OE1 31.76

ILE281.N-SER284.O 31.76

LYS269.N-CYS265.O 32.49

CYS265.N-VAL261.O 32.67

ALA255.N-GLY251.O 33.21

ILE136.N-HSE172.O 33.39

SER139.N-TYR126.OH 33.76

GLN69.N-GLN19.O 33.76

ASN203.ND2-ASP289.O 33.76

TYR118.N-SER121.O 34.30

ARG131.N-THR135.O 32.12

PHE112.N-CYS128.O 32.49

ALA266.N-LEU262.O 32.67

LYS61.NZ-ASP48.OD1 33.21

CYS265.N-VAL261.O 31.58 CYS160.N-GLY149.O 31.22 ASN221.N-SER267.OG 30.67

SER254.N-LEU250.O 32.85 LYS269.N-CYS265.O 31.03 TYR54.OH-ASP187.O 31.03

VAL104.N-PHE159.O 31.22

TYR209.OH-ILE259.O 31.03

ASN180.N-ASP176.OD2 31.03

LYS269.N-CYS265.O 32.12

CYS160.N-GLY149.O 31.94

ILE200.N-ASP289.OD2 34.12

ASN133.ND2-GLY195.O 34.48

ALA255.N-GLY251.O 34.66

CYS160.N-GLY149.O 35.39

GLY120.N-ASN28.OD1 35.57

ARG131.N-THR135.O 31.76

SER254.N-LEU250.O 32.85 THR243.OG1-HSE246.ND1 32.12

TYR209.OH-ILE259.O 33.03 CYS265.N-VAL261.O 32.85

GLN69.N-GLN19.O 32.49

SER139.N-TYR126.OH 31.94

THR175.OG1-ASP176.O 32.49

ALA70.N-VAL73.O 32.30

ASN203.ND2-ASP289.O 33.21 THR175.OG1-ASP176.O 33.21

ARG105.NH1-ASP176.OD1 33.76 LEU30.N-TYR37.O 33.03

TYR182.N-GLY174.O 33.21

LYS269.N-CYS265.O 32.85

ALA255.N-GLY251.O 32.67

VAL173.N-MET165.O 32.67

CYS38.N-LEU87.O 33.94 PHE159.N-LYS102.O 33.58

SER144.OG-LEU141.O 34.85 CYS128.N-PHE112.O 34.85

PHE159.N-LYS102.O 33.94

ALA255.N-GLY251.O 33.39

ASN180.N-ASP176.OD2 33.03

ALA266.N-LEU262.O 32.85

2.4 Concluding Remarks 155

156

2 3C-Like Protease (3CLpro)

Fig. 2.26 The secondary structures of the optimized Mpro-wt, Mpro-delP168-and-a173v, MprodelP168, and Mpro-a173v dimer models

2.4 Concluding Remarks

157

Fig. 2.27 MD secondary structures of the Mpro-wt-7bb2 model from the 550 ns MD trajectories (amarolab.ucsd.edu/covid19.php)

Fig. 2.28 MD secondary structures of the Mpro-delP168-and-a173v-7bb2 model from the 550 ns MD trajectories (amarolab.ucsd.edu/covid19.php)

158

2 3C-Like Protease (3CLpro)

Fig. 2.29 MD secondary structures of the Mpro-delP168-7bb2 model from the 550 ns MD trajectories (amarolab.ucsd.edu/covid19.php)

Fig. 2.30 MD secondary structures of the Mpro-a173v-7bb2 model from the 550 ns MD trajectories (amarolab.ucsd.edu/covid19.php)

Fig. 2.31 MD-RMSFs of the Mpro-wt-7bb2 model from the 550 ns MD trajectories (amarolab.ucsd.edu/covid19.php)

2.4 Concluding Remarks

159

Fig. 2.32 MD-RMSFs of the Mpro-delP168-a173v-7bb2 model from the 550 ns MD trajectories (amarolab.ucsd.edu/covid19.php)

Fig. 2.33 MD-RMSFs of the Mpro-delP168-7bb2 model from the 550 ns MD trajectories (amarolab.ucsd.edu/covid19.php)

Fig. 2.34 MD-RMSFs of the Mpro-a173v-7bb2 model from the 550 ns MD trajectories (amarolab.ucsd.edu/covid19.php)

Chapter 3

RNA-Dependent RNA Polymerase (RdRp)

Abstract This chapter firstly did the work skillfully and locally by optimizing the structures of RNA-dependent RNA polymerase (RdRp) in complex with its cofactors, i.e., NSP7 and NSP8 (6M71.pdb and 7BTF.pdb), respectively, from COVID-19 virus; then some new structural bioinformatics from the structures optimized for developing therapies of the currently fatal COVID-19 virus are reported. Currently, lots of researchers are using optimization to screen, dock, and design new therapies for COVID-19 but it is not used professionally. The hybrid strategy of mathematical optimization’s neighboring different (local search) algorithms is used professionally in this chapter. For RdRp, we found two new salt bridges: A:GLU729-A:HIS725 and A:GLU610-A:HIS752. The polar contacts A:ASP274-B:ARG111 and A:ARG331-B:ASP112 and the hydrogen bond A:VAL330.NB:VAL115.O (with 51.98% occupancy rate during 10 .μs of molecular dynamics simulation), etc. strongly make the in complex between RdRp and its cofactor Nsp8. Keywords COVID-19 virus · RNA-dependent RNA polymerase (RdRp) · Optimizing cryo-EM structures · Molecular dynamics studies · New structural bioinformatics

3.1 Introduction The COVID-19 virus’ RNA-dependent RNA polymerase (RdRp, also named NSP12) is the central component of coronaviral replication/transcription machinery and appears to be a primary target for the antiviral drug remdesivir [118]. The cryoEM structures for RdRp cofactors (with PDB IDs 6M71 and 7BTF) were recently released into the PDB (www.rcsb.org). This brief chapter will study these structures (optimized) and seek additional useful structural bioinformatics for COVID-19. We also notice that recently the mechanism of RNA capping of SARS-CoV-2 has been presented in [265, 390]; the RNA genome of SARS-CoV-2 contains the 5’ cap that facilitates the translation of viral proteins, protection from exonucleases, and

© The Author(s), under exclusive license to Springer Nature Switzerland AG 2023 J. Zhang, Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures, Springer Series in Biophysics 23, https://doi.org/10.1007/978-3-031-36773-1_3

161

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3 RNA-Dependent RNA Polymerase (RdRp)

evasion of the host immune response, and decoration of the cap on viral RNA plays essential roles in SARS-CoV-2 proliferation.

3.2 Materials and Methods The materials used in this chapter are 6M71.pdb and 7BTF.pdb. The methods of this chapter are optimizing the structures and confirming from MD trajectory data analyses. The hybrid strategy of mathematical optimization’s neighboring different algorithms is completely the same as the one used in [405, 413]. We optimized the structures locally and slightly, looking at the optimization problem as a three-body problem. The decreased energies (KJ/mol) are .−62125.531 (E102), .−64080.008 (E149), and .−64111.469 (E152) for 6M71.pdb and .−72227.188 (E102), .−75893.664 (E204), and .−76871.992 (E256) for 7BTF.pdb, respectively. The RMSD ([412], Chapter 1) values of the optimized structures from the original structures are 4.783784 Å for 6M71.pdb and 3.040042 Å for 7BTF.pdb, respectively; thus the optimized RdRp cofactor structures are very much different from their original structures. The differences of the 3D structure and secondary structure between each optimized and original structure can be detected by the package MOLMOL [184] and its CalcSecondary output files produced. We also find the openly accessible trajectory data of MD simulations of SARSCoV-2-RdRp with or without template RNA and remdesivir triphosphate from [384], where “the MD simulations were performed using Desmond; the complex models were placed in the orthorhombic box with a buffer distance of 10 Å in order to create a hydration model; TIP3P water model was used for creation of the hydration model; and the MD simulations were performed under the NPT ensemble for 1 .μs on three complex structures using OPLS3e force field.” Six .β-hairpin peptides ◦ ◦ .◦ .◦ .◦ .◦ . .

YKRAKTKYTKRVAGFAKKRK (peptide A), MKRAKTIYTKRVAGFAKKRR (peptide B), MYRAKTIYTKRVAGFAKKLK (peptide C), CKRAKTKYTKRVAGFAKKRC-CONH2 (peptide A-dis), CKRAKTIYTKRVAGFAKKRC-CONH2 (peptide B-dis), and CYRAKTIYTKRVAGFAKKLC-CONH2 (peptide C-dis)

highly affiliated to the N-terminal binding site of the SARS-CoV-2-RdRp NiRAN domain are designed in [321], where for each model of the peptide-RdRp complex (generated from 6M71.pdb and from the peptide VYRAFDIYNDKVAGFAKFLK [136, 204, 263, 321]), the MD trajectories of 20 .μs were released on June 22, 2022, in [321] with DESRES-ANTON codes 15235449, 15235455, 15235444, 15256598, 15256602, and 15256595 in turns for the peptideA-RdRp, peptideBRdRp, peptideC-RdRp, peptideAdis-RdRp, peptideBdis-RdRp, and peptideCdisRdRp models. We will optimize the six models of the peptide-RdRp complex and then confirm our findings from the 20 .μs MD trajectories of each model (Tables 3.1, 3.2 and 3.3).

3.3 New Results and Discussions

163

3.3 New Results and Discussions For the optimized RdRp cofactors, its Ramachandran plots for 6M71optimized and 7BTFoptimized models are shown in Fig. 3.1 (there is a slight difference between these two plots) implying to us our 6M71optimized and 7BTFoptimized models should be reasonable. The Ramachandran plots are with large percentage of residues in most favored regions so that RdRp factor protein structures could be suitable for docking studies with the compounds.

Fig. 3.1 The Ramachandran plots for the 6M71optimized model and the 7BTFoptimized model

The 3D structures of the 6M71optimized and 7BTFoptimized models have ABCD-Chains: A-Chain is RdRp (i.e., Nsp12) with a .β-hairpin Y21-F48 (Fig. S5 [118] – this is a potential binding site for remdesivir [118]) – C-Chain is Nsp7, and D- and B-Chains are Nsp8 [118]. In this structure of RdRp, there are two disulfide bonds between A:C301 and A:C306 and between A:C487 and A:C645, respectively (Fig. S3 of [118]), binding two Zn.2+ . More theoretical binding sites for the 6M71optimized model may be seen from [235]. The 6M71optimized model has 287 HBs and the 7BTFoptimized model has 385 HBs. The 6M71optimized model has the following 24 SBs: A:GLU665-A:LYS676, A:GLU83-A:LYS73, A:GLU744-A:ARG726, A:ASP452-A:ARG624, A:ASP194A:LYS288, A:GLU729-A:HIS725, A:GLU474-A:ARG305, A:ASP170-A:ARG 173, A:GLU610-A:HIS752, A:GLU474-A:ARG640, A:ASP421-A:LYS417, A:ASP499-A:ARG513, A:ASP258-A:LYS263, A:ASP304-A:ARG640, A:ASP 465-A:ARG132, A:ASP477-A:ARG640, A:ASP274-A:LYS272, A:GLU180A:ARG183, A:GLU136-A:LYS783, A:ASP804-A:LYS807, C:ASP38-C:LYS51, D:ASP112-D:ARG111, A:ASP274-B:ARG111, and D/B:ASP112-A:ARG331, where A:GLU83-A:LYS73 was confirmed by the MD of [321]: “LYS73 in .β3 forms a salt bridge with GLU83 in .αC for most of the simulation” (with HBs A:LYS73.NZ-A:GLU83.OE2 (10.54%) and A:LYS73.NZ-A:GLU83.OE1 (10.54%)). The 7BTFoptimized model has 17 SBs: A:ASP804-A:LYS807, A:ASP291-A:ARG735, A:ASP499-A:ARG513, A:GLU744-A:ARG726, A:ASP 865-A:LYS593, A:GLU474-A:ARG640, C:ASP38-C:LYS51, A:GLU254A:ARG285, A:ASP477-A:ARG640, A:ASP269-B:ARG111, A:GLU474-A:ARG

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3 RNA-Dependent RNA Polymerase (RdRp)

305, A:GLU136-A:LYS783, A:ASP465-A:ARG132, A:ASP421-A:LYS417, A:GLU180-A:ARG183, A:ASP170-A:ARG173, and A:ASP304-A:ARG640. For the 6M71optimized model, we found four .π -cations: B:ARG.+ 111.NH2A:TYR273, A:ARG.+ 624.NH2-A:TYR456, A:ARG.+ 735.NH2-A:TRP290, and A:LYS.+ 272.NZA:PHE275; in A-Chain (i.e., RaRp, Nsp12) 31 .π -.π stackings were found:

PHE415-TYR420, PHE422-TYR887-PHE419-PHE859, PHE881-TYR867, TRP916-PHE594-TYR915, HIS872-TYR831, HIS810-TRP800, TRP617-PHE782, TYR732-TYR728 (with HB TYR732.N-TYR728.O (33.17%)), TYR456-TYR453, PHE571-HIS642, TYR479-TYR746, TYR748-HIS752-TYR770 (with HB HID752.ND1-TYR748.O (11.8%)), TYR787-PHE134, TYR346-PHE348, HIS133TYR129 (with HBs HID133.N-TYR129.O (4.43%) and HID133.ND1-TYR129.O (1.56%)), (2) TYR163-TRP162-PHE157 (2), TYR787-PHE134, (2) TRP268THE275-PHE321, TRP290-PHE313-PHE283, and PHE287-TYR238-TYR237. From [321] with MD trajectory data ID DESRES-ANTON-10917618, we find that the model has 1182 residues and the 10002 ns MD trajectory of data has 8335 frames (with a frame interval of 1.2 ns). We pick up 835 frames with a frame interval of 12 ns to analyze the performances of the 10 .μs MD trajectory. We know that during 2.4–10 .μs, the protein equilibrates around the RMSD value of 5.7 Å. We observe the secondary structure of the whole .10 μs of the MD (Fig. 3.2) and get to know that the following segments have structural changes: A-Chain 446–455, 562–571, 622–625, 733–740, 870–879, 843–855, and 889–917, B-Chain 78–101, C-Chain 17–20 and 62–71, and D-Chain 84–88, 96–113, and 169–179. From the RMSF ([412], Chap. 1) values during the whole 10 .μs (Fig. 3.3), we know that segments 51–71 (the N-terminal part of NiRAN), 258–268, 508–518, and 898–908 (the C-terminal) vary very much during the whole MD of 10 .μs.

Fig. 3.2 The secondary structural developments during the whole 10 .μs of MD

3.3 New Results and Discussions

165

The MD data of [321] can confirm all our SBs of the 6M71optimized model, except that the HIS residues of A:GLU729-A:HIS725 and A:GLU610-A:HIS752 were replaced by ARG726/733/LYS41 and LYS751, respectively. We have shown

Fig. 3.3 The root mean square fluctuation (RMSF) of each residue (numbered from down to up) during the whole 10 .μs of MD

166

3 RNA-Dependent RNA Polymerase (RdRp)

in Fig. 3.7 our SBs (A:ASP274-B:ARG111, B:ASP112-A:ARG331, B:ASP112B:ARG111, D:ASP112-D:ARG111, C:ASP38-C:LYS51, A:GLU665-A:LYS676, A:GLU83-A:LYS73, A:GLU744-A:ARG726, A:ASP452-A:ARG624, A:ASP170A:ARG173, A:GLU174-A:ARG640, A:ASP499-A:ARG513, A:ASP304-A:ARG 640, A:ASP465-A:ARG132, A:ASP477-A:ARG640, A:GLU136-A:LYS783) confirmed by the MD data and our HBs confirmed in Table 3.4. We found 5221 HBs; during the whole 10 .μs of MD, most of the HBs in Table 3.4 are not broken except for A:TYR294.OH-ASN314.OD1 (61.92%), broken during 0–47 frames; A:SER343.OG-A:ASP377.OD1 (50.78%), broken during 118–243 and 733–834 frames; and A:SER239.OG-A:ASP465.OD1 (50.54%), broken during 0–38 and 166–203 frames; from Table 3.4 we also found one important HB, A:VAL330.NB:VAL115.O (51.98%), between AB-Chains. These four HBs are shown in Fig. 3.8. The strong polar contacts A:GLU665-A:LYS676, A:GLU744-A:ARG726, A:ASP452-A:ARG624, A:ASP170-A:ARG173, and A:GLU:474-A:ARG640 are with high HB occupancy rates (Table 3.5), and there are two polar contacts, A:ARG331-B:ASP112 and A:ASP274-B:ARG111, between RdRp and Nsp8 (Table 3.5). In addition to these basic and preliminary results, we will further reveal more structural bioinformatics for the PDB entries 6M71, 7BTF, and 7BV1 and 7BV2 [394]. We analyze the MD data of [384] – MD trajectory data of SARS-CoV-2-RdRp with or without template RNA and remdesivir triphosphate. Tables 3.6, 3.8 and 3.9 respectively list the HBs (with more than 55% occupancy rates from the analyses of the 1 .μs MD trajectory data) and all the existing SBs (from the analyses of the 1 .μs MD trajectory data) of SARS-CoV-2 RdRp with template RNA and remdesivir triphosphate, and Tables 3.7, 3.10 and 3.11 respectively list the HBs (with more than 55% occupancy rates from the analyses of the 1 .μs MD trajectory data) and all the existing SBs (from the analyses of the 1 .μs MD trajectory data) of SARSCoV-2 RdRp without template RNA and remdesivir triphosphate. From MD data of [384], we can confirm all the SBs of the 6M71optimized and 7BTFoptimized models except for SBs A:GLU83-A:LYS73 and A:GLU610-A:HIS752, and the SB A:GLU610-A:HIS752 was replaced by A:GLU610-A:LYS751 (Tables 3.8, 3.9, 3.10 and 3.11). For Mpro, Yamamoto et al. (2020) reported that “although nitro groups were enriched in the substructure of the hit compounds, they did not significantly contribute to the binding interaction in the predicted docking poses” [385]. Next, we specially discuss the SARS-CoV-2-RdRp domain (mainly in the NiRAN domain) binding with some .β-hairpin peptides. We optimized the six models of peptideA-RdRp, peptideB-RdRp, peptideC-RdRp, peptideAdis-RdRp, peptideBdis-RdRp, and peptideCdis-RdRp [321] and got the following RdRp residues binding with each peptide (Fig. 3.4): ◦ peptide A: LYS11, TYR12, THR13, ALA15, ASP16, VAL18, TYR19, ALA20, ARG22, HIS23, ASN28, THR31, LEU32, GLU34, ILE35, VAL94, THR96, LEU97, ASP98, ASN99, TYR107, ASP108, ASP111, SER126, LEU130, ASN595, LEU598, SER599, THR600, ASP601, GLY602, ASN603, LYS604,

.

3.3 New Results and Discussions

167

ARG611, GLN614, HIS615, LEU617, TYR618, GLU619, ARG623; ◦ peptide B: ILE4, ARG6, LYS11, TYR12, THR13, ALA15, ASP16, VAL18, TYR19, ARG22, HIS23, CYS29, ASP30, THR31, LEU32, ILE35, VAL94, THR96, LEU97, ASP98, ASN99, TYR107, ASP108, GLY110, VAL123, SER126, LEU130, ASN595, LEU598, SER599, THR600, ASP601, GLY602, ASN603, LYS604, ARG611, ASN612, GLN614, HIS615, TYR618, GLU619, TYR622, ARG623; .◦ peptide C: THR10, LYS11, TYR12, THR13, ALA15, ASP16, VAL18, TYR19, ARG22, HIS23, ASN28, CYS29, THR31, LEU32, VAL94, THR96, LEU97, ASP98, SER126, LEU130, LEU598, SER599, THR600, ASP601, GLY602, ASN603, LYS604, ILE605, ARG611, GLN614, HIS615, TYR618, GLU619, TYR622, ARG623; .◦ peptide A-dis: LYS11, TYR12, THR13, ALA15, ASP16, VAL18, TYR19, HIS23, GLY27, ASN28, THR31, VAL94, THR96, LEU97, ASP98, ASN99, TYR107, ASP111, SER126, TYR127, LEU130, GLN358, LEU598, SER599, THR600, ASP601, GLY602, ASN603, LYS604, ILE605, ARG611, GLN614, HIS615, TYR618, GLU619, ARG623; .◦ peptide B-dis: THR10, LYS11, TYR12, THR13, ALA15, ASP16, VAL18, TYR19, ALA20, ARG22, HIS23, ASP25, GLY27, ASN28, ASP30, THR31, VAL94, THR96, LEU97, ASP98, ASN99, TYR107, ASP108, ASP111, SER126, LEU130, ASN595, LEU598, SER599, THR600, ASP601, GLY602, ASN603, LYS604, ILE605, LYS608, ARG611, ASN612, GLN614, HIS615, TYR618, GLU619, TYR622, ARG623; .◦ peptide C-dis: LEU9, LYS11, TYR12, THR13, ALA15, ASP16, VAL18, TYR19, ALA20, ARG22, HIS23, PHE24, ASN28, CYS29, THR31, LEU32, THR96, LEU97, VAL94, ASP98, ASN99, TYR107, SER126, LEU130, GLN358, ASN595, LEU598, SER599, THR600, ASP601, GLY602, ASN603, LYS604, ILE605, ARG611, ASN612, GLN614, HIS615, TYR618, GLU619, TYR622, ARG623; .

where the RdRp residues are labeled as aa PRO2-LEU786 (with ACE and NME at the N- and C-terminals, respectively; the residue labels plus 110 will agree with the ones in A-chain of PDB 6M71 where A:CYS301.SG-A:CYS306.SG and A:CYS487.SG-A:CYS645.SG) and the peptide is labeled as aa 31–50. Thus, the RdRp residues are aa ILE114-LEU240 in NiRAN domain (aa 51–249), GLN468 in Finger, and aa ASN705-ARG633 in the palm subdomain (aa 680–815). Each peptide should insert into the groove clamped by the NiRAN domain (aa 51–249) and the palm subdomain (aa 680–815) in the SARS-Cov-2-RdRp [118] and link to the RdRp Finger by residue GLN468. All the six models have the same SB P:LYS48-A:ASP711 (Tables 3.1 and 3.2 and Fig. 3.6) as confirmed below (but for model peptideC-RdRp, it is broken during 13.9–20 .μs). For the optimized peptideA-RdRp, peptideB-RdRp, peptideC-RdRp, peptideAdis-RdRp, peptideBdis-RdRp, and peptideCdis-RdRp models, we find the HBs, SBs, and .π -interactions between the peptide and the RaRp from Table 3.1 and Fig. 3.4, where P-chain is the peptide aa 31–50 and A-chain is the RdRp aa PRO2-LEU786 (where these residue labels plus 110 will agree with the ones

168

3 RNA-Dependent RNA Polymerase (RdRp)

in the A-chain of PDB 6M71). Table 3.12 lists the SBs within the RaRp of the optimized peptideA-RdRp, peptideB-RdRp, peptideC-RdRp, peptideAdis-RdRp, peptideBdis-RdRp, and peptideCdis-RdRp models in [321]. All the six peptides in the optimized models have positive Poisson-Boltzmann electrostatic potential surfaces (EPS), and within RaRp around residues GLU364 and ASP389, and bottom residues CYS42.→AS342.→ASP54.→THR31.→TYR509 .→PHE672.→SER599.→ALA652-ALA667.→THR600 have positive EPS. The MD secondary structural performance of the peptideA-RdRp, peptideBRdRp, peptideC-RdRp, peptideAdis-RdRp, peptideBdis-RdRp, and peptideCdisRdRp models in [321] can be seen from Fig. 3.5. We may see that some .α-helices unfold: ◦ model peptideA-RdRp: segment aa VAL147-LYS162; ◦ model peptideB-RdRp: segment aa ASN387-ALA402; .◦ model peptideC-RdRp: segments aa HID252-ASP267, around ASP342 (8– 20 .μs), aa ASN387-ALA402 (3.8–10.2 .μs); .◦ model peptideAdis-RdRp: around LEU327; .◦ model peptideBdis-RdRp: around ASP342 (17.4–20 .μs), ALA402 (8.9– 11.4 .μs); . .

Fig. 3.4 The six peptides (YKRAKTKYTKRVAGFAKKRK, MKRAKTIYTKRVAGFAKKRR, MYRAKTIYTKRVAGFAKKLK, CKRAKTKYTKRVAGFAKKRC-CONH2, CKRAKTIYTKRVAGFAKKRC-CONH2, CYRAKTIYTKRVAGFAKKLC-CONH2) interacting with SARS-CoV-2-RdRp in their optimized models of [321]: up from left to right – peptideARdRp, peptideB-RdRp, and peptideC-RdRp ; down from left to right – peptideAdis-RdRp, peptideBdis-RdRp, and peptideCdis-RdRp

3.3 New Results and Discussions

169

◦ model peptideCdis-RdRp: around ASP342 (11.4–20 .μs), ALA402 (8–20 .μs).

.

The SBs of RdRp in the optimized models and during 20 .μs MDs can be seen from Tables 3.12 and 3.13. The MD-HBs between the peptide and RdRp (with occupancy rates .≥5%) and within the peptide (with occupancy rates .≥5%) can be seen from Table 3.3. Within RdRp, during 20 .μs MDs, the SBs and HBs (with occupancy rates .≥35%) can be seen from Tables 3.13, 3.14 and Tables 3.15, 3.16, respectively. Do remember in these tables the residue labels plus 110 will agree with the ones in the A-chain of PDB 6M71. From Tables 3.13 and 3.14, we can confirm the following SBs: A:GLU744A:ARG726 (GLU634-ARG616), A:ASP452-A:ARG624 (ASP342-ARG514), A:ASP170-A:ARG173 (ASP60-ARG63), A:GLU474-A:ARG640 (GLU364ARG530), A:ASP499-A:ARG513 (ASP389-ARG403), A:ASP304-A:ARG640 (ASP194-ARG530), A:ASP465-A:ARG132 (ASP355-ARG22), A:ASP477A:ARG640 (ASP367-ARG530), A:GLU136-A:LYS783 (GLU26-LYS673) of RdRp during the 20 .μs MD simulations for the peptideA-RdRp, peptideB-RdRp, peptideC-RdRp, peptideAdis-RdRp, peptideBdis-RdRp, and peptideCdis-RdRp models (Fig. 3.6).

Fig. 3.5 The MD secondary structures of the six models of [321]; each model has 20 .μs MD trajectories – here we pick up 200 frames with “frameStride .= 0.1 .μs”: up from left to right – peptideA-RdRp, peptideB-RdRp, and peptideC-RdRp ; down from left to right – peptideAdisRdRp, peptideBdis-RdRp, and peptideCdis-RdRp

170

3 RNA-Dependent RNA Polymerase (RdRp)

Fig. 3.6 The six models, peptideA-RdRp, peptideB-RdRp, peptideC-RdRp, peptideAdis-RdRp, peptideBdis-RdRp, and peptideCdis-RdRp, all have the same MD-SB P:LYS48-A:ASP711 (but for model peptideC-RdRp, it is broken during 13.9–20 .μs)

3.4 Concluding Remarks In molecular structural studies, optimization is a very useful tool; for example, in [406] the author used optimization hybrid strategies of simulated annealing and local search methods and found that the prion AGAAAA amyloid fibril structure is the Class 7 structure of amyloid fibrils – recently the Class 7 was confirmed by Glynn et al. [124]. Thus, the hybrid strategy of mathematical optimization’s neighboring different (local search) algorithms could be very effective in this chapter. Moreover, this chapter will also present some preliminary structural bioinformatics for developing therapies of the currently fatal COVID-19 virus (Figs 3.7 and 3.8).

Supplementary Information

171

Supplementary Information

Fig. 3.7 Some interesting SBs of the 6M71optimized model confirmed by the 10 μs MD trajectory data of [321]

172

Fig. 3.7 (continued)

3 RNA-Dependent RNA Polymerase (RdRp)

A:ASP98.OD1-P:LYS35.NZ*P:THR36.N-A:ASP98.OD2

P:TYR38.OH-A:GLU619.OE1 P:ARG41.NH1-A:ASN603.OD1

P:ARG33.NE-A:ASP16.OD2 *

P:ALA34.N-A:ASP16.OD2

P:LYS48.NZ-A:ASP601.OD1*-

P:LYS48.NZ-A:ASP601.OD1 *

P:ARG33.NH1-A:ASP16.OD2 *

P:ARG33.NH2-A:LYS11.O

P:ALA34.N-A:ASP16.OD1

P:LYS35.NZ-A:ASP98.OD1 *

P:LYS48-A:ASP601

P:ILE37.N-P:GLY44.O P:LYS48.N-P:ARG33.O

P:LYS35-A:ASP98

P:LYS48-A:ASP601

A:TYR19-P:LYS47.NZ+

P:LYS32.NZ-P:LYS47.O

P:ARG33.N-P:LYS48.O

P:ILE37.N-P:GLY44.O

P:LYS48.N-P:ARG33.O

P:LYS48-A:ASP601

P:TYR38-A:ARG623.NE+

P:TYR31.N-P:LYS50.OXT

P:LYS50.NZ-P:LYS50.O

P:LYS50.OXT-P:TYR31.N P:LYS50.O-P:LYS35.NZ

P:LYS35.NZ-P:LYS50.O

P:ARG33.N-P:LYS48.O

A:TYR12-P:ARG33.NH2+

P:ARG33-A:ASP16

P:ARG33-A:ASP16

P:LYS35-A:ASP98

P:LYS47.NZ-P:LYS32.O

P:ARG33.N-P:LYS48.O

P:CYS31.N-P:CYS50.O

P:ARG49.NH2-P:ARG49.O

P:LYS48.N-P:ARG33.O

P:LYS48-A:ASP601

P:LYS48-A:ASP601 A:TYR19-P:LYS47.NZ+

P:LYS35-A:ASP98

P:ARG33-A:ASP16

P:LYS32-A:ASP30

A:ASP601.OD1-P:LYS48.NZ*-

P:LYS48.NZ-A:ASP601.OD1 *

P:LYS47.NZ-A:THR31.OG1

P:LYS47-A:ASP16

P:LYS37-A:ASP98

P:LYS35-A:ASP98

P:ALA43.N-A:GLN614.OE1 P:PHE45.N-A:LEU598.O

P:LYS48.NZ-A:ASP601.OD1 * A:ASP601.OD1-P:LYS48.NZ*-

A:ASP601.OD1-P:LYS48.NZ*-

P:LYS48.NZ-A:ASP601.OD1 *

P:ALA43.N-A:GLN614.OE1

P:THR36.N-A:ASP98.OD1 P:THR36.OG1-A:ASP98.OD1

P:LYS47.NZ-A:ASP16.OD1 * P:LYS47.NZ-A:THR31.OG1

P:THR36.OG1-A:ASP98.OD2

P:TYR38.OH-A:GLU619.OE2

P:LYS35.NZ-A:ASP98.OD2 * A:ASP98.OD2-P:LYS35.NZ*-

P:LYS37.NZ-A:ASP98.OD1 * P:TYR38.OH-A:GLU619.OE1

P:ALA34.N-A:ASP16.OD1

A:ASP16.OD2-P:ARG33.NH1*-

P:ARG33.NH1-A:ASP16.OD2 *

A:ASP30.OD2-P:LYS32.NZ*-

A:ASP98.OD1-P:LYS35.NZ*-

P:LYS37.NZ-A:ASN99.OD1

P:LYS35.NZ-A:ASP98.OD1 *

Model peptideBdis-RdRp P:LYS32.NZ-A:ASP30.OD2 *

P:THR36.N-A:ASP98.OD2

P:LYS48.NZ-A:ASP601.OD1 *

P:THR36.N-A:ASP98.OD1

Model peptideAdis-RdRp P:ARG33.NH2-A:LYS11.O

Model peptideC-RdRp P:ARG33.NH2-A:LYS11.O

Model peptideB-RdRp

P:ARG33.NH2-A:ASP16.OD1 *

Model peptideA-RdRp

P:TYR31.OXTYR12.OH

P:LYS48.N-P:ARG33.O

P:LYS35.N-P:ALA46.O

P:ARG33.N-P:LEU49.O

P:TYR38-A:AR623.NH2+

A:TYR12-P:ARG33.NH2+

P:LYS48-A:ASP601

P:LYS35-A:ASP98

P:ARG33-A:ASP16

A:ASP601.OD1-P:LYS48.NZ*-

P:LYS48.NZ-A:ASP601.OD1 *

P:THR36.OG1-A:ASP98.OD2

P:THR36.N-A:ASP98.OD2

A:ASP98.OD1-P:LYS35.NZ*-

P:LYS35.NZ-A:ASP98.OD1 *

P:ALA34.N-A:ASP16.OD1

P:ARG33.NH2-A:LYS11.O

P:ARG33.NH1-A:ASP16.OD2 *

Model peptideCdis-RdRp

Table 3.1 The HBs, SBs, and π-cations between the peptide (P-chain) and the RaRp (A-chain) of the peptideA-RdRp, peptideB-RdRp, peptideC-RdRp, peptideAdis-RdRp, peptideBdis-RdRp, and peptideCdis-RdRp models in [321] are optimized, where * means that at the same time, there exists an SB between the residues. The HBs within each peptide are also shown

Supplementary Information 173

174

3 RNA-Dependent RNA Polymerase (RdRp)

Table 3.2 The 20 μs MD-SBs between the peptide (P-chain) and the RaRp (A-chain) of the peptideA-RdRp, peptideB-RdRp, peptideC-RdRp, peptideAdis-RdRp, peptideBdis-RdRp, and peptideCdis-RdRp models in [321] Model peptideA-RdRp

Model peptideB-RdRp

Model peptideC-RdRp

Model peptideAdis-RdRp

Model peptideBdis-RdRp

Model peptideCdis-RdRp

A:ASP111-P:LYS37

A:ASP16-P:ARG33

A:ASP16-P:ARG33

A:ASP111-P:LYS37

A:ASP108-P:ARG33

A:ASP16-P:ARG33

A:ASP16-P:ARG33

A:ASP25-P:LYS47

A:ASP601-P:LYS47

A:ASP16-P:ARG33

A:ASP111-P:LYS35

A:ASP25-P:LYS47

A:ASP25-P:ARG49

A:ASP30-P:ARG49

A:ASP601-P:LYS48

A:ASP16-P:LYS35

A:ASP16-P:ARG33

A:ASP601-P:LYS47

A:ASP25-P:LYS32

A:ASP30-P:LYS32

A:ASP98-P:ARG33

A:ASP30-P:LYS32

A:ASP16-P:LYS35

A:ASP601-P:LYS48

A:ASP25-P:LYS47

A:ASP601-P:ARG49

A:ASP98-P:LYS35

A:ASP601-P:ARG49

A:ASP25-P:LYS32

A:ASP98-P:ARG33

A:ASP30-P:ARG33

A:ASP601-P:LYS48

A:ASP98-P:LYS48

A:ASP601-P:LYS37

A:ASP25-P:LYS47

A:ASP98-P:LYS35

A:ASP30-P:LYS32

A:ASP98-P:ARG50

A:ASP98-P:LYS50

A:ASP601-P:LYS47

A:ASP30-P:LYS32

A:ASP601-P:ARG49

A:ASP98-P:LYS35

A:ASP601-P:LYS48

A:ASP601-P:LYS47

A:ASP601-P:LYS37

A:GLU26-P:ARG49

A:ASP98-P:LYS35

A:ASP601-P:LYS48

A:ASP601-P:LYS48

A:GLU26-P:LYS32

A:ASP98-P:LYS37

A:ASP98-P:LYS35

A:ASP601-P:LYS50

A:GLU26-P:LYS47

A:ASP98-P:LYS48

A:ASP98-P:LYS48

A:ASP98-P:ARG33 A:ASP98-P:LYS35 A:ASP98-P:LYS37 A:ASP98-P:LYS48

Fig. 3.8 Some interesting HBs of the 6M71optimized model confirmed by the 10 μs MD trajectory data of [321]

P:LYS47.NZ-SER599.O 7.46 P:CYX31.N-ASP30.OD1 5.97

P:THR36.N-ASP98.OD2 21.89

P:THR36.N-ASP98.OD1 19.40

P:THR36.OG1-ASP98.OD1 14.93

P:ALA34.N-ASP16.OD2 11.94

P:THR36.OG1-ASP98.OD2 10.95

P:ALA34.N-ASP16.OD1 9.45

P:LYS48.NZ-ASP601.OD2 9.45

P:LYS47.NZ-ASP25.OD2 9.45

GLN614.NE2-P:ALA43.O 7.46

P:LYS48.NZ-ASP601.OD1 6.97

P:LYS47.NZ-THR31.OG1 6.47

P:ARG33.NH2-ASP16.OD1 6.47

P:LYS47.NZ-ASP25.OD1 5.97

P:THR36.N-ASP98.OD1 24.88

P:ALA34.N-ASP16.OD2 19.90

P:THR36.N-ASP98.OD2 17.41

P:ARG33.NE-ASP16.OD2 11.94

GLN614.NE2-P:ALA43.O 11.44

P:ALA34.N-ASP16.OD1 9.95

P:TYR31.OH-ASP16.OD1 9.45

P:ARG33.NH2-ASP16.OD1 7.96

P:ALA43.N-GLN614.OE1 6.97

P:TYR31.N-ASN28.OD1 5.97

P:THR36.OG1-ASP98.OD2 5.47

P:LYS32.N-THR31.OG1 5.47

TYR618.OH-P:THR36.OG1 5.47

P:THR39.N-P:VAL42.O 50.75

P:LYS35.N-P:ALA46.O 42.79

P:VAL42.N-P:THR39.OG1 38.81

P:LYS48.N-P:ARG33.O 28.86

P:ARG33.N-P:LYS48.O 15.92

P:ALA46.N-P:LYS35.O 7.46

P:VAL42.N-P:THR39.OG1 29.35

P:LYS37.N-P:GLY44.O 28.86

P:LYS35.N-P:ALA46.O 28.86

P:LYS48.N-P:ARG33.O 25.37

P:ALA46.N-P:LYS35.O 17.41

P:GLY44.N-P:LYS37.O 10.45

P:MET31.N-P:ARG50.OXT 5.47

P:ARG50.N-P:MET31.O 7.46

P:ILE37.N-P:GLY44.O 53.73

P:THR39.N-P:VAL42.O 53.23

P:LYS35.NZ-ASP98.OD1 5.47

Model peptideAdis-RdRp

P:GLY44.N-P:LYS37.O 8.96

P:LYS50.N-P:MET31.O 5.47

P:LYS47.NZ-P:PHE45.O 7.46

P:ARG33.NH1-P:LYS32.O 7.46

P:ALA46.N-P:LYS35.O 19.40

P:LYS48.N-P:ARG33.O 24.88

P:LYS37.N-P:GLY44.O 27.36

P:VAL42.N-P:THR39.OG1 28.86

P:ARG33.N-P:LYS48.O 33.33

P:LYS35.N-P:ALA46.O 41.79

P:THR39.N-P:VAL42.O 43.28

P:LYS32.N-THR31.OG1 7.96

P:ALA34.N-ASP16.OD2 10.45

P:LYS47.NZ-ASP601.OD1 14.43

P:LYS47.NZ-ASP601.OD2 14.43

P:PHE45.N-LEU598.O 17.91

GLN614.NE2-P:ALA43.O 18.91

P:THR36.N-ASP98.OD2 22.89

P:THR36.N-ASP98.OD1 27.36

P:ARG33.N-P:LYS48.O 10.95

P:ALA46.N-P:LYS35.O 15.42

P:VAL42.N-P:THR39.OG1 34.33

P:LYS48.N-P:ARG33.O 39.30

P:LYS35.N-P:ALA46.O 40.80

P:ILE37.N-P:GLY44.O 44.28

P:THR39.N-P:VAL42.O 56.22

P:LYS48.NZ-ASP601.OD1 6.47

P:THR36.OG1-ASP98.OD1 8.46

P:ALA34.N-ASP16.OD2 8.96

P:THR36.OG1-ASP98.OD2 12.44

GLN614.NE2-P:ALA43.O 13.43

P:THR36.N-ASP98.OD2 19.90

P:ALA34.N-ASP16.OD1 20.90

P:THR36.N-ASP98.OD1 29.35

P:ALA34.N-ASP16.OD1 36.82

HIP615.NE2-P:THR39.O 46.77

Model peptideC-RdRp

P:PHE45.N-LEU598.O 41.29

P:PHE45.N-LEU598.O 32.84 P:PHE45.N-LEU598.O 35.82

HIP615.NE2-P:THR39.O 49.25

Model peptideB-RdRp

HIP615.NE2-P:THR39.O 47.26

Model peptideA-RdRp

HIP615.NE2-P:THR39.O 36.32

P:ARG33.NH1-P:LYS32.O 7.46

P:CYX50.N-P:CYX31.O 13.93

P:ALA46.N-P:LYS35.O 13.93

P:ARG33.N-P:LYS48.O 29.85

P:VAL42.N-P:THR39.OG1 31.84

P:ILE37.N-P:GLY44.O 36.32

P:LYS48.N-P:ARG33.O 36.32

P:LYS35.N-P:ALA46.O 49.75

P:THR39.N-P:VAL42.O 53.23

P:THR36.OG1-ASP98.OD2 9.45

P:THR36.OG1-ASP98.OD1 9.45

P:ALA34.N-ASP16.OD1 14.93

GLN614.NE2-P:ALA43.O 15.42

P:THR36.N-ASP98.OD1 16.92

P:ALA34.N-ASP16.OD2 17.91

P:THR36.N-ASP98.OD2 23.88

P:PHE45.N-LEU598.O 33.83

HIP615.NE2-P:THR39.O 56.72

Model peptideBdis-RdRp

P:ALA46.N-P:LYS35.O 11.94

P:CYX50.N-P:CYX31.O 13.93

P:ARG33.N-P:LYS48.O 26.87

P:VAL42.N-P:THR39.OG1 35.32

P:ILE37.N-P:GLY44.O 39.80

P:LYS35.N-P:ALA46.O 41.29

P:LYS48.N-P:ARG33.O 47.26

P:THR39.N-P:VAL42.O 55.72

P:THR36.OG1-ASP98.OD2 8.96

P:THR36.OG1-ASP98.OD1 8.96

P:ALA34.N-ASP16.OD1 10.45

P:ALA34.N-ASP16.OD2 11.44

GLN614.NE2-P:ALA43.O 16.42

P:THR36.N-ASP98.OD2 18.91

P:THR36.N-ASP98.OD1 24.38

P:PHE45.N-LEU598.O 38.81

HIP615.NE2-P:THR39.O 50.75

Model peptideCdis-RdRp

Table 3.3 The 20 μs MD-HBs (with occupancy rates ≥5%) between the peptide (P-chain) and the RaRp (A-chain) of the peptideA-RdRp, peptideB-RdRp, peptideC-RdRp, peptideAdis-RdRp, peptideBdis-RdRp, and peptideCdis-RdRp models in [321] and the MD-HBs (with occupancy rates ≥5%) within the peptide (P-chain)

Supplementary Information 175

176 Table 3.4 The HBs with more than 50% occupancy rates from the analyses of the 10 μs MD trajectory data of [321]

3 RNA-Dependent RNA Polymerase (RdRp) Donor

Acceptor

Occupancy

B/D:ILE132.N

B/D:LEU184.O

79.04%

B/D:THR141.OG1

B/D:THR137.O

78.20%

B/D:LYS139.N

B/D:TYR135.O

74.85%

B/D:ALA188.N

B/D:LEU128.O

74.49%

B/D:ILE185.N

B/D:VAL160.O

73.77%

B/D:VAL186.N

B/D:VAL130.O

73.17%

B/D:LEU128.N

B/D:ALA188.O

71.74%

B/D:GLN157.N

B/D:THR187.O

71.50%

B/D:GLU155.N

B/D:LEU189.O

69.10%

A:THR319.OG1

A:LEU316.O

68.26%

C:THR9.OG1

C:ASP5.O

68.14%

B/D:THR187.N

B/D:GLN158.O

67.19%

A:THR148.OG1

A:GLU144.O

67.07%

A:THR701.OG1

A:CYS697.O

66.23%

B/D:VAL130.N

B/D:VAL186.O

65.87%

A:VAL764.N

A:MET615.O

64.91%

B/D:ASN176.ND2

B/D:GLU171.O

64.91%

B/D:TRP154.NE1

B/D:TYR149.O

64.19%

A:THR248.OG1

A:ILE244.O

63.23%

B/D:SER177.OG

B/D:SER173.O

63.11%

B/D:THR137.OG1

B/D:ASP134.OD1

62.75%

A:TYR294.OH

A:ASN314.OD1

61.92%

B/D:ILE156.N

B/D:THR145.O

61.56%

B/D:THR137.OG1

B/D:ASP134.OD2

61.32%

A:TYR237.OH

A:GLN210.OE1

61.08%

B/D:ALA191.N

B/D:LEU153.O

61.08%

B/D:THR123.OG1

B/D:ILE119.O

59.64%

A:SER681.OG

A:GLU665.OE2

59.40%

B/D:THR124.OG1

B/D:ILE120.O

59.16%

A:THR604.OG1

A:ASN600.O

59.16%

B/D:CYS142.N

B/D:TYR138.O

58.20%

A:ASP211.N

A:ASN215.O

57.13%

A:THR870.OG1

A:TYR867.O

56.53%

A:VAL535.N

A:ASN356.OD1

56.17%

A:GLN789.NE2

A:GLN698.OE1

55.09%

B/D:PHE147.N

B/D:TRP154.O

54.97%

A:THR582.OG1

A:SER578.O

54.49%

A:TYR787.OH

A:TYR163.O

54.37%

A:THR252.OG1

A:ARG249.O

54.13%

C:SER57.OG

C:VAL53.O

53.53%

B/D:THR93.OG1

B/D:THR89.O

52.69%

B/D:LEU189.N

B/D:GLU155.O

52.22%

A:VAL330.N

B:VAL115.O

51.98%

A:GLN822.N

A:ASP825.O

51.50%

B/D:VAL160.N

B/D:ILE185.O

50.90%

A:TYR884.OH

A:ILE837.O

50.90%

A:SER343.OG

A:ASP377.OD1

50.78%

A:TRP216.N

A:ALA95.O

50.78%

A:SER709.OG

A:ASN705.O

50.66%

A:VAL820.N

A:VAL827.O

50.54%

A:SER239.OG

A:ASP465.OD1

50.54%

A:VAL202.N

A:ILE223.O

50.18%

A:VAL667.N

A:TYR674.O

50.18%

A:ASN416.N

A:CYS842.O

50.18%

A:SER384.OG

A:MET380.O

50.18%

Supplementary Information Table 3.5 The HBs for some important SBs of the 6M71optimized model from the analyses of the 10 μs MD trajectory data of [321]

177 Donor

Acceptor

Occupancy

A:ARG331.NH1

B:ASP112.O

A:ARG331.NH2

B:ASP112.OD2

A:ARG331.NH2

B:ASP112.O

A:ARG331.NH2

B:ASP112.OD1

A:ARG331.NH1

B:ASP112.OD1

A:ARG331.NH1

B:ASP112.OD2

A:ARG331.NE

B:ASP112.O

B:ARG111.NH2

A:ASP274.OD2

B:ARG111.NH2

A:ASP274.OD1

B:ARG111.NH1

A:ASP274.OD1

B:ARG111.NH1

A:ASP274.OD2

B:ARG111.NE

A:ASP274.OD1

B:ARG111.NE

A:ASP274.OD2

D/B:ARG111.NE

D/B:ASP112.OD1

D/B:ARG111.NH2

D/B:ASP112.OD1

D/B:ARG111.NH2

D/B:ASP112.OD2

D/B:ARG111.NE

D/B:ASP112.OD2

D/B:ARG111.NH1

D/B:ASP112.OD1

D/B:ARG111.NH1

D/B:ASP112.OD2

D/B:ARG111.NE

D/B:ASP112.O

C:LYS51.NZ

C:ASP38.OD2

C:LYS51.NZ

C:ASP38.OD1

C:LYS51.NZ

C:ASP38.O

A:LYS676.NZ

A:GLU665.OE1

A:LYS676.N

A:GLU665.O

10.78% 4.55% 4.43% 4.43% 0.60% 0.48% 0.24% 13.29% 11.38% 3.95% 3.59% 3.23% 2.28% 7.90% 7.90% 7.66% 6.83% 1.44% 1.08% 0.24% 19.88% 18.32% 0.48% 40.00% 34.01% 0.96% 10.54% 10.54% 19.28% 18.20% 18.20% 17.60% 37.01% 19.40% 2.04% 0.84% 0.60% 26.23% 25.75% 20.60% 17.60% 3.95% 1.08% 0.60% 31.98% 28.14% 27.78% 22.75% 13.05% 10.06% 9.70% 9.46% 3.11% 22.28% 19.52% 17.25% 17.49% 11.26% 15.21% 13.29% 0.12% 0.12% 17.96% 15.69%

A:LYS676.NZ

A:GLU665.OE2

A:LYS73.NZ

A:GLU83.OE2

A:LYS73.NZ

A:GLU83.OE1

A:ARG726.NH1

A:GLU744.OE2

A:ARG726.NH2

A:GLU744.OE1

A:ARG726.NH2

A:GLU744.OE2

A:ARG726.NH1

A:GLU744.OE1

A:ARG624.NH2

A:ASP452.OD1

A:ARG624.NH2

A:ASP452.OD2

A:ARG624.NE

A:ASP452.OD2

A:ARG624.NE

A:ASP452.OD1

A:ARG624.NE

A:ASP452.O

A:ARG173.NE

A:ASP170.OD2

A:ARG173.NH2

A:ASP170.OD1

A:ARG173.NH2

A:ASP170.OD2

A:ARG173.NE

A:ASP170.OD1

A:ARG173.N

A:ASP170.O

A:ARG173.NH1

A:ASP170.OD1

A:ARG173.NH1

A:ASP170.OD2

A:ARG640.NH2

A:GLU474.OE2

A:ARG640.NH2

A:GLU474.OE1

A:ARG640.NH1

A:GLU474.OE1

A:ARG640.NH1

A:GLU474.OE2

A:ARG513.NH2

A:ASP499.OD1

A:ARG513.NH2

A:ASP499.OD2

A:ARG513.NE

A:ASP499.OD2

A:ARG513.NE

A:ASP499.OD1

A:ARG513.NH1

A:ASP499.OD1

A:ARG640.NH2

A:ASP304.OD2

A:ARG640.NH2

A:ASP304.OD1

A:ARG640.NE

A:ASP304.OD2

A:ARG132.NH1

A:ASP465.OD2

A:ARG132.NH2

A:ASP465.OD2

A:ARG640.NH1

A:ASP477.OD1

A:ARG640.NH1

A:ASP477.OD2

A:ARG640.NH2

A:ASP477.OD1

A:ARG640.NE

A:ASP477.OD2

A:LYS783.NZ

A:GLU136.OE2

A:LYS783.NZ

A:GLU136.OE1

Table 3.6 The HBs with more than 55% occupancy rates from the analyses of the 1 μs MD trajectory data of SARS-CoV-2 RdRp with template RNA and remdesivir triphosphate [384]

Donor-acceptor

Occupancy

ARG392.NE-ASP390.OD1

87.72%

ARG173.NE-ASP170.OD1

87.33%

ARG392.NH2-ASP390.OD2

86.56%

ARG173.NH2-ASP170.OD2

86.28%

ARG132.NH2-ASP465.OD2

83.78%

ARG640.NH2-GLU474.OE2

82.92%

TYR156.OH-ASP170.OD2

78.60%

THR394.N-ASP454.OD1

78.60%

ARG654.NH2-ASN568.OD1

77.74%

ARG640.NH1-GLU474.OE1

75.34%

ARG513.NH2-ASP499.OD1

74.47%

HIP256.ND1-LYS263.O

74.18%

ARG197.NE-TYR289.OH

73.32%

SER343.N-ASP377.OD2

72.84%

THR531.OG1-PHE528.O

72.65%

ARG513.NE-ASP499.OD2

72.36%

TYR653.OH-HIS355.O

69.96%

TYR674.OH-ASP390.OD2

69.87%

ALA512.N-LYS500.O

69.29%

ARG640.NE-ASP304.OD2

68.91%

ARG197.NH2-ASP194.OD1

68.81%

TYR787.OH-TYR163.O

68.52%

THR701.OG1-CYS697.O

67.66%

SER239.OG-ASP465.OD1

67.18%

THR319.OG1-LEU316.O

67.08%

LEU469.N-ASP465.O

66.89%

ARG624.NH2-ASP452.OD1

66.41%

TYR884.OH-ILE837.O

66.31%

CYS765.N-SER754.O

66.12%

ASN37.ND2-ALA443.O

66.03%

SER692.OG-ALA688.O

65.83%

THR394.OG1-ASP454.OD1

65.74%

ASP336.N-SER363.O

65.74%

TYR237.OH-GLN210.OE1

64.97%

MET668.N-THR540.O

64.11%

SER26.OG-ASP163.OD1

63.63%

ARG624.NE-ASP452.OD2

62.96%

VAL130.N-VAL186.O

62.96%

VAL202.N-ILE223.O

62.86%

THR124.OG1-ILE120.O

62.67%

GLN724.NE2-LEU707.O

62.67%

HIS816.N-TYR831.O

62.48%

THR148.OG1-GLU144.O

61.32%

TYR175.OH-TYR787.OH

60.75%

ASN657.ND2-ASN534.O

60.65%

TRP154.NE1-TYR149.O

60.56%

ASN416.ND2-GLY841.O

60.56%

TYR175.N-ILE171.O

60.36%

SER384.OG-MET380.O

59.88%

GLY559.N-GLN541.O

59.88%

ARG305.NH1-GLU474.OE2

59.88%

LYS676.NZ-GLU665.OE1

59.79%

VAL186.N-VAL130.O

59.60%

HIS347.N-GLY327.O

59.50%

ALA400.N-ASN386.O

59.12%

THR604.OG1-ASN600.O

58.64%

ASN416.N-CYS842.O

58.45%

VAL472.N-GLN468.O

58.35%

VAL535.N-ASN356.OD1

58.25%

TYR595.N-TYR915.O

57.97%

ILE185.N-VAL160.O

57.68%

ARG640.NH2-ASP304.OD1

57.68%

THR93.OG1-THR89.O

57.68%

ASN695.ND2-SER759.O

57.49%

LYS577.N-GLN573.O

57.20%

THR870.OG1-TYR867.O

57.20%

TYR674.N-VAL667.O

57.10%

LEU614.N-GLU802.O

57.01%

ASN705.ND2-TYR788.OH

56.91%

ARG654.NH1-THR531.OG1

56.91%

THR248.OG1-ILE244.O

56.72%

THR9.OG1-ASP5.O

56.53%

ILE757.N-THR586.O

56.43%

LYS27.NZ-ASP163.OD2

56.43%

Supplementary Information Table 3.7 The HBs with more than 55% occupancy rates from the analyses of the 1 μs MD trajectory data of SARS-CoV-2 RdRp without template RNA and remdesivir triphosphate [384]

179 Donor-acceptor

Occupancy

ILE132.N-LEU184.O

87.14%

ARG392.NE-ASP390.OD1

83.01%

ILE185.N-VAL160.O

82.44%

ARG392.NH2-ASP390.OD2

81.57%

ALA188.N-LEU128.O

80.33%

VAL186.N-VAL130.O

78.31%

THR540.OG1-GLU665.OE2

77.93%

TRP154.NE1-TYR149.O

77.35%

ARG640.NE-ASP304.OD1

76.97%

LYS676.NZ-GLU665.OE1

76.58%

ARG631.NH2-ASP684.OD2

76.01%

TRP154.N-PHE147.O

76.01%

THR93.OG1-THR89.O

75.62%

GLN157.N-THR187.O

74.95%

ILE156.N-THR145.O

73.70%

LEU128.N-ALA188.O

73.61%

ARG197.NE-TYR289.OH

72.84%

HIP256.ND1-LYS263.O

71.40%

THR89.OG1-SER85.O

70.35%

CYS765.N-SER754.O

69.87%

VAL472.N-GLN468.O

69.77%

SER26.N-ASP163.OD1

69.77%

TYR595.N-TYR915.O

69.77%

TYR674.OH-ASP390.OD2

69.00%

ARG640.NH2-GLU474.OE1

68.71%

ARG640.NH1-GLU474.OE2

68.52%

THR9.OG1-ASP5.O

67.66%

VAL130.N-VAL186.O

67.27%

ARG640.NH2-ASP304.OD2

67.18%

GLU155.N-LEU189.O

66.12%

THR701.OG1-CYS697.O

65.16%

HIS347.N-GLY327.O

64.97%

THR187.N-GLN158.O

64.40%

THR556.OG1-ASP452.OD2

64.20%

GLN724.NE2-LEU707.O

63.72%

TYR237.OH-GLN210.OE1

63.53%

ASN628.ND2-GLU350.OE2

62.96%

PHE92.N-GLN88.O

62.76%

THR556.N-ASP452.OD2

62.00%

SER26.OG-ASP163.OD1

61.80%

LEU189.N-GLU155.O

61.42%

SER384.OG-MET380.O

60.65%

TYR653.OH-HIE355.O

60.36%

CYS142.N-TYR138.O

60.36%

LEU117.N-PRO328.O

60.17%

MET668.N-THR540.O

59.98%

CYS464.N-ASN312.OD1

59.50%

LEU614.N-GLU802.O

59.21%

THR84.OG1-ARG80.O

59.02%

TYR175.OH-TYR787.OH

58.93%

THR248.OG1-ILE244.O

58.73%

ASP336.N-SER363.O

58.64%

ASN416.N-CYS842.O

58.45%

ALA400.N-ASN386.O

58.35%

ASP421.N-LYS417.O

58.16%

VAL535.N-ASN356.OD1

58.06%

TYR787.OH-TYR163.O

57.87%

THR148.OG1-GLU144.O

57.68%

ASN734.N-GLU729.O

57.49%

ALA311.N-ILE307.O

57.29%

THR686.OG1-ASP684.OD1

57.10%

ARG555.NH1-ASP623.OD1

56.81%

TYR175.N-ILE171.O

56.72%

THR531.OG1-PHE528.O

56.62%

LEU469.N-ASP465.O

56.62%

VAL353.N-ASN297.OD1

56.53%

THR137.OG1-ASP134.OD1

56.43%

THR870.OG1-TYR867.O

56.24%

180

3 RNA-Dependent RNA Polymerase (RdRp)

Table 3.8 All the existing SBs from the analyses of the 1 μs MD trajectory data of SARS-CoV-2 RdRp with template RNA and remdesivir triphosphate [384] In MD

-

In opt

-

A:ASP100-A:ARG118

B:ASP101-B:LYS97

A:ASP135-A:LYS780

B:GLU171-B:LYS165

A:ASP100-A:HIS99

B:ASP112-B:ARG111

A:ASP140-A:LYS143

A:ASP100-A:LYS91

B:ASP143-B:LYS139

A:ASP161-A:LYS160

C:ASP38-C:LYS51

A:ASP100-A:LYS98

B:ASP161-B:LYS165

A:ASP170-A:ARG173

C:GLU47-C:LYS43

A:ASP126-A:ARG33

B:ASP163-B:LYS165

A:ASP194-A:ARG197

A:ASP126-A:LYS47

B:ASP78-B:ARG80

A:ASP194-A:LYS288

A:ASP135-A:HIS133

B:ASP78-B:LYS79

A:ASP235-A:ARG467

A:ASP135-A:LYS780

B:ASP78-B:LYS82

A:ASP235-A:ARG735

A:ASP135-A:LYS783

B:ASP99-B:ARG96

A:ASP258-A:LYS263

A:ASP140-A:LYS143

B:GLU171-B:LYS165

A:ASP260-A:LYS263

C:ASP38-C:LYS51

A:ASP291-A:ARG735

A:ASP269-A:LYS272

A:ASP153-A:ARG118 A:ASP154-A:ARG118 A:ASP161-A:LYS160

C:ASP44-C:LYS43

A:ASP304-A:ARG640

A:ASP170-A:ARG173

C:ASP5-C:LYS2

A:ASP304-A:ARG651

A:ASP170-A:LYS159

C:GLU23-C:ARG21

A:ASP358-A:ARG533

A:ASP194-A:ARG197

C:GLU47-C:LYS43

A:ASP390-A:ARG392

A:ASP194-A:LYS288

C:GLU47-C:LYS51

A:ASP40-A:LYS41

A:ASP211-A:ARG118

C:GLU50-C:LYS51

A:ASP418-A:LYS890

A:ASP218-A:ARG118

A:ASP421-A:LYS417

A:ASP218-A:ARG33

A:ASP269-B:ARG111

A:ASP452-A:ARG624

A:ASP218-A:HIS99

A:ASP274-B:ARG111

A:ASP452-A:LYS621

A:ASP218-A:LYS50

A:ASP517-B:ARG80

A:ASP454-A:ARG457

A:ASP221-A:LYS50

A:ASP517-B:LYS79

A:ASP235-A:ARG467

A:ASP523-B:ARG80

A:ASP477-A:ARG640

A:ASP235-A:ARG735

A:GLU277-B:ARG111

A:ASP477-A:LYS641

A:GLU431-C:LYS2

A:ASP484-A:LYS574

A:ASP481-A:LYS478

A:ASP258-A:LYS263 A:ASP260-A:ARG183

A:ASP465-A:ARG132

A:ASP260-A:LYS263

A:GLU431-C:LYS43

A:ASP499-A:ARG513

A:ASP269-A:LYS267

A:GLU436-C:LYS2

A:ASP523-A:LYS369

A:ASP269-A:LYS272

A:GLU436-C:LYS43

A:ASP608-A:LYS751 A:ASP618-A:LYS798 X

A:ASP274-A:LYS272 A:ASP284-A:LYS281

B:ASP99-A:LYS332

A:ASP284-A:LYS288

B:ASP112-A:ARG331

A:ASP684-A:ARG631 A:ASP711-A:LYS714 A:ASP736-A:ARG305

A:ASP291-A:ARG735 A:ASP303-A:ARG651

B:ASP161-C:LYS27

A:ASP804-A:LYS807

A:ASP304-A:ARG640

B:ASP163-C:LYS27

A:ASP825-A:HIS599 X A:ASP833-A:LYS438

A:ASP304-A:ARG651 A:ASP336-A:ARG365 A:ASP358-A:ARG533

C:ASP5-A:LYS430

A:ASP845-A:ARG858 A:ASP846-A:LYS411

A:ASP36-A:LYS50

A:ASP865-A:LYS593

A:ASP390-A:ARG392

A:ASP879-A:HIS882

A:ASP40-A:LYS41

A:ASP879-A:LYS426

A:ASP418-A:LYS417

A:ASP893-A:HIS892

A:ASP418-A:LYS849

A:GLU136-A:LYS783

A:ASP418-A:LYS890

A:GLU144-A:LYS121

A:ASP421-A:LYS417

A:GLU180-A:ARG181

A:ASP452-A:ARG624

A:GLU254-A:ARG183

A:ASP452-A:LYS621

A:GLU254-A:ARG285

A:ASP454-A:ARG457

A:GLU277-A:LYS281

A:ASP465-A:ARG132

A:GLU278-A:LYS281

A:ASP477-A:ARG640

A:GLU350-A:ARG349

A:ASP477-A:LYS478

A:GLU474-A:ARG640

A:ASP477-A:LYS641

A:GLU658-A:ARG631

A:ASP481-A:LYS478

A:GLU658-A:ARG654

A:ASP481-A:LYS641

A:GLU665-A:LYS676

A:ASP484-A:LYS574

A:GLU729-A:HIS725 X

A:ASP499-A:ARG513

A:GLU744-A:ARG726

A:ASP499-A:LYS511

A:GLU796-A:LYS783

A:ASP523-A:LYS369

A:GLU802-A:LYS807

A:ASP608-A:ARG750

A:GLU811-A:LYS798 X

A:ASP608-A:LYS751

A:GLU876-A:LYS430

A:ASP623-A:ARG624

A:GLU894-A:LYS890

A:ASP623-A:LYS621

A:GLU917-A:LYS871

Supplementary Information Table 3.9 All the existing SBs from the analyses of the 1 μs MD trajectory data of SARS-CoV-2 RdRp with template RNA and remdesivir triphosphate [384] (continuation)

181 In MD A:ASP684-A:ARG631 A:ASP711-A:LYS50 A:ASP711-A:LYS714 A:ASP736-A:ARG305 A:ASP738-A:ARG726 A:ASP740-A:ARG726 A:ASP804-A:LYS807 A:ASP824-A:LYS821 A:ASP825-A:LYS603 A:ASP833-A:LYS438 A:ASP845-A:ARG858 A:ASP845-A:LYS411 A:ASP846-A:LYS411 A:ASP846-A:LYS849 A:ASP865-A:LYS593 A:ASP879-A:HIS882 A:ASP879-A:LYS426 A:ASP893-A:ARG889 A:ASP893-A:HIS892 A:ASP893-A:LYS890 A:ASP910-A:ARG914 A:ASP92-A:LYS91 A:ASP92-A:LYS98 A:GLU136-A:LYS143 A:GLU136-A:LYS780 A:GLU136-A:LYS783 A:GLU144-A:ARG118 A:GLU144-A:LYS121 A:GLU144-A:LYS143 A:GLU167-A:LYS159 A:GLU167-A:LYS160 A:GLU167-A:LYS621 A:GLU180-A:ARG181 A:GLU180-A:ARG183 A:GLU254-A:ARG183 A:GLU254-A:ARG285 A:GLU277-A:LYS272 A:GLU277-A:LYS281 A:GLU278-A:LYS272 A:GLU278-A:LYS281 A:GLU350-A:ARG349 A:GLU370-A:LYS369 A:GLU431-A:LYS430 A:GLU436-A:LYS438 A:GLU474-A:ARG305 A:GLU474-A:ARG640 A:GLU610-A:LYS751 A:GLU658-A:ARG631 A:GLU658-A:ARG654 A:GLU665-A:LYS676 A:GLU729-A:ARG733 A:GLU744-A:ARG726 A:GLU796-A:LYS780 A:GLU796-A:LYS783 A:GLU802-A:HIS810 A:GLU802-A:LYS807 A:GLU811-A:HIS810 A:GLU84-A:HIS99 A:GLU84-A:LYS91 A:GLU84-A:LYS98 A:GLU876-A:LYS426 A:GLU876-A:LYS430 A:GLU894-A:LYS890 A:GLU917-A:ARG914 A:GLU917-A:LYS871 A:GLU919-A:ARG583 A:GLU919-A:ARG914

-

In opt

-

182

3 RNA-Dependent RNA Polymerase (RdRp)

Table 3.10 All the existing SBs from the analyses of the 1 μs MD trajectory data of SARS-CoV2 RdRp without template RNA and remdesivir triphosphate [384] In MD

-

In opt

-

A:ASP100-A:ARG118

B:ASP101-B:ARG190

A:ASP135-A:LYS780

B:ASP161-B:LYS165 B:ASP163-B:LYS165

A:ASP100-A:HIS99

B:ASP101-B:LYS97

A:ASP140-A:LYS143

A:ASP100-A:LYS91

B:ASP112-B:ARG111

A:ASP161-A:LYS160

A:ASP100-A:LYS98

B:ASP161-B:LYS165

A:ASP170-A:ARG173

C:ASP38-C:LYS51

A:ASP126-A:ARG33

B:ASP163-B:LYS165

A:ASP194-A:ARG197

C:GLU23-C:ARG21 C:GLU47-C:LYS43

A:ASP126-A:LYS47

B:ASP78-B:ARG80

A:ASP194-A:LYS288

A:ASP135-A:HIS133

B:ASP78-B:LYS79

A:ASP208-A:LYS50

A:ASP135-A:LYS780

B:ASP78-B:LYS82

A:ASP235-A:ARG467

A:ASP135-A:LYS783

B:GLU171-B:LYS165

A:ASP235-A:ARG735

A:ASP140-A:LYS143

C:ASP38-C:LYS51

A:ASP258-A:LYS263

A:ASP143-A:LYS139

C:ASP44-C:LYS43

A:ASP260-A:LYS263

A:ASP161-A:LYS160

C:ASP5-C:LYS2

A:ASP274-A:LYS272

A:ASP170-A:ARG173

C:GLU23-C:ARG21

A:ASP284-A:LYS281

A:ASP170-A:LYS159

C:GLU47-C:LYS43

A:ASP291-A:ARG735

A:ASP194-A:ARG197

C:GLU47-C:LYS51

A:ASP303-A:ARG651

A:ASP194-A:LYS288

C:GLU50-C:LYS51

A:ASP304-A:ARG640

A:ASP208-A:LYS50

D:ASP112-D:ARG111

A:ASP304-A:ARG651

A:ASP211-A:ARG118

D:ASP143-D:LYS139

A:ASP358-A:ARG533

A:ASP218-A:ARG118

D:ASP161-D:LYS165

A:ASP36-A:ARG733

A:ASP218-A:ARG33

D:ASP163-D:LYS127

A:ASP390-A:ARG392

A:ASP218-A:HIS99

D:ASP163-D:LYS165

A:ASP40-A:LYS41

A:ASP218-A:LYS50

D:ASP99-D:ARG96

A:ASP418-A:LYS890 A:ASP421-A:LYS417

A:ASP218-A:LYS98 A:ASP235-A:ARG467

A:ASP274-B:ARG111

A:ASP452-A:ARG624

A:ASP235-A:ARG735

A:ASP517-B:LYS79

A:ASP452-A:LYS621 X

A:ASP258-A:LYS263

A:ASP523-B:ARG80

A:ASP454-A:ARG457

A:ASP260-A:LYS263

A:GLU277-B:ARG111

A:ASP465-A:ARG132

A:GLU431-C:LYS2

A:ASP477-A:LYS641

A:ASP477-A:LYS478

A:ASP269-A:LYS267 A:ASP269-A:LYS272 A:ASP274-A:LYS272

A:GLU431-C:LYS43

A:ASP481-A:LYS478

A:ASP284-A:LYS281

A:GLU436-C:LYS2

A:ASP481-A:LYS641

A:ASP284-A:LYS288

A:GLU436-C:LYS43

A:ASP484-A:LYS577

A:ASP421-D:LYS97

A:ASP618-A:LYS798

A:ASP291-A:ARG467 A:ASP291-A:ARG735 A:ASP303-A:ARG305

A:ASP499-A:ARG513 A:GLU431-D:LYS97

A:ASP623-A:ARG624

B:ASP99-A:LYS332

A:ASP833-A:ARG836

A:ASP304-A:ARG651

B:ASP161-C:LYS27

A:ASP879-A:HIS882

A:ASP336-A:ARG365

B:ASP163-C:LYS27

A:ASP711-A:LYS714

A:ASP303-A:ARG651 A:ASP304-A:ARG305 A:ASP304-A:ARG640

A:ASP845-A:ARG858

A:ASP358-A:ARG533

A:ASP879-A:LYS426 A:ASP893-A:ARG889

B:ASP175-D:LYS127

A:GLU136-A:LYS780

A:ASP40-A:LYS41

C:ASP5-A:LYS430

A:GLU144-A:LYS121

A:ASP418-A:LYS417

C:GLU23-A:LYS411

A:ASP36-A:ARG733

A:GLU136-A:LYS783

A:ASP390-A:ARG392

A:ASP418-A:LYS849 A:ASP418-A:LYS890

C:ASP5-D:LYS97

A:GLU278-A:LYS272

D:ASP99-C:LYS2

A:GLU436-A:LYS438

A:GLU431-A:LYS430

A:ASP421-A:LYS417 A:ASP445-A:ARG553

A:GLU167-A:LYS159 A:GLU254-A:ARG285

A:ASP452-A:ARG553

A:GLU474-A:ARG640

A:ASP452-A:ARG624

A:GLU610-A:LYS751

A:ASP454-A:ARG457

A:GLU658-A:ARG654

A:ASP465-A:ARG132

A:GLU665-A:LYS676

A:ASP477-A:ARG640

A:GLU744-A:ARG726

A:ASP477-A:LYS478

A:GLU796-A:LYS780

A:ASP477-A:LYS641

A:GLU796-A:LYS783

A:ASP481-A:LYS478

A:GLU802-A:LYS807

A:ASP481-A:LYS641

A:GLU811-A:ARG836

A:ASP484-A:LYS574

A:GLU894-A:LYS890

A:ASP484-A:LYS577

A:GLU919-A:ARG583

A:ASP523-B:ARG80 C:GLU23-A:LYS411 D:ASP99-C:LYS2

Supplementary Information Table 3.11 All the existing SBs from the analyses of the 1 μs MD trajectory data of SARS-CoV-2 RdRp without template RNA and remdesivir triphosphate [384] (continuation)

183 In MD

-

In opt

-

A:ASP499-A:ARG513 A:ASP499-A:LYS500 A:ASP499-A:LYS511 A:ASP523-A:LYS369 A:ASP608-A:ARG750 A:ASP608-A:LYS751 A:ASP618-A:LYS621 A:ASP618-A:LYS798 A:ASP623-A:ARG555 A:ASP623-A:ARG624 A:ASP684-A:ARG631 A:ASP711-A:LYS714 A:ASP736-A:ARG305 A:ASP736-A:ARG735 A:ASP738-A:ARG726 A:ASP740-A:ARG726 A:ASP760-A:LYS621 A:ASP761-A:LYS621 A:ASP804-A:LYS807 A:ASP824-A:LYS821 A:ASP833-A:ARG836 A:ASP833-A:HIS439 A:ASP833-A:LYS438 A:ASP845-A:ARG858 A:ASP845-A:LYS411 A:ASP846-A:LYS411 A:ASP846-A:LYS849 A:ASP851-A:LYS511 A:ASP865-A:LYS593 A:ASP879-A:HIS882 A:ASP879-A:LYS426 A:ASP893-A:ARG889 A:ASP893-A:HIS892 A:ASP893-A:LYS890 A:ASP910-A:ARG914 A:ASP92-A:LYS91 A:ASP92-A:LYS98 A:GLU136-A:LYS780 A:GLU136-A:LYS783 A:GLU144-A:ARG118 A:GLU144-A:ARG33 A:GLU144-A:LYS121 A:GLU144-A:LYS143 A:GLU167-A:LYS159 A:GLU167-A:LYS160 A:GLU180-A:ARG183 A:GLU254-A:ARG183 A:GLU254-A:ARG285 A:GLU254-A:LYS281 A:GLU277-A:LYS272 A:GLU277-A:LYS281 A:GLU278-A:LYS272 A:GLU278-A:LYS281 A:GLU350-A:ARG349 A:GLU370-A:LYS369 A:GLU431-A:LYS430 A:GLU436-A:LYS438 A:GLU474-A:ARG305

(continued)

184 Table 3.11 (continued)

3 RNA-Dependent RNA Polymerase (RdRp) In MD A:GLU474-A:ARG640 A:GLU610-A:LYS751 A:GLU658-A:ARG631 A:GLU658-A:ARG654 A:GLU665-A:LYS676 A:GLU729-A:ARG733 A:GLU729-A:HIS725 A:GLU744-A:ARG726 A:GLU796-A:LYS780 A:GLU796-A:LYS783 A:GLU802-A:HIS810 A:GLU802-A:LYS807 A:GLU811-A:ARG836 A:GLU811-A:HIS810 A:GLU811-A:LYS798 A:GLU84-A:HIS99 A:GLU84-A:LYS91 A:GLU84-A:LYS98 A:GLU876-A:LYS426 A:GLU876-A:LYS430 A:GLU894-A:LYS890 A:GLU917-A:ARG914 A:GLU917-A:LYS871 A:GLU919-A:ARG583 A:GLU919-A:ARG914 ASP208-A:ARG33

-

In opt

-

Supplementary Information

185

Table 3.12 The SBs within the RaRp (A-chain) of the peptideA-RdRp, peptideB-RdRp, peptideC-RdRp, peptideAdis-RdRp, peptideBdis-RdRp, and peptideCdis-RdRp models in [321] optimized Model peptideA-RdRp

Model peptideB-RdRp

Model peptideC-RdRp

Model peptideAdis-RdRp

Model peptideBdis-RdRp

Model peptideCdis-RdRp

ASP108-ARG6

ASP108-ARG6

ASP108-ARG6

ASP108-ARG6

ASP108-ARG6

ASP108-ARG6

ASP125-ARG357

ASP125-ARG357

ASP125-ARG357

ASP111-ARG623

ASP125-ARG357

ASP125-ARG357

ASP125-ARG625

ASP125-ARG625

ASP125-ARG625

ASP125-ARG357

ASP125-ARG625

ASP125-ARG625

ASP148-LYS153

ASP148-LYS153

ASP148-LYS153

ASP125-ARG625

ASP148-LYS153

ASP148-LYS153

ASP164-LYS162

ASP164-LYS162

ASP164-LYS162

ASP148-LYS153

ASP150-LYS153

ASP150-LYS153

ASP181-ARG625

ASP174-LYS178

ASP174-LYS178

ASP150-LYS153

ASP159-LYS157

ASP159-LYS157

ASP194-ARG530

ASP181-ARG625

ASP181-ARG625

ASP159-LYS157

ASP164-LYS162

ASP164-LYS162

ASP248-ARG423

ASP194-ARG530

ASP194-ARG530

ASP164-LYS162

ASP174-LYS178

ASP174-LYS178

ASP25-LYS673

ASP248-ARG423

ASP194-ARG541

ASP181-ARG625

ASP181-ARG625

ASP181-ARG625

ASP280-ARG282

ASP280-ARG282

ASP248-ARG423

ASP194-ARG530

ASP194-ARG530

ASP194-ARG541

ASP30-LYS33

ASP30-LYS33

ASP280-ARG282

ASP194-ARG541

ASP194-ARG541

ASP248-ARG423

ASP311-LYS307

ASP311-LYS307

ASP30-LYS33

ASP248-ARG423

ASP248-ARG423

ASP25-LYS670

ASP342-ARG443

ASP342-ARG443

ASP311-LYS307

ASP280-ARG282

ASP25-LYS673

ASP280-ARG282

ASP342-ARG514

ASP342-ARG514

ASP342-ARG443

ASP30-LYS33

ASP280-ARG282

ASP308-LYS739

ASP344-ARG347

ASP344-ARG347

ASP342-ARG514

ASP342-ARG443

ASP308-LYS739

ASP30-LYS33

ASP355-ARG22

ASP355-ARG22

ASP344-ARG347

ASP342-LYS511

ASP311-LYS307

ASP311-LYS307

ASP367-LYS368

ASP367-LYS531

ASP355-ARG22

ASP344-ARG347

ASP342-ARG443

ASP342-ARG443

ASP371-LYS368

ASP371-LYS368

ASP367-ARG530

ASP355-ARG22

ASP342-ARG514

ASP342-ARG514

ASP374-LYS464

ASP371-LYS531

ASP371-LYS368

ASP367-ARG530

ASP344-ARG347

ASP344-ARG347

ASP389-ARG403

ASP374-LYS464

ASP371-LYS531

ASP367-LYS531

ASP355-ARG22

ASP355-ARG22

ASP498-LYS641

ASP389-ARG403

ASP374-LYS464

ASP371-LYS368

ASP367-ARG530

ASP367-ARG530

ASP508-LYS441

ASP498-LYS641

ASP389-ARG403

ASP374-LYS464

ASP367-LYS368

ASP367-LYS531

ASP513-ARG443

ASP508-LYS688

ASP498-LYS641

ASP389-ARG403

ASP371-LYS368

ASP371-LYS368

ASP513-ARG514

ASP513-ARG514

ASP508-LYS441

ASP508-LYS688

ASP371-LYS531

ASP374-LYS464

ASP51-LYS50

ASP60-ARG63

ASP513-ARG443

ASP574-LYS390

ASP374-LYS464

ASP389-ARG403

ASP54-LYS688

ASP714-LYS711

ASP513-ARG514

ASP601-LYS604

ASP389-ARG403

ASP498-LYS641

ASP601-LYS604

ASP715-HIS489

ASP51-LYS50

ASP60-ARG63

ASP44-LYS33

ASP513-ARG514

ASP607-LYS608

ASP755-LYS483

ASP601-LYS604

ASP714-LYS711

ASP498-LYS641

ASP54-LYS688

ASP60-ARG63

ASP769-HIS772

ASP60-ARG63

ASP715-LYS493

ASP513-ARG514

ASP60-ARG63

ASP626-ARG195

ASP783-LYS780

ASP626-ARG195

ASP735-ARG748

ASP601-LYS604

ASP626-ARG195

ASP694-LYS697

ASP84-ARG87

ASP714-LYS711

ASP736-LYS301

ASP60-ARG63

ASP694-LYS697

ASP714-LYS711

GLU144-ARG175

ASP715-HIS489

ASP755-LYS483

ASP626-ARG195

ASP714-LYS711

ASP735-ARG748

GLU168-LYS171

ASP735-ARG748

ASP84-ARG87

ASP694-LYS697

ASP715-LYS493

ASP736-LYS301

GLU260-LYS259

ASP755-LYS483

ASP84-LYS178

ASP714-LYS711

ASP735-ARG748

ASP755-LYS483

GLU26-LYS673

ASP769-HIS772

GLU144-ARG175

ASP715-LYS493

ASP736-LYS301

ASP769-HIS772

GLU326-LYS328

ASP783-LYS780

GLU167-LYS162

ASP735-ARG748

ASP755-LYS483

ASP783-LYS780

GLU34-LYS11

ASP84-ARG87

GLU168-LYS171

ASP736-LYS301

ASP769-HIS772

ASP84-LYS178

GLU364-ARG195

ASP84-LYS178

GLU260-LYS259

ASP755-LYS483

ASP783-LYS780

GLU144-ARG175

GLU364-ARG530

GLU144-ARG175

GLU26-LYS670

ASP769-HIS772

ASP84-LYS178

GLU168-LYS171

GLU500-LYS641

GLU168-LYS171

GLU26-LYS673

ASP769-LYS316

GLU144-ARG175

GLU260-LYS259

GLU548-ARG544

GLU260-LYS259

GLU321-LYS320

ASP783-LYS780

GLU167-LYS162

GLU26-LYS673

GLU548-HIS462

GLU26-LYS673

GLU326-LYS328

ASP84-ARG87

GLU168-LYS171

GLU326-LYS328

GLU555-LYS566

GLU326-LYS328

GLU34-LYS11

GLU144-ARG175

GLU260-LYS259

GLU34-LYS11

GLU619-HIS615

GLU34-LYS11

GLU364-ARG195

GLU144-ARG73

GLU26-LYS673

GLU364-ARG195

GLU634-ARG616

GLU364-ARG530

GLU364-ARG530

GLU167-LYS162

GLU321-LYS320

GLU364-ARG530

GLU686-LYS673

GLU500-LYS641

GLU500-HIS642

GLU168-LYS171

GLU326-LYS328

GLU548-ARG544

GLU692-LYS697

GLU548-ARG544

GLU500-LYS641

GLU260-LYS259

GLU34-LYS11

GLU555-LYS566

GLU70-ARG73

GLU555-LYS566

GLU548-ARG521

GLU26-LYS673

GLU364-ARG195

GLU619-HIS615

GLU784-LYS780

GLU619-HIS615

GLU555-LYS566

GLU326-LYS328

GLU364-ARG530

GLU634-ARG616

GLU634-ARG616

GLU57-LYS49

GLU34-LYS11

GLU500-HIS642

GLU686-LYS673

GLU686-LYS673

GLU619-HIS615

GLU364-ARG195

GLU500-LYS641

GLU692-LYS697

GLU692-LYS697

GLU634-ARG616

GLU364-ARG530

GLU548-ARG544

GLU701-LYS441

GLU701-LYS441

GLU686-LYS670

GLU500-HIS642

GLU548-HIS462

GLU70-ARG73

GLU70-ARG73

GLU686-LYS673

GLU548-HIS462

GLU555-LYS566

GLU766-LYS320

GLU784-LYS780

GLU784-LYS780

GLU692-LYS697

GLU555-LYS566

GLU619-HIS615

GLU70-ARG73

GLU619-ARG623

GLU634-ARG616

GLU784-LYS780

GLU634-ARG616

GLU686-LYS673

GLU686-LYS670

GLU692-HIS700

GLU686-LYS673

GLU692-LYS697

GLU692-LYS697

GLU70-ARG73

GLU70-ARG73

GLU784-LYS780

GLU784-LYS780

186

3 RNA-Dependent RNA Polymerase (RdRp)

Table 3.13 The 20 μs MD-SBs within the RaRp (A-chain) of the peptideA-RdRp, peptideBRdRp, peptideC-RdRp, peptideAdis-RdRp, peptideBdis-RdRp, and peptideCdis-RdRp models in [321] Model peptideA-RdRp

Model peptideB-RdRp

Model peptideC-RdRp

Model peptideAdis-RdRp

Model peptideBdis-RdRp

Model peptideCdis-RdRp

ASP101-ARG6

ASP101-LYS11

ASP101-ARG8

ASP101-ARG8

ASP101-ARG6

ASP101-ARG6

ASP101-ARG8

ASP108-ARG6

ASP101-LYS11

ASP101-LYS11

ASP101-ARG8

ASP101-ARG8

ASP101-LYS11

ASP108-ARG8

ASP108-ARG6

ASP108-ARG6

ASP101-LYS11

ASP101-LYS11

ASP108-ARG6

ASP111-ARG623

ASP108-ARG8

ASP108-ARG8

ASP108-ARG6

ASP108-ARG6

ASP108-ARG8

ASP125-ARG357

ASP111-ARG6

ASP111-ARG623

ASP108-ARG8

ASP108-ARG8

ASP125-ARG357

ASP125-ARG623

ASP111-ARG623

ASP125-ARG357

ASP111-ARG8

ASP125-ARG357

ASP125-ARG623

ASP125-ARG625

ASP125-ARG357

ASP125-ARG623

ASP125-ARG357

ASP125-ARG623

ASP125-ARG625

ASP148-ARG139

ASP125-ARG623

ASP125-ARG625

ASP125-ARG623

ASP125-ARG625

ASP148-ARG63

ASP148-ARG175

ASP125-ARG625

ASP148-ARG139

ASP125-ARG625

ASP148-LYS153

ASP148-LYS153

ASP148-ARG282

ASP148-ARG139

ASP148-ARG175

ASP148-LYS153

ASP150-LYS153

ASP148-LYS157

ASP148-ARG63

ASP148-ARG282

ASP148-ARG63

ASP150-LYS153

ASP159-ARG282

ASP150-LYS153

ASP148-LYS153

ASP148-LYS153

ASP148-LYS153

ASP159-LYS162

ASP159-LYS157

ASP159-ARG221

ASP148-LYS157

ASP148-LYS171

ASP148-LYS157

ASP164-ARG221

ASP159-LYS162

ASP159-LYS157

ASP148-LYS171

ASP148-LYS281

ASP150-ARG175

ASP164-LYS162

ASP159-LYS281

ASP159-LYS162

ASP150-ARG282

ASP150-ARG282

ASP150-ARG63

ASP16-ARG8

ASP164-LYS162

ASP159-LYS222

ASP150-LYS153

ASP150-LYS153

ASP150-LYS153

ASP174-LYS171

ASP174-LYS171

ASP164-LYS162

ASP159-ARG221

ASP150-LYS281

ASP159-ARG221

ASP174-LYS178

ASP174-LYS178

ASP174-LYS171

ASP159-ARG282

ASP159-ARG221

ASP159-LYS153

ASP181-ARG357

ASP181-ARG357

ASP174-LYS178

ASP159-LYS157

ASP159-ARG282

ASP159-LYS157

ASP181-ARG625

ASP181-ARG625

ASP181-ARG357

ASP159-LYS162

ASP159-LYS162

ASP159-LYS162

ASP193-ARG195

ASP193-ARG195

ASP181-ARG625

ASP159-LYS222

ASP164-LYS162

ASP159-LYS222

ASP194-ARG195

ASP194-ARG530

ASP193-ARG195

ASP164-ARG169

ASP174-LYS171

ASP164-LYS157

ASP194-ARG530

ASP248-ARG423

ASP193-ARG541

ASP164-LYS162

ASP174-LYS178

ASP164-LYS162

ASP194-ARG541

ASP25-LYS670

ASP194-ARG195

ASP174-LYS171

ASP181-ARG357

ASP174-ARG175

ASP226-ARG255

ASP25-LYS673

ASP194-ARG530

ASP174-LYS178

ASP181-ARG625

ASP174-LYS171

ASP248-ARG423

ASP280-ARG282

ASP194-ARG541

ASP181-ARG357

ASP193-ARG195

ASP174-LYS178

ASP25-LYS670

ASP280-LYS157

ASP226-ARG255

ASP181-ARG625

ASP194-ARG530

ASP181-ARG195

ASP25-LYS673

ASP280-LYS281

ASP226-ARG282

ASP193-ARG195

ASP226-ARG255

ASP181-ARG357

ASP267-ARG255

ASP308-LYS739

ASP248-ARG221

ASP194-ARG195

ASP226-ARG403

ASP181-ARG625

ASP280-ARG282

ASP30-LYS33

ASP248-ARG255

ASP194-ARG530

ASP248-ARG423

ASP193-ARG195

ASP308-LYS307

ASP311-LYS307

ASP248-ARG423

ASP248-ARG423

ASP25-LYS670

ASP194-ARG195

ASP308-LYS739

ASP335-ARG726

ASP25-LYS670

ASP25-LYS670

ASP25-LYS673

ASP194-ARG530

ASP308-LYS780

ASP335-LYS301

ASP25-LYS673

ASP25-LYS673

ASP280-ARG282

ASP194-ARG541

ASP30-LYS33

ASP335-LYS307

ASP267-ARG255

ASP267-ARG255

ASP280-LYS157

ASP226-ARG255

ASP311-LYS307

ASP335-LYS435

ASP267-LYS398

ASP280-ARG282

ASP280-LYS222

ASP248-ARG423

ASP335-ARG443

ASP342-ARG443

ASP280-ARG255

ASP280-LYS162

ASP280-LYS281

ASP25-LYS670

ASP335-ARG445

ASP342-ARG445

ASP280-ARG282

ASP280-LYS222

ASP308-LYS307

ASP25-LYS673

ASP342-ARG443

ASP342-ARG514

ASP280-ARG347

ASP280-LYS281

ASP308-LYS739

ASP267-ARG282

ASP342-ARG445

ASP342-LYS511

ASP280-ARG445

ASP308-LYS307

ASP30-LYS33

ASP267-LYS398

ASP342-ARG514

ASP344-ARG347

ASP280-LYS281

ASP308-LYS739

ASP311-LYS307

ASP280-ARG282

ASP342-LYS511

ASP344-ARG443

ASP280-LYS441

ASP308-LYS780

ASP335-ARG445

ASP280-LYS281

ASP344-ARG282

ASP344-ARG514

ASP308-LYS307

ASP30-ARG6

ASP335-LYS301

ASP308-LYS307

ASP344-ARG347

ASP344-LYS511

ASP308-LYS739

ASP30-LYS33

ASP335-LYS398

ASP308-LYS780

ASP344-LYS511

ASP355-ARG22

ASP308-LYS780

ASP311-LYS307

ASP342-ARG347

ASP30-LYS33

ASP355-ARG22

ASP367-ARG530

ASP30-LYS33

ASP335-ARG443

ASP342-ARG443

ASP311-LYS307

ASP367-ARG530

ASP367-LYS368

ASP311-LYS307

ASP335-LYS301

ASP342-ARG445

ASP335-ARG443

ASP367-LYS368

ASP367-LYS531

ASP311-LYS328

ASP335-LYS441

ASP342-ARG514

ASP335-LYS328

ASP367-LYS531

ASP371-LYS368

ASP335-ARG282

ASP335-LYS566

ASP342-LYS328

ASP342-ARG443

ASP371-LYS368

ASP371-LYS531

ASP335-ARG347

ASP342-ARG347

ASP342-LYS441

ASP342-ARG445

ASP371-LYS531

ASP374-LYS464

ASP335-ARG443

ASP342-ARG443

ASP342-LYS511

ASP342-ARG514

ASP374-ARG473

ASP389-ARG403

ASP335-ARG445

ASP342-ARG514

ASP344-ARG282

ASP342-LYS441

ASP374-LYS464

ASP389-ARG459

ASP335-ARG726

ASP342-LYS301

ASP344-ARG347

ASP342-LYS511

ASP389-ARG403

ASP389-LYS401

ASP335-LYS301

ASP344-ARG347

ASP344-ARG445

ASP344-ARG347

ASP389-ARG459

ASP389-LYS711

ASP335-LYS328

ASP355-ARG22

ASP344-LYS566

ASP344-ARG445

ASP389-LYS390

ASP407-ARG403 ASP407-ARG459

ASP335-LYS483

ASP367-ARG530

ASP355-ARG22

ASP344-ARG514

ASP389-LYS401

ASP335-LYS566

ASP367-LYS368

ASP367-ARG530

ASP344-LYS566

ASP407-ARG403

ASP407-LYS390

ASP342-ARG282

ASP367-LYS531

ASP367-LYS531

ASP355-ARG22

ASP413-LYS259

ASP407-LYS401

ASP342-ARG347

ASP371-LYS368

ASP371-ARG530

ASP367-ARG530

ASP43-ARG6

ASP413-LYS259

ASP342-ARG443

ASP371-LYS531

ASP371-LYS368

ASP367-LYS531

ASP43-ARG63

ASP43-ARG63

ASP342-ARG445

ASP374-ARG473

ASP371-LYS531

ASP371-LYS368

ASP44-LYS33

ASP45-LYS49

ASP342-ARG514

ASP374-LYS464

ASP374-LYS464

ASP371-LYS531

ASP498-ARG640

ASP498-ARG640

ASP342-LYS281

ASP389-ARG403

ASP389-ARG403

ASP374-LYS464

ASP498-LYS641

ASP498-LYS641

(continued)

Supplementary Information

187

Table 3.13 (continued) Model peptideA-RdRp

Model peptideB-RdRp

Model peptideC-RdRp

Model peptideAdis-RdRp

Model peptideBdis-RdRp

Model peptideCdis-RdRp

ASP342-LYS301

ASP389-ARG459

ASP389-ARG459

ASP389-ARG403

ASP508-LYS688

ASP508-LYS688

ASP342-LYS441

ASP389-LYS259

ASP389-LYS301

ASP389-ARG459

ASP513-ARG445

ASP513-ARG347

ASP342-LYS511

ASP389-LYS301

ASP389-LYS390

ASP389-LYS390

ASP513-ARG514

ASP513-ARG443

ASP344-ARG282

ASP389-LYS390

ASP389-LYS401

ASP389-LYS401

ASP51-LYS50

ASP513-ARG445

ASP344-ARG347

ASP389-LYS401

ASP389-LYS435

ASP389-LYS435

ASP574-ARG445

ASP513-ARG514

ASP344-ARG443

ASP407-ARG255

ASP407-ARG403

ASP389-LYS739

ASP574-ARG459

ASP513-LYS441

ASP344-ARG445

ASP407-ARG403

ASP407-LYS259

ASP407-ARG403

ASP574-LYS390

ASP513-LYS511

ASP344-ARG514

ASP407-LYS259

ASP407-LYS390

ASP413-LYS259

ASP574-LYS435

ASP513-LYS688

ASP344-LYS281

ASP413-LYS259

ASP413-LYS259

ASP43-ARG63

ASP601-LYS604

ASP51-LYS50

ASP344-LYS441

ASP415-LYS398

ASP43-ARG63

ASP44-ARG6

ASP60-ARG63

ASP574-LYS390

ASP344-LYS566

ASP43-ARG6

ASP45-LYS49

ASP45-LYS49

ASP60-LYS49

ASP574-LYS467

ASP355-ARG22

ASP43-ARG8

ASP498-ARG640

ASP498-ARG640

ASP626-ARG195

ASP574-LYS483

ASP367-ARG530

ASP43-LYS49

ASP498-LYS641

ASP498-LYS641

ASP626-ARG625

ASP601-LYS604

ASP367-LYS531

ASP44-ARG6

ASP508-LYS441

ASP508-ARG514

ASP628-ARG616

ASP60-ARG63

ASP371-LYS368

ASP44-ARG8

ASP508-LYS688

ASP508-LYS511

ASP630-ARG616

ASP60-LYS49

ASP374-ARG473

ASP45-ARG6

ASP513-ARG347

ASP508-LYS688

ASP650-ARG445

ASP626-ARG195

ASP374-LYS464

ASP45-LYS33

ASP513-ARG443

ASP513-ARG347

ASP650-ARG514

ASP626-ARG625

ASP389-ARG403

ASP498-ARG473

ASP513-ARG445

ASP513-ARG443

ASP650-LYS511

ASP628-ARG616

ASP389-ARG445

ASP498-ARG640

ASP513-ARG514

ASP513-ARG445

ASP651-ARG514

ASP630-ARG616

ASP389-ARG459

ASP508-ARG443

ASP513-LYS511

ASP513-ARG514

ASP694-LYS697

ASP650-ARG514

ASP389-LYS390

ASP508-LYS441

ASP513-LYS566

ASP513-LYS441

ASP714-LYS711

ASP650-LYS441

ASP389-LYS401

ASP508-LYS688

ASP51-LYS50

ASP513-LYS688

ASP715-LYS493

ASP650-LYS483

ASP407-ARG403

ASP513-ARG443

ASP574-ARG459

ASP51-LYS50

ASP723-ARG726

ASP650-LYS511

ASP407-LYS390

ASP513-ARG445

ASP574-ARG521

ASP54-ARG347

ASP723-LYS328

ASP651-LYS483

ASP413-ARG255

ASP513-ARG514

ASP601-LYS604

ASP574-ARG445

ASP723-LYS441

ASP694-LYS697

ASP413-LYS259

ASP513-LYS511

ASP60-ARG63

ASP574-ARG459

ASP735-ARG748

ASP714-LYS401

ASP43-ARG6

ASP513-LYS566

ASP60-LYS49

ASP574-LYS390

ASP735-LYS301

ASP714-LYS467

ASP43-ARG63

ASP51-LYS441

ASP626-ARG195

ASP574-LYS435

ASP735-LYS390

ASP714-LYS711

ASP44-ARG6

ASP51-LYS50

ASP626-ARG625

ASP601-LYS604

ASP735-LYS401

ASP715-ARG403

ASP45-LYS49

ASP51-LYS673

ASP628-ARG616

ASP60-ARG63

ASP736-ARG748

ASP715-ARG473

ASP498-ARG640

ASP54-ARG443

ASP630-ARG616

ASP60-LYS49

ASP736-LYS301

ASP715-LYS390

ASP498-LYS641

ASP574-ARG445

ASP650-ARG443

ASP626-ARG195

ASP736-LYS390

ASP715-LYS401

ASP508-ARG443

ASP574-ARG459

ASP650-ARG445

ASP626-ARG625

ASP736-LYS739

ASP715-LYS467

ASP508-ARG514

ASP574-LYS390

ASP650-LYS441

ASP628-ARG616

ASP741-LYS739

ASP723-ARG726

ASP508-LYS441

ASP601-LYS604

ASP650-LYS511

ASP630-ARG616

ASP755-ARG726

ASP723-LYS328

ASP508-LYS511

ASP60-ARG63

ASP651-ARG443

ASP650-ARG445

ASP755-ARG748

ASP735-ARG748

ASP508-LYS688

ASP60-LYS49

ASP651-LYS441

ASP650-ARG514

ASP755-LYS483

ASP735-LYS301

ASP513-ARG347

ASP626-ARG195

ASP694-LYS697

ASP650-LYS441

ASP783-ARG779

ASP735-LYS435

188

3 RNA-Dependent RNA Polymerase (RdRp)

Table 3.14 The 20 μs MD-SBs within the RaRp (A-chain) of the peptideA-RdRp, peptideBRdRp, peptideC-RdRp, peptideAdis-RdRp, peptideBdis-RdRp, and peptideCdis-RdRp models in [321] (continuation) Model peptideA-RdRp

Model peptideB-RdRp

Model peptideC-RdRp

Model peptideAdis-RdRp

Model peptideBdis-RdRp

Model peptideCdis-RdRp

ASP513-ARG443

ASP626-ARG625

ASP714-LYS467

ASP650-LYS511

ASP783-LYS780

ASP735-LYS739

ASP513-ARG445

ASP628-ARG616

ASP714-LYS711

ASP651-ARG514

ASP84-ARG87

ASP736-ARG748

ASP513-ARG514

ASP630-ARG616

ASP715-LYS467

ASP694-LYS697

ASP84-LYS178

ASP736-LYS301

ASP513-ARG521

ASP650-ARG443

ASP715-LYS483

ASP714-LYS711

GLU144-ARG175

ASP736-LYS398

ASP513-LYS511

ASP650-ARG445

ASP723-ARG443

ASP723-ARG726

GLU144-ARG73

ASP736-LYS739

ASP513-LYS566

ASP650-LYS441

ASP723-ARG726

ASP723-LYS441

GLU167-LYS162

ASP741-LYS739

ASP51-LYS50

ASP650-LYS483

ASP723-LYS328

ASP735-ARG748

GLU167-LYS171

ASP755-ARG726

ASP574-ARG459

ASP650-LYS511

ASP723-LYS441

ASP735-LYS301

GLU168-ARG175

ASP755-ARG748

ASP574-ARG521

ASP651-ARG443

ASP735-ARG445

ASP735-LYS435

GLU168-LYS162

ASP755-LYS398

ASP601-LYS604

ASP651-LYS441

ASP735-ARG748

ASP736-ARG748

GLU168-LYS171

ASP755-LYS401

ASP60-ARG63

ASP651-LYS483

ASP735-LYS301

ASP736-LYS301

GLU240-ARG239

ASP755-LYS483

ASP60-LYS49

ASP651-LYS688

ASP736-ARG445

ASP736-LYS390

GLU260-ARG255

ASP783-ARG779

ASP626-ARG195

ASP694-LYS697

ASP736-ARG748

ASP736-LYS435

GLU260-LYS259

ASP783-LYS780

ASP626-ARG625

ASP714-ARG459

ASP736-LYS301

ASP741-LYS739

GLU26-LYS33

ASP84-ARG87

ASP628-ARG616

ASP714-LYS467

ASP736-LYS739

ASP755-ARG726

GLU26-LYS670

ASP84-LYS178

ASP630-ARG616

ASP714-LYS711

ASP741-LYS401

ASP755-ARG748

GLU26-LYS673

ASP98-ARG8

ASP650-ARG443

ASP715-LYS467

ASP741-LYS739

ASP755-LYS483

GLU326-ARG443

GLU144-ARG175

ASP650-ARG445

ASP715-LYS483

ASP755-ARG748

ASP783-ARG779

GLU326-ARG726

GLU144-ARG73

ASP650-LYS511

ASP715-LYS493

ASP755-LYS483

ASP783-LYS780

GLU326-LYS328

GLU167-LYS162

ASP651-ARG443

ASP723-ARG726

ASP783-ARG779

ASP84-ARG175

GLU326-LYS441

GLU167-LYS171

ASP651-LYS483

ASP723-LYS328

ASP783-LYS780

ASP84-ARG87

GLU34-ARG6

GLU168-ARG175

ASP651-LYS511

ASP735-ARG445

ASP84-ARG175

ASP84-LYS178

GLU34-ARG8

GLU168-LYS162

ASP694-LYS697

ASP735-ARG748

ASP84-ARG87

GLU144-ARG139

GLU34-LYS11

GLU168-LYS171

ASP714-LYS711

ASP735-LYS435

ASP84-LYS178

GLU144-ARG175

GLU34-LYS33

GLU240-ARG239

ASP723-ARG726

ASP736-ARG748

GLU144-ARG139

GLU144-ARG63

GLU364-ARG195

GLU260-ARG255

ASP735-ARG445

ASP736-LYS301

GLU144-ARG175

GLU144-ARG73

GLU364-ARG530

GLU260-LYS259

ASP735-ARG748

ASP736-LYS435

GLU144-ARG63

GLU144-LYS153

GLU500-LYS641

GLU26-LYS670

ASP735-LYS301

ASP736-LYS739

GLU144-ARG71

GLU144-LYS171

GLU548-ARG521

GLU26-LYS673

ASP735-LYS435

ASP741-ARG748

GLU144-ARG73

GLU167-LYS153

GLU548-ARG544

GLU321-LYS320

ASP735-LYS441

ASP741-LYS401

GLU167-LYS153

GLU167-LYS157

GLU555-LYS566

GLU321-LYS328

ASP735-LYS739

ASP741-LYS739

GLU167-LYS162

GLU167-LYS162

GLU57-ARG347

GLU321-LYS441

ASP736-ARG443

ASP755-ARG726

GLU167-LYS171

GLU167-LYS171

GLU57-LYS49

GLU326-LYS307

ASP736-ARG445

ASP755-ARG748

GLU168-ARG169

GLU168-LYS153

GLU619-ARG616

GLU326-LYS320

ASP736-ARG748

ASP755-LYS483

GLU168-LYS162

GLU168-LYS157

GLU634-ARG616

GLU326-LYS328

ASP736-LYS301

ASP783-ARG779

GLU168-LYS171

GLU168-LYS162

GLU686-LYS670

GLU326-LYS441

ASP736-LYS441

ASP783-LYS401

GLU240-ARG239

GLU168-LYS171

GLU686-LYS673

GLU34-ARG6

ASP736-LYS739

ASP783-LYS780

GLU260-ARG221

GLU240-ARG239

GLU692-LYS697

GLU34-ARG8

ASP741-ARG443

ASP84-ARG175

GLU260-ARG255

GLU260-ARG255

GLU701-LYS441

GLU34-LYS11

ASP741-LYS301

ASP84-ARG87

GLU260-LYS259

GLU26-LYS670

GLU70-ARG71

GLU364-ARG195

ASP741-LYS739

ASP84-LYS178

GLU26-LYS50

GLU26-LYS673

GLU70-ARG73

GLU364-ARG530

ASP755-LYS483

GLU144-ARG175

GLU26-LYS673

GLU321-LYS320

GLU747-ARG403

GLU412-LYS259

ASP783-ARG779

GLU144-ARG73

GLU321-ARG443

GLU321-LYS328

GLU784-LYS780

GLU500-LYS641

ASP783-LYS780

GLU167-LYS162

GLU321-ARG445

GLU326-ARG726

GLU548-ARG521

ASP84-ARG175

GLU167-LYS171

GLU321-ARG514

GLU326-LYS301

GLU548-ARG544

ASP84-ARG87

GLU168-LYS153

GLU321-LYS328

GLU326-LYS307

GLU555-LYS566

ASP84-LYS178

GLU168-LYS162

GLU321-LYS441

GLU326-LYS320

GLU57-ARG347

GLU144-ARG139

GLU168-LYS171

GLU321-LYS511

GLU326-LYS328

GLU57-ARG443

GLU144-ARG175

GLU240-ARG239

GLU326-ARG443

GLU34-ARG6

GLU57-ARG514

GLU144-ARG63

GLU260-ARG255

GLU326-ARG445

GLU34-ARG8

GLU57-LYS441

GLU144-ARG73

GLU260-LYS259

GLU326-LYS328

GLU34-LYS11

GLU57-LYS511

GLU144-LYS153

GLU26-LYS670

GLU326-LYS441

GLU364-ARG195

GLU619-ARG616

GLU144-LYS171

GLU26-LYS673

GLU326-LYS511

GLU364-ARG530

GLU634-ARG616

GLU167-LYS157

GLU321-LYS328

GLU34-ARG6

GLU412-LYS259

GLU686-LYS50

GLU167-LYS162

GLU326-ARG726

GLU34-ARG8

GLU500-LYS641

GLU686-LYS670

GLU167-LYS171

GLU326-LYS328

GLU34-LYS11

GLU548-ARG521

GLU686-LYS673

GLU168-ARG169

GLU34-ARG6

GLU364-ARG195

GLU548-ARG544

GLU686-LYS688

GLU168-ARG175

GLU34-ARG8

GLU364-ARG530

GLU555-ARG347

GLU692-LYS697

GLU168-LYS162

GLU34-LYS11

GLU412-ARG403

GLU555-ARG514

GLU701-ARG726

GLU168-LYS171

GLU364-ARG195

GLU412-LYS259

GLU555-LYS566

GLU701-LYS328

GLU240-ARG239

GLU364-ARG530

GLU412-LYS390

GLU57-ARG347

GLU701-LYS483

GLU260-ARG255

GLU412-LYS398

GLU500-LYS641

GLU57-LYS49

GLU701-LYS688

GLU260-LYS259

GLU500-LYS641

GLU548-ARG521

GLU57-LYS50

GLU701-LYS697

GLU26-LYS50

GLU548-ARG521

GLU548-ARG544

GLU619-ARG616

GLU70-ARG6

(continued)

Supplementary Information

189

Table 3.14 (continued) Model peptideA-RdRp

Model peptideB-RdRp

Model peptideC-RdRp

Model peptideAdis-RdRp

GLU26-LYS670

GLU548-ARG541

GLU555-LYS566

GLU634-ARG616

Model peptideBdis-RdRp

GLU70-ARG71

Model peptideCdis-RdRp GLU70-ARG73

GLU26-LYS673

GLU548-ARG544

GLU57-ARG514

GLU686-LYS511

GLU321-ARG726

GLU555-LYS566

GLU57-LYS441

GLU686-LYS670

GLU747-ARG403

GLU326-ARG726

GLU57-ARG443

GLU57-LYS511

GLU686-LYS673

GLU747-ARG748

GLU326-LYS328

GLU57-ARG514

GLU619-ARG616

GLU686-LYS688

GLU747-LYS390

GLU326-LYS441

GLU57-LYS441

GLU634-ARG616

GLU692-LYS697

GLU747-LYS401

GLU34-ARG6

GLU57-LYS49

GLU686-LYS670

GLU701-ARG726

GLU747-LYS739

GLU34-ARG8

GLU619-ARG616

GLU686-LYS673

GLU70-ARG63

GLU784-ARG779

GLU34-LYS11

GLU619-ARG623

GLU692-LYS697

GLU70-ARG71

GLU784-LYS780

GLU364-ARG195

GLU634-ARG616

GLU701-ARG443

GLU70-ARG73

GLU364-ARG530

GLU686-LYS50

GLU701-LYS441

GLU747-ARG748

GLU412-ARG255

GLU686-LYS670

GLU701-LYS483

GLU747-LYS739

GLU412-LYS259

GLU686-LYS673

GLU701-LYS697

GLU784-ARG779 GLU784-LYS780

GLU500-LYS641

GLU692-LYS697

GLU70-ARG6

GLU548-ARG521

GLU701-ARG726

GLU70-ARG63

GLU548-ARG544

GLU701-LYS688

GLU70-ARG71

GLU555-ARG347

GLU701-LYS697

GLU70-ARG73

GLU555-ARG443

GLU70-ARG63

GLU766-LYS435

GLU555-ARG445

GLU70-ARG71

GLU784-ARG779

GLU555-LYS441

GLU70-ARG73

GLU784-LYS780

GLU555-LYS566

GLU747-ARG459

GLU57-ARG347

GLU747-ARG748

GLU57-LYS441

GLU747-LYS390

GLU619-ARG616

GLU747-LYS401

GLU619-ARG623

GLU747-LYS483

GLU634-ARG616

GLU766-LYS320

GLU686-LYS670

GLU784-ARG779

GLU686-LYS673

GLU784-LYS780

GLU692-LYS697 GLU701-ARG726 GLU701-LYS328 GLU70-ARG63 GLU70-ARG71 GLU70-ARG73 GLU747-LYS739 GLU784-ARG779 GLU784-LYS739 GLU784-LYS780

CYS620.N-ARG616.O 60.70 ALA667.N-ASN593.OD1 60.20

VAL654.N-MET505.O 63.68

ALA667.N-ASN593.OD1 63.18

VAL366.N-VAL362.O 63.18

CYS620.N-ARG616.O 63.18

TYR677.OH-TYR53.O 63.18

TYR127.OH-GLN100.OE1 62.69

ARG616.N-ASN612.O 62.19

PHE635.N-PHE631.O 61.69

LYS673.N-ILE669.O 61.69

LEU676.N-PHE672.O 61.69

ALA313.N-PHE309.O 61.69

TYR184.OH-ASN204.OD1 61.19

LEU359.N-ASP355.O 61.19

ASN306.N-CYS732.O 60.70

ALA201.N-ILE197.O 60.70

VAL366.N-VAL362.O 64.18

LYS673.N-ILE669.O 63.68

ARG73.N-GLY69.O 63.68

TYR127.OH-GLN100.OE1 63.18

ALA667.N-ASN593.OD1 63.18

LEU359.N-ASP355.O 62.69

TYR677.OH-TYR53.O 62.69

CYS200.N-CYX196.O 62.19

VAL314.N-TYR310.O 62.19

TYR767.OH-PRO722.O 62.19

CYS620.N-ARG616.O 61.69

THR38.OG1-GLU34.O 60.70

LEU676.N-PHE672.O 60.70

ARG640.N-TYR636.O 58.71

LEU728.N-PRO724.O 58.71

ALA546.N-PHE542.O 65.67

LEU359.N-ASP355.O 64.68

TYR127.OH-GLN100.OE1 55.72

VAL362.N-GLN358.O 57.71

ASN581.N-THR577.O 58.21

ASN204.N-CYS200.O 57.71

ARG640.N-TYR636.O 57.71

ILE223.N-PHE230.O 57.21

THR138.OG1-ILE134.O 57.21

ARG73.N-GLY69.O 56.72

MET523.N-MET519.O 55.72

VAL363.N-LEU359.O 55.22

HID237.N-GLY217.O 55.22

PHE230.N-ILE223.O 54.73

LEU781.N-TYR777.O 54.73

ASN595.N-THR591.O 54.23

TYR65.N-ILE61.O 54.23

MET86.N-PHE82.O 53.73

VAL590.N-ILE586.O 53.73

CYS354.N-ASN202.OD1 57.21

ASN306.N-CYS732.O 57.21

MET456.N-ILE452.O 56.22

ASN397.N-GLY393.O 55.72

TYR184.OH-ASN204.OD1 55.22

LEU781.N-TYR777.O 55.22

LEU76.N-VAL72.O 55.22

CYS587.N-VAL583.O 54.73

VAL750.N-ILE746.O 54.23

THR138.OG1-ILE134.O 54.23

CYS655.N-SER644.O 53.73

ALA201.N-ILE197.O 53.73

VAL717.N-VAL710.O 53.73

ALA592.N-GLN588.O 53.23

TYR65.OH-TYR677.OH 53.23

VAL362.N-GLN358.O 58.71

VAL750.N-ILE746.O 58.21

ALA546.N-PHE542.O 58.21

TYR622.OH-ASP355.OD2 57.21

ASN306.N-CYS732.O 55.72

THR136.OG1-PRO351.O 58.21

VAL425.N-ASN246.OD1 59.20

LYS531.NZ-TYR373.O 59.20

ASP415.N-TYR411.O 58.21

MET86.N-PHE82.O 53.23

ARG640.N-TYR636.O 53.73

ASN306.N-CYS732.O 53.73

ASP311.N-LYS307.O 54.23

ILE647.N-THR476.O 54.73

LEU492.N-TRP488.O 55.72

VAL717.N-VAL710.O 55.72

VAL750.N-ILE746.O 55.72

ASN58.N-ASP54.O 55.72

ASN518.ND2-GLU240.OE2 56.22

VAL366.N-VAL362.O 56.72

THR591.OG1-CYS587.O 56.72

TYR127.OH-GLN100.OE1 56.72

CYS354.N-ASN202.OD1 57.21

ALA592.N-GLN588.O 57.21

ASN595.N-THR591.O 57.21

LEU359.N-ASP355.O 59.70

THR591.OG1-CYS587.O 57.71

MET86.N-PHE82.O 52.24

THR138.OG1-ILE134.O 52.74

ASN547.N-TYR543.O 53.23

ILE778.N-TYR774.O 53.23

ALA201.N-ILE197.O 53.23

CYS83.N-THR79.O 53.23

LEU198.N-ASP194.O 53.73

GLN679.N-VAL675.O 53.73

VAL590.N-ILE586.O 53.73

VAL717.N-VAL710.O 54.23

LEU219.N-GLY235.O 54.23

LEU76.N-VAL72.O 54.73

ARG640.N-TYR636.O 54.73

TYR677.OH-TYR53.O 55.22

TYR184.OH-ASN204.OD1 55.22

LYS673.N-ILE669.O 55.72

VAL750.N-ILE746.O 55.72

ALA546.N-PHE542.O 57.71

TYR19.N-ALA15.O 58.21

TYR184.OH-ASN204.OD1 59.70

ALA546.N-PHE542.O 60.20

CYS655.N-SER644.O 59.70

MET558.N-THR430.O 58.71

ILE426.N-ASN547.OD1 58.21

ALA313.N-PHE309.O 58.21

CYS354.N-ASN202.OD1 58.21

CYS655.N-SER644.O 58.21

VAL425.N-ASN246.OD1 58.71

THR136.OG1-PRO351.O 58.71

LEU676.N-PHE672.O 58.71

ARG73.N-GLY69.O 58.71

VAL366.N-VAL362.O 59.20

CYS620.N-ARG616.O 60.20

CYS200.N-CYX196.O 60.70

VAL363.N-LEU359.O 61.19

SER668.N-ASN671.OD1 61.69

ARG616.N-ASN612.O 61.69

ALA667.N-ASN593.OD1 62.19

TYR19.N-ALA15.O 62.69

TYR543.OH-HID245.O 63.68

PHE635.N-PHE631.O 64.18

THR591.OG1-CYS587.O 58.71

VAL654.N-MET505.O 60.70

ARG73.N-GLY69.O 60.70

THR591.N-CYS587.O 61.19

ASN581.N-THR577.O 61.69

LEU781.N-TYR777.O 62.19

ALA201.N-ILE197.O 62.19

ARG616.N-ASN612.O 62.69

TYR543.OH-HID245.O 62.69

PHE635.N-PHE631.O 62.69

CYS200.N-CYX196.O 62.69

ALA313.N-PHE309.O 63.18

VAL363.N-LEU359.O 63.18

ASN547.N-TYR543.O 64.18

TYR767.OH-PRO722.O 64.68

PHE584.N-ALA580.O 64.68

VAL314.N-TYR310.O 65.17

TYR543.OH-HID245.O 64.18

THR136.OG1-PRO351.O 65.17

VAL590.N-ILE586.O 64.18

VAL425.N-ASN246.OD1 66.67

TYR19.N-ALA15.O 67.16

CYS200.N-CYX196.O 66.17

TYR19.N-ALA15.O 65.67

PHE635.N-PHE631.O 68.16

GLN588.N-PHE584.O 70.15

ALA313.N-PHE309.O 65.17

Model peptideAdis-RdRp ASN397.N-GLY393.O 66.67

Model peptideC-RdRp

Model peptideB-RdRp

CYS354.N-ASN202.OD1 71.14

Model peptideA-RdRp

ARG616.N-ASN612.O 69.15

LEU781.N-TYR777.O 52.74

MET558.N-THR430.O 52.74

VAL590.N-ILE586.O 52.74

ARG73.N-GLY69.O 53.73

TYR65.OH-TYR677.OH 53.73

HID146.ND1-LYS153.O 53.73

GLN614.N-VAL610.O 53.73

ALA667.N-ASN593.OD1 54.73

TYR543.OH-HID245.O 55.22

ALA201.N-ILE197.O 56.22

VAL425.N-ASN246.OD1 56.22

ALA272.N-PRO268.O 56.72

TYR678.OH-ASN595.OD1 57.21

ILE426.N-ASN547.OD1 57.71

CYS354.N-ASN202.OD1 57.71

CYS655.N-SER644.O 57.71

LEU563.N-ALA289.O 58.21

ASN547.ND2-ASN424.O 58.21

LEU504.N-GLU692.O 58.21

VAL362.N-GLN358.O 58.21

VAL123.N-GLY93.O 58.71

LEU676.N-PHE672.O 59.20

TYR19.N-ALA15.O 59.70

VAL717.N-VAL710.O 60.20

TYR127.OH-GLN100.OE1 61.19

ASN306.N-CYS732.O 61.69

VAL363.N-LEU359.O 61.69

VAL366.N-VAL362.O 62.19

ARG640.N-TYR636.O 62.69

VAL314.N-TYR310.O 63.68

ALA313.N-PHE309.O 65.67

ASN595.N-THR591.O 65.67

ARG616.N-ASN612.O 65.67

LYS673.N-ILE669.O 66.17

CYS620.N-ARG616.O 66.67

ALA546.N-PHE542.O 66.67

PHE635.N-PHE631.O 67.16

TYR184.OH-ASN204.OD1 67.16

ASN204.OD1-TYR184.OH 67.16

CYS200.N-CYX196.O 70.15

LEU359.N-ASP355.O 70.15

Model peptideBdis-RdRp

LEU219.N-GLY235.O 52.74

HID146.ND1-LYS153.O 52.74

GLN614.N-VAL610.O 52.74

ASP415.N-TYR411.O 53.23

ARG87.N-CYS83.O 53.23

VAL244.N-TYR236.O 53.23

VAL750.N-ILE746.O 53.73

GLN588.N-PHE584.O 53.73

LEU639.N-PHE635.O 54.23

VAL717.N-VAL710.O 54.73

VAL654.N-MET505.O 55.22

LEU359.N-ASP355.O 55.22

ALA313.N-PHE309.O 55.72

ARG73.N-GLY69.O 55.72

MET558.N-THR430.O 56.22

CYS655.N-SER644.O 56.72

ALA592.N-GLN588.O 56.72

ALA546.N-PHE542.O 56.72

TYR767.OH-PRO722.O 57.21

ASN458.N-SER454.O 57.21

ASN306.N-CYS732.O 57.71

ALA201.N-ILE197.O 57.71

TYR65.OH-TYR677.OH 57.71

VAL590.N-ILE586.O 57.71

ALA667.N-ASN593.OD1 58.21

VAL314.N-TYR310.O 58.71

VAL366.N-VAL362.O 58.71

VAL362.N-GLN358.O 58.71

ARG640.N-TYR636.O 58.71

ILE522.N-ASN518.O 59.70

VAL363.N-LEU359.O 59.70

VAL147.N-PRO154.O 60.20

LYS673.N-ILE669.O 60.20

THR209.OG1-LEU206.O 61.19

CYS587.N-VAL583.O 62.69

CYS620.N-ARG616.O 63.18

TYR127.OH-GLN100.OE1 64.68

CYS200.N-CYX196.O 65.67

TYR19.N-ALA15.O 65.67

PHE635.N-PHE631.O 66.67

ARG616.N-ASN612.O 66.67

Model peptideCdis-RdRp

Table 3.15 The 20 μs MD-HBs (with occupancy rates ≥35%) within the RaRp (A-chain) of the peptideA-RdRp, peptideB-RdRp, peptideC-RdRp, peptideAdis-RdRp, peptideBdis-RdRp, and peptideCdis-RdRp models in [321]

190 3 RNA-Dependent RNA Polymerase (RdRp)

PHE238.N-GLY242.O 53.73

ASN547.ND2-ASN424.O 53.23

LYS566.N-GLU555.O 52.74

VAL244.N-TYR236.O 51.74

GLN614.N-VAL610.O 51.24

VAL717.N-VAL710.O 51.24

LEU728.N-PRO724.O 51.24

ALA592.N-GLN588.O 50.75

TYR65.OH-TYR677.OH 50.75

SER668.N-ASN671.OD1 50.25

GLN679.NE2-GLN588.OE1 49.75

SER554.N-CYS549.O 49.25

VAL243.N-ASN187.OD1 48.76

TYR128.N-VAL124.O 48.76

LEU466.N-HIE462.O 48.76

VAL232.N-ARG221.O 48.26

THR138.N-ILE134.O 47.76

LEU639.N-PHE635.O 47.76

THR38.OG1-GLU34.O 47.76

LEU76.N-VAL72.O 47.76

MET14.N-GLN100.O 47.26

LYS33.N-CYS29.O 47.26

ILE426.N-ASN547.OD1 47.26

TYR107.N-ASN99.O 47.26

SER599.OG-ASN595.O 46.77

ASN458.N-SER454.O 46.77

ILE35.N-THR31.O 46.77

ASN397.N-GLY393.O 46.77

LEU360.N-ILE356.O 46.27

ASP311.N-LYS307.O 46.27

THR38.N-GLU34.O 46.27

CYS559.N-SER562.O 46.27

CYS83.N-THR79.O 45.77

LEU198.N-ASP194.O 45.77

LYS435.N-ARG445.O 45.77

ASN612.N-LYS608.O 45.77

GLN712.N-ASP715.O 45.27

ALA550.N-ALA546.O 45.27

GLN614.NE2-LEU597.O 44.78

ILE469.N-LEU465.O 44.28

ASN518.ND2-GLU240.OE2 44.28

MET646.N-VAL653.O 44.28

LYS531.NZ-PHE370.O 44.28

SER658.N-ASN501.O 43.78

MET708.N-LEU719.O 52.74

LEU198.N-ASP194.O 51.74

ASN581.N-THR577.O 51.74

TYR678.OH-ASN595.OD1 51.24

ASN458.N-SER454.O 50.75

CYS83.N-THR79.O 50.75

LEU360.N-ILE356.O 50.25

VAL362.N-GLN358.O 50.25

CYS549.N-LEU545.O 50.25

GLN614.N-VAL610.O 49.75

ASN595.N-THR591.O 49.75

LEU219.N-GLY235.O 49.75

LYS493.N-HIE489.O 49.25

ILE469.N-LEU465.O 49.25

ALA580.N-THR576.O 48.76

ASN204.N-CYS200.O 48.76

VAL64.N-ASP60.O 48.76

MET86.N-PHE82.O 48.26

VAL557.N-TYR564.O 48.26

ARG22.N-VAL18.O 48.26

GLU692.N-LEU504.O 48.26

PHE207.N-PHE203.O 48.26

THR38.N-GLU34.O 47.76

ILE223.N-PHE230.O 47.76

ASP311.N-LYS307.O 47.76

MET14.N-GLN100.O 47.76

THR591.N-CYS587.O 47.26

VAL363.N-LEU359.O 47.26

MET523.N-MET519.O 47.26

GLN614.NE2-LEU597.O 46.77

ASN624.N-GLU619.O 46.77

TYR65.N-ILE61.O 46.77

ILE426.N-ASN547.OD1 46.77

TYR622.N-TYR618.O 46.27

HID772.N-ALA768.O 46.27

THR138.N-ILE134.O 45.77

THR209.OG1-LEU206.O 45.77

VAL243.N-ASN187.OD1 45.77

LEU492.N-TRP488.O 45.77

VAL123.N-GLY93.O 44.78

TYR636.N-VAL632.O 44.28

VAL244.N-TYR236.O 44.28

ILE35.N-THR31.O 44.28

LEU466.N-HIE462.O 44.28

ASP367.N-VAL363.O 44.78

HID237.N-GLY217.O 45.27

LEU76.N-VAL72.O 45.27

ARG541.N-SER537.O 45.27

GLN712.N-ASP715.O 45.27

VAL590.N-ILE586.O 45.77

VAL244.N-TYR236.O 45.77

CYS549.N-LEU545.O 45.77

LEU504.N-GLU692.O 45.77

VAL92.N-ILE113.O 45.77

ILE426.N-ASN547.OD1 45.77

ASN547.ND2-ASN424.O 45.77

ILE522.N-ASN518.O 45.77

ASP174.N-LEU170.O 46.27

ASN246.N-THR234.O 47.26

SER129.OG-ASP355.OD1 47.26

GLN679.N-VAL675.O 47.26

CYS83.N-THR79.O 47.26

TYR622.N-TYR618.O 47.26

ILE35.N-THR31.O 47.76

GLN358.N-ASP355.OD1 48.26

CYS655.N-SER644.O 48.26

VAL64.N-ASP60.O 48.76

TYR622.OH-ASP355.OD2 48.76

LEU360.N-ILE356.O 49.25

VAL557.N-TYR564.O 49.75

TYR678.OH-ASN595.OD1 50.25

TYR65.N-ILE61.O 50.25

LYS531.NZ-PHE370.O 50.25

LYS673.N-ILE669.O 50.25

GLN614.N-VAL610.O 50.25

THR38.OG1-GLU34.O 50.25

LEU130.N-SER126.O 50.75

VAL314.N-TYR310.O 50.75

PHE238.N-GLY242.O 50.75

HID772.N-ALA768.O 50.75

ILE223.N-PHE230.O 51.24

THR138.OG1-ILE134.O 51.24

MET14.N-GLN100.O 52.24

THR38.N-GLU34.O 52.24

LEU728.N-PRO724.O 52.74

TYR677.OH-TYR53.O 52.74

LEU198.N-ASP194.O 52.74

MET646.N-VAL653.O 53.23

LYS33.N-CYS29.O 44.78

ASN246.N-THR234.O 45.27

ASP174.N-LEU170.O 45.27

MET456.N-ILE452.O 45.77

GLU692.N-LEU504.O 46.27

LEU639.N-PHE635.O 46.27

LYS531.NZ-TYR373.O 46.77

CYS587.N-VAL583.O 46.77

ILE647.N-THR476.O 47.26

ARG169.N-PHE165.O 47.26

LYS531.NZ-PHE370.O 47.76

TYR678.OH-ASN595.OD1 47.76

LEU417.N-ASP413.O 47.76

ALA89.N-ALA85.O 47.76

TYR128.N-VAL124.O 48.26

ILE223.N-PHE230.O 48.26

HID237.N-GLY217.O 48.26

TYR622.OH-ASP355.OD2 48.76

VAL232.N-ARG221.O 48.76

VAL362.N-GLN358.O 48.76

VAL243.N-ASN187.OD1 48.76

ILE469.N-LEU465.O 48.76

VAL654.N-MET505.O 49.25

VAL557.N-TYR564.O 49.25

ASN458.N-SER454.O 49.25

ASN88.N-ASP84.O 49.25

GLN614.N-VAL610.O 49.25

LYS493.N-HIE489.O 49.75

TYR65.OH-TYR677.OH 49.75

ASN58.N-ASP54.O 49.75

ASP311.N-LYS307.O 49.75

ALA592.N-GLN588.O 49.75

LEU360.N-ILE356.O 49.75

LEU781.N-TYR777.O 50.25

VAL314.N-TYR310.O 50.25

PHE238.N-GLY242.O 50.25

MET523.N-MET519.O 50.75

TYR264.N-GLU260.O 51.24

LEU261.N-SER257.O 51.24

LEU466.N-HIE462.O 51.24

ILE522.N-ASN518.O 51.74

LEU36.N-LEU32.O 51.74

ASN595.N-THR591.O 51.74

THR38.N-GLU34.O 52.24

ILE647.N-THR476.O 45.27

VAL557.N-TYR564.O 45.77

VAL244.N-TYR236.O 45.77

VAL243.N-ASN187.OD1 45.77

PHE230.N-ILE223.O 46.27

LEU545.N-ARG541.O 46.27

MET646.N-VAL653.O 46.27

VAL288.N-LEU563.O 46.27

HID237.N-GLY217.O 46.27

ALA419.N-ASP415.O 46.77

ALA524.N-LEU520.O 46.77

VAL654.N-MET505.O 46.77

ASN246.N-THR234.O 47.26

LEU36.N-LEU32.O 47.26

MET523.N-MET519.O 47.76

VAL447.N-ASN433.O 47.76

TYR128.N-VAL124.O 47.76

THR138.N-ILE134.O 48.26

TYR638.OH-LEU665.O 48.76

ASP415.N-TYR411.O 48.76

ILE522.N-ASN518.O 48.76

ASP84.N-VAL80.O 48.76

THR591.OG1-CYS587.O 48.76

LEU360.N-ILE356.O 48.76

SER668.N-ASN671.OD1 49.25

ASP311.N-LYS307.O 49.25

CYS559.N-SER562.O 49.25

ASN612.N-LYS608.O 49.25

THR38.N-GLU34.O 49.75

THR38.OG1-GLU34.O 50.25

LEU198.N-ASP194.O 50.25

VAL750.N-ILE746.O 50.25

ILE778.N-TYR774.O 50.25

ALA592.N-GLN588.O 50.75

ASN58.N-ASP54.O 50.75

LYS33.N-CYS29.O 51.24

CYS549.N-LEU545.O 51.24

TYR677.OH-TYR53.O 51.24

THR591.N-CYS587.O 52.24

CYS83.N-THR79.O 52.24

MET86.N-PHE82.O 52.24

ILE223.N-PHE230.O 52.24

CYS587.N-VAL583.O 52.74

ASN397.N-GLY393.O 52.74

ASN204.N-CYS200.O 43.78

ASN612.N-LYS608.O 43.78

MET14.N-GLN100.O 44.28

ILE469.N-LEU465.O 44.28

GLN74.N-GLU70.O 44.28

GLN712.N-ASP715.O 44.28

ARG459.N-THR455.O 44.78

GLN776.N-HID772.O 44.78

VAL565.N-PHE286.O 45.27

HID772.N-ALA768.O 45.27

LEU76.N-VAL72.O 45.27

PHE230.N-ILE223.O 45.77

ILE426.N-ASN547.OD1 45.77

VAL583.N-TYR579.O 45.77

PHE542.N-LEU538.O 45.77

VAL64.N-ASP60.O 46.27

GLN679.N-VAL675.O 46.27

MET86.N-PHE82.O 46.27

LYS33.N-CYS29.O 46.77

LEU360.N-ILE356.O 46.77

THR138.OG1-ILE134.O 46.77

LEU781.N-TYR777.O 47.26

ILE35.N-THR31.O 47.26

MET456.N-ILE452.O 47.26

THR136.OG1-PRO351.O 47.76

ILE156.N-SER145.O 47.76

ASN581.N-THR577.O 47.76

LEU617.N-LEU613.O 47.76

LEU36.N-LEU32.O 48.26

ILE223.N-PHE230.O 48.26

CYS354.N-ASN202.OD1 48.26

ASN88.N-ASP84.O 48.76

LEU504.N-GLU692.O 48.76

TYR264.N-GLU260.O 49.75

VAL123.N-GLY93.O 49.75

CYS83.N-THR79.O 49.75

THR138.N-ILE134.O 50.25

ASN397.N-GLY393.O 50.75

TYR184.OH-ASN204.OD1 50.75

LEU598.N-VAL594.O 50.75

THR591.N-CYS587.O 51.74

THR38.N-GLU34.O 51.74

ASP174.N-LEU170.O 52.24

SER668.N-ASN671.OD1 52.24

Supplementary Information 191

TYR496.N-LEU492.O 43.28

ASP174.N-LEU170.O 43.78

ASN547.N-TYR543.O 43.28

VAL92.N-ILE113.O 43.78

ALA419.N-ASP415.O 43.78

THR138.N-ILE134.O 43.28

THR138.N-ILE134.O 42.29

GLN358.N-ASP355.OD1 41.79

PHE230.N-ILE223.O 41.79

ALA524.N-LEU520.O 42.29

HIE271.N-ASP267.O 40.80

ASN624.N-GLU619.O 40.80

GLU167.N-TYR163.O 40.30

LEU36.N-LEU32.O 37.31

ARG541.N-SER537.O 37.31

TYR564.N-VAL557.O 36.82

TYR264.N-GLU260.O 36.82

MET491.N-GLY487.O 39.30

TYR496.N-LEU492.O 39.30

ILE384.N-GLN463.OE1 39.30

TYR128.N-VAL124.O 38.81

CYS549.N-LEU545.O 37.31

VAL123.N-GLY93.O 37.31

ASP174.N-LEU170.O 39.80

HID237.N-GLY217.O 39.80

LEU598.N-VAL594.O 37.81

ARG22.NH2-ASP355.OD2 37.31

THR494.OG1-ASN490.O 39.80

ASN246.N-THR234.O 39.80

THR591.N-CYS587.O 38.31

ALA89.N-ALA85.O 37.81

ILE452.N-ALA392.O 40.30

TYR369.N-VAL365.O 40.30

SER599.OG-ASN595.O 38.81

ASN612.N-LYS608.O 38.81

ILE384.N-ALA380.O 39.30

ARG239.NE-GLU240.OE1 39.30

ALA578.N-ASP574.O 39.30

ASN204.ND2-GLU240.O 39.30

CYS559.N-SER562.O 39.30

ASN624.N-GLU619.O 39.30

TYR107.N-ASN99.O 39.80

LEU617.N-LEU613.O 41.29

MET646.N-VAL653.O 39.30

TYR636.N-VAL632.O 39.30

LEU613.N-TYR609.O 39.30

ARG459.N-THR455.O 39.80

ASP367.N-VAL363.O 39.80

LYS566.N-GLU555.O 40.30

ASN612.N-LYS608.O 40.30

GLY449.N-GLN431.O 40.30

ASP248.N-ASN424.OD1 40.30

THR352.OG1-ASN681.OD1 41.29 THR472.OG1-SER468.O 40.80

LEU219.N-GLY235.O 40.30 TYR65.OH-TYR677.OH 40.30 TYR46.OH-ASN58.OD1 40.30

VAL552.N-GLU548.O 38.81

TYR767.OH-PRO722.O 38.81

GLU692.N-LEU504.O 38.31

LEU613.N-TYR609.O 40.30

ASN518.ND2-GLU240.OE2 41.29

LEU504.N-GLU692.O 41.29

SER662.N-SER658.O 41.29

VAL92.N-ILE113.O 41.29

ILE452.N-ALA392.O 41.79

VAL123.N-GLY93.O 41.79

VAL583.N-TYR579.O 40.30

VAL552.N-GLU548.O 40.30

LEU613.N-TYR609.O 40.30

LEU598.N-VAL594.O 40.30

LYS33.N-CYS29.O 41.29

LEU130.N-SER126.O 40.30

VAL557.N-TYR564.O 38.81

TYR236.N-VAL244.O 38.81

PHE238.N-GLY242.O 40.30

ILE754.N-VAL750.O 40.30

LEU528.N-ALA524.O 39.30

LEU95.N-VAL123.O 38.81

PHE230.N-ILE223.O 40.80

ASN547.ND2-ASN424.O 41.79

ALA419.N-ASP415.O 41.29 LEU617.N-LEU613.O 40.80

ALA75.N-ARG71.O 39.30

VAL583.N-TYR579.O 39.30

ASN88.N-ASP84.O 40.80

SER658.N-ASN501.O 40.80

TYR564.N-VAL557.O 40.80

THR13.N-ASP16.OD2 41.79

LYS171.N-GLU167.O 41.29

LYS78.NZ-ASN103.O 39.80

CYS587.N-VAL583.O 39.30

LEU261.N-SER257.O 41.29

LEU728.N-PRO724.O 41.79

ILE586.N-SER582.O 41.29

SER668.N-ASN671.OD1 41.29

LEU261.N-SER257.O 39.80

ILE778.N-TYR774.O 39.80

ASN58.N-ASP54.O 41.29

GLN551.NE2-ILE426.O 41.29

LEU719.N-MET708.O 42.29 TYR564.N-VAL557.O 42.29

TYR636.N-VAL632.O 41.79 SER208.N-ASN204.O 41.79 THR760.OG1-TYR757.O 41.79

ASP367.N-VAL363.O 40.30

LEU613.N-TYR609.O 40.30

THR421.N-LEU417.O 39.80

TYR718.N-HIE489.ND1 41.29

THR115.N-GLY90.O 42.29

VAL710.N-VAL717.O 42.79

TYR65.N-ILE61.O 42.79

VAL64.N-ASP60.O 43.78

PHE584.N-ALA580.O 41.29

ALA89.N-ALA85.O 41.79

LYS78.NZ-ASN103.O 42.29

ASN397.N-GLY393.O 42.29

CYS587.N-VAL583.O 42.79

ALA524.N-LEU520.O 41.29

ASN246.N-THR234.O 40.80

LEU492.N-TRP488.O 40.80

LEU617.N-LEU613.O 41.79

CYS559.N-SER562.O 41.79

TYR636.N-VAL632.O 41.29

ASP248.N-ASN424.OD1 40.80

LEU36.N-LEU32.O 41.79

ASN204.ND2-GLU240.O 43.28 MET14.N-GLN100.O 43.28

TYR128.N-VAL124.O 42.79 ILE778.N-TYR774.O 42.79

SER582.OG-ALA578.O 41.29

LEU219.N-GLY235.O 41.29

ASN612.N-LYS608.O 42.29

LYS78.NZ-ASN103.O 42.29

LYS566.N-GLU555.O 41.79

LYS435.N-ARG445.O 43.28

ILE754.N-VAL750.O 42.79

ASN88.N-ASP84.O 42.29

LEU617.N-LEU613.O 41.79

GLU548.N-ARG544.O 42.79

TYR264.N-GLU260.O 42.79

PHE230.N-ILE223.O 43.78

ASN204.N-CYS200.O 43.78

LYS566.N-GLU555.O 43.28 ARG544.N-HIE540.O 43.28 LEU466.N-HIE462.O 43.28

THR591.OG1-CYS587.O 43.28

GLN588.NE2-ASN680.OD1 43.28

VAL447.N-ASN433.O 42.79

ILE778.N-TYR774.O 43.28

THR38.OG1-GLU34.O 43.78

ASN585.N-ASN581.O 44.28 VAL18.N-MET14.O 44.28

ARG221.N-VAL232.O 43.28

THR760.OG1-TYR757.O 43.28

TYR721.N-HID706.O 43.78

THR591.N-CYS587.O 44.28 LEU130.N-SER126.O 44.28

ILE469.N-LEU465.O 44.28 LEU639.N-PHE635.O 43.28

ASN681.ND2-ALA515.O 43.78

MET708.N-LEU719.O 43.78

ALA89.N-ALA85.O 43.78

LYS398.N-PRO395.O 43.78

Model peptideAdis-RdRp TYR107.N-ASN99.O 44.78

MET558.N-THR430.O 44.78

Model peptideB-RdRp

LYS171.N-GLU167.O 43.78

Model peptideA-RdRp

THR115.N-GLY90.O 43.78

Model peptideC-RdRp

LEU492.N-TRP488.O 39.30

VAL18.N-MET14.O 39.30

TYR496.N-LEU492.O 39.80

ALA265.N-LEU261.O 39.80

VAL232.N-ARG221.O 39.80

GLY217.N-HID237.O 39.80

THR472.OG1-SER468.O 39.80

LYS531.NZ-TYR373.O 39.80

VAL565.N-PHE286.O 40.30

LEU728.N-PRO724.O 40.30

LEU261.N-SER257.O 40.30

LEU262.N-PHE258.O 40.30

ASN204.N-CYS200.O 40.80

ARG87.N-CYS83.O 40.80

GLN614.NE2-LEU597.O 40.80

ARG459.N-THR455.O 41.29

TYR622.N-TYR618.O 41.29

TYR622.OH-ASP355.OD2 41.79

ILE156.N-SER145.O 41.79

ALA550.N-ALA546.O 41.79

MET708.N-LEU719.O 41.79

GLN712.N-ASP715.O 42.29

ILE469.N-LEU465.O 42.29

THR138.OG1-ILE134.O 42.29

ILE35.N-THR31.O 42.79

LEU76.N-VAL72.O 42.79

TYR176.OH-GLU144.OE1 43.28

GLU692.N-LEU504.O 43.28

ASP174.N-LEU170.O 43.28

ASP248.N-ASN424.OD1 43.78

MET14.N-GLN100.O 43.78

GLN74.N-GLU70.O 43.78

ASP367.N-VAL363.O 44.28

LEU553.N-CYS549.O 44.78

LYS493.N-HIE489.O 44.78

VAL147.N-PRO154.O 44.78

ARG169.N-PHE165.O 44.78

LEU291.N-GLY561.O 44.78

LYS435.N-ARG445.O 44.78

TYR543.N-SER539.O 45.27

LEU617.N-LEU613.O 45.27

TYR564.N-VAL557.O 45.27

Model peptideBdis-RdRp

LEU492.N-TRP488.O 38.81

LYS493.N-HIE489.O 38.81

ASN624.N-GLU619.O 38.81

VAL594.N-VAL590.O 38.81

THR760.OG 1-TYR757.O 39.30

VAL18.N-MET14.O 39.30

SER129.OG-ASP355.OD1 39.30

LEU291.N-GLY561.O 39.80

VAL232.N-ARG221.O 39.80

ARG221.N-VAL232.O 39.80

ARG530.N-LEU526.O 39.80

LYS467.N-GLN463.O 40.30

ASN547.N-TYR543.O 40.80

TYR65.N-ILE61.O 40.80

MET646.N-VAL653.O 40.80

ASN595.N-THR591.O 40.80

CYS559.N-SER562.O 40.80

SER658.N-ASN501.O 40.80

TYR176.OH-GLU144.OE2 40.80

LYS566.N-GLU555.O 41.29

TYR564.N-VAL557.O 41.29

TYR622.OH-ASP355.OD2 41.79

HID237.N-GLY217.O 41.79

PHE584.N-ALA580.O 41.79

THR38.OG1-GLU34.O 42.29

ASN585.N-ASN581.O 42.29

ALA89.N-ALA85.O 42.29

VAL288.N-LEU563.O 42.29

LYS171.N-GLU167.O 42.29

PHE207.N-PHE203.O 42.29

THR591.OG1-CYS587.O 42.29

SER599.OG-ASN595.O 42.79

LEU728.N-PRO724.O 42.79

ASP311.N-LYS307.O 42.79

TYR636.N-VAL632.O 42.79

ASN58.N-ASP54.O 42.79

LYS435.N-ARG445.O 42.79

TYR496.N-LEU492.O 43.28

TYR677.OH-TYR53.O 43.28

LEU261.N-SER257.O 43.28

ASP84.N-VAL80.O 43.28

THR430.N-MET556.O 43.78

Model peptideCdis-RdRp

Table 3.16 The 20 μs MD-HBs (with occupancy rates ≥35%) within the RaRp (A-chain) of the peptideA-RdRp, peptideB-RdRp, peptideC-RdRp, peptideAdis-RdRp, peptideBdis-RdRp, and peptideCdis-RdRp models in [321] (continuation)

192 3 RNA-Dependent RNA Polymerase (RdRp)

ALA419.N-ASP415.O 36.82

VAL653.N-MET646.O 36.32

ASN657.ND2-HIE642.ND1 36.32

VAL594.N-VAL590.O 36.32

ASN58.N-ASP54.O 36.32

VAL18.N-MET14.O 36.32

THR760.OG1-TYR757.O 36.32

ASP415.N-TYR411.O 35.82

TYR622.N-TYR618.O 35.82

PHE207.N-PHE203.O 35.82

VAL675.N-ASN671.O 35.82

ASN624.N-GLU619.O 35.32

ARG459.N-THR455.O 35.32

GLU747.N-THR743.O 35.32

ARG87.N-CYS83.O 34.83

ALA580.N-THR576.O 34.83

GLU548.N-ARG544.O 34.83

TYR622.OH-ASP355.OD2 34.83

ARG169.N-PHE165.O 34.83

ARG221.N-VAL232.O 34.83

LEU130.N-SER126.O 34.33

SER525.N-ARG521.O 34.33

ASN204.ND2-GLU240.O 33.83

ASN204.ND2-PRO186.O 33.33

VAL710.N-VAL717.O 33.33

PHE542.N-LEU538.O 33.33

ILE727.N-ASP723.O 33.33

HID772.N-ALA768.O 33.33

THR13.N-ASP16.OD1 33.33

ARG530.NH2-GLU364.OE2 32.84

TYR420.N-ALA416.O 32.84

LEU719.N-MET708.O 32.84

GLN100.NE2-GLY104.O 32.84

GLN776.N-HID772.O 32.84

HIE271.N-ASP267.O 32.84

LEU77.N-ARG73.O 32.84

ARG611.N-ASP607.O 32.84

ASN349.ND2-MET516.O 32.84

VAL225.N-VAL228.O 32.34

TYR310.N-ASN306.O 32.34

ALA637.N-ASN633.O 32.34

ASN349.ND2-ARG514.O 32.34

ALA661.N-ASN657.O 32.34

ILE522.N-ASN518.O 31.84

SER662.N-SER658.O 38.81

LYS33.N-CYS29.O 38.81

GLN712.N-ASP715.O 38.81

GLN776.N-HID772.O 38.81

ARG459.N-THR455.O 38.81

VAL232.N-ARG221.O 38.81

VAL18.N-MET14.O 38.31

VAL552.N-GLU548.O 37.81

ARG22.NH2-ASP355.OD2 37.81

LEU95.N-VAL123.O 37.31

CYX377.N-THR534.O 36.82

GLY217.N-HID237.O 36.82

GLU701.N-GLU692.OE1 36.82

ARG87.N-CYS83.O 36.32

LYS171.N-GLU167.O 36.32

ASN547.ND2-ASN424.O 36.32

THR352.OG1-ASN681.OD1 36.32

VAL654.N-MET505.O 36.32

LEU719.N-MET708.O 36.32

ILE522.N-ASN518.O 35.82

VAL225.N-VAL228.O 35.82

LEU639.N-PHE635.O 35.82

ARG521.N-PRO517.O 35.82

HIE462.N-ASN458.O 35.82

LEU598.N-VAL594.O 35.32

LEU170.N-THR166.O 35.32

THR13.N-ASP16.OD1 35.32

TYR107.N-ASN99.O 34.83

TRP690.N-GLY506.O 34.83

LEU528.N-ALA524.O 34.83

ASN204.ND2-GLU240.O 34.83

ALA753.N-PHE749.O 34.83

ASN547.N-TYR543.O 34.33

ALA20.N-ASP16.O 33.83

HID237.ND1-SER215.O 33.83

THR707.N-PRO699.O 33.83

TRP180.NE1-HID199.NE2 33.33

HID532.ND1-LEU528.O 33.33

THR430.N-MET556.O 33.33

TYR46.OH-ASN58.OD1 33.33

VAL770.N-GLU766.O 33.33

GLY400.N-PHE396.O 33.33

VAL594.N-VAL590.O 32.84

ARG611.N-ASP607.O 32.84

ARG530.NH1-GLU364.OE2 33.33

MET456.N-ILE452.O 33.33

ALA470.N-LEU466.O 33.33

ARG611.N-ASP607.O 33.83

PHE211.N-PHE207.O 34.33

TYR564.N-VAL557.O 34.33

MET708.N-LEU719.O 34.33

GLN614.NE2-LEU597.O 34.33

PHE286.N-PHE216.O 34.83

TYR310.N-ASN306.O 34.83

ASP248.N-ASN424.OD1 34.83

TYR509.OH-ASN585.OD1 35.32

LYS78.NZ-ASN105.OD1 35.32

VAL527.N-MET523.O 35.32

PHE418.N-GLN414.O 35.32

ARG530.NE-ASP194.OD2 35.32

SER662.N-SER658.O 35.32

TYR264.N-GLU260.O 35.32

THR352.OG1-ASN681.OD1 35.32

GLN100.NE2-GLY104.O 35.82

VAL18.N-MET14.O 35.82

VAL232.N-ARG221.O 35.82

VAL123.N-GLY93.O 35.82

LEU563.N-VAL288.O 36.32

ALA637.N-ASN633.O 36.32

THR421.N-LEU417.O 36.32

THR457.OG1-CYS453.O 36.32

GLN776.N-HID772.O 36.82

VAL478.N-ILE647.O 37.31

THR472.OG1-SER468.O 37.31

PHE207.N-PHE203.O 37.31

VAL243.N-ASN187.OD1 37.31

LEU170.N-THR166.O 37.81

SER658.N-ASN501.O 37.81

ASN88.N-ASP84.O 37.81

TYR638.OH-LEU665.O 38.31

LEU775.N-PHE771.O 38.31

VAL710.N-VAL717.O 38.31

GLU747.N-THR743.O 38.31

ALA550.N-ALA546.O 38.31

GLU692.N-LEU504.O 38.31

THR115.N-GLY90.O 38.81

THR430.N-MET556.O 38.81

ARG22.N-VAL18.O 38.81

ALA753.N-PHE749.O 33.83

ILE586.N-SER582.O 33.83

ASP84.N-VAL80.O 33.83

ARG544.N-HIE540.O 33.83

LYS171.N-GLU167.O 33.83

ALA589.N-ASN585.O 34.33

ILE727.N-ASP723.O 34.33

ASN657.N-HIE642.O 34.83

TYR718.OH-LEU695.O 34.83

LYS78.N-GLN74.O 34.83

TYR622.N-TYR618.O 34.83

VAL632.N-ASP628.O 34.83

PHE173.N-ARG169.O 35.32

TYR236.N-VAL244.O 35.32

TYR774.OH-ILE727.O 35.32

THR494.OG1-ASN490.O 35.82

ARG530.NE-ASP194.OD2 35.82

GLN414.N-SER410.O 35.82

TYR420.N-ALA416.O 35.82

LYS78.NZ-ASN103.O 35.82

HID237.ND1-SER215.O 35.82

THR421.OG1-LEU417.O 36.32

TYR718.N-HIE489.ND1 36.32

ILE384.N-GLN463.OE1 36.32

ALA419.N-ASP415.O 36.32

GLU747.N-THR743.O 36.32

ASP415.N-TYR411.O 36.32

VAL244.N-TYR236.O 36.32

ARG541.N-SER537.O 36.82

THR760.OG1-TYR757.O 36.82

TYR721.N-HID706.O 36.82

ARG611.N-ASP607.O 36.82

THR209.OG1-LEU206.O 36.82

ARG87.N-CYS83.O 37.31

GLN712.N-ASP715.O 37.81

SER525.N-ARG521.O 37.81

SER582.OG-ALA578.O 37.81

LEU775.N-PHE771.O 38.31

THR421.N-LEU417.O 38.31

PHE207.N-PHE203.O 38.81

TYR46.OH-ASN58.OD1 39.30

ILE35.N-THR31.O 39.30

CYS559.N-SER562.O 39.30

VAL447.N-ASN433.O 39.30

LEU130.N-SER126.O 35.32

ILE429.N-ALA266.O 35.32

ASN204.ND2-PRO186.O 35.32

LYS566.N-GLU555.O 35.32

ASN458.N-SER454.O 35.32

TYR721.N-HID706.O 35.32

SER658.N-ASN501.O 35.32

TYR39.OH-ASN103.OD1 35.82

THR136.OG1-PRO351.O 35.82

ARG611.N-ASP607.O 35.82

VAL710.N-VAL717.O 36.32

HIE271.NE2-ALA265.O 36.32

TYR636.N-VAL632.O 36.32

ARG221.N-VAL232.O 36.32

LEU598.N-VAL594.O 36.82

ALA380.N-ASP415.OD2 36.82

MET456.N-ILE452.O 36.82

ARG73.NE-GLU70.OE2 37.31

GLN776.N-HID772.O 37.31

HIE462.N-ASN458.O 37.31

LEU613.N-TYR609.O 37.31

PHE238.N-GLY242.O 37.31

TYR65.N-ILE61.O 37.31

PHE173.N-ARG169.O 37.31

LEU466.N-HIE462.O 37.81

VAL64.N-ASP60.O 37.81

TYR236.N-VAL244.O 37.81

ASN518.ND2-GLU240.OE2 37.81

ILE586.N-SER582.O 37.81

TYR420.N-ALA416.O 38.31

LEU639.N-PHE635.O 38.31

ASN88.N-ASP84.O 38.31

ILE91.N-MET86.O 38.31

MET432.N-MET558.O 38.81

TYR107.N-ASN99.O 38.81

ILE384.N-GLN463.OE1 38.81

LEU95.N-VAL123.O 38.81

HID237.ND1-SER215.O 38.81

LYS171.N-GLU167.O 38.81

TYR46.OH-ASN58.OD1 39.30

LEU775.N-PHE771.O 39.30

LEU219.N-GLY235.O 39.30

ASN624.N-GLU619.O 39.30

ILE727.N-ASP723.O 39.30

PHE177.N-PHE173.O 32.84

ALA637.N-ASN633.O 32.84

ARG73.NH2-GLU70.OE1 33.33

TYR46.OH-ASN58.OD1 33.33

GLN460.NE2-ILE378.O 33.33

THR421.N-LEU417.O 33.33

MET708.N-LEU719.O 33.33

VAL557.N-TYR564.O 33.83

TYR176.OH-GLU144.OE1 33.83

LEU613.N-TYR609.O 33.83

HIE462.N-ASN458.O 33.83

LEU676.N-PHE672.O 34.33

ARG541.N-SER537.O 34.33

ARG611.N-ASP607.O 34.33

VAL632.N-ASP628.O 34.33

THR115.N-GLY90.O 34.33

GLU692.N-LEU504.O 34.33

GLN551.NE2-ILE426.O 34.83

HIE271.N-ASP267.O 34.83

VAL243.N-ASN187.OD1 34.83

VAL675.N-ASN671.O 35.32

ASN458.ND2-GLN551.OE1 35.32

TYR420.N-ALA416.O 35.32

GLN100.NE2-GLY104.O 35.32

GLN614.NE2-LEU597.O 35.32

THR352.OG1-ASN681.OD1 35.82

ASN595.ND2-THR591.O 35.82

ARG169.N-PHE165.O 35.82

ILE754.N-VAL750.O 36.32

TYR128.N-VAL124.O 36.32

MET523.N-MET519.O 36.32

SER208.N-ASN204.O 36.32

VAL225.N-VAL228.O 36.82

LEU198.N-ASP194.O 36.82

ILE778.N-TYR774.O 36.82

ALA524.N-LEU520.O 36.82

VAL92.N-ILE113.O 36.82

ARG73.NE-GLU70.OE2 37.31

ASP367.N-VAL363.O 37.81

GLU747.N-THR743.O 37.81

TYR622.N-TYR618.O 37.81

ALA272.N-PRO268.O 38.31

ALA580.N-THR576.O 38.31

LEU95.N-VAL123.O 38.31

Supplementary Information 193

Chapter 4

RNA Helicase

Abstract Helicase and polymerase are coupling in the SARS-CoV-2 replicationtranscription complex (RTC). RNA helicase (NSP13) is a SARS-CoV-2 antiviral target too. It facilitates/stimulates SARS-CoV-2 RdRp backtracking. Molecular dynamics (MD) simulations of the NSP13.2 -BTC.−1U +1C and NSP13.2 BTC.−1U +1U complexes were done in Malone et al. (Proc Natl Acad Sci USA 118(19):e2102516118, 2021) and confirmed the results: “the single-stranded 3’segment of the product-RNA generated by backtracking extrudes through the RdRp NTP-entry tunnel, that a mismatched nucleotide at the product-RNA 3’end frays and enters the NTP-entry tunnel to initiate backtracking” but without detailed structural bioinformatics such as hydrogen bonds (HBs), salt bridges (SBs), .π -interactions (PIs), and hydrophobic interactions (HYDs) of the SARS-CoV-2NSP13 RNA helicase. This chapter presents some detailed structural bioinformatics such as HBs, SBs, PIs, and HYDs of the SARS-CoV-2-NSP13 RNA helicase in its optimized structure and then during its MD simulations. Keywords COVID-19 virus · RNA helicase (NSP13) · Binding with holo-RdRp and RNA · Optimization and MD (molecular dynamics) studies · Basic structural bioinformatics

4.1 Introduction The COVID-19 virus’ RNA-dependent RNA polymerase (RdRp, also named NSP12) is the central component of coronaviral replication/transcription machinery and appears to be a primary drug target for antivirals such as remdesivir [118, 225]. Structures of SARS-CoV-2 RdRp (RNA-dependent RNA polymerase) bound to the essential RNA helicase (NSP13) and RNA suggested the helicase facilitates/stimulates SARS-CoV-2 RdRp backtracking; backtracking is the reverse/backward motion of the RdRp on the template RNA, and backtracking may aid proofreading, viral transcription, and replication [64, 225]. The RdRp holoenzyme (holo-RdRp: NSP7/NSP8.2 /NSP12) is thought to coordinate with many © The Author(s), under exclusive license to Springer Nature Switzerland AG 2023 J. Zhang, Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures, Springer Series in Biophysics 23, https://doi.org/10.1007/978-3-031-36773-1_4

195

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cofactors (such as the NSP13 helicase and the NSP10/NSP14 proofreading assembly) to carry out its function. These cofactors are also essential for viral replication and are antiviral targets. Molecular dynamics (MD) simulations of the NSP13.2 -BTC.−1U +1C and NSP13.2 -BTC.−1U +1U complexes were done in [225], to confirm the results: “the single-stranded 3’-segment of the product-RNA generated by backtracking extrudes through the RdRp NTP-entry tunnel, that a mismatched nucleotide at the productRNA 3’-end frays and enters the NTP-entry tunnel to initiate backtracking.” This chapter presents detailed structural bioinformatics such as hydrogen bonds (HBs), salt bridges (SBs), .π -interactions (PIs), and hydrophobic interactions (HYDs) of the SARS-CoV-2-NSP13 RNA helicase in its optimized structure and its MD simulations.

4.2 Materials and Methods Six 5 .μs MD simulation trajectories (numbered 12366060, 12366092, 12366129, 12376232, 12376233, and 12376234) are presented in open databases [321]; in this chapter, we denote them as replicate 1 (rep1), replicate 2 (rep2), replicate 3 (rep3), replicate 4 (rep4), replicate 5 (rep5), replicate 6 (rep6), respectively, of the NSP13-bound SARS-CoV-2 replication-transcription complex (RTC) which are starting from a backtracked state [225] by the use of 7KRO.pdb (cryo-EM structure of NSP13.2 -BTC.5 ). Three replicates of trajectories [numbered 12366060, 12366092, and 12366129] are featuring p-RNA with a matched .−1U and a mismatched +1C, and another three replicates of trajectories [numbered 12376232, 12376233, and 12376234] are featuring p-RNA with a matched -1U, and +1C/U. A-, B-, C-, D-, E-, F-, P-, and T-chains of 7KRO.pdb are NSP12, NSP8a, NSP7, NSP8b, NSP13.1, NSP13.2, p-RNA, and t-RNA, respectively with ions Zn.2+ , Mg.2+ , and ADPs. We optimized the structures of NSP13, i.e., the EF-chains of 7KRO.pdb, and got some basic structural bioinformatics (such as HBs, SBs, PIs, and HYDs) about NSP13 helicase and then confirmed these basic bioinformatics during 5 .μs’ long MD simulations.

4.3 New Results and Discussions The optimized-12366060-EFchains model has 152 HBs, 48 SBs (within Echain: GLU142-ARG409, ASP204-LYS524, ASP223-ARG186, GLU136-ARG21, GLU162-LYS524, GLU551-LYS477, GLU201-ARG178, GLU353-LYS347, ASP32-LYS28, GLU420-ARG427, ASP328-LYS347, ASP534-ARG560, ASP344LYS345, ASP450-LYS460, GLU540-LYS320, GLU197-ARG337, GLU128LYS131, GLU261-ARG442, GLU201-ARG212, ASP315-ARG332, ASP583ARG579, GLU319-LYS569; within F-chain: GLU142-ARG409, ASP204-LYS524, ASP223-ARG186, GLU136-ARG21, GLU162-LYS524, GLU551-LYS477, GLU201-ARG178, GLU353-LYS347, ASP32-LYS28, GLU420-ARG427,

4.3 New Results and Discussions

197

ASP328-LYS347, ASP534-ARG560, ASP344-LYS345, GLU498-ARG502, ASP466-LYS467, GLU420-LYS430, ASP374-LYS288, ASP315-LYS345, GLU375-LYS288, ASP101-LYS28, GLU244-LYS276, GLU143-LYS146, GLU540-ARG443, GLU418-LYS430, ASP369-LYS394; between E-chain and F-chain: E:ASP160-F:ARG248), 9 .π -cations (F:LYS76.NZ-F:TYR64, E:LYS473.NZ-E:TYR582, F:LYS473.NZ-F:TYR582, E:LYS192.NZ-E:TYR185, F:LYS192.NZ-F:TYR185, F:ARG15.NH2-F:PHE24, E:LYS139.NZ-E:TYR182, E:LYS276.NZ-E:HID395, E:ARG332.NH2-E:HID311), and 21 .π -.π stackings (F:TYR70-F:TYR48, F:PHE81-F:PHE90, F:HID39-F:HID33-F:PHE106, F:HID395-F:TYR246, F:TYR299-F:TYR298, F:TYR114-F:TYR120, F:PHE200F:TYR198-F:PHE182, F:TYR198-F:PHE225, F:PHE262-F:TYR324, F:PHE499F:TRP506, E:PHE225-E:PHE200, E:TYR149-E:PHE145, E:TRP114-E:TYR120, E:TYR299-E:TYR298, E:TYR269-E:PHE291, E:PHE262-E:TYR324, E:PHE499E:TRP506-E:TYR543-E:TRP506). The optimized-12376232-EFchains model has 164 HBs, 49 SBs (within E-chain: GLU447-LYS462, GLU353-LYS347, GLU540-LYS320, GLU197ARG337, GLU197-ARG339, GLU201-LYS524, ASP223-ARG186, ASP534ARG560, ASP583-ARG579, ASP32-LYS28, GLU128-LYS131, GLU498ARG502, GLU201-ARG212, GLU142-LYS139, GLU143-LYS146, ASP369LYS394, ASP328-LYS347, ASP466-LYS465, ASP435-LYS271, GLU168LYS171, ASP483-LYS202, ASP204-ARG490, ASP315-ARG332, ASP542LYS569; within F-chain: GLU447-LYS465, GLU447-LYS467, GLU353-LYS347, GLU197-ARG337, GLU201-ARG178, ASP223-ARG186, ASP534-ARG560, ASP583-LYS460, ASP32-LYS28, GLU128-LYS131, GLU143-LYS146, ASP369LYS394, ASP328-LYS347, GLU168-LYS171, ASP315-ARG332, GLU418LYS430, GLU142-ARG409, GLU341-ARG212, ASP101-LYS28, GLU420LYS430, GLU162-ARG161, GLU551-LYS477, GLU136-ARG21, GLU244LYS276; between E-chain and F-chain: E:GLU341-F:ARG248), 13 .π -cations (F:HID245-E:LYS218.NZ+, F:LYS76.NZ+-F:TYR64, E:LYS76.NZ+-E:TYR64, E:LYS473.NZ+-E:TYR582, F:LYS473.NZ+-F:TYR582, E:LYS192.NZ+-E:TYR 185, F:ARG15.NH2+-F:PHE24, F:LYS139.NZ+-F:TYR382, E:LYS276.NZ+E:HID395, E:ARG332.NH2+-E:HID311, E:TYR211-E:ARG161.NH2+, E:TYR 205-E:ARG490.NH2+, E:TYR93-E:ALA1.N+), and 22 .π -.π stackings (F:TYR149F:PHE145, F:TRP167-F:TRP167, F:TYR198-F:PHE225-F:PHE200, F:PHE499F:TRP506-F:PHE499, F:PHE546-F:PHE561, F:TYR120-F:TRP114, F:HID290F:ADP1003, F:TYR324-F:PHE262, F:PHE106-F:PHE133, F:TYR298-F:TYR299, F:HID33-F:HID39, F:TYR48-F:TYR70, F:PHE81-F:PHE90, E:PHE200-E:PHE 225, E:TYR180-E:TYR149, E:PHE499-E:TRP506-E:TYR543-E:TRP506, E:TYR 298-E:TYR299, E:PHE106-E:PHE133). The RMSD value between the optimized-12366060-EFchains model and the optimized-12376232-EFchains model is 5.77368 Å. The ADP1003 ligand interaction diagrams with the E-chain and F-chain for each optimized model are shown in Fig. 4.1, where EF-chains’ residues 285, 286, 287, 289, 290, 320, 442, and 443 and Mg.2+ 1004 are always binding ADP1003. Seeing Fig. 4.2, we may know that the NSP13.1 residues ASP101-ASN102 are always exposed to the surface with negative charges; the two Ramachandran plots are also slightly different to each other.

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4 RNA Helicase

Fig. 4.1 RNA helicases NSP13.1 and NSP13.2 binding with the ADP. The first two graphs from left to right are for the optimized-12366060-EFchains model, and the last two graphs from left to right are for the optimized-12376232-EFchains model

Fig. 4.2 The Poisson-Boltzmann electrostatic surfaces and the Ramachandran plots for the optimized-12366060-EFchains model and the optimized-12376232-EFchains model respectively

The hydrophobic-hydrophilic surfaces for the optimized-12366060-EFchains model and the optimized-12376232-EFchains model of NSP13 helicase are shown in Fig. 4.3.

Fig. 4.3 The hydrophobic-hydrophilic surfaces for the optimized-12366060-EFchains model (left) and the optimized-12376232-EFchains model (right)

Tables 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9 and 4.10 list the SBs linking Echain NSP13.1 with ABCDFchains NSP12-NSP8a-NSP7-NSP8b-NSP13.2, the SBs linking Fchain NSP13.2 with ABCDEchains NSP12-NSP8a-NSP7-NSP8b-

With A-chain NSP12

A:ASP901-E:LYS94

A:ASP901-E:LYS94

A:ASP901-E:LYS94

A:ASP901-E:LYS94

A:ASP901-E:LYS94

A:ASP901-E:LYS94

.\E:

Rep1

Rep2

Rep3

Rep4

Rep5

Rep6

E:GLU341-B:LYS97

E:ASP328/GLU353-B:LYS165

F:GLU244-E:ARG186/LYS189/LYS218

C:ASP67/GLU74-E:ARG248

C:ASP67/GLU74-E:ARG248

E:ASP160-F:ARG248/LYS271 E:ASP344/GLU341-F:ARG248

D:ASP78/GLU77-E:ARG392 E:GLU244-D:LYS82

E:ASP344/GLU341-F:ARG248 F:ASP435-E:LYS218

E:ASP160-F:ARG248 E:GLU244-D:LYS82

F:ASP435-E:LYS218

D:GLU171-E:ARG248

F:ASP101/ASP105/GLU128-E:LYS189

E:GLU341-F:ARG248

D:GLU77-E:ARG392

D:GLU77-E:ARG392

E:ASP160-F:ARG248/LYS271

E:ASP260-D:LYS165

D:ASP52/GLU48-E:LYS76

F:ASP101/ASP105/GLU128-E:LYS189

D:ASP175-E:LYS271

F:ASP435-E:ARG161/LYS218

F:ASP101/ASP105/GLU128-E:LYS189

D:ASP52/GLU48-E:LYS76

F:GLU365-E:LYS189

F:GLU128/GLU244-E:LYS189

E:GLU244-C:LYS70 C:ASP67/GLU73/GLU74-E:ARG248

F:ASP328/GLU244/GLU353-E:LYS218

E:ASP160/GLU156-F:ARG248

E:GLU156-F:ARG248

F:ASP369-E:LYS218

E:ARG392-C:GLU23

D:ASP134-E:ARG248

E:GLU365-C:ARG21,

C:ASP67-E:ARG392/LYS276/LYS394

F:GLU128/GLU365-E:LYS189

E:GLU244-C:LYS70

F:GLU244-E:LYS189/LYS218

E:ASP160-F:ARG248/ARG392/LYS394

C:ASP67-E:ARG392/LYS276/LYS394 E:GLU365-C:ARG21

F:ASP101-E:LYS189

E:GLU341-F:ARG248

E:ASP328/GLU353-B:LYS165

D:ASP134-E:ARG248

F:GLU128-E:LYS189 F:GLU244-E:ARG186/LYS218

E:ASP160-F:ARG248/LYS271

F:ASP101-E:LYS189

With F-chain NSP13.2

E:GLU244-C:LYS70

D:ASP134-E:ARG248

With D-chain NSP8b

E:ASP369-C:ARG21

C:ASP67-E:ARG392/LYS276/LYS394

With C-chain NSP7

E:GLU341-B:ARG96

E:ASP328/GLU353-B:LYS165

With B-chain NSP8a

Table 4.1 The SBs linking E-chain NSP13.1 with ABCDF-chains NSP12-NSP8a-NSP7-NSP8b-NSP13.2 during the six replicates’ (each with 5 .μs) MD simulations

4.3 New Results and Discussions 199

Rep6

Rep5

Rep4

Rep3

Rep2

F:GLU244-E:LYS189/LYS218

B:GLU77-F:ARG15

F:ASP101/ASP105/GLU128-E:LYS189

E:ASP160-F:ARG248

F:ASP369/GLU353-B:ARG96

F:GLU365-A:ARG365

F:ASP435-E:LYS218

E:ASP344/GLU341-F:ARG248

F:ASP101/ASP105/GLU128-E:LYS189

B:ASP101-F:LYS329

A:ASP336-F:ARG390

F:ASP435-E:LYS218

F:ASP101/ASP105/GLU128-E:LYS189 E:ASP160-F:ARG248/LYS271 E:GLU341-F:ARG248

B:ASP78/GLU77-F:LYS94 B:ASP99/ASP101-F:LYS329 F:ASP369-B:ARG96

A:ASP336-F:ARG392

F:GLU365-A:ARG365

E:ASP344/GLU341-F:ARG248 F:ASP435-E:ARG161/LYS218

E:ASP160-F:ARG248/LYS271

B:ASP99-F:LYS329

F:ASP369/GLU353-B:ARG96

F:GLU365-A:ARG365

F:GLU365-E:LYS189

B:ASP101-F:LYS347

B:ASP78/GLU77-F:LYS94

F:GLU128/GLU244-E:LYS189 F:GLU244-E:ARG186/LYS189/LYS218

A:ASP284/ASP303/GLU277-F:LYS189

A:GLU522-F:ARG15/ARG22

A:ASP336-F:ARG390

E:ASP160/GLU156-F:ARG248 F:ASP328/GLU244/GLU353-E:LYS218

A:ASP336-F:ARG390/ARG392/LYS394

F:GLU365-A:ARG365

E:GLU156-F:ARG248

F:ASP369-E:LYS218

E:ASP160-F:ARG248/ARG392/LYS394 F:GLU128/GLU365-E:LYS189

F:ASP101-E:LYS189

B:ASP101-F:LYS347

F:GLU365-A:ARG365 B:ASP112-F:ARG339/LYS189

B:ASP64/GLU60-F:LYS94

A:ASP336-F:ARG392/ARG337/ARG390

E:GLU341-F:ARG248

F:GLU244-E:ARG186/LYS218

F:GLU128-E:LYS189

E:ASP160-F:ARG248/LYS271

With E-chain NSP13.1 F:ASP101-E:LYS189

With D-chain NSP8b

F:GLU365-A:ARG365

With C-chain NSP7

A:ASP336-F:ARG392

Rep1

With B-chain NSP8a

With A-chain NSP12

.\F:

Table 4.2 The SBs linking F-chain NSP13.2 with ABCDE-chains NSP12-NSP8a-NSP7-NSP8b-NSP13.1 during the six replicates’ (each with 5 .μs) MD simulations

200 4 RNA Helicase

4.3 New Results and Discussions

201

NSP13.1, and the SBs within Echain NSP13.1, Fchain NSP13.2, and Achain NSP12, during the six replicates’ (each with 5 .μs) MD simulations. Tables 4.1 and 4.2 can confirm the following SBs: F:ARG248-E:ASP160/GLU 341 (for replicate 5, with HBs F:ARG248.NH2-E:GLU341.OE2 19.38%, E:ARG248.NH2-F:GLU341.OE2 13.64%, F:ARG248.NH2-E:GLU341.OE1 13.16%, F:ARG248.NH1-E:GLU341.OE1 12.92%), E:LYS218-F:GLU244/ASP435 (GLU244 is for replicates 1–3 and ASP435 is for replicates 4–6), E:LYS189F:ASP101/GLU128 (for replicate 4, there is HB E:LYS189.NZ-F:ASP101.OD2 7.42%); A:ASP901-E:LYS94, A:ASP336-F:ARG392/390, A:ARG365-F:GLU365; B:LYS165-E:ASP328/GLU353 for replicates 1–3, and B:ARG96-F:ASP369 for replicates 4–6. However, the SBs B:LYS165-E:ASP328, E:LYS218-F:ASP435, E:LYS218-F:GLU244, and F:ARG248-E:ASP160 are very weak during each 5 .μs MD replicate. We have shown SBs A:ARG365-F:GLU365, F:ARG248-E:GLU341, A:ASP901-E:LYS94, A:ASP336-F:ARG392, B:LYS165-E:GLU353, E:LYS189F:GLU128, E:LYS189-F:ASP101, A:ASP336-F:ARG390, and B:ARG96-F:ASP369 in Fig. 4.4. The SBs A:ARG365-F:GLU365, F:ARG248-E:GLU341, A:ASP901E:LYS94, and A:ASP336-F:ARG392/ARG390 are polar contacts (Table 4.3).

The following SBs within E and within F can be confirmed from Tables 4.7 and 4.8, within E: ASP223-ARG186, ASP315-ARG332, ASP328-LYS347, ASP32LYS28, ASP534-ARG560, ASP583-ARG579, GLU128-LYS131, GLU197-ARG337, GLU201-ARG212, GLU353-LYS347, GLU540-LYS320, ASP204-LYS524/ARG490 (replicates 1–3/4 and 6), and GLU142-ARG409/LYS139 (replicates 1–3/4–6) – all

202

4 RNA Helicase

these SBs within E-chain NSP13.1 are shown in Fig. 4.5, within F: ASP101-LYS28, ASP223-ARG186, ASP328-LYS347, ASP32-LYS28, ASP369-LYS394, ASP534ARG560 (broken for replicates 1, 5, and 6 (4500–5000 ns)), GLU136-ARG21, GLU142-ARG409, GLU143-LYS146, GLU201-ARG178, GLU244-LYS276, GLU353-LYS347, GLU418-LYS430, GLU420-LYS430, GLU551-LYS477 (broken for replicate 1), ASP315-LYS345/ARG332 (replicates 1–2/4–6), and GLU162LYS524 (replicates 1–3 (but for replicate 2 broken during 1344–3204 ns)) – all these SBs within E-chain NSP13.2 are shown in Fig. 4.6, within both E and F respectively: ASP223-ARG186, ASP328-LYS347, ASP32-LYS28, ASP534-ARG560,

4.4 Concluding Remarks

203

Fig. 4.4 The 13 SBs linking A-, B-, E-, and F-chains (i.e., NSP12 RdRp, NSP8a, NSP13.1, and NSP13.2, respectively) during the six replicates’ MD simulations, where each replicate has 5000 ns MD

and GLU353-LYS347. We also can confirm the following SBs (Tables 4.9 and 4.10) of NSP12 RdRp in Chap. 3: A:ASP170-A:ARG173, A:ASP304-A:ARG640, A:ASP421-A:LYS417, A:ASP465-A:ARG132, A:ASP477-A:ARG640 (for replicate 1 existing only during 3960–5000 ns), A:ASP499-A:ARG513 (broken for replicate 4 during 324–432 ns and for replicate 5 during 684–2388 ns), A:ASP804-A:LYS807, A:GLU136-A:LYS783 (broken for replicates 4–6), A:GLU180-A:ARG183 (broken for replicate 4), A:GLU474-A:ARG305 (always broken), A:GLU474-A:ARG640 (broken for replicate 1 during 4236–5000 ns), and A:GLU744-A:ARG726 (broken for replicate 2 during 1860–3156 ns and for replicate 3 during 4308–5000 ns) – all these SBs within A-chain NSP12 RaRp are shown in Fig. 4.7. The SBs A:ASP274/269-B:ARG111 and A:ARG331-B:ASP112 between RdRp and NSP8a and an SB C:ASP38-C:LYS51 within NSP7 are shown in Fig. 4.8. All these SBs within C-chain, linking A-chain and B-chain, within A-chain, within E-chain, and within F-chain at the same time own strong or weak HBs – we list them with occupancy rates (.≥10%) in Tables 4.4, 4.5, and 4.6.

4.4 Concluding Remarks NSP13 RNA helicase is a SARS-CoV-2 antiviral target. This chapter presents the bioinformatics of polar contacts within NSP13.1: E:ASP223-E:ARG186, E:ASP315-E:ARG332, E:ASP328-E:LYS347, E:ASP32-E:LYS28, E:ASP534E:ARG560, E:ASP583-E:ARG579, E:GLU128-E:LYS131, E:GLU197-E:ARG337, E:GLU201-E:ARG212, E:GLU353-E:LYS347, E:GLU540-E:LYS320, E:ASP204E:LYS524, E:ASP204-E:ARG490, E:GLU142-E:ARG409, E:GLU142-E:LYS139 and within NSP13.2: F:ASP101-F:LYS28, F:ASP223-F:ARG186, F:ASP328F:LYS347, F:ASP32-F:LYS28, F:ASP369-F:LYS394, F:ASP534-F:ARG560, F:GLU136-F:ARG21, F:GLU142-F:ARG409, F:GLU143-F:LYS146, F:GLU201F:ARG178, F:GLU244-F:LYS276, F:GLU353-F:LYS347, F:GLU418-F:LYS430, F:GLU420-F:LYS430, F:GLU551-F:LYS477, F:GLU162-F:LYS524, F:ASP315F:LYS345, and F:ASP315-F:F:ARG332 of the SARS-CoV-2-NSP13 RNA helicase in its optimized structure and confirmed in its six replicates (each replicate has 5 .μs’ long) of MD simulations. During the long MD of each of the six replicates, the polar contacts among NSP13.1, NSP13.2, RdRp NSP13, NSP7, NSP8a, and

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4 RNA Helicase

NSP8b are also studied in this chapter. Other structural bioinformatics for NSP13 helicase such as .π -interactions F:HID245-E:LYS218.NZ+, etc. are also presented in this chapter.

LYS94.NZ-ASP901.OD2 10.53%

Rep2

LYS94.NZ-ASP901.OD1 11.72%

LYS94.NZ-ASP901.OD2 13.64%

ARG390.NH2-ASP336.OD1 11.96%

ARG390.NH1-ASP336.OD1 20.10%

ARG390.NH2-ASP336.OD2 21.77%

LYS94.NZ-ASP901.OD2 11.72%

LYS94.NZ-ASP901.OD1 13.88%

ARG365.NE-GLU365.OE1 10.05%

ARG365.NE-GLU365.OE2 10.77%

ARG392.NH1-ASP336.OD1 11.48%

ARG392.NH2-ASP336.OD2 12.68%

ARG248.NH1-GLU341.OE1 12.92%

ARG248.NH2-GLU341.OE1 13.16%

ARG248.NH2-GLU341.OE2 19.38%

ARG365.NH2-GLU365.OE2 13.40%

ARG365.NH2-GLU365.OE1 16.03%

ARG365.NH2-GLU365.OE2 11.00%

ARG365.NH2-GLU365.OE1 18.90% ARG365.NH2-GLU365.OE2 15.79%

ARG365.NH2-GLU365.OE1 16.99%

ARG365.NH2-GLU365.OE2 16.27%

ARG365.NH2-GLU365.OE1 15.07%

Rep6

Rep5

Rep4

Rep3

Table 4.3 The HBs (with occupancy rates .≥10) of the SB A:ARG365-F:GLU365, F:ARG248-E:GLU341, A:ASP901-E:LYS94, A:ASP336-F:ARG392, and A:ASP336-F:ARG390 linking A-, E-, and F-chains (i.e., NSP12 RdRp, NSP13.1, and NSP13.2, respectively) during the six replicates’ (each with 5 .μs) MD simulations

4.4 Concluding Remarks 205

ARG111.NH1-ASP274.OD1 14.11

ARG111.NH1-ASP274.OD1 18.42

ARG640.NH2-ASP304.OD1 27.27 ASP421.N-LYS417.O 55.74 LYS417.NZ-ASP421.OD1 30.86 LYS417.NZ-ASP421.OD2 23.44 ARG132.NH2-ASP465.OD2 46.89

ARG640.NH2-ASP304.OD2 35.89 ASP421.N-LYS417.O 57.42 LYS417.NZ-ASP421.OD2 39.23 LYS417.NZ-ASP421.OD1 19.38 ARG132.NH2-ASP465.OD2 67.7

ARG640.NH1-ASP477.OD1 27.99 ARG513.NE-ASP499.OD2 44.26

ARG173.NH2-ASP170.OD2 37.56

ARG173.NH2-ASP170.OD1 30.38

ARG173.NE-ASP170.OD2 30.14

ARG640.NE-ASP304.OD2 58.13

ARG640.NH2-ASP304.OD1 51.91

ARG640.NE-ASP304.OD1 28.95

ARG640.NH2-ASP304.OD2 26.79

ASP421.N-LYS417.O 56.70

LYS417.NZ-ASP421.OD2 32.06

LYS417.NZ-ASP421.OD1 22.25

ARG132.NH2-ASP465.OD2 75.36

ARG640.NH1-ASP477.OD1 29.90

ARG640.NH1-ASP477.OD2 28.23

ARG513.NE-ASP499.OD1 44.98

ARG513.NE-ASP499.OD2 42.11

ARG513.NH2-ASP499.OD1 41.87

ARG513.NH2-ASP499.OD2 40.19

LYS783.NZ-GLU136.OE1 33.01

LYS783.NZ-GLU136.OE2 32.54

ARG173.NH2-ASP170.OD1 40.91

ARG173.NE-ASP170.OD1 33.49

ARG173.NH2-ASP170.OD2 32.06

ARG640.NE-ASP304.OD2 41.63

ARG640.NH2-ASP304.OD1 39.23

ARG640.NE-ASP304.OD1 27.03

ARG640.NH2-ASP304.OD2 24.88

ASP421.N-LYS417.O 56.46

LYS417.NZ-ASP421.OD1 30.86

LYS417.NZ-ASP421.OD2 22.73

ARG132.NH2-ASP465.OD2 69.62

ARG640.NH1-ASP477.OD2 23.21

ARG640.NH1-ASP477.OD1 22.73

ARG513.NE-ASP499.OD1 46.41

ARG513.NH2-ASP499.OD2 42.58

ARG513.NE-ASP499.OD2 40.43

ARG513.NH2-ASP499.OD1 38.04

LYS783.NZ-GLU136.OE2 30.38

LYS783.NZ-GLU136.OE1 23.92

LYS783.NZ-GLU136.OE2 22.97

LYS783.NZ-GLU136.OE1 25.12

ARG513.NH2-ASP499.OD2 36.84

ARG513.NH2-ASP499.OD1 41.15

ARG513.NE-ASP499.OD1 43.06

ARG640.NH1-ASP477.OD2 28.23

ARG640.NH2-ASP304.OD1 40.91

ARG640.NE-ASP304.OD1 40.91

ARG640.NE-ASP304.OD2 46.65

ARG173.NE-ASP170.OD2 33.01

ARG173.NH2-ASP170.OD1 33.73

ARG513.NH2-ASP499.OD1 37.80

ARG513.NH2-ASP499.OD2 39.23

ARG513.NE-ASP499.OD2 41.63

ARG513.NE-ASP499.OD1 42.11

ARG640.NH1-ASP477.OD1 25.60

ARG640.NH1-ASP477.OD2 29.67

ARG132.NH1-ASP465.OD2 18.42

ARG640.NE-ASP304.OD2 36.84

ARG640.NH2-ASP304.OD2 37.56

ARG640.NE-ASP304.OD1 48.56

ARG173.NE-ASP170.OD1 22.49

ARG173.NH2-ASP170.OD2 25.60

ARG173.NE-ASP170.OD2 27.99

ARG173.NH2-ASP170.OD1 29.43

ARG173.NH2-ASP170.OD2 40.91

ARG173.NE-ASP170.OD1 37.80 ARG173.NE-ASP170.OD1 37.32

VAL115.N-VAL330.O 14.83

VAL115.N-VAL330.O 15.07

VAL115.N-VAL330.O 18.42

VAL330.N-VAL115.O 73.21

VAL330.N-VAL115.O 50.00

VAL330.N-VAL115.O 55.74

VAL115.N-VAL330.O 16.51

ARG111.NH2-ASP274.OD1 11.96

ARG111.NH2-ASP274.OD2 13.40

ARG173.NE-ASP170.OD2 42.11

VAL330.N-VAL115.O 57.42

ARG331.NH2-ASP112.OD1 11.96

ARG331.NH2-ASP112.OD2 13.40

ARG111.NH1-ASP274.OD2 13.40

ARG331.NH2-ASP112.OD2 13.88

ARG331.NH2-ASP112.OD1 16.27

ARG331.NH1-ASP112.O 10.53

ARG331.NH1-ASP112.O 13.88

ARG513.NH2-ASP499.OD2 25.12

ARG513.NH2-ASP499.OD1 26.08

ARG513.NE-ASP499.OD1 27.03

ARG513.NE-ASP499.OD2 29.19

ARG640.NH1-ASP477.OD2 16.75

ARG640.NH1-ASP477.OD1 18.90

ARG132.NH2-ASP465.OD2 53.83

LYS417.NZ-ASP421.OD1 23.68

LYS417.NZ-ASP421.OD2 34.45

ASP421.N-LYS417.O 52.39

ARG640.NH2-ASP304.OD1 31.10

ARG640.NH2-ASP304.OD2 33.73

ARG640.NE-ASP304.OD2 42.82

ARG640.NE-ASP304.OD1 45.93

ARG173.NE-ASP170.OD1 10.77

ARG173.NH2-ASP170.OD1 12.92

ARG173.NH2-ASP170.OD2 15.55

VAL115.N-VAL330.O 24.40

VAL330.N-VAL115.O 67.46

LYS51.NZ-ASP38.OD2 18.42

ARG513.NH2-ASP499.OD2 31.1

ARG513.NE-ASP499.OD1 35.65

ARG513.NH2-ASP499.OD1 46.17

ARG513.NE-ASP499.OD2 48.09

ARG640.NH1-ASP477.OD1 14.35

ARG640.NH1-ASP477.OD2 21.05

ARG132.NH2-ASP465.OD2 53.83

LYS417.NZ-ASP421.OD1 24.16

LYS417.NZ-ASP421.OD2 33.01

ASP421.N-LYS417.O 50.48

ARG640.NH2-ASP304.OD2 23.44

ARG640.NH2-ASP304.OD1 29.90

ARG640.NE-ASP304.OD1 34.69

ARG640.NE-ASP304.OD2 43.30

ARG173.NH2-ASP170.OD1 30.62

ARG173.NE-ASP170.OD2 32.78

ARG173.NH2-ASP170.OD2 40.19

ARG173.NE-ASP170.OD1 40.91

VAL115.N-VAL330.O 16.27

VAL330.N-VAL115.O 58.13

LYS51.NZ-ASP38.OD1 22.49

LYS51.NZ-ASP38.OD2 23.21

LYS51.NZ-ASP38.OD1 23.92

Rep6

LYS51.NZ-ASP38.OD2 20.33

LYS51.NZ-ASP38.OD1 29.67

Rep5

LYS51.NZ-ASP38.OD1 22.25

LYS51.NZ-ASP38.OD2 26.79

Rep4

LYS51.NZ-ASP38.OD2 26.79

LYS51.NZ-ASP38.OD1 27.27

LYS51.NZ-ASP38.OD2 25.84

LYS51.NZ-ASP38.OD1 29.67

Rep3

Rep2

Rep1

Table 4.4 The HBs (with occupancy rates .≥10%) of SBs C:ASP38-C:LYS51 within C-chain, A:ARG331-B:ASP112, A:ASP274-B:ARG111, and A:VAL330-B:VAL115 linking AB chains, and A:ASP170-A:ARG173, A:ASP304-A:ARG640, A:ASP421-A:LYS417, A:ASP465-A:ARG132, A:ASP477A:ARG640, A:ASP499-A:ARG513, A:GLU136-A:LYS783, A:GLU180-A:ARG183, A:GLU474-A:ARG305, A:GLU474-A:ARG640, and A:GLU744A:ARG726 within A-chain (i.e., within NSP7, linking NSP12 RdRp and NSP8a, within NSP12 RdRp) during the six replicates’ (each with 5 .μs) MD simulations

206 4 RNA Helicase

ARG305.NE-GLU474.OE1 36.36

ARG305.NE-GLU474.OE1 47.61

ARG305.NH1-GLU474.OE1 9.57

ARG640.NH2-GLU474.OE1 80.62

ARG640.NH1-GLU474.OE2 72.49

ARG305.NE-GLU474.OE2 39.95

ARG305.NE-GLU474.OE1 27.03

ARG640.NH2-GLU474.OE2 45.45

ARG640.NH1-GLU474.OE1 43.54 ARG640.NH1-GLU474.OE1 35.17 ARG726.NH1-GLU744.OE2 44.02

ARG726.NH2-GLU744.OE2 34.21

ARG726.NH1-GLU744.OE1 32.78

ARG726.NH1-GLU744.OE2 31.58

ARG726.NH2-GLU744.OE1 31.10

ARG640.NH1-GLU474.OE2 29.67

ARG726.NH1-GLU744.OE1 43.78

ARG726.NH2-GLU744.OE2 43.78

ARG726.NH2-GLU744.OE1 40.19

ARG726.NH1-GLU744.OE2 39.71 ARG726.NH2-GLU744.OE2 36.60

ARG726.NH1-GLU744.OE1 39.47

ARG726.NH2-GLU744.OE1 40.67

ARG640.NH2-GLU474.OE2 35.41

ARG640.NH2-GLU474.OE1 32.54

ARG640.NH1-GLU474.OE2 48.80

ARG640.NH2-GLU474.OE1 49.28

ARG305.NE-GLU474.OE2 13.40

ARG183.NH2-GLU180.OE2 16.03

ARG183.NH2-GLU180.OE1 39.71

ARG183.NH2-GLU180.OE1 69.14

ARG183.NE-GLU180.OE2 72.25 ARG183.NE-GLU180.OE1 17.22

ARG183.NH2-GLU180.OE2 86.36

ARG183.NE-GLU180.OE2 40.43

ARG183.NE-GLU180.OE1 89.23

ARG183.NE-GLU180.OE1 46.65

ARG183.NH2-GLU180.OE2 44.74

ARG726.NH1-GLU744.OE2 38.52

ARG726.NH2-GLU744.OE1 39.71

ARG726.NH2-GLU744.OE2 45.93

ARG726.NH1-GLU744.OE1 46.89

ARG640.NH1-GLU474.OE2 33.73

ARG640.NH2-GLU474.OE1 36.60

ARG640.NH1-GLU474.OE1 43.06

ARG640.NH2-GLU474.OE2 44.02

ARG305.NE-GLU474.OE1 9.81

ARG305.NE-GLU474.OE2 17.94

ARG183.NE-GLU180.OE1 13.88

ARG183.NH2-GLU180.OE2 16.51

ARG183.NE-GLU180.OE2 22.25

ARG183.NH2-GLU180.OE1 23.68

ARG726.NH1-GLU744.OE1 39.95

ARG726.NH2-GLU744.OE2 40.67

ARG726.NH1-GLU744.OE2 46.17

ARG726.NH2-GLU744.OE1 46.89

ARG640.NH1-GLU474.OE2 37.32

ARG640.NH2-GLU474.OE1 38.04

ARG640.NH2-GLU474.OE2 41.15

ARG640.NH1-GLU474.OE1 44.98

ARG183.NH2-GLU180.OE2 10.53

ARG183.NE-GLU180.OE1 11.00

ARG183.NH2-GLU180.OE1 73.21

ARG183.NE-GLU180.OE2 80.14

ARG726.NH1-GLU744.OE2 40.67

ARG726.NH2-GLU744.OE1 42.82

ARG726.NH1-GLU744.OE1 43.30

ARG726.NH2-GLU744.OE2 43.78

ARG640.NH2-GLU474.OE1 30.14

ARG640.NH1-GLU474.OE2 30.86

ARG640.NH2-GLU474.OE2 47.61

ARG640.NH1-GLU474.OE1 50.00

ARG183.NH2-GLU180.OE2 29.90

ARG183.NE-GLU180.OE1 32.06

ARG183.NH2-GLU180.OE1 55.74

ARG183.NE-GLU180.OE2 60.77

4.4 Concluding Remarks 207

ARG186.NE-ASP223.OD1 98.80

ARG186.NH2-ASP223.OD2 99.04

ARG186.NE-ASP223.OD1 98.56

ASP223.OD2-ARG186.NH2 90.43

ARG332.NH2-ASP315.OD1 26.32

ARG332.NE-ASP315.OD2 23.68

ARG332.NE-ASP315.OD1 18.18

ARG186.NH2-ASP223.OD2 99.76

ARG186.NE-ASP223.OD1 97.61

ASP223.OD2-ARG186.NH2 87.80

ARG332.NH2-ASP315.OD2 32.30

ARG332.NH2-ASP315.OD1 26.79

ARG332.NE-ASP315.OD1 16.51

LYS28.NZ-ASP32.OD2 36.12

ASP32.N-LYS28.O 33.25

ARG560.NE-ASP534.OD2 61.96

ARG560.NE-ASP534.OD1 60.77

ARG560.NH2-ASP534.OD2 36.84

ARG560.NH2-ASP534.OD1 33.49

ASP583.N-ARG579.O 34.45

ARG579.NE-ASP583.OD2 22.25

ARG579.NE-ASP583.OD1 20.10

ARG579.NH2-ASP583.OD1 13.40

ARG579.NH2-ASP583.OD2 12.92

LYS28.NZ-ASP32.OD1 46.41

LYS28.NZ-ASP32.OD2 39.47

ARG560.NE-ASP534.OD1 61.72

ARG560.NE-ASP534.OD2 45.45

ARG560.NH2-ASP534.OD2 42.34

ARG560.NH2-ASP534.OD1 36.60

ASP583.N-ARG579.O 34.69

ARG579.NE-ASP583.OD2 22.25

ARG579.NE-ASP583.OD1 21.29

ARG579.NH2-ASP583.OD2 12.68

ARG579.NH2-ASP583.OD1 11.24

LYS347.NZ-ASP328.OD2 14.11

LYS347.NZ-ASP328.OD1 19.14

LYS347.NZ-ASP328.O 11.24

ARG579.NH2-ASP583.OD1 10.53

ARG579.NH1-ASP583.OD2 10.77

ARG579.NH2-ASP583.OD2 12.68

ARG579.NE-ASP583.OD2 20.33

ARG579.NE-ASP583.OD1 20.33

ASP583.N-ARG579.O 33.49

ARG560.NH2-ASP534.OD1 59.33

ARG560.NH2-ASP534.OD2 62.44

ARG560.NE-ASP534.OD2 63.40

ARG560.NE-ASP534.OD1 64.59

LYS28.NZ-ASP32.OD1 34.93

ASP32.N-LYS28.O 38.76

LYS28.NZ-ASP32.OD2 43.78

ARG579.NH2-ASP583.OD2 12.68

ARG579.NH2-ASP583.OD1 13.88

ARG579.NE-ASP583.OD1 18.66

ARG579.NE-ASP583.OD2 18.90

ARG579.NH2-ASP583.OD1 9.81

ARG579.NH2-ASP583.OD2 12.44

ARG579.NE-ASP583.OD2 17.46

ARG579.NE-ASP583.OD1 19.86

ASP583.N-ARG579.O 39.71

ARG579.NH2-ASP583.OD1 12.92

ARG579.NH2-ASP583.OD2 17.46

ARG579.NE-ASP583.OD2 21.05

ARG579.NE-ASP583.OD1 22.49

ASP583.N-ARG579.O 41.15

ARG560.NH1-ASP534.OD2 15.79

ASP583.N-ARG579.O 40.91

ARG560.NH1-ASP534.OD1 19.14

ARG560.NE-ASP534.OD1 33.49

ARG560.NH2-ASP534.OD2 41.15

ARG560.NE-ASP534.OD2 51.91

ARG560.NH2-ASP534.OD1 53.35

LYS28.NZ-ASP32.OD1 34.69

LYS28.NZ-ASP32.OD2 37.56

ASP32.N-LYS28.O 39.00

LYS347.NZ-ASP328.OD1 22.25

LYS347.NZ-ASP328.OD2 22.25

LYS347.NZ-ASP328.O 26.56

ARG332.NH1-ASP315.OD1 11.96

ARG332.NH2-ASP315.OD1 63.64

ARG186.NE-ASP223.OD1 98.56

ARG186.NH2-ASP223.OD2 99.04

Rep6

ARG560.NH1-ASP534.OD2 10.29

ARG560.NE-ASP534.OD1 29.43

ARG560.NE-ASP534.OD2 31.10

ARG560.NH2-ASP534.OD2 38.52

ARG560.NH2-ASP534.OD1 44.26

LYS28.NZ-ASP32.OD2 31.10

LYS28.NZ-ASP32.OD1 42.82

ASP32.N-LYS28.O 47.13

LYS347.NZ-ASP328.OD2 20.33

LYS347.NZ-ASP328.OD1 21.77

LYS347.NZ-ASP328.O 23.92

ARG332.NH2-ASP315.OD1 66.03

ARG186.NE-ASP223.OD1 97.85

ARG186.NH2-ASP223.OD2 99.76

Rep5

ARG560.NH1-ASP534.OD1 22.49

ARG560.NE-ASP534.OD2 38.04

ARG560.NH2-ASP534.OD1 47.37

ARG560.NE-ASP534.OD1 52.87

ARG560.NH2-ASP534.OD2 67.22

LYS28.NZ-ASP32.OD2 32.06

LYS28.NZ-ASP32.OD1 32.54

ASP32.N-LYS28.O 43.30

LYS347.NZ-ASP328.OD1 21.05

LYS28.NZ-ASP32.OD1 42.11

LYS347.NZ-ASP328.O 24.16

LYS347.NZ-ASP328.OD2 22.97

LYS347.NZ-ASP328.OD1 27.27

LYS347.NZ-ASP328.OD1 27.75

ASP32.N-LYS28.O 47.13

ARG332.NH1-ASP315.OD1 12.20

LYS347.NZ-ASP328.OD2 28.71 LYS347.NZ-ASP328.O 42.34

ARG332.NH2-ASP315.OD2 17.94

ARG332.NH1-ASP315.OD2 14.59

ARG332.NH2-ASP315.OD2 30.86

ARG332.NH2-ASP315.OD1 43.78

ARG186.NE-ASP223.OD1 96.89

ARG186.NH2-ASP223.OD2 99.28

Rep4

LYS347.NZ-ASP328.OD2 30.14

ARG332.NE-ASP315.OD2 33.25

ARG332.NH2-ASP315.OD1 42.58

ARG332.NH2-ASP315.OD2 65.55

ASP223.OD2-ARG186.NH2 90.67

ARG186.NH2-ASP223.OD2 98.80

Rep3

Rep2

Rep1

Table 4.5 The HBs (with occupancy rates .≥10%) of SBs E:ASP223-E:ARG186, E:ASP315-E:ARG332, E:ASP328-E:LYS347, E:ASP32-E:LYS28, E:ASP534-E:ARG560, E:ASP583-E:ARG579, E:GLU128-E:LYS131, E:GLU197-E:ARG337, E:GLU201-E:ARG212, E:GLU353-E:LYS347, E:GLU540E:LYS320, E:ASP204-E:LYS524, E:ASP204-E:ARG490, E:GLU142-E:ARG409, and E:GLU142-E:LYS139 within E chain (i.e., within NSP13.1) during the six replicates’ (each with 5 .μs) MD simulations

208 4 RNA Helicase

ARG337.NH1-GLU197.OE1 18.66

ARG337.NE-GLU197.OE2 15.79

ARG337.NE-GLU197.OE1 15.31

ARG212.NH1-GLU201.OE2 34.93

ARG212.NH1-GLU201.OE1 28.71

LYS347.NZ-GLU353.OE1 56.22

LYS347.NZ-GLU353.OE2 41.15

ARG337.NH1-GLU197.OE1 42.11

ARG337.NH1-GLU197.OE2 34.21

ARG337.NE-GLU197.OE1 31.34

ARG212.NH1-GLU201.OE2 10.53

ARG212.NH1-GLU201.OE1 10.05

LYS347.NZ-GLU353.OE2 52.87

LYS347.NZ-GLU353.OE1 51.20 LYS347.NZ-GLU353.OE1 52.63

LYS347.NZ-GLU353.OE2 54.55

ARG212.NH1-GLU201.OE1 27.75

ARG212.NH1-GLU201.OE2 29.19

ARG337.NH1-GLU197.OE2 50.48

ARG337.NE-GLU197.OE1 53.11

ARG337.NE-GLU197.OE2 58.13

ARG337.NH1-GLU197.OE1 58.85

LYS131.NZ-GLU128.OE1 39.00

LYS524.NZ-ASP204.OD2 41.15

ARG409.NE-GLU142.OE2 83.25

ARG409.NH2-GLU142.OE1 81.34

ARG409.NH2-GLU142.OE2 47.13

ARG409.NE-GLU142.OE1 36.60

GLU142.OE2-ARG409.NH2 31.58

LYS524.NZ-ASP204.OD2 54.31

ARG409.NE-GLU142.OE2 65.31

ARG409.NH2-GLU142.OE1 57.18

ARG409.NE-GLU142.OE1 55.74

ARG409.NH2-GLU142.OE2 48.09

GLU142.OE2-ARG409.NH2 26.56 LYS139.NZ-GLU142.OE2 31.34 LYS139.NZ-GLU142.OE1 30.38

LYS139.NZ-GLU142.OE1 13.88

ARG409.NE-GLU142.OE2 19.14

ARG409.NE-GLU142.OE1 20.33

ARG409.NH2-GLU142.OE1 24.40

ARG409.NH2-GLU142.OE2 26.56

LYS139.NZ-GLU142.OE2 14.11

GLU142.OE2-ARG409.NH2 38.52

ARG409.NH2-GLU142.OE1 55.50

ARG409.NH2-GLU142.OE2 57.18

ARG409.NE-GLU142.OE2 58.13

ARG409.NE-GLU142.OE1 60.53

ARG490.NE-ASP204.OD1 69.86 ARG490.NH2-ASP204.OD2 68.66

ARG490.NH2-ASP204.OD2 11.24

LYS320.NZ-GLU540.OE2 47.61

LYS139.NZ-GLU142.OE1 12.68

LYS139.NZ-GLU142.OE2 14.83

ARG409.NE-GLU142.OE1 37.56

ARG409.NH2-GLU142.OE2 41.39

ARG409.NH2-GLU142.OE1 45.69

ARG409.NE-GLU142.OE2 45.93

ARG490.NH2-ASP204.OD2 81.10

ARG490.NE-ASP204.OD1 88.52

LYS320.NZ-GLU540.OE1 41.63

LYS139.NZ-GLU142.OE1 24.88

LYS139.NZ-GLU142.OE2 26.32

ARG409.NE-GLU142.OE2 27.03

ARG409.NE-GLU142.OE1 28.71

ARG409.NH2-GLU142.OE1 30.86

ARG409.NH2-GLU142.OE2 37.56

ARG490.NH2-ASP204.OD2 39.00

ARG490.NE-ASP204.OD1 40.91

LYS320.NZ-GLU540.OE2 12.92

LYS320.NZ-GLU540.OE1 36.36

LYS347.NZ-GLU353.OE1 47.61

LYS347.NZ-GLU353.OE2 58.85

ARG212.NH1-GLU201.OE1 12.68 LYS347.NZ-GLU353.OE2 47.37

ARG212.NH1-GLU201.OE1 21.29 LYS347.NZ-GLU353.OE1 53.11

LYS347.NZ-GLU353.OE2 54.55

ARG212.NH2-GLU201.OE1 22.25 ARG212.NH1-GLU201.OE2 12.92

ARG212.NE-GLU201.OE2 22.73

ARG212.NH2-GLU201.OE2 23.92

ARG212.NE-GLU201.OE1 27.03

ARG337.NH1-GLU197.OE1 46.17

ARG337.NE-GLU197.OE2 47.13

ARG337.NE-GLU197.OE1 48.09

ARG337.NH1-GLU197.OE2 51.67

LYS131.NZ-GLU128.OE2 42.82

ARG212.NE-GLU201.OE2 24.88

LYS347.NZ-GLU353.OE1 52.87

ARG212.NH1-GLU201.OE2 14.83

ARG212.NH1-GLU201.OE1 15.31

ARG337.NH1-GLU197.OE1 34.93

ARG337.NE-GLU197.OE2 36.36

ARG337.NH1-GLU197.OE2 39.71

ARG337.NE-GLU197.OE1 41.63

LYS131.NZ-GLU128.OE1 36.60

ARG212.NH2-GLU201.OE2 22.73

ARG212.NH2-GLU201.OE1 25.12

ARG212.NE-GLU201.OE1 25.84

ARG212.NH1-GLU201.OE2 26.56

ARG337.NH1-GLU197.OE2 42.11

ARG337.NE-GLU197.OE1 44.98

ARG337.NH1-GLU197.OE1 49.52

ARG337.NE-GLU197.OE2 49.76

LYS131.NZ-GLU128.OE2 37.56

ARG490.NH1-ASP204.OD1 12.20

LYS524.NZ-ASP204.OD2 48.56

LYS320.NZ-GLU540.OE1 21.05 LYS524.NZ-ASP204.OD1 50.96

LYS524.NZ-ASP204.OD1 47.13

LYS320.NZ-GLU540.OE2 15.79

LYS524.NZ-ASP204.OD1 54.31

LYS320.NZ-GLU540.OE2 23.21

ARG337.NH1-GLU197.OE2 19.14

ARG337.NE-GLU197.OE2 43.06

LYS320.NZ-GLU540.OE1 47.13

LYS131.NZ-GLU128.OE2 33.01

LYS131.NZ-GLU128.OE2 35.89

4.4 Concluding Remarks 209

LYS347.NZ-ASP328.OD1 21.05 LYS347.NZ-ASP328.OD2 14.11

LYS347.NZ-ASP328.OD2 22.97 LYS347.NZ-ASP328.OD1 19.14

ASP223.OD2-ARG186.NH2 90.43

LYS347.NZ-ASP328.OD2 28.71

LYS347.NZ-ASP328.OD1 27.27

LYS347.NZ-ASP328.O 11.24

ASP223.OD2-ARG186.NH2 87.80

LYS347.NZ-ASP328.OD2 30.14

LYS347.NZ-ASP328.OD1 27.75

ARG21.NE-GLU136.OE1 50.48

ARG409.NE-GLU142.OE2 83.25

ARG409.NH2-GLU142.OE1 81.34

ARG409.NH2-GLU142.OE2 47.13

ARG409.NE-GLU142.OE1 36.60

LYS146.NZ-GLU143.OE2 57.42

LYS146.NZ-GLU143.OE1 48.56

ARG21.NE-GLU136.OE2 34.21

ARG409.NE-GLU142.OE2 65.31

ARG409.NH2-GLU142.OE1 57.18

ARG409.NE-GLU142.OE1 55.74

ARG409.NH2-GLU142.OE2 48.09

LYS146.NZ-GLU143.OE2 54.55

LYS146.NZ-GLU143.OE1 48.09

ARG178.NH2-GLU201.OE2 25.60

ARG21.NE-GLU136.OE2 56.46

ARG21.NE-GLU136.OE1 49.04

ARG178.NH2-GLU201.OE2 34.93

ARG178.NE-GLU201.OE2 41.63

ARG560.NH2-ASP534.OD1 33.49

ARG560.NH2-ASP534.OD1 36.60

ARG178.NH2-GLU201.OE1 31.34

ARG560.NH2-ASP534.OD2 36.84

ARG560.NH2-ASP534.OD2 42.34

ARG178.NE-GLU201.OE2 39.00

LYS146.NZ-GLU143.OE1 51.91

ARG560.NE-ASP534.OD1 60.77

ARG560.NE-ASP534.OD2 45.45

ARG178.NE-GLU201.OE1 35.41

ARG409.NE-GLU142.OE1 60.53

ARG560.NE-ASP534.OD2 61.96

ARG178.NE-GLU201.OE1 48.09

ARG21.NE-GLU136.OE1 52.63

LYS394.NZ-ASP369.OD1 19.14

LYS394.NZ-ASP369.OD1 12.68

ARG560.NE-ASP534.OD1 61.72

ARG178.NH2-GLU201.OE1 48.09

LYS394.NZ-ASP369.OD2 22.25

LYS394.NZ-ASP369.OD2 17.70

LYS394.NZ-ASP369.OD2 21.05

LYS394.NZ-ASP369.OD2 14.59

ARG178.NE-GLU201.OE2 65.31

LYS394.NZ-ASP369.OD1 29.19

LYS394.NZ-ASP369.OD1 18.18

ASP32.N-LYS28.O 33.25

ARG178.NH2-GLU201.OE2 28.23

ARG178.NH2-GLU201.OE1 30.86

ARG178.NE-GLU201.OE1 38.04

LYS146.NZ-GLU143.OE2 41.87

ARG178.NH2-GLU201.OE2 22.25

ARG178.NH2-GLU201.OE1 22.49

ARG178.NE-GLU201.OE2 28.23

ARG178.NE-GLU201.OE1 31.82

LYS146.NZ-GLU143.OE1 37.32

ARG409.NE-GLU142.OE2 19.14

LYS146.NZ-GLU143.OE2 52.63

ARG409.NE-GLU142.OE1 20.33

ARG409.NH2-GLU142.OE1 24.40

ARG409.NH2-GLU142.OE2 26.56

ARG21.NE-GLU136.OE1 20.81

ARG21.NE-GLU136.OE2 43.30

ARG21.NE-GLU136.OE2 57.18

ARG178.N-GLU201.OE2 10.77

ARG178.NH2-GLU201.OE2 32.78

ARG178.NH2-GLU201.OE1 35.17

ARG178.NE-GLU201.OE1 46.41

ARG178.NE-GLU201.OE2 50.96

LYS146.NZ-GLU143.OE1 48.80

LYS146.NZ-GLU143.OE2 64.59

ARG409.NE-GLU142.OE1 37.56

ARG409.NH2-GLU142.OE2 41.39

ARG409.NH2-GLU142.OE1 45.69

ARG409.NE-GLU142.OE2 45.93

ARG21.NE-GLU136.OE1 52.15

ARG178.NH2-GLU201.OE1 25.12

ARG178.NH2-GLU201.OE2 27.75

ARG178.NE-GLU201.OE1 32.78

ARG178.NE-GLU201.OE2 34.45

LYS146.NZ-GLU143.OE1 48.80

LYS146.NZ-GLU143.OE2 50.48

ARG409.NE-GLU142.OE2 27.03

ARG409.NE-GLU142.OE1 28.71

ARG409.NH2-GLU142.OE1 30.86

ARG409.NH2-GLU142.OE2 37.56

ARG21.NE-GLU136.OE2 34.45

ARG21.NE-GLU136.OE1 44.02

ARG560.NH1-ASP534.OD1 19.14 ARG560.NH1-ASP534.OD2 15.79

ARG560.NE-ASP534.OD1 33.49

ARG560.NH2-ASP534.OD2 41.15

ARG560.NE-ASP534.OD2 51.91

ARG560.NH2-ASP534.OD1 53.35

LYS394.NZ-ASP369.OD1 28.71

LYS394.NZ-ASP369.OD2 29.90

LYS28.NZ-ASP32.OD1 34.69

LYS28.NZ-ASP32.OD2 37.56

ASP32.N-LYS28.O 39.00

LYS347.NZ-ASP328.OD1 22.25

LYS347.NZ-ASP328.OD2 22.25

LYS347.NZ-ASP328.O 26.56

ARG186.NE-ASP223.OD1 98.56

ARG186.NH2-ASP223.OD2 99.04

ARG560.NH1-ASP534.OD2 10.29

ARG560.NE-ASP534.OD1 29.43

ARG560.NE-ASP534.OD2 31.10

ARG560.NH2-ASP534.OD2 38.52

ARG560.NH2-ASP534.OD1 44.26

LYS394.NZ-ASP369.OD2 34.69

LYS394.NZ-ASP369.OD1 34.69

LYS28.NZ-ASP32.OD2 31.10

LYS28.NZ-ASP32.OD1 42.82

ASP32.N-LYS28.O 47.13

LYS347.NZ-ASP328.OD2 20.33

LYS347.NZ-ASP328.OD1 21.77

LYS347.NZ-ASP328.O 23.92

ARG186.NE-ASP223.OD1 97.85

ARG186.NH2-ASP223.OD2 99.76

LYS28.NZ-ASP101.OD2 14.83

LYS28.NZ-ASP101.OD1 18.66

Rep6

ARG560.NH1-ASP534.OD1 22.49

ARG560.NE-ASP534.OD2 38.04

ARG560.NH2-ASP534.OD1 47.37

ARG560.NE-ASP534.OD1 52.87

ARG560.NH2-ASP534.OD2 67.22

LYS28.NZ-ASP32.OD2 32.06

ARG409.NH2-GLU142.OE1 55.50

ARG409.NH2-GLU142.OE2 57.18

ARG409.NE-GLU142.OE2 58.13

ARG21.NE-GLU136.OE2 57.18

ARG560.NH2-ASP534.OD1 59.33

ARG560.NH2-ASP534.OD2 62.44

ARG560.NE-ASP534.OD2 63.40

ARG560.NE-ASP534.OD1 64.59

LYS28.NZ-ASP32.OD1 34.93

LYS28.NZ-ASP32.OD1 32.54

ASP32.N-LYS28.O 43.30

LYS28.NZ-ASP32.OD2 39.47

ASP32.N-LYS28.O 38.76

LYS28.NZ-ASP32.OD2 36.12

LYS28.NZ-ASP32.OD2 43.78

LYS28.NZ-ASP32.OD1 42.11

LYS28.NZ-ASP32.OD1 46.41

LYS347.NZ-ASP328.O 24.16

ASP32.N-LYS28.O 47.13

LYS347.NZ-ASP328.O 42.34

ASP223.OD2-ARG186.NH2 90.67

ARG186.NE-ASP223.OD1 96.89

ARG186.NE-ASP223.OD1 98.56

ARG186.NE-ASP223.OD1 97.61 ARG186.NH2-ASP223.OD2 98.80

ARG186.NH2-ASP223.OD2 99.04

ARG186.NH2-ASP223.OD2 99.76

ARG186.NH2-ASP223.OD2 99.28

LYS28.NZ-ASP101.OD1 12.20

LYS28.NZ-ASP101.OD1 14.83

LYS28.NZ-ASP101.OD2 16.51 ARG186.NE-ASP223.OD1 98.80

LYS28.NZ-ASP101.OD2 13.88

Rep5

LYS28.NZ-ASP101.OD1 18.18

LYS28.NZ-ASP101.OD1 11.00

Rep4

LYS28.NZ-ASP101.OD2 15.31

Rep2

Rep1

Rep3

Table 4.6 The HBs (with occupancy rates .≥10%) of SBs F:ASP101-F:LYS28, F:ASP223-F:ARG186, F:ASP328-F:LYS347, F:ASP32-F:LYS28, F:ASP369F:LYS394, F:ASP534-F:ARG560, F:GLU136-F:ARG21, F:GLU142-F:ARG409, F:GLU143-F:LYS146, F:GLU201-F:ARG178, F:GLU244-F:LYS276, F:GLU353-F:LYS347, F:GLU418-F:LYS430, F:GLU420-F:LYS430, F:GLU551-F:LYS477, F:GLU162-F:LYS524, F:ASP315-F:LYS345, and F:ASP315F:F:ARG332 within F chain (i.e., within NSP13.2) during the six replicates’ (each with 5 .μs) MD simulations

210 4 RNA Helicase

LYS276.NZ-GLU244.OE2 20.33

LYS276.NZ-GLU244.OE1 17.22

LYS347.NZ-GLU353.OE1 56.22

LYS347.NZ-GLU353.OE2 41.15

LYS430.NZ-GLU418.OE2 40.19

LYS430.NZ-GLU418.OE1 37.32

LYS430.NZ-GLU420.OE2 52.63

LYS430.NZ-GLU420.OE1 44.74

LYS477.NZ-GLU551.OE1 56.22

LYS477.NZ-GLU551.OE2 49.28

LYS524.NZ-GLU162.OE1 36.36

LYS524.NZ-GLU162.OE2 34.69

LYS345.NZ-ASP315.OD1 38.76

LYS345.NZ-ASP315.OD2 36.84

ARG332.NH2-ASP315.OD1 26.32

ARG332.NE-ASP315.OD2 23.68

ARG332.NE-ASP315.OD1 18.18

LYS276.NZ-GLU244.OE2 33.73

LYS276.NZ-GLU244.OE1 30.62

LYS347.NZ-GLU353.OE2 52.87

LYS347.NZ-GLU353.OE1 51.20

LYS430.NZ-GLU418.OE1 35.89

LYS430.NZ-GLU418.OE2 29.67

LYS430.NZ-GLU420.OE1 41.87

LYS430.NZ-GLU420.OE2 41.15

LYS477.NZ-GLU551.OE2 37.80

LYS477.NZ-GLU551.OE1 36.60

LYS524.NZ-GLU162.OE1 47.13

LYS524.NZ-GLU162.OE2 44.02

LYS345.NZ-ASP315.OD2 29.90

LYS345.NZ-ASP315.OD1 27.51

ARG332.NH2-ASP315.OD2 32.30

ARG332.NH2-ASP315.OD1 26.79

ARG332.NE-ASP315.OD1 16.51

ARG332.NH2-ASP315.OD2 17.94

LYS276.N-GLU244.O 22.49

LYS276.N-GLU244.O 37.32

ARG332.NE-ASP315.OD2 33.25

ARG332.NH2-ASP315.OD1 42.58

ARG332.NH2-ASP315.OD2 65.55

LYS524.NZ-GLU162.OE2 41.63

LYS524.NZ-GLU162.OE1 42.34

LYS477.NZ-GLU551.OE1 52.63

LYS477.NZ-GLU551.OE2 53.59

LYS430.NZ-GLU420.OE2 37.80

LYS430.NZ-GLU420.OE1 47.85

LYS430.NZ-GLU418.OE2 28.95

LYS430.NZ-GLU418.OE1 30.38

LYS347.NZ-GLU353.OE1 52.63

LYS347.NZ-GLU353.OE2 54.55

LYS276.NZ-GLU244.OE1 15.07

LYS276.NZ-GLU244.OE2 17.46

LYS276.N-GLU244.O 23.44

ARG332.NH1-ASP315.OD1 12.20

ARG332.NH1-ASP315.OD2 14.59

ARG332.NH2-ASP315.OD2 30.86

ARG332.NH2-ASP315.OD1 43.78

LYS345.NZ-ASP315.OD2 28.95 ARG332.NH2-ASP315.OD1 66.03

LYS345.NZ-ASP315.OD1 24.64

LYS524.NZ-GLU162.OE1 30.38

LYS345.NZ-ASP315.OD1 18.66

LYS524.NZ-GLU162.OE2 31.34

LYS477.NZ-GLU551.OE1 33.01

LYS477.NZ-GLU551.OE2 35.65

LYS430.NZ-GLU420.OE2 47.85

LYS430.NZ-GLU420.OE1 51.91

LYS430.NZ-GLU418.OE1 40.43

LYS430.NZ-GLU418.OE2 46.17

LYS347.NZ-GLU353.OE2 47.37

LYS347.NZ-GLU353.OE1 52.87

LYS276.NZ-GLU244.OE1 14.11

LYS276.NZ-GLU244.OE2 14.83

LYS276.N-GLU244.O 15.55

LYS524.NZ-GLU162.OE1 14.83

LYS524.NZ-GLU162.OE2 18.18

LYS477.NZ-GLU551.OE2 38.76

LYS477.NZ-GLU551.OE1 42.58

LYS430.NZ-GLU420.OE1 38.52

LYS430.NZ-GLU420.OE2 40.19

LYS430.NZ-GLU418.OE1 27.27

LYS430.NZ-GLU418.OE2 30.38

LYS347.NZ-GLU353.OE1 53.11

LYS347.NZ-GLU353.OE2 54.55

LYS276.NZ-GLU244.OE2 16.27

LYS276.NZ-GLU244.OE1 16.99

LYS276.N-GLU244.O 17.7

ARG332.NH1-ASP315.OD1 11.96

ARG332.NH2-ASP315.OD1 63.64

LYS345.NZ-ASP315.OD2 15.07

LYS345.NZ-ASP315.OD1 20.33

LYS477.NZ-GLU551.OE1 47.13

LYS477.NZ-GLU551.OE2 50.72

LYS430.NZ-GLU420.OE2 33.97

LYS430.NZ-GLU420.OE1 39.47

LYS430.NZ-GLU418.OE1 30.38

LYS430.NZ-GLU418.OE2 32.54

LYS347.NZ-GLU353.OE1 47.61

LYS347.NZ-GLU353.OE2 58.85

LYS276.NZ-GLU244.OE2 18.18

LYS276.N-GLU244.O 18.42

LYS276.NZ-GLU244.OE1 18.66

4.4 Concluding Remarks 211

212

4 RNA Helicase

Fig. 4.5 The SBs within E-chain (i.e., NSP13.1) during the six replicates’ MD simulations, where each replicate has 5 .μs MD

4.4 Concluding Remarks

Fig. 4.5 (continued)

213

214

4 RNA Helicase

Fig. 4.6 The SBs within F-chain (i.e., NSP13.2) during the six replicates’ MD simulations, where each replicate has 5 .μs MD

4.4 Concluding Remarks

Fig. 4.6 (continued)

215

216

Fig. 4.6 (continued)

4 RNA Helicase

4.4 Concluding Remarks

217

Fig. 4.7 The SBs within A-chain (i.e., NSP12) during the six replicates’ MD simulations, where each replicate has 5 .μs MD

218

Fig. 4.7 (continued)

4 RNA Helicase

4.4 Concluding Remarks

219

Fig. 4.8 The SBs linking A- and B-chains (i.e., NSP12, NSP8a) and within C-chain (i.e., NSP7) during the six replicates’ MD simulations, where each replicate has 5 .μs MD

220

4 RNA Helicase

Table 4.7 The SBs within E-chain NSP13.1 during the six replicates’ (each with 5 .μs) MD simulations Rep1

Rep2

Rep3

Rep4

Rep5

ASP101-LYS28

ASP101-LYS28

ASP101-LYS28

ASP101-LYS28

ASP101-LYS28

ASP101-LYS28

ASP160-ARG161

ASP160-ARG161

ASP160-ARG161

ASP113-LYS414

ASP160-ARG161

ASP160-ARG161

Rep6

ASP160-LYS218

ASP160-ARG212

ASP160-LYS218

ASP160-ARG161

ASP160-LYS218

ASP160-LYS218

ASP204-ARG490

ASP160-LYS218

ASP204-LYS524

ASP160-LYS218

ASP204-ARG490

ASP204-ARG161

ASP204-LYS524

ASP204-ARG161

ASP207-ARG155

ASP204-ARG490

ASP207-ARG155

ASP204-ARG490

ASP207-ARG155

ASP204-ARG490

ASP207-ARG173

ASP204-LYS524

ASP207-ARG173

ASP204-LYS524

ASP207-ARG173

ASP204-LYS524

ASP223-ARG186

ASP207-ARG155

ASP207-LYS202

ASP207-ARG155

ASP223-ARG186

ASP207-ARG155

ASP315-ARG332

ASP207-ARG173

ASP223-ARG186

ASP207-ARG173

ASP315-ARG332

ASP207-ARG173

ASP328-LYS329

ASP207-LYS202

ASP315-ARG332

ASP207-LYS202

ASP315-ARG339

ASP223-ARG186

ASP328-LYS347

ASP223-ARG186

ASP315-LYS345

ASP223-ARG186

ASP315-LYS345

ASP260-ARG442

ASP32-LYS28

ASP315-ARG332

ASP315-LYS508

ASP260-ARG442

ASP328-LYS329

ASP315-ARG332

ASP344-ARG332

ASP315-LYS345

ASP328-LYS329

ASP315-ARG332

ASP328-LYS347

ASP315-LYS345

ASP344-LYS345

ASP328-LYS329

ASP328-LYS347

ASP315-ARG339

ASP32-LYS28

ASP328-LYS329

ASP369-ARG303

ASP328-LYS347

ASP32-LYS28

ASP315-LYS345

ASP344-ARG332

ASP328-LYS345

ASP369-LYS394

ASP32-LYS28

ASP344-ARG332

ASP328-LYS329

ASP344-LYS345

ASP328-LYS347

ASP383-LYS139

ASP344-ARG332

ASP344-LYS345

ASP328-LYS347

ASP369-ARG303

ASP32-LYS28

ASP401-LYS430

ASP344-LYS345

ASP344-LYS508

ASP32-LYS28

ASP369-LYS394

ASP344-ARG332

ASP435-LYS271

ASP369-ARG303

ASP369-ARG303

ASP344-ARG332

ASP374-LYS288

ASP344-LYS345

ASP450-LYS460

ASP369-LYS394

ASP369-LYS394

ASP344-ARG339

ASP383-LYS139

ASP369-ARG303

ASP458-LYS460

ASP401-LYS430

ASP383-ARG409

ASP344-LYS345

ASP401-LYS430

ASP369-LYS394

ASP466-ARG442

ASP435-LYS271

ASP401-LYS430

ASP369-ARG303

ASP435-LYS271

ASP374-LYS320

ASP466-LYS465

ASP450-LYS460

ASP435-LYS271

ASP369-LYS394

ASP450-LYS460

ASP383-LYS139

ASP466-LYS467

ASP450-LYS462

ASP450-LYS460

ASP401-LYS430

ASP466-LYS465

ASP401-LYS430

ASP483-ARG490

ASP450-LYS465

ASP450-LYS462

ASP435-LYS271

ASP466-LYS467

ASP435-LYS271

ASP534-ARG560

ASP458-LYS584

ASP450-LYS465

ASP450-LYS460

ASP483-ARG490

ASP450-LYS460

ASP542-LYS508

ASP466-LYS465

ASP458-LYS584

ASP450-LYS462

ASP534-ARG560

ASP450-LYS462

ASP542-LYS569

ASP466-LYS467

ASP466-LYS462

ASP450-LYS465

ASP542-LYS508

ASP450-LYS465

ASP580-ARG579

ASP466-LYS473

ASP466-LYS465

ASP458-LYS584

ASP542-LYS569

ASP466-LYS465

ASP580-LYS584

ASP483-LYS202

ASP466-LYS467

ASP466-LYS462

ASP580-ARG579

ASP466-LYS467

ASP583-ARG579

ASP534-ARG560

ASP483-ARG490

ASP466-LYS465

ASP580-LYS584

ASP483-ARG490

ASP583-LYS584

ASP542-ARG507

ASP483-LYS202

ASP466-LYS467

ASP583-ARG579

ASP534-ARG560

ASP59-LYS40

ASP542-LYS508

ASP534-ARG560

ASP483-ARG173

ASP59-LYS40

ASP542-ARG507

GLU128-ARG129

ASP542-LYS569

ASP534-LYS414

ASP483-LYS202

GLU128-ARG129

ASP542-LYS508

GLU128-LYS131

ASP580-ARG579

ASP542-ARG507

ASP534-ARG560

GLU128-LYS131

ASP542-LYS569

GLU136-ARG21

ASP580-LYS584

ASP542-LYS508

ASP542-ARG443

GLU136-ARG21

ASP580-ARG579

GLU142-ARG409

ASP583-ARG579

ASP542-LYS569

ASP542-ARG507

GLU142-ARG409

ASP580-LYS584

GLU142-LYS139

ASP583-LYS584

ASP56-ARG22

ASP542-LYS508

GLU142-LYS139

ASP583-ARG579

GLU143-LYS139

ASP59-LYS40

ASP580-ARG579

ASP542-LYS569

GLU143-LYS139

ASP583-LYS584

GLU143-LYS146

ASP59-LYS73

ASP580-LYS584

ASP56-ARG22

GLU143-LYS146

ASP59-LYS40

GLU156-ARG155

GLU128-ARG129

ASP583-ARG579

ASP56-LYS73

GLU156-ARG155

GLU128-ARG129

GLU162-ARG161

GLU128-LYS131

ASP59-LYS40

ASP580-ARG579

GLU162-ARG161

GLU128-LYS131

GLU162-LYS524

GLU136-ARG15

GLU128-ARG129

ASP580-LYS584

GLU162-LYS524

GLU136-ARG21

GLU168-LYS171

GLU136-ARG21

GLU128-LYS131

ASP583-ARG579

GLU168-LYS171

GLU142-ARG409

GLU197-ARG337

GLU142-ARG409

GLU136-ARG21

ASP583-LYS584

GLU197-ARG337

GLU142-LYS139

GLU197-ARG339

GLU142-LYS139

GLU142-ARG409

ASP59-LYS40

GLU197-ARG339

GLU143-LYS139

GLU201-ARG178

GLU142-LYS146

GLU142-LYS139

ASP59-LYS73

GLU201-ARG161

GLU143-LYS146

GLU201-ARG212

GLU143-ARG21

GLU142-LYS146

GLU201-ARG178

GLU156-ARG155

GLU244-LYS276

GLU143-LYS139

GLU143-ARG21

GLU128-LYS131

GLU201-ARG212

GLU162-ARG161

GLU261-ARG442

GLU143-LYS146

GLU143-LYS139

GLU136-ARG15

GLU244-LYS276

GLU162-LYS524

GLU261-LYS465

GLU156-ARG155

GLU143-LYS146

GLU136-ARG21

GLU261-ARG442

GLU168-LYS171

GLU319-LYS320

GLU162-ARG161

GLU156-ARG155

GLU136-ARG22

GLU261-LYS465

GLU197-ARG337

GLU319-LYS323

GLU162-LYS524

GLU162-ARG161

GLU142-ARG409

GLU319-LYS323

GLU197-ARG339

GLU319-LYS345

GLU168-LYS171

GLU162-LYS524

GLU142-LYS139

GLU319-LYS345

GLU201-ARG178

GLU319-LYS569

GLU197-ARG337

GLU168-LYS171

GLU142-LYS146

GLU319-LYS569

GLU201-ARG212

GLU341-ARG178

GLU197-ARG339

GLU197-ARG337

GLU143-ARG21

GLU341-ARG178

GLU244-LYS276

GLU341-ARG212

GLU201-ARG178

GLU197-ARG339

GLU143-LYS139

GLU341-ARG212

GLU261-ARG442

GLU341-LYS345

GLU201-ARG212

GLU201-ARG178

GLU143-LYS146

GLU341-ARG339

GLU261-LYS323

GLU353-LYS329

GLU201-ARG339

GLU201-ARG212

GLU156-ARG155

GLU353-LYS347

GLU261-LYS467

GLU353-LYS347

GLU201-LYS524

GLU201-ARG339

GLU162-ARG161

GLU365-ARG392

GLU319-LYS323

GLU365-ARG390

GLU244-LYS276

GLU201-LYS524

GLU162-LYS524

GLU128-ARG427

(continued)

4.4 Concluding Remarks

221

Table 4.7 (continued) Rep1

Rep2

Rep3

Rep4

Rep5

Rep6

GLU375-LYS288

GLU319-LYS345

GLU365-ARG392

GLU261-ARG442

GLU244-LYS276

GLU168-LYS171

GLU418-LYS430

GLU319-LYS508

GLU418-LYS430

GLU261-ARG443

GLU261-ARG442

GLU197-ARG337

GLU420-ARG427

GLU319-LYS569

GLU420-ARG427

GLU261-LYS323

GLU261-LYS323

GLU197-ARG339

GLU420-LYS430

GLU341-ARG178

GLU420-LYS430

GLU319-LYS323

GLU319-LYS320

GLU201-ARG178

GLU447-LYS467

GLU341-ARG212

GLU447-LYS467

GLU319-LYS345

GLU319-LYS323

GLU201-ARG212

GLU498-ARG497

GLU341-ARG339

GLU498-ARG497

GLU319-LYS508

GLU319-LYS345

GLU201-ARG339

GLU498-ARG502

GLU353-LYS329

GLU498-ARG502

GLU319-LYS569

GLU319-LYS508

GLU201-LYS524

GLU540-ARG443

GLU353-LYS347

GLU540-ARG443

GLU341-ARG178

GLU319-LYS569

GLU244-LYS276

GLU540-ARG567

GLU365-ARG390

GLU540-ARG567

GLU341-ARG212

GLU341-ARG212

GLU261-ARG442

GLU540-LYS320

GLU365-ARG392

GLU540-LYS320

GLU341-ARG332

GLU341-ARG339

GLU261-ARG443

GLU540-LYS569

GLU375-LYS288

GLU540-LYS569

GLU341-ARG339

GLU353-LYS329

GLU261-LYS323

GLU551-ARG579

GLU418-LYS430

GLU551-LYS477

GLU341-LYS345

GLU353-LYS347

GLU319-LYS345

GLU551-LYS477

GLU420-ARG427

GLU341-LYS508

GLU365-ARG392

GLU319-LYS508

GLU420-LYS430

GLU353-LYS329

GLU375-ARG567

GLU319-LYS569

GLU447-LYS465

GLU353-LYS347

GLU418-LYS430

GLU341-ARG178

GLU447-LYS467

GLU365-ARG392

GLU420-ARG427

GLU341-ARG212

GLU447-LYS584

GLU375-ARG567

GLU420-LYS430

GLU341-ARG332

GLU498-ARG497

GLU418-LYS430

GLU447-LYS462

GLU341-ARG339

GLU498-ARG502

GLU420-ARG427

GLU447-LYS465

GLU341-LYS345

GLU540-ARG443

GLU420-LYS430

GLU447-LYS467

GLU341-LYS508

GLU540-ARG567

GLU447-LYS462

GLU498-ARG497

GLU353-LYS329

GLU540-LYS320

GLU447-LYS465

GLU498-ARG502

GLU353-LYS347

GLU551-LYS477

GLU447-LYS467

GLU540-ARG443

GLU365-ARG392

GLU498-ARG497

GLU540-LYS320

GLU375-ARG567

GLU498-ARG502

GLU540-LYS569

GLU418-LYS430

GLU540-ARG443

GLU551-ARG579

GLU420-ARG427

GLU540-LYS320

GLU551-LYS477

GLU420-LYS430

GLU540-LYS569

GLU447-LYS462

GLU551-ARG579

GLU447-LYS465

GLU551-LYS477

GLU447-LYS467 GLU498-ARG497 GLU498-ARG502 GLU540-ARG443 GLU540-LYS320 GLU540-LYS569 GLU551-LYS477

222

4 RNA Helicase

Table 4.8 The SBs within F-chain NSP13.2 during the six replicates’ (each with 5 .μs) MD simulations Rep1

Rep2

Rep3

Rep4

Rep5

ASP101-LYS28

ASP101-ARG129

ASP101-ARG129

ASP101-LYS28

ASP101-LYS28

ASP101-LYS28

ASP160-ARG161

ASP101-LYS28

ASP101-LYS28

ASP160-ARG161

ASP160-ARG161

ASP160-ARG161

Rep6

ASP160-LYS218

ASP160-ARG161

ASP160-ARG161

ASP160-ARG212

ASP160-ARG339

ASP160-ARG339

ASP204-ARG161

ASP160-ARG212

ASP160-LYS218

ASP160-ARG339

ASP160-LYS218

ASP160-LYS218

ASP204-ARG490

ASP160-LYS218

ASP204-ARG490

ASP160-LYS218

ASP204-ARG161

ASP204-ARG161

ASP204-LYS524

ASP204-ARG161

ASP204-LYS524

ASP204-ARG161

ASP204-ARG560

ASP204-ARG560

ASP207-ARG155

ASP204-ARG490

ASP207-ARG155

ASP204-LYS202

ASP204-LYS202

ASP204-LYS202

ASP207-ARG173

ASP204-LYS202

ASP207-ARG173

ASP204-LYS524

ASP207-ARG155

ASP207-ARG155

ASP207-LYS202

ASP204-LYS524

ASP207-LYS202

ASP207-ARG155

ASP207-ARG173

ASP207-ARG173

ASP223-ARG186

ASP207-ARG155

ASP223-ARG186

ASP207-ARG173

ASP207-ARG560

ASP207-LYS202

ASP315-ARG332

ASP207-ARG173

ASP260-ARG442

ASP207-LYS202

ASP207-LYS202

ASP223-ARG186

ASP315-LYS345

ASP207-LYS202

ASP260-LYS465

ASP223-ARG186

ASP223-ARG186

ASP260-LYS323

ASP328-LYS329

ASP207-LYS524

ASP315-ARG332

ASP315-ARG178

ASP260-ARG442

ASP315-ARG178

ASP328-LYS345

ASP223-ARG186

ASP315-ARG339

ASP315-ARG332

ASP260-ARG443

ASP315-ARG332

ASP328-LYS347

ASP260-ARG442

ASP315-LYS345

ASP328-LYS329

ASP315-ARG178

ASP315-LYS202

ASP32-LYS28

ASP315-ARG212

ASP328-LYS329

ASP328-LYS347

ASP315-ARG332

ASP328-LYS329

ASP344-ARG332

ASP315-ARG332

ASP328-LYS347

ASP32-LYS28

ASP328-LYS329

ASP328-LYS347

ASP344-LYS345

ASP315-LYS345

ASP32-LYS28

ASP32-LYS94

ASP328-LYS345

ASP32-LYS28

ASP369-ARG303

ASP328-LYS329

ASP344-ARG332

ASP344-LYS345

ASP328-LYS347

ASP344-LYS345

ASP369-LYS394

ASP328-LYS347

ASP344-LYS345

ASP369-LYS394

ASP32-LYS28

ASP369-ARG303

ASP374-LYS288

ASP32-LYS28

ASP369-ARG303

ASP383-LYS139

ASP344-ARG339

ASP369-LYS394

ASP383-ARG409

ASP344-ARG332

ASP369-LYS394

ASP401-LYS288

ASP344-LYS345

ASP383-LYS139

ASP383-LYS139

ASP344-LYS345

ASP374-LYS288

ASP435-LYS271

ASP369-ARG303

ASP401-LYS288

ASP401-LYS430

ASP369-LYS394

ASP435-LYS271

ASP450-LYS462

ASP369-LYS394

ASP435-LYS271

ASP401-LYS460

ASP374-LYS288

ASP450-LYS462

ASP450-LYS465

ASP374-LYS288

ASP450-LYS462

ASP435-LYS271

ASP435-LYS271

ASP466-LYS465

ASP458-LYS460

ASP401-LYS288

ASP458-LYS460

ASP450-LYS462

ASP450-LYS462

ASP466-LYS467

ASP458-LYS584

ASP435-LYS271

ASP458-LYS462

ASP458-LYS460

ASP458-LYS460

ASP483-ARG490

ASP466-LYS462

ASP450-LYS462

ASP458-LYS584

ASP466-LYS465

ASP458-LYS462

ASP483-LYS202

ASP466-LYS465

ASP458-LYS460

ASP466-LYS462

ASP466-LYS467

ASP466-ARG442

ASP534-ARG560

ASP466-LYS467

ASP458-LYS584

ASP466-LYS465

ASP483-ARG490

ASP466-LYS465

ASP542-LYS508

ASP483-ARG490

ASP466-LYS465

ASP466-LYS467

ASP483-LYS202

ASP466-LYS467

ASP542-LYS569

ASP483-LYS524

ASP466-LYS467

ASP483-ARG490

ASP534-ARG560

ASP483-ARG490

ASP580-ARG579

ASP534-ARG178

ASP483-ARG490

ASP483-LYS524

ASP542-ARG507

ASP483-LYS202

ASP580-LYS584

ASP534-ARG560

ASP483-LYS524

ASP534-ARG161

ASP542-LYS508

ASP534-ARG560

ASP583-ARG579

ASP542-LYS508

ASP534-ARG560

ASP534-ARG560

ASP542-LYS569

ASP542-LYS508

ASP583-LYS584

ASP542-LYS569

ASP534-LYS202

ASP534-ARG567

ASP580-ARG579

ASP542-LYS569

ASP59-LYS40

ASP580-ARG579

ASP542-ARG443

ASP542-ARG443

ASP580-LYS584

ASP580-ARG579

GLU128-ARG129

ASP580-LYS460

ASP542-LYS508

ASP542-LYS508

ASP583-ARG579

ASP580-LYS584

GLU128-LYS131

ASP580-LYS584

ASP542-LYS569

ASP542-LYS569

ASP583-LYS584

ASP583-ARG579

GLU136-ARG21

ASP583-ARG579

ASP578-LYS477

ASP580-ARG579

ASP59-LYS40

ASP59-LYS73

GLU142-ARG409

ASP583-LYS460

ASP580-ARG579

ASP580-LYS460

GLU128-ARG129

GLU128-ARG129

GLU142-LYS139

ASP583-LYS462

ASP580-LYS460

ASP580-LYS584

GLU128-LYS131

GLU128-LYS131

GLU142-LYS146

ASP59-LYS40

ASP580-LYS584

ASP583-ARG579

GLU136-ARG21

GLU136-ARG129

GLU143-LYS139

GLU128-ARG129

ASP583-ARG579

ASP583-LYS460

GLU142-ARG409

GLU136-ARG21

GLU143-LYS146

GLU128-LYS131

ASP583-LYS460

ASP583-LYS462

GLU142-LYS139

GLU142-ARG409

GLU156-ARG155

GLU136-ARG21

ASP59-LYS40

ASP59-LYS40

GLU142-LYS146

GLU142-LYS139

GLU162-ARG161

GLU142-ARG409

GLU128-ARG129

GLU143-LYS139

GLU143-LYS139

GLU162-LYS524

GLU142-LYS139

GLU128-LYS131

GLU128-LYS131

GLU143-LYS146

GLU143-LYS146

GLU168-LYS171

GLU142-LYS146

GLU136-ARG21

GLU136-ARG21

GLU156-ARG155

GLU156-ARG155

GLU197-ARG337

GLU143-LYS139

GLU142-ARG409

GLU142-ARG409

GLU162-ARG161

GLU162-ARG161

GLU197-ARG339

GLU143-LYS146

GLU142-LYS139

GLU142-LYS139

GLU162-LYS524

GLU162-LYS524

GLU201-ARG178

GLU156-ARG155

GLU143-LYS139

GLU143-LYS139

GLU168-LYS171

GLU168-LYS171

GLU201-ARG212

GLU162-ARG161

GLU143-LYS146

GLU143-LYS146

GLU197-ARG337

GLU197-ARG337

GLU244-LYS276

GLU162-LYS524

GLU156-ARG155

GLU156-ARG155

GLU197-ARG339

GLU197-ARG339

GLU261-ARG442

GLU168-LYS171

GLU162-ARG161

GLU162-ARG161

GLU201-ARG178

GLU201-ARG178

GLU261-LYS323

GLU197-ARG337

GLU168-LYS171

GLU162-ARG560

GLU201-ARG212

GLU201-ARG212

GLU261-LYS465

GLU201-ARG178

GLU197-ARG337

GLU168-LYS171

GLU244-LYS276

GLU244-LYS276

GLU319-LYS320

GLU201-ARG212

GLU201-ARG178

GLU197-ARG337

GLU261-LYS323

GLU244-LYS394

GLU319-LYS323

GLU244-LYS276

GLU201-ARG212

GLU197-ARG339

GLU261-LYS467

GLU261-ARG442

GLU319-LYS345

GLU261-ARG442

GLU244-LYS276

GLU201-ARG178

GLU319-LYS320

GLU261-ARG443

GLU319-LYS569

GLU261-ARG443

GLU261-ARG442

GLU201-ARG212

GLU319-LYS323

GLU261-LYS320

GLU341-ARG212

GLU261-LYS323

GLU261-ARG443

GLU201-ARG339

GLU128-ARG129

(continued)

4.4 Concluding Remarks

223

Table 4.8 (continued) Rep1

Rep2

Rep3

Rep4

Rep5

Rep6

GLU319-LYS345

GLU261-LYS323

GLU341-ARG339

GLU319-LYS320

GLU261-LYS320

GLU244-LYS276

GLU319-LYS569

GLU319-LYS320

GLU353-LYS329

GLU319-LYS323

GLU261-LYS323

GLU261-ARG442

GLU341-ARG332

GLU319-LYS323

GLU353-LYS347

GLU341-ARG161

GLU261-LYS508

GLU261-LYS323

GLU341-ARG337

GLU319-LYS345

GLU365-ARG390

GLU341-ARG178

GLU319-LYS320

GLU261-LYS508

GLU341-ARG339

GLU341-ARG332

GLU365-ARG392

GLU341-ARG212

GLU319-LYS323

GLU319-LYS320

GLU353-LYS329

GLU341-ARG337

GLU375-ARG567

GLU341-ARG339

GLU341-ARG161

GLU319-LYS323

GLU353-LYS347

GLU341-ARG339

GLU375-LYS288

GLU353-LYS329

GLU341-ARG178

GLU341-ARG161

GLU365-ARG390

GLU353-LYS329

GLU418-LYS430

GLU353-LYS347

GLU341-ARG212

GLU341-ARG178

GLU365-ARG392

GLU353-LYS347

GLU420-ARG427

GLU365-ARG390

GLU341-ARG332

GLU341-ARG212

GLU375-LYS288

GLU365-ARG390

GLU420-LYS430

GLU365-ARG392

GLU341-ARG337

GLU341-ARG339

GLU418-LYS430

GLU365-ARG392

GLU447-LYS467

GLU418-LYS430

GLU341-ARG339

GLU353-LYS329

GLU420-ARG427

GLU375-ARG567

GLU498-ARG497

GLU420-ARG427

GLU353-LYS329

GLU353-LYS347

GLU420-LYS430

GLU375-LYS288

GLU498-ARG502

GLU420-LYS430

GLU353-LYS347

GLU365-ARG390

GLU498-ARG497

GLU418-ARG560

GLU540-ARG443

GLU447-LYS462

GLU365-ARG390

GLU365-ARG392

GLU498-ARG502

GLU418-LYS430

GLU540-LYS569

GLU447-LYS465

GLU365-ARG392

GLU418-LYS430

GLU540-ARG443

GLU420-ARG427

GLU551-LYS477

GLU447-LYS467

GLU375-LYS288

GLU420-ARG427

GLU540-LYS569

GLU420-LYS430

GLU498-ARG497

GLU418-LYS430

GLU420-LYS430

GLU551-ARG579

GLU498-ARG497

GLU498-ARG502

GLU420-ARG427

GLU447-LYS462

GLU551-LYS477

GLU498-ARG502

GLU551-ARG579

GLU420-LYS430

GLU447-LYS465

GLU540-ARG443

GLU551-LYS477

GLU447-LYS462

GLU447-LYS467

GLU540-ARG567

GLU447-LYS465

GLU498-ARG497

GLU540-LYS320

GLU447-LYS467

GLU498-ARG502

GLU540-LYS569

GLU498-ARG497

GLU551-LYS477

GLU551-LYS477

GLU498-ARG502 GLU540-ARG567 GLU540-LYS569 GLU551-ARG579 GLU551-LYS477

224

4 RNA Helicase

Table 4.9 The SBs within A-chain NSP12 during the six replicates’ (each with 5 .μs) MD simulations Rep1

Rep2

Rep3

Rep4

Rep5

Rep6

ASP100-ARG10

ASP100-ARG10

ASP100-ARG10

ASP100-ARG10

ASP100-ARG10

ASP100-ARG10

ASP107-ARG74

ASP126-ARG33

ASP107-ARG74

ASP100-LYS98

ASP107-ARG74

ASP107-ARG74

ASP126-ARG33

ASP135-LYS47

ASP126-ARG33

ASP107-ARG74

ASP109-ARG74

ASP109-ARG74

ASP126-LYS47

ASP135-LYS780

ASP126-LYS47

ASP126-ARG33

ASP126-ARG33

ASP126-ARG33

ASP135-LYS47

ASP135-LYS783

ASP135-LYS47

ASP135-LYS780

ASP135-LYS47

ASP135-LYS47

ASP135-LYS780

ASP140-LYS143

ASP135-LYS780

ASP135-LYS783

ASP135-LYS780

ASP135-LYS780

ASP135-LYS783

ASP153-ARG173

ASP135-LYS783

ASP140-LYS143

ASP135-LYS783

ASP135-LYS783

ASP140-LYS143

ASP155-LYS159

ASP140-LYS143

ASP153-ARG173

ASP140-LYS143

ASP140-LYS143

ASP140-LYS47

ASP161-LYS159

ASP140-LYS47

ASP154-LYS143

ASP140-LYS160

ASP140-LYS160

ASP153-ARG173

ASP161-LYS160

ASP153-ARG173

ASP161-LYS159

ASP153-ARG173

ASP153-ARG173

ASP153-LYS159

ASP164-LYS159

ASP154-LYS143

ASP161-LYS160

ASP153-LYS159

ASP154-LYS143

ASP154-LYS143

ASP170-ARG173

ASP155-LYS159

ASP164-LYS159

ASP154-ARG173

ASP161-LYS159

ASP155-LYS159

ASP170-LYS159

ASP161-LYS159

ASP170-ARG173

ASP154-LYS159

ASP161-LYS160

ASP161-LYS159

ASP194-ARG197

ASP161-LYS160

ASP170-LYS159

ASP155-ARG173

ASP164-LYS159

ASP161-LYS160

ASP194-LYS288

ASP170-ARG173

ASP194-ARG197

ASP155-LYS159

ASP170-ARG173

ASP170-ARG173

ASP218-ARG116

ASP194-ARG197

ASP194-LYS288

ASP161-LYS159

ASP194-ARG197

ASP170-LYS159

ASP218-LYS73

ASP194-LYS288

ASP208-ARG33

ASP161-LYS160

ASP194-LYS288

ASP194-ARG197

ASP235-ARG467

ASP218-ARG116

ASP218-ARG116

ASP164-LYS159

ASP208-ARG33

ASP194-LYS288

ASP235-ARG733

ASP218-LYS73

ASP235-ARG467

ASP170-ARG173

ASP218-ARG116

ASP218-ARG116

ASP235-ARG735

ASP235-ARG467

ASP235-ARG733

ASP170-LYS159

ASP218-LYS50

ASP218-LYS73

ASP258-LYS263

ASP235-ARG733

ASP235-ARG735

ASP194-ARG197

ASP235-ARG467

ASP235-ARG467

ASP260-LYS263

ASP235-ARG735

ASP258-ARG183

ASP194-LYS288

ASP235-ARG733

ASP235-ARG733

ASP269-LYS267

ASP258-LYS263

ASP258-ARG285

ASP208-ARG33

ASP235-ARG735

ASP235-ARG735

ASP269-LYS272

ASP260-LYS263

ASP258-LYS263

ASP218-ARG116

ASP258-LYS263

ASP258-LYS263

ASP274-LYS272

ASP269-LYS267

ASP258-LYS267

ASP235-ARG467

ASP260-LYS263

ASP260-LYS263

ASP284-LYS281

ASP269-LYS272

ASP258-LYS281

ASP235-ARG733

ASP269-LYS267

ASP269-LYS267

ASP284-LYS288

ASP274-LYS272

ASP260-ARG249

ASP258-LYS263

ASP269-LYS272

ASP269-LYS272

ASP291-ARG467

ASP284-LYS281

ASP260-LYS263

ASP260-ARG173

ASP274-LYS272

ASP274-LYS272

ASP291-ARG735

ASP284-LYS288

ASP260-LYS267

ASP260-LYS263

ASP284-LYS281

ASP284-LYS281

ASP29-ARG55

ASP291-ARG467

ASP260-LYS272

ASP269-LYS267

ASP284-LYS288

ASP284-LYS288

ASP303-ARG305

ASP291-ARG735

ASP260-LYS281

ASP269-LYS272

ASP291-ARG467

ASP291-ARG467

ASP303-ARG651

ASP29-ARG55

ASP269-LYS267

ASP274-LYS272

ASP291-ARG733

ASP291-ARG735

ASP304-ARG640

ASP303-ARG305

ASP269-LYS272

ASP284-LYS281

ASP291-ARG735

ASP29-ARG55

ASP304-ARG651

ASP304-ARG640

ASP274-LYS263

ASP284-LYS288

ASP303-ARG305

ASP29-LYS121

ASP336-ARG365

ASP304-ARG651

ASP274-LYS272

ASP291-ARG467

ASP303-ARG651

ASP303-ARG305

ASP358-ARG533

ASP336-ARG365

ASP284-ARG285

ASP291-ARG735

ASP304-ARG640

ASP304-ARG640

ASP390-ARG392

ASP358-ARG533

ASP284-LYS281

ASP29-ARG55

ASP304-ARG651

ASP304-ARG651

ASP3-ARG105

ASP36-ARG733

ASP284-LYS288

ASP29-ARG74

ASP336-ARG365

ASP336-ARG365

ASP3-ARG18

ASP390-ARG392

ASP291-ARG467

ASP303-ARG305

ASP358-ARG533

ASP358-ARG533

ASP40-ARG721

ASP3-ARG105

ASP291-ARG735

ASP304-ARG640

ASP390-ARG392

ASP36-ARG733

ASP40-LYS41

ASP40-ARG721

ASP303-ARG305

ASP336-ARG365

ASP3-ARG105

ASP390-ARG392

ASP40-LYS718

ASP40-LYS41

ASP303-ARG651

ASP358-ARG331

ASP3-ARG10

ASP3-ARG105

ASP418-LYS417

ASP40-LYS718

ASP304-ARG305

ASP358-ARG533

ASP40-ARG721

ASP3-ARG18

ASP418-LYS890

ASP418-LYS890

ASP304-ARG640

ASP390-ARG392

ASP40-LYS41

ASP40-ARG721

ASP421-LYS417

ASP421-LYS417

ASP304-ARG651

ASP3-ARG105

ASP40-LYS718

ASP40-LYS41

ASP452-ARG553

ASP445-ARG553

ASP336-ARG365

ASP3-ARG10

ASP421-LYS417

ASP40-LYS718

ASP452-ARG624

ASP452-ARG553

ASP358-ARG533

ASP3-ARG18

ASP452-ARG553

ASP418-LYS417

ASP452-LYS551

ASP452-ARG624

ASP36-ARG733

ASP40-ARG721

ASP452-ARG624

ASP418-LYS890

ASP454-ARG457

ASP454-ARG457

ASP390-ARG392

ASP40-LYS41

ASP452-LYS621

ASP421-LYS417

ASP465-ARG132

ASP465-ARG132

ASP3-ARG105

ASP40-LYS718

ASP454-ARG457

ASP445-ARG553

ASP477-ARG640

ASP477-ARG640

ASP3-ARG10

ASP421-LYS417

ASP465-ARG132

ASP452-ARG553

ASP477-LYS478

ASP477-LYS478

ASP3-ARG18

ASP452-ARG624

ASP477-ARG640

ASP452-ARG624

ASP481-LYS478

ASP481-LYS478

ASP3-LYS103

ASP452-LYS621

ASP477-LYS478

ASP454-ARG457

ASP481-LYS641

ASP481-LYS641

ASP3-LYS59

ASP454-ARG457

ASP477-LYS641

ASP465-ARG132

ASP484-LYS574

ASP484-LYS574

ASP40-ARG721

ASP465-ARG132

ASP481-LYS478

ASP477-ARG640

ASP499-ARG513

ASP499-ARG513

ASP40-LYS41

ASP477-ARG640

ASP481-LYS641

ASP477-LYS478

ASP499-LYS511

ASP499-LYS511

ASP40-LYS718

ASP477-LYS478

ASP484-LYS574

ASP481-LYS478

ASP523-LYS369

ASP523-LYS369

ASP418-LYS890

ASP477-LYS641

ASP499-ARG513

ASP484-LYS574

ASP608-ARG750

ASP608-ARG750

ASP421-LYS417

ASP481-LYS478

ASP499-LYS511

ASP499-ARG513

ASP608-LYS751

ASP608-LYS751

ASP452-ARG624

ASP481-LYS641

ASP523-LYS369

ASP499-LYS511

ASP60-ARG18

ASP60-ARG18

ASP452-LYS621

ASP484-LYS574

ASP608-ARG750

ASP517-ARG513

ASP618-LYS621

ASP618-LYS621

ASP454-ARG457

ASP499-ARG513

ASP608-LYS751

ASP523-LYS369

ASP618-LYS798

ASP618-LYS798

ASP465-ARG132

ASP499-LYS511

ASP60-ARG18

ASP608-ARG750

ASP623-ARG553

ASP623-ARG553

ASP477-ARG640

ASP517-ARG513

ASP618-ARG553

ASP608-LYS751

ASP623-ARG624

ASP623-ARG555

ASP477-LYS478

ASP523-LYS369

ASP618-LYS551

ASP60-ARG18

ASP623-LYS551

ASP623-LYS551

ASP477-LYS641

ASP608-ARG750

ASP618-LYS798

(continued)

4.4 Concluding Remarks

225

Table 4.9 (continued) Rep1

Rep2

Rep3

Rep4

Rep5

Rep6

ASP618-LYS798

ASP623-LYS621

ASP623-LYS621

ASP481-LYS478

ASP608-LYS751

ASP623-ARG624

ASP623-ARG553

ASP62-ARG18

ASP63-ARG18

ASP481-LYS641

ASP60-ARG18

ASP623-LYS621

ASP623-ARG555

ASP62-LYS59

ASP63-LYS59

ASP484-LYS574

ASP618-ARG553

ASP63-LYS59

ASP623-ARG624

ASP63-ARG18

ASP67-LYS121

ASP499-ARG513

ASP618-LYS551

ASP67-LYS121

ASP63-ARG18

ASP63-LYS59

ASP711-LYS41

ASP499-LYS511

ASP618-LYS798

ASP711-LYS47

ASP63-LYS59

ASP67-LYS121

ASP711-LYS714

ASP523-LYS369

ASP623-ARG624

ASP711-LYS714

ASP67-LYS121

ASP711-LYS714

ASP736-ARG305

ASP608-ARG750

ASP623-LYS621

ASP711-LYS780

ASP684-ARG631

ASP736-ARG305

ASP736-ARG735

ASP608-LYS603

ASP63-ARG18

ASP717-LYS714

ASP711-LYS714

ASP736-ARG735

ASP738-ARG726

ASP608-LYS751

ASP63-LYS59

ASP736-ARG305

ASP711-LYS780

ASP738-ARG726

ASP740-ARG726

ASP618-ARG553

ASP67-LYS121

ASP736-ARG735

ASP717-LYS718

ASP760-LYS621

ASP760-LYS621

ASP618-LYS551

ASP711-LYS47

ASP760-ARG553

ASP736-ARG305

ASP761-LYS621

ASP761-LYS621

ASP618-LYS798

ASP711-LYS714

ASP760-LYS551

ASP736-ARG735

ASP804-LYS807

ASP804-LYS807

ASP623-ARG624

ASP711-LYS780

ASP761-LYS551

ASP760-LYS621

ASP824-LYS821

ASP824-LYS821

ASP623-LYS621

ASP717-LYS714

ASP804-LYS807

ASP761-LYS621

ASP825-LYS603

ASP825-LYS603

ASP63-ARG18

ASP736-ARG305

ASP824-LYS821

ASP804-LYS807

ASP833-ARG836

ASP833-ARG836

ASP63-LYS59

ASP736-ARG735

ASP833-ARG836

ASP824-LYS821

ASP833-LYS438

ASP833-LYS438

ASP67-LYS121

ASP761-LYS551

ASP833-LYS438

ASP825-LYS603

ASP845-LYS849

ASP845-LYS849

ASP684-ARG569

ASP804-LYS807

ASP845-LYS411

ASP833-ARG836

ASP846-LYS849

ASP846-LYS849

ASP711-LYS47

ASP824-LYS821

ASP845-LYS545

ASP833-LYS438

ASP865-LYS593

ASP865-ARG836

ASP711-LYS714

ASP825-LYS603

ASP845-LYS849

ASP845-LYS411

ASP879-LYS426

ASP865-LYS593

ASP711-LYS780

ASP833-ARG836

ASP846-LYS411

ASP845-LYS849

ASP893-ARG889

ASP879-LYS426

ASP717-LYS714

ASP833-LYS438

ASP846-LYS849

ASP846-LYS411

ASP893-LYS890

ASP893-ARG889

ASP736-ARG305

ASP845-LYS411

ASP865-ARG836

ASP846-LYS849

ASP910-ARG914

ASP893-LYS890

ASP736-ARG735

ASP845-LYS545

ASP865-ARG858

ASP865-ARG836

ASP92-LYS91

ASP910-ARG889

ASP738-ARG305

ASP845-LYS849

ASP865-LYS593

ASP865-LYS593

ASP92-LYS98

ASP910-ARG914

ASP760-ARG553

ASP846-LYS411

ASP879-LYS426

ASP879-LYS426

GLU136-LYS160

ASP92-LYS91

ASP760-LYS551

ASP846-LYS849

ASP893-ARG889

ASP893-ARG889

GLU136-LYS780

GLU136-LYS160

ASP761-ARG553

ASP865-LYS593

ASP910-ARG889

ASP893-LYS890

GLU136-LYS783

GLU136-LYS780

ASP761-LYS551

ASP893-ARG889

ASP910-ARG914

ASP92-LYS91

GLU144-LYS121

GLU136-LYS783

ASP804-LYS807

ASP893-LYS890

ASP92-LYS91

GLU136-LYS160

GLU167-LYS159

GLU144-LYS121

ASP824-LYS821

ASP910-ARG889

GLU136-LYS160

GLU136-LYS780

GLU167-LYS160

GLU144-LYS143

ASP833-ARG836

ASP910-ARG914

GLU136-LYS47

GLU136-LYS783

GLU180-ARG183

GLU167-LYS159

ASP833-LYS438

ASP92-LYS91

GLU136-LYS780

GLU144-LYS121

GLU254-ARG183

GLU167-LYS160

ASP845-LYS849

GLU136-LYS160

GLU136-LYS783

226

4 RNA Helicase

Table 4.10 The SBs within A-chain NSP12 during the six replicates’ (each with 5 .μs) MD simulations (continuation) Rep1

Rep2

Rep3

Rep4

Rep5

GLU167-LYS159

GLU254-ARG285

GLU180-ARG183

ASP846-LYS411

GLU136-LYS47

GLU144-LYS121

GLU167-LYS160

GLU277-LYS272

GLU254-ARG183

ASP846-LYS849

GLU136-LYS780

GLU167-ARG457

Rep6

GLU180-ARG183

GLU277-LYS281

GLU254-ARG285

ASP865-ARG836

GLU136-LYS783

GLU167-LYS159

GLU254-ARG183

GLU278-LYS272

GLU277-LYS281

ASP865-LYS593

GLU144-LYS121

GLU180-ARG183

GLU254-ARG285

GLU278-LYS281

GLU278-LYS272

ASP879-LYS426

GLU144-LYS143

GLU254-ARG183

GLU277-LYS272

GLU350-ARG349

GLU278-LYS281

ASP893-ARG889

GLU167-ARG457

GLU254-ARG285

GLU277-LYS281

GLU370-ARG365

GLU350-ARG349

ASP893-LYS890

GLU167-LYS159

GLU277-LYS281

GLU278-LYS272

GLU370-LYS369

GLU370-ARG365

ASP910-ARG889

GLU180-ARG183

GLU278-LYS272

GLU278-LYS281

GLU431-LYS430

GLU370-LYS369

ASP910-ARG914

GLU254-ARG183

GLU278-LYS281

GLU350-ARG349

GLU436-LYS438

GLU431-LYS430

ASP92-LYS91

GLU254-ARG285

GLU350-ARG349

GLU370-ARG365

GLU474-ARG305

GLU436-LYS438

GLU136-LYS160

GLU277-LYS281

GLU370-LYS369

GLU370-LYS369

GLU474-ARG640

GLU474-ARG305

GLU136-LYS780

GLU278-LYS272

GLU431-LYS430

GLU431-LYS430

GLU522-LYS369

GLU474-ARG640

GLU136-LYS783

GLU278-LYS281

GLU436-LYS438

GLU436-LYS438

GLU58-ARG118

GLU58-ARG118

GLU144-LYS121

GLU350-ARG349

GLU474-ARG305

GLU474-ARG305

GLU610-LYS751

GLU610-LYS751

GLU144-LYS143

GLU370-ARG365

GLU474-ARG640

GLU474-ARG640

GLU61-ARG18

GLU61-ARG18

GLU167-ARG457

GLU370-LYS369

GLU58-ARG118

GLU522-LYS369

GLU658-ARG631

GLU658-ARG631

GLU167-LYS159

GLU431-LYS430

GLU58-ARG18

GLU58-ARG118

GLU658-ARG654

GLU658-ARG654

GLU167-LYS160

GLU436-LYS438

GLU610-LYS751

GLU58-ARG18

GLU665-LYS676

GLU665-LYS676

GLU180-ARG181

GLU474-ARG305

GLU61-ARG18

GLU610-LYS751

GLU729-ARG726

GLU729-ARG726

GLU180-ARG183

GLU474-ARG640

GLU61-LYS59

GLU61-ARG18

GLU729-ARG733

GLU729-ARG733

GLU254-ARG183

GLU522-LYS369

GLU658-ARG631

GLU658-ARG631

GLU744-ARG726

GLU729-LYS41

GLU254-ARG285

GLU58-ARG118

GLU665-LYS676

GLU658-ARG654

GLU796-LYS780

GLU744-ARG726

GLU254-LYS267

GLU58-ARG18

GLU729-ARG733

GLU665-LYS676

GLU796-LYS783

GLU796-LYS780

GLU277-LYS263

GLU610-LYS751

GLU744-ARG726

GLU729-ARG733

GLU802-LYS807

GLU796-LYS783

GLU277-LYS272

GLU61-ARG18

GLU796-LYS780

GLU744-ARG726

GLU811-ARG836

GLU802-LYS807

GLU277-LYS281

GLU658-ARG631

GLU796-LYS783

GLU796-LYS780

GLU811-LYS798

GLU811-ARG836

GLU278-LYS263

GLU658-ARG654

GLU802-LYS807

GLU796-LYS783

GLU83-LYS73

GLU811-LYS798

GLU278-LYS267

GLU665-LYS676

GLU811-ARG836

GLU802-LYS807

GLU876-LYS430

GLU83-LYS73

GLU278-LYS272

GLU729-ARG733

GLU811-LYS438

GLU811-LYS798

GLU894-LYS890

GLU876-LYS430

GLU278-LYS281

GLU744-ARG726

GLU811-LYS551

GLU811-LYS807

GLU917-ARG914

GLU894-LYS890

GLU350-ARG349

GLU796-LYS780

GLU811-LYS798

GLU83-LYS73

GLU919-ARG914

GLU917-ARG889

GLU370-LYS369

GLU796-LYS783

GLU83-ARG116

GLU857-ARG858

GLU922-LYS871

GLU917-ARG914

GLU431-LYS430

GLU802-LYS807

GLU83-LYS73

GLU876-LYS430

GLU919-ARG914

GLU436-LYS438

GLU811-ARG836

GLU857-ARG914

GLU894-LYS890

GLU922-LYS871

GLU474-ARG305

GLU811-LYS438

GLU894-LYS890

GLU917-ARG914

GLU474-ARG640

GLU811-LYS551

GLU917-ARG889

GLU919-ARG914

GLU58-ARG118

GLU811-LYS798

GLU917-ARG914

GLU922-LYS871

GLU58-ARG18

GLU83-ARG116

GLU919-ARG914

GLU610-LYS751

GLU83-LYS73

GLU922-LYS871

GLU61-ARG18

GLU857-ARG914

GLU658-ARG631

GLU876-LYS807

GLU658-ARG654

GLU894-LYS890

GLU665-LYS676

GLU917-ARG914

GLU729-ARG733

GLU919-ARG914

GLU744-ARG726

GLU922-LYS871

GLU796-LYS780 GLU796-LYS783 GLU802-LYS807 GLU811-ARG836 GLU811-LYS438 GLU811-LYS551 GLU83-ARG116 GLU83-LYS73 GLU876-LYS430 GLU876-LYS807 GLU894-LYS890 GLU917-ARG914 GLU919-ARG914 GLU922-LYS871

Chapter 5

RNA Helicase Binding with RdRp, NSP7, NSP8a, NSP8b, pRNA, tRNA, ADP-Mg2+ , and ATP-Mg2+

.

.

Abstract Firstly, we optimized the molecular structure of the NSP13-bound SARS-CoV-2 replication-transcription complex (RTC, starting from the NSP13.1open conformation with three cytosines (chain P and residues 36, 37, and 38) manually built onto the 3’ end of chain P, extending the product RNA into the NTP-entry channel of NSP12 to mimic the backtracked state of NSP12). We got some basic structural bioinformatics about the NSP13-bound SARS-CoV-2 replication-transcription complex and then confirmed these basic bioinformatics by analysis of an openly online accessible 500 .μs MD simulation trajectory. Interesting backtracking performance can be observed. Keywords COVID-19 virus · RNA helicase (NSP13) · Binding with RdRp, NSP7, NSP8a, NSP8b - pRNA, tRNA, ADP-Mg.2+ , ATP-Mg.2+ · Optimization and MD (molecular dynamics) studies · Basic structural bioinformatics

5.1 Introduction The COVID-19 pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The SARS-CoV-2 genome is replicated and transcribed by its RNA-dependent RNA polymerase (RdRp), which is the target for antivirals such as remdesivir. In [225], the authors used a combination of approaches to show that backtracking (backward motion of the RdRp on the template RNA) is a feature of SARS-CoV-2 replication/transcription and concluded that backtracking may play a critical role in proofreading, a crucial process for SARS-CoV-2 resistance against many antivirals. The SARS-CoV-2 nonstructural proteins coordinate genome 26 replication and gene expression. Structural analyses revealed the basis for coupling of the essential NSP13 helicase with the RNA-dependent RNA polymerase (RdRp) where the holo-RdRp and RNA substrate (the replication-transcription complex, or RTC) are associated with two copies of NSP13 (NSP13.2 -RTC). One copy of NSP13 interacts with the template RNA in an opposing polarity to the RdRp and is envisaged to drive the RdRp backward on the RNA template (backtracking), © The Author(s), under exclusive license to Springer Nature Switzerland AG 2023 J. Zhang, Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures, Springer Series in Biophysics 23, https://doi.org/10.1007/978-3-031-36773-1_5

227

228

5 RNA Helicase Binding with RdRp, NSP7, NSP8a, NSP8b, pRNA, tRNA,. . .

prompting questions as to how the RdRp can efficiently synthesize RNA in the presence of NSP13. The results of [66] suggest a mechanism for the NSP13.2 -RTC to turn backtracking on and off, using an allosteric mechanism to switch between RNA synthesis and backtracking in response to stimuli at the RdRp active site. In this chapter, we will study the NSP13 in complex with [RdRp, NSP7, NSP8a, NSP8b, pRNA, tRNA, ADP-Mg.2+ , ATP-Mg.2+ ] from optimization and MD point of view.

5.2 Materials and Methods A 500-.μs trajectory featuring nsp13-bound SARS-CoV-2 replication-transcription complex, starting from the NSP13.1-open conformation with three cytosines (chain P and residues 36, 37, and 38), is manually built onto the 3’ end of chain P, extending the product RNA into the NTP-entry channel of NSP12 to mimic the backtracked state of NSP12. In the MD simulation of data of DESRES-ANTON-13795965 of [321], both copies of NSP13 reoriented themselves while remaining bound to NSP12 [321]. For 500-.μs MD trajectories [321], we select 522 frames. In this chapter, firstly we optimized the structures of the NSP13-bound SARS-CoV-2 RTC and got some basic structural bioinformatics about the NSP13-bound SARS-CoV-2 replicationtranscription complex and then confirmed these basic bioinformatics by analysis of the 500 .μs MD simulation trajectories.

5.3 New Results and Discussions The optimized model studied in this chapter can be seen in Fig. 5.1a.

Fig. 5.1 (a) The 3D structure of the optimized NSP12-NSP8-NSP7-NSP13-tpRNA model (where A-chain is NSP12, B-chain is NSP8a, D-chain is NSP8b, C-chain is NSP7, EF-chains are NSP13, and P- and T-chains are p-RNA and t-RNA, respectively). (b, c, d) The ligands ADP2003, ATP1003, and ATP1003 interact with A-, E-, and F-chains, respectively

In Fig. 5.1b, the ligand ADP2003-MG2002 binds with A-chain (NSP12) residues PHE35, LYS50, ASN52, CYS53, LYS73, ARG74, HIS75, GLU83, ARG116, ASP208, ASN209, TYR217, ASP218, PHE219, and GLY220; in Fig. 5.1c, the

5.3 New Results and Discussions

229

ligand ATP1003-MG1004 binds with NSP13 E-chain residues GLU261, SER264, PRO283, PRO284, GLY285, THR286, GLY287, LYS288, SER289, HIS290, LYS320, LYS323, GLU375, GLN404, ARG442, ARG443, HIS464, GLY538, GLU540, THR566, ARG567, and LYS569; and in Fig. 5.1d, the ligand ATP1003MG1004 binds with NSP13 F-chain residues GLU261, PHE262, ASN265, PRO284, GLY285, THR286, GLY287, LYS288, SER289, HIS290, LYS320, ASP374, GLU375, GLN404, ARG442, ARG443, GLU540, ARG567, and LYS569.

Fig. 5.2 The optimized NSP12-NSP8-NSP7-NSP13-tpRNA model binding with ZN2000ZN2001, ZN1000-ZN1001-ZN1002, and ZN1000-ZN1001-ZN1002 for A (NSP12), E (NSP13), and F (NSP13) chains, respectively

In Fig. 5.2, the ZN2000-ZN2001 bind with A-chain (NSP12) residues HIS295, CYM301, LEU302, CYM306, ILE307, HIS309, CYM310; GLY486, CYM487, LYS532, HIS642, CYM645, and CYM646; the ZN1000-ZN1001-ZN1002 bind with NSP13 E-chain residues CYM5, LEU7, CYM8, ASN9, SER10, CYM26, CYM29; CYM50, ALA52, CYM55, VAL57, CYM72, HIS75; CYM16, CYM19, HIS33, HIS39, and ALA110; and the ZN1000-ZN1001-ZN1002 bind with NSP13 F-chain residues CYM5, LEU7, CYM8, ASN9, SER10, CYM26, CYM29, GLY99; CYM50, ALA52, CYM55, CYM72, HIS75; CYM16, CYM19, HIS33, HIS39, and ALA110. Table 5.1 and Fig. 5.3 show us the ABCDEF-chains’ residues of optimized NSP12-NSP8-NSP7-NSP13-tpRNA, binding with pRNA and tRNA. Table 5.2 lists the SBs in ABCDEF-chains of the optimized NSP12-NSP8-NSP7NSP13-tpRNA model. Among the SBs listed in Table 5.2, there are nine stronger SBs (with stronger HBs) among the A-B-C-D-E-F-chains during the 500 .μs MD; we list them in Table 5.3 and show them in Fig. 5.5. Within each chain of the NSP12-NSP8-NSP7-NSP13-tpRNA model, we also get some stronger SBs (with stronger HBs), which are listed in Tables 5.4 and 5.5. During the 500 .μs MD, the NSP12-NSP8-NSP7-NSP13-tpRNA model has some strong HBs listed in Table 5.6 to refer.

230

5 RNA Helicase Binding with RdRp, NSP7, NSP8a, NSP8b, pRNA, tRNA,. . .

Table 5.1 The ABCDEF-chains’ residues of optimized NSP12-NSP8-NSP7-NSP13-tpRNA, binding with pRNA and tRNA tRNA

A408, A409, A410, A411, A495, A496, A497, A500, A501, A502, A503, A507, A508, A509, A511, A541, A543, A544, A545, A546, A547, A557, A558, A559, A560, A565, A569, A573, A576, A577, A580, A583, A589, A590, A591, A592, A594, A593, A595, A682, A683, A684, A685, A686, A687, A689, A849, A857, A864, A911, A914, A915, A920, A924; B39, B40, B43, B44, B46, B47, B57, B58, B61, B82; C21; D39, D40, D43, D44, D61, D62, D65, D69, D80; E15, E139, E142, E143, E147, E174, E175, E176, E177, E178, E179, E180, E230, E231, E232, E233, E234, E309, E310, E311, E335, E336, E337, E338, E339, E340, E359, E360, E361, E382, E408, E410, E516, E532, E534, E535

pRNA

A438, A439, A497, A513, A545, A548, A549, A550, A551, A553, A555, A593, A594, A619, A620, A621, A688, A758, A759, A760, A761, A798, A811, A813, A814, A815, A832, A836, A837, A840, A845, A849, A855, A857, A858, A861, A862, A865; B33, B36, B37, B46, B50, B51, B54, B57, B65, B72, B75; D33, D36, D46, D47, D50, D51, D54, D57, D58;

ptRNA p

A438, A439, A513, A548, A549, A550, A551, A553, A555, A563, A593, A619, A621, A688, A758, A759, A760, A761, A798, A811, A813, A814, A815, A832, A836, A837, A840, A845, A849, A855, A858, A861, A862, A865; B33, B36, B37, B50, B51, B54, B65, B72, B75; D33, D36, D46, D47, D50, D51, D54, D57, D58;

t

A408, A409, A410, A411, A495, A496, A497, A500, A501, A502, A503, A507, A508, A509, A511, A543, A544, A545, A546, A547, A558, A559, A565, A567, A569, A573, A576, A577, A580, A583, A589, A590, A591, A592, A594, A595, A560, A682, A684, A685, A686, A687, A689, A857, A864, A920, A924; B39, B40, B43, B44, B46, B47, B57, B58, B61, B82; C21; D39, D40, D43, D44, D61, D62, D65, D69, D80; E15, E139, E142, E143, E147, E174, E175, E176, E177, E178, E179, E180, E230, E231, E232, E233, E234, E309, E310, E311, E335, E336, E337, E338, E339, E340, E338, E359, E360, E361, E382, E408, E410, E516, E532, E534, E535

During the 500 .μs MD of the NSP12-NSP8-NSP7-NSP13-tpRNA model, we also find the changes of .α-helices as follows: in A-chain, for ASP154-ASN158 its .αhelix unfolds into turn and G-3-10-helix, for MET242-THR248 its .α-helix unfolds into G-3-10-helix and turn during frames 284–525, for ASN447-ASP454 its .α-helix unfolds into turn during frames 144–525, for GLY597-ASN600 its .α-helix unfolds into C-T-E during frames 354–525, for SER768-GLN773 its .α-helix unfolds into TE-G during frames 424–525; within B-chain, for LEU169-SER173 its G-3-10-helix changes into .α-helix and turn during frames 95–525; within D-chain, for LEU169SER173 its .α-helix unfolds during frames 25–484; within E-chain, for ALA446VAL456 its .α-helix is not stable and for VAL533-GLN537 its .α-helix is also not stable; and within F-chain, for ASN516-ILE525 its .α-helix unfolds into C-T-E-G during frames 344–525. Table 5.7 lists the .α-helices’ HBs which become weaker, leading to the unfolding of .α-helices.

5.4 Concluding Remarks

231

Lastly, we observe the PT-chains (T-C54.∼C6, P-G2.∼C38) during the 500 .μs MD. Backtracking [66, 225] can be observed from the seven snapshots: at 0th frame T-U21, P-A35; at 100th frame T-A22, P-U34; at 200th frame T-A22, P-U34; at 300th frame T-A22, P-U34; at 400th frame T-G53, P-C3 – T-A22, P-U34 – others T-C54, P-G2; at 500th frame T-A22, P-U34; and at 512th frame T-A22, P-U34. We have shown the interesting backtracking in Fig. 5.4.

5.4 Concluding Remarks During 500 .μs MD, there are the following strong polar contacts among NSP12 and its cofactors NSP7 and NSP8a, NSP8b: A:ASP517-B:LYS79, A:ASP846-D:ARG80, A:ASP851-D:ARG75, C:ASP5-D:LYS97, C:GLU73D:ARG111, C:GLU50-D:ARG190, A:GLU857-D:LYS72, A:GLU436-C:LYS43, and A:ASP274-B:ARG111, where A-chain is NSP12, B-chain is NSP8a, D-chain

Fig. 5.3 The ABCDEF-chains’ residues of optimized NSP12-NSP8-NSP7-NSP13-tpRNA, binding with pRNA and tRNA

232

5 RNA Helicase Binding with RdRp, NSP7, NSP8a, NSP8b, pRNA, tRNA,. . .

Fig. 5.4 NSP12-NSP8-NSP7-NSP13-tpRNA’s PT-chains at frames 0, 100, 200, 300, 400, 500, and 512 during the 500 .μs MD

is NSP8b, and C-chain is NSP7. With each chain of the NSP12-NSP8-NSP7NSP13-tpRNA model, we also get some stronger polar contacts during the 500 .μs MD (Fig. 5.5). The .α-helices of NSP12’s ASP154-ASN158, MET242-THR248, ASN447-ASP454, GLY597-ASN600, and SER768-GLN773, NSP8a’s LEU169SER173, NSP8b’s LEU169-SER173, NSP13a’s ALA446-VAL456, and NSP13b’s ASN516-ILE525 are unfolding during the 500 .μs MD. Backtracking [66, 225] can be observed from the 500 .μs MD.

5.4 Concluding Remarks Table 5.2 SBs in A-, B-, C-, D-, E-, F-chains of the optimized NSP12-NSP8NSP7-NSP13-tpRNA model

233 A:ASP100-A:ARG10

B:ASP143-B:LYS139

E:ASP113-E:LYS414

F:ASP113-F:LYS414

A:ASP100-A:LYS98

B:ASP163-B:LYS165

E:ASP160-E:LYS218

F:ASP160-F:LYS218

A:ASP126-A:LYS47

B:ASP50-B:LYS46

E:ASP207-E:LYS202

F:ASP204-F:LYS524

A:ASP135-A:LYS780

B:GLU77-B:ARG80

E:ASP223-E:ARG186 F:ASP207-F:ARG173

A:ASP135-A:LYS783

E:ASP315-E:ARG332 F:ASP223-F:ARG186

A:ASP140-A:LYS143

C:ASP5-C:LYS2

E:ASP344-E:LYS345

F:ASP315-F:ARG332

A:ASP161-A:LYS160

C:GLU47-C:LYS51

E:ASP369-E:LYS394

F:ASP328-F:LYS329

A:ASP170-A:ARG173 C:GLU74-C:LYS70

E:ASP450-E:LYS462

F:ASP328-F:LYS347

A:ASP194-A:LYS288

E:ASP458-E:LYS460

F:ASP344-F:LYS345

A:ASP235-A:ARG467 D:ASP161-D:LYS165 E:ASP534-E:ARG560 F:ASP369-F:LYS394 A:ASP235-A:ARG735 D:ASP163-D:LYS165 E:ASP580-E:LYS584

F:ASP435-F:LYS271

A:ASP260-A:LYS263

D:ASP50-D:LYS46

E:ASP583-E:LYS584

F:ASP450-F:LYS462

A:ASP274-A:LYS272

D:ASP78-D:ARG75

E:GLU128-E:LYS131 F:ASP483-F:ARG490

A:ASP291-A:ARG735 D:ASP78-D:LYS82

E:GLU136-E:ARG129 F:ASP534-F:ARG560

A:ASP29-A:ARG55

E:GLU136-E:ARG21

F:ASP542-F:LYS508

A:ASP304-A:ARG640 A:ASP274-B:ARG111 E:GLU142-E:LYS139 F:ASP580-F:ARG579 A:ASP358-A:ARG533 A:ASP517-B:LYS72

E:GLU143-E:LYS139 F:ASP583-F:ARG579

A:ASP390-A:ARG392 A:ASP517-B:LYS79

E:GLU168-E:LYS171 F:GLU128-F:LYS131

A:ASP40-A:LYS41

E:GLU197-E:ARG22

A:ASP418-A:LYS890

A:GLU436-C:LYS43

F:GLU136-F:ARG21

E:GLU244-E:LYS276 F:GLU142-F:LYS139

A:ASP421-A:LYS417

E:GLU353-E:LYS347 F:GLU142-F:LYS146

A:ASP452-A:ARG553 A:ASP846-D:ARG80

E:GLU365-E:ARG390 F:GLU143-F:LYS139

A:ASP452-A:ARG624 A:ASP851-D:ARG75

E:GLU375-E:LYS288 F:GLU143-F:LYS146

A:ASP454-A:ARG457 A:ASP851-D:LYS79

E:GLU420-E:ARG427 F:GLU156-F:HIS164

A:ASP465-A:ARG132 A:GLU857-D:LYS72

E:GLU498-E:ARG502 F:GLU162-F:LYS524

A:ASP477-A:ARG640

E:GLU540-E:LYS569 F:GLU168-F:LYS171

A:ASP477-A:LYS641

B:ASP112-A:ARG331 E:GLU551-E:LYS477 F:GLU197-F:ARG339

A:ASP481-A:LYS478 A:ASP484-A:LYS574

F:GLU201-F:ARG161 B:GLU60-F:LYS94

A:ASP499-A:ARG513

F:GLU244-F:LYS276 F:GLU261-F:ARG442

A:ASP523-A:LYS369

C:ASP5-D:LYS97

F:GLU319-F:LYS323

A:ASP618-A:LYS798

C:GLU50-D:ARG190

F:GLU353-F:LYS329

A:ASP623-A:ARG624 C:GLU73-D:ARG111

F:GLU353-F:LYS347

A:ASP623-A:LYS621

F:GLU365-F:ARG390

A:ASP62-A:ARG18

D:ASP112-E:ARG248

A:ASP63-A:LYS59

F:GLU418-F:LYS430 F:GLU420-F:ARG427

A:ASP684-A:ARG631 E:ASP207-F:ARG392

F:GLU447-F:LYS467

A:ASP711-A:LYS714

E:ASP207-F:LYS276

F:GLU498-F:ARG497

A:ASP824-A:LYS821

E:GLU156-F:ARG129

F:GLU540-F:LYS569

A:ASP833-A:HIS439 A:ASP845-A:ARG858 F:GLU244-E:ARG155 A:ASP845-A:LYS849 A:ASP865-A:LYS593 A:ASP879-A:HIS882 A:ASP893-A:HIS892 A:ASP92-A:LYS91 A:GLU136-A:LYS783 A:GLU144-A:LYS121 A:GLU167-A:LYS160 A:GLU180-A:ARG183 A:GLU254-A:ARG285 A:GLU277-A:LYS281 A:GLU278-A:LYS272 A:GLU350-A:ARG349 A:GLU474-A:ARG305 A:GLU474-A:ARG640 A:GLU58-A:ARG118 A:GLU610-A:LYS751 A:GLU61-A:ARG18 A:GLU658-A:ARG631 A:GLU658-A:ARG654 A:GLU665-A:LYS676 A:GLU744-A:ARG726 A:GLU796-A:LYS783 A:GLU811-A:HIS810 A:GLU811-A:LYS438 A:GLU83-A:LYS73 A:GLU894-A:LYS890 A:GLU922-A:LYS871

F:GLU551-F:LYS477

234

5 RNA Helicase Binding with RdRp, NSP7, NSP8a, NSP8b, pRNA, tRNA,. . .

Table 5.3 During the 500 .μs MD, there are nine stronger SBs (with stronger HBs) among the A-B-C-D-E-F-chains of the NSP12-NSP8-NSP7-NSP13-tpRNA model A:ASP517-B:LYS79

LYS79.NZ-ASP517.OD2 31.99%, LYS79.NZ-ASP517.OD1 28.74%

A:ASP846-D:ARG80

ARG80.NH1-ASP846.OD2 25.48%, ARG80.NH1-ASP846.OD1 25.10%, ARG80.NH2-ASP846.OD1 22.80%, ARG80.NH2-ASP846.OD2 22.03%

A:ASP851-D:ARG75

ARG75.NE-ASP851.OD2 34.29%, ARG75.NH2-ASP851.OD1 32.95%, ARG75.NH2-ASP851.OD2 29.31%, ARG75.NE-ASP851.OD1 29.31%

C:ASP5-D:LYS97

LYS97.NZ-ASP5.OD1 33.72%, LYS97.NZ-ASP5.OD2 21.46%

C:GLU73-D:ARG111 ARG111.NE-GLU73.OE2 17.24%, ARG111.NH2-GLU73.OE1 15.13%, ARG111.NE-GLU73.OE1 13.79%, ARG111.NH2-GLU73.OE2 12.45% C:GLU50-D:ARG190 ARG190.NH2-GLU50.OE1 15.33%, ARG190.NH1-GLU50.OE2 14.56%, ARG190.NH1-GLU50.OE1 13.41%, ARG190.NH2-GLU50.OE2 11.49% A:GLU857-D:LYS72

LYS72.NZ-GLU857.OE1 14.37%, LYS72.NZ-GLU857.OE2 12.26%

A:GLU436-C:LYS43

LYS43.NZ-GLU436.OE1 8.05%, LYS43.NZ-GLU436.OE2 6.13%

A:ASP274-B:ARG111 ARG111.NH2-ASP274.OD1 7.47%, ARG111.NH2-ASP274.OD2 6.32%, ARG111.NH1-ASP274.OD2 5.56%, ARG111.NH1-ASP274.OD1 5.17%

Table 5.4 Within each chain, there are some stronger SBs (with stronger HBs) during the 500 .μs MD of the NSP12-NSP8-NSP7-NSP13-tpRNA model B:ASP112-A:ARG331 ARG331.NE-ASP112.O 10.15% B:ASP50-B:LYS46

ASP50.N-LYS46.O 82.95%, LYS46.NZ-ASP50.OD2 47.89%, LYS46.NZ-ASP50.OD1 46.93%, ASP50.OD2-LYS46.NZ 8.24%

B:GLU77-B:ARG80

ARG80.NE-GLU77.OE1 16.67%, ARG80.NE-GLU77.OE2 14.18%, ARG80.NH1-GLU77.OE2 12.07%, ARG80.NH2-GLU77.OE2 11.11%, ARG80.NH1-GLU77.OE1 10.73%, ARG80.NH2-GLU77.OE1 10.54%

B:ASP163-B:LYS165

LYS165.NZ-ASP163.OD1 14.37%, LYS165.NZ-ASP163.OD2 13.03%

B:ASP143-B:LYS139

LYS139.NZ-ASP143.OD1 10.73%, LYS139.NZ-ASP143.OD2 9.96%

C:GLU47-C:LYS51

LYS51.N-GLU47.O 22.22%, LYS51.NZ-GLU47.OE1 15.90%, LYS51.NZ-GLU47.OE2 15.71%

D:ASP50-D:LYS46

ASP50.N-LYS46.O 82.95%, LYS46.NZ-ASP50.OD2 47.89%, LYS46.NZ-ASP50.OD1 46.93%, ASP50.OD2-LYS46.NZ 8.24% -

D:ASP161-D:LYS165 ASP161.N-LYS165.O 43.87%, LYS165.N-ASP161.OD2 26.05%, LYS165.N-ASP161.OD1 23.75%, LYS165.NZ-ASP161.OD2 10.92%, LYS165.NZ-ASP161.OD1 8.24% D:ASP78-D:LYS82

LYS82.N-ASP78.O 41.57%, LYS82.NZ-ASP78.OD2 38.51%, LYS82.NZ-ASP78.OD1 34.67%

D:ASP163-D:LYS165 LYS165.NZ-ASP163.OD1 14.37%, LYS165.NZ-ASP163.OD2 13.03%, D:ASP78-D:ARG75

ARG75.NH1-ASP78.OD1 12.45%, ARG75.NH1-ASP78.OD2 11.30%

E:ASP223-E:ARG186 ARG186.NH2-ASP223.OD1 90.80%, ARG186.NH2-ASP223.OD2 89.08%, ARG186.NE-ASP223.OD2 87.93%, ARG186.NE-ASP223.OD1 85.82% E:GLU143-E:LYS139 GLU143.N-LYS139.O 61.49%, LYS139.NZ-GLU143.OE2 18.20%, LYS139.NZ-GLU143.OE1 15.90% E:GLU353-E:LYS347 LYS347.NZ-GLU353.OE1 54.98%, LYS347.NZ-GLU353.OE2 51.34%, GLU353.OE1-LYS347.NZ 9.20% E:GLU168-E:LYS171 LYS171.NZ-GLU168.OE2 49.62%, LYS171.NZ-GLU168.OE1 45.79%, LYS171.N-GLU168.O 8.81% E:GLU498-E:ARG502 ARG502.N-GLU498.O 45.79%, ARG502.NE-GLU498.OE2 31.61%, ARG502.NE-GLU498.OE1 29.31%, ARG502.NH2-GLU498.OE1 23.75%, ARG502.NH2-GLU498.OE2 21.65%, ARG502.NH1-GLU498.OE2 4.02% E:GLU136-E:ARG21

ARG21.NE-GLU136.OE1 40.42%, ARG21.NE-GLU136.OE2 38.12%, ARG21.NH2-GLU136.OE1 33.14%, ARG21.NH2-GLU136.OE2 32.95%, ARG21.NH1-GLU136.OE2 25.10%, ARG21.NH1-GLU136.OE1 22.99%, GLU136.OE2-ARG21.NE 11.49% -

E:ASP315-E:ARG332 ARG332.NH2-ASP315.OD1 40.23%, ARG332.NH2-ASP315.OD2 38.51%, ARG332.NE-ASP315.OD2 22.03%, ARG332.NE-ASP315.OD1 18.97%, ARG332.NH1-ASP315.OD1 5.75%E:GLU128-E:LYS131 LYS131.NZ-GLU128.OE2 30.08%, LYS131.NZ-GLU128.OE1 29.12% E:GLU244-E:LYS276 LYS276.N-GLU244.O 28.74%, LYS276.NZ-GLU244.OE1 23.75%, LYS276.NZ-GLU244.OE2 21.65% E:ASP534-E:ARG560 ARG560.NH2-ASP534.OD2 27.39%, ARG560.NE-ASP534.OD1 26.25%, ARG560.NH2-ASP534.OD1 24.71%, ARG560.NE-ASP534.OD2 23.75% E:GLU197-E:ARG22

ARG22.NH2-GLU197.OE2 24.71%, ARG22.NH2-GLU197.OE1 23.18%, ARG22.NH1-GLU197.OE2 21.07%, ARG22.NH1-GLU197.OE1 19.35%, ARG22.NE-GLU197.OE1 9.39%, ARG22.NE-GLU197.OE2 8.81%

E:GLU142-E:LYS139 LYS139.NZ-GLU142.OE2 22.61%, LYS139.NZ-GLU142.OE1 20.69% – E:GLU420-E:ARG427 ARG427.NH1-GLU420.OE2 19.54%, ARG427.NH1-GLU420.OE1 18.77%, ARG427.NE-GLU420.OE1 4.60% E:ASP369-E:LYS394

LYS394.NZ-ASP369.OD1 14.37%, LYS394.NZ-ASP369.OD2 10.92% -

E:ASP580-E:LYS584

LYS584.N-ASP580.O 13.60%, LYS584.NZ-ASP580.OD2 8.05%, LYS584.NZ-ASP580.OD1 7.28%

E:ASP450-E:LYS462

LYS462.NZ-ASP450.OD1 10.54%, LYS462.NZ-ASP450.OD2 9.39% -

E:ASP160-E:LYS218

LYS218.NZ-ASP160.OD2 10.34%, LYS218.NZ-ASP160.OD1 8.62% -

E:ASP458-E:LYS460

LYS460.NZ-ASP458.OD1 9.00%, LYS460.NZ-ASP458.OD2 8.62%

E:GLU540-E:LYS569 LYS569.NZ-GLU540.OE2 7.66%, LYS569.NZ-GLU540.OE1 6.70% F:ASP223-F:ARG186 ARG186.NH2-ASP223.OD1 90.80%, ARG186.NH2-ASP223.OD2 89.08%, ARG186.NE-ASP223.OD2 87.93%, ARG186.NE-ASP223.OD1 85.82%

(continued)

5.4 Concluding Remarks

235

Table 5.4 (continued) F:GLU156-F:HIS164

HID164.N-GLU156.O 74.14%, HID164.ND1-GLU156.OE1 18.77%, HID164.ND1-GLU156.OE2 13.98%

F:GLU143-F:LYS139

GLU143.N-LYS139.O 61.49%, LYS139.NZ-GLU143.OE2 18.20%, LYS139.NZ-GLU143.OE1 15.90%

F:GLU353-F:LYS347

LYS347.NZ-GLU353.OE1 54.98%, LYS347.NZ-GLU353.OE2 51.34%, GLU353.OE1-LYS347.NZ 9.20%

F:GLU418-F:LYS430

LYS430.NZ-GLU418.OE2 52.68%, LYS430.NZ-GLU418.OE1 50.77%

F:GLU143-F:LYS146

LYS146.NZ-GLU143.OE2 53.64%, LYS146.NZ-GLU143.OE1 52.87%

F:GLU168-F:LYS171

LYS171.NZ-GLU168.OE2 49.62%, LYS171.NZ-GLU168.OE1 45.79%, LYS171.N-GLU168.O 8.81%

F:ASP583-F:ARG579

ASP583.N-ARG579.O 47.70%, ARG579.NE-ASP583.OD1 35.82%, ARG579.NE-ASP583.OD2 34.48%, ARG579.NH2-ASP583.OD1 18.58%, ARG579.NH2-ASP583.OD2 18.39%, ARG579.NH1-ASP583.OD2 6.90%, ARG579.NH1-ASP583.OD1 4.60%

F:GLU136-F:ARG21

ARG21.NE-GLU136.OE1 40.42%, ARG21.NE-GLU136.OE2 38.12%, ARG21.NH2-GLU136.OE1 33.14%, ARG21.NH2-GLU136.OE2 32.95%, ARG21.NH1-GLU136.OE2 25.10%, ARG21.NH1-GLU136.OE1 22.99%, GLU136.OE2-ARG21.NE 11.49%

F:ASP315-F:ARG332

ARG332.NH2-ASP315.OD1 40.23%, ARG332.NH2-ASP315.OD2 38.51%, ARG332.NE-ASP315.OD2 22.03%, ARG332.NE-ASP315.OD1 18.97%, ARG332.NH1-ASP315.OD1 5.75%

F:ASP328-F:LYS347

LYS347.NZ-ASP328.OD1 30.84%, LYS347.NZ-ASP328.OD2 30.27%, LYS347.NZ-ASP328.O 16.67%

F:GLU128-F:LYS131

LYS131.NZ-GLU128.OE2 30.08%, LYS131.NZ-GLU128.OE1 29.12%

F:GLU244-F:LYS276

LYS276.N-GLU244.O 28.74%, LYS276.NZ-GLU244.OE1 23.75%, LYS276.NZ-GLU244.OE2 21.65%

F:ASP534-F:ARG560

ARG560.NH2-ASP534.OD2 27.39%, ARG560.NE-ASP534.OD1 26.25%, ARG560.NH2-ASP534.OD1 24.71%, ARG560.NE-ASP534.OD2 23.75%

F:GLU261-F:ARG442 ARG442.NH2-GLU261.OE1 23.95%, ARG442.NH1-GLU261.OE2 19.92%, ARG442.NH2-GLU261.OE2 18.20%, ARG442.NH1-GLU261.OE1 15.52% F:GLU142-F:LYS139

LYS139.NZ-GLU142.OE2 22.61%, LYS139.NZ-GLU142.OE1 20.69%

F:ASP542-F:LYS508

LYS508.N-ASP542.OD1 21.07%, LYS508.N-ASP542.OD2 19.54%, LYS508.NZ-ASP542.OD1 8.05%, LYS508.NZ-ASP542.OD2 5.36%

F:GLU420-F:ARG427 ARG427.NH1-GLU420.OE2 19.54%, ARG427.NH1-GLU420.OE1 18.77%, ARG427.NE-GLU420.OE1 4.60% F:ASP369-F:LYS394

LYS394.NZ-ASP369.OD1 14.37%, LYS394.NZ-ASP369.OD2 10.92%

F:ASP435-F:LYS271

LYS271.NZ-ASP435.O 13.03%, LYS271.NZ-ASP435.OD1 9.58%, LYS271.NZ-ASP435.OD2 8.43%

F:GLU142-F:LYS146

LYS146.N-GLU142.O 12.26%

F:ASP450-F:LYS462

LYS462.NZ-ASP450.OD1 10.54%, LYS462.NZ-ASP450.OD2 9.39%

F:ASP160-F:LYS218

LYS218.NZ-ASP160.OD2 10.34%, LYS218.NZ-ASP160.OD1 8.62%

F:GLU353-F:LYS329

LYS329.NZ-GLU353.OE1 7.85%, LYS329.NZ-GLU353.OE2 6.90%

F:GLU540-F:LYS569

LYS569.NZ-GLU540.OE2 7.66%, LYS569.NZ-GLU540.OE1 6.70%

F:ASP483-F:ARG490

ARG490.NH2-ASP483.OD1 7.09%, ARG490.NH2-ASP483.OD2 6.32%, ARG490.NE-ASP483.OD1 5.17%

F:ASP207-F:ARG173

ARG173.NH1-ASP207.OD2 6.90%, ARG173.NH1-ASP207.OD1 6.51%

F:GLU197-F:ARG339 ARG339.NH2-GLU197.OE1 6.90%, ARG339.NH1-GLU197.OE2 6.13%, ARG339.NH2-GLU197.OE2 4.98% F:GLU162-F:LYS524

LYS524.NZ-GLU162.OE1 5.94%, LYS524.NZ-GLU162.OE2 5.36%

A:ASP421-A:LYS417

ASP421.N-LYS417.O 60.15%, LYS417.NZ-ASP421.OD2 30.08%, LYS417.NZ-ASP421.OD1 22.80%

A:GLU658-A:ARG654 GLU658.N-ARG654.O 59.00%, ARG654.NH2-GLU658.OE2 27.59%, ARG654.NH2-GLU658.OE1 21.26% A:GLU665-A:LYS676 LYS676.N-GLU665.O 55.94%, LYS676.NZ-GLU665.OE2 42.91%, LYS676.NZ-GLU665.OE1 20.31% A:ASP390-A:ARG392 ARG392.NE-ASP390.OD2 52.49%, ARG392.NH2-ASP390.OD1 45.79%, ARG392.NE-ASP390.OD1 32.95%, ARG392.NH2-ASP390.OD2 30.08% A:ASP304-A:ARG640 ARG640.NE-ASP304.OD1 47.51%, ARG640.NE-ASP304.OD2 42.15%, ARG640.NH2-ASP304.OD2 40.23%, ARG640.NH2-ASP304.OD1 34.67% A:ASP358-A:ARG533 ARG533.NE-ASP358.OD2 44.06%, ARG533.NH2-ASP358.OD1 40.04%, ARG533.NE-ASP358.OD1 38.51%, ARG533.NH2-ASP358.OD2 36.59% A:GLU474-A:ARG640 ARG640.NH2-GLU474.OE2 42.72%, ARG640.NH1-GLU474.OE1 41.00%, ARG640.NH2-GLU474.OE1 39.27%, ARG640.NH1-GLU474.OE2 38.12% A:GLU58-A:ARG118

ARG118.NH2-GLU58.OE2 41.95%, ARG118.NH2-GLU58.OE1 39.85%, ARG118.NE-GLU58.OE2 39.27%, ARG118.NE-GLU58.OE1 39.08%

A:GLU277-A:LYS281 LYS281.N-GLU277.O 39.46% A:GLU658-A:ARG631 ARG631.NH2-GLU658.OE1 37.74%, ARG631.NH2-GLU658.OE2 30.65% A:ASP499-A:ARG513 ASP499.OD1-ARG513.NE 36.97%, ARG513.NE-ASP499.OD1 36.97%, ARG513.NE-ASP499.OD2 32.38%, ARG513.NH2-ASP499.OD2 31.42%, ARG513.NH2-ASP499.OD1 31.23% A:ASP845-A:LYS849

LYS849.NZ-ASP845.OD2 34.87%, YS849.NZ-ASP845.OD1 33.72%, ASP845.OD2-LYS849.NZ 11.49%

A:ASP100-A:ARG10

ARG10.NH1-ASP100.OD1 34.10%, ARG10.NH2-ASP100.OD2 31.23%, ARG10.NH1-ASP100.OD2 28.54%, ARG10.NH2-ASP100.OD1 26.05%

A:GLU796-A:LYS783 LYS783.NZ-GLU796.OE1 33.33%, LYS783.NZ-GLU796.OE2 28.35% A:GLU744-A:ARG726 ARG726.NH1-GLU744.OE1 32.95%, ARG726.NH1-GLU744.OE2 31.99%, ARG726.NH2-GLU744.OE2 30.65%, ARG726.NH2-GLU744.OE1 28.54% A:ASP29-A:ARG55

ARG55.NE-ASP29.OD1 31.61%, ARG55.NE-ASP29.OD2 29.50%, ARG55.NH2-ASP29.OD2 27.01%, ARG55.NH2-ASP29.OD1 25.48%

A:GLU894-A:LYS890 LYS890.NZ-GLU894.OE1 31.23%, LYS890.NZ-GLU894.OE2 26.05%, GLU894.N-LYS890.O 18.58%, GLU894.OE1-LYS890.NZ 12.07%

(continued)

236

5 RNA Helicase Binding with RdRp, NSP7, NSP8a, NSP8b, pRNA, tRNA,. . .

Table 5.4 (continued) A:ASP477-A:ARG640 ARG640.NH1-ASP477.OD2 27.78%, ARG640.NH1-ASP477.OD1 23.75% A:ASP865-A:LYS593

LYS593.NZ-ASP865.OD2 27.59%, LYS593.NZ-ASP865.OD1 26.63%, ASP865.OD2-LYS593.NZ 11.49%

A:GLU144-A:LYS121 LYS121.NZ-GLU144.OE1 27.39%, LYS121.NZ-GLU144.OE2 26.82% A:GLU350-A:ARG349 ARG349.NE-GLU350.OE1 27.39%, ARG349.NE-GLU350.OE2 26.25% A:GLU180-A:ARG183 ARG183.NE-GLU180.OE1 26.63%, ARG183.NH2-GLU180.OE2 26.25%, ARG183.NE-GLU180.OE2 18.58%, ARG183.NH2-GLU180.OE1 17.43% A:GLU922-A:LYS871 LYS871.NZ-GLU922.OE1 20.31%, LYS871.NZ-GLU922.OE2 17.43% A:GLU254-A:ARG285 ARG285.NH1-GLU254.OE2 18.01%, ARG285.NH2-GLU254.OE1 17.82%, ARG285.NH2-GLU254.OE2 17.24%, ARG285.NH1-GLU254.OE1 13.79%, ARG285.NE-GLU254.OE1 5.75% A:ASP260-A:LYS263

LYS263.N-ASP260.O 17.05%, LYS263.NZ-ASP260.OD1 12.64%, LYS263.NZ-ASP260.OD2 8.62%

A:ASP618-A:LYS798

ASP618.N-LYS798.O 17.05%, LYS798.NZ-ASP618.OD2 9.39%, LYS798.NZ-ASP618.OD1 6.70%

A:ASP454-A:ARG457 ARG457.NH2-ASP454.OD1 16.86%, ARG457.NH2-ASP454.OD2 14.75%, ARG457.NH1-ASP454.OD2 13.79%, ARG457.NH1-ASP454.OD1 12.07% A:ASP274-A:LYS272

LYS272.NZ-ASP274.OD1 15.90%, LYS272.NZ-ASP274.OD2 10.92%

A:ASP879-A:HIS882

HID882.ND1-ASP879.OD1 13.98%, HID882.ND1-ASP879.OD2 13.79%

A:ASP235-A:ARG467 ARG467.NH2-ASP235.OD1 13.41%, ARG467.NH2-ASP235.OD2 12.64%, ARG467.NH1-ASP235.OD2 11.30%, ARG467.NH1-ASP235.OD1 10.92% A:ASP135-A:LYS780

LYS780.NZ-ASP135.OD2 13.22%, LYS780.NZ-ASP135.OD1 11.30%

A:ASP170-A:ARG173 ARG173.NH2-ASP170.OD2 13.22%, ARG173.NH2-ASP170.OD1 11.69%, ARG173.NE-ASP170.OD1 7.66%, ARG173.NE-ASP170.OD2 5.56% A:ASP291-A:ARG735 ARG735.NH2-ASP291.OD1 12.84%, ARG735.NH2-ASP291.OD2 11.88%, ARG735.NH1-ASP291.OD2 5.56%, ARG735.NH1-ASP291.OD1 4.60% A:ASP481-A:LYS478

LYS478.NZ-ASP481.OD2 12.26%, LYS478.NZ-ASP481.OD1 11.88%

A:GLU278-A:LYS272 LYS272.NZ-GLU278.OE2 11.88%, LYS272.NZ-GLU278.OE1 9.39% A:ASP161-A:LYS160

LYS160.NZ-ASP161.OD1 11.69%, LYS160.NZ-ASP161.OD2 10.34%

A:GLU474-A:ARG305 ARG305.NE-GLU474.OE1 9.39%, ARG305.NE-GLU474.OE2 5.75%, ARG305.NH1-GLU474.OE2 4.98% A:ASP63-A:LYS59

LYS59.NZ-ASP63.OD2 9.20%, LYS59.NZ-ASP63.OD1 8.24%

A:ASP235-A:ARG735 ARG735.NH2-ASP235.OD2 8.81%, ARG735.NH2-ASP235.OD1 7.85% A:ASP452-A:ARG624 ARG624.NH1-ASP452.OD1 8.81%, ARG624.NH2-ASP452.OD2 7.09% A:ASP40-A:LYS41

LYS41.NZ-ASP40.OD2 8.62%, LYS41.NZ-ASP40.OD1 5.56%

A:ASP465-A:ARG132 ARG132.NH2-ASP465.OD2 8.24%, ARG132.NH2-ASP465.OD1 6.13% A:ASP194-A:LYS288

LYS288.NZ-ASP194.OD1 7.66%, LYS288.NZ-ASP194.OD2 5.17%

A:GLU136-A:LYS783 LYS783.NZ-GLU136.OE2 7.47%, LYS783.NZ-GLU136.OE1 5.56% A:ASP140-A:LYS143

LYS143.NZ-ASP140.OD1 6.90%, LYS143.NZ-ASP140.OD2 6.32%

Table 5.5 Within each chain, there are some stronger SBs (with stronger HBs) during the 500 .μs MD of the NSP12-NSP8-NSP7-NSP13-tpRNA model (continuation) A:ASP135-A:LYS783

LYS783.NZ-ASP135.OD1 6.70%, LYS783.NZ-ASP135.OD2 6.70%

A:ASP711-A:LYS714

LYS714.NZ-ASP711.OD1 6.70%, LYS714.NZ-ASP711.OD2 5.17%

A:ASP484-A:LYS574

LYS574.NZ-ASP484.OD1 5.17%

A:GLU610-A:LYS751

LYS751.NZ-GLU610.OE2 4.79%, LYS751.NZ-GLU610.OE1 4.60%

GLU155.N-LEU189.O 69.16%

TYR306.N-VAL356.O 68.97%

LEU25.N-LEU14.O 68.77%

TYR925.OH-ILE864.O 68.77%

GLU23.N-GLN19.O 68.58%

ASN37.N-VAL33.O 68.39%

TYR294.OH-ASN314.OD1 68.39%

TYR396.N-LYS276.O 67.82%

LEU500.N-VAL496.O 67.62%

TYR299.OH-TYR269.O 67.62%

LYS46.N-LEU42.O 67.62%

TYR185.N-TYR224.O 67.62%

THR199.N-ARG212.O 67.62%

ILE35.N-TYR31.O 67.43%

THR566.OG1-ASN562.O 67.43%

ASN43.N-LYS39.O 67.05%

ALA110.N-PHE106.O 66.86%

ILE333.N-PHE357.O 66.86%

PHE546.N-LEU573.O 66.67%

ALA123.N-ASP119.O 66.67%

LEU38.N-VAL34.O 66.48%

GLY400.N-LEU280.O 66.48%

VAL209.N-LEU163.O 66.09%

ALA512.N-LYS500.O 65.90%

ALA423.N-PHE419.O 65.52%

GLU142.N-LEU138.O 65.33%

GLY3.N-THR12.O 65.13%

LEU91.N-MET87.O 65.13%

SER385.OG-ALA237.O 64.75%

VAL193.N-ARG186.O 64.75%

ALA74.N-MET70.O 64.75%

MET576.N-MET474.O 64.18%

ILE334.N-ASN349.OD1 64.18%

LEU98.N-MET94.O 64.18%

GLY184.N-GLY196.O 63.98%

ASN423.ND2-ALA379.O 63.98%

LEU885.N-PHE881.O 63.79%

TYR246.OH-LYS394.O 63.41%

SER331.OG-LYS347.O 63.41%

ARG75.N-TYR71.O 63.41%

THR141.OG1-THR137.O 91.57%

ARG186.NH2-ASP223.OD1 90.80%

ARG186.NH2-ASP223.OD2 89.08%

LEU65.N-PHE81.O 88.31%

CYM5.N-SER10.O 87.93%

ARG186.NE-ASP223.OD2 87.93%

LEU43.N-ARG15.O 87.55%

THR12.OG1-LEU25.O 85.82%

ARG186.NE-ASP223.OD1 85.82%

CYS30.N-CYM26.O 85.06%

PHE373.N-VAL397.O 84.87%

ALA134.N-LEU130.O 84.87%

VAL397.N-VAL371.O 84.67%

ILE132.N-LEU184.O 84.10%

ARG497.N-ILE493.O 83.91%

THR307.N-VAL372.O 83.14%

ASP50.N-LYS46.O 82.95%

ILE185.N-VAL160.O 82.57%

VAL371.N-HID395.O 81.61%

LEU280.N-TYR398.O 81.42%

CYS426.N-ASN423.OD1 81.03%

LEU573.N-VAL544.O 80.08%

CYS574.N-PHE472.O 79.89%

VAL372.N-VAL305.O 79.89%

ASN51.N-TYR70.O 79.31%

PHE357.N-SER331.O 79.12%

TYR306.OH-ALA292.O 79.12%

PHE225.N-ALA152.O 78.93%

TYR64.N-TYR71.O 78.93%

LYS473.NZ-TYR582.O 78.93%

LEU325.N-ALA321.O 78.54%

ILE545.N-VAL510.O 78.35%

ILE156.N-THR145.O 78.35%

PHE511.N-PRO529.O 77.78%

LYS569.N-TYR541.O 77.78%

ASN104.N-ASN100.O 77.59%

TRP154.N-PHE147.O 77.59%

ILE512.N-ILE545.O 77.20%

ALA16.N-TYR12.O 76.82%

CYS142.N-TYR138.O 76.44%

PHE348.N-GLY352.O 57.47%

LEU184.N-ILE132.O 57.47%

GLN56.N-ASP52.O 57.47%

VAL44.N-LYS40.O 57.47%

TYR269.N-ASN265.O 57.47%

THR68.N-ASP64.O 57.66%

THR701.N-CYS697.O 57.66%

VAL700.N-ILE696.O 57.66%

LEU138.N-ALA134.O 57.85%

ARG390.N-VAL386.O 57.85%

THR111.OG1-ASN107.O 57.85%

LYS131.N-THR127.O 58.24%

TYR398.N-SER278.O 58.24%

TYR129.N-ALA125.O 58.43%

GLN470.N-VAL570.O 58.81%

PHE90.N-LEU83.O 58.81%

TYR87.N-GLU83.O 58.81%

GLU658.N-ARG654.O 59.00%

PHE70.N-PHE56.O 59.20%

VAL330.N-VAL115.O 59.39%

ALA14.N-PRO10.O 59.39%

VAL473.N-LEU469.O 59.58%

VAL210.N-GLU201.O 59.77%

GLN19.N-PHE15.O 59.77%

ASP315.N-HID311.O 59.96%

ARG443.NH1-THR566.O 59.96%

ILE493.N-ASN489.O 59.96%

ASP421.N-LYS417.O 60.15%

GLY222.N-VAL154.O 60.34%

LYS79.N-ARG75.O 60.34%

ALA86.N-LYS82.O 60.34%

LEU428.N-SER424.O 60.34%

THR183.N-VAL226.O 60.34%

VAL353.N-ASN297.OD1 60.34%

LEU103.N-ASN100.OD1 60.54%

TYR246.N-MET274.O 60.54%

GLU60.N-GLN56.O 60.54%

GLN281.N-MET436.O 60.54%

LYS430.NZ-GLU420.OE1 60.73%

MET62.N-LYS58.O 60.92%

MET633.N-MET629.O 52.49%

THR137.OG1-ASP134.OD1 52.49%

SER57.OG-SER54.O 52.49%

ILE572.N-GLN470.O 52.68%

SER263.N-SER259.O 52.68%

LYS430.NZ-GLU418.OE2 52.68%

SER523.N-ASN519.O 52.68%

CYS697.N-VAL693.O 52.68%

LYS146.NZ-GLU143.OE1 52.87%

VAL34.N-CYS30.O 52.87%

LEU329.N-GLY345.O 53.07%

THR89.N-SER85.O 53.26%

LYS40.N-LYS36.O 53.26%

THR431.N-ARG427.O 53.26%

TYR237.OH-GLN210.OE1 53.45%

ASN507.N-GLY503.O 53.45%

ASN705.N-THR701.O 53.45%

THR137.OG1-ASP134.OD2 53.45%

ARG303.N-ASP369.OD2 53.45%

ASP525.N-TYR521.O 53.64%

LEU389.N-MET129.O 53.64%

TYR277.N-GLN243.OE1 53.64%

LYS146.NZ-GLU143.OE2 53.64%

ILE304.N-GLN354.O 53.64%

MET196.N-PHE192.O 53.83%

ARG178.NE-GLU201.OE1 54.02%

LYS39.N-LEU35.O 54.21%

CYS464.N-ASN312.OD1 54.41%

VAL667.N-TYR674.O 54.41%

MET129.N-LEU387.O 54.41%

SER36.OG-ASP32.O 54.60%

ASN568.N-SER564.O 54.60%

MET668.N-THR540.O 54.60%

TYR421.N-GLU418.O 54.60%

VAL26.N-TYR22.O 54.79%

ASN356.N-THR344.O 54.79%

CYS765.N-SER754.O 54.79%

VAL424.N-TYR420.O 54.79%

LYS347.NZ-GLU353.OE1 54.98%

PHE92.N-GLN88.O 54.98%

Table 5.6 During the 500 .μs MD of the NSP12-NSP8-NSP7-NSP13-tpRNA model, the strong HBs with occupancy rates (.≥50%) are

(continued)

5.4 Concluding Remarks 237

ILE107.N-LEU103.O 62.64%

ASN28.N-GLN24.O 62.64%

MET87.N-VAL83.O 62.45%

THR187.N-GLN158.O 62.26%

TYR48.OH-VAL42.O 62.26%

SER331.N-TYR355.O 62.07%

ALA656.N-PHE652.O 62.07%

LEU83.N-LEU63.O 62.07%

VAL535.N-ASN356.OD1 61.88%

PHE291.N-GLY287.O 61.69%

LEU322.N-CYS318.O 61.69%

LEU891.N-TYR887.O 61.69%

LEU673.N-ALA399.O 61.69%

LYS72.N-THR68.O 61.69%

GLU143.N-LYS139.O 61.49%

ASN388.ND2-PRO238.O 61.30%

ILE888.N-TYR884.O 61.30%

VAL226.N-THR183.O 61.30%

GLY294.N-HID290.O 61.11%

CYS358.N-TYR306.O 74.90%

SER166.N-THR153.O 74.52%

ALA53.N-PHE49.O 74.33%

HID164.N-GLU156.O 74.14%

ILE399.N-PHE373.O 73.95%

LEU128.N-ALA188.O 73.37%

LEU95.N-LEU91.O 72.99%

ALA191.N-LEU153.O 72.99%

GLN157.N-THR187.O 72.80%

VAL305.N-ILE370.O 72.61%

ILE565.N-PHE561.O 72.61%

ASN108.N-ASN104.O 72.03%

CYS318.N-VAL314.O 72.03%

ASN562.N-VAL558.O 71.84%

ARG186.NH2-LYS218.O 71.84%

ASN349.N-ARG332.O 71.65%

VAL186.N-VAL130.O 70.69%

PHE472.N-ILE572.O 70.50%

TYR71.N-MET67.O 70.50%

THR153.N-SER166.O 60.92%

MET67.N-ALA63.O 62.64%

TYR120.OH-TRP114.O 75.10%

PHE182.N-TYR198.O 70.31%

HID113.N-PHE102.O 50.00%

LYS783.N-ILE779.O 62.84%

GLY66.N-SER69.O 75.29%

SER41.N-LYS37.O 61.11%

THR137.N-PHE133.O 62.84%

LYS139.N-TYR135.O 75.48%

VAL167.N-VAL159.O 60.92%

ARG560.N-CYS556.O 63.03%

ALA140.N-GLU136.O 75.48%

MET566.N-ILE562.O 70.50%

TYR476.N-MET576.O 63.03%

ALA321.N-LEU317.O 75.48%

VAL130.N-VAL186.O 70.31%

ASP358.N-ASN534.OD1 50.00%

GLN270.N-VAL266.O 63.22%

LEU59.N-MET55.O 76.05%

TYR355.N-LYS329.O 55.17%

GLN88.N-THR84.O 55.17%

GLN354.NE2-ALA302.O 55.17%

PHE745.N-PHE741.O 55.36%

THR9.OG1-ASP5.O 55.36%

VAL563.N-ASN559.O 55.56%

LYS676.N-GLU665.O 55.94%

LYS430.NZ-GLU420.OE2 55.94%

THR501.OG1-ARG497.O 56.13%

THR37.OG1-HID33.O 56.32%

TYR595.N-MET924.O 56.32%

SER115.N-ASP100.O 56.51%

ARG567.NE-SER539.O 56.51%

THR9.N-ASP5.O 56.51%

ARG507.NE-LEU500.O 56.51%

ASN416.N-CYS842.O 56.70%

TYR382.OH-MET233.O 56.70%

ARG186.N-VAL193.O 56.70%

VAL387.N-ASP383.O 56.70%

THR850.OG1-ILE847.O 56.90%

LYS36.N-GLU32.O 56.90%

PHE694.N-ALA690.O 56.90%

VAL72.N-CYS54.O 57.09%

HID395.N-ASP369.O 57.09%

LEU56.N-MET52.O 57.28%

VAL476.N-VAL472.O 50.00%

LYS545.N-ARG555.O 50.00%

THR359.OG1-ASN361.OD1 50.00%

SER47.N-ASN43.O 50.19%

ALA522.N-GLN518.O 50.57%

ILE579.N-LEU575.O 50.57%

GLN243.NE2-TYR277.O 50.57%

LYS430.NZ-GLU418.OE1 50.77%

VAL33.N-TRP29.O 50.77%

GLN492.N-ASN489.OD1 50.96%

ILE333.N-PHE340.O 50.96%

TYR374.N-GLU370.O 50.96%

MET124.N-GLN210.O 51.15%

VAL233.N-GLY203.O 51.15%

TYR71.N-TYR64.O 51.15%

ARG303.N-ASP369.OD1 51.34%

GLU498.N-GLY494.O 51.34%

LYS347.NZ-GLU353.OE2 51.34%

THR144.OG1-ALA140.O 51.72%

SER635.N-ARG631.O 51.72%

VAL160.N-ILE185.O 51.72%

ASN691.N-THR687.O 51.72%

CYS669.N-SER672.O 51.92%

TYR138.N-ASP134.O 52.11%

ALA21.N-THR17.O 52.11%

ALA575.N-PHE546.O 52.11%

ARG750.N-TYR746.O 52.30%

ARG392.NE-ASP390.OD2 52.49%

ILE575.N-PHE546.O 52.49%

SER278.N-TYR396.O 63.22%

ARG116.N-VAL71.O 52.49%

TYR198.N-PHE182.O 76.05%

ARG57.N-ALA53.O 57.28%

ILE109.N-ASP105.O 63.22%

MET429.N-VAL425.O 76.05%

LEU117.N-MET129.O 57.28%

ALA368.N-ARG392.O 63.41%

VAL154.N-ASP223.O 76.25%

Table 5.6 (continued)

238 5 RNA Helicase Binding with RdRp, NSP7, NSP8a, NSP8b, pRNA, tRNA,. . .

5.4 Concluding Remarks

239

Table 5.7 The following .α-helices’ HBs become weaker, leading to the unfolding of .α-helices A:ASP154

ASN158.N-ASP154.O 8.81%

A:ASP155

LYS159.N-ASP155.O 7.85%

A:TYR156

LYS143.NZ-TYR156.O 11.30%, TYR156.N-ASP153.O 5.36%

A:PHE157

PHE157.N-ASP153.O 8.24%

A:ASN158

ASN158.N-ASP154.O 8.81%

A:LEU241

ILE244.N-LEU241.O 14.37%, LEU245.N-LEU241.O 14.18%, LEU241.N-TYR237.O 5.56%

A:MET242

MET242.N-TYR238.O 27.39%, LEU245.N-MET242.O 6.70%, THR246.N-MET242.O 6.70%, THR246.OG1-MET242.O 4.98%

A:PRO243

LEU247.N-PRO243.O 19.54%, TYR788.OH-PRO243.O 8.62%

A:ILE244

THR248.OG1-ILE244.O 35.63%, THR248.N-ILE244.O 31.61%, ILE244.N-LEU241.O 14.37%

A:LEU245

LEU245.N-LEU241.O 14.18%, ALA250.N-LEU245.O 11.69%, LEU245.N-MET242.O 6.70%

A:THR246

MET463.N-THR246.OG1 42.34%, THR246.N-MET242.O 6.70%, ASN791.ND2-THR246.O 6.70%

A:LEU247

LEU247.N-PRO243.O 19.54%, ARG249.NH2-LEU247.O 7.47%

A:THR248

THR248.OG1-ILE244.O 35.63%, THR248.N-ILE244.O 31.61%

A:ASN447

SER451.N-ASN447.O 40.04%, GLN408.N-ASN447.OD1 23.56%, ASN447.ND2-ALA406.O 13.98%, ILE450.N-ASN447.O 7.66%, ALA449.N-ASN447.OD1 5.56%

A:ALA448

ALA448.N-GLN408.O 25.29%

A:ALA449

ALA449.N-ASN447.OD1 5.56%

A:ILE450

ARG392.NH1-ILE450.O 48.47%, ILE450.N-ASN447.O 7.66%

A:SER451

SER451.N-ASN447.O 40.04%

A:ASP452

ARG624.NH1-ASP452.OD1 8.81%, ARG624.NH2-ASP452.OD2 7.09%, THR556.N-ASP452.OD2 6.13%, THR556.OG1-ASP452.OD2 4.60%

A:TYR453

TYR453.N-ALA449.O 4.41%

A:ASP454

ARG457.NH2-ASP454.OD1 16.86%, ARG457.NH2-ASP454.OD2 14.75%, ARG457.NH1-ASP454.OD2 13.79%, THR556.N-ASP454.O 12.64%, ARG457.NH1-ASP454.OD1 12.07%, ARG553.NE-ASP454.OD2 12.07%, ARG553.NE-ASP454.OD1 11.88%, ARG553.NH2-ASP454.OD2 11.49%, ARG553.NH2-ASP454.OD1 11.49%

A:TYR455

SER681.OG-TYR455.O 23.75%

A:TYR456

ARG457.NH1-TYR456.O 10.34%

A:ARG457

ARG457.N-THR680.O 27.97%, ARG457.NE-CYS622.O 19.54%, ARG457.NH2-ASP454.OD1 16.86%, ARG457.NH2-ASP454.OD2 14.75%, ARG457.NH1-ASP454.OD2 13.79%, ARG457.NH1-ASP454.OD1 12.07%, ARG457.NH1-TYR456.O 10.34%, ARG457.NH1-ASP760.OD1 5.75%, ARG457.NH1-ASP760.OD2 5.36%, THR680.N-ARG457.O 4.98%, ARG457.NH2-ASP760.OD2 4.60%

A:TYR458

ALA625.N-TYR458.O 14.18%

A:ASN459

ASN459.N-GLY678.O 21.84%, ASN459.ND2-MET626.O 16.86%, ASN459.N-SER453.O 16.09%

A:GLY596

ASN600.N-GLY596.O 32.57%

A:GLY597

MET601.N-GLY597.O 11.49%, GLY597.N-PHE594.O 8.24%

A:TRP598

LEU602.N-TRP598.O 23.18%, TRP598.NE1-THR817.OG1 5.94%

A:HID599

LYS603.N-HID599.O 6.51%

A:ASN600

ASN600.N-GLY596.O 32.57%, LYS603.NZ-ASN600.OD1 9.96%, THR604.OG1-ASN600.O 7.09%, THR604.N-ASN600.O 5.17%, LYS603.N-ASN600.OD1 4.79%

A:MET601

THR604.OG1-MET601.O 15.33%, MET601.N-GLY597.O 11.49%, VAL605.N-MET601.O 9.77%, THR604.N-MET601.O 4.60%

A:LEU602

LEU602.N-TRP598.O 23.18%, TYR606.N-LEU602.O 22.41%

A:LYS603

LYS603.NZ-ASN600.OD1 9.96%, SER607.OG-LYS603.O 7.28%, LYS603.N-HID599.O 6.51%, LYS603.N-ASN600.OD1 4.79%

A:THR604

THR604.OG1-MET601.O 15.33%, ALA585.N-THR604.OG1 14.75%, SER754.OG-THR604.O 9.20%, THR604.OG1-ASN600.O 7.09%, THR604.N-ASN600.O 5.17%, THR604.N-MET601.O 4.60%

A:VAL605

VAL605.N-MET601.O 9.77%

A:TYR606

TYR606.N-LEU602.O 22.41%

A:SER607

SER607.OG-LYS603.O 7.28%, ARG750.NH1-SER607.O 5.17%

A:ASP608

LYS751.NZ-ASP608.O 9.39%

A:ASN767

ASN611.N-ASN767.OD1 23.95%, ASN767.N-HID752.O 15.90%, TYR770.N-ASN767.OD1 13.79%, ASN767.ND2-GLU610.O 9.39%, ALA771.N-ASN767.O 8.43%, ASN767.ND2-THR769.OG1 7.28%

A:SER768

SER768.N-ASN611.O 19.54%, SER772.N-SER768.O 16.67%, SER768.OG-ASN611.O 6.13%

A:THR769

GLN773.N-THR769.O 9.00%, ASN767.ND2-THR769.OG1 7.28%

A:TYR770

LEU775.N-TYR770.O 14.56%, TYR770.N-ASN767.OD1 13.79%

A:ALA771

ALA771.N-ASN767.O 8.43%

A:SER772

SER772.N-SER768.O 16.67%

A:GLN773

GLN773.N-THR769.O 9.00%

A:GLY774 A:LEU775

LEU775.N-TYR770.O 14.56%

A:VAL776

ASN713.N-VAL776.O 6.32%

A:ALA777

ALA777.N-ASN703.OD1 18.58%

A:SER778

SER778.N-ASN781.OD1 21.84%, PHE782.N-SER778.O 15.71%

B/D:LEU169 SER173.N-LEU169.O 22.22%, SER173.OG-LEU169.O 16.48% B/D:SER170 B/D:GLU171 SER177.OG-GLU171.O 16.28%, GLU171.N-GLN168.O 15.33%, ASN176.ND2-GLU171.O 10.15% B/D:ILE172 ILE172.N-GLN168.O 19.35%, TYR135.OH-ILE172.O 7.85% B/D:SER173 SER173.N-LEU169.O 22.22%, SER173.OG-LEU169.O 16.48%

(continued)

240

5 RNA Helicase Binding with RdRp, NSP7, NSP8a, NSP8b, pRNA, tRNA,. . .

Table 5.7 (continued) E:ALA446

ASP450.N-ALA446.O 30.65%

E:GLU447

THR451.OG1-GLU447.O 41.38%, LYS584.NZ-GLU447.OE2 19.35%, LYS584.NZ-GLU447.OE1 15.52%, THR451.N-GLU447.O 14.37%

E:ILE448

VAL452.N-ILE448.O 45.40%, ILE448.N-PRO445.O 8.24%

E:VAL449

SER453.N-VAL449.O 41.00%, VAL449.N-PRO445.O 23.56%, SER453.OG-VAL449.O 10.73%

E:ASP450

ASP450.N-ALA446.O 30.65%, ALA454.N-ASP450.O 23.95%, LYS462.NZ-ASP450.OD1 10.54%, LYS460.NZ-ASP450.OD2 9.77%, LYS462.NZ-ASP450.OD2 9.39%, LYS460.NZ-ASP450.OD1 9.20%

E:THR451

THR451.OG1-GLU447.O 41.38%, LEU455.N-THR451.O 36.21%, THR451.N-GLU447.O 14.37%

E:VAL452

VAL452.N-ILE448.O 45.40%, VAL456.N-VAL452.O 39.66%, TYR457.N-VAL452.O 12.45%, LEU455.N-VAL452.O 7.09%

E:SER453

SER453.N-VAL449.O 41.00%, ASN459.N-SER453.O 16.09%, SER453.OG-VAL449.O 10.73%, LEU461.N-SER453.OG 5.75%

E:ALA454

ALA454.N-ASP450.O 23.95%

E:LEU455

LEU455.N-THR451.O 36.21%, LEU455.N-VAL452.O 7.09%

E:VAL456

VAL456.N-VAL452.O 39.66%

F:ASN516

ALA520.N-ASN516.O 38.51%, ASN519.N-ASN516.OD1 17.24%

F:SER517

VAL521.N-SER517.O 15.52%, SER517.OG-SER485.O 7.47%

F:GLN518

ALA522.N-GLN518.O 50.57%, SER513.OG-GLN518.OE1 28.74%, THR547.OG1-GLN518.OE1 15.71%, GLN518.NE2-SER486.O 13.41%

F:ASN519

SER523.N-ASN519.O 52.68%, SER523.OG-ASN519.O 23.18%, ASN519.N-ASN516.OD1 17.24%, ASN519.N-TYR515.O 13.60%, ASN519.ND2-SER513.O 13.60%, ASN519.ND2-PRO514.O 13.03%, SER513.OG-ASN519.OD1 7.66%, ALA522.N-ASN519.OD1 6.70%, ASN519.ND2-GLN531.O 4.60%

F:ALA520

ALA520.N-ASN516.O 38.51%, LYS524.N-ALA520.O 28.54%

F:VAL521

ILE525.N-VAL521.O 35.44%, VAL521.N-SER517.O 15.52%, LEU526.N-VAL521.O 13.03%

F:ALA522

ALA522.N-GLN518.O 50.57%, LEU528.N-ALA522.O 35.82%, LEU526.N-ALA522.O 29.12%, ALA522.N-ASN519.OD1 6.70%

F:SER523

SER523.N-ASN519.O 52.68%, SER523.OG-ASN519.O 23.18%, LEU528.N-SER523.O 11.49%, THR530.N-SER523.OG 7.09%, SER523.OG-LEU528.O 4.98%

F:LYS524

LYS524.N-ALA520.O 28.54%, LYS524.NZ-GLN270.OE1 7.09%, LYS524.NZ-GLU162.OE1 5.94%, LYS524.NZ-LEU252.O 5.36%, LYS524.NZ-GLU162.OE2 5.36%

F:ILE525

ILE525.N-VAL521.O 35.44%, ARG497.NH2-ILE525.O 14.37%

F:LEU526

LEU526.N-ALA522.O 29.12%, LEU526.N-VAL521.O 13.03%

E/F:VAL533

GLN537.NE2-VAL533.O 7.09%

E/F:ASP534

GLN537.NE2-ASP534.O 8.24%, THR532.OG1-ASP534.OD1 6.51%, THR532.OG1-ASP534.OD2 6.13%, ARG560.NE-ASP534.OD2 23.75%, ARG560.NH2-ASP534.OD1 24.71%, ARG560.NE-ASP534.OD1 26.25%, ARG560.NH2-ASP534.OD2 27.39%

E/F:SER535

THR532.N-SER535.OG 35.63%, SER535.OG-GLN531.OE1 23.75%, SER535.N-THR532.OG1 21.26%, SER535.OG-THR532.OG1 6.70%

E/F:SER536

SER536.OG-THR532.O 45.02%, TYR541.OH-SER536.OG 30.46%, SER539.N-SER536.O 17.82%, SER536.N-THR532.O 14.18%

5.4 Concluding Remarks

241

Fig. 5.5 During the 500 .μs MD, there are nine stronger SBs (with stronger HBs) among the A-BC-D-E-F-chains

242

5 RNA Helicase Binding with RdRp, NSP7, NSP8a, NSP8b, pRNA, tRNA,. . .

Fig. 5.5 (continued)

Chapter 6

RNA Helicase Binding with ADP-Mg2+ , ATP-Mg2+ , and RNA .

.

Abstract This chapter studied the six models of model-NSP13-ATPMg.2+ RNA, model-NSP13-ADPMg.2+ -RNA, model-NSP13-ATPMg.2+ , model-NSP13ADPMg.2+ , model-NSP13.1-open-ADPMg.2+ , and model-NSP13.1-closeADPMg.2+ by using optimization and MD technologies. NSP13’s segments such as ASN51-GLY91, 151–221, 471–531, and 441/461/481/541/551–581 have larger root mean square fluctuations during MDs. NSP13’s residues 139, 142, 177, 179, 180, 230, 231, 311, 337, 361, 382, 383, 390, 408, 409, 410, 485, 486, 514, 515, 516, 532, 534, 535, and 554 bind RNA-6CCCAUGUG13 in the optimized model-NSP13ATPMg.2+ -RNA and model-NSP13-ADPMg.2+ -RNA. NSP13’s residues 283, 284, 285, 286, 287, 288, 289, 290, 375, 442, 443, and 540 bind ATP1003/ADP1003 and MG1004 in all the six optimized models. Rich MD-HBs and Opt-SBs are presented in this chapter. Keywords COVID-19 virus · RNA helicase (NSP13) · Binding with ADP-Mg.2+ , ATP-Mg.2+ , and RNA · Optimization and MD (molecular dynamics) studies · Basic structural bioinformatics

6.1 Introduction The SARS-CoV-2 nonstructural proteins (NSPs) coordinate genome 26 replication and gene expression. Structural analyses revealed the basis for coupling of the essential NSP13 helicase with the RNA-dependent RNA polymerase (RdRp), where the holo-RdRp and RNA substrate (the replication-transcription complex, or RTC) are associated with two copies of NSP13 (NSP13.2 -RTC). One copy of NSP13 interacts with the template RNA in an opposing polarity to the RdRp and is envisaged to drive the RdRp backward on the RNA template (backtracking [225]), prompting questions as to how the RdRp can efficiently synthesize RNA in the presence of NSP13. In [66] the authors use cryo-electron microscopy and MD simulations to analyze the NSP13.2 -RTC, revealing four distinct conformational states of the helicases, and their results suggest a mechanism for the NSP13.2 -RTC to © The Author(s), under exclusive license to Springer Nature Switzerland AG 2023 J. Zhang, Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures, Springer Series in Biophysics 23, https://doi.org/10.1007/978-3-031-36773-1_6

243

244

6 RNA Helicase Binding with .ADP-Mg2+ , .ATP-Mg2+ , and RNA

turn backtracking on and off, using an allosteric mechanism to switch between RNA synthesis and backtracking in response to stimuli at the RdRp active site [66]. In this chapter, we will study the NSP13 in complex with ADP-Mg.2+ , ATP-Mg.2+ , and RNA from optimization and MD point of view; some basic structural bioinformatics such as HBs, SBs, RMSF, etc. will be presented.

6.2 Materials and Methods Two sets of MD simulation trajectories of the SARS-CoV-2 helicase NSP13 were gotten from the openly online accessible website [321]. These trajectories are described in [66]. Set 1 contains 12 5 .μs simulation trajectories of NSP13 bound to various substrates starting from the ATPMg.2+ —and RNA-bound conformation; in trajectories [12970406, 12970408, 12970412] NSP13 was bound to ATPMg.2+ and RNA; in trajectories [12258863, 12258865, 12251869] NSP13 was bound to ADPMg.2+ and RNA; in trajectories [12258868, 12257092, 12259873] NSP13 was bound to ATPMg.2+ ; and in trajectories [12257049, 12251866, 12251868] NSP13 was bound to ADPMg.2+ . Set 2 contains ten 25 .μs simulation trajectories of NSP13 bound to ADPMg.2+ ; trajectories [12212701, 12212688, 12212691, 12212689, 12212693] started from the NSP13.1-open conformation and trajectories [12225252, 12225258, 12225255, 12225240, 12225249] started from the NSP13.1closed conformation. We optimized the structures of the six models (model-NSP13-ATPMg.2+ -RNA, model-NSP13-ADPMg.2+ -RNA, model-NSP13.1-open-ADPMg.2+ , model-NSP13ATPMg.2+ , model-NSP13-ADPMg.2+ , and model-NSP13.1-close-ADPMg.2+ ), and got some basic structural bioinformatics (such as HBs, SBs, PIs, and HYDs) about the optimized six models and then confirmed these basic bioinformatics by the MD simulation trajectories [12970406, 12970408, 12970412; 12258863, 12258865, 12251869; 12258868, 12257092, 12259873; 12257049, 12251866, 12251868; 12212701, 12212688, 12212691, 12212689, 12212693; 12225252, 12225258, 12225255, 12225240, 12225249] of [321].

6.3 New Results and Discussions We optimized the following six models (Fig. 6.1): model-NSP13-ATPMg.2+ -RNA, model-NSP13-ADPMg.2+ -RNA, model-NSP13.1-open-ADPMg.2+ , model-NSP13ATPMg.2+ , model-NSP13-ADPMg.2+ , and model-NSP13.1-close-ADPMg.2+ . The RMSD values between the optimized and unoptimized models are 2.735522 Å, 1.665655 Å, 7.605859 Å, respectively, for NSP13-ATPMg.2+ -RNA/NSP13ADPMg.2+ -RNA, NSP13-ATPMg.2+ /NSP13-ADPMg.2+ , open / close models. The optimized six models are shown in Fig. 6.1 and their residues’ numbers binding with ATP1003/ADP1003 and MG1004 are listed in Table 6.1 and shown in Fig. 6.2.

6.3 New Results and Discussions

245

Fig. 6.1 3D structures of the six optimized models of model-NSP13-ATPMg.2+ -RNA, modelNSP13-ADPMg.2+ -RNA, model-NSP13.1-open-ADPMg.2+ , model-NSP13-ATPMg.2+ , modelNSP13-ADPMg.2+ , and model-NSP13.1-close-ADPMg.2+

Fig. 6.2 The ligand ATP1003/ADP1003 and MG1004 interaction diagram of each optimized model

Figure 6.3 shows the Poisson-Boltzmann electrostatic potential surface (EPS) charges’ distributions of the optimized NSP13.1-open-ADPMg.2+ 5-1_12212701 model and the optimized NSP13.1-close-ADPMg.2+ 6-1_12225252 model, where we might see that the close model has more positive EPS than the open model. Table 6.2 lists all the SBs of the optimized models of NSP13-ATPMg.2+ -RNA, NSP13-ADPMg.2+ -RNA, NSP13-ATPMg.2+ , and NSP13-ADPMg.2+ , and Table 6.3 lists all the SBs of the optimized models of NSP13.1-open-ADPMg.2+ and NSP13.1close-ADPMg.2+ . Tables 6.4, 6.5, 6.6, 6.7, 6.8 and 6.9 present some stronger

246

6 RNA Helicase Binding with .ADP-Mg2+ , .ATP-Mg2+ , and RNA

Fig. 6.3 The Poisson-Boltzmann electrostatic potential surface charges’ distributions of the optimized NSP13.1-open-ADPMg.2+ 5-1_12212701 model and the optimized NSP13.1-closeADPMg.2+ 6-1_12225252 model

HBs during MDs’ rep1-rep3 of model-NSP13-ATPMg.2+ -RNA, model-NSP13ADPMg.2+ -RNA, model-NSP13-ATPMg.2+ , model-NSP13-ADPMg.2+ , and rep1rep5 of model-NSP13.1-open-ADPMg.2+ and model-NSP13.1-close-ADPMg.2+ ; Table 6.10 shows that the segment ASN51-GLY91 of NSP13 has large RMSF values during all the MDs. Figures 6.4 and 6.5 show the RNA-6CCCAUGUG13 binding with NSP13ATP-Mg.2+ in the optimized NSP13-ATPMg.2+ -RNA model and the RNA6CCCAUGUG13 binding with NSP13-ADP-Mg.2+ in the optimized NSP13ADPMg.2+ -RNA model, respectively. Table 6.11 lists NSP13’s residue binding with RNA-6CCCAUGUG13 of each optimized model.

6.4 Concluding Remarks This chapter studied the six models of model-NSP13-ATPMg.2+ -RNA, modelNSP13-ADPMg.2+ -RNA, model-NSP13-ATPMg.2+ , model-NSP13-ADPMg.2+ , model-NSP13.1-open-ADPMg.2+ , and model-NSP13.1-close-ADPMg.2+ by the use of optimization and MD technologies. NSP13’s segments such as ASN51GLY91, 151–221, 471–531, and 441/461/481/541/551–581 have larger root mean

6.4 Concluding Remarks

247

Fig. 6.4 RNA-6CCCAUGUG13 binding with NSP13-ATP-Mg.2+ in the optimized NSP13ATPMg.2+ -RNA model

Fig. 6.5 RNA-6CCCAUGUG13 binding with NSP13-ADP-Mg.2+ in the optimized NSP13ADPMg.2+ -RNA model

square fluctuations during MDs. NSP13’s residues 139, 142, 177, 179, 180, 230, 231, 311, 337, 361, 382, 383, 390, 408, 409, 410, 485, 486, 514, 515, 516, 532, 534, 535, and 554 bind RNA-6CCCAUGUG13 in the optimized model-NSP13ATPMg.2+ -RNA and model-NSP13-ADPMg.2+ -RNA. NSP13’s residues 283, 284, 285, 286, 287, 288, 289, 290, 375, 442, 443, and 540 bind ATP1003/ADP1003 and MG1004 in all the six optimized models. Rich MD-HBs and Opt-SBs are presented in this chapter.

NSP13.1-close-ADPMg.2+

NSP13.1-open-ADPMg.2+

NSP13-ADPMg.2+

NSP13-ATPMg.2+

NSP13-ADPMg.2+ -RNA

NSP13-ATPMg.2+ -RNA

261, 264, 283, 284, 265, 285, 286, 287, 288, 289, 290, 319, 320, 323, 324, 374, 375, 442, 443, 465, 538, 540, 567, 569, ADP1003, MG1004 261, 264, 265, 283, 284, 285, 286, 287, 288, 289, 290, 319, 320, 323, 324, 374, 375, 442, 443, 465, 538, 540, 567, 569, ADP1003, MG1004 261, 264, 265, 283, 284, 285, 286, 287, 288, 289, 290, 319, 320, 323, 324, 374, 375, 442, 443, 465, 538, 540, 567, 569, ADP1003, MG1004 261, 264, 265, 283, 284, 285, 286, 287, 288, 289, 290, 319, 320, 323, 324, 374, 375, 442, 443, 465, 538, 540, 567, 569, ADP1003, MG1004

6-4_12225240

6-5_12225249

261, 264, 265, 283, 284, 285, 286, 287, 288, 289, 290, 320, 374, 375, 442, 443, 540, MG1004

6-3_12225255

261, 264, 265, 283, 284, 285, 286, 287, 288, 289, 290, 320, 374, 375, 442, 443, 540, MG1004

5-5_12212693

261, 264, 265, 283, 284, 285, 286, 287, 288, 289, 290, 319, 320, 323, 324, 374, 375, 442, 443, 465, 538, 540, 567, 569, ADP1003, MG1004

261, 264, 265, 283, 284, 285, 286, 287, 288, 289, 290, 320, 374, 375, 442, 443, 540, MG1004

5-4_12212689

6-2_12225258

261, 264, 265, 283, 284, 285, 286, 287, 288, 289, 290, 320, 374, 375, 442, 443, 540, MG1004

5-3_12212691

6-1_12225252

261, 264, 265, 283, 284, 285, 286, 287, 288, 289, 290, 320, 374, 375, 442, 443, 540, MG1004

261, 262, 283, 284, 285, 286, 287, 288, 289, 290, 319, 320, 323, 324, 375, 440, 441, 442, 443, 465, 538, 540, 569, ADP1003, MG1004

5-2_12212688

261, 262, 283, 284, 285, 286, 287, 288, 289, 290, 319, 320, 323, 324, 375, 440, 441, 442, 443, 465, 538, 540, 569, ADP1003, MG1004

4-3_12251868

5-1_12212701

261, 262, 283, 284, 285, 286, 287, 288, 289, 290, 319, 320, 323, 324, 375, 440, 441, 442, 443, 465, 538, 540, 569, ADP1003, MG1004

261, 283, 284, 285, 286, 287, 288, 289, 290, 320, 323, 375, 440, 441, 442, 443, 465, 537, 538, 540, 567, 569, ATP1003, MG1004

4-2_12251866

261, 283, 284, 285, 286, 287, 288, 289, 290, 320, 323, 375, 440, 441, 442, 443, 465, 537, 538, 540, 567, 569, ATP1003, MG1004

3-3_12259873

4-1_12257049

261, 283, 284, 285, 286, 287, 288, 289, 290, 320, 323, 375, 440, 441, 442, 443, 465, 537, 538, 540, 567, 569, ATP1003, MG1004

261, 262, 283, 284, 285, 286, 287, 288, 289, 290, 375, 442, 443, 538, 540, ADP1003, MG1004

3-2_12257092

261, 262, 283, 284, 285, 286, 287, 288, 289, 290, 375, 442, 443, 538, 540, ADP1003, MG1004

2-3_12251869

3-1_12258868

261, 262, 283, 284, 285, 286, 287, 288, 289, 290, 375, 442, 443, 538, 540, ADP1003, MG1004

283, 284, 285, 286, 287, 288, 289, 290, 320, 323, 375, 404, 442, 443, 540, 567, 569, ATP1003, MG1004

1-3_12970412

2-2_12258865

283, 284, 285, 286, 287, 288, 289, 290, 320, 323, 375, 404, 442, 443, 540, 567, 569, ATP1003, MG1004

1-2_12970408

2-1_12258863

261, 283, 284, 285, 286, 287, 288, 289, 290, 320, 324, 375, 442, 443, 540, ATP1003, MG1004

1-1_12970406

Table 6.1 The NSP13’s residues binding with ATP1003/ADP1003, MG1004 of each optimized model

248 6 RNA Helicase Binding with .ADP-Mg2+ , .ATP-Mg2+ , and RNA

6.4 Concluding Remarks

249

Table 6.2 The SBs of the optimized models of NSP13-ATPMg.2+ -RNA, NSP13-ADPMg.2+ RNA, NSP13-ATPMg.2+ , and NSP13-ADPMg.2+ 1_NSP13-ATPMg2+-RNA

1_NSP13-ATPMg2+-RNA

2_NSP13-ADPMg2+-RNA

3_NSP13-ATPMg2+

4_NSP13-ADPMg2+

seed1

seed2-seed3

seed1-seed3

seed1-seed3

seed1-seed3

ASP204-ARG490

ASP204-ARG490

ASP204-ARG490

ASP113-LYS414

ASP113-LYS414

ASP207-ARG155

ASP207-ARG173

ASP315-ARG332

ASP204-ARG490

ASP160-LYS218

ASP315-ARG332

ASP315-ARG332

ASP458-LYS460

ASP204-LYS524

ASP204-ARG490

ASP344-LYS345

ASP369-ARG303

ASP483-LYS202

ASP207-ARG173

ASP315-ARG332

ASP369-LYS394

ASP383-ARG409

ASP534-ARG560

ASP315-ARG332

ASP344-LYS345

ASP483-ARG173

ASP435-LYS271

ASP542-LYS569

ASP344-LYS345

ASP369-LYS394

GLU136-ARG21

ASP534-ARG560

GLU128-LYS131

ASP369-LYS394

ASP383-LYS139

GLU142-ARG409

ASP542-LYS569

GLU136-ARG21

ASP435-LYS271

ASP435-LYS271

GLU143-LYS146

ASP580-ARG579

GLU142-LYS139

ASP450-LYS467

ASP534-ARG560

GLU168-LYS171

GLU136-ARG21

GLU143-LYS139

ASP458-LYS460

ASP542-LYS569

GLU201-ARG178

GLU143-LYS146

GLU143-LYS146

ASP483-LYS202

ASP580-LYS584

GLU261-ARG442

GLU201-ARG178

GLU197-ARG337

ASP542-LYS569

ASP583-ARG579

GLU353-LYS347

GLU244-LYS276

GLU319-LYS320

ASP580-LYS584

GLU128-LYS131

GLU365-ARG392

GLU353-LYS347

GLU353-LYS347

ASP583-ARG579

GLU136-ARG21

GLU540-LYS569

GLU418-LYS430

GLU375-LYS288

ASP583-LYS584

GLU143-HIS230

GLU420-ARG427

GLU447-LYS467

GLU128-LYS131

GLU143-LYS146

GLU420-LYS430

GLU498-ARG502

GLU136-ARG21

GLU156-HIS164

GLU498-ARG502

GLU540-ARG443

GLU143-HIS230

GLU168-LYS171

GLU540-ARG443

GLU540-LYS320

GLU143-LYS139

GLU197-ARG337

GLU551-LYS477

GLU143-LYS146

GLU201-ARG212

GLU168-LYS171

GLU201-LYS524

GLU197-ARG337

GLU244-LYS276

GLU201-ARG212

GLU261-LYS323

GLU244-LYS276

GLU319-LYS320

GLU261-LYS323

GLU353-LYS347

GLU353-LYS347

GLU365-ARG392

GLU365-ARG390

GLU375-LYS288

GLU498-ARG497

GLU420-LYS430

GLU540-ARG443

GLU498-ARG502

GLU540-LYS320

GLU540-ARG443

GLU551-LYS477

GLU540-LYS320 GLU540-LYS569 GLU551-LYS477

250 Table 6.3 The SBs of the optimized models of NSP13.1-open-ADPMg.2+ and NSP13.1-close-ADPMg.2+

6 RNA Helicase Binding with .ADP-Mg2+ , .ATP-Mg2+ , and RNA NSP13.1-open-ADPMg.2+

NSP13.1-close-ADPMg.2+

seed1-seed5

seed1-seed5

ASP113-LYS414

ASP113-LYS414

ASP160-LYS218

ASP204-ARG490

ASP207-ARG173

ASP207-ARG173

ASP315-ARG332

ASP223-ARG186

ASP328-LYS329

ASP315-ARG332

ASP328-LYS347

ASP369-LYS394

ASP32-LYS28

ASP450-LYS467

ASP344-ARG339

ASP458-LYS460

ASP369-LYS394

ASP483-ARG173

ASP450-LYS462

ASP534-ARG560

ASP483-ARG490

ASP542-LYS569

ASP534-ARG560

ASP56-HIS75

ASP542-LYS508

ASP580-LYS584

ASP542-LYS569

ASP583-ARG579

ASP583-ARG579

ASP59-LYS40

GLU128-LYS131

GLU128-ARG427

GLU136-ARG21

GLU128-LYS131

GLU142-ARG409

GLU136-ARG21

GLU142-LYS139

GLU142-LYS139

GLU143-LYS139

GLU143-LYS139

GLU143-LYS146

GLU143-LYS146

GLU156-ARG155

GLU156-HIS164

GLU156-HIS164

GLU168-LYS171

GLU162-ARG161

GLU197-ARG337

GLU168-LYS171

GLU197-ARG339

GLU197-ARG22

GLU201-ARG212

GLU201-ARG178

GLU244-LYS276

GLU201-ARG212

GLU261-LYS323

GLU244-LYS276

GLU319-LYS569

GLU319-LYS569

GLU341-ARG178

GLU341-HIS311

GLU353-LYS347

GLU353-LYS329

GLU365-ARG390

GLU353-LYS347

GLU420-LYS430

GLU365-ARG390

GLU498-ARG497

GLU375-LYS288

GLU540-ARG443

GLU420-LYS430

GLU540-LYS320

GLU447-LYS467

GLU551-LYS477

GLU498-ARG502 GLU540-ARG443 GLU540-LYS320

6.4 Concluding Remarks

251

Table 6.4 Stronger HBs during MDs’ rep1-rep3 of model-NSP13-ATPMg.2+ -RNA 1_NSP13-ATPMg2+-RNA 1-1_12970406

1-2_12970408

1-3_12970412

THR12.OG1-LEU25.O 78.10%

SER289.OG-ASP374.OD2 78.10%

SER513.OG-ASN519.OD1 75.24%

SER289.OG-ASP374.OD2 68.57%

SER513.OG-ASN519.OD1 64.76%

THR12.OG1-LEU25.O 74.29%

TYR120.OH-TRP114.O 66.67%

ASN489.N-GLN518.OE1 61.90%

THR286.OG1-PRO283.O 62.86%

THR141.OG1-THR137.O 65.71%

TYR306.N-VAL356.O 61.90%

SER289.OG-ASP374.OD1 62.86%

TYR185.N-TYR224.O 61.90%

THR451.OG1-GLU447.O 60.95%

THR451.OG1-GLU447.O 62.86%

TYR306.OH-ALA292.O 60.00%

THR141.OG1-THR137.O 60.00%

SER229.OG-GLU143.O 61.90%

LEU65.N-PHE81.O 60.00%

THR380.OG1-ASP383.OD2 59.05%

THR141.OG1-THR137.O 59.05%

CYM5.N-SER10.O 60.00%

CYS441.N-LYS462.O 58.10%

TYR306.N-VAL356.O 59.05%

THR451.OG1-GLU447.O 58.10%

TYR306.OH-ALA292.O 57.14%

PHE546.N-LEU573.O 58.10%

THR144.OG1-ALA140.O 57.14%

SER80.OG-PRO77.O 57.14%

CYS441.N-LYS462.O 57.14%

SER331.OG-SER350.O 56.19%

PHE472.N-ILE572.O 56.19%

PHE373.N-VAL397.O 57.14%

THR111.OG1-ASN107.O 55.24%

TYR185.N-TYR224.O 55.24%

SER453.OG-VAL449.O 56.19%

SER513.OG-ASN519.OD1 55.24%

THR111.OG1-ASN107.O 55.24%

TYR64.N-TYR71.O 55.24%

SER536.OG-THR532.O 54.29%

LEU43.N-ARG15.O 54.29%

SER331.OG-SER350.O 54.29%

ARG443.NH1-THR566.O 54.29%

SER453.OG-VAL449.O 53.33%

ILE195.N-GLY184.O 54.29%

TYR306.N-VAL356.O 54.29%

LEU325.N-ALA321.O 53.33%

LEU25.N-LEU14.O 54.29%

THR125.OG1-ILE121.O 53.33%

THR12.OG1-LEU25.O 52.38%

TYR306.OH-ALA292.O 53.33%

PHE472.N-ILE572.O 53.33%

TYR198.N-PHE182.O 52.38%

VAL452.N-ILE448.O 52.38%

ASN388.ND2-PRO238.O 52.38%

TYR299.OH-TYR269.O 52.38%

ARG409.NH1-PRO408.O 52.38%

SER555.OG-THR552.OG1 50.48%

TYR120.OH-TRP114.O 51.43%

PHE511.N-PRO529.O 52.38%

ASP374.N-THR307.O 49.52%

PHE357.N-SER331.O 51.43%

GLY150.N-PRO172.O 52.38%

TYR515.OH-THR550.OG1 49.52%

THR286.OG1-PRO283.O 50.48%

TYR185.N-TYR224.O 52.38%

TYR198.N-PHE182.O 48.57%

SER385.OG-ALA237.O 50.48%

ASN489.N-GLN518.OE1 51.43%

SER80.OG-PRO77.O 47.62%

ILE488.N-THR481.O 49.52%

PHE357.N-SER331.O 50.48%

VAL372.N-VAL305.O 47.62%

MET429.N-VAL425.O 49.52%

ILE333.N-PHE357.O 50.48%

GLY184.N-GLY196.O 47.62%

PHE511.N-PRO529.O 49.52%

TYR198.OH-TYR217.O 50.48%

TYR71.N-TYR64.O 46.67%

ARG409.NH1-PRO408.O 47.62%

LEU43.N-ARG15.O 50.48%

PHE546.N-LEU573.O 46.67%

LEU65.N-PHE81.O 47.62%

THR144.OG1-ALA140.O 50.48%

SER385.OG-ALA237.O 45.71%

TYR64.N-TYR71.O 47.62%

THR111.OG1-ASN107.O 50.48%

ILE545.N-VAL510.O 45.71%

LEU25.N-LEU14.O 47.62%

ASN388.ND2-PRO238.O 49.52%

SER577.OG-TYR476.O 45.71%

ASN388.ND2-PRO238.O 47.62%

LEU65.N-PHE81.O 49.52%

THR550.OG1-SER555.OG 44.76%

VAL452.N-ILE448.O 46.67%

THR12.N-GLY3.O 48.57%

TYR246.N-MET274.O 44.76%

LEU165.N-ASP207.O 46.67%

PHE182.N-TYR198.O 48.57%

PHE182.N-TYR198.O 44.76%

PHE373.N-VAL397.O 46.67%

SER385.OG-ALA237.O 48.57%

ILE333.N-PHE357.O 44.76%

CYM5.N-SER10.O 45.71%

MET429.N-VAL425.O 47.62%

LEU325.N-ALA321.O 44.76%

PHE546.N-LEU573.O 45.71%

TYR198.N-PHE182.O 47.62%

TYR64.N-TYR71.O 43.81%

VAL209.N-LEU163.O 45.71%

GLY184.N-GLY196.O 47.62%

PHE357.N-SER331.O 43.81%

GLN518.NE2-ASN489.O 44.76%

VAL154.N-ASP223.O 47.62%

SER577.N-GLN548.OE1 43.81%

LEU500.N-VAL496.O 42.86%

THR413.N-THR115.O 46.67%

PHE511.N-PRO529.O 43.81%

THR481.N-ILE488.O 42.86%

TYR120.OH-TRP114.O 46.67%

SER453.OG-VAL449.O 42.86%

THR144.OG1-ALA140.O 42.86%

VAL372.N-VAL305.O 45.71%

ALA368.N-ARG392.O 42.86%

SER331.OG-SER350.O 42.86%

CYM5.N-SER10.O 45.71%

ASN381.ND2-ASN124.OD1 42.86%

ALA186.N-VAL193.O 42.86%

ASP374.N-THR307.O 45.71%

ARG560.NH1-ASP534.OD1 42.86%

ALA110.N-PHE106.O 42.86%

VAL210.N-GLU201.O 44.76%

ARG155.N-HID164.O 40.95%

ILE333.N-PHE357.O 41.90%

PHE472.N-ILE572.O 44.76%

VAL210.N-GLU201.O 40.95%

ILE195.N-GLY184.O 41.90%

TYR48.OH-PHE90.O 44.76%

ALA575.N-PHE546.O 40.95%

ILE334.N-ASN349.OD1 40.95%

GLN548.N-ALA575.O 44.76%

VAL193.N-ALA186.O 40.95%

HID164.N-GLU156.O 40.95%

CYS358.N-TYR306.O 42.86%

GLN243.NE2-TYR277.O 40.95%

PHE182.N-TYR198.O 40.95%

THR228.OG1-VAL181.O 42.86%

LEU83.N-LEU63.O 40.00%

ILE525.N-VAL521.O 40.95%

VAL232.N-ILE20.O 41.90%

THR37.OG1-HID33.O 40.00%

SER536.OG-THR532.O 40.00%

ALA186.N-VAL193.O 41.90%

ALA134.N-LEU130.O 40.00%

TYR476.N-MET576.O 40.00%

LEU280.N-TYR398.O 40.95%

LEU43.N-ARG15.O 40.00%

SER377.OG-ASP401.O 40.00%

VAL209.N-LEU163.O 40.95%

MET429.N-VAL425.O 39.05%

VAL210.N-GLU201.O 40.00%

ARG155.N-HID164.O 40.95%

VAL226.N-THR183.O 39.05%

GLY184.N-GLY196.O 40.00%

MET576.N-MET474.O 40.95%

ASN562.N-VAL558.O 39.05%

ASN489.ND2-LYS477.O 40.00%

TYR457.OH-ASP401.OD1 40.00%

TYR299.OH-TYR269.O 39.05%

TYR246.N-MET274.O 39.05%

THR125.OG1-ILE121.O 40.00%

LEU391.N-VAL387.O 39.05%

ARG303.N-ASP369.OD2 39.05%

ASN489.ND2-LYS477.O 40.00%

ASN349.N-ARG332.O 39.05%

VAL154.N-ASP223.O 39.05%

LEU163.N-VAL209.O 40.00%

GLN492.NE2-GLN548.O 38.10%

VAL372.N-VAL305.O 39.05%

CYS30.N-CYM26.O 40.00%

THR286.OG1-PRO283.O 38.10%

TYR149.OH-PHE145.O 39.05%

SER80.OG-PRO77.O 40.00%

SER166.N-THR153.O 37.14%

THR307.N-VAL372.O 39.05%

TYR541.N-ARG567.O 40.00%

PHE373.N-VAL397.O 37.14%

ASP374.N-THR307.O 38.10%

GLN492.NE2-GLN548.O 39.05%

(continued)

252

6 RNA Helicase Binding with .ADP-Mg2+ , .ATP-Mg2+ , and RNA

Table 6.4 (continued) 1_NSP13-ATPMg2+-RNA 1-1_12970406

1-2_12970408

1-3_12970412

ILE109.N-ASP105.O 37.14%

GLY150.N-PRO172.O 38.10%

TYR541.OH-GLN531.OE1 39.05%

THR199.N-ARG212.O 37.14%

THR431.OG1-ARG427.O 37.14%

LEU325.N-ALA321.O 39.05%

LEU138.N-ALA134.O 37.14%

ILE304.N-GLN354.O 37.14%

THR566.OG1-ASN562.O 39.05%

THR115.OG1-ASP113.OD2 37.14%

GLN548.N-ALA575.O 37.14%

SER377.OG-ASP401.O 38.10%

ILE195.N-GLY184.O 36.19%

THR501.OG1-ARG497.O 37.14%

GLN275.NE2-SER278.OG 38.10%

VAL154.N-ASP223.O 36.19%

LEU590.N-ALA473.O 36.19%

PHE90.N-LEU83.O 38.10%

THR566.OG1-ASN562.O 35.24%

ARG560.NH2-ASP534.OD2 36.19%

HID164.N-GLU156.O 38.10%

CYS441.N-LYS462.O 35.24%

TYR71.N-TYR64.O 36.19%

ILE304.N-GLN354.O 38.10%

Table 6.5 Stronger HBs during MDs’ rep1-rep3 of model-NSP13-ADPMg.2+ -RNA 2_NSP13-ADPMg2+-RNA 2-1_12258863

2-2_12258865

2-3_12251869

THR12.OG1-LEU25.O 70.48%

THR12.OG1-LEU25.O 68.57%

THR12.OG1-LEU25.O 79.05%

THR451.OG1-GLU447.O 65.71%

THR451.OG1-GLU447.O 65.71%

ASN489.N-GLN518.OE1 63.81%

THR566.OG1-ASN562.O 64.76%

TYR306.N-VAL356.O 62.86%

THR451.OG1-GLU447.O 63.81%

ASN489.N-GLN518.OE1 62.86%

TYR185.N-TYR224.O 61.90%

THR566.OG1-ASN562.O 62.86%

THR141.OG1-THR137.O 62.86%

SER513.OG-ASN519.OD1 60.95%

TYR541.OH-GLN531.OE1 61.90%

THR37.OG1-HID33.O 61.90%

THR141.OG1-THR137.O 60.00%

TYR306.OH-ALA292.O 61.90%

TYR185.N-TYR224.O 58.10%

TYR306.OH-ALA292.O 60.00%

SER513.OG-ASN519.OD1 60.00%

SER513.OG-ASN519.OD1 58.10%

THR125.OG1-ILE121.O 58.10%

TYR306.N-VAL356.O 59.05%

PHE182.N-TYR198.O 57.14%

TYR64.N-TYR71.O 56.19%

THR141.OG1-THR137.O 58.10%

TYR306.N-VAL356.O 56.19%

TYR120.OH-TRP114.O 53.33%

TYR185.N-TYR224.O 58.10%

ASN388.ND2-PRO238.O 54.29%

THR566.OG1-ASN562.O 51.43%

THR125.OG1-ILE121.O 57.14%

SER80.OG-PRO77.O 53.33%

PHE472.N-ILE572.O 51.43%

CYM5.N-SER10.O 57.14%

ILE545.N-VAL510.O 53.33%

SER331.OG-SER350.O 51.43%

ARG560.NH2-ASP534.OD2 56.19%

THR286.OG1-PRO283.O 53.33%

ASN388.ND2-PRO238.O 51.43%

ASP374.N-THR307.O 56.19%

CYM5.N-SER10.O 52.38%

VAL210.N-GLU201.O 50.48%

SER331.OG-SER350.O 54.29%

TYR306.OH-ALA292.O 52.38%

PHE373.N-VAL397.O 50.48%

ARG560.NH1-ASP534.OD1 54.29%

PHE357.N-SER331.O 51.43%

VAL154.N-ASP223.O 50.48%

ASN381.ND2-ASN124.OD1 54.29%

TYR299.OH-TYR269.O 51.43%

CYM5.N-SER10.O 49.52%

SER536.OG-VAL533.O 53.33%

TYR120.OH-TRP114.O 51.43%

SER453.OG-VAL449.O 48.57%

THR286.OG1-PRO283.O 52.38%

TYR48.OH-VAL42.O 51.43%

ASN489.N-GLN518.OE1 48.57%

TYR120.OH-TRP114.O 51.43%

ILE195.N-GLY184.O 50.48%

GLY184.N-GLY196.O 47.62%

MET576.N-MET474.O 49.52%

GLY66.N-SER69.O 50.48%

ASP374.N-THR307.O 47.62%

PHE357.N-SER331.O 49.52%

SER377.OG-ASP401.O 49.52%

LEU65.N-PHE81.O 47.62%

GLN492.NE2-TYR476.O 48.57%

TYR198.N-PHE182.O 49.52%

HID164.N-GLU156.O 47.62%

GLY184.N-GLY196.O 48.57%

SER385.OG-ALA237.O 49.52%

PHE511.N-PRO529.O 46.67%

PHE472.N-ILE572.O 48.57%

SER453.OG-VAL449.O 49.52%

SER536.OG-VAL533.O 46.67%

TYR198.N-PHE182.O 48.57%

THR144.OG1-ALA140.O 47.62%

TYR299.OH-TYR269.O 46.67%

LEU65.N-PHE81.O 47.62%

ILE333.N-PHE357.O 47.62%

PHE546.N-LEU573.O 45.71%

VAL210.N-GLU201.O 47.62%

SER331.OG-SER350.O 47.62%

SER577.OG-TYR476.O 45.71%

TYR299.OH-TYR269.O 47.62%

LEU65.N-PHE81.O 47.62%

ILE545.N-VAL510.O 44.76%

TYR457.OH-ASP401.OD1 47.62%

VAL452.N-ILE448.O 46.67%

TYR541.N-ARG567.O 44.76%

MET429.N-VAL425.O 47.62%

CYS441.N-LYS462.O 46.67%

CYS441.N-LYS462.O 44.76%

TYR541.N-ARG567.O 46.67%

CYS30.N-CYM26.O 45.71%

TYR457.OH-ASP401.OD1 44.76%

SER453.OG-VAL449.O 45.71%

PHE511.N-PRO529.O 45.71%

THR137.OG1-PHE133.O 43.81%

THR37.OG1-HID33.O 45.71%

VAL372.N-VAL305.O 45.71%

GLN243.NE2-TYR277.O 43.81%

CYS358.N-TYR306.O 45.71%

LEU43.N-ARG15.O 44.76%

TYR71.N-TYR64.O 43.81%

PHE546.N-LEU573.O 45.71%

PHE90.N-LEU83.O 44.76%

MET429.N-VAL425.O 43.81%

CYS441.N-LYS462.O 44.76%

SER166.N-THR153.O 44.76%

SER148.OG-THR144.O 43.81%

THR431.OG1-ARG427.O 43.81%

THR12.N-GLY3.O 44.76%

ASN562.N-VAL558.O 42.86%

SER80.OG-PRO77.O 43.81%

PHE546.N-LEU573.O 43.81%

ILE195.N-GLY184.O 42.86%

LEU138.N-ALA134.O 42.86%

THR125.OG1-ILE121.O 43.81%

VAL372.N-VAL305.O 42.86%

ILE333.N-PHE357.O 42.86%

LEU138.N-ALA134.O 43.81%

TYR198.N-PHE182.O 42.86%

GLN243.NE2-TYR277.O 42.86%

LEU280.N-TYR398.O 43.81%

SER80.OG-PRO77.O 41.90%

HID164.N-GLU156.O 42.86%

GLN243.NE2-TYR277.O 43.81%

GLY3.N-THR12.O 41.90%

ASN388.ND2-PRO238.O 42.86%

LEU25.N-LEU14.O 43.81%

ILE512.N-ILE545.O 41.90%

TYR71.N-TYR64.O 41.90%

ASN349.N-ARG332.O 43.81%

THR431.OG1-ARG427.O 40.95%

VAL372.N-VAL305.O 41.90%

TYR64.N-TYR71.O 43.81%

THR12.N-GLY3.O 40.95%

LEU500.N-VAL496.O 40.95%

THR307.N-VAL372.O 43.81%

ALA186.N-VAL193.O 40.95%

THR144.OG1-ALA140.O 40.95%

TYR457.OH-ASP401.OD2 43.81%

CYS30.N-CYM26.O 40.00%

LEU43.N-ARG15.O 40.95%

(continued)

6.4 Concluding Remarks

253

Table 6.5 (continued) 2_NSP13-ADPMg2+-RNA 2-1_12258863

2-2_12258865

2-3_12251869

ALA186.N-VAL193.O 43.81%

ILE334.N-ASN349.OD1 40.00%

ALA575.N-PHE546.O 40.95%

LEU590.N-ALA473.O 42.86%

TYR457.OH-ASP401.OD2 40.00%

ALA186.N-VAL193.O 40.95%

GLY184.N-GLY196.O 42.86%

THR549.OG1-ALA487.O 40.00%

THR61.OG1-ASP59.OD2 40.95%

ASP374.N-THR307.O 42.86%

LEU43.N-ARG15.O 39.05%

LEU325.N-ALA321.O 40.95%

ILE304.N-GLN354.O 42.86%

GLY150.N-PRO172.O 39.05%

THR137.OG1-PHE133.O 40.95%

HID164.N-GLU156.O 42.86%

PHE182.N-TYR198.O 39.05%

PHE511.N-PRO529.O 40.00%

PHE472.N-ILE572.O 42.86%

SER577.N-GLN548.OE1 39.05%

VAL452.N-ILE448.O 40.00%

VAL154.N-ASP223.O 42.86%

ASN349.N-ARG332.O 38.10%

ALA368.N-ARG392.O 40.00%

TYR476.N-MET576.O 42.86%

CYS426.N-ASN423.OD1 37.14%

PHE182.N-TYR198.O 39.05%

TYR70.OH-GLY91.O 42.86%

ARG303.N-ASP369.OD1 37.14%

ILE334.N-ASN349.OD1 39.05%

THR137.OG1-PHE133.O 41.90%

ALA368.N-ARG392.O 37.14%

CYS30.N-CYM26.O 39.05%

LEU325.N-ALA321.O 41.90%

VAL193.N-ALA186.O 37.14%

THR12.N-GLY3.O 39.05%

TYR382.OH-MET233.O 41.90%

SER377.OG-LEU405.O 37.14%

GLN548.NE2-SER555.O 39.05%

THR153.N-SER166.O 41.90%

TYR246.N-MET274.O 37.14%

THR307.N-VAL372.O 39.05%

THR199.N-ARG212.O 41.90%

LEU590.N-ALA473.O 36.19%

LYS131.N-THR127.O 39.05%

ALA368.N-ARG392.O 41.90%

LEU325.N-ALA321.O 36.19%

GLY3.N-THR12.O 39.05%

ALA575.N-PHE546.O 40.95%

TYR541.OH-GLN531.OE1 36.19%

ILE512.N-ILE545.O 38.10%

VAL209.N-LEU163.O 40.95%

THR286.OG1-PRO283.O 36.19%

SER424.OG-ASN381.OD1 38.10%

THR61.OG1-ASP59.OD2 40.95%

THR307.OG1-CYS358.O 36.19%

LEU384.N-THR380.O 38.10%

THR111.OG1-ASN107.O 40.95%

ASN423.ND2-ALA379.O 35.24%

ARG155.N-HID164.O 38.10%

TYR71.N-TYR64.O 40.00%

ASP450.N-ALA446.O 35.24%

SER166.N-THR153.O 37.14%

ILE512.N-ILE545.O 40.00%

PHE357.N-SER331.O 35.24%

TYR64.N-TYR71.O 37.14%

Table 6.6 Stronger HBs during MDs’ rep1-rep3 of model-NSP13-ATPMg.2+ 3_NSP13-ATPMg2+ 3-1_12258868

3-2_12257092

3-3_12259873

THR12.OG1-LEU25.O 72.38%

THR12.OG1-LEU25.O 70.48%

THR12.OG1-LEU25.O 76.19%

SER513.OG-ASN519.OD1 70.48%

THR451.OG1-GLU447.O 68.57%

THR451.OG1-GLU447.O 71.43%

THR451.OG1-GLU447.O 64.76%

ASN489.N-GLN518.OE1 66.67%

ASN489.N-GLN518.OE1 69.52%

TYR306.N-VAL356.O 63.81%

TYR306.OH-ALA292.O 65.71%

SER513.OG-ASN519.OD1 66.67%

THR141.OG1-THR137.O 61.90%

THR125.OG1-ILE121.O 65.71%

TYR306.OH-ALA292.O 64.76%

SER331.OG-SER350.O 61.90%

TYR299.OH-TYR269.O 63.81%

TYR306.N-VAL356.O 62.86%

ASN489.N-GLN518.OE1 61.90%

SER513.OG-ASN519.OD1 60.95%

MET576.N-MET474.O 61.90%

TYR120.OH-TRP114.O 60.95%

THR141.OG1-THR137.O 60.95%

THR111.OG1-ASN107.O 60.95%

PHE472.N-ILE572.O 59.05%

SER331.OG-SER350.O 60.95%

GLN492.NE2-TYR476.O 60.95%

THR125.OG1-ILE121.O 58.10%

THR144.OG1-ALA140.O 58.10%

THR286.OG1-PRO283.O 59.05%

THR144.OG1-ALA140.O 58.10%

TYR306.N-VAL356.O 56.19%

ASP315.N-HID311.O 58.10%

TYR185.N-TYR224.O 57.14%

VAL154.N-ASP223.O 56.19%

VAL210.N-GLU201.O 57.14%

THR137.OG1-PHE133.O 56.19%

THR286.OG1-PRO283.O 55.24%

SER331.OG-SER350.O 57.14%

THR566.OG1-ASN562.O 55.24%

CYM5.N-SER10.O 55.24%

SER385.OG-ASN381.O 57.14%

TYR306.OH-ALA292.O 55.24%

TYR120.OH-TRP114.O 54.29%

THR37.OG1-ASP32.O 57.14%

THR286.OG1-PRO283.O 52.38%

TYR185.N-TYR224.O 54.29%

PHE511.N-PRO529.O 55.24%

VAL154.N-ASP223.O 52.38%

GLN492.NE2-TYR476.O 53.33%

GLY184.N-GLY196.O 55.24%

SER80.OG-PRO77.O 51.43%

THR431.OG1-ARG427.O 53.33%

TYR198.N-PHE182.O 54.29%

THR111.OG1-ASN107.O 50.48%

ILE333.N-PHE357.O 53.33%

TYR185.N-TYR224.O 53.33%

ASP374.N-THR307.O 50.48%

PHE511.N-PRO529.O 52.38%

THR566.OG1-ASN562.O 52.38%

TYR299.OH-TYR269.O 50.48%

ASN381.ND2-ASN124.OD1 52.38%

THR144.OG1-ALA140.O 52.38%

GLY184.N-GLY196.O 49.52%

ALA575.N-PHE546.O 52.38%

LEU43.N-ARG15.O 52.38%

ASN388.ND2-PRO238.O 49.52%

PHE472.N-ILE572.O 51.43%

PHE472.N-ILE572.O 51.43%

HID164.N-GLU156.O 47.62%

ALA134.N-LEU130.O 51.43%

PHE357.N-SER331.O 51.43%

TYR541.N-ARG567.O 46.67%

THR566.OG1-ASN562.O 50.48%

GLN243.NE2-TYR277.O 51.43%

GLN492.NE2-TYR476.O 46.67%

LEU43.N-ARG15.O 50.48%

PHE373.N-VAL397.O 50.48%

TYR64.N-TYR71.O 46.67%

SER80.OG-PRO77.O 49.52%

MET429.N-VAL425.O 48.57%

PHE511.N-PRO529.O 46.67%

THR111.OG1-ASN107.O 49.52%

HID164.N-GLU156.O 48.57%

THR183.N-VAL226.O 45.71%

ASN388.ND2-PRO238.O 49.52%

VAL154.N-ASP223.O 47.62%

THR431.OG1-ARG427.O 45.71%

GLY184.N-GLY196.O 49.52%

ASP374.N-THR307.O 47.62%

PHE357.N-SER331.O 45.71%

TYR198.N-PHE182.O 48.57%

THR481.N-ILE488.O 47.62%

SER453.OG-VAL449.O 45.71%

LEU325.N-ALA321.O 48.57%

TYR541.N-ARG567.O 47.62%

(continued)

254

6 RNA Helicase Binding with .ADP-Mg2+ , .ATP-Mg2+ , and RNA

Table 6.6 (continued) 3_NSP13-ATPMg2+ 3-1_12258868

3-2_12257092

3-3_12259873

TYR198.N-PHE182.O 44.76%

GLN243.NE2-TYR277.O 47.62%

THR125.OG1-ILE121.O 47.62%

TYR71.N-TYR64.O 44.76%

PHE546.N-LEU573.O 47.62%

LEU25.N-LEU14.O 46.67%

PHE546.N-LEU573.O 44.76%

SER453.OG-VAL449.O 46.67%

ASN388.ND2-PRO238.O 45.71%

GLU142.N-LEU138.O 43.81%

SER385.OG-ALA237.O 46.67%

CYS441.N-LYS462.O 45.71%

TYR543.OH-GLN470.OE1 43.81%

TYR71.N-TYR64.O 46.67%

THR137.OG1-PHE133.O 44.76%

ALA134.N-LEU130.O 43.81%

CYS441.N-LYS462.O 46.67%

SER80.OG-PRO77.O 44.76%

LEU325.N-ALA321.O 43.81%

HID164.N-GLU156.O 45.71%

THR431.OG1-ARG427.O 43.81%

LEU25.N-LEU14.O 43.81%

GLY150.N-PRO172.O 44.76%

TYR64.N-TYR71.O 43.81%

ARG332.N-LYS347.O 42.86%

ASN423.ND2-ALA379.O 44.76%

LEU325.N-ALA321.O 43.81%

ARG303.N-ASP369.OD1 42.86%

SER166.N-THR153.O 44.76%

TYR299.OH-TYR269.O 42.86%

ALA368.N-ARG392.O 42.86%

LEU65.N-PHE81.O 44.76%

VAL452.N-ILE448.O 42.86%

MET576.N-MET474.O 42.86%

MET576.N-MET474.O 44.76%

ILE195.N-GLY184.O 41.90%

ALA575.N-PHE546.O 42.86%

ILE545.N-VAL510.O 43.81%

VAL372.N-VAL305.O 41.90%

CYS441.N-LYS462.O 41.90%

THR199.N-ARG212.O 43.81%

LEU65.N-PHE81.O 41.90%

SER289.OG-ASP374.OD1 41.90%

ALA186.N-VAL193.O 43.81%

THR12.N-GLY3.O 41.90%

LEU65.N-PHE81.O 41.90%

TYR198.OH-TYR217.O 43.81%

TYR71.N-TYR64.O 41.90%

ALA186.N-VAL193.O 41.90%

THR137.OG1-PHE133.O 43.81%

THR153.N-SER166.O 41.90%

MET429.N-VAL425.O 41.90%

VAL210.N-GLU201.O 42.86%

SER453.OG-VAL449.O 40.95%

CYS426.N-ASN423.OD1 40.95%

PHE373.N-VAL397.O 42.86%

ILE376.N-ILE399.O 40.95%

GLN354.NE2-ALA302.O 40.95%

SER289.OG-ASP374.OD2 42.86%

ALA368.N-ARG392.O 40.95%

VAL210.N-GLU201.O 40.95%

ILE376.N-ILE399.O 41.90%

THR380.OG1-ASP383.OD1 40.95%

SER166.N-THR153.O 40.00%

ILE195.N-GLY184.O 40.95%

THR141.OG1-THR137.O 40.00%

GLN243.NE2-TYR277.O 40.00%

MET429.N-VAL425.O 40.95%

ILE333.N-PHE357.O 40.00%

ILE304.N-GLN354.O 40.00%

LEU138.N-ALA134.O 40.95%

ARG303.N-ASP369.OD2 40.00%

CYM5.N-SER10.O 40.00%

PHE357.N-SER331.O 40.95%

GLN354.NE2-ALA302.O 40.00%

ILE195.N-GLY184.O 40.00%

GLU143.N-LYS139.O 40.95%

TYR543.OH-GLN470.OE1 40.00%

LEU43.N-ARG15.O 39.05%

ASP374.N-THR307.O 40.95%

ALA575.N-PHE546.O 39.05%

THR380.OG1-ASP383.OD1 39.05%

TYR48.OH-VAL42.O 40.00%

CYM5.N-SER10.O 39.05%

ASN489.ND2-LYS477.O 39.05%

CYS30.N-CYM26.O 40.00%

ASN489.ND2-THR549.O 39.05%

TYR211.N-ALA161.O 39.05%

TYR64.N-TYR71.O 40.00%

PHE546.N-LEU573.O 39.05%

GLU201.N-VAL210.O 38.10%

ILE488.N-THR481.O 39.05%

GLY150.N-PRO172.O 39.05%

THR37.OG1-HID33.O 37.14%

ARG303.N-ASP369.OD1 39.05%

ILE304.N-GLN354.O 38.10%

SER385.OG-ALA237.O 37.14%

THR153.N-SER166.O 38.10%

ILE525.N-VAL521.O 37.14%

VAL372.N-VAL305.O 37.14%

ILE304.N-GLN354.O 38.10%

TYR211.N-ALA161.O 37.14%

THR199.N-ARG212.O 37.14%

TYR543.OH-GLN470.OE1 38.10%

SER536.OG-THR532.O 37.14%

SER555.OG-THR550.OG1 36.19%

ILE334.N-ASN349.OD1 37.14%

VAL209.N-LEU163.O 37.14%

ASN381.ND2-ASN124.OD1 36.19%

TYR246.N-MET274.O 37.14%

PHE182.N-TYR198.O 37.14%

ILE512.N-ILE545.O 36.19%

THR501.OG1-ARG497.O 37.14%

VAL193.N-ALA186.O 37.14%

GLY150.N-PRO172.O 36.19%

PHE90.N-LEU83.O 37.14%

TYR382.OH-MET233.O 37.14%

Table 6.7 Stronger HBs during MDs’ rep1-rep3 of model-NSP13-ADPMg.2+ 4_NSP13-ADPMg2+ 4-1_12257049

4-2_12251866

4-3_12251868

ASN489.N-GLN518.OE1 71.43%

THR12.OG1-LEU25.O 80.00%

THR141.OG1-THR137.O 67.62%

THR12.OG1-LEU25.O 68.57%

SER331.OG-SER350.O 66.67%

THR451.OG1-GLU447.O 66.67%

TYR306.N-VAL356.O 66.67%

THR451.OG1-GLU447.O 62.86%

THR12.OG1-LEU25.O 66.67%

THR141.OG1-THR137.O 65.71%

TYR306.OH-ALA292.O 62.86%

SER513.OG-ASN519.OD1 65.71%

THR451.OG1-GLU447.O 61.90%

THR141.OG1-THR137.O 59.05%

ASN489.N-GLN518.OE1 59.05%

SER513.OG-ASN519.OD1 59.05%

THR125.OG1-ILE121.O 59.05%

TYR120.OH-TRP114.O 58.10%

TYR48.OH-PHE90.O 57.14%

ALA407.N-LEU417.O 59.05%

VAL154.N-ASP223.O 58.10%

TYR541.OH-GLN531.OE1 57.14%

TYR306.N-VAL356.O 57.14%

THR566.OG1-ASN562.O 57.14%

(continued)

6.4 Concluding Remarks

255

Table 6.7 (continued) 4_NSP13-ADPMg2+ 4-1_12257049

4-2_12251866

4-3_12251868

SER331.OG-SER350.O 55.24%

SER536.OG-THR532.O 56.19%

THR125.OG1-ILE121.O 56.19%

TYR185.N-TYR224.O 54.29%

VAL210.N-GLU201.O 54.29%

THR144.OG1-ALA140.O 55.24%

PHE472.N-ILE572.O 54.29%

THR111.OG1-ASN107.O 54.29%

GLY184.N-GLY196.O 55.24%

TYR457.OH-ASP401.OD2 54.29%

TYR185.N-TYR224.O 53.33%

TYR185.N-TYR224.O 54.29%

TYR120.OH-TRP114.O 53.33%

CYS30.N-CYM26.O 52.38%

TYR198.N-PHE182.O 54.29%

THR566.OG1-ASN562.O 52.38%

THR566.OG1-ASN562.O 51.43%

TYR306.N-VAL356.O 54.29%

TYR306.OH-ALA292.O 52.38%

ASN388.ND2-PRO238.O 50.48%

TYR306.OH-ALA292.O 53.33%

LEU65.N-PHE81.O 52.38%

GLY150.N-PRO172.O 49.52%

ASN388.ND2-PRO238.O 53.33%

THR144.OG1-ALA140.O 50.48%

GLY184.N-GLY196.O 49.52%

THR286.OG1-PRO283.O 53.33%

GLN492.NE2-TYR476.O 50.48%

THR144.OG1-ALA140.O 46.67%

ALA575.N-PHE546.O 51.43%

ASN388.ND2-PRO238.O 49.52%

LEU138.N-ALA134.O 46.67%

CYM5.N-SER10.O 51.43%

LEU325.N-ALA321.O 49.52%

PHE357.N-SER331.O 46.67%

SER331.OG-SER350.O 51.43%

SER536.OG-VAL533.O 49.52%

PHE472.N-ILE572.O 46.67%

ASN381.ND2-ASN124.OD1 51.43%

VAL154.N-ASP223.O 48.57%

ILE545.N-VAL510.O 45.71%

ASP374.N-THR307.O 50.48%

THR125.OG1-ILE121.O 48.57%

SER453.OG-VAL449.O 45.71%

TYR299.OH-TYR269.O 50.48%

HID164.N-GLU156.O 47.62%

ILE512.N-ILE545.O 44.76%

THR199.N-ARG212.O 50.48%

PHE357.N-SER331.O 47.62%

ARG560.N-ASN557.OD1 44.76%

LEU43.N-ARG15.O 48.57%

LEU43.N-ARG15.O 47.62%

MET429.N-VAL425.O 44.76%

VAL210.N-GLU201.O 46.67%

TYR64.N-TYR71.O 47.62%

LYS131.N-THR127.O 43.81%

THR111.OG1-ASN107.O 46.67%

SER289.OG-ASP374.OD1 46.67%

TYR64.N-TYR71.O 43.81%

GLN548.N-ALA575.O 45.71%

PHE511.N-PRO529.O 46.67%

THR12.N-GLY3.O 43.81%

PHE511.N-PRO529.O 45.71%

TYR299.OH-TYR269.O 46.67%

PHE511.N-PRO529.O 42.86%

LEU65.N-PHE81.O 45.71%

PHE373.N-VAL397.O 45.71%

VAL154.N-ASP223.O 42.86%

HID164.N-GLU156.O 45.71%

VAL372.N-VAL305.O 45.71%

TYR198.N-PHE182.O 42.86%

ILE195.N-GLY184.O 45.71%

PHE546.N-LEU573.O 44.76%

TYR541.N-ARG567.O 42.86%

PHE373.N-VAL397.O 45.71%

CYS441.N-LYS462.O 44.76%

ASN381.ND2-ASN124.OD1 42.86%

PHE472.N-ILE572.O 43.81%

TYR198.N-PHE182.O 44.76%

PHE373.N-VAL397.O 42.86%

MET429.N-VAL425.O 43.81%

ILE333.N-PHE357.O 44.76%

LEU163.N-VAL209.O 41.90%

ILE333.N-PHE357.O 43.81%

TYR246.N-MET274.O 43.81%

ARG303.N-ASP369.OD2 41.90%

ILE304.N-GLN354.O 43.81%

ASN423.ND2-ALA379.O 43.81%

TYR48.OH-VAL42.O 41.90%

SER453.OG-VAL449.O 43.81%

THR111.OG1-ASN107.O 43.81%

THR183.N-VAL226.O 40.95%

PHE546.N-LEU573.O 42.86%

CYM5.N-SER10.O 43.81%

CYS441.N-LYS462.O 40.95%

GLY150.N-PRO172.O 42.86%

LEU25.N-LEU14.O 43.81%

ARG332.N-LYS347.O 40.95%

THR431.OG1-ARG427.O 42.86%

GLN281.NE2-ASP401.OD1 42.86%

THR137.OG1-PHE133.O 40.00%

VAL372.N-VAL305.O 42.86%

THR481.N-ILE488.O 41.90%

HID164.N-GLU156.O 40.00%

TYR198.OH-TYR217.O 42.86%

ARG443.NH1-THR566.O 41.90%

TYR120.OH-TRP114.O 40.00%

ASP315.N-HID311.O 42.86%

GLY66.N-SER69.O 41.90%

LEU43.N-ARG15.O 39.05%

ALA368.N-ARG392.O 42.86%

MET576.N-MET474.O 40.95%

PHE90.N-LEU83.O 39.05%

SER577.N-GLN548.OE1 41.90%

ASN489.ND2-THR549.O 40.95%

LEU65.N-PHE81.O 39.05%

PHE357.N-SER331.O 41.90%

SER555.OG-THR550.OG1 40.95%

ALA186.N-VAL193.O 39.05%

ARG443.NH1-THR566.O 41.90%

MET429.N-VAL425.O 40.95%

CYM5.N-SER10.O 39.05%

GLN243.NE2-TYR277.O 41.90%

SER453.OG-VAL449.O 40.95%

ASP315.N-HID311.O 39.05%

LEU280.N-TYR398.O 41.90%

THR153.N-SER166.O 40.95%

SER385.OG-ALA237.O 38.10%

ILE334.N-ASN349.OD1 41.90%

THR199.N-ARG212.O 40.00%

ILE195.N-GLY184.O 38.10%

TYR211.N-ALA161.O 40.95%

VAL193.N-ALA186.O 40.00%

ALA134.N-LEU130.O 38.10%

MET576.N-MET474.O 40.95%

ALA186.N-VAL193.O 40.00%

SER80.OG-PRO77.O 38.10%

THR137.OG1-PHE133.O 40.95%

ILE304.N-GLN354.O 40.00%

SER229.OG-GLU143.O 38.10%

TYR476.N-MET576.O 40.95%

GLN243.NE2-TYR277.O 40.00%

ALA368.N-ARG392.O 38.10%

ALA134.N-LEU130.O 40.95%

TYR543.OH-GLN470.OE1 40.00%

THR431.OG1-ARG427.O 38.10%

ASN562.ND2-ALA403.O 40.95%

VAL209.N-LEU163.O 40.00%

VAL209.N-LEU163.O 38.10%

GLN354.NE2-ALA302.O 40.00%

ILE512.N-ILE545.O 39.05%

ASP374.N-THR307.O 37.14%

TYR246.N-MET274.O 40.00%

TYR541.N-ARG567.O 39.05%

LEU325.N-ALA321.O 37.14%

CYS441.N-LYS462.O 39.05%

PHE225.N-ALA152.O 39.05%

MET576.N-MET474.O 37.14%

THR12.N-GLY3.O 39.05%

ARG332.N-LYS347.O 39.05%

THR501.OG1-ARG497.O 37.14%

TYR71.N-TYR64.O 39.05%

CYS30.N-CYM26.O 39.05%

THR153.N-SER166.O 37.14%

ARG332.N-LYS347.O 39.05%

THR286.OG1-PRO283.O 39.05%

TYR71.N-TYR64.O 37.14%

SER166.N-THR153.O 38.10%

LEU280.N-TYR398.O 39.05%

VAL226.N-THR183.O 36.19%

LEU138.N-ALA134.O 38.10%

GLY184.N-GLY196.O 39.05%

TYR211.N-ALA161.O 36.19%

TYR541.N-ARG567.O 38.10%

ASN489.ND2-LYS477.O 38.10%

ILE333.N-PHE357.O 36.19%

ASN489.ND2-THR549.O 37.14%

THR183.N-VAL226.O 38.10%

LEU590.N-ALA473.O 36.19%

THR380.OG1-ASP383.OD1 37.14%

ILE334.N-ASN349.OD1 38.10%

GLY66.N-SER69.O 36.19%

ILE545.N-VAL510.O 36.19%

ALA140.N-GLU136.O 38.10%

TYR70.OH-GLY91.O 36.19%

THR61.OG1-ASP59.OD2 36.19%

ALA368.N-ARG392.O 38.10%

THR547.OG1-ALA487.O 36.19%

LEU165.N-ASP207.O 36.19%

MET576.N-MET474.O 66.99 ILE545.N-VAL510.O 63.64

ALA134.N-LEU130.O 63.64 ILE545.N-VAL510.O 61.72

ARG186.NE-ASP223.OD1 85.17

ALA134.N-LEU130.O 72.25

ARG186.NE-ASP223.OD1 87.08

ALA134.N-LEU130.O 70.33

GLN548.N-ILE575.O 58.85

THR307.N-VAL372.O 55.98

VAL452.N-ILE448.O 54.55

MET429.N-VAL425.O 54.55 PHE357.N-SER331.O 54.07

LEU500.N-VAL496.O 55.02

ILE512.N-ILE545.O 54.55

ILE109.N-ASP105.O 53.59

ALA321.N-LEU317.O 53.59

TYR306.OH-ALA292.O 56.46

LYS473.NZ-TYR582.O 53.11 LEU500.N-VAL496.O 53.11

ALA321.N-LEU317.O 51.20 LEU325.N-ALA321.O 51.20

CYM5.N-SER10.O 53.59

ARG497.N-ILE493.O 53.11

LYS473.NZ-TYR582.O 53.11

LEU500.N-VAL496.O 53.11

PHE511.N-PRO529.O 49.76 ARG186.NH2-LYS218.O 49.76

GLN492.NE2-GLN548.O 52.15

TYR306.OH-ALA292.O 52.15

ASN489.N-GLN518.OE1 52.15

PHE546.N-LEU573.O 51.67

LEU455.N-THR451.O 50.72 LEU325.N-ALA321.O 50.72 ASN349.N-ARG332.O 50.72

VAL154.N-ASP223.O 48.33 LYS473.NZ-TYR582.O 48.33 ASN388.ND2-PRO238.O 47.85

GLU142.N-LEU138.O 50.72

SER523.N-ASN519.O 50.72

PHE357.N-SER331.O 50.24

ASP32.N-LYS28.O 51.20

ALA123.N-ASP119.O 50.24

GLN492.NE2-GLN548.O 49.28

LEU325.N-ALA321.O 50.24

GLN548.N-ILE575.O 50.24

PHE546.N-LEU573.O 50.72

LEU573.N-VAL544.O 48.80

ARG186.NH2-LYS218.O 51.20

LEU138.N-ALA134.O 50.72

ALA140.N-GLU136.O 51.20

SER166.N-THR153.O 52.15 TYR185.N-TYR224.O 51.20

LEU280.N-TYR398.O 51.20

ARG567.NE-SER539.O 49.28

GLN548.N-ILE575.O 52.15

ASN489.N-GLN518.OE1 51.67

VAL452.N-ILE448.O 51.67

LEU573.N-VAL544.O 52.15

ASP450.N-ALA446.O 52.63

THR12.OG1-LEU25.O 52.63

MET429.N-VAL425.O 53.59

MET429.N-VAL425.O 51.20

CYS358.N-TYR306.O 49.76

SER523.N-ASN519.O 50.72

PHE182.N-TYR198.O 52.63

MET429.N-VAL425.O 52.15

PHE472.N-ILE572.O 52.63

VAL154.N-ASP223.O 52.15

LEU280.N-TYR398.O 51.20

ASN489.N-GLN518.OE1 54.07

HID164.N-GLU156.O 54.55

TYR198.N-PHE182.O 52.63 LEU500.N-VAL496.O 52.15 MET576.N-MET474.O 51.67

TYR120.OH-TRP114.O 54.55

LEU325.N-ALA321.O 54.07

PHE225.N-ALA152.O 53.59

VAL154.N-ASP223.O 55.98

THR307.N-VAL372.O 55.98

CYM5.N-SER10.O 53.11

LYS569.N-TYR541.O 54.55

ASN388.ND2-PRO238.O 53.11

TYR306.OH-ALA292.O 53.59

LYS569.N-TYR541.O 54.55

ILE575.N-PHE546.O 54.55

VAL154.N-ASP223.O 55.98

CYS358.N-TYR306.O 55.50

VAL397.N-VAL371.O 55.50

PHE373.N-VAL397.O 57.42 LEU280.N-TYR398.O 56.46

ILE575.N-PHE546.O 54.07

VAL397.N-VAL371.O 55.02 TYR120.OH-TRP114.O 54.55

LYS473.NZ-TYR582.O 56.94

VAL372.N-VAL305.O 55.98

VAL372.N-VAL305.O 57.42

VAL397.N-VAL371.O 57.42

ARG497.N-ILE493.O 57.89

LEU25.N-LEU14.O 57.89

CYS426.N-ASN423.OD1 57.89

PHE225.N-ALA152.O 58.37

ILE575.N-PHE546.O 63.16

MET576.N-MET474.O 56.94

GLY400.N-LEU280.O 55.02

ASN489.N-GLN518.OE1 55.02

ILE512.N-ILE545.O 55.02

VAL372.N-VAL305.O 55.50

CYS426.N-ASN423.OD1 55.98

ARG507.NE-LEU500.O 55.98

PHE472.N-ILE572.O 58.85

SER523.N-ASN519.O 55.50

THR307.N-VAL372.O 57.42

TYR71.N-TYR64.O 56.94

ASP450.N-ALA446.O 57.42

TYR71.N-TYR64.O 56.94

HID164.N-GLU156.O 57.89

TYR64.N-TYR71.O 57.42

PHE373.N-VAL397.O 57.42

ILE545.N-VAL510.O 57.42

ILE545.N-VAL510.O 59.33

ALA321.N-LEU317.O 58.85

CYS426.N-ASN423.OD1 57.89

VAL372.N-VAL305.O 59.33

ARG129.NE-ASN9.OD1 59.33

ALA134.N-LEU130.O 62.20 ALA321.N-LEU317.O 59.33

LEU65.N-PHE81.O 56.94 TYR306.OH-ALA292.O 56.94

VAL397.N-VAL371.O 60.29

VAL452.N-ILE448.O 59.33

TYR64.N-TYR71.O 59.81

TYR120.OH-TRP114.O 59.33

SER385.OG-ALA237.O 58.37

ILE512.N-ILE545.O 62.68

PHE373.N-VAL397.O 57.42

PHE472.N-ILE572.O 60.77

ILE109.N-ASP105.O 60.77

LEU138.N-ALA134.O 61.24

PHE472.N-ILE572.O 63.64

THR307.N-VAL372.O 60.29

ARG497.N-ILE493.O 61.72

ILE575.N-PHE546.O 65.07

PHE373.N-VAL397.O 62.20

ILE512.N-ILE545.O 65.07

ARG186.NE-ASP223.OD1 88.52

CYS426.N-ASN423.OD1 64.11

ARG186.NE-ASP223.OD2 88.04

5-4_12212689 ARG186.NH2-ASP223.OD2 89.95

5-3_12212691

ARG186.NH2-ASP223.OD2 89.00

ARG186.NH2-ASP223.OD1 93.30

5-2_12212688

ARG186.NH2-ASP223.OD2 86.60

5-1_12212701

Open

Table 6.8 Stronger HBs (with occupancy rates .≥40%) during MDs’ rep1-rep5 of model-NSP13.1-open-ADPMg.2+ 5-5_12212693

ALA140.N-GLU136.O 50.24

VAL452.N-ILE448.O 50.72

LEU65.N-PHE81.O 50.72

TYR198.N-PHE182.O 50.72

TYR306.N-VAL356.O 51.20

GLY294.N-HID290.O 51.20

GLY184.N-GLY196.O 52.63

VAL154.N-ASP223.O 52.63

THR307.N-VAL372.O 53.11

GLN548.N-ILE575.O 53.11

VAL371.N-HID395.O 53.11

ALA321.N-LEU317.O 53.59

ILE575.N-PHE546.O 54.07

TYR306.OH-ALA292.O 54.07

ASN489.N-GLN518.OE1 54.55

CYM5.N-SER10.O 54.55

PHE225.N-ALA152.O 55.50

HID164.N-GLU156.O 55.50

LEU500.N-VAL496.O 55.98

CYS426.N-ASN423.OD1 56.46

PHE472.N-ILE572.O 56.46

LYS569.N-TYR541.O 56.46

LEU138.N-ALA134.O 56.46

VAL372.N-VAL305.O 57.42

LEU325.N-ALA321.O 57.42

LYS94.NZ-CYM29.SG 57.89

MET576.N-MET474.O 57.89

LYS473.NZ-TYR582.O 58.37

TYR120.OH-TRP114.O 58.37

ARG129.NE-ASN9.OD1 58.85

ILE109.N-ASP105.O 58.85

PHE373.N-VAL397.O 59.33

VAL397.N-VAL371.O 60.29

ILE545.N-VAL510.O 61.72

ILE512.N-ILE545.O 62.68

ALA134.N-LEU130.O 65.07

ARG186.NE-ASP223.OD1 85.17

ARG186.NH2-ASP223.OD2 89.95

256 6 RNA Helicase Binding with .ADP-Mg2+ , .ATP-Mg2+ , and RNA

ASN349.N-ARG332.O 46.89

TYR299.OH-TYR269.O 46.41

ASN388.ND2-PRO238.O 46.41

GLY66.N-SER69.O 46.41

LEU455.N-THR451.O 45.93

ASN220.N-ASP223.OD2 45.45

THR12.OG1-LEU25.O 45.45

ILE399.N-PHE373.O 49.28

THR125.OG1-ILE121.O 48.80

ARG186.NH2-LYS218.O 48.80

CYS318.N-VAL314.O 48.33

PHE357.N-SER331.O 48.33

ASN107.N-VAL103.O 47.37

LYS131.N-THR127.O 47.37

GLN492.NE2-GLN548.O 47.37

THR566.OG1-ASN562.O 46.89 ALA140.N-GLU136.O 46.89 ARG560.N-ASN557.OD1 46.89 TYR396.N-LYS276.O 46.41 ASP578.N-GLN548.OE1 46.41

VAL193.N-ARG186.O 45.45 THR141.OG1-THR137.O 45.45

GLU142.N-LEU138.O 44.50 ASP315.N-HID311.O 44.50 ASN220.N-ASP223.OD1 44.50 ASN349.N-ARG332.O 44.02 ASN107.N-VAL103.O 44.02 THR199.N-ARG212.O 44.02 ALA110.N-PHE106.O 43.54 SER166.N-THR153.O 43.54 VAL209.N-LEU163.O 43.54

ASN562.N-VAL558.O 45.45

ASN423.ND2-ALA379.O 44.50

LEU280.N-TYR398.O 44.50

GLY184.N-GLY196.O 44.02

TYR398.N-SER278.O 44.02

LEU83.N-LEU63.O 44.02

GLY294.N-HID290.O 44.02

VAL371.N-HID395.O 43.54

ILE525.N-VAL521.O 43.54

TYR211.OH-SER159.O 43.54

GLU143.N-LYS139.O 43.54

SER80.OG-PRO77.O 43.06

ASN107.N-VAL103.O 42.58

TYR382.OH-MET233.O 42.58

ARG332.NH2-ASP315.OD1 42.58

SER385.OG-ALA237.O 42.58

PHE561.N-ASN557.O 42.11

THR451.OG1-GLU447.O 42.11

CYS318.N-VAL314.O 42.11

THR125.OG1-ILE121.O 41.63

SER278.N-TYR396.O 41.63

LYS569.N-TYR541.O 41.63

PHE225.N-ALA152.O 47.37

CYS358.N-TYR306.O 46.89

LEU65.N-PHE81.O 45.93

TYR396.N-LYS276.O 45.93

ARG567.NE-SER539.O 45.45

TYR185.N-TYR224.O 45.45

ASN220.N-ASP223.OD2 45.45

SER166.N-THR153.O 44.98

HID164.N-GLU156.O 44.98

LYS569.N-TYR541.O 44.50

GLY294.N-HID290.O 44.50

ARG497.N-ILE493.O 44.50

TYR299.OH-TYR269.O 44.02

LEU573.N-VAL544.O 44.02

VAL6.N-PHE24.O 44.02

THR183.N-VAL226.O 44.02

GLU136.N-LEU132.O 44.02

LYS94.NZ-CYM29.SG 44.02

ARG332.NH2-ASP315.OD1 43.54

ILE333.N-PHE357.O 43.06

GLU143.N-LYS139.O 42.58

SER278.N-TYR396.O 42.58

GLN492.NE2-GLN548.O 43.54

ASN423.ND2-ALA379.O 43.54

GLY66.N-SER69.O 42.58

ILE35.N-TYR31.O 43.54

VAL305.N-ILE370.O 42.58

THR451.OG1-GLU447.O 43.54

THR231.N-ASN179.O 44.02

CYM5.N-SER10.O 43.06 GLY222.N-VAL154.O 42.58

TYR120.OH-TRP114.O 44.02

GLY294.N-HID290.O 44.02

PHE546.N-LEU573.O 43.06 VAL371.N-HID395.O 43.06

THR566.N-ASN562.O 44.50

VAL193.N-ARG186.O 43.06

GLY494.N-ARG490.O 44.50

PHE182.N-TYR198.O 43.06

THR183.N-VAL226.O 44.50

CYS358.N-TYR306.O 44.98

THR141.OG1-THR137.O 43.06 TYR185.N-TYR224.O 43.06

PHE561.N-ASN557.O 44.98

ALA292.N-LYS288.O 45.45

TYR71.N-TYR64.O 43.54 LEU428.N-SER424.O 43.06

GLU142.N-LEU138.O 45.45

TYR306.N-VAL356.O 43.54

SER385.OG-ALA237.O 45.45

THR144.OG1-ALA140.O 45.93

PHE357.N-SER331.O 47.37

LEU138.N-ALA134.O 44.50

ILE399.N-PHE373.O 48.33

THR183.N-VAL226.O 44.98 LEU438.N-GLN281.O 47.37

VAL371.N-HID395.O 48.33

ASN562.N-VAL558.O 45.45 GLY294.N-HID290.O 44.98

TYR306.N-VAL356.O 48.33

ILE333.N-PHE357.O 45.45

PHE511.N-PRO529.O 48.80

TYR198.N-PHE182.O 46.89

SER513.OG-ASN519.OD1 49.28 ASP450.N-ALA446.O 45.93

PHE546.N-LEU573.O 47.37

ARG507.NE-LEU500.O 49.28 SER513.OG-ASN519.OD1 48.80

PHE182.N-TYR198.O 49.28

SER513.OG-ASN519.OD1 46.41

SER166.N-THR153.O 47.37

PHE511.N-PRO529.O 49.28 PHE225.N-ALA152.O 45.93

LEU65.N-PHE81.O 49.28

TYR299.OH-TYR269.O 46.41

PHE511.N-PRO529.O 47.85

VAL456.N-VAL452.O 49.28 LEU138.N-ALA134.O 49.28

GLY184.N-GLY196.O 49.28

LEU25.N-LEU14.O 46.89

THR199.N-ARG212.O 47.85

ASN349.N-ARG332.O 49.76

LYS131.N-THR127.O 46.41

SER523.N-ASN519.O 49.28

HID164.N-GLU156.O 47.37

TYR198.N-PHE182.O 49.76

TYR185.N-TYR224.O 47.85

MET576.N-MET474.O 48.33

VAL305.N-ILE370.O 49.76 VAL181.N-SER229.O 49.28

VAL305.N-ILE370.O 49.76

TYR70.OH-LEU25.O 47.85

ILE333.N-PHE357.O 49.28

GLU142.N-LEU138.O 49.76 VAL456.N-VAL452.O 47.37

ILE109.N-ASP105.O 49.76

VAL452.N-ILE448.O 47.85

TYR198.N-PHE182.O 50.72

VAL305.N-ILE370.O 49.28

ASP315.N-HID311.O 49.76

GLN548.N-ILE575.O 47.85 ARG186.NH2-LYS218.O 50.24

PHE182.N-TYR198.O 49.76 ALA140.N-GLU136.O 47.85

ILE399.N-PHE373.O 49.76

ALA140.N-GLU136.O 49.76

VAL371.N-HID395.O 49.76

TYR299.OH-TYR269.O 41.63

PHE546.N-LEU573.O 42.11

(continued)

ASN423.ND2-ALA379.O 42.11

ASN107.N-VAL103.O 42.11

THR231.N-ASN179.O 42.11

LEU573.N-VAL544.O 42.58

VAL210.N-GLU201.O 43.06

SER513.OG-ASN519.OD1 43.06

GLY66.N-SER69.O 43.54

GLN492.NE2-GLN548.O 43.54

LYS131.N-THR127.O 44.02

PHE511.N-PRO529.O 44.02

TYR396.N-LYS276.O 44.02

VAL193.N-ARG186.O 44.02

SER278.N-TYR396.O 44.02

ILE35.N-TYR31.O 44.02

ASN388.ND2-PRO238.O 44.50

CYS358.N-TYR306.O 44.98

THR12.OG1-LEU25.O 44.98

ASN349.N-ARG332.O 45.45

TYR71.N-TYR64.O 45.45

PHE357.N-SER331.O 45.45

ARG567.NE-SER539.O 45.45

ARG497.N-ILE493.O 45.93

SER385.OG-ALA237.O 45.93

VAL305.N-ILE370.O 46.41

CYS318.N-VAL314.O 46.89

SER166.N-THR153.O 46.89

CYS574.N-PHE472.O 46.89

GLU142.N-LEU138.O 46.89

THR144.OG1-ALA140.O 47.37

ARG409.NE-GLU142.OE1 47.37

ARG186.NH2-LYS218.O 47.85

ARG409.NH2-GLU142.OE2 47.85

VAL181.N-SER229.O 48.80

SER523.N-ASN519.O 48.80

MET429.N-VAL425.O 48.80

TYR64.N-TYR71.O 49.28

TYR185.N-TYR224.O 49.28

PHE182.N-TYR198.O 49.76

6.4 Concluding Remarks 257

5-2_12212688

VAL226.N-THR183.O 41.63

GLY222.N-VAL154.O 41.63

LEU25.N-LEU14.O 41.15

LEU573.N-VAL544.O 41.15

VAL210.N-GLU201.O 41.15

THR431.N-ARG427.O 40.67

TYR246.N-MET274.O 40.67

LYS131.N-THR127.O 40.19

SER513.OG-ASN519.OD1 40.19

LEU428.N-SER424.O 40.19

GLY3.N-THR12.O 40.19

VAL193.N-ARG186.O 40.19

TYR306.N-VAL356.O 40.19

GLY400.N-LEU280.O 39.71

ARG507.NE-LEU500.O 39.71

TYR396.N-LYS276.O 39.71

ARG560.N-ASN557.OD1 39.71

THR12.N-GLY3.O 39.71

ALA123.N-ASP119.O 39.23

THR183.N-VAL226.O 39.23

5-1_12212701

ARG409.NH2-GLU142.OE2 42.58

THR451.OG1-GLU447.O 42.11

ASN423.ND2-ALA379.O 41.63

VAL226.N-THR183.O 41.63

TYR421.N-GLU418.O 41.63

TYR246.N-MET274.O 41.15

TYR306.N-VAL356.O 41.15

PHE291.N-GLY287.O 41.15

ILE525.N-VAL521.O 41.15

LEU25.N-LEU14.O 40.67

PHE561.N-ASN557.O 40.67

THR199.N-ARG212.O 40.67

GLY3.N-THR12.O 40.67

SER278.N-TYR396.O 40.19

ALA368.N-ARG392.O 40.19

THR144.OG1-ALA140.O 40.19

ARG560.N-ASN557.OD1 40.19

THR431.N-ARG427.O 39.71

THR12.OG1-LEU25.O 38.76

LEU391.N-VAL387.O 38.76

Open

Table 6.8 (continued)

ILE399.N-PHE373.O 39.23

LEU322.N-CYS318.O 39.71

SER331.N-TYR355.O 39.71

THR451.OG1-GLU447.O 39.71

GLU143.N-LYS139.O 40.19

TYR398.N-SER278.O 40.19

GLY3.N-THR12.O 40.19

ASP578.N-GLN548.OE1 40.19

THR153.N-SER166.O 40.67

ALA123.N-ASP119.O 40.67

LYS430.NZ-GLU420.OE1 40.67

THR255.N-TYR298.O 40.67

TYR421.N-GLU418.O 41.15

ASN423.ND2-ALA379.O 41.15

CYS574.N-PHE472.O 41.63

ARG409.NH2-GLU142.OE2 41.63

LEU455.N-THR451.O 41.63

CYS318.N-VAL314.O 41.63

GLN243.NE2-TYR277.O 41.63

GLY184.N-GLY196.O 42.58

5-3_12212691

LEU322.N-CYS318.O 39.23

VAL226.N-THR183.O 39.71

SER577.N-GLN548.OE1 39.71

GLU136.N-LEU132.O 39.71

GLN281.N-MET436.O 39.71

TYR398.N-SER278.O 40.19

VAL456.N-VAL452.O 40.19

GLU143.N-LYS139.O 40.67

THR431.OG1-ARG427.O 40.67

CYS318.N-VAL314.O 41.15

VAL210.N-GLU201.O 41.15

LYS131.N-THR127.O 41.15

ILE525.N-VAL521.O 41.63

SER331.N-TYR355.O 42.11

TYR299.OH-TYR269.O 42.11

ARG390.NH1-LEU363.O 42.58

ASN562.N-VAL558.O 42.58

ASN220.N-ASP223.OD2 42.58

THR431.N-ARG427.O 42.58

ASP315.N-HID311.O 43.06

5-4_12212689

GLY17.N-LEU41.O 37.80

GLY222.N-VAL154.O 38.28

TYR398.N-SER278.O 38.28

ASP450.N-ALA446.O 38.76

THR137.N-PHE133.O 38.76

LEU83.N-LEU63.O 38.76

PHE106.N-ASN102.O 39.23

ASN220.N-ASP223.OD2 39.71

THR141.OG1-THR137.O 39.71

ARG303.NE-GLU353.O 40.19

THR199.N-ARG212.O 40.19

ILE333.N-PHE357.O 40.19

GLU143.N-LYS139.O 40.19

ALA123.N-ASP119.O 40.19

LEU455.N-THR451.O 40.67

ASP315.N-HID311.O 40.67

ASN562.N-VAL558.O 40.67

ILE399.N-PHE373.O 41.15

TYR246.N-MET274.O 41.15

LEU280.N-TYR398.O 41.63

5-5_12212693

258 6 RNA Helicase Binding with .ADP-Mg2+ , .ATP-Mg2+ , and RNA

PHE373.N-VAL397.O 61.24 CYM5.N-SER10.O 58.37

THR307.N-VAL372.O 57.89 CYS30.N-CYM26.O 57.89

THR307.N-VAL372.O 58.85

ILE575.N-PHE546.O 58.85

ARG129.NE-ASN9.OD1 59.33

ASP450.N-ALA446.O 56.94 VAL372.N-VAL305.O 56.94

LEU138.N-ALA134.O 57.42

PHE225.N-ALA152.O 56.94

ALA140.N-GLU136.O 57.42

THR307.N-VAL372.O 57.42

ASN107.N-VAL103.O 56.46

ILE545.N-VAL510.O 54.55 LYS473.NZ-TYR582.O 54.55 VAL372.N-VAL305.O 54.07

CYM5.N-SER10.O 53.59 ILE109.N-ASP105.O 53.59 ARG507.NE-LEU500.O 52.63 ILE545.N-VAL510.O 52.63

ASP315.N-HID311.O 55.50

ARG332.NH2-ASP315.OD2 55.02

THR37.OG1-HID33.O 55.02

ILE35.N-TYR31.O 54.55

CYM5.N-SER10.O 55.98

ASN349.N-ARG332.O 55.02

LEU500.N-VAL496.O 54.55

ALA321.N-LEU317.O 53.59

PHE182.N-TYR198.O 53.59 LEU325.N-ALA321.O 53.59

TYR198.N-PHE182.O 52.63 ALA321.N-LEU317.O 52.63

ARG186.NH2-LYS218.O 51.20 ALA321.N-LEU317.O 51.20

ARG507.NE-LEU500.O 53.59

ASN107.N-VAL103.O 53.59

HID164.N-GLU156.O 53.59

PHE472.N-ILE572.O 53.11

TYR299.OH-TYR269.O 51.67

LYS473.NZ-TYR582.O 51.67

VAL154.N-ASP223.O 51.20

ARG332.NH2-ASP315.OD2 51.20

LEU325.N-ALA321.O 50.24

VAL305.N-ILE370.O 51.67

ILE399.N-PHE373.O 52.63

ILE575.N-PHE546.O 52.63

ASP450.N-ALA446.O 53.11

CYS426.N-ASN423.OD1 52.63 ASN562.N-VAL558.O 52.15 HID164.N-GLU156.O 51.67

LYS131.N-THR127.O 54.55

GLN548.N-ILE575.O 54.07

ARG497.N-ILE493.O 53.59

VAL305.N-ILE370.O 54.07

PHE472.N-ILE572.O 55.98

SER166.N-THR153.O 52.15

LEU138.N-ALA134.O 54.55

CYS426.N-ASN423.OD1 52.15

LYS569.N-TYR541.O 53.11

LEU138.N-ALA134.O 55.02

LEU43.N-ARG15.O 53.59

VAL371.N-HID395.O 56.46

VAL452.N-ILE448.O 55.98

MET429.N-VAL425.O 55.98

CYS426.N-ASN423.OD1 56.46 PHE225.N-ALA152.O 55.98

LEU325.N-ALA321.O 55.98

PHE357.N-SER331.O 56.46

SER166.N-THR153.O 56.46

LYS473.NZ-TYR582.O 56.46

ARG497.N-ILE493.O 56.46

LEU500.N-VAL496.O 56.94

SER385.OG-ALA237.O 57.42

ILE334.N-ASN349.OD1 57.89

ILE493.N-ASN489.O 58.37

ARG567.NE-SER539.O 58.37

PHE357.N-SER331.O 58.37

VAL397.N-VAL371.O 61.24

LEU280.N-TYR398.O 56.46

ILE399.N-PHE373.O 56.94 PHE225.N-ALA152.O 56.46

VAL397.N-VAL371.O 56.94

ILE545.N-VAL510.O 56.46

ILE109.N-ASP105.O 56.46

VAL397.N-VAL371.O 56.94

PHE225.N-ALA152.O 56.94

ILE109.N-ASP105.O 56.94

ARG129.NE-ASN9.OD1 57.42

VAL154.N-ASP223.O 57.42

ILE512.N-ILE545.O 57.89

MET429.N-VAL425.O 57.89

TYR120.OH-TRP114.O 57.89

ASN489.N-GLN518.OE1 57.42

CYS574.N-PHE472.O 58.85

CYS358.N-TYR306.O 62.68 LEU65.N-PHE81.O 62.20

PHE546.N-LEU573.O 58.85

ARG497.N-ILE493.O 60.77 LEU65.N-PHE81.O 59.81

CYS426.N-ASN423.OD1 59.33

VAL372.N-VAL305.O 59.33

TYR306.OH-ALA292.O 60.29

VAL372.N-VAL305.O 59.33

TYR306.OH-ALA292.O 62.68

ARG497.N-ILE493.O 63.64

ILE512.N-ILE545.O 61.72

PHE373.N-VAL397.O 61.72

TYR306.OH-ALA292.O 62.20

CYM5.N-SER10.O 62.20

SER385.OG-ALA237.O 61.24

THR125.OG1-ILE121.O 60.77

ALA134.N-LEU130.O 71.77 ILE512.N-ILE545.O 67.46 ILE109.N-ASP105.O 66.03

TYR306.OH-ALA292.O 65.55 VAL397.N-VAL371.O 64.11 SER385.OG-ALA237.O 61.72

SER385.OG-ALA237.O 65.07

ALA134.N-LEU130.O 63.16

PHE373.N-VAL397.O 63.16

PHE373.N-VAL397.O 62.68

LEU138.N-ALA134.O 61.24

PHE511.N-PRO529.O 64.11

ARG186.NE-ASP223.OD1 86.12

ALA134.N-LEU130.O 68.42

ARG186.NH2-ASP223.OD2 88.52 ARG332.NE-ASP315.OD1 73.68

ALA134.N-LEU130.O 68.90

ARG186.NE-ASP223.OD1 83.73

LYS94.NZ-CYM29.SG 68.90

ARG186.NH2-ASP223.OD2 91.39 ARG186.NE-ASP223.OD1 80.86

6-4_12225240 ARG186.NE-ASP223.OD1 90.43

6-3_12225255 ARG186.NH2-ASP223.OD2 92.34

6-2_12225258

ARG186.NH2-ASP223.OD2 89.47

6-1_12225252

Close

Table 6.9 Stronger HBs (with occupancy rates .≥40%) during MDs’ rep1-rep5 of model-NSP13.1-close-ADPMg.2+ 6-5_12225249

THR481.N-ILE488.O 51.20

LEU43.N-ARG15.O 51.20

ASN349.N-ARG332.O 51.67

ARG129.NE-ASN9.OD1 51.67

CYS574.N-PHE472.O 52.15

LEU325.N-ALA321.O 52.15

SER385.OG-ALA237.O 52.15

TYR120.OH-TRP114.O 52.15

(continued)

SER513.OG-ASN519.OD1 52.63

PHE225.N-ALA152.O 53.11

PHE546.N-LEU573.O 53.59

MET429.N-VAL425.O 53.59

HID164.N-GLU156.O 53.59

ASP315.N-HID311.O 54.07

PHE511.N-PRO529.O 54.07

ALA321.N-LEU317.O 55.50

GLN548.N-ILE575.O 55.50

VAL154.N-ASP223.O 56.46

CYM5.N-SER10.O 56.94

THR12.OG1-LEU25.O 57.89

LYS569.N-TYR541.O 57.89

ILE575.N-PHE546.O 58.37

CYS426.N-ASN423.OD1 58.85

VAL397.N-VAL371.O 59.33

VAL372.N-VAL305.O 60.29

THR307.N-VAL372.O 60.77

LEU280.N-TYR398.O 63.64

PHE373.N-VAL397.O 64.11

MET576.N-MET474.O 66.03

ASN489.N-GLN518.OE1 67.94

ILE512.N-ILE545.O 69.38

ALA134.N-LEU130.O 73.68

ARG186.NE-ASP223.OD1 87.56

ARG186.NH2-ASP223.OD2 88.52

6.4 Concluding Remarks 259

6-2_12225258

PHE511.N-PRO529.O 52.63

CYS318.N-VAL314.O 52.63

ALA321.N-LEU317.O 52.63

ARG129.NE-ASN9.OD1 52.63

LEU500.N-VAL496.O 52.15

ALA123.N-ASP119.O 52.15

SER523.N-ASN519.O 52.15

TYR120.OH-TRP114.O 52.15

THR431.OG1-ARG427.O 51.67

ASN349.N-ARG332.O 51.67

ILE399.N-PHE373.O 51.20

LEU325.N-ALA321.O 50.72

VAL154.N-ASP223.O 49.76

TYR198.N-PHE182.O 49.76

LEU573.N-VAL544.O 49.76

CYS358.N-TYR306.O 49.76

PHE291.N-GLY287.O 49.28

THR125.OG1-ILE121.O 48.80

VAL305.N-ILE370.O 48.80

PHE357.N-SER331.O 48.80

GLY222.N-VAL154.O 48.33

LYS569.N-TYR541.O 48.33

TYR306.N-VAL356.O 48.33

SER453.N-VAL449.O 47.85

TYR269.N-ASN265.O 47.85

TYR299.OH-TYR269.O 47.37

LEU322.N-CYS318.O 46.41

TYR398.N-SER278.O 46.41

VAL210.N-GLU201.O 46.41

LYS94.NZ-ASP32.OD1 45.93

LEU25.N-LEU14.O 44.98

TYR396.N-LYS276.O 44.98

ARG186.NH2-LYS218.O 44.98

LYS288.NZ-ASP374.OD1 44.98

TYR71.N-TYR64.O 44.50

PHE182.N-TYR198.O 44.02

6-1_12225252

ILE512.N-ILE545.O 51.20

ILE575.N-PHE546.O 50.72

HID164.N-GLU156.O 50.24

ASP315.N-HID311.O 50.24

LYS131.N-THR127.O 50.24

ALA123.N-ASP119.O 50.24

VAL452.N-ILE448.O 49.76

CYS358.N-TYR306.O 49.28

PHE472.N-ILE572.O 49.28

TYR306.N-VAL356.O 49.28

ASN388.ND2-PRO238.O 49.28

ILE399.N-PHE373.O 48.33

TYR185.N-TYR224.O 47.85

CYS318.N-VAL314.O 47.37

PHE357.N-SER331.O 46.89

ILE525.N-VAL521.O 46.89

GLN492.NE2-GLN548.O 46.41

ASN107.N-VAL103.O 45.93

PHE561.N-ASN557.O 45.45

CYS574.N-PHE472.O 44.98

SER453.N-VAL449.O 44.50

TYR398.N-SER278.O 44.50

TYR246.N-MET274.O 44.50

SER36.OG-ASP32.O 44.50

LEU573.N-VAL544.O 44.50

VAL305.N-ILE370.O 44.50

THR183.N-VAL226.O 44.02

ARG186.NH2-LYS218.O 44.02

SER523.N-ASN519.O 43.54

GLY294.N-HID290.O 43.06

ILE334.N-ASN349.OD1 43.06

GLN492.NE2-TYR476.O 43.06

ASP450.N-ALA446.O 42.58

TYR198.N-PHE182.O 42.58

THR431.N-ARG427.O 42.11

SER278.N-TYR396.O 42.11

Close

Table 6.9 (continued)

ILE333.N-PHE357.O 44.50

SER453.N-VAL449.O 44.50

ILE35.N-TYR31.O 44.98

TYR299.OH-TYR269.O 44.98

LEU83.N-LEU63.O 44.98

PHE472.N-ILE572.O 45.45

TYR398.N-SER278.O 45.93

GLY294.N-HID290.O 45.93

THR12.OG1-LEU25.O 45.93

LEU25.N-LEU14.O 45.93

TYR185.N-TYR224.O 45.93

PHE511.N-PRO529.O 46.41

VAL34.N-CYS30.O 46.41

THR125.OG1-ILE121.O 46.41

VAL371.N-HID395.O 46.41

ALA140.N-GLU136.O 46.89

TYR198.N-PHE182.O 46.89

MET576.N-MET474.O 46.89

ILE334.N-ASN349.OD1 46.89

THR183.N-VAL226.O 46.89

SER166.N-THR153.O 46.89

CYS318.N-VAL314.O 47.37

SER36.OG-ASP32.O 47.37

VAL89.N-CYS27.O 47.37

ASN349.N-ARG332.O 47.37

ILE575.N-PHE546.O 47.85

ALA123.N-ASP119.O 47.85

THR286.OG1-LEU438.O 47.85

ASN388.ND2-PRO238.O 48.33

LEU573.N-VAL544.O 48.33

VAL456.N-VAL452.O 48.80

MET429.N-VAL425.O 48.80

ILE565.N-PHE561.O 49.28

PHE546.N-LEU573.O 49.28

TYR120.OH-TRP114.O 49.76

ASN220.N-ASP223.OD2 49.76

6-3_12225255

LEU25.N-LEU14.O 43.06

THR37.OG1-HID33.O 43.06

LYS569.N-TYR541.O 43.06

TYR185.N-TYR224.O 43.54

LEU573.N-VAL544.O 44.50

VAL6.N-PHE24.O 44.50

TYR299.OH-TYR269.O 44.50

THR183.N-VAL226.O 44.50

ALA123.N-ASP119.O 44.98

ARG337.NH2-GLU197.OE2 44.98

ASN423.ND2-ALA379.O 44.98

GLY66.N-SER69.O 45.45

SER523.N-ASN519.O 45.45

PHE511.N-PRO529.O 45.93

ALA520.N-ASN516.O 45.93

CYS30.N-CYM26.O 46.41

MET429.N-VAL425.O 47.37

VAL371.N-HID395.O 47.85

THR125.OG1-ILE121.O 47.85

GLY294.N-HID290.O 48.33

TYR64.N-TYR71.O 48.80

ARG178.NE-GLU201.OE1 49.28

ARG337.NE-GLU197.OE1 49.28

HID164.N-GLU156.O 49.28

THR199.N-ARG212.O 49.76

LYS131.N-THR127.O 49.76

ASN388.ND2-PRO238.O 49.76

VAL210.N-GLU201.O 50.24

ARG129.NE-ASN9.OD1 50.72

THR307.N-VAL372.O 51.20

SER166.N-THR153.O 51.20

TYR476.N-MET576.O 51.67

CYS574.N-PHE472.O 52.15

THR12.OG1-LEU25.O 52.15

VAL154.N-ASP223.O 52.15

TYR120.OH-TRP114.O 52.15

6-4_12225240

GLY184.N-GLY196.O 43.54

GLY66.N-SER69.O 44.02

LEU25.N-LEU14.O 44.02

TYR71.N-TYR64.O 44.02

VAL193.N-ARG186.O 44.98

ASN489.ND2-THR549.O 44.98

SER166.N-THR153.O 44.98

LEU65.N-PHE81.O 44.98

VAL210.N-GLU201.O 45.93

ARG497.N-ILE493.O 45.93

THR125.OG1-ILE121.O 45.93

ILE545.N-VAL510.O 45.93

ASN388.ND2-PRO238.O 45.93

THR451.OG1-GLU447.O 45.93

TYR541.N-ARG567.O 46.41

CYS358.N-TYR306.O 46.41

LEU138.N-ALA134.O 46.41

TYR185.N-TYR224.O 46.89

ALA123.N-ASP119.O 46.89

ILE333.N-PHE357.O 46.89

LYS131.N-THR127.O 47.37

ILE399.N-PHE373.O 47.37

LEU500.N-VAL496.O 47.37

THR532.N-SER535.OG 47.85

TYR299.OH-TYR269.O 47.85

ASN220.N-ASP223.OD2 48.33

ALA522.N-GLN518.O 48.80

ALA140.N-GLU136.O 49.28

ARG186.NH2-LYS218.O 49.76

TYR198.N-PHE182.O 49.76

SER523.N-ASN519.O 50.24

VAL371.N-HID395.O 50.24

CYS318.N-VAL314.O 50.24

PHE357.N-SER331.O 50.72

ILE109.N-ASP105.O 51.20

TYR306.OH-ALA292.O 51.20

6-5_12225249

260 6 RNA Helicase Binding with .ADP-Mg2+ , .ATP-Mg2+ , and RNA

ALA140.N-GLU136.O 42.11 ARG507.NE-LEU500.O 42.11 ASN107.N-VAL103.O 41.63 ARG390.NH1-LEU363.O 41.63 TYR398.N-SER278.O 41.63 VAL387.N-ASP383.O 41.63 MET576.N-MET474.O 41.15 GLY222.N-VAL154.O 41.15

THR37.OG1-HID33.O 44.50 TYR476.N-MET576.O 44.02 TYR64.N-TYR71.O 44.02 GLY150.N-PRO172.O 43.54 TYR306.N-VAL356.O 43.54 THR255.N-TYR298.O 43.54 THR451.OG1-GLU447.O 43.06 LYS131.N-THR127.O 43.06

ASN381.ND2-ASN124.OD1 43.54

THR141.OG1-THR137.O 43.54

ARG390.NH1-LEU363.O 43.54

ASN423.ND2-ALA379.O 43.06

ILE333.N-PHE357.O 43.06

TYR185.N-TYR224.O 41.15

ASN562.N-VAL558.O 40.67

TYR421.N-GLU418.O 40.67

PHE561.N-ASN557.O 40.67

MET576.N-MET474.O 40.19

VAL209.N-LEU163.O 40.19

ALA140.N-GLU136.O 40.19

ARG337.NE-GLU197.OE1 40.19

PHE546.N-LEU573.O 39.71

VAL456.N-VAL452.O 39.71

GLY184.N-GLY196.O 39.71

GLU142.N-LEU138.O 39.23

ASN388.ND2-PRO238.O 39.23

TYR246.N-MET274.O 39.23

GLN270.N-VAL266.O 39.23

ARG560.NE-VAL533.O 39.23

LYS146.NZ-GLU143.OE1 38.76

THR12.OG1-LEU25.O 38.76

THR183.N-VAL226.O 38.76

LEU280.N-TYR398.O 38.76

ILE334.N-ASN349.OD1 38.28

THR199.N-ARG212.O 41.63

VAL371.N-HID395.O 41.63

ALA578.N-GLN548.OE1 41.15

PHE182.N-TYR198.O 41.15

THR141.OG1-THR137.O 41.15

GLN270.N-VAL266.O 41.15

LEU25.N-LEU14.O 40.67

MET576.N-MET474.O 40.67

THR12.OG1-LEU25.O 40.67

VAL193.N-ARG186.O 40.67

ASN423.ND2-ALA379.O 40.19

CYS30.N-CYM26.O 40.19

ARG337.NE-GLU197.OE1 40.19

VAL6.N-PHE24.O 40.19

LEU590.N-LYS473.O 40.19

PHE106.N-ASN102.O 39.71

ALA522.N-GLN518.O 39.23

LEU438.N-GLN281.O 39.23

ILE35.N-TYR31.O 39.23

ASN220.N-ASP223.OD2 39.23

ASN381.ND2-ASN124.OD1 39.23

VAL209.N-LEU163.O 38.76

ARG129.NH1-SER236.O 38.76

TYR355.N-LYS329.O 38.76

THR255.N-TYR298.O 38.76

THR451.OG1-GLU447.O 38.76

GLN492.N-ASN489.OD1 39.71

SER523.N-ASN519.O 40.19

SER278.N-TYR396.O 39.23

VAL193.N-ARG186.O 39.23

HID395.ND1-GLN275.O 39.23 ARG129.NH1-SER236.O 39.23

TYR246.N-MET274.O 39.23

LEU322.N-CYS318.O 39.71

SER331.OG-LYS347.O 39.23

LYS146.NZ-THR228.O 39.71

ARG332.NH2-ASP315.OD1 40.67 TYR396.N-LYS276.O 40.19

THR255.N-TYR298.O 39.71

GLY400.N-LEU280.O 39.71

TYR71.N-TYR64.O 40.67

LEU280.N-TYR398.O 40.19

THR359.OG1-ASN361.OD1 40.19

ASP315.N-HID311.O 41.63 CYS358.N-TYR306.O 40.67

GLN548.N-ILE575.O 40.19

LYS569.N-TYR541.O 41.63 VAL210.N-GLU201.O 40.67

GLN270.N-VAL266.O 40.19

ILE333.N-PHE357.O 40.67

THR199.N-ARG212.O 42.11 GLN492.N-ASN489.OD1 41.63

ASN220.N-ASP223.OD2 40.67

ALA368.N-ARG392.O 42.11

ARG186.NH2-LYS218.O 41.15

TYR246.N-MET274.O 42.58 ARG178.NH2-GLU201.OE2 41.15

ILE35.N-TYR31.O 41.15

VAL452.N-ILE448.O 42.58 PHE182.N-TYR198.O 42.11

VAL34.N-CYS30.O 41.15

LEU500.N-VAL496.O 42.58

GLY150.N-PRO172.O 42.11

ILE493.N-ASN489.O 44.50

ASP450.N-ALA446.O 43.54

TYR71.N-TYR64.O 42.58

GLY3.N-THR12.O 44.50

ASN220.N-ASP223.OD2 44.02

ARG409.NH2-GLU142.OE2 42.11

GLN492.N-ASN489.OD1 42.11

THR183.N-VAL226.O 40.19

ARG409.NH2-GLU142.OE2 40.67

ARG409.NE-GLU142.OE1 40.67

ARG390.NH1-LEU363.O 40.67

TYR398.N-SER278.O 40.67

THR199.N-ARG212.O 40.67

VAL209.N-LEU163.O 41.15

GLY3.N-THR12.O 41.15

GLN270.N-VAL266.O 41.15

TYR306.N-VAL356.O 41.63

ALA368.N-ARG392.O 41.63

VAL6.N-PHE24.O 41.63

THR153.N-SER166.O 41.63

GLN281.N-MET436.O 41.63

GLY494.N-ARG490.O 41.63

THR255.N-TYR298.O 42.11

GLY222.N-VAL154.O 42.11

PHE182.N-TYR198.O 42.11

ASP450.N-ALA446.O 42.11

ILE525.N-VAL521.O 42.11

TYR476.N-MET576.O 42.11

VAL387.N-ASP383.O 42.58

VAL305.N-ILE370.O 42.58

ASN562.N-VAL558.O 42.58

THR431.N-ARG427.O 42.58

ALA578.N-GLN548.OE1 43.06

THR286.OG1-LEU438.O 43.06

CYS30.N-CYM26.O 43.54

6.4 Concluding Remarks 261

262 Table 6.10 All the MDs show that the segment ASN51-GLY91 of NSP13 has large RMSFs

6 RNA Helicase Binding with .ADP-Mg2+ , .ATP-Mg2+ , and RNA NSP13-ATPMg.2+ -RNA

NSP13-ADPMg.2+ -RNA

NSP13-ATPMg.2+

NSP13-ADPMg.2+

NSP13.1-open-ADPMg.2+

NSP13.1-close-ADPMg.2+

1-1_12970406

51-91

1-2_12970408

51-91

1-3_12970412

51–91, 191

2-1_12258863

51–91, 151–221, 341, 481

2-2_12258865

51–91, 151–221, 341, 481

2-3_12251869

41–91

3-1_12258868

51–91

3-2_12257092

51–91, 151–221, 501

3-3_12259873

51–91

4-1_12257049

51–91

4-2_12251866

51–91, 151–221, 341, 481

4-3_12251868

51–91

5-1_12212701

51–91, 151–221, 471–531, 541–581

5-2_12212688

51–91, 151–221, 471–531, 551–581

5-3_12212691

51–91, 151–221, 471–531

5-4_12212689

51–91, 151–221, 471–581

5-5_12212693

51–91, 151–221, 471–531, 541–581

6-1_12225252

51–91, 151–231, 481, 551

6-2_12225258

51–91, 191–221, 441–581

6-3_12225255

51–91, 151–221, 461–581

6-4_12225240

51–91, 151–221, 481–581

6-5_12225249

51–91, 191, 461

Table 6.11 The residues of NSP13 binding with RNA-6CCCAUGUG13 of each optimized model NSP13-ATPMg.2+ -RNA_1-1_12970406

139, 142, 146, 175, 177, 179, 180, 230, 231, 232, 233, 234, 311, 333, 334, 335, 336, 337, 360, 361, 362, 363, 382, 383, 386, 390, 408, 409, 410, 412, 413, 414, 415, 416, 481, 482, 485, 486, 487, 514, 515, 516, 532, 534, 535, 550, 554

NSP13-ATPMg.2+ -RNA_1-2_12970408

139, 142, 143, 177, 178, 179, 180, 181, 197, 202, 228, 230, 231, 311, 336, 337, 360, 361, 382, 383, 386, 390, 408, 409, 410, 412, 413, 415, 416, 417, 485, 486, 514, 515, 516, 517, 532, 534, 535, 554, 560

NSP13-ATPMg.2+ -RNA_1-3_12970412

139, 142, 143, 177, 178, 179, 180, 181, 197, 202, 228, 230, 231, 311, 336, 337, 360, 361, 382, 383, 386, 390, 408, 409, 410, 412, 413, 415, 416, 417, 485, 486, 514, 515, 516, 517, 532, 534, 535, 554, 560

NSP13-ADPMg.2+ -RNA_2-1_12258863

139, 142, 143, 145, 146, 149, 175, 177, 178, 179, 180, 230, 231, 233, 310, 311, 335, 337, 340, 361, 362, 363, 364, 365, 378, 380, 382, 383, 390, 406, 407, 408, 409, 410, 480, 482, 485, 486, 487, 514, 515, 516, 517, 532, 534, 535, 550, 552, 554, 555, 560

NSP13-ADPMg.2+ -RNA_2-2_12258865

139, 142, 143, 145, 146, 149, 175, 177, 178, 179, 180, 230, 231, 233, 310, 311, 335, 337, 340, 361, 362, 363, 364, 365, 378, 380, 382, 383, 390, 406, 407, 408, 409, 410, 480, 482, 485, 486, 487, 514, 515, 516, 517, 532, 534, 535, 550, 552, 555, 554, 560

NSP13-ADPMg.2+ -RNA_2-3_12251869

139, 142, 143, 145, 146, 149, 175, 177, 178, 179, 180, 230, 231, 233, 310, 311, 335, 337, 340, 361, 362, 363, 364, 365, 378, 380, 382, 383, 390, 406,407, 408, 409, 410, 480, 482, 485, 486, 487, 514, 515, 516, 517, 532, 534, 535, 550, 552, 554, 555, 560

Chapter 7

Spike (S) Glycoprotein

Abstract Coronavirus SARS-CoV-2 spike glycoproteins (S-proteins) promote entry into cells and are the main target of antibodies and inhibitors. Angiotensinconverting enzyme 2 (ACE2) is the cellular receptor for SARS-CoV-2 and is an antiviral drug target against SARS-CoV-2. This chapter is doing molecular dynamics (MD) studies of their structures and presenting some structural bioinformatics for developing therapies of the currently fatal COVID-19 virus. From SARS-CoV-2 S, we found (i) a strong polar contact between ASP442 and ARG509 in the receptor-binding domain (RBD) of each monomer, (ii) strong hydrogen bond (HB) PHE43.N-PHE565.O and their side-chain .π -.π stackings between each two monomers, and (iii) strong polar contacts between GLU1031 and ARG1039/LYS1038 in the central helix-connector domain (CHCD) between each two monomers; thus holding the three monomers tightly from both ends to the middle of the spike; in the spike HB C:TYR369.OHA:THR415.OG1 also has high occupancy rate, i.e., 50.30%. From the bindings of SARS-CoV-2 S (denoted as F-chain) and human ACE2 (denoted as D-/B-chain), we found that polar contacts F:LYS417-D:ASP30, F:ARG439-B:GLU329, and HB F:THR500.OG1-D:ASP355.OD1 are very strong during MD of 10 .μs, and salt bridges (SBs) F:LYS458-D/B:GLU23 (but D/B:GLU23 is with high HB occupancy rates with D/B:THR27), F:ARG403-D/B:GLU37 (also with low HB occupancy rates), F:GLU484-D/B:LYS31, and F:ARG403-D/B:ASP38 (but HB D/B:ASP38F:TYR449 is strong) are weak during the whole 10 .μs; during the whole 10 .μs, spike SBs F:ASP398-F:ARG355 and F:ASP442-F:ARG509 and the human ACE2 SBs GLU182-ARG115, GLU208-ARG219, GLU406-ARG518, GLU435-LYS541, GLU310-ARG306, GLU433-LYS288, and GLU189-LYS112 are always strong in MD of 10 .μs. Keywords Coronavirus SARS-CoV-2 spike · Human angiotensin-converting enzyme 2 · Receptor bindings · Optimization-based molecular dynamics studies · New structural bioinformatics

© The Author(s), under exclusive license to Springer Nature Switzerland AG 2023 J. Zhang, Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures, Springer Series in Biophysics 23, https://doi.org/10.1007/978-3-031-36773-1_7

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7.1 Introduction “Coronavirus” (CoV) is an umbrella term for a family of viruses that share similar properties. Some coronaviruses have been behind concerning disease outbreaks, namely, SARS, MERS, and SARS-CoV-2. The SARS-CoV-2 (severe acute respiratory syndrome (SARS) coronavirus 2) is the disease at the center of our current global health crisis of COVID-19. Coronavirus spike (S) glycoproteins promote entry into cells and are the main target of antibodies. The cryo-EM structures of the SARS-CoV-2 S ectodomain trimer were determined with PDB entries 6VXX (closed SARS-CoV-2 S) and 6VYB (SARS-CoV-2 S with one SB open) [363, 372]. The angiotensin-converting enzyme (ACE)-related carboxypeptidase, ACE2, is a type I integral membrane protein of 805 amino acids that contains one HEXXH + E zinc-binding consensus sequence, and it has been implicated in the regulation of heart function and also as a functional receptor for coronavirus such as SARS and SARS-CoV-2 [359]. To gain further insights into this enzyme, the first crystal structures of the native (PDB entry 1R42) and inhibitor-bound (PDB entry 1R4L) forms of the ACE2 extracellular domains were solved to 2.2- and 3.0-Å resolution, respectively [359]. ACE2 is the cellular receptor for SARS-CoV-2; the cryo-EM structure for the SARS-CoV-2 S receptor-binding domain (RBD) in complex with ACE2 (in the presence of a neutral amino acid transporter B.0 AT1) was determined with PDB entry 6M71 [387]. Another SARS-CoV-2 S-RBD in complex with human ACE2 structure is the crystal structure with PDB entry 6VW1. SARS-CoV-2 and SARS recognize the same ACE2 in humans. The structure was determined by molecular replacement using the structure of SARS RBD complexed with ACE2 as the search template (PDB entry 2AJF) [317]. This chapter will perform MD computations of these six structures (with PDB entries 6VXX, 6VYB, 1R4L, 1R42, 6M17, and 6VW1) to reveal some structural bioinformatics for developing therapies of the currently fatal COVID-19.

7.2 Materials and Methods 7.2.1 Trimeric SARS-CoV-2 S For the SARS-CoV-2 trimeric spike, its MD materials and methods can be seen from [321]: “Two 10 .μs simulation trajectories of the trimeric SARS-CoV-2 spike glycoprotein with additional loop structures and glycan chains. Trajectory 1 was initiated in the closed state (PDB entry 6VXX), and trajectory 2 in a partially opened state (PDB entry 6VYB). The simulations used the Amber ff99SB-ILDN force field for proteins, the TIP3P model for water, and the Amber Glycam force field for the glycosylated parts of the system. The C- and N-peptide termini are capped with

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amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.” We denote the trimeric spike models as the 6VXX-trimeric-spike-closed-model-1 and the 6VYBtrimeric-spike-opened-model-2, respectively.

7.2.2 Human ACE2 For the human ACE2 ectodomain, in [321] two trajectories were initiated in an inhibitor-bound closed state (PDB entry 1R4L) and in an apo open state (PDB entry 1R42), respectively. Their simulations “used the Amber ff99SB-ILDN force field for proteins, the TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and A-peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.” We denote the ACE2 models as the 1R4L-ACE2-closed-model-3 and the 1R42-ACE2-opened-model-4, respectively.

7.2.3 Binding of SARS-CoV-2 S-RBD and Human ACE2 For the SARS-CoV-2 spike receptor-binding domain (RBD) in complex with ACE2, in [321], we find two trajectories for PDB entries 6M17 and 6VW1, respectively. For 6M17.pdb, D-chain 21–612 (i.e., the peptidase domain (PD) [359] of ACE2) and Fchain 336–518 (i.e., SARS-CoV-2 S-RBD) were used in the MD simulation; and for 6VW1.pdb, the dimers of B-chain (i.e., the PD of ACE2) (with Zn.2+ 703) and F-chain 331–527 (i.e., SARS-CoV-2 S-RBD) were used in the MD simulation. The simulation methods are the same as all the above models. We denote the S-ACE2 bindings as the 6M17-spike-ACE2-binding-model-5 and the 6VW1-spike-ACE2binding-model-6, respectively. The MD data of trajectories can be downloaded under the Creative Commons Attribution 4.0 International Public License from [321], and the data IDs are 11021566 (6VXX.pdb), 11021571 (6VYB.pdb), 10875754 (1R4L.pdb), 10875753 (1R42.pdb), 10905033 (6M17.pdb), and 10875775 (6VW1.pdb), respectively, for the six models. In the below, (i) firstly, all these PDB entries will be optimized into a much more stable transition state—the hybrid strategy [405] of mathematical optimization’s neighboring different (local search) algorithms is used in the optimization; (ii) secondly, we will present some important structural bioinformatics from the optimized structures; and (iii) we then only prove the structural bioinformatics of

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(ii) from the analyses of the MD data of [321] (in order to reduce the numerously large structural bioinformatics obtained from the MD data). Currently, lots of researchers are using optimization to screen, find, and design new therapies for COVID-19 but it is not always used professionally. The hybrid strategy of mathematical optimization’s neighboring different (local search) algorithms is used professionally in this chapter. Basing on this optimization approach, we will catch some basic structural bioinformatics. The optimized structure is at a transition state with the best stability and the lowest energy. To really understand the stability of molecules and their mechanisms of action, we should consider not only the static NMR, X-ray, or cryo-EM structures concerned but also the dynamical information obtained by MD or quantum mechanics/molecular mechanics (QM/MM) simulating their internal motions or dynamic processes. We will just use and analyze the MD trajectory data of others to confirm our optimizationbased structural bioinformatics. We can get numerously large bioinformatics from the large-scale MD or QM/MM raw trajectory data. The optimization strategy will significantly reduce the scale of data and at the same time get rid of useless bioinformatics. The structural bioinformatics approach used here is also quite appealing for studying various in-depth biological phenomena. Although currently, the MD trajectory data is already present, X-ray or cryo-EM experimental structures are also available, interaction profiling is also performed by the data collectors, and many aspects are still needed for the author to study further; for example, the spike experimental structures are not complete (so that the trajectory data DESRES-ANTON-10897136 and DESRES-ANTON-10897850 (released on March 27, 2020) are without additional loop structures and glycan chains) and many other spike molecular modeling (MM) models around the world are not definitely complete and correct yet. Thus, currently, we still need to deeply analyze the many spike MM models and their MD trajectory data around the world. The MD trajectory data of the six models is huge. We focus on/represent them into six optimized structures; and we only confirm their structural bioinformatics from the analyses of the huge collected MD trajectory data. The representation is clear and scientific, because only the optimized structures are the most stable ones and with lowest energies. Our optimization strategy might be the most correct and professional one, because many people are using optimization to screen compounds now but almost all failed in the clinical drug tests. The noncovalent interactions of hydrogen bonds (HBs), salt bridges (SBs), and van der Waals (vdWs) contacts and hydrophobic interactions (HYDs) are driving a protein to be able to perform its biological functions. This chapter will find out the HBs, SBs, HYDs, and vdWs of each model from the large MD trajectory data and evaluate the reliability of the MD trajectory data, presenting basic structural bioinformatics (Figs. 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 7.10, 7.11 and 7.12) to drug designers or discovery. We will not aim to design a drug against the COVID-19 virus in this chapter because designing a drug takes a long time and it takes 8 or 10 years to have a successful clinical test.

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7.3 Results and Discussions 7.3.1 The 6VXX (SARS-CoV-2 S Close) Model: Model1 We optimized the A-chain of 6VXX.pdb and got an optimized structure (denoted as 6VXX-Achain-Optimized ) with 5.923734 Å of RMSD (root mean square deviation) value from its original structure. For the 6VXX-Achain-Optimized structure, we found 20 SBs: ASP467-ARG454, ASP53-LYS195, ASP389-LYS528, ASP398-ARG355, GLU1031-ARG1039, ASP820-ARG815, ASP442-ARG509, GLU725-HIS1064, GLU583-LYS535, ASP228-LYS202, GLU96-ARG190, GLU324-LYS537, ASP820-LYS811, ASP663-LYS310, GLU773-ARG1019, ASP775-LYS733, GLU340-LYS356, ASP578-ARG328, ASP574-LYS557, ASP40-ARG44; 140 HBs; 5 .π -cations, TYR396-ARG.+ 355.NH2, ARG.+ 355.NH2PHE464, LYS.+ 1028.NZ-PHE1042, LYS.+ 278.NZ-PHE306, and ARG.+ 44.NH2HIS49; 19 .π -.π stackings, TYR1110-PHE1075, TYR1067-PHE906, PHE800PHE898, PHE898-PHE802, PHE802-PHE1052/PHE927, TYR660-TYR695, HIS655-PHE643, TYR612-PHE318, PHE275-PHE58, PHE92-TRP104 (2), PHE201-PHE106, HIS519-PHE565, PHE423-TRP353 (2), PHE377-TYR369, TRP436-PHE374, and PHE338-TYR365; and its Poison-Boltzmann electrostatic potential surface, hydrophobic/hydrophilic surface, Ramachandran plot, phi, psi, secondary structure, SASA (solvent accessible/accessibility surface area) etc.; we know that NAGs have positive electrostatics, there is a large hydrophobic hole under the .α-helices around GLY744-VAL1040 (where GLY889-ALA890GLY891-ALA892-ALA893 construct a hydrophobic core), and residues TYR904-ARG905-PHE906 construct one solvent accessible surface, etc. For the 10 .μs MD simulation trajectory data [321], there are 8335 frames and each frame has 1.2 ns MD. We picked up 835 frames with a frame interval of 12 ns. From the 835 frames, we can confirm all the above SBs except for the very weak SBs ASP467-ARG454, GLU725-HIS1064, ASP228-LYS202, and ASP663-LYS201; in addition, we find SBs A:GLU1031-B:ARG1039, B:GLU1031-C:ARG1039, C:GLU1031-A:ARG1039, A:ASP574-C:LYS854, B:ASP574-A:LYS854, and C:GLU773-A:LYS974 are among the three monomers of the trimeric spike. The SBs have an oxygen-nitrogen cutoff of 3.2 Å, and in all we found 537 SBs from the 835 frames and we have shown the above SBs in Fig. 7.7. From the 835 frames, for HBs we set 3.0 Å as the donor-acceptor cutoff distance and 20.◦ as the cutoff angle and find 13,817 HBs during the 10 .μs MD; all the 140 HBs of the 6VXX-Achain-Optimized model can be confirmed and we list the HBs with more than 50% occupancy rates during the 10 .μs MD simulations for the 6VXX-trimeric-spike-closed-model-1 in Table 7.1. All the abovementioned SBs are polar contacts (SB and HB) and the SB ASP442-ARG509 has strong HB contacts: C:ASP442.OD1-C:ARG509.NE (during 28–834 frames with an average value of 2.860864 Å) with an occupancy rate of 54.13% and B:ASP442.OD1B:ARG509.NH2 (during the whole 835 frames with an average value of 2.848252 Å) with an occupancy rate of 53.45% (Table 7.1 and Fig. 7.13)—the strong polar

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contact between ASP442 and ARG509 is in the RBD (receptor-binding domain) region of spike, with the polar contact GLU1031-ARG1039 on another side of the spike (central helix-connector domain (CH-CD)), holding the trimeric spike at both ends tightly. From Table 7.1, we know some strong HBs among A-B-Cchains: B:PHE43.N-C:PHE565.O (during the whole 835 frames with an average value of 2.919316 Å) with an occupancy rate of 54.13%—with a strong side-chain .π − π stacking too (Fig. 7.13), C:TYR369.OH-A:THR415.OG1 (during 83–834 frames with an average value of 3.650197 Å during the whole 835 frames) with an occupancy rate of 50.30% (Fig. 7.13). For the MD, from the performances of the MD secondary structures, RMSD, potential energies, kinetic energies, and RMSF developments, we know that it reached equilibration and it is in a production phase, where RMSF is the RMS (root mean square) fluctuation—the segments 68–78, 142–152, 180–186, 244–261, 622–636, 677–787, and 833–853 of the 6VXX-trimeric-spike-closed-model-1 have larger RMSF values than other regions.

7.3.2 The 6VYB (SARS-CoV-2 S with One SB Open) Model: Model2 We optimized the A-chain of 6VYB.pdb and got an optimized structure (denoted as 6VYB-Achain-Optimized ) with an RMSD value of 6.182470 Å from its original structure. For the 6VYB-Achain-Optimized structure, we found 20 salt bridges (SBs), ASP820-ARG815, ASP578-ARG328, ASP820LYS811, ASP442-ARG509, ASP467-ARG454, ASP53-LYS195, ASP663-LYS310, GLU583-LYS535, ASP775-LYS733, GLU773-ARG1019, GLU340-LYS356, ASP574-LYS557, ASP40-ARG44, GLU1031-ARG1039, GLU725-HIS1064, ASP1084-LYS1086, ASP571-ARG567, ASP405-ARG403, GLU465-ARG457, GLU191-ARG34 (without ASP389-LYS528, ASP398-ARG355, GLU324LYS537, GLU96-ARG190, and ASP228-LYS202 of the 6VXX-Achain-Optimized structure), 264 hydrogen bonds (HBs); 7 .π -cations, TYR396-ARG.+ 355.NH2, ARG.+ 355.NH2-PHE464, LYS.+ 1028.NZ-PHE1042, LYS.+ 278.NZ-PHE306, ARG.+ 44.NH2-HIS49, ARG.+ 466.NH2-TRP353, and LYS.+ 1073.NZ-PHE1075; 17 .π − π stackings, TYR1110-PHE1075, PHE800-PHE898, PHE898-PHE802, PHE802-PHE1052/PHE927, TYR660-TYR695, PHE92-TRP104 (2), PHE201PHE106, PHE423-TRP353 (2), PHE377-TYR369, TRP436-PHE374, PHE58PHE275, TYR495-TYR453, PHE515-PHE392, PHE192-TRP104 (without TYR1067-PHE906, HIS655-PHE643, TYR612-PHE318, HIS519-PHE565, and PHE338-TYR365 of the 6VXX-Achain-Optimized structure); and its PoisonBoltzmann electrostatic potential surface, hydrophobic/hydrophilic surface, Ramachandran plot, phi, psi, secondary structure, SASA, etc.—we know that the NAGs have positive electrostatics, there is a large hydrophobic hole under the .α-helices around GLY744-VAL1040 (where GLY889-ALA890-GLY891-ALA892-

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ALA893 and GLY667-ALA668-GLY669 construct two respective hydrophobic cores), and residues TYR904-ARG905-PHE906 and ARG355-LYS356-ARG357 construct two respective solvent accessible surfaces, etc. From the 835 frames (with a frame interval of 12 ns) of the 10 .μs MD simulation trajectory data [321], we can confirm all the above 20 SBs except for GLU725-HIS1064; in addition, we find SBs (1) A:GLU1031B:ARG1039, B:GLU1031-C:ARG1039, and C:GLU1031-A:ARG1039 (with weak SBs A:GLU1031-B:LYS1038, B:GLU1031-A:LYS1038, and C:GLU1031A:LYS1038), (2) C:ASP574-B:LYS854, and (3) B:GLU773-C:ARG1014 among the three monomers of the trimeric spike. In all we found 556 SBs and have shown the above SBs in Fig. 7.8. We found 13,652 HBs during the 10 .μs MD; all the 264 HBs of the 6VYB-Achain-Optimized model can be confirmed and we list the HBs with more than 50% occupancy rates during the 10 .μs MD simulations for the 6VYB-trimeric-spike-opened-model-2 in Table 7.2. All the abovementioned SBs are polar contacts and the SB ASP442-ARG509 has strong HB contacts: B:ARG509.NE-B:ASP442.OD2 with an occupancy rate of 58.44% (during the whole 835 frames with an average value of 2.826612 Å) and B:ARG509.NH2B:ASP442.OD1 with an occupancy rate of 51.62% (during the whole 835 frames with an average value of 2.827929 Å) (Table 7.2 and Fig. 7.14)—the polar contact between ASP442 and ARG509 is in RBD of spike, with the polar contacts GLU1031-ARG1039 and GLU1031-LYS1038 in the CH-CD of the spike, holding the trimeric spike at both ends tightly. From Table 7.2, we know some strong HBs among A-B-C-chains: A:PHE43.N-B:PHE565.O (Fig. 7.14) with an occupancy rate of 51.38% (during the whole 835 frames with an average value of 2.937867 Å), B:PHE43.N-C:PHE565.O (Fig. 7.14) with an occupancy rate of 54.01% (during the whole 835 frames with an average value of 2.933415 Å), and C:PHE43.NA:PHE565.O (Fig. 7.14) with an occupancy rate of 54.37% (during the whole 835 frames with an average value of 2.911408 Å)—between the side-chains of PHE43 and PHE565, there are strong .π -.π stackings too. For the MD, from the performances of the MD secondary structures, RMSD, potential energies, kinetic energies, and RMSF developments, we know it reached equilibration and it is in a production phase. The RMSF values show us that the segments 68–78, 142–152, 181–184, 247–257, 477–487, 622–635, 677–687, 842– 844, 941–944, and 1140–1148 of the 6VYB-trimeric-spike-opened-model-2 have larger RMSF values than other regions. For the above two (closed and opened) spike models, we may see in each monomer that there is a strong polar contact between ASP442 and ARG509, and there is a strong HB (at the same time, a .π − π stacking) between PHE43.N and PHE565.O among the three monomers.

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7.3.3 The 1R4L (ACE2 Close) Model: Model3 We optimized 1R4L.pdb and got an optimized structure (denoted as 1R4Loptimized ) with an RMSD value of 0.961113 Å from its original structure. For the 1R4Loptimized structure, we found 18 SBs, GLU406-ARG518, GLU402ARG514, GLU181-ARG177, GLU406-HIS374, GLU433-LYS288, GLU232ARG582, ASP30-HIS34, GLU310-ARG306, ASP201-ARG219, ASP206LYS562, GLU457-ARG460, GLU182-ARG115, GLU435-LYS541, GLU479LYS475, GLU208-ARG219, GLU22-LYS26, GLU145-LYS363, and GLU402HIS374; 50 HBs; 10 .π -cations, TRP48-ARG357.NE (2), TRP302-ARG306.NE, TRP215-LYS577.NZ, ARG514.NE-TYR515, TYR515-ARG273.NE, TRP461ARG204.NE, TYR497-LYS174.NZ, TRP478-LYS481.NZ, and TRP165-ARG169. NH2; 22 .π -.π stackings, PHE72-TRP69, TRP349-TRP48 (3), TRP328-PHE327, PHE314-HIS417, HIS265-TYR158, TYR158-TYR255, TRP473-TRP459, (3) TRP459-TRP477, TRP477-TRP478 (2), PHE230-TYR454, TYR202-TYR196, PHE504-HIS345, HIS345-HIS505, HIS505-PHE512, HIS401-HIS378, HIS378HIS374, and HIS374-Zn2.+ , Zn2.+ -HIS378; and its Poison-Boltzmann electrostatic potential surface, hydrophobic/hydrophilic surface, phi, psi, secondary structure, SASA, ligand (XX5 804) interaction diagram, and Ramachandran plot (Fig. 7.1). We can see that the Ramachandran plot has a dark area, in SASA graph the SER411-ALA412-ALA413 area is highly hydrophobic, and there are three most solvent accessible areas: TYR202-TRP203-ARG204, TRP459-ARG460-TRP461, and ARG514-TYR515-TYR516 (where the HB TYR516.OH-THR229.OG1 has an occupancy rate of 53.05% during the 10 .μs MD (Table 7.3)).

Fig. 7.1 The ligand (XX5 804) interaction diagram and the Ramachandran plot of the 1R4Loptimized model

From the 8335 frames (with a frame interval of 1.2 ns) of the 10 .μs MD trajectory data [321], we get 146 SBs and we can confirm all the 15 SBs except for the ones (GLU406-HIS374, ASP30-HIS34, GLU402-HIS374)

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with HIS residues—these three SBs are replaced by SBs GLU406-ARG518, ASP30-LYS26/31, and GLU402-ARG514/518; some strong SBs such as GLU435LYS541, GLU182-ARG115, ASP206-LYS562, ASP201-ARG219, GLU22-LYS26, GLU208-ARG219, GLU433-LYS288, and GLU406-ARG518 are shown in Fig. 7.9. From the 8335 frames, we got 4033 HBs and all the 50 HBs in the 1R4Loptimized structure can be confirmed from them, and we list the HBs with more than 50% occupancy rates in Table 7.3, where TYR237.OH-VAL485.O (with an average value of 2.907522 Å and broken during frames 103–169 and 211–235 with a frame interval of 12 ns), TYR252.OH-LEU156.O (with an average value of 3.143333 Å and broken during frames 1–32, 103–202, 272–279, and 380–404 with a frame interval of 12 ns), and THR516.OH-THR229.OG1 (with an average value of 2.921907 Å) (Fig. 7.15) span 248, 96, and 287 residues, respectively. For the MD, the RMSD values from the 2600th frame equilibrate around 3.5 Å and the whole RMSD values of 8335 frames vary within 2 Å—this implies that the MD is very reliable; the secondary structural changes happened in the region around ALA36 unfolding from .α-helices to turns starting from the 3700th frame, in the region around VAL172 unfolding from .α-helices to turns even starting from beginning, and in the region around PHE274 even starting from the .α-helices to the 3.10 -helices; and for the RMSF values, the THR129-GLN139 region has large RMSF values from the 1600th frame, the region around PRO289 has large RMSF values from the 5050th frame, and the C-terminal THR609-ASP615 has large RMSF values even since the beginning of MD.

7.3.4 The 1R42 (ACE2 Open) Model: Model4 We optimized 1R42.pdb and get an optimized structure (denoted as 1R42optimized ) with an RMSD value of 0.978346 Å from its original structure. For the 1R42optimized structure, we found 18 SBs, GLU181-ARG177, GLU433LYS288, GLU310-ARG306, ASP201-ARG219, GLU182-ARG115, GLU208ARG219, GLU402-HIS374, GLU37-ARG393, ASP355-ARG357, GLU231LYS234, GLU495-ARG177, GLU489-ARG482, GLU430-LYS541, ASP509LYS187, GLU402-HIS378, GLU227-LYS458, GLU189-LYS112, and ASP543HIS417 (without the SBs GLU406-ARG518, GLU402-ARG514, GLU406HIS374, GLU232-ARG582, ASP30-HIS34, ASP206-LYS562, GLU457-ARG460, GLU435-LYS541, GLU479-LYS475, GLU22-LYS26, and GLU145-LYS363 of the 1R4Loptimized structure); 230 HBs; 13 .π -cations, ARG306.NE-TRP302, ARG357.NE-TRP48 (2), LYS577.NZ-TYR215, ARG514.NE-TYR515, TYR515ARG273.NE, ARG204.NE-TRP461 (2), ARG169.NE-TRP165, LYS174.NZTYR494, LYS309.NZ-TYP328, LYS288.NZ-PHE285, and LYS441.NZ-TYR279 (without TRP478-LYS481.NZ of the 1R4Loptimized structure); 29 .π -.π stackings, PHE390-PHE40, PHE40-TRP69, TRP48-TRP349 (2), PHE327-TRP328 (2), HIS373-PHE314, PHE314-PHE315, HIS374-HIS378, HIS378-HIS401, HIS401-TYR385/TYR381, PHE400-PHE525, TYR587-PHE588, TRP566-

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TYR217, TYR515-HIS505, HIS505-PHE504/PHE512, TYR196-TYR202, PHE464-TYR199, TYR594-TYR243, TYR255-TYR158, TYR158-HIS265, HIS493-TYR497, (2) TRP459-TRP477, TRP477-TRP478 (2), and TRP473TRP459 (without PHE72-TRP69, PHE314-HIS417, and PHE230-TYR454 of the 1R4Loptimized structure); and its Poison-Boltzmann electrostatic potential surface, hydrophobic/hydrophilic surface, secondary structure, phi, psi, SASA, etc. We know that in the SASA graph the SER411-ALA412-ALA413 area is highly hydrophobic and there are three most solvent accessible areas: TYR202-TRP203-ARG204, TRP459-ARG460-TRP461, and ARG514-TYR515-TYR516 (where there is a HB TYR516.OH-THR229.OG1 with an occupancy rate of 52.27% during the 10 .μs MD). From the 8335 frames (with a frame interval of 1.2 ns) of the 10 .μs MD trajectory data [321], we get 134 SBs and we can confirm all the 15 SBs except for the ones (ASP543-HIS417, GLU402-HIS374/378) with HIS residues—these three SBs are replaced by SBs ASP543-LYS416/419/534/541 and GLU402-ARG514/518; some strong SBs such as GLU182-ARG115, ASP201-ARG219, GLU208-ARG219, ASP355-ARG357, GLU231-LYS234, GLU489-ARG482, GLU227-LYS458, and GLU189-LYS112 are shown in Fig. 7.10. From the 8335 frames, we got 4340 HBs and all the 230 HBs in the 1R42optimized structure can be confirmed from them, and we list the HBs with more than 50% occupancy rates in Fig. 7.4, where TYR237.OH-VAL485.O (with an average value of 2.827859 Å), THR567.OG1TYR215.O (with an average value of 2.824532 Å), and THR516.OH-THR229.OG1 (with an average value of 2.940768 Å) (Fig. 7.16) span 248, 352, and 287 residues, respectively (where there is a .π -cation TYR215-LYS577.NZ), and from Tables 7.3 and 7.4 and Figs. 7.15 and 7.16, we know that both 1R42-ACE2-closed-model-4 and 1R4L-ACE2-opened-model-3 have three very strong HBs THR229.OG1ASP225.O (with occupancy rates of 61.90 and 66.27%, during the whole 835 frames (with a frame interval of 12 ns) with average values of 2.835496 and 2.803843 Å), THR371.OG1-ASP367.O (with occupancy rates of 61.73 and 61.87%, during the whole 835 frames with average values of 2.726547 and 2.725134 Å), and HID241.N-TYR237.O (with occupancy rates of 58.96 and 61.37%, during the whole 835 frames with average values of 2.818753 and 2.832368 Å). We can see that the three residues, i.e., TYR237, THR229, and TYR215, play an important role. For the MD, the RMSD values for all the 8335 frames equilibrate around 3.3 Å and the whole RMSD values of 8335 frames vary within 2 Å—this implies that the MD is very reliable; the secondary structural changes happened in the region around PHE274, starting from .α-helices to 3.10 -helices; in the region around GLN325, unfolding from .α-helices to turns; in the region around PHE512, unfolding from .α-helices to turns or 3.10 -helices; and in the region around NAG546-SER563, unfolding from .α-helices to turns or 3.10 -helices from the 6850th frame; and for the RMSF values, the GLU329-TRP349 region, the region around PRO289, and the C-terminal THR609-ASP615 have large RMSF values even since the beginning of MD. For the human ACE2, we found that strong HBs, i.e., TYR237.OH-VAL485.O, THR516.OH-THR229.OG1, TYR252.OH-LEU156.O, and THR567.OG1-

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TYR215.O (where there is a .π -cation, TYR215-LYS577.NZ), have large spans of residues, and three very strong HBs, THR229.OG1-ASP225.O, THR371.OG1ASP367.O, and HID241.N-TYR237.O, have large occupancy rates; thus, we may see that the three residues, TYR237, THR229, and TYR215, play an important role.

7.3.5 The 6M17 (B0 AT1) Model: Model5 We optimized the DF-chains of 6M17.pdb and got an optimized structure (denoted as 6M17-DFchains-Optimized ) with an RMSD value of 3.281984 Å from its original structure. For the 6M17-DFchains-Optimized structure, we found 1 SB, ASP467-ARG457, in the F-chain; 22 SBs in the D-chain, ASP719-ARG708, GLU182-ARG115, ASP335-LYS363, GLU406-ARG518, GLU723-ARG621, GLU312-LYS309, GLU375-HIS378, GLU435-HIS540, ASP201-ARG219, GLU310-ARG306, GLU457-ARG460, GLU701-ARG697, GLU208-ARG219, GLU430-LYS419, GLU181-ARG177, GLU495-ARG177, GLU433-LYS288, ASP509-LYS187, GLU667-ARG644, GLU37-ARG393, GLU189-LYS112, and GLU402-HIS378; 28 hydrogen bonds (HBs); 8 .π -cations, TRP168-LYS.+ 174.NZ, TRP165-ARG.+ 169.NH2, TYR515-ARG.+ 273.NH2, TRP48-ARG.+ 357.NH2, PHE592-LYS.+ 596.NZ, TYR41-LYS.+ 353.NZ, and TRP461-ARG.+ 204.NH2 (2); 24 .π -.π stackings, TYR423-TRP353 (2), TRP566-TYR217, TYR521PHE400, TYR381-TYR385, TYR202-TYR196, TYR199-PHE464, HIS239PHE592, PHE588-TYR587, TRP349-TRP48, TRP328-PHE327, TYR497HIS373, TYR255-TYR158-HIS265, PHE681-PHE643, (2) TRP459-TRP477, TRP477-TRP478 (2), PHE314-PHE315, HIS505-PHE504/PHE512/TYR515, and HIS378-HIS374; and its Poison-Boltzmann electrostatic potential surface, hydrophobic/hydrophilic surface, secondary structure, SASA, etc. We know that residues F:NAG, F:LEU387, F:ALA435, D:GLN728 have positive electrostatics; residue TYR459-ARG460-TRP467 in the D-chain constructs one solvent accessible surface; and F-chain residues SER371-ALA372-SER373, ALA411-PRO412-GLY413, and ALA475-GLY476-SER477-THR478-PRO479 and D-chain residues GLY104-SER105-SER106, THR334-ASP335-PRO336GLY337, SER411-ALA412-ALA413, VAL485-GLY486-VAL487-VAL488, PRO500-ALA501-SER502, VAL685-THR667-ALA687-PRO688, GLY732PRO733-PRO734, and PRO737-PRO738-VAL739-SER740 construct hydrophobic cores, etc. For the 10 .μs MD simulation trajectory data [321], there are 8335 frames and each frame has 1.2 ns MD. From the 8335 frames, we got 188 SBs; we can confirm the SBs in the F-chain (i.e., the RBD of spike), the D-chain (i.e., the PD of human ACE2, especially the following SBs in 1R4L-ACE2-closed-model3 and 1R42-ACE2-opened-model-4 (Figs. 7.9, 7.10 and 7.11): GLU182-ARG115, ASP201/GLU208-ARG219, GLU406-ARG518, GLU435-LYS541, GLU310-ARG306, GLU181ARG177, GLU433-LYS288, and GLU189-LYS112), and between the F-chain and D-chain

of the 6M17-DFchains-Optimized model, and some important SBs have been

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shown in Fig. 7.2, where we know that the SB D:ASP30-F:LYS417 is very strong, but SBs D:GLU23-F:LYS458 (where the .α-helix HB D:GLU23.O-D:THR27.OG1 has an occupancy rate of 54.57%, with an average value of 2.859609 Å during the whole 835 frames), D:GLU37-F:ARG403, and F:GLU484-D:LYS31 do not always exist during the 10 .μs of MD, and for the SB D:ASP38-F:ARG403, we just find one snapshot at the 5681st frame. From the 8335 frames, we found 4987 HBs but we cannot find a strong HB being always kept during the 10 .μs between D- and F-chains: D:LYS31.NZ-F:GLU484.OE1 (0.89%), D:LYS31.NZ-F:GLU484.OE2 (0.74%), D:LYS31.NZ-F:GLU484.CD (0.01%); F:LYS458.NZ-D:GLN24.OE1 (0.01%), F:LYS458.NZ-D:GLU23.OE1 (0.47%), F:LYS458.NZ-D:GLU23.OE2 (0.41%); F:LYS417.NZD:ASP30.OD2 (7.95%), F:LYS417.NZ-D:ASP30.OD1 (8.36%) (Fig. 7.17), F:LYS417.NZD:HIS34.NE2 (3.60%); F:ARG403.NH2-D:HIS34.NE2 (0.04%), F:ARG403.NH1-D:HIS34.NE2 (0.01%), F:ARG403.NH2-D:GLU37.OE2 (3.34%), F:ARG403.NH2-D:GLU37.OE1 (4.56%), F:ARG403.NH1-D:GLU37.OE2 (0.29%), F:ARG403.NH1-D:GLU37.OE1 (0.41%) (Fig. 7.17), and F:ARG403.NH1-D:ASP38.OD1 (0.01%)—where in the brackets are the occupancy

rates during 10 .μs. We list the HBs with more than 50% occupancy rates during the 10 .μs MD simulations for the 6M17-spike-ACE2-binding-model-5 in Table 7.5 and shown in Fig. 7.17. The HB F:THR500.OG1-D:ASP355.OD1 (with an occupancy rate of 53.51%, with an average value of 2.917075 Å during the whole 835 frames) links the spike and the ACE2 strongly. In Fig. 7.17, we have shown four HBs, VAL433.N-LYS378.O (with an occupancy rate of 61%, with an average value of 2.849615 Å during the whole 835 frames), LEU513.N-CYS432.O (with an occupancy rate of 57.08%, with an average value of 2.903840 Å during the whole 835 frames), VAL511.N-ILE434.O (with an occupancy rate of 56.02%, with an average value of 2.904051 Å during the whole 835 frames), and ARG454.N-ASN422.OD1 (with an occupancy rate of 63.83%, with an average value of 2.827907 Å during the whole 835 frames) in the spike; four HBs, THR567.OG1-TYR215.O (with an occupancy rate of 57.78%, with an average value of 2.803045 Å during the whole 835 frames), TYR516.OH-THR229.OG1 (with an occupancy rate of 56.66%, with an average value of 2.881762 Å during the whole 835 frames), TYR41.OH-ASP355.OD1 (with an occupancy rate of 53.47%, with an average value of 2.747765 Åduring frames 85–835), and TYR237.OHVAL485.O (with an occupancy rate of 69.54%, with an average value of 2.803158 Å during the whole 835 frames—where it is broken during frames 41–55, 166–205, and 280–287) in the ACE2; and two polar contacts, F:LYS417.NZ-D:ASP30.OD2/1 and F:ARG403-D:GLU37. For the MD, during the 10 .μs, its RMSD values equilibrate around 3.1 Å and the whole RMSD values of 8335 frames vary within about 2 Å—this implies that the MD is very reliable; the secondary structural developments show us starting from the 2700th frame .α-helix structure of spike ASN360-VAL382 (and human ACE2 VAL488-TYR510) had unfolded into turns, and around LYS288 of human ACE2 starting from the 5660th frame, more turns appear; and the RMSF values show us that the spike PRO337-VAL382 region, human ACE2 ASN134, LEU333, etc. have large RMSF values during the 10 .μs of MD.

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Fig. 7.2 Some important SBs and HBs of the 6M17-spike-ACE2-binding-model-5 confirmed by MD data in [321]

7.3.6 The 6VW1 (Chimera) Model: Model6 We optimized the BF-chains of 6VW1.pdb and got an optimized structure (denoted as 6VW1-BFchains-Optimized ) with an RMSD value of 2.177343 Å from its original structure. For the 6VW1-BFchains-Optimized structure, we found 4 SBs, ASP467-ARG457, GLU465-ARG457, ASP398-ARG355, and ASP442-ARG509 in the F-chain, and 16 SBs in the B-chain, ASP201-ARG219, GLU457-ARG460, GLU495-ARG177, GLU37-ARG393, GLU181-ARG177, ASP509-LYS187, GLU189-LYS112, GLU208-ARG219, ASP499-HIS493, GLU402-HIS374, ASP355-ARG357, GLU489-ARG482, ASP382-HIS401, ASP38-LYS353, GLU406-HIS374, and GLU166-HIS493; 83 HBs (where HB F:TYR449.HH-B:ASP38.OD2 is with distance 1.82 Å); 15 .π -cations, TRP165-ARG169.NE, TRP48-ARG357.NE(2), TRP461-ARG204.NE-TRP271, ARG514.NETYR515-ARG273.NE, TYR380-LYS378.NZ, PHE464-ARG355.NH2, TRP353-ARG466.NE(2),

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TRP302-ARG306.NE(2), TYR279-LYS441.NZ, and TYR215-LYS577.NZ; 27 .π -.π stackings, TYR423-TRP353(2), TYR196-TYR202, HIS505-TYR515, TYR515-PHE512, PHE512HIS505, HIS505-PHE504, (2)TRP477-TRP459, TRP459-TRP477, TRP477-TRP478(2), TRP48-TRP349(2), TYR497-HIS493, HIS265-TYR158, TYR158-TYR255, PHE523-TYR587, TYR587-PHE588, PHE486-TYR83, PHE390-PHE40, TRP459-TRP473, and TRP594-TYR243;

and its Poison-Boltzmann electrostatic potential surface, hydrophobic/hydrophilic surface, secondary structure, SASA, etc.; we know that residues F:GLY431, TRP436, ILE358, ALA397, B:GLU310, GLN325, SER366, ALA372, and NAG712-713 have positive electrostatics, and the F-chain (i.e., RBD of spike) has high psi degrees and low phi degrees. For the 10 .μs MD simulation trajectory data [321], there are 8335 frames with a frame interval of 1.2 ns. From the 8335 frames, we got 147 SBs and 4187 HBs. We can confirm the strong SBs F:ASP398-F:ARG355 and F:ASP442F:ARG509 in the F-chain (i.e., the RBD of spike), the B-chain (i.e., the PD of human ACE2, especially the following SBs in 1R4L-ACE2-closed-model-3, 1R42-ACE2-opened-model-4, and 6M17-spike-ACE2-binding-model-5 (Figs. 7.9, 7.10, 7.11 and 7.12): GLU182-ARG115, GLU208-ARG219, GLU406-ARG518, GLU435LYS541, GLU310-ARG306, GLU433-LYS288, and GLU189-LYS112), and between the F-chain and B-chain of the 6VW1-BFchains-Optimized model, B:GLU329F:ARG439, F:GLU484-B:LYS31, and B:GLU23-F:LYS458 (where the .α-helix HB B:GLU23.O-B:THR27.OG1 has an occupancy rate of 50.81%, with an average value of 2.858096 Å during the whole 835 frames), and some important SBs have been shown in Fig. 7.3, where we know that the SB B:GLU329-F:ARG439 is very strong, F:GLU484-B:LYS31 is weaker, and SB B:GLU23-F:LYS458 is the weakest, but here the strong .α-helix HB B:GLU23.O-B:THR27.OG1 is found with an occupancy rate of 50.81%, with an average value of 2.858096 Å during the whole 835 frames. From the 8335 frames, we found 4187 HBs and we found two strong HBs being always kept during the 10 .μs between B- and F-chains (Fig. 7.18): F:ARG439.NH1-B:GLU329.OE1 (19.47%), F:ARG439.NH2-B:GLU329.OE2 (19.98%), F:ARG439.NH1-B:GLU329.OE2 (18.68%), F:ARG439.NH2-B:GLU329.OE1 (19.56%), F:TYR449.OH-B:ASP38.OD1 (30.47%), and F:TYR449.OH-B:ASP38.OD2 (29.02%); we also found a very weak HB between B- and F-chains: B:LYS31.NZ-F:GLU484.OE1 (0.65%), B:LYS31.NZ-F:GLU484.OE2 (0.84%), and B:LYS31.NZ-F:GLU484.CD (0.01%), where in the

brackets are the occupancy rates during 10 .μs. We list the HBs with more than 50% occupancy rates during the 10 .μs MD simulations for the 6VW1-spike-ACE2binding-model-6 in Table 7.6 and shown in Fig. 7.18.

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Fig. 7.3 Some important SBs of the 6VW1-spikeACE2-binding-model-6 confirmed by MD data in [321]

In Fig. 7.18, we have shown six HBs, VAL433.N-LYS378.O (with an occupancy rate of 55.27%, with an average value of 2.868132 Å during the whole 835 frames), LEU513.N-CYS432.O (with an occupancy rate of 58.81%, with an average value of 2.865653 Å during the whole 835 frames), VAL511.N-ILE434.O (with an occupancy rate of 53.86%, with an average value of 2.921195 Å during the whole 835 frames), ARG454.N-ASN422.OD1 (with an occupancy rate of 69.92%, with an average value of 2.814954 Å during the whole 835 frames), ASP398.NVAL512.O (with an occupancy rate of 54.78%, with an average value of 2.920962 Å during the whole 835 frames), and LEU461.N-ASP420.O (with an occupancy rate of 50.53%, with an average value of 2.900633 Å during the whole 835 frames) in the spike; four HBs, THR567.OG1-TYR215.O (with an occupancy rate of 59.34%, with an average value of 2.913999 Å during the whole 835 frames, broken during frames 204–206 and 705–723), TYR516.OH-THR229.OG1 (with an occupancy rate of 54.91%, with an average value of 2.912548 Å during the whole 835 frames), TYR41.OH-ASP355.OD2 (with an occupancy rate of 64.94%, with an average

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value of 2.715280 Å during the whole 835 frames), and TYR243.OH-THR282.O (with an occupancy rate of 50.08%, with an average value of 2.791970 Å during the whole 835 frames—where it is broken during frames 86–89, 547–553, and 166– 205) in the ACE2; and the strong HBs, F:ARG439.NH1/2-B:GLU329.OE1/2 and F:TYR449.OH-B:ASP38.OD1/2 between the spike and the ACE2. For the MD, during the 10 .μs starting from about 1900th frame, RMSD values equilibrate around 3.3 Å and the whole RMSD values of 8335 frames vary within about 2 Å—this implies that the MD is very reliable; the secondary structural developments show us that starting from the 1920th frame, .α-helix structure of human ACE2 around the HIS195 region had unfolded into turns, and around GLY173 of human ACE2 and the N-terminal 331–350 region, both have slightly changed into turns from .α-helices and changed back to .α-helices; and the RMSF values of human ACES show us that the regions of 129–139 and 329–335 and Cterminal 612–614 have large RMSF values during the 10 .μs of MD. For the bindings of spike (denoted as F-chain) and human ACE2 (denoted as D/B-chain), polar contacts F:LYS417-D:ASP30, F:ARG403-D:GLU37, F:ARG439B:GLU329, and F:TYR449-B:ASP38 and HB F:THR500.OG1-D:ASP355.OD1 are strong during MD of 10 .μs, salt bridges (SBs) F:LYS458-D/B:GLU23 (but D/B:GLU23 has high HB occupancy rates with D/B:THR27), F:ARG403D/B:GLU37 (has low HB occupancy rates), F:GLU484-D/B:LYS31, and F:ARG403-D/B:ASP38 (but HB D/B:ASP38-F:TYR449 is strong) are weak during the whole 10 .μs; during the whole 10 .μs, in the spike SBs F:ASP398-F:ARG355, and F:ASP442-F:ARG509 and in the human ACE2 SBs GLU182-ARG115, GLU208-ARG219, GLU406-ARG518, GLU435-LYS541, GLU310-ARG306, GLU433-LYS288, and GLU189-LYS112 are always strong in MD of 10 .μs. For HBs, during the whole 10 .μs, in the spike VAL433.N-LYS378.O, LEU513.NCYS432.0, VAL511.N-ILE434.O, and ARG454.N-ASN422.OD1 and in the ACE2 THR567.OG1-TYR215.O, TYR516.OH-THR229.OG1, and TYR41.OHASP355.OD2 are always very strong. The 500 ns MD trajectory data of spikeRBD-and-ACE2 (6M0J.pdb) [99] can confirm the strong polar contact between LYS417 and ASP30 (Fig. 7.4): A:ASP30E:LYS417 (E:LYS417.NZ-A:ASP30.OD2 with an occupancy rate of 43.21% and with an average value of 4.261707 Å during the whole 500 ns, E:LYS417.NZA:ASP30.OD1 with an occupancy rate of 11.58% and with an average value of 3.488454 Å during the whole 500 ns) with an average value of 3.781951 Å during the whole 500 ns. In addition, two weak polar contacts E:GLU484-A:LYS31 (A:LYS31.NZ-E:GLU484.OE1 0.40%, A:LYS31.NZ-E:GLU484.OE2 0.40%), A:GLU23E:LYS458 (E:LYS458.NZ-A:GLU23.OE2 0.40%, E:LYS458.NZ-A:GLU23.OE1 0.40%) are

also found from the analyses of the MD dataset [99]. The top 100 drugs (except for enloplatin) are binding at the interface of SARS-CoV-2-spike-RBD and human ACE2 [100] to disturb the interactions of LYS417 and ASP30 (Table 7.7). The MD trajectory data of [55] (amarolab.ucsd.edu/covid19.php) on the dimer of spike-RBD R-chain binding with human-ACE2 A-chain can also confirm the strong polar contact between LYS417 and ASP30 (Fig. 7.5):

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Fig. 7.4 The strong polar contact (left: SBs, right: HBs) between LYS417 and ASP30 is confirmed by MD data in [99] (PDB template 6M0J)

SBs ACEAA:ASP30-RBDBR:LYS417 and ACECA:ASP30-RBDDR:LYS417 with HBs RBDD:LYS417.NZ-ACEC:ASP30.OD1 21.92%, RBDB:LYS417.NZ-ACEA:ASP30.OD2 20.55%, RBDB:LYS417.NZ-ACEA:ASP30.OD1 15.75%, and RBDD:LYS417.NZ-ACEC:ASP30. OD2 15.75%. The weaker polar contact between GLU484 and LYS31 is also confirmed: SBs RBDBR:GLU484-ACEAA:LYS31 and RBDDR:GLU484-ACECA:LYS31 with HBs ACEC:LYS31.NZ-RBDD:GLU484.OE2 9.59%, ACEA:LYS31.NZ-RBDB:GLU484.OE2 8.9%, ACEC:LYS31.NZ-RBDD:GLU484.OE1 7.53%, and ACEA:LYS31.NZ-RBDB:GLN493. OE1 6.85%. We can confirm the following HBs: RBDD:THR500.OG1-ACEC:ASP355.OD2 43.84% and RBDB:THR500.OG1-ACEA:ASP355.OD2 27.4% . The main SBs and HBs

between the R-chain of spike-RBD-B/D and A-chain of human-ACE2-A/C by analyses of the open MD data in amarolab.ucsd.edu/covid19.php are listed as follows: – The SBs between R-chain of spike-RBD-B/D and A-chain of human-ACE2-A/C:

.·

.· .· .·

.·

.·

.· .· .· .· .· .· .· .· .· .· .·

ACEAA:GLU23-RBDBR:LYS458, ACECA:GLU23-RBDDR:LYS458, . RBDBR:ASP420-ACEAA:LYS26, ACEAA:ASP30-RBDBR:LYS417, ACECA:ASP30-RBDDR:LYS417, RBDBR:GLU484-ACEAA:LYS31, RBDDR:GLU484-ACECA:LYS31, . ACEAA:GLU37-RBDBR:ARG403, ACECA:GLU37-RBDDR:ARG403, . RBDBR:ASP405-ACEAA:ARG393; SBs between chainA of ACEA (i.e., dimeric-ACE monomer-A)—A-chain of ACEC (i.e. dimeric-ACE monomer-C): C:ASP136-A:ARG115, A:ASP136-C:ARG115, A:ASP136-C:LYS174, C:GLU140-A:LYS131, A:GLU140-C:LYS131, C:GLU171-A:LYS131, C:GLU634-A:LYS657, A:GLU634-C:LYS657, A:GLU639-C:ARG710, C:GLU639-A:ARG710, C:GLU667-A:ARG652, A:GLU667-C:ARG652, A:ASP713-C:LYS631, C:ASP713-A:ARG716, A:ASP713-C:ARG716, A:ASP719-C:ARG716, C:ASP799-A:LYS788;

– The HBs (with occupancy rates .≥5%) between spike-RBD-B/D and humanACE2-A/C:

280 .· .· .·

.·

.· .· .· .·

.·

.· .·

.· .· .·

7 Spike (S) Glycoprotein

RBDD:GLY502.N-ACEC:LYS353.O 50%, RBDB:GLY502.N-ACEA:LYS353.O 25.34%, RBDD:THR500.OG1-ACEC:ASP355.OD2 43.84%, RBDB:THR500.OG1-ACEA:ASP355. OD2 27.4%, RBDD:LYS417.NZ-ACEC:ASP30.OD1 21.92%, RBDB:LYS417.NZ-ACEA:ASP30.OD2 20.55%, RBDB:LYS417.NZ-ACEA:ASP30.OD1 15.75%, RBDD:LYS417.NZ-ACEC:ASP30. OD2 15.75%, RBDD:TYR505.OH-ACEC:GLU37.OE1 17.81%, RBDD:TYR505.OH-ACEC:GLU37.OE2 13.01%, RBDB:TYR505.OH-ACEA:GLU37.OE1 6.16%, RBDB:TYR505.OH-ACEA: GLU37.OE2 6.16%, . ACEA:TYR83.OH-RBDB:ASN487.OD1 37.67%, ACEC:TYR83.OH-RBDD:ASN487.OD1 21.23%, RBDD:TYR489.OH-ACEC:TYR83.OH 13.01% (with .π -.π stacking), ACEC:GLN24.NE2-RBDD:ALA475.O 6.16%, RBDB:TYR473.OH-ACEA:GLN24.OE1 5.48%, ACEA:LYS26.NZ-RBDB:THR415.OG1 5.48%, RBDD:LYS417.NZ-ACEC:ASP30.OD1 21.92%, RBDB:LYS417.NZ-ACEA:ASP30.OD2 20.55%, RBDB:LYS417.NZ-ACEA:ASP30.OD1 15.75%, RBDD:LYS417.NZ-ACEC:ASP30. OD2 15.75%, ACEC:LYS31.NZ-RBDD:GLU484.OE2 9.59%, ACEA:LYS31.NZ-RBDB:GLU484.OE2 8.9%, ACEC:LYS31.NZ-RBDD:GLU484.OE1 7.53%, . ACEA:LYS31.NZ-RBDB:GLN493. OE1 6.85%, RBDD:GLN493.NE2-ACEC:GLU35.OE2 9.59%, RBDB:GLN493.NE2-ACEA:GLU35.OE1 6.85%, RBDD:GLN493.NE2-ACEC:GLU35.OE1 6.85%, RBDD:TYR505.OH-ACEC:GLU37.OE1 17.81%, RBDD:TYR505.OH-ACEC:GLU37.OE2 13.01%, RBDB:TYR505.OH-ACEA:GLU37.OE1 6.16%, RBDB:TYR505.OH-ACEA: GLU37.OE2 6.16%, . RBDD:TYR449.OH-ACEC:ASP38.OD2 7.53%, RBDB:TYR449.OH-ACEA:ASP38.OD1 5.48%, . RBDB:THR500.OG1-ACEA:TYR41.OH 7.53%, RBDD:THR500.OG1-ACEC:TYR41.OH 5.48%, ACEA:TYR83.OH-RBDB:ASN487.OD1 37.67%, ACEC:TYR83.OH-RBDD:ASN487.OD1 21.23%, RBDD:TYR489.OH-ACEC:TYR83.OH 13.01%.

Fig. 7.5 The strong polar contact (left: SBs, right: HBs) between LYS417 and ASP30 is confirmed by MD data in https://amarolab.ucsd.edu/covid19.php ([55]) for dimeric spike-RBDACE2 binding, where for the MD data, the frame stride is 200; thus, we picked up 146 frames in all, and at the picked-up frame numbered 47, its SB distance is 161.388718 Å and its HBs distances are 160.428131 Å and 162.351318 Å (i.e., its SBs and HBs are broken)

The analyses of MD data in https://amarolab.ucsd.edu/covid19.php can also confirm some strong polar contacts, i.e., ASP442-ARG509 and ASP398-ARG355,

7.3 Results and Discussions

281

inside each spike-RBD monomer, and GLU182-ARG115, GLU208-ARG219, GLU435-LYS541, GLU310-ARG306, and GLU433-LYS288 inside each human ACE2 monomer, with the following HBs with occupancy rates .≥5%: – The HBs (with occupancy rates .≥5%) inside the spike-RBD-B/D or inside the human-ACE2-A/C:

.·

.·

.·

.·

.·

.·

.·

RBDD:ARG355.NE-RBDD:ASP398.OD1 36.30%, RBDD:ARG355.NH2-RBDD:ASP398.OD2 34.93%, RBDD:ARG355.NE-RBDD:ASP398.OD2 33.56%, RBDD:ARG355.NH2-RBDD:ASP398.OD1 32.19%, RBDB:ARG355.NH2-RBDB:ASP398.OD2 23.97%, RBDB:ARG355.NE-RBDB:ASP398.OD2 17.12%, RBDB:ARG355.NH2-RBDB:ASP398.OD1 13.7%, RBDD:ARG509.NE-RBDD:ASP442.OD2 61.64%, RBDD:ARG509.NH2-RBDD:ASP442.OD1 52.74%, RBDD:ARG509.NE-RBDD:ASP442.OD1 8.9%, RBDD:ARG509.NH2-RBDD:ASP442.OD2 5.48%, RBDB:ARG509.NE-RBDB:ASP442.OD2 51.37%, RBDB:ARG509.NH2-RBDB:ASP442.OD1 38.36%, RBDB:ARG509.NE-RBDB:ASP442.OD1 17.81%, RBDB:ARG509.NH2-RBDB:ASP442.OD2 15.75%, ACEC:ARG115.NH1-ACEC:GLU182.OE1 33.56%, ACEC:ARG115.NE-ACEC:GLU182.OE2 32.88%, ACEC:ARG115.NE-ACEC:GLU182.OE1 24.66%, ACEC:ARG115.NH1-ACEC:GLU182.OE2 21.92%, ACEA:ARG115.NE-ACEA:GLU182.OE1 31.51%, ACEA:ARG115.NH1-ACEA:GLU182.OE1 29.45%, ACEA:ARG115.NE-ACEA:GLU182.OE2 28.08%, ACEA:ARG115.NH1-ACEA:GLU182.OE2 28.08%, ACEA:ARG219.NH1-ACEA:GLU208.OE2 29.45%, ACEA:ARG219.NH1-ACEA:GLU208.OE1 25.34%, ACEC:ARG219.NH1-ACEC:GLU208.OE1 26.71%, ACEC:ARG219.NH1-ACEC:GLU208.OE2 26.03%, ACEC:ARG518.NE-ACEC:GLU406.OE2 8.22%, ACEC:ARG518.NH1-ACEC:GLU406.OE1 6.85%, ACEC:ARG518.NH1-ACEC:GLU406.OE2 6.85%, ACEC:ARG518.NE-ACEC:GLU406.OE1 5.48%, ACEA:LYS541.NZ-ACEA:GLU435.OE1 32.19%, ACEA:LYS541.NZ-ACEA:GLU435.OE2 25.34%, ACEA:HSE540.NE2-ACEA:GLU435.OE2 23.97%, ACEA:HSE540.NE2-ACEA:GLU435.OE1 8.9%, ACEC:LYS541.NZ-ACEC:GLU435.OE2 31.51%, ACEC:LYS541.NZ-ACEC:GLU435.OE1 24.66%, ACEC:HSE540.NE2-ACEC:GLU435.OE1 13.70%, ACEC:HSE540.NE2-ACEC:GLU435.OE2 13.01%, ACEA:GLU310.N-ACEA:ARG306.O 36.99%, ACEA:ARG306.NE-ACEA:GLU310.OE1 17.12%, ACEA:ARG306.NE-ACEA:GLU310.OE2 8.90%, ACEA:ARG306.NH1-ACEA:GLU310.OE1 5.48%, ACEC:GLU310.N-ACEC:ARG306.O 28.77%, ACEC:ARG306.NE-ACEC:GLU310.OE1 13.70%, ACEC:ARG306.NE-ACEC:GLU310.OE2 12.33%, ACEC:ARG306.NH2-ACEC:GLU310.OE1 5.48%, ACEC:LYS288.NZ-ACEC:GLU433.OE2 41.10%, ACEC:LYS288.NZ-ACEC:GLU433.OE1 27.40%, ACEA:LYS288.NZ-ACEA:GLU433.OE2 18.49%, ACEA:LYS288.NZ-ACEA:GLU433.OE1 12.33%.

7.3.7 Glycans’ Shields Despite the relatively modest contribution of the glycans to the total molecular weight of the spike trimer (17% for the HEK293 glycoform), the glycans shield approximately 40% of the spike protein surface [127] from antibody recognition by glycans, with the notable exception of the human ACE2 RBD. The degree of shielding is largely insensitive to the specific glycoform [127]. Here we will analyze the glycosylated Swiss model MD trajectory (5_Swiss_5_SS.prmtop and 5_Swiss_5_SS_Combined.nc) of SARS-CoV-2 spike glycoprotein with glycans [127, 128] built based on the cryo-EM structure 6VSB.pdb. The HBs (with more than 55.00% occupancy rates) of the MD trajectory are listed as follows: TYR2251.OH-LEU2268.O 77%, TYR11.OH-LEU28.O 75%, THR276.OG1-GLU272.O 74%, TYR1131.OH-LEU1148.O 70%, SER3265.OG-HIE3278.ND1 70%, MET671.N-GLY643.O 68%, LEU2799.NVAL2790.O 67%, TYR2527.OH-GLU2523.O 66%, TYR2305.N-GLY2482.O 66%, LEU2825.N-SER2810.O 66%, THR2516.OG1-GLU2512.O 66%, TYR1185.N-GLY1362.O 65%, THR1040.OG1-LYS1019.O 65%, THR273.OG1PRO269.O 64%, TYR287.OH-GLU283.O 64%, VAL2647.N-LYS2592.O 64%, PHE1486.N-VAL1618.O 64%, PHE2156.N-GLU1819.O 63%, SER2145.OG-HIE2158.ND1 63%, THR3280.OG1-LYS3259.O 62%, SER3030.OGGLN3268.OE1 62%, TYR1407.OH-GLU1403.O 61%, PHE17.N-PHE2779.O 61%, THR3241.OG1-ASN3237.O 61%, ASN893.ND2-VAL889.O 61%, THR2121.OG1-ASN2117.O 61%, ASP552.N-GLU557.O 60%, ILE572.N-ALA583.O

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7 Spike (S) Glycoprotein

60%, CYX645.N-TYR669.O 60%, LEU585.N-SER570.O 60%, PHE2606.N-VAL2738.O 60%, VAL2190.NPHE2197.O 60%, THR1396.OG1-GLU1392.O 59%, LEU1212.N-LYS1223.O 58%, THR1001.OG1-ASN997.O 58%, THR3220.OG1-GLN3216.O 58%, THR2513.OG1-PRO2509.O 58%, SER1025.OG-HIE1038.ND1 58%, GLN3250.NE2-HIE3262.O 58%, THR2171.OG1-PHE2189.O 58%, LEU1705.N-SER1690.O 57%, TYR2955.OHLEU3176.O 57%, ASN2013.ND2-VAL2009.O 57%, ASN902.N-ALA898.O 57%, ILE971.N-ILE967.O 57%, THR857.OG1-ALA853.O 57%, ALA642.N-PRO1957.O 56%, SER2033.OG-GLN2029.O 56%, ASP2792.NGLU2797.O 56%, PHE2257.N-PHE1659.O 56%, ASN2335.N-ARG2316.O 56%, THR3097.OG1-ALA3093.O 56%, VAL2753.N-GLY2764.O 56%, PHE1200.N-LEU1211.O 56%, THR3095.OG1-LEU3091.O 56%, GLU1005.NTHR1001.O 56%, TYR65.N-GLY242.O 55%, ASN2022.N-ALA2018.O 55%, THR1872.OG1-GLN1868.O 55%, PHE3276.N-GLU2939.O 55%, LEU1679.N-VAL1670.O 55%, THR983.OG1-GLN979.O 55%, VAL1456.N-

We also optimized the 5_Swiss_5_SS-6VSB model and got its ligand interactions as presented in Table 7.8 (see Fig. 7.19) to illuminate the recognition by glycans. An “O-Follow-N” rule for the O-glycosylation pattern of SARS-CoV-2 spike protein was revealed in [354].

ASN1428.O 55%.

7.3.8 Spike-Trimer Binding with Nanobody-Nb6c In the website www.rbvi.ucsf.edu/chimerax/data/nanobody-feb2021/, a pdb file “production_Nb6cRBD1.pdb” is presented for “How to View Nanobody Molecular Dynamics in ChimeraX”; this is an MD trajectory file with 600 frames for spiketrimer aa THR2-PRO196, GLN198-SER316, and THR318-PRO512 binding with the nanobody-Nb6c 4YB514-0YB515 and 4YB516-0YB517. We optimized the last frame and got its structural bioinformatics as follows: the optimized spike has 9 .π -.π stackings, PHE11-PHE43, TRP22-TYR92-TRP22, PHE61-PHE184, TYR292TRP306, PHE377-PHE500, PHE385-TYR408-(2), and TRP338 (2)-ARG451.NH2; 8 .π -cations, TYR118-ARG250.NH2+, PHE159-ARG251.NH2+, TYR174-ARG72.NH2+, TYR277ARG216.NH2+, PHE332-LYS341.NZ+, TRP338-ARG451.NH2+-TRP338, and TYR381ARG340.NH2+; 28 SBs, GLU9-LYS25, ASP67-ARG24, ASP74-ARG72, ASP74-ARG77, GLU75-ARG72, ASP96-LYS371, ASP96-LYS93, ASP111-ARG178, GLU134-ARG126, GLU134-LYS131, ASP136-ARG123, ASP136-ARG126, GLU140-ARG123, GLU153-ARG251, ASP259-LYS262, ASP270-LYS273, GLU286-LYS284, ASP287-ARG264, ASP296-ARG242, ASP304-ARG228, GLU325-LYS240, ASP383-ARG340, ASP390-ARG393, GLU391-ARG388, ASP405-LYS409, ASP427-ARG494, ASP452-ARG442, and GLU501-ARG342; and 209 HBs.

The optimal structure has NLN12, THR14, and LEU110 residues binding with 4YB514-0YB515 and GLY145, SER146, LYS240, SER299, PRO300, ALA301, PRO302, GLY303, TYR305, GLY324, PHE327, NLN328, VAL352, and LEU353 residues binding with 4YB516-0YB517. The MD performances show that the RMSD values level off after the 25th frame; the RMSF values have large variations in the loops aa 142–152 and aa 233–243 mainly because turns change into coils during 179–498 frames; the variations of MD secondary structures are mainly in segments aa PRO53-ASP58 and ALA404-TRP406 which has .α-helix changed into .310 -helix from the 520th frame. The MD HBs with more than 10.00% occupancy rates are listed in Table 7.9.

7.4 Concluding Remarks

283

7.3.9 The RGD Motif of Spike-RBD In “the MD-trajectories of SARS-CoV-2-spike-RBD from accelerated molecular simulation” [258], we are told that SARS-CoV-2 spike protein is unlikely to bind to integrins via the ARG70-GLY71-ASP72 RGD motif of the receptorbinding domain. We take 100 as the frame stride and can get 100 frames for “amd2_rbd_glycan.nc,” “amd3_rbd_glycan.nc,” and “amd4_rbd_glycan.nc,” respectively; the MD secondary structural graphs can be seen in Fig. 7.6 where for rep3 around the RGD motif, the .α-helix seems to unfold into .310 -helix completely. The spike residues are labeled with aa ASN1-LYS195 and with a ligand 4YB196-197 binding with spike residues GLY6 and NLN10; we optimized the model and get four .π -interactions: PHE41-TRP103, TYR162-TYR120LYS84.NZ, TRP20-TYR90-TRP20-ARG133.NH2, and PHE131-ARG22.NH2. The MD SBs and HBs can be seen in Tables 7.10, 7.11 and 7.12, where the MD-SBs ARG75/LYS84-AS72-ARG70-GLU73-ARG75/LYS84 are around the RGD motif, and around the RGD motif at residue ARG70, there are HBs, ARG70.NE-GLU73.OE1, ARG70.NE-GLU73.OE2, ARG70.NH1-GLU73.OE1, and ARG70.NH1-GLU73.OE2, during MD-rep2-3-4; at residue GLY71, there is an HB, GLY71.N-GLN173.O, during MD-rep2-3-4; and at residue ASP72, there are HBs, ASP72.N-GLY171.O, ARG75.NH1-ASP72.OD2, and ARG75.NH2ASP72.OD1.

Fig. 7.6 The MD secondary structures of 100 frames (with frame stride .= 10) of aa ASN1LYS195 [258]

7.4 Concluding Remarks Coronavirus SARS-CoV-2 S promote entry into cells and are the main target of antibodies and inhibitors. Human ACE2 is the cellular receptor for SARS-CoV-2 and is an antiviral drug target against SARS-CoV-2. The spike and the human ACE2 clearly are very helpful and useful for revealing secrets of COVID-19 virus and for structure-based drug design or discovery. Fortunately, the molecular structures of SARS-CoV-2 S, human ACE2, and their bindings were already determined and released into the Protein Data Bank (PDB) with PDB entries 6VXX, 6VYB, 1R4L, 1R42, 6M71, and 6VW1, respectively. This chapter perform MD studies of these six structures and present some structural bioinformatics (based on the optimized

284

7 Spike (S) Glycoprotein

monomers) for developing therapies of the currently fatal COVID-19 virus. For the trimeric spike, we found (i) a strong polar contact between ASP442 and ARG509 in the receptor-binding domain (RBD) of each monomer (where we found that the compounds megestrol acetate, nitazoxanide, and ritonavir bind with ARG509.NH1 with HB occupancy rates of 0.6%, 17.26%, and 0.6%, respectively, during 2 .μs of MD (Table 7.7)), (ii) strong hydrogen bond (HB) PHE43.N-PHE565.O and their side-chain .π -.π stackings between each two monomers, and (iii) strong polar contacts between GLU1031 and ARG1039/LYS1038 in the central helix-connector domain (CH-CD) between each two monomers; thus, holding the three monomers tightly from both ends to the middle of the spike; in the spike HB C:TYR369.OHA:THR415.OG1 has also a high occupancy rate of 50.30% (where we found the compound tadalafil binds with TYR369.OH with an HB occupancy rate of 1.79% during 2 .μs of MD, and the compounds fluticasone propionate and nebivolol bind with THR415 with an HB occupancy rates of 13.61% and 0.6%, respectively, during 2 .μs of MD (Table 7.7)). We think these compounds broke the strong polar contact ASP442-ARG509 and the strong HB C:TYR369.OH-A:THR415.OG1 so that the spike lost its protein functions. For the human ACE2, we found that the strong HBs TYR237.OH-VAL485.O, THR516.OH-THR229.OG1, TYR252.OH-LEU156.O, and THR567.OG1-TYR215.O (where there is a .π -cation, TYR215-LYS577.NZ) have large spans of residues, and three very strong HBs, THR229.OG1-ASP225.O (with occupancy rates of 61.90 and 66.27%), THR371.OG1-ASP367.O (with occupancy rates of 61.73 and 61.87%), and HID241.N-TYR237.O (with occupancy rates of 58.96 and 61.37%), have large occupancy rates; thus, we may see that the three residues, i.e., TYR237, THR229, and TYR215, play an important role. For the bindings of spike (denoted as F-chain) and human ACE2 (denoted as D/B-chain), polar contacts F:LYS417-D:ASP30, F:ARG439-B:GLU329, and HB F:THR500.OG1-D:ASP355.OD1 are very strong during MD of 10 .μs, and salt bridges (SBs) F:LYS458-D/B:GLU23 (but D/B:GLU23 has high HB occupancy rates with D/B:THR27), F:ARG403-D/B:GLU37 (has low HB occupancy rates), F:GLU484-D/B:LYS31, and F:ARG403-D/B:ASP38 (but HB D/B:ASP38F:TYR449 is strong) are weak during the whole 10 .μs; during the whole 10 .μs, in the spike SBs F:ASP398-F:ARG355 and F:ASP442-F:ARG509 and in the human ACE2 SBs GLU182-ARG115, GLU208-ARG219, GLU406-ARG518, GLU435LYS541, GLU310-ARG306, GLU433-LYS288, and GLU189-LYS112 are always strong in MD of 10 .μs. These MD structural bioinformatics were obtained which are based on the optimized monomer. The MD data of [321] is numerously large; thus, detailed structural bioinformatics will be further studied and presented very soon. By the analyses (Table 7.7) of the 2 .μs MD data of DESRES-ANTON10906555 (6VXX.pdb and 6VW1.pdb)—50 drugs respectively in complex with SARS-CoV-2-trimericspike-RBDs—we know that (1) the compounds alprostadil, AZD-8330, azilsartan, captopril, cefamandole nafate, cefixime, CP195543, darunavir, levomefolate, lometrexol, pelitrexol, raltitrexed, rebamipide, recoflavone, and vorapaxar broke the polar contact F:ARG439-B:GLU329 to make the spike lost its protein functions; (2) the compounds AZD-8330, azilsartan,

7.4 Concluding Remarks

285

levomefolate, lometrexol, pelitrexol, recoflavone, and vorapaxar broke the HB F:THR500.OG1-D:ASP355.OD1 to make the spike lost its protein functions; (3) the compounds aprepitant, calcifediol, clobazam, and terazosin broke the HB F:GLU484-D/B:LYS31 to make the spike lost its protein functions; (4) the compounds megestrol acetate, nitazoxanide, and ritonavir disturbed the strong polar contact F:ASP442-F:ARG509 to make the spike lost its protein functions; (5) the compounds fluticasone propionate and nebivolol made the loss of contacts with F:THR415; and (6) the compound tadalafil broke the HB C:TYR369.OHA:THR415.OG1 to make the spike lost its protein functions. Lastly, we review some literatures to further confirm the findings in this chapter. The SB F:ARG439-B:GLU329 is confirmed in [317, 387]. The SB F:LYS417D/B:ASP30 is confirmed in [13, 21, 123, 248, 336, 353, 376, 428]. In [13] the HB F:TYR449-D/B:ASP38 is also confirmed. The SB F:GLU484-D/B:LYS31 is confirmed in [380]. We wanted to perform deep protein-protein or protein-ligand profiling in terms of interactions and in lieu of the biological functioning of individual proteins or the complexes. We have presented the targeted interaction profiling between different biomolecules as they are operational inside the body. This will provide us more understanding how the spike protein and the ACE2 protein become the main windows in the spread of the COVID-19. Basically, in this chapter, we can find that there is a strong polar contacts between LYS417 of the SARS-CoV-2-spike and ASP30 of the ACE2: our MD and optimization studies showed us that we cannot find it from SARS-CoV-1 and MERS, and even the SARS-CoV-2-D614G mutant will not change it at all. The noncovalent interactions of hydrogen bonds (HBs), salt bridges (SBs), van der Waals (vdWs) contacts, and hydrophobic interactions (HYDs) are driving a protein to be able to perform its biological functions. This chapter presented fundamental and basic bioinformatics of the HBs, SBs, HYDs, and vdWs of each model from the large MD trajectory data and evaluate the reliability of the MD trajectory data of 10 .μs. Clearly, the basic bioinformatics presented in this chapter cannot solve current hard work of COVID-19 problems. A more concrete information and pathway should be determined to provide insights how this virus can be stopped from entering inside the human body. A detailed interaction profile of various inhibitors along with the interaction mechanism of the two proteins can help in understanding why all drugs till now are failing and what precautions we should take in developing any new drug molecule against the deadly disease. Basing on the fundamental bioinformatics of this chapter, we will further study the databases DESRES-ANTON-10906555 and DESERS-ANTON-10918441 of (all the FDAapproved) drugs binding with the SARS-CoV-2 trimeric spike and the ectodomain of human ACE2 in Chaps. 17 and 18. The optimized structure is at a transition state with the best stability and the lowest energy. Currently, a lot of researchers are using optimization to screen and design compounds but they do not definitely use optimization algorithms professionally. The hybrid strategy of mathematical optimization’s neighboring different (local search) algorithms is used professionally in this chapter. Currently

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7 Spike (S) Glycoprotein

the spike’s structures are still not complete yet and static molecular structures are not enough to reveal the secrets of COVID-19 virus; MD is still needed. Optimization strategy can also catch main bioinformatics from the huge MD trajectory databases and reduce the large-scale datasets. This chapter studied the MD trajectory databases from the optimization strategies and should have a value to COVID-19 researchers as a reference. For SARS-CoV-2, we also found some interesting results on (monomeric and dimeric) Mpro and PLpro, RdRp, etc. Furthermore, research will be revealing more secrets of the SARS-CoV-2.

Supplementary Information

Table 7.1 The HBs with more than 50% occupancy rates during the 10 μs MD simulations for the 6VXX-trimeric-spike-closedmodel-1

Donor

Acceptor

Occupancy

Cchain-TYR37-Side-OH

Cchain-LEU54-Main-O

75.09%

Achain-TYR37-Side-OH

Achain-LEU54-Main-O

73.05%

Bchain-TYR37-Side-OH

Bchain-LEU54-Main-O

70.78%

Bchain-ARG454-Main-N

Bchain-ASN422-Side-OD1

68.98%

Bchain-TYR91-Main-N

Bchain-GLY268-Main-O

68.26%

Cchain-TYR91-Main-N

Cchain-GLY268-Main-O

65.63%

Cchain-TYR313-Side-OH

Cchain-GLU309-Main-O

65.39%

Bchain-TYR741-Side-OH

Bchain-LEU962-Main-O

65.27%

Achain-THR299-Side-OG1

Achain-PRO295-Main-O

64.31%

Bchain-THR299-Side-OG1

Bchain-PRO295-Main-O

63.23%

Bchain-THR302-Side-OG1

Bchain-GLU298-Main-O

63.23%

Achain-TYR91-Main-N

Achain-GLY268-Main-O

63.23%

Bchain-LEU513-Main-N

Bchain-CYS432-Main-O

62.28%

Cchain-THR883-Side-OG1

Cchain-ALA879-Main-O

61.80%

Cchain-ARG454-Main-N

Cchain-ASN422-Side-OD1

61.32%

Bchain-SER438-Side-OG

Bchain-ASP442-Side-OD2

61.20%

Cchain-LEU455-Main-N

Cchain-PRO491-Main-O

60.72%

Cchain-LEU513-Main-N

Cchain-CYS432-Main-O

60.72%

Bchain-LEU611-Main-N

Bchain-SER596-Main-O

60.60%

Bchain-TYR269-Side-OH

Bchain-PRO85-Main-O

60.36%

Cchain-LEU611-Main-N

Cchain-SER596-Main-O

60.00%

Cchain-LEU585-Main-N

Cchain-VAL576-Main-O

59.52%

Cchain-THR299-Side-OG1

Cchain-PRO295-Main-O

59.16%

Achain-TYR313-Side-OH

Achain-GLU309-Main-O

58.92%

Bchain-ASP398-Main-N

Bchain-VAL512-Main-O

58.80%

Achain-THR881-Side-OG1

Achain-LEU877-Main-O

58.68%

Bchain-TYR451-Side-OH

Bchain-ASP442-Side-OD1

58.68%

Achain-THR302-Side-OG1

Achain-GLU298-Main-O

58.56%

Cchain-VAL433-Main-N

Cchain-LYS378-Main-O

58.44%

Achain-SER112-Side-OG

Achain-GLU132-Main-O

58.44%

Achain-ARG454-Main-N

Achain-ASN422-Side-OD1

58.32%

Bchain-VAL433-Main-N

Bchain-LYS378-Main-O

58.20%

Bchain-LEU455-Main-N

Bchain-PRO491-Main-O

57.84%

Cchain-SER438-Side-OG

Cchain-ASP442-Side-OD1

57.84%

Bchain-SER982-Side-OG

Bchain-ASN978-Main-O

57.49%

Achain-LEU611-Main-N

Achain-SER596-Main-O

57.13%

Cchain-THR302-Side-OG1

Cchain-GLU298-Main-O

57.01%

Achain-LEU513-Main-N

Achain-CYS432-Main-O

56.89%

Bchain-PHE106-Main-N

Bchain-LEU117-Main-O

56.89%

(continued)

Supplementary Information Table 7.1 (continued)

287 Donor

Acceptor

Occupancy

Bchain-THR883-Side-OG1

Bchain-ALA879-Main-O

56.77%

Bchain-GLN1054-Side-NE2

Bchain-PRO1053-Main-O

56.65%

Achain-THR883-Side-OG1

Achain-ALA879-Main-O

56.65%

Bchain-CYS671-Main-N

Bchain-TYR695-Main-O

56.65%

Achain-GLN1054-Side-NE2

Achain-PRO1053-Main-O

56.53%

Achain-SER1003-Side-OG

Achain-GLY999-Main-O

56.53%

Bchain-TYR695-Main-N

Bchain-CYS671-Main-O

56.41%

Bchain-VAL539-Main-N

Bchain-GLY550-Main-O

56.17%

Achain-THR1066-Side-OG1

Achain-LYS1045-Main-O

56.17%

Achain-LEU585-Main-N

Achain-VAL576-Main-O

56.05%

Cchain-TYR269-Side-OH

Cchain-PRO85-Main-O

55.93%

Achain-PHE106-Main-N

Achain-LEU117-Main-O

55.93%

Cchain-PHE1103-Main-N

Cchain-VAL1096-Main-O

55.81%

Achain-HIS1064-Side-ND1

Achain-SER1051-Side-OG

55.81%

Bchain-ALA694-Main-N

Bchain-GLU654-Main-O

55.81%

Bchain-HIS1064-Side-ND1

Bchain-SER1051-Side-OG

55.81%

Achain-VAL511-Main-N

Achain-ILE434-Main-O

55.69%

Achain-ASN777-Main-N

Achain-GLU773-Main-O

55.57%

Bchain-ILE651-Main-N

Bchain-VAL610-Main-O

55.57%

Achain-VAL551-Main-N

Achain-THR588-Main-O

55.57%

Cchain-GLN1054-Side-NE2

Cchain-PRO1053-Main-O

55.45%

Bchain-ILE598-Main-N

Bchain-ALA609-Main-O

55.21%

Bchain-ASN919-Side-ND2

Bchain-VAL915-Main-O

55.09%

Bchain-PHE275-Main-N

Bchain-THR51-Main-O

54.97%

Achain-VAL433-Main-N

Achain-LYS378-Main-O

54.97%

Achain-VAL539-Main-N

Achain-GLY550-Main-O

54.97%

Cchain-ASP398-Main-N

Cchain-VAL512-Main-O

54.97%

Bchain-PHE1089-Main-N

Bchain-PHE1121-Main-O

54.73%

Cchain-ILE651-Main-N

Cchain-VAL610-Main-O

54.61%

Cchain-SER803-Side-OG

Cchain-NLM1172-Side-OD1

54.49%

Bchain-THR1066-Side-OG1

Bchain-LYS1045-Main-O

54.25%

Bchain-VAL511-Main-N

Bchain-ILE434-Main-O

54.13%

Cchain-SER816-Side-OG

Cchain-GLN1054-Side-OE1

54.13%

Bchain-PHE43-Main-N

Cchain-PHE565-Main-O

54.13%

Cchain-ARG509-Side-NE

Cchain-ASP442-Side-OD1

54.13%

Achain-TYR266-Main-N

Achain-ALA93-Main-O

54.01%

Achain-LEU277-Main-N

Achain-HIS49-Main-O

53.89%

Achain-PHE541-Main-N

Achain-GLY548-Main-O

53.77%

Achain-LEU461-Main-N

Achain-ASP420-Main-O

53.77%

Achain-PHE1089-Main-N

Achain-PHE1121-Main-O

53.65%

Achain-ASP398-Main-N

Achain-VAL512-Main-O

53.65%

Cchain-PHE275-Main-N

Cchain-THR51-Main-O

53.53%

Cchain-LEU118-Main-N

Cchain-LYS129-Main-O

53.53%

Cchain-PHE106-Main-N

Cchain-LEU117-Main-O

53.29%

Cchain-CYS671-Main-N

Cchain-TYR695-Main-O

53.29%

Cchain-VAL1096-Main-N

Cchain-PHE1103-Main-O

53.05%

Cchain-ILE598-Main-N

Cchain-ALA609-Main-O

53.05%

Bchain-ARG509-Side-NH2

Bchain-ASP442-Side-OD1

53.05%

Achain-ALA1022-Main-N

Achain-ILE1018-Main-O

52.93%

Achain-ASN928-Main-N

Achain-ALA924-Main-O

52.81%

Cchain-VAL551-Main-N

Cchain-THR588-Main-O

52.81%

Cchain-ASP586-Main-N

Cchain-THR553-Main-O

52.81%

Achain-LEU223-Main-N

Achain-VAL36-Main-O

52.81%

Cchain-LEU277-Main-N

Cchain-HIS49-Main-O

52.57%

Cchain-VAL729-Main-N

Cchain-HIS1058-Main-O

52.46%

Cchain-SER640-Side-OG

Cchain-HIS625-Side-NE2

52.46%

Achain-MET697-Main-N

Achain-GLY669-Main-O

52.34%

Achain-PHE59-Main-N

Achain-PHE32-Main-O

52.34%

Bchain-PHE392-Main-N

Bchain-VAL524-Main-O

52.34%

Cchain-LEU117-Main-N

Cchain-PHE106-Main-O

52.34%

Cchain-LEU223-Main-N

Cchain-VAL36-Main-O

52.34%

Bchain-LEU241-Main-N

Bchain-GLY103-Main-O

52.22%

Cchain-LEU1063-Main-N

Cchain-PHE1052-Main-O

52.10%

Cchain-SER939-Side-OG

Cchain-GLN935-Main-O

52.10%

Achain-VAL1104-Main-N

Achain-GLN1113-Main-O

52.10%

(continued)

288

7 Spike (S) Glycoprotein

Fig. 7.7 Some strong SBs of the 6VXX-trimeric-spike-closed-model-1 confirmed by MD data in [321]

Supplementary Information

Fig. 7.7 (continued)

289

290 Table 7.1 (continued)

Table 7.2 The HBs with more than 50% occupancy rates during the 10 μs MD simulations for the 6VYB-trimeric-spikeopened-model-2

7 Spike (S) Glycoprotein Donor

Acceptor

Occupancy

Cchain-PHE1089-Main-N

Cchain-PHE1121-Main-O

51.98%

Achain-THR1120-Side-OG1

Achain-THR1116-Main-O

51.98%

Achain-GLN493-Main-N

Achain-TYR453-Main-O

51.98%

Cchain-THR881-Side-OG1

Cchain-LEU877-Main-O

51.74%

Achain-ILE598-Main-N

Achain-ALA609-Main-O

51.74%

Cchain-ASN919-Side-ND2

Cchain-VAL915-Main-O

51.74%

Cchain-VAL127-Main-N

Cchain-VAL120-Main-O

51.74%

Achain-CYS671-Main-N

Achain-TYR695-Main-O

51.50%

Cchain-THR1027-Side-OG1

Cchain-ASN1023-Main-O

51.38%

Cchain-PHE541-Main-N

Cchain-GLY548-Main-O

50.30%

Cchain-CYS1082-Main-N

Cchain-VAL1133-Main-O

50.30%

Bchain-VAL729-Main-N

Bchain-HIS1058-Main-O

50.30%

Bchain-TYR423-Main-N

Bchain-ILE418-Main-O

50.30%

Cchain-VAL511-Main-N

Cchain-ILE434-Main-O

50.30%

Bchain-VAL551-Main-N

Bchain-THR588-Main-O

50.30%

Bchain-PHE541-Main-N

Bchain-GLY548-Main-O

50.30%

Cchain-TYR451-Side-OH

Cchain-ASP442-Side-OD2

50.30%

Achain-THR1066-Main-N

Achain-SER721-Main-O

50.30%

Bchain-SER939-Side-OG

Bchain-GLN935-Main-O

50.30%

Cchain-TYR369-Side-OH

Achain-THR415-Side-OG1

50.30%

Achain-ILE651-Main-N

Achain-VAL610-Main-O

50.30%

Achain-LEU118-Main-N

Achain-LYS129-Main-O

50.30%

Achain-VAL362-Main-N

Achain-ASN334-Main-O

50.30%

Bchain-LEU118-Main-N

Bchain-LYS129-Main-O

50.30%

Achain-TYR695-Main-N

Achain-CYS671-Main-O

50.30%

Achain-PHE275-Main-N

Achain-THR51-Main-O

50.30%

Cchain-HIS1064-Side-ND1

Cchain-SER1051-Side-OG

50.30%

Achain-SER982-Side-OG

Achain-ASN978-Main-O

50.30%

Cchain-GLU132-Main-N

Cchain-ASN164-Main-O

50.30%

Bchain-HIS1088-Main-N

Bchain-ILE1081-Main-O

50.30%

Bchain-PHE59-Main-N

Bchain-PHE32-Main-O

50.30%

Bchain-TYR313-Side-OH

Bchain-GLU309-Main-O

50.30%

Bchain-ASP586-Main-N

Bchain-THR553-Main-O

50.30%

Achain-THR167-Side-OG1

Achain-GLN115-Side-OE1

50.30%

Donor

Acceptor

Occupancy

Achain-TYR37-Side-OH

Achain-LEU54-Main-O

72.10%

Bchain-TYR91-Main-N

Bchain-GLY268-Main-O

71.98%

Bchain-TYR37-Side-OH

Bchain-LEU54-Main-O

70.78%

Cchain-TYR37-Side-OH

Cchain-LEU54-Main-O

70.66%

Bchain-TYR269-Side-OH

Bchain-PRO85-Main-O

68.98%

Achain-ARG454-Main-N

Achain-ASN422-Side-OD1

68.38%

Cchain-TYR91-Main-N

Cchain-GLY268-Main-O

66.35%

Bchain-SER438-Side-OG

Bchain-ASP442-Side-OD2

64.31%

Bchain-LEU611-Main-N

Bchain-SER596-Main-O

64.07%

Achain-TYR313-Side-OH

Achain-GLU309-Main-O

64.07%

Achain-THR302-Side-OG1

Achain-GLU298-Main-O

63.59%

Bchain-TYR741-Side-OH

Bchain-LEU962-Main-O

63.11%

Cchain-ARG454-Main-N

Cchain-ASN422-Side-OD1

62.51%

Achain-TYR91-Main-N

Achain-GLY268-Main-O

62.28%

Cchain-THR299-Side-OG1

Cchain-PRO295-Main-O

62.04%

Achain-LEU118-Main-N

Achain-LYS129-Main-O

61.32%

Bchain-THR299-Side-OG1

Bchain-PRO295-Main-O

61.20%

Bchain-THR302-Side-OG1

Bchain-GLU298-Main-O

61.20%

Bchain-SER982-Side-OG

Bchain-ASN978-Main-O

60.72%

Bchain-VAL433-Main-N

Bchain-LYS378-Main-O

60.60%

Achain-ILE598-Main-N

Achain-ALA609-Main-O

60.00%

Cchain-THR302-Side-OG1

Cchain-GLU298-Main-O

59.76%

Cchain-LEU455-Main-N

Cchain-PRO491-Main-O

59.76%

Bchain-LEU455-Main-N

Bchain-PRO491-Main-O

59.52%

Bchain-TYR313-Side-OH

Bchain-GLU309-Main-O

59.28%

Achain-THR299-Side-OG1

Achain-PRO295-Main-O

59.16%

Bchain-LEU585-Main-N

Bchain-VAL576-Main-O

58.92%

(continued)

Supplementary Information Table 7.2 (continued)

291 Donor

Acceptor

Occupancy

Bchain-LEU513-Main-N

Bchain-CYS432-Main-O

58.92%

Achain-LEU611-Main-N

Achain-SER596-Main-O

58.80%

Achain-VAL433-Main-N

Achain-LYS378-Main-O

58.80%

Bchain-ARG509-Side-NE

Bchain-ASP442-Side-OD2

58.44%

Bchain-THR883-Side-OG1

Bchain-ALA879-Main-O

58.08%

Cchain-TYR269-Side-OH

Cchain-PRO85-Main-O

57.84%

Bchain-GLN1054-Side-NE2

Bchain-PRO1053-Main-O

57.84%

Achain-THR883-Side-OG1

Achain-ALA879-Main-O

57.49%

Cchain-VAL433-Main-N

Cchain-LYS378-Main-O

57.13%

Cchain-ILE598-Main-N

Cchain-ALA609-Main-O

57.13%

Bchain-ARG454-Main-N

Bchain-ASN422-Side-OD1

56.89%

Achain-GLN1054-Side-NE2

Achain-PRO1053-Main-O

56.77%

Achain-LEU585-Main-N

Achain-VAL576-Main-O

56.41%

Bchain-CYS671-Main-N

Bchain-TYR695-Main-O

56.41%

Bchain-LEU223-Main-N

Bchain-VAL36-Main-O

56.29%

Bchain-ILE598-Main-N

Bchain-ALA609-Main-O

56.17%

Cchain-LEU585-Main-N

Cchain-VAL576-Main-O

56.05%

Achain-VAL511-Main-N

Achain-ILE434-Main-O

56.05%

Achain-THR881-Side-OG1

Achain-LEU877-Main-O

55.93%

Cchain-LEU611-Main-N

Cchain-SER596-Main-O

55.81%

Achain-CYS1082-Main-N

Achain-VAL1133-Main-O

55.69%

Achain-PHE106-Main-N

Achain-LEU117-Main-O

55.69%

Bchain-ASP398-Main-N

Bchain-VAL512-Main-O

55.69%

Cchain-LEU650-Main-N

Cchain-PHE643-Main-O

55.69%

Achain-VAL539-Main-N

Achain-GLY550-Main-O

55.45%

Cchain-GLN1054-Side-NE2

Cchain-PRO1053-Main-O

55.45%

Cchain-SER1021-Side-OG

Cchain-GLU1017-Main-O

55.45%

Achain-THR1066-Side-OG1

Achain-LYS1045-Main-O

55.45%

Bchain-ILE651-Main-N

Bchain-VAL610-Main-O

55.33%

Bchain-GLN271-Main-N

Bchain-PHE55-Main-O

55.33%

Achain-ASP578-Main-N

Achain-GLU583-Main-O

55.33%

Cchain-THR883-Side-OG1

Cchain-ALA879-Main-O

55.09%

Achain-ASN777-Main-N

Achain-GLU773-Main-O

55.09%

Bchain-PHE106-Main-N

Bchain-LEU117-Main-O

55.09%

Cchain-LEU223-Main-N

Cchain-VAL36-Main-O

55.09%

Cchain-THR1066-Side-OG1

Cchain-LYS1045-Main-O

54.97%

Achain-CYS671-Main-N

Achain-TYR695-Main-O

54.85%

Cchain-VAL511-Main-N

Cchain-ILE434-Main-O

54.73%

Achain-SER1003-Side-OG

Achain-GLY999-Main-O

54.73%

Achain-SER939-Side-OG

Achain-GLN935-Main-O

54.61%

Cchain-PHE43-Main-N

Achain-PHE565-Main-O

54.37%

Bchain-HIS1088-Main-N

Bchain-ILE1081-Main-O

54.13%

Cchain-PHE106-Main-N

Cchain-LEU117-Main-O

54.13%

Bchain-PHE43-Main-N

Cchain-PHE565-Main-O

54.01%

Bchain-ASN919-Side-ND2

Bchain-VAL915-Main-O

54.01%

Achain-TYR741-Main-N

Achain-ASP737-Main-O

54.01%

Cchain-VAL539-Main-N

Cchain-GLY550-Main-O

53.89%

Bchain-SER1003-Side-OG

Bchain-GLY999-Main-O

53.77%

Cchain-LEU84-Main-N

Cchain-PHE238-Main-O

53.77%

Cchain-VAL551-Main-N

Cchain-THR588-Main-O

53.65%

Achain-THR1077-Side-OG1

Achain-PHE1095-Main-O

53.65%

Bchain-SER939-Side-OG

Bchain-GLN935-Main-O

53.53%

Achain-LEU513-Main-N

Achain-CYS432-Main-O

53.53%

Cchain-LEU560-Main-N

Cchain-GLN563-Side-OE1

53.41%

Bchain-TYR266-Main-N

Bchain-ALA93-Main-O

53.17%

Achain-ALA1022-Main-N

Achain-ILE1018-Main-O

53.05%

Cchain-ARG190-Main-N

Cchain-SER94-Main-O

53.05%

Cchain-THR881-Side-OG1

Cchain-LEU877-Main-O

52.93%

Cchain-ASP586-Main-N

Cchain-THR553-Main-O

52.93%

Cchain-HIS1064-Side-ND1

Cchain-SER1051-Side-OG

52.93%

Achain-PHE275-Main-N

Achain-THR51-Main-O

52.93%

Cchain-MET697-Main-N

Cchain-GLY669-Main-O

52.81%

Achain-GLN271-Main-N

Achain-PHE55-Main-O

52.81%

Cchain-ASN777-Main-N

Cchain-GLU773-Main-O

52.81%

Cchain-SER939-Side-OG

Cchain-GLN935-Main-O

52.69%

Cchain-ILE651-Main-N

Cchain-VAL610-Main-O

52.46%

Bchain-VAL539-Main-N

Bchain-GLY550-Main-O

52.46%

(continued)

292 Table 7.2 (continued)

Table 7.3 The HBs with more than 50% occupancy rates during the 10 μs MD simulations for the 1R4L-ACE2-closed-model-3

7 Spike (S) Glycoprotein Donor

Acceptor

Occupancy

Cchain-ASP442-Main-N

Cchain-SER438-Main-O

52.46%

Achain-LEU241-Main-N

Achain-GLY103-Main-O

52.34%

Cchain-TYR266-Main-N

Cchain-ALA93-Main-O

52.34%

Achain-ASN928-Main-N

Achain-ALA924-Main-O

52.34%

Cchain-CYS671-Main-N

Cchain-TYR695-Main-O

52.22%

Achain-THR1027-Side-OG1

Achain-ASN1023-Main-O

52.10%

Achain-HIS1064-Side-ND1

Achain-SER1051-Side-OG

52.10%

Cchain-THR531-Main-N

Cchain-VAL327-Main-O

51.86%

Achain-PHE1103-Main-N

Achain-VAL1096-Main-O

51.74%

Bchain-PHE59-Main-N

Bchain-PHE32-Main-O

51.74%

Achain-SER982-Side-OG

Achain-ASN978-Main-O

51.74%

Cchain-VAL512-Main-N

Cchain-ASP398-Main-O

51.74%

Achain-ASN919-Side-ND2

Achain-VAL915-Main-O

51.62%

Achain-PHE59-Main-N

Achain-PHE32-Main-O

51.62%

Bchain-ARG509-Side-NH2

Bchain-ASP442-Side-OD1

51.62%

Cchain-TYR695-Main-N

Cchain-CYS671-Main-O

51.62%

Bchain-PHE1089-Main-N

Bchain-PHE1121-Main-O

51.62%

Bchain-ARG158-Side-NH1

Bchain-GLU156-Side-OE2

51.62%

Cchain-VAL1096-Main-N

Cchain-PHE1103-Main-O

51.50%

Bchain-NLM1160-Side-ND2

Bchain-GLY339-Main-O

51.38%

Achain-PHE43-Main-N

Bchain-PHE565-Main-O

51.38%

Bchain-MET697-Main-N

Bchain-GLY669-Main-O

51.14%

Achain-ILE651-Main-N

Achain-VAL610-Main-O

51.02%

Cchain-PHE275-Main-N

Cchain-THR51-Main-O

51.02%

Bchain-TYR612-Main-N

Bchain-CYS649-Main-O

50.90%

Cchain-PHE59-Main-N

Cchain-PHE32-Main-O

50.90%

Bchain-ARG273-Main-N

Bchain-ASP53-Main-O

50.90%

Bchain-LEU118-Main-N

Bchain-LYS129-Main-O

50.90%

Achain-SER116-Main-N

Achain-CYS131-Main-O

50.90%

Achain-MET697-Main-N

Achain-GLY669-Main-O

50.78%

Bchain-VAL511-Main-N

Bchain-ILE434-Main-O

50.78%

Bchain-VAL551-Main-N

Bchain-THR588-Main-O

50.66%

Cchain-TYR741-Main-N

Cchain-ASP737-Main-O

50.66%

Bchain-SER803-Side-OG

Bchain-NLM1172-Side-OD1

50.54%

Bchain-TYR380-Main-N

Bchain-GLY431-Main-O

50.54%

Achain-LEU223-Main-N

Achain-VAL36-Main-O

50.54%

Achain-HIS245-Main-N

Achain-TYR248-Main-O

50.54%

Bchain-LEU650-Main-N

Bchain-PHE643-Main-O

50.42%

Bchain-LEU241-Main-N

Bchain-GLY103-Main-O

50.42%

Cchain-LEU118-Main-N

Cchain-LYS129-Main-O

50.42%

Bchain-THR1120-Side-OG1

Bchain-THR1116-Main-O

50.42%

Achain-LEU1063-Main-N

Achain-PHE1052-Main-O

50.42%

Cchain-TYR265-Main-N

Cchain-PHE65-Main-O

50.42%

Cchain-VAL729-Main-N

Cchain-HIS1058-Main-O

50.30%

Achain-TYR612-Main-N

Achain-CYS649-Main-O

50.30%

Achain-VAL512-Main-N

Achain-ASP398-Main-O

50.30%

Cchain-LEU277-Main-N

Cchain-HIS49-Main-O

50.18%

Bchain-PHE275-Main-N

Bchain-THR51-Main-O

50.18%

Bchain-GLU96-Main-N

Bchain-ASN188-Main-O

50.18%

Bchain-SER31-Main-N

Bchain-SER60-Main-O

50.06%

Bchain-TYR695-Side-OH

Bchain-GLU661-Main-O

50.06%

Donor

Acceptor

Occupancy

THR229-Side-OG1

ASP225-Main-O

66.27%

THR282-Side-OG1

LEU278-Main-O

62.86%

THR371-Side-OG1

ASP367-Main-O

61.87%

HID241-Main-N

TYR237-Main-O

61.37%

THR122-Side-OG1

THR118-Main-O

59.81%

TYR237-Side-OH

VAL485-Main-O

58.79%

LEU95-Main-N

LEU91-Main-O

53.68%

TYR516-Side-OH

THR229-Side-OG1

53.05%

SER77-Side-OG

LEU73-Main-O

51.01%

TYR252-Side-OH

LEU156-Main-O

50.64%

Supplementary Information Table 7.4 The HBs with more than 50% occupancy rates during the 10 μs MD simulations for the 1R42-ACE2-opened-model-4

Table 7.5 The HBs with more than 50% occupancy rates during the 10 μs MD simulations for the 6M17-spike-ACE2-bindingmodel-5

Table 7.6 Table S6. The HBs with more than 50% occupancy rates during the 10 μs MD simulations for the 6VW1-spike-ACE2-bindingmodel-6

293 Donor

Acceptor

Occupancy

TYR237-Side-OH

VAL485-Main-O

64.75%

THR229-Side-OG1

ASP225-Main-O

61.90%

THR371-Side-OG1

ASP367-Main-O

61.73%

TRP461-Main-N

GLU457-Main-O

61.25%

HID241-Main-N

TYR237-Main-O

58.96%

THR567-Side-OG1

TYR215-Main-O

58.78%

TYR516-Side-OH

THR229-Side-OG1

52.27%

HID373-Side-ND1

PHE369-Main-O

52.20%

THR129-Side-OG1

THR125-Main-O

51.70%

TYR521-Main-N

THR517-Main-O

51.27%

Donor

Acceptor

Occupancy

D:TYR237-Side-OH

D:VAL485-Main-O

69.54%

D:ARG357-Side-NH1

D:ASP355-Side-OD1

64.97%

F:ARG454-Main-N

F:ASN422-Side-OD1

63.83%

D:THR229-Side-OG1

D:ASP225-Main-O

63.29%

D:TRP461-Main-N

D:GLU457-Main-O

62.44%

D:HIS241-Main-N

D:TYR237-Main-O

61.56%

F:VAL433-Main-N

F:LYS378-Main-O

61.00%

D:THR567-Side-OG1

D:TYR215-Main-O

57.78%

D:SER331-Side-OG

D:PHE327-Main-O

57.30%

F:LEU513-Main-N

F:CYS432-Main-O

57.08%

D:TYR516-Side-OH

D:THR229-Side-OG1

56.66%

D:TYR521-Main-N

D:THR517-Main-O

56.56%

F:VAL511-Main-N

F:ILE434-Main-O

56.02%

D:THR27-Side-OG1

D:GLU23-Main-O

54.57%

D:THR129-Side-OG1

D:THR125-Main-O

54.03%

D:ASN49-Main-N

D:LEU45-Main-O

53.59%

F:THR500-Side-OG1

D:ASP355-Side-OD1

53.51%

D:TYR41-Side-OH

D:ASP355-Side-OD1

53.47%

D:THR371-Side-OG1

D:ASP367-Main-O

52.24%

D:GLU238-Main-N

D:LYS234-Main-O

50.57%

D:ASN194-Side-ND2

D:MET190-Main-O

50.03%

Donor

Acceptor

Occupancy

F:ARG454-Main-N

F:ASN422-Side-OD1

69.92%

B:TYR237-Side-OH

B:VAL485-Main-O

66.83%

B:SER317-Side-OG

B:PHE314-Main-O

66.21%

B:ARG357-Side-NH1

B:ASP355-Side-OD2

65.48%

B:TYR41-Side-OH

B:ASP355-Side-OD2

64.94%

B:THR229-Side-OG1

B:ASP225-Main-O

64.84%

B:HID241-Main-N

B:TYR237-Main-O

62.89%

B:TYR521-Main-N

B:THR517-Main-O

60.89%

B:THR282-Side-OG1

B:LEU278-Main-O

60.42%

B:THR567-Side-OG1

B:TYR215-Main-O

59.34%

F:LEU513-Main-N

F:CYX432-Main-O

58.81%

B:THR371-Side-OG1

B:ASP367-Main-O

57.92%

B:SER502-Side-OG

B:ASP499-Main-O

56.59%

F:VAL433-Main-N

F:LYS378-Main-O

55.27%

B:TYR516-Side-OH

B:THR229-Side-OG1

54.91%

F:ASP398-Main-N

F:VAL512-Main-O

54.78%

F:VAL511-Main-N

F:LEU434-Main-O

53.86%

B:LEU95-Main-N

B:LEU91-Main-O

53.43%

B:SER70-Side-OG

B:GLY66-Main-O

52.53%

B:THR414-Side-OG1

B:SER411-Main-O

52.24%

B:THR125-Side-OG1

B:ASN121-Main-O

51.69%

B:ASN33-Main-N

B:LEU29-Main-O

51.52%

B:THR27-Side-OG1

B:GLU23-Main-O

50.81%

F:THR438-Side-OG1

F:ASP442-Side-OD1

50.67%

B:VAL244-Main-N

B:LEU240-Main-O

50.56%

F:LEU461-Main-N

F:ASP420-Main-O

50.53%

B:TYR243-Side-OH

B:THR282-Main-O

50.08%

294

7 Spike (S) Glycoprotein

Table 7.7 The 50 drugs binding with SARS-CoV-2-trimericspike-RBDs of 2 μs MD trajectory data in [321] 01

Drug name

MD Data ID

ChEMBL

Spike-D, E, F

HBs

Alprostadil

10930523

1318789

F

lig.O-ASP364.O 45.83% lig.O-NMG343.O7 27.38% NMG343.O6-lig.O 7.14% NMG343.O3-lig.O 3.57% NMG343.O2-lig.O 1.19% SER371.OG-lig.O 19.64% ARG439.NH2-lig.O 4.76% ARG439.NH1-lig.O 4.17% ASP364.N-lig.O 3.57% PHE338.N-lig.O 3.57% GLY339.N-lig.O 1.19% THR372.OG1-lig.O 1.19%

02

Amcinonide

10940986

1200732

E

03

Aprepitant

10942625

1471

E: GLY482, GLU484

ASP364.N-lig.F 13.10%

F

lig.N-GLU484.OE2 11.31%

lig.O-ASP364.O 52.38% ASP364.N-lig.O 20.83%

lig.N-GLU484.OE1 6.55% GLU484.N-lig.O 5.95% VAL483.N-lig.O 2.98% lig.N-SER366.OG 0.60% lig.N-ASN481.O 0.60% lig.N-ASN481.OD1 0.60% VAL483.N-lig.N 0.60% GLY485.N-lig.O 0.60% 04

Atazanavir

10921672

1163

D

lig.O-ASP364.OD1 46.43%

F

lig.N-ASP364.OD1 42.86% lig.O-ASP364.OD2 23.81% lig.N-ASP364.OD2 17.26% TYR489.OH-lig.O 14.88% ASN370.ND2-lig.O 7.14% NMG343.O4-lig.O 2.98% lig.N-SER371.OG 2.38% lig.N-TYR489.OH 1.79% lig.N-ASN370.OD1 1.19% lig.N-ASN331.OD1 0.60% ASN331.N-lig.O 0.60% GLN493.NE2-lig.N 0.60% SER371.OG-lig.O 0.60% lig.N-NMG343.O2 0.60% NMG343.O2-lig.O 0.60%

05

Atorvastatin

10930821

1487

E

lig.O-ASN487.O 22.02%

F

ASN487.ND2-lig.O 14.29% ALA475.N-lig.O 13.69% lig.O-lig.O 13.10% lig.O-ASN487.OD1 8.33% lig.O-GLN474.OE1 3.57% lig.N-lig.C 2.38% SER477.N-lig.F 1.79% ASN487.N-lig.O 1.79% NMG343.O3/4-lig.O 1.19% lig.O-ASP389.OD1 0.60% ASN331.ND2-lig.O 0.60% lig.O-ASP389.OD2 0.60% THR333.OG1-lig.O 0.60% ASN388.ND2-lig.C 0.60% lig.O-PRO527.O 0.60%

06

Atropine

10942532

1396281

E

lig.N-ASP420.OD1 45.83%

F

lig.O-SER477.OG 32.74% lig.N-ASP420.OD2 22.02% ASN370.ND2-lig.O 1.19% THR385.OG1-lig.O 0.60%

(continued)

Supplementary Information

295

Table 7.7 (continued) 07

Drug name

MD Data ID

ChEMBL

Spike-D, E, F

AZD-8330

10941318

3182621

D

ARG439.NH2-lig.O 27.98%

E

GLN506.NE2-lig.O 13.10%

F

HBs

lig.O-PRO499.O 7.74% ARG439.NE-lig.O 5.36% GLN506.NE2-lig.F 4.17% ARG439.NH1-lig.O 3.57% lig.O-ARG439.O 1.19% lig.O-ASN440.OD1 1.19% lig.O-lig.N 1.19% lig.N-THR500.O 1.19% TYR508.OH-lig.O 1.19% ARG439.NE-lig.N/C 0.60% NMG343.O6-lig.O 0.60% ASN440.ND2-lig.O 0.60%

08

Azilsartan

10941382

57242

D

ARG439.NH2-lig.O 40.48%

E

GLN506.NE2-lig.N 15.48%

F

ARG439.NH2-lig.N 11.31% ARG439.NH1-lig.O 11.31% ARG439.NE-lig.O 10.12% ASN440.ND2-lig.O 5.95% GLN506.NE2-lig.O 4.76% ASN501.ND2-lig.N 4.17% GLY502.N-lig.O 4.17% ASN437.ND2-lig.O 2.98% ARG439.NH1-lig.N 1.79% ASN440.ND2-lig.N 1.79% VAL503.N-lig.O 1.19% THR500.OG1-lig.O 1.19% VAL503.N-lig.N 0.60% ASN437.ND2-lig.N 0.60%

09

Brigatinib

10930748

3545311

D

lig.N-ASP389.OD2 17.86%

E

lig.N-ASP389.OD1 13.69% ASN370.ND2-lig.N 3.57% lig.N-TYR453.OH 2.98% SER477.OG-lig.N 2.98% TYR453.OH-lig.O 2.98% lig.N-GLY476.O 1.79% lig.N-PRO527.O 1.19% GLN493.NE2-lig.N 1.19% ASN370.ND2-lig.O 0.60% TYR421.OH-lig.N 0.60% GLN493.NE2-lig.O 0.60% lig.N-ASN388.O 0.60% lig.N-SER477.OG 0.60% THR372.OG1-lig.O 0.60% lig.N-lig.O 0.60%

10

Calcifediol

10941841

1040

E

lig.O-PRO337.O 41.07%

F

lig.O-GLU484.OE1 8.93% NMG343.N2-lig.O 7.74% lig.O-GLU484.OE2 6.55% lig.O-ASP364.O 1.79% lig.O-ASN437.O 1.79% lig.O-VAL483.O 1.19% lig.O-NMG343.O7/4 0.60% lig.O-TYR365.OH 0.60% lig.O-GLU484.O 0.60%

11

Captopril

10940762

27686

D

ARG408.NH2-lig.O 27.38%

E: LYS378

ARG408.NH1-lig.O 15.48%

F

LYS378.NZ-lig.O 12.50% ARG439.NH1-lig.O 5.36% ARG439.NH2-lig.O 3.57% VAL503.N-lig.O 2.98% ARG408.NE-lig.O 1.79%

(continued)

296

7 Spike (S) Glycoprotein

Table 7.7 (continued) 12

Drug name

MD Data ID

ChEMBL

Spike-D, E, F

Cefamandole nafate

10941424

1484057

D

HBs GLN506.NE2-lig.O 48.21%

E

VAL503.N-lig.O 19.05%

F

ARG439.NH2-lig.O 13.69% ARG439.NH1-lig.O 10.71% ASN437.N-lig.N 1.19% ARG439.NE-lig.O 1.19%

13

Cefixime

10918686

1317573

D

GLN506.NE2-lig.O 57.14%

E

ARG439.NH2-lig.O 48.81%

F

ARG439.NE-lig.O 31.55% VAL503.N-lig.O 16.67% lig.N-ASN440.OD1 5.36% ARG439.NE-lig.N 0.60%

14

Clobazam

10941112

70418

D

CYX488.N-lig.O 19.64%

F

ASN487.N-lig.O 11.31% VAL483.N-lig.O 7.14% GLY485.N-lig.O 2.38% GLU484.N-lig.O 1.79% ASN487.ND2-lig.O 0.60%

15

Cobimetinib

10941772

2146883

E

lig.N-GLU340.OE1 16.07% lig.N-GLU340.OE2 14.88% lig.O-GLU340.OE1 14.29% lig.O-GLU340.OE2 13.10% lig.O-PRO337.O 13.10% lig.N-LEU335.O 0.60% LYS356.NZ-lig.O 0.60% lig.O-GLU340.O 0.60%

16

CP-195543

10941273

301829

D

ARG439.NH2-lig.O 23.81%

E

ARG439.NE-lig.O 22.02%

F

ASN440.ND2-lig.O 10.12% ARG439.NH1-lig.O 1.79% GLN506.NE2-lig.O 1.19%

17

Darunavir

10918731

1201127

D

lig.O-lig.O 58.93%

F

lig.N-SER375.OG 26.79% SER375.OG-lig.O 19.05% lig.N-SER371.O 11.31% TYR508.OH-lig.N 10.12% GLY502.N-lig.O 8.93% lig.N-THR376.OG1 5.95% ARG439.NH1-lig.O 3.57% GLY496.N-lig.O 2.38% ARG439.NH2-lig.O 1.79% lig.N-PHE373.O 1.79% lig.N-ASP405.OD1 1.19% NMG343.N2-lig.O 1.19% GLN506.NE2-lig.O 0.60% NMG343.O3-lig.O 0.60% GLN493.NE2-lig.O 0.60% ASN437.ND2-lig.O 0.60% lig.N-GLY504.O 0.60% GLN498.NE2-lig.O 0.60% TYR508.OH-lig.C 0.60% lig.O-GLY496.O 0.60% LYS403.NZ-lig.O 0.60% lig.N-SER494.O 0.60% lig.O-PHE373.O 0.60%

18

Deferasirox

10941722

550348

E

lig.O-lig.N 8.33% LYS356.NZ-lig.O 6.55% ASP364.N-lig.O 5.95% ASN360.ND2-lig.O 2.98% lig.O-GLU340.OE2 1.79%

(continued)

Supplementary Information

297

Table 7.7 (continued) 19

Drug name

MD Data ID

ChEMBL

Spike-D, E, F

HBs

Dihydroergotamine

10942525

3561903

D

lig.N-SER366.OG 19.05%

F

lig.O-ASP364.OD1 4.17% lig.N-ASP364.OD2 3.57% lig.N-ASP364.OD1 2.98% lig.O-ASP364.OD2 2.38% ASN370.ND2-lig.O 1.19% lig.N-ASP389.OD2 1.19% NMG343.O6-lig.O 0.60% lig.N-ASN388.OD1 0.60% lig.O-lig.C 0.60% ASN481.ND2-lig.O 0.60% TYR489.OH-lig.O 0.60% lig.O-SER366.OG 0.60%

20

Divalproex sodium

10931330

109

E

lig.O-PRO337.O 43.45% ASP364.N-lig.O 12.50% TYR365.N-lig.O 9.52% lig.O-ASP364.OD1 9.52% lig.O-ASP364.OD2 4.17% lig.O-ASP364.O 1.19%

21

Duloxetine

10918694

424660

D

lig.N-ASP389.OD1 18.45%

E

lig.N-ASP389.OD2 14.88% lig.N-ASP364.OD1 0.60% lig.N-ASP389.CG 0.60%

22 23

Efavirenz Fluticasone propionate

10931344 10930719

59507 1473

D

lig.N-GLY476.O 44.64%

E

lig.N-ASN388.OD1 0.60%

E: THR415

THR415.OG1-lig.O 10.12%

F

lig.O-THR415.O 2.38% lig.O-THR415.OG1 1.19%

24

Iloprost

10906572

494

D: PHE486

lig.O-PRO337.O 49.40%

E

LYS356.NZ-lig.O 32.14% lig.O-CYX336.O 22.62% lig.O-GLU340.OE1 6.55% lig.O-GLU340.OE2 4.76% lig.O-lig.C 1.19% THR345.OG1-lig.O 1.19% SER399.OG-lig.O 0.60% GLU340.N-lig.O 0.60%

25

Isocarboxazid

10941783

1201168

26

Ketoconazole

10941101

157101

D

ASP364.N-lig.O 7.74%

F

lig.N-ASP364.O 4.17%

D

ASP364.N-lig.O 9.52%

F: PHE486

ASN487.ND2-lig.O 3.57% NMG343.O6-lig.N 1.19% TYR489.OH-lig.C 0.60% TYR489.OH-lig.O 0.60%

27

Lapatinib

10942558

1076241

D

lig.N-ASP364.OD1 14.29%

F

lig.N-ASP364.OD2 13.69% lig.N-CYX336.O 5.95% NMG343.N2-lig.O 2.38% lig.N-NMG343.O7 1.79% NMG343.O2-lig.N 1.79% lig.N-GLN474.O 1.19% GLN474.NE2-lig.O 1.19% NMG343.O3-lig.O 0.60% ASN487.N-lig.O 0.60% ASN487.ND2-lig.O 0.60% NMG343.O6-lig.O 0.60% lig.N-ILE332.O 0.60% lig.N-LEU335.O 0.60% THR333.OG1-lig.O 0.60%

(continued)

298

7 Spike (S) Glycoprotein

Table 7.7 (continued) 28

Drug name

MD Data ID

ChEMBL

Spike-D, E, F

Levomefolate calcium

10941419

1221561

D

ARG439.NH2-lig.O 53.57%

E

ARG439.NH1-lig.O 29.17%

F

HBs

TYR508.OH-lig.O 25.60% GLN506.NE2-lig.O 22.02% ARG439.NE-lig.O 16.67% lig.N-ASN501.O 5.36% GLN506.NE2-lig.N 2.38% lig.N-ALA435.O 2.38% ASN440.ND2-lig.O 1.79% lig.N-lig.O 0.60% lig.N-SER375.OG 0.60% lig.N-PRO499.O 0.60% VAL503.N-lig.O 0.60% lig.N-THR500.O 0.60%

29

Lometrexol

10941234

170101

D

ARG439.NH2-lig.O 51.19%

E

ARG439.NE-lig.O 32.14%

F

ARG439.NH1-lig.O 31.55% ASN440.ND2-lig.O 16.67% GLN506.NE2-lig.O 5.36% TYR508.OH-lig.N 2.98% ASN437.N-lig.O 1.79% lig.N-lig.O 1.19% THR500.OG1-lig.O 0.60% NMG343.N2-lig.N 0.60% SER375.OG-lig.N 0.60% NMG343.O6-lig.O 0.60% ARG439.NH1-lig.C 0.60% lig.N-PHE373.O 0.60% GLY504.N-lig.N 0.60%

30

Lomibuvir

10931493

3182952

D E

lig.O-lig.N 10.71% PHE374.N-lig.O 3.57% TRP436.NE1-lig.O 2.98% lig.O-PHE342.O 2.38% ASN440.ND2-lig.O 1.79% NMG343.O6-lig.O 1.19% GLN493.NE2-lig.O 1.19% lig.O-ASN437.O 0.60%

31

Megestrol acetate

10932268

1201139

D

lig.O-NMG343.OD1 69.05%

E

THR372.OG1-lig.O 29.17% lig.N-PHE342.O 19.05% THR372.N-lig.O 6.55% TRP436.NE1-lig.C 1.19% ARG509.NH1-lig.N 0.60% GLN493.NE2-lig.O 0.60%

32

Methsuximide

10906575

697

D

THR376.OG1-lig.O 5.95%

F: SER477

ARG408.NH1-lig.O 2.38% ARG408.NE-lig.O 1.19% ARG408.NH2-lig.O 0.60% LYS378.NZ-lig.O 0.60%

33

Naloxone

10906602

609673

D

lig.O-ASP405.OD1 62.50%

E

lig.N-ASP405.OD2 47.02% ALA384.N-lig.O 35.71% lig.O-ASP405.OD2 11.31% lig.O-VAL382.O 6.55% ARG408.NH2-lig.O 6.55% lig.N-ASP405.OD1 5.36%

34

Nebivolol

10918707

1201731

D

lig.O-ASP420.OD2 42.86%

E

lig.O-ASP420.OD1 17.26% ASN460.ND2-lig.O 4.17% lig.N-ASP420.OD2 4.17%

A

lig.O-A:ASP985.OD2 1.19%

A

lig.O-A:ASP985.OD1 1.19% lig.N-ASP420.OD1 1.19% lig.N-ASN460.OD1 0.60% lig.N-THR415.OG1 0.60% lig.O-TYR421.OH 0.60% lig.O-THR385.OG1 0.60%

(continued)

Supplementary Information

299

Table 7.7 (continued) 35

Drug name

MD Data ID

ChEMBL

Spike-D, E, F

HBs

Nilutamide

10942574

1274

F

ASP364.N-lig.O 10.71% VAL367.N-lig.O 1.79% lig.N-ASP364.OD1 1.19% lig.N-ASP364.OD2 0.60% lig.N-NMG343.OD1 0.60% PHE342.N-lig.O 0.60% lig.N-NMG343.O7 0.60% NMG343.N2-lig.O 0.60% lig.N-NMG343.O4 0.60%

36 37

Nitazoxanide Pelitrexol

10930676 10941210

1401 2107361

D

ARG509.NH1-lig.O 17.26%

F: VAL503, TYR505

lig.N-PHE342.O 0.60%

D

TYR508.OH-lig.O 42.86%

E

ARG439.NH2-lig.O 35.12%

F

ARG439.NH1-lig.O 33.93% NMG343.O4-lig.O 13.69% NMG343.O3-lig.O 11.31% GLN506.NE2-lig.O 5.36% ARG439.NE-lig.O 4.76% TYR508.OH-lig.N 3.57% lig.N-THR500.O 2.98% ASN440.ND2-lig.O 1.79% VAL503.N-lig.O 1.79% THR500.OG1-lig.O 1.19% lig.N-THR376.OG1 1.19% ASN437.ND2-lig.N 1.19% VAL503.N-lig.N 0.60% SER375.OG-lig.N 0.60% lig.N-lig.O 0.60% NMG343.O3-lig.N 0.60% GLN498.NE2-lig.O 0.60% TYR508.OH-lig.C 0.60% lig.N-ALA435.O 0.60%

38

Raltitrexed

10941177

140144

D

ARG439.NH2-lig.O 60.12%

E

ARG439.NH1-lig.O 34.52%

F

ARG439.NE-lig.O 22.02% NMG343.O4-lig.O 12.50% NMG343.O3-lig.O 10.71% NMG343.O6-lig.O 8.93% GLN506.NE2-lig.O 8.33% ASN437.N-lig.O 6.55% ASN440.ND2-lig.O 6.55% lig.N-PHE373.O 5.36% NMG343.O2-lig.O 4.76% ASN437.N-lig.N 1.79% TYR508.OH-lig.C 1.19% ASN440.N-lig.O 0.60% lig.N-ASN440.OD1 0.60% TYR508.OH-lig.O 0.60% GLY504.N-lig.O 0.60% TYR508.OH-lig.N 0.60% lig.N-TYR505.OH 0.60%

39

Rebamipide

10941364

1697771

D

GLN506.NE2-lig.O 45.24%

E

ARG439.NH2-lig.O 34.52%

F

ARG439.NH1-lig.O 23.81% GLN506.NE2-lig.C 4.76% lig.N-ASN501.O 3.57% ARG439.NE-lig.O 2.38% GLN506.NE2-lig.N 1.19%

40

Recoflavone

10941282

4297606

D

ARG439.NH2-lig.O 20.24%

E

ARG439.NH1-lig.O 13.69%

F

ASN437.N-lig.O 9.52% ARG439.NE-lig.O 7.74% GLN506.NE2-lig.O 5.36% THR500.OG1-lig.O 4.17% TYR508.OH-lig.C 1.79% TYR508.OH-lig.O 0.60% SER375.OG-lig.O 0.60%

(continued)

300

7 Spike (S) Glycoprotein

Table 7.7 (continued) 41

Drug name

MD Data ID

ChEMBL

Spike-D, E, F

Ritonavir

10921687

159496

D

HBs lig.O-NMG343.OD1 69.05%

F

THR372.OG1-lig.O 29.17% lig.N-PHE342.O 19.05% THR372.N-lig.O 6.55% TRP436.NE1-lig.C 1.19% ARG509.NH1-lig.N 0.60% GLN493.NE2-lig.O 0.60%

42

Rivaroxaban

10940767

3183768

D

THR376.OG1-lig.O 5.95%

E: SER371

ARG408.NH1-lig.O 2.38% ARG408.NE-lig.O 1.19% ARG408.NH2-lig.O 0.60% LYS378.NZ-lig.O 0.60%

43

Tadalafil

10942509

1671905

D

lig.N-LEU455.O 28.57%

E

TYR365.N-lig.O 3.57% TYR369.OH-lig.C 1.79% PHE490.N-lig.O 1.79%

44

Telaprevir

10931335

231813

D F

lig.N-ALA475.O 26.19% SER477.OG-lig.O 4.76% lig.N-SER366.OG 2.98% THR372.OG1-lig.O 2.98% ASN370.ND2-lig.O 2.38% lig.N-lig.O 1.79% NMG343.N2-lig.O 0.60%

45

Tenofovir

10931329

315593

D E

lig.O-ASP406.OD1 38.10% LYS403.NZ-lig.O 21.43% lig.O-ASP405.OD2 16.67% lig.O-ASP405.OD1 13.69% ASN370.ND2-lig.N 8.93% lig.O-ASP406.OD2 7.74% lig.O-ASP389.OD1 6.55% lig.O-ASP389.OD2 5.36% lig.N-ASN370.OD1 5.36% ASN481.ND2-lig.N 2.98% lig.O-ASP420.OD1 2.38% lig.N-TYR453.OH 1.19% TYR453.OH-lig.N 1.19% GLN409.NE2-lig.O 1.19% GLN493.NE2-lig.N 1.19% lig.N-GLN409.NE2 0.60% lig.N-ASP406.OD2 0.60% ASN388.ND2-lig.O 0.60% lig.N-ALA384.O 0.60% lig.O-THR385.OG1 0.60% ASN388.ND2-lig.N 0.60% lig.N-ASN370.ND2 0.60% lig.N-ASP389.OD1 0.60% lig.N-THR385.O 0.60% lig.N-GLN493.OE1 0.60%

46

Terazosin

10918688

1201091

D

lig.N-VAL483.O 29.76%

F

lig.N-GLY485.O 24.40% THR372.OG1-lig.O 8.33% lig.N-GLU484.OE1 1.79% lig.N-GLU484.OE2 1.19% THR372.OG1-lig.C 0.60% lig.N-ASN370.OD1 0.60% TYR489.OH-lig.N 0.60% SER494.OG-lig.O 0.60% lig.N-SER371.OG 0.60%

47

Treprostinil

10906555

3561314

E

NMG343.ND2-lig.O 42.26% lig.O-ASP364.O 22.02% NMG343.N2-lig.O 8.93% NMG343.O6-lig.O 1.19% ASP364.N-lig.O 0.60% lig.O-ASP364.OD1 0.60% ASN487.ND2-lig.O 0.60%

(continued)

Supplementary Information

301

Table 7.7 (continued) 48 49

Drug name

MD Data ID

ChEMBL

Spike-D, E, F

HBs

Triazolam

10941754

646

D

GLN493.NE2-lig.C 1.19%

E

TYR365.N-lig.N 0.60%

D

GLN506.NE2-lig.N 16.67%

Vorapaxar

10930743

2107386

E F

lig.N-PRO499.O 14.29% GLN506.NE2-lig.O 10.12% lig.N-THR500.O 3.57% VAL503.N-lig.O 1.79% ARG439.NE-lig.O 1.79% ARG439.NH2-lig.O 1.19% ARG439.NH1-lig.O 1.19% ASN440.ND2-lig.O 1.19%

50

Zileuton

10930851

93

D: ASP405, ARG408 E

lig.O-ASP405.OD1 30.95% lig.O-ASP405.OD2 4.17% lig.N-ASP405.O 2.98% ARG408.NE-lig.O 1.79% ARG408.NH1-lig.O 1.79% lig.N-ASP405.OD2 0.60% lig.N-ASP405.OD1 0.60% lig.N-GLY404.O 0.60%

302

Fig. 7.7 (continued)

7 Spike (S) Glycoprotein

Supplementary Information

303

Fig. 7.8 Some strong SBs of the 6VYB-trimeric-spike-opened-model-2 confirmed by MD data in [321]

304

Fig. 7.8 (continued)

7 Spike (S) Glycoprotein

Supplementary Information

305

Fig. 7.9 Some strong SBs of the 1R4L-ACE2-closed-model-3 confirmed by MD data in [321]

306

7 Spike (S) Glycoprotein

Fig. 7.10 Some strong SBs of the 1R42-ACE2-opened-model-4 confirmed by MD data in [321]

Supplementary Information

307

Fig. 7.11 Some SBs of the 6M17-spike-ACE2-binding-model-5 confirmed by MD data in [321]

308

Fig. 7.12 Some data in [321]

7 Spike (S) Glycoprotein

Supplementary Information

Fig. 7.12 (continued)

309

310

7 Spike (S) Glycoprotein

Fig. 7.13 Some strong and important HBs (with average values of 2.860864, 2.848252, 2.919316, and 3.650197 Å, respectively) of the 6VXX-trimeric-spike-closed-model-1 confirmed by MD data in [321]

Fig. 7.14 Some strong and important HBs (with average values of 2.826612, 2.827929, 2.937867, 2.933415, and 2.911408 Å, respectively) of the 6VYB-trimeric-spike-opened-model-2 confirmed by MD data in [321]

Supplementary Information

311

Fig. 7.15 Some strong and important HBs (with average values of 2.907522 (broken during frames 103–169 and 211–235), 3.143333 (broken during frames 1–32, 103–202, 272–279, and 380–404), and 2.921907 Å, respectively) of the 1R4L-ACE2-closed-model-3 confirmed by MD data in [321]

Fig. 7.16 Some strong and important HBs (with average values of 2.827859, 2824532, and 2.940768 Å, respectively) of the 1R42-ACE2-opened-model-4 confirmed by MD data in [321]

312

7 Spike (S) Glycoprotein

Fig. 7.17 Some strong and important HBs (with average values of 2.849615, 2.903840, 2.904051, 2.827907, 2.803045, 2.881762, 3.173316, and 2.803158 Å, respectively) of the 6M17-spikeACE2-binding-model-5 confirmed by MD data in [321]

Supplementary Information

313

Fig. 7.18 Some strong and important HBs (with average values of 2.868132, 2.865653, 2.921195, 2.814954, 2.920962, 2.900633, 2.913999, 2.912548, 2.71528, and 2.791970 Å, respectively) of the 6VW1-spike-ACE2-binding-model-6 confirmed by MD data in [321]

314

Fig. 7.18 continued

7 Spike (S) Glycoprotein

Supplementary Information

315

Fig. 7.19 The 115 ligand interaction diagrams of the optimized 5_Swiss_5_SS-6VSB model of [127]

316

Fig. 7.19 continued

7 Spike (S) Glycoprotein

Supplementary Information

Fig. 7.19 continued

317

318

Fig. 7.19 continued

7 Spike (S) Glycoprotein

Table 7.8 The 115 glycan shields and their binding residues of SARS-CoV-2-spike in the optimized 5_Swiss_5_SS-6VSB model of [127] The glycan shield

Spike residues binding with the glycan shield

Ligand-3361-4YB

TYR2, NLN35, THR37, PHE39, LEU58, PRO59, TYR243

Ligand-3366-OMA

ARG211

Ligand-3368-UYB

GLY46, NLN48, THR50, GLN108, PHE109, CYS110, ASN111

Ligand-3373-OYB

ASP112, ARG132

Ligand-3374-2MA

LYS51, PHE53, ASN111, ASP112, PHE114, GLY116, VAL117, TYR118, ARG132

Ligand-3376-OfA

GLY46, THR50, LYS51, ARG52, PHE53, PHE109, ASN111

Ligand-3377-4YB

NLN96, THR98, ASN99, MET127, PHE131, VAL145

Ligand-3384-UYB

GLN108, VAL117, LYS121, NLN123, SER135, ASN138

Ligand-3389-2MA

SER86, GLN108, PHE109, CYS110

Ligand-3391-OfA

LYS103, NLN123, GLU128, SER129, TYR134, SER135

Ligand-3392-UYB

ASN138, NLN139, TYR2565, ILE2682, SER2683, THR2684, GLU2685, ILE2686, PHE2704

Ligand-3399-OfA

LYS87, THR88, GLN89, GLU106, ARG2680, ASP2681, ILE2682, SER2683

Ligand-3406-2MA

GLN26, ASP27, LEU28, ASP62, ILE171, PRO246, PRO605, VMB3402, VMA3403

Ligand-3408-2MA

GLU298, SER299, ASN514, THR1841, VMB3402, OMA3405

Ligand-3410-UYB

PRO148, PHE149, LEU150, MET151, LEU153, GLU154, NLN256, LEU2774, PRO2775

Ligand-3418-OfA

TYR12, LEU150, MET151, ASP152, LYS180, HIS181, GLU198, THR258, LEU2774

Ligand-3419-UYB

NLN305, ILE306, THR307, ASN1219, VAL1265, GLN1267

Ligand-3424-2MA

VAL1221, LYS1223, GLU1250, TYR1254, GLU1263, VAL1265

Ligand-3426-OfA

NLN305, ILE306, THR307, LEU309, VAL336, PRO501

Ligand-3427-UYB

NLN317

Ligand-3434-OfA

GLU314, NLN317, ALA318, THR319

Ligand-3435-4YB

THR281, GLU283, NLN577, LYS809, GLN810, TYR811, SER913, SER914

Ligand-3440-OMA

LEU795, ASN798, LYS799, LEU802, GLN810, TYR811, GLY812, SER913

Ligand-3441-OMA

GLN810, TYR811, GLY812, ASP813

Ligand-3442-UYB

NLN590, THR592, GLN618

Ligand-3449-OfA

NLN590, THR592, GLU593

Ligand-3450-4YB

NLN590, GLN618, HIS629, NLN631

Ligand-3455-OMA

ASP588, ARG620

Ligand-3456-2MA

ARG620, PRO1906, SER1907, ARG1909, ASP1961, GLU1962

Ligand-3458-4YB

NLN683, ASN684, ASP1890

Ligand-3464-OMA

ILE1104

Ligand-3465-4YB

THR690, NLN691, LEU896, GLN1045, ASN3339, VAL3342

Ligand-3470-OMA

PRO1086

Ligand-3472-4YB

LYS769, NLN775, SER777, GLN778, PHE791, GLN810, ILE905, GLY906, GLN909, ASP910, SER913, SER914

Ligand-3479-4YB

ALA680, SER682, ASN684, SER685, NLN1048, PHE1049, THR1050, PRO1997, ILE1888, LYS1889, GLN1989

Ligand-3486-4YB

NLN1072, GLY1073, THR1074, HIS1075, PHE1077

Ligand-3491-2MA

THR1110, TYR1112

Ligand-3493-UYB

NLN1108, ASN1109, HIS1075

Ligand-3501-4YB

LEU1150, PRO1151, SER1154, NLN1155, VAL1156, ASN1181, GLY1362, TYR1363, LEU1364, GLN1365, PRO1416, THR1417, GLU1418, SER1419, ASN1634, VMB3542, VMA3543, 2MA3544, OMA3545

Ligand-3506-OMA

GLN1365, 0MA3545

Ligand-3507-OMA

PRO1179, PHE1180, ASN1181, ASP1182, NLN1328, ILE1329, THR1330, ARG1331, 4YB3540, 2MA3544

Ligand-3508-UYB

VAL1164, GLY1166, THR1167, NLN1168, ARG1172, GLN1228, ASN1231, ASP1232

Ligand-3516-OfA

NLN1168, ARG1172, PHE1173, ASP1174, PHE1229, ASN1231

Ligand-3517-4YB

ARG1196, NLN1216, VAL1221, TYR1238, GLU1248, SER1249, GLU1250, PHE1251, TYR1254

Ligand-3524-UYB

HIS1240, ASN1242, NLN1243

Ligand-3531-OfA

ALA1217, THR1218

Ligand-3532-UYB

PRO437, ARG440, CYS454, ASN455, ASN1258, NLN1259

Ligand-3537-2MA

PRO437, GLU439, ARG440, ASP441, ILE442

Ligand-3539-OfA

LYS1207, THR1208, GLN1209, GLU1226

Ligand-3546-2MA

GLN1146, THR2961, GLU2962, SER2964, ASN2965, LEU2968, LYS3200, 4YB3540, 4YB3541, VMA3542, VMA3543

Ligand-3548-2MA

SER1419, LYS1480, ASP1483, THR1641, LEU3195, SER3196, 4YB3541, VMB3542

Ligand-3550-UYB

ASN530, LYS531, GLU1375, NLN1376, ALA1940, ASP1942

Ligand-3556-2MA

ASN1918, ALA1923, ASP1924, ASP1942

Ligand-3558-OfA

ASN1374, GLU1375

Ligand-3559-UYB

PRO1424, NLN1425, ILE1426,PRO1673, GLN1674

Ligand-3564-2MA

ASN1454, THR2338, ASN2339

Ligand-3566-OfA

NLN1425, ILE1426, THR1427, ASN1428

Ligand-3567-UYB

SER433, ASN434, LEU435, PHE1436, NLN1437, ALA1466, SER1467, PHE1468, SER1469, TRP1530, ASN1531, SER1532,ASN1533, ASN1534, LEU1535, VAL1597, GLN1600

Ligand-3572-2MA

SER433, ASN434, LEU435, LYS436, PRO437, PHE438, ALA1466

Ligand-3574-OfA

NLN1437, ALA1438, THR1439, LEU1535

Ligand-3575-4YB

THR1401, ARG1776, LYS1919, LYS1929, TYR1931, ASP1933, CYS1934, LEU1935, ASP1937, SER2033, SER2034, THR2035, ALA2036, SER2037

Ligand-3581-OMA

GLY1936, ASP1937, ILE1938

Ligand-3582-UYB

NLN1710, CYS1711, THR1712

Ligand-3589-OfA

CYS1711, THR1712, VAL1736

Ligand-3590-4YB

NLN1751, SER1753, CYS3054, LEU3055, GLY3056

Ligand-3596-2MA

SER3024, LYS3025, PHE3047, GLN3050, TYR30511, GLY3052, CYS3054, LEU3055

Ligand-3598-4YB

NLN1803, ASN1804, THR2171, ALA2172, PRO2173, GLY2225, ILE2226, VAL2227

(continued)

320

7 Spike (S) Glycoprotein

Table 7.8 (continued) The glycan shield

Spike residues binding with the glycan shield

Ligand-3604-OMA

CYS2220, ASP2221, ILE2226, NLN2228

Ligand-3605-4YB

THR1810, NLN1811, TYR2204, PRO2206, PRO2237, LEU2239, ASP2240

Ligand-3610-OMA

GLU2205, PRO2206, GLN2207, ILE2208, PHE2197, PRO2237

Ligand-3611-OMA

ASN1099, ASP1101, VAL1102

Ligand-3612-4YB

SER1897, GLN1898, PHE1911, GLY2026, GLN2029, ASP2030, SER2033

Ligand-3619-4YB

ALA1800, TYR1801, SER1802, SER1805, SER1802, NLN2168, THR2170, NLN2192, GLN3109

Ligand-3626-4YB

THR1810, NLN1811, GLN2165, GLU2166, LYS2167, PHE2169, NLN2192, PHE2197, TYR2204, PRO2206

Ligand-3633-UYB

ILE2226, VAL2227

Ligand-3641-4YB

NLN2275, THR2277, PRO2296, LEU2298, PRO2229, PHE2279, ASN2301, TYR2483, 2MA3684, 0MA3685

Ligand-3646-OMA

ILE2283, ARG2292, PRO2296

Ligand-3648-UYB

THR2287, NLN2288, THR2290, LYS2291, PHE2293, LEU2355, HIS2459, ARG2460

Ligand-3653-OYB

TRP2366, ARG2372

Ligand-3654-2MA

PHE2354, LEU2355, ASN2362, SER2369, GLU2370, PHE2371, ARG2372, ASP2352, ALA2457, LEU2458, HIS2459

Ligand-3656-OfA

THR2287, ARG2460

Ligand-3657-4YB

NLN2336, THR2338, ASN2339, VAL2341, LYS2343, VAL2385

Ligand-3664-UYB

TYR2359, TYR2374, SER2375, NLN2363, SER2376, ALA2377, ASN2378

Ligand-3669-2MA

GLU2346, NLN2379

Ligand-3671-OfA

LYS2361, ASN2362, NLN2363

Ligand-3672-UYB

ARG1440, NLN2379

Ligand-3677-2MA

THR1439, ARG1440, LYS1538, GLY1541, ASN1542, TYR1543

Ligand-3679-OfA

ARG1440, NLN2379, CYS2380

Ligand-3686-2MA

LYS1552, SER1553, ASN1554, LEU1555, LYS1556, THR2450, 4YB3680, VMA3683, 2MA3684

Ligand-3688-2MA

ARG1551, LYS1552, ILE1566, GLN1568, ALA1569, GLY1570, SER1571, THR1572, PRO1573, CYS1574, ASN1575, GLY1576, ASN1581, VMB3682

Ligand-3690-UYB

SER1649, ASN1650, LYS1651, LYS1652, PHE1653, LEU1654, GLU1677, PHE2257, NLN2496, GLY2497

Ligand-3696-2MA

GLU1648, SER1649, ASN1650

Ligand-3699-UYB

NLN2545, GLN2794, THR2795

Ligand-3706-OfA

THR2547

Ligand-3707-UYB

PHE2556, NLN2557, ALA2558, THR2559, ARG2560, SER2587, PHE2588, TRP2650, ASN2653, ASN2654, LEU2655, ASP2656, SER2657, LYS2658, VAL2659, ARG2723

Ligand-3714-OfA

GLU2554, NLN2557, ALA2558, THR2559

Ligand-3715-4YB

ILE1663, SER2519, THR2521, GLU2523, THR2816, NLN2817

Ligand-3720-OMA

SER2260, LYS2492, TYR2493, ASN2494, GLU2495, THR2500

Ligand-3721-OMA

ILE1663, LEU2517, LYS2518, SER2519, LEU2262

Ligand-3722-UYB

NLN2830, CYS2831, THR2832, ASP2841, GLN2842, THR2846, TRP2847, PHE2857, GLN2858, THR2859, ARG2860, HIS2869, NLN2871, ILE2884, THR2910

Ligand-3727-2MA

ARG2848, GLU2868, HIS2869, VAL2870, NLN2871

Ligand-3729-OfA

GLN2858, THR2859, ARG2860

Ligand-3730-4YB

PRO783, SER784, LYS785, PRO786, LYS788, NLN2871, ASN2872, SER2873

Ligand-3735-OMA

SER784

Ligand-3736-2MA

LYS764, PRO783, LYS788, GLN846, GLU2916

Ligand-3738-4YB

SER2922, NLN2923, ASN2924

Ligand-3745-4YB

THR2930, NLN2931, PHE2932, GLU3132, ASN3133, LEU3136, LYS3287, PHE3323, TYR3324

Ligand-3750-OMA

ASP3360

Ligand-3751-OMA

LYS2180, GLY2218, ASN2219, GLU3325, ASP3360

Ligand-3752-4YB

LYS3009, ASP3010, NLN3015, SER3017, GLN3018, PHE3031, ASN3142, ILE3145, GLY3146, GLN3149, ASP3150, SER3153, SER3154

Ligand-3759-4YB

NLN3288, PHE3289, THR3290, SER3311, NLN3312

Ligand-3766-4YB

LYS3287, PHE3289, NLN3312, PHE3317, TYR3324, PRO3326

Ligand-3773-UYB

CYS3296, HIS3297, ASP3298, GLY3299, NLN3348, ASN3349, THR3350

Ligand-3778-2MA

GLU1118, LEU1119, ASP1120

Ligand-3780-OfA

CYS3296, ASP3298, GLY3299, NLN3348

ARG24.NE-ASP67.OD1 26.33

ILE71.N-TYR177.O 25.33 TYR381.OH-GLU501.OE1 25.33

TYR164.N-TYR120.O 37.50

TYR493.N-ILE387.O 37.33

ASN433.ND2-ASP427.O 57.17

PHE377.N-VAL509.O 56.50

THR310.N-TYR291.O 26.17

GLN279.NE2-ASN281.OD1 19.00

ASN63.ND2-GLU185.OE2 18.17

ARG264.NH1-ASP287.OD1 17.33

ARG264.NH2-ASP287.OD2 23.50 THR249.N-ILE254.O 23.33 CYX101.N-LEU182.O 23.17 TYR256.N-GLY247.O 23.17

SER35.OG-ASP33.OD2 35.33

VAL312.N-ALA289.O 35.00

ILE27.N-VAL64.O 35.00

ARG250.N-ASN229.O 34.83

SER218.N-SER204.O 34.33

GLN162.N-TYR122.O 34.17

ARG126.NH1-SER128.O 34.17

ASN229.N-GLN162.OE1 51.83

ASP427.N-SER423.O 50.67

ASP67.N-VAL181.O 50.50

VAL276.N-CYX219.O 50.50

ASP111.N-SER107.O 49.83

LEU124.N-PRO160.O 49.17

SER107.N-PRO176.O 33.33

SER35.OG-ASP33.OD1 33.17

GLN491.NE2-ASN486.O 47.50

ASP89.N-GLY85.O 46.50

VAL209.N-THR313.O 22.50 GLN459.NE2-GLY461.O 22.33

ARG340.NH2-ASP383.OD1 16.83

THR249.OG1-ARG251.O 16.83

ARG251.NH1-GLU153.OE2 17.00

THR275.N-ASP270.O 17.00

TYR65.OH-GLU185.OE2 17.00

VAL193.N-PHE61.O 22.83 THR400.OG1-ASP405.OD2 22.83 ARG269.NH2-GLY252.O 22.50

ASP287.N-LYS284.O 33.67

GLY223.N-GLN167.OE1 33.67

ILE387.N-TYR493.O 33.50

VAL181.N-ASP67.O 47.83

ASN29.N-THR192.OG1 17.00

ASN379.ND2-GLU501.OE2 17.17

ARG24.NH2-ASP67.OD1 17.33

ASN424.N-ASN422.OD1 17.50

ALA420.N-THR361.O 17.50

GLY389.N-GLN491.O 17.50

CYX321.N-VAL347.O 23.17

TYR256.OH-ASP296.OD2 23.50

ASP270.N-THR275.O 47.50

VAL496.N-ILE419.O 48.17

ARG251.NH1-GLU153.OE1 17.33

ARG340.NH2-ASP383.OD2 23.67

ASN422.ND2-GLN491.OE1 35.33

ASP383.N-VAL497.O 52.00

SER358.OG-PRO302.O 51.83 SER183.N-TYR65.O 23.67

LYS25.N-ALA66.O 17.83 GLY100.N-TYR49.O 17.67 ARG126.NE-ASP136.OD1 17.50

SER18.OG-LEU121.O 24.17 ALA144.N-ASN156.O 23.83 LYS363.N-VAL418.O 23.83

GLN279.N-THR266.O 35.67

SER423.N-PRO492.O 35.50

TYR158.N-TYR142.O 35.50

ARG123.NH1-ASP136.OD1 18.00

SER107.OG-ASP111.OD2 18.00

TYR234.OH-ASP296.OD2 18.17

VAL180.N-ILE103.O 52.67

ARG264.NH2-ASP287.OD1 24.17

SER356.OG-VAL352.O 25.00

VAL418.N-LYS363.O 52.17

ASN117.ND2-ASP111.O 53.17

ALA258.N-VAL245.O 18.00

CYX417.N-LEU498.O 24.17

TYR158.OH-ASP296.OD1 35.67

VAL31.N-ASN3.O 35.67

LEU130.N-ASP89.O 53.50

GLN143.NE2-GLY145.O 24.33 LYS47.N-VAL102.O 24.17

LEU498.N-CYX417.O 36.00

ILE103.N-VAL180.O 35.83

VAL102.N-LYS47.O 54.33

ARG494.NH2-ASP427.OD1 53.50

LEU446.N-ASP405.O 53.33

SER204.N-SER218.O 18.00

ARG178.N-TRP105.O 24.67

SER315.N-VAL209.O 36.50

LYS284.N-ASP287.OD2 36.50

ARG123.N-ASN91.OD1 55.67

ARG126.NE-ASP136.OD2 18.33 NLN12.N-GLY8.O 18.33

TRP233.N-ALA246.O 54.33

TYR118.OH-GLY115.O 25.00

ARG264.NH1-ASP287.OD2 36.83

THR266.N-GLN279.O 36.67

TYR277.N-SER268.O 55.83

TRP421.N-ARG494.O 18.33

SER334.OG-LEU437.O 18.50

GLY416.N-TYR365.O 18.50

VAL314.N-THR288.OG1 18.67

ASN39.N-SER35.O 18.67

LYS341.N-ALA382.O 19.00

ARG494.NE-ASP427.OD2 55.83

TYR38.OH-PRO53.O 25.67

SER138.OG-GLU140.OE1 26.00

ARG24.NE-ASP67.OD2 26.17

MET280.N-LEU215.O 38.33

SER428.OG-ASN424.O 37.83

ALA295.N-GLN198.OE1 37.50

ARG439.N-ASN407.OD1 62.67

TYR291.OH-ASP287.O 62.67

CYX5.N-VAL31.O 26.17

TYR291.N-THR310.O 57.33

TYR142.N-TYR158.O 38.50

TYR122.N-GLN162.O 38.33

TYR436.OH-ASP427.OD1 64.83

SER423.OG-ASP427.OD2 63.17

Table 7.9 The HBs (with more than 10.00% occupancy rates) of the spike-trimer 600 frames’ MD file “production_Nb6cRBD1.pdb” PHE159.N-ASN229.OD1 13.33

(continued)

GLN394.NE2-GLU391.OE2 11.00

ALA460.N-ASN472.O 11.00

GLN483.NE2-THR485.OG1 11.00

ASN57.ND2-ASP33.OD1 11.17

SER222.OG-ASN170.OD1 11.33

ALA294.N-GLY232.O 11.33

TYR142.OH-ALA298.O 11.50

ASN229.ND2-PHE159.O 11.50

ARG126.NH2-ASP136.OD1 11.50

VAL468.N-CYX465.O 11.67

ALA88.N-GLN78.OE1 11.67

SER68.N-ASN23.O 12.00

THR62.N-GLU185.O 12.00

GLU243.N-ARG235.O 12.00

GLN394.NE2-GLU391.OE1 12.17

LYS447.N-GLU450.OE1 12.17

LYS93.NZ-ASP89.OD2 12.33

LEU37.N-TYR34.O 12.33

LEU503.N-THR378.OG1 12.67

TYR234.OH-ASP296.OD1 12.67

SER360.N-ALA420.O 12.67

SER268.N-TYR277.O 12.67

PHE500.N-THR415.O 12.67

SER384.N-ASN339.O 12.67

ARG442.NE-ASP452.OD1 12.83

THR62.OG1-PRO190.O 12.83

ARG123.NH1-ASP136.OD2 13.00

LYS113.N-PHE166.O 13.00

ARG439.NH2-SER454.O 13.17

ARG135.NH1-TRP22.O 13.17

Supplementary Information 321

ALA66.N-LYS25.O 32.67

CYX473.N-GLY470.O 32.50

TYR458.N-TYR474.O 32.33

TYR92.OH-ASP67.OD1 32.33

TYR92.OH-ASP67.OD2 32.00

TYR438.N-GLN478.O 31.33

TYR164.OH-GLU75.OE1 31.33

TYR408.N-ILE403.O 31.33

ARG340.NE-ASP383.OD1 31.17

ILE419.N-VAL496.O 31.00

GLY154.N-CYX157.O 30.83

ASN355.N-SER351.O 30.67

THR508.N-PHE377.O 30.67

VAL495.N-PHE385.O 30.50

ALA382.N-LYS341.O 30.50

ASN274.ND2-GLY115.O 30.33

LEU278.N-LEU217.O 29.17

SER112.OG-ASN108.O 29.00

THR288.OG1-PRO285.O 28.67

VAL179.N-PHE69.O 28.67

ASN433.N-PHE482.O 28.33

TYR158.OH-ASP296.OD2 28.17

ILE248.N-MET231.O 28.00

ALA32.N-CYX194.O 28.00

ASN91.ND2-ARG123.O 27.83

SER351.OG-ASP349.OD1 27.83

SER454.OG-ASP452.OD1 27.50

TYR474.N-TYR458.O 27.33

ASP296.N-ALA230.O 27.17

ARG235.N-GLU243.O 27.17

LEU440.N-PRO476.O 26.83

SER138.OG-GLU140.OE2 26.67

TYR480.N-TYR436.O 26.67

ARG494.N-TRP421.O 26.50

TYR408.OH-ASP383.OD1 26.50

THR275.OG1-LYS273.O 26.33

SER107.OG-ASP111.OD1 46.33

TYR234.N-TYR292.O 46.00

TYR49.N-GLY100.O 46.00

TYR365.N-GLY416.O 45.83

VAL497.N-ASP383.O 45.67

PHE61.N-VAL193.O 45.67

PHE226.N-SER222.O 45.17

GLY212.N-LEU283.O 45.17

ALA348.N-CYX510.O 45.00

LEU217.N-LEU278.O 45.00

THR508.OG1-THR378.O 45.00

THR192.OG1-THR62.O 44.50

VAL245.N-TRP233.O 43.83

GLY232.N-ALA294.O 43.67

GLN175.NE2-ASN170.O 43.50

TYR120.OH-ASP111.OD2 43.50

ASP405.N-GLY401.O 43.50

TYR177.N-ILE71.O 42.67

ARG178.NH2-ASP111.OD2 42.50

TYR292.N-TYR234.O 42.17

TYR92.N-ILE87.O 41.50

ARG178.NE-ASP111.OD1 41.33

VAL347.N-ASN319.O 41.17

TYR381.N-SER499.O 41.17

ILE343.N-VAL380.O 40.33

SER454.OG-ASP452.OD2 40.17

SER351.OG-ASP349.OD2 39.83

TYR65.N-SER183.O 39.67

TYR256.OH-ASP296.OD1 39.67

GLN478.N-TYR438.O 39.33

ARG442.NH1-SER444.O 39.33

TYR408.OH-ASP383.OD2 39.17

ASN106.ND2-GLN175.OE1 39.17

THR192.N-PHE61.O 39.00

LEU182.N-CYX101.O 39.00

TYR354.OH-ASN373.OD1 39.00

Table 7.9 (continued)

ARG340.NE-ASP383.OD2 19.17

PHE449.N-LYS409.O 19.17

TRP105.N-ARG178.O 19.17

MET231.N-ILE248.O 19.17

THR84.OG1-ASP89.OD2 19.33

SER112.OG-ASN108.OD1 19.33

TYR65.OH-GLU185.OE1 19.33

THR400.OG1-ASP405.OD1 19.33

GLN78.N-GLU75.O 19.50

ASN424.ND2-PRO484.O 19.50

ASN108.N-ASN106.OD1 19.67

TYR120.OH-ASP111.OD1 19.83

ASN379.ND2-GLU501.OE1 19.83

GLY73.N-GLN175.O 19.83

LEU215.N-MET280.O 19.83

VAL509.N-PHE377.O 20.00

TYR381.OH-GLU501.OE2 20.00

SER299.OG-SER358.OG 20.17

THR84.OG1-ASP89.OD1 20.33

ASN407.ND2-ARG439.O 20.33

ASN117.N-PHE166.O 20.33

ALA220.N-VAL202.O 20.50

GLY247.N-TYR256.O 20.50

THR313.N-GLY207.O 20.50

TYR493.OH-VAL488.O 20.67

LEU283.N-GLY213.O 20.67

PHE133.N-LYS93.O 20.83

VAL202.N-ALA220.O 20.83

ARG451.NH1-TRP338.O 21.00

ARG24.NH2-ASP67.OD2 21.17

GLN394.N-GLU391.O 21.17

NLN328.N-GLY324.O 21.33

TYR164.OH-GLU75.OE2 21.33

ARG439.NH2-ASP452.O 22.00

ALA104.N-THR45.O 22.00

VAL386.N-ALA333.O 22.17

VAL380.N-ILE343.O 13.50

ARG388.NH1-ASP390.OD2 13.50

LYS447.N-GLU450.OE2 13.50

SER428.OG-ASN424.OD1 13.50

LEU426.N-SER423.O 13.67

CYX219.N-VAL276.O 13.67

ASP74.N-GLY173.O 13.67

ASN345.N-THR508.OG1 13.83

ASP390.N-GLY489.O 13.83

ARG388.NE-ASP390.OD1 14.00

GLN236.N-VAL290.O 14.17

ARG123.NH2-GLU140.OE1 14.33

ASN229.ND2-LEU161.O 14.33

ASN57.ND2-ASP33.OD2 14.33

TYR434.OH-GLY431.O 14.33

TRP421.NE1-TYR305.OH 14.83

ARG123.NH2-GLU140.OE2 15.00

LYS86.NZ-LEU124.O 15.33

SER40.OG-VAL36.O 15.33

ILE267.N-TYR257.OH 15.33

ARG178.NH2-ASP111.OD1 15.33

PHE265.N-VAL261.O 15.33

ARG251.NE-GLU153.OE2 15.50

GLU185.N-ASN63.O 15.50

VAL70.N-ALA17.O 15.50

ALA404.N-GLN394.OE1 15.83

GLU501.N-ASN379.O 15.83

ARG269.NH1-THR249.O 15.83

PHE327.N-PHE323.O 16.00

SER499.N-TYR381.O 16.17

VAL64.N-ILE27.O 16.17

GLY470.N-CYX473.O 16.17

SER138.N-TYR20.OH 16.50

LYS429.N-PHE482.O 16.50

SER163.N-GLY227.O 16.67

ASN63.ND2-GLU185.OE1 16.67

ARG264.NH2-SER260.O 9.50

ILE395.N-VAL392.O 9.50

ALA221.N-ASN274.O 9.50

TYR438.OH-GLN478.OE1 9.67

LYS93.NZ-ASP89.OD1 9.67

THR62.OG1-GLU185.OE2 9.67

THR139.N-GLU140.OE2 9.83

ARG178.NE-ASP111.OD2 9.83

GLY85.N-ASP89.OD1 10.00

GLN483.N-ASN486.OD1 10.00

ARG77.NH2-ASP74.OD2 10.00

LEU372.N-SER368.O 10.17

SER479.OG-TYR434.O 10.17

ARG126.NH2-ASP136.OD2 10.17

LEU437.N-SER334.OG 10.33

ASN379.N-GLU501.O 10.50

ARG251.NE-GLU153.OE1 10.50

GLN200.NE2-THR169.O 10.50

TYR34.N-ASN57.OD1 10.67

VAL261.N-ALA258.O 10.67

ASN425.ND2-TRP306.O 10.67

ARG228.NH1-ASP304.OD2 10.83

ALA357.N-SER299.OG 11.00

322 7 Spike (S) Glycoprotein

Supplementary Information Table 7.10 The SBs of the spike aa ASN1-LYS195 100 frames’ (with frame stride = 10) MD files of [258]

323 MD-rep2

MD-rep3

MD-rep4

Optimized model

ASP109-ARG176

ASP109-ARG176

ASP109-ARG176

ASP109-ARG176

ASP134-ARG121

ASP134-ARG121

ASP134-ARG121

ASP134-ARG121

ASP134-ARG124

ASP134-ARG124

ASP134-ARG124

ASP134-ARG124

ASP31-LYS195

ASP31-LYS195

ASP31-LYS195

ASP56-LYS195

ASP56-LYS195

ASP56-LYS195

ASP56-LYS195

ASP56-LYS53

ASP56-LYS53

ASP56-LYS53

ASP56-LYS53

ASP65-ARG22

ASP65-ARG22

ASP65-ARG22

ASP65-ARG22

ASP72-ARG70

ASP72-ARG70

ASP72-ARG70

ASP72-ARG70

ASP72-ARG75

ASP72-ARG75

ASP72-ARG75

ASP72-LYS84

ASP72-LYS84

ASP72-LYS84

ASP87-LYS91

ASP87-LYS91

ASP87-LYS91

ASP94-LYS91

ASP94-LYS91

GLU132-ARG124

GLU132-ARG124

ASP87-LYS84

ASP87-LYS84

GLU132-LYS129

ASP94-LYS91 GLU132-ARG124

GLU132-LYS129

GLU132-LYS129

GLU138-ARG121

GLU138-ARG121

GLU138-ARG121

GLU138-ARG124

GLU138-ARG124 GLU138-LYS125

GLU138-LYS125

GLU132-ARG124

GLU138-LYS125

GLU138-ARG13 GLU138-ARG133 GLU151-ARG121 GLU151-ARG124 GLU151-LYS111 GLU151-ARG70

GLU151-ARG70

GLU151-LYS84

GLU151-ARG70 GLU151-LYS125

GLU151-LYS125 GLU151-LYS84

GLU151-LYS84

GLU183-ARG24

GLU183-ARG24

GLU183-ARG24

GLU73-ARG70

GLU73-ARG70

GLU73-ARG70

GLU73-ARG75

GLU73-ARG75

GLU73-ARG75

GLU73-LYS84

GLU73-LYS84

GLU73-LYS84

GLU7-LYS23

GLU7-LYS23

GLU7-LYS23

GLU7-ARG13

324

7 Spike (S) Glycoprotein

Table 7.11 The HBs (with more than 10% occupancy rates) of the spike aa ASN1-LYS195 100 frames’ (with frame stride = 10) MD files of [258] Rep2

Rep3

Rep4

LEU180.N-CYX99.O 57%

ASP87.N-GLY83.O 53%

SER105.OG-ASP109.OD1 49%

VAL178.N-ILE101.O 52%

SER16.OG-LEU119.O 53%

TYR118.OH-ASP109.OD2 49%

TYR175.N-ILE69.O 51%

VAL100.N-LYS45.O 51%

ILE69.N-TYR175.O 48%

CYX3.N-VAL29.O 49%

VAL179.N-ASP65.O 50%

SER38.OG-VAL34.O 48%

VAL100.N-LYS45.O 48%

VAL178.N-ILE101.O 47%

VAL100.N-LYS45.O 47%

SER33.OG-ASP31.OD2 48%

ILE69.N-TYR175.O 45%

ASP87.N-GLY83.O 45%

ASP87.N-GLY83.O 46%

CYX3.N-VAL29.O 44%

VAL178.N-ILE101.O 45%

SER105.OG-ASP109.OD1 46%

ALA64.N-LYS23.O 42%

SER16.OG-LEU119.O 45%

ARG121.N-ASN89.OD1 45%

TYR175.N-ILE69.O 42%

VAL179.N-ASP65.O 44%

ILE69.N-TYR175.O 42%

VAL68.N-ALA15.O 41%

TYR36.N-TYR32.O 44%

ALA102.N-THR43.O 41%

LEU128.N-ASP87.O 40%

ALA64.N-LYS23.O 44%

TYR47.N-GLY98.O 41%

PHE59.N-VAL191.O 40%

TYR120.N-GLN160.O 43%

ARG176.N-TRP103.O 40%

ASP65.N-VAL179.O 39%

ARG22.NE-ASP65.OD2 43%

ASP65.N-VAL179.O 40%

TYR47.N-GLY98.O 38%

LEU180.N-CYX99.O 42%

ARG22.NH2-ASP65.OD2 40%

GLN160.N-TYR120.O 38%

ARG121.N-ASN89.OD1 39%

VAL29.N-ASN1.O 39%

ARG121.N-ASN89.OD1 37%

TYR90.N-ILE85.O 39%

SER66.N-ASN21.O 39%

TYR162.N-TYR118.O 37%

VAL177.N-PHE67.O 38%

ILE25.N-VAL62.O 39%

ARG176.N-TRP103.O 36%

TYR162.N-TYR118.O 38%

VAL179.N-ASP65.O 39%

ARG176.NH2-ASP109.OD1 36%

TYR47.N-GLY98.O 38%

ARG22.NE-ASP65.OD1 38%

TYR162.OH-GLU73.OE1 35%

VAL68.N-ALA15.O 38%

TYR63.N-SER181.O 37%

TYR90.N-ILE85.O 35%

ARG176.N-TRP103.O 38%

ALA30.N-CYX192.O 36%

GLU183.N-ASN61.O 35%

GLN160.N-TYR120.O 36%

PHE9.N-PHE5.O 36%

ILE101.N-VAL178.O 34%

SER66.N-ASN21.O 35%

ALA64.N-LYS23.O 36%

SER105.OG-ASP109.OD2 34%

ARG22.NE-ASP65.OD1 34%

VAL177.N-PHE67.O 35%

TYR162.OH-GLU73.OE2 34%

SER110.OG-ASN106.O 34%

LEU122.N-PRO158.O 33%

SER33.OG-ASP31.OD1 34%

VAL29.N-ASN1.O 34%

PHE59.N-VAL191.O 33%

LEU180.N-CYX99.O 33%

TYR162.OH-GLU73.OE1 34%

LYS45.N-VAL100.O 33%

ALA30.N-CYX192.O 33%

ILE101.N-VAL178.O 33%

TYR118.OH-ASP109.OD2 33%

TYR36.OH-PRO51.O 33%

TYR175.N-ILE69.O 33%

TYR90.OH-ASP65.OD2 32%

ARG22.NE-ASP65.OD1 32%

TYR90.OH-ASP65.OD1 33%

TYR162.N-TYR118.O 30%

ALA102.N-THR43.O 32%

ILE25.N-VAL62.O 33%

TRP103.N-ARG176.O 30%

SER105.OG-ASP109.OD1 32%

TYR162.OH-GLU73.OE2 33%

GLN160.N-TYR120.O 29%

VAL177.N-PHE67.O 31%

ASP65.N-VAL179.O 31%

ASN89.ND2-ARG121.O 29%

TYR90.OH-ASP65.OD2 30%

LEU128.N-ASP87.O 30%

TYR120.N-GLN160.O 29%

TRP103.N-ARG176.O 30%

TRP103.N-ARG176.O 30%

ARG176.NE-ASP109.OD1 29%

ASP109.N-SER105.O 29%

PHE131.N-LYS91.O 29%

ILE101.N-VAL178.O 28%

LYS23.N-ALA64.O 29%

ARG22.NH2-ASP65.OD1 29%

GLU183.N-ASN61.O 27%

TYR63.N-SER181.O 29%

LYS45.N-VAL100.O 29%

LYS23.N-ALA64.O 26%

ILE25.N-VAL62.O 29%

ARG176.NE-ASP109.OD1 29%

PHE131.N-LYS91.O 26%

VAL29.N-ASN1.O 29%

NLN10.ND2-GLY6.O 28%

SER181.N-TYR63.O 26%

ARG22.NE-ASP65.OD2 29%

ALA102.N-THR43.O 28%

VAL68.N-ALA15.O 26%

SER33.OG-ASP31.OD2 28%

SER33.OG-ASP31.OD1 28%

ARG176.NH2-ASP109.OD2 26%

THR190.OG1-THR60.O 28%

SER181.N-TYR63.O 27%

ALA11.N-GLU7.O 26%

ARG176.NE-ASP109.OD1 28%

PHE9.N-PHE5.O 27%

TYR90.OH-ASP65.OD1 24%

TYR18.OH-ASP134.OD1 28%

LYS23.N-ALA64.O 26%

ARG22.NE-ASP65.OD2 24%

ARG121.NH1-PHE123.O 27%

ARG22.NH2-ASP65.OD2 26%

VAL191.N-PHE59.O 24%

ARG176.NE-ASP109.OD2 26%

ASP72.N-GLY171.O 26%

TYR63.OH-GLU183.OE2 24%

TYR120.N-GLN160.O 26%

ALA30.N-CYX192.O 25%

LEU54.N-SER50.O 23%

TYR18.OH-ASP134.OD2 26%

ASP109.N-SER105.O 25%

THR137.OG1-ASP134.O 23%

VAL191.N-PHE59.O 25%

TYR63.N-SER181.O 24%

ASP109.N-SER105.O 22%

ARG22.NH2-ASP65.OD2 25%

GLY98.N-TYR47.O 24%

SER33.OG-ASP31.OD1 22%

ARG176.NH2-ASP109.OD2 25%

ASN89.ND2-ARG121.O 23%

ASP31.N-CYX3.O 22%

ASP31.N-CYX3.O 25%

GLN76.N-GLU73.O 23%

GLY71.N-GLN173.O 22%

GLN76.N-GLU73.O 24%

SER33.OG-ASP31.OD2 23%

SER110.OG-ASN106.O 22%

TYR90.OH-ASP65.OD1 24%

TYR118.OH-ASP109.OD1 22%

TYR116.N-VAL112.O 22%

CYX99.N-LEU180.O 24%

CYX3.N-VAL29.O 22%

TYR162.OH-GLU73.OE1 21%

SER181.N-TYR63.O 24%

SER105.OG-ASP109.OD2 21%

THR190.OG1-THR60.O 21%

ARG22.NH2-ASP65.OD1 23%

TYR90.OH-ASP65.OD2 21%

LEU35.N-TYR32.O 21%

GLY71.N-GLN173.O 22%

GLY71.N-GLN173.O 21%

ARG22.NH2-ASP65.OD1 21%

LYS129.N-GLU132.OE1 22%

CYX99.N-LEU180.O 21%

ASN104.ND2-GLN173.OE1 21%

ASN89.ND2-ARG121.O 22%

ILE85.N-GLN76.OE1 21%

CYX99.N-LEU180.O 21%

SER66.N-ASN21.O 22%

ASN104.ND2-GLN173.OE1 20%

NLN10.ND2-GLY6.O 21%

TYR118.OH-PHE14.O 22%

PHE59.N-VAL191.O 20%

TYR90.N-ILE85.O 20%

TYR118.OH-ASP109.OD2 20%

LYS129.N-GLU132.OE1 19%

Supplementary Information

325

Table 7.12 The HBs (with more than 10% occupancy rates) of the spike aa ASN1-LYS195 100 frames’ (with frame stride = 10) MD files of [258] (continuation) Rep2

Rep3

Rep4

LEU128.N-ASP87.O 20%

NLN10.N-GLY6.O 20%

THR190.OG1-THR60.O 19%

VAL62.N-ILE25.O 20%

THR190.N-PHE59.O 20%

VAL112.N-LEU108.O 19%

GLN76.N-GLU73.O 20%

LYS91.NZ-ALA86.O 20%

ARG176.NH1-ASP109.OD2 19%

THR190.N-PHE59.O 20%

SER161.N-CYX147.O 20%

SER105.N-PRO174.O 18%

THR12.OG1-VAL8.O 20%

ASN104.ND2-GLN173.OE1 19%

GLU183.N-ASN61.O 18%

ASN21.ND2-ARG13.O 20%

GLY98.N-TYR47.O 19%

ASN37.N-SER33.O 18%

TYR162.OH-GLU73.OE2 19%

VAL62.N-ILE25.O 19%

LEU122.N-PRO158.O 18%

LYS91.NZ-ASP87.OD2 19%

GLN165.N-TYR172.O 19%

ARG176.NE-ASP109.OD2 18%

SER136.OG-ASP134.OD2 19%

SER110.OG-ASN106.O 19%

NLN10.N-GLY6.O 18%

SER105.N-PRO174.O 18%

PHE9.N-PHE5.O 19%

THR82.OG1-GLN76.O 18%

LEU57.N-LYS53.O 18%

SER136.OG-GLU138.OE2 19%

TYR120.OH-GLU73.OE1 18%

TYR118.OH-ASP109.OD1 17%

TYR118.OH-ASP109.OD1 18%

NLN10.ND2-SER38.O 18%

SER136.OG-ASP134.OD1 17%

ARG121.NH1-GLU138.OE1 18%

ARG176.NH2-ASP109.OD1 17%

GLY98.N-TYR47.O 17%

ARG70.NH2-GLY163.O 18%

SER136.OG-ASP134.OD2 17%

PHE5.N-ASP31.O 17%

LEU57.N-LYS53.O 18%

LEU57.N-LYS53.O 17%

PHE67.N-VAL177.O 17%

THR43.N-ALA102.O 18%

ARG176.NH2-ASP109.OD2 17%

GLY113.N-ASP109.O 17%

ALA142.N-GLU138.O 18%

THR43.N-ALA102.O 16%

SER105.OG-ASP109.OD2 16%

LEU35.N-TYR32.O 17%

ALA39.N-LEU35.O 16%

ARG176.NH2-ASP109.OD1 16%

ASP72.N-GLY171.O 17%

TYR120.OH-GLU73.OE2 16%

SER16.OG-LEU119.O 16%

ARG70.NE-GLU73.OE1 17%

THR60.N-GLU183.O 15%

THR43.N-ALA102.O 16%

LYS45.N-VAL100.O 17%

VAL62.N-ILE25.O 15%

TYR36.OH-PRO51.O 15%

SER105.N-PRO174.O 17%

PHE67.N-VAL177.O 15%

ASN61.ND2-GLU183.OE2 15%

ARG70.NE-GLU73.OE2 17%

TYR18.OH-ASP134.OD1 15%

TYR90.N-ALA86.O 15%

ARG176.NH2-THR12.O 16%

LEU54.N-SER50.O 14%

ASN89.ND2-ILE85.O 15%

ILE85.N-GLN76.OE1 15%

LEU35.N-ASP31.O 14%

VAL112.N-LEU108.O 15%

SER110.OG-ASN106.OD1 15%

ARG70.NE-GLU73.OE1 14%

TYR63.OH-GLU183.OE1 14%

ASN106.N-ASN104.OD1 15%

TYR18.OH-ASP134.OD2 14%

ARG176.NE-ASP109.OD2 14%

ARG70.NH1-GLU73.OE1 15%

ARG124.NH1-GLU132.OE1 13%

ASN27.N-THR190.OG1 14%

ARG124.NH2-SER126.O 15%

ARG70.NE-GLU73.OE2 13%

SER161.OG-ASN117.OD1 14%

THR145.OG1-LEU159.O 15%

THR60.OG1-ALA187.O 13%

ARG124.NH1-SER126.O 13%

ARG121.NH1-GLU138.OE2 14%

TYR118.N-GLY114.O 13%

ASN115.N-PHE164.O 13%

TYR120.OH-GLU73.OE1 14%

SER42.N-ALA102.O 13%

ARG124.NE-SER126.O 13%

LEU54.N-SER50.O 13%

ARG70.NH1-GLU73.OE1 13%

THR60.N-GLU183.O 13%

ARG121.NH2-GLU138.OE1 13%

ARG121.NH2-GLU138.OE2 13%

PHE182.N-THR97.O 13%

GLN173.NE2-THR167.O 13%

ARG121.NH2-GLU138.OE1 13%

TYR140.N-SER136.O 13%

CYX28.N-THR190.O 13%

ARG121.NH2-PHE123.O 13%

SER40.OG-ASN37.O 13%

ARG24.NE-ASN61.OD1 13%

THR190.N-PHE59.O 12%

TYR140.N-TYR156.O 12%

ASN61.ND2-GLU183.OE1 13%

LYS129.N-GLU132.OE2 12%

THR82.OG1-ASP87.OD2 12%

LYS91.NZ-LEU128.O 13%

GLN160.NE2-PHE157.O 12%

ASN115.ND2-ASP109.O 12%

VAL112.N-LEU108.O 13%

PHE59.N-CYX28.O 12%

LYS129.N-GLU132.OE1 12%

NLN10.ND2-GLY6.O 12%

LYS91.NZ-LEU128.O 11%

ASN61.N-GLU183.O 12%

LYS129.N-GLU132.OE2 12%

ARG124.NH2-SER126.O 11%

ARG70.NE-GLU73.OE1 12%

PHE5.N-ASP31.O 12%

ASN117.N-GLY113.O 11%

ASN61.ND2-GLU183.OE1 12%

GLU132.N-LYS129.O 12%

THR12.OG1-VAL8.O 11%

GLN173.NE2-ASN168.O 12%

TYR63.OH-GLU183.OE1 12%

SER40.OG-TYR36.O 11%

ASN37.N-SER33.O 12%

GLN141.N-THR137.O 12%

GLN160.NE2-THR145.O 11%

ARG124.NH2-SER126.O 12%

ARG176.NH1-ALA11.O 11%

SER136.OG-ASP134.OD1 10%

ASP72.N-GLY171.O 11%

PHE131.N-LYS91.O 11%

SER110.OG-ASN106.OD1 10%

ALA86.N-GLN76.OE1 11%

THR60.OG1-ALA187.O 11%

ASN61.ND2-GLU183.OE1 10%

TYR18.OH-ASP134.OD2 11%

ASN127.ND2-ASP87.OD2 11%

ARG124.NH1-GLU132.OE2 10%

ARG75.NH1-ASP72.OD2 11%

ARG70.NH1-GLU73.OE2 11%

SER161.OG-TYR116.O 10%

ARG133.NH1-TRP20.O 11%

ASN61.ND2-GLU183.OE2 10%

ASP56.N-LYS53.O 10%

LYS129.N-GLU132.OE2 11%

THR82.OG1-ASP87.OD2 10%

ARG124.NE-ASP134.OD2 10%

SER38.OG-LEU35.O 11%

ASN37.N-SER33.O 10%

GLN165.N-TYR172.O 10%

GLN165.N-TYR172.O 11%

ARG124.NE-ASP134.OD1 10%

ARG124.NH2-GLU132.OE2 10%

TYR18.OH-CYX155.O 11%

GLY83.N-ASP87.OD2 10%

ARG121.NH1-GLU138.OE1 10%

TYR156.N-TYR140.O 10%

ARG133.NH2-TRP20.O 10%

ARG124.NH2-ASP134.OD1 10%

ARG124.NH1-GLU132.OE1 10%

ARG124.NH2-GLU132.OE2 10%

SER136.OG-ASP134.OD1 10%

ASN104.N-SER42.OG 10%

ARG124.NE-SER126.O 10%

CYX28.N-THR190.O 10%

ARG75.NH2-ASP72.OD1 10%

THR12.N-VAL8.O 10%

ARG121.NE-ASP134.OD1 10%

TYR172.N-ASN168.OD1 10%

ARG70.NH1-GLU151.OE2 10% PHE67.N-VAL177.O 10% ALA11.N-GLU7.O 10%

Chapter 8

Spike (S) Glycoprotein D614G Mutant

Abstract Recently, the SARS-CoV-2 D614G mutant has been reported to be potentially more transmissible (“contagious”) than its wild-type. When there is no laboratory structure for the mutant, we made two homology ones (with close and open spikes, respectively). In this brief chapter, we will give a note on the two (6vxx-, 6vyb-) homology structures for D614G mutant and present a comparison with its wild-type SARS-CoV-2. We found the mutant has stronger hydrogen bonds between GLY614 and ALA647 in each monomer and changed the molecular structure at residue ASN616. MD studies find that the D614G mutant produced new strong hydrogen bonds between ALA845 and GLY614. Keywords SARS-CoV-2 D614G mutant · More contagious · Homology structures · Structural bioinformatics · Compared with wild-type

8.1 Introduction Several recent papers [37, 83, 185, 186, 429] caused world attentions to the D614G mutant of SARS-CoV-2. It has been reported the mutant is more contagious than its wild-type virus. When its laboratory NMR, X-ray, or cryo-EM structures are not determined yet, we made two homology structures. This brief chapter is to do homology modeling first to get two molecular structures for the D614G mutant and then gives a note of preliminary analyses of their structural bioinformatics. A comparison with its wild-type will also be given in this brief chapter.

8.2 Homology Structures of D614G Mutant For 6vxx.pdb (structure of the SARS-CoV-2 spike (S) glycoprotein (closed state)) and 6vyb.pdb (SARS-CoV-2 spike ectodomain structure (open state)) downloaded from the Protein Data Bank (https://www.rcsb.org/), we used the Swiss-PdbViewer © The Author(s), under exclusive license to Springer Nature Switzerland AG 2023 J. Zhang, Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures, Springer Series in Biophysics 23, https://doi.org/10.1007/978-3-031-36773-1_8

327

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8 Spike (S) Glycoprotein D614G Mutant

4.1.0 (https://spdbv.vital-it.ch/) [133, 134] (a free package for comparative protein modeling) to make a mutation of residue 614 from aspartic acid (D) into glycine (G) for A, B, and C chains, respectively. Then we used Maestro 10.1 (Academic Use Only) (https://www.schrodinger.com/maestro) to optimize the models: “Edit.→Select Atoms.→All” and then “Tools.→Minimize.→All Atoms” for 100 cycles (backbone RMSD values between the unoptimized and optimized models are 0.450160 Åand 0.464231 Å, respectively, for the close and open models). We denote the models as 6vxx-close-D614G-mutant and 6vyb-open-D614G-mutant, respectively.

8.3 Structural Bioinformatics of D614G Mutant The noncovalent interactions of hydrogen bonds (HBs), salt bridges (SBs), van der Waals (vdWs) contacts, and hydrophobic (HYD) interactions are driving a protein to be able to perform its biological functions. In the below, we will find out the HBs, SBs, HYD interactions, and vdWs contacts of the 6vxx-close-D614G-mutant and 6vyb-open-D614G-mutant models.

8.3.1 6vxx-Close-D614G-Mutant In Sect. 7.3.1 for the trimeric SARS-CoV-2 S wild-type 6vxx-close-model, our analyses of the molecular dynamics (MD) trajectories data of 10 .μs confirm us: (1) SBs: – In each chain: ASP442-ARG509, ASP53-LYS195, ASP389-LYS528, ASP398-ARG355, GLU1031-ARG1039, ASP820-ARG815, GLU583LYS535, GLU96-ARG190, GLU324-LYS537, ASP820-LYS811, ASP663LYS310, GLU773-ARG1019, ASP775-LYS733, GLU340-LYS356, ASP578-ARG328, ASP574-LYS557, ASP40-ARG44 – Among chains: A:GLU1031-B:ARG1039, B:GLU1031-C:ARG1039, C:GLU1031-A:ARG1039; A:ASP574-C:LYS854, B:ASP574-A:LYS854; C:GLU773-A:LYS974 (2) HBs: – In each chain: C:ASP442.OD1-C:ARG509.NE with occupancy rate 54.13% and B:ASP442.OD1-B:ARG509.NH2 with occupancy rate 53.45% – Among chains: B:PHE43.N-C:PHE565.O with occupancy rate 54.13% – with strong side-chain .π -.π stacking too – and C:TYR369.OHA:THR415.OG1 with occupancy rate 50.30%

8.3 Structural Bioinformatics of D614G Mutant

329

(3) .π -interactions: – 5 .π -cations: in each chain, TYR396-ARG.+ 355.NH2-PHE464, LYS.+ 1028.NZ-PHE1042, LYS.+ 278.NZ-PHE306, ARG.+ 44.NH2-HIS49 – 19 .π -.π stackings: in each chain, TYR1110-PHE1075, TYR1067-PHE906, PHE800-PHE898-PHE802-PHE1052/PHE927, TYR660-TYR695, HIS655PHE643, TYR612-PHE318, PHE275-PHE58, PHE92-TRP104 (2), PHE201-PHE106, HIS519-PHE565, PHE423-TRP353 (2), PHE377TYR369, TRP436-PHE374, PHE338-TYR365 For the 6vxx-close-D614G-mutant, for the SBs, we find 137 SBs, where ASP442-ARG509 is in each chain, GLU1031-ARG1039 exists not only among chains but also in each chain (C:GLU1031-C:ARG1039, B:GLU1031-B:ARG1039, A:GLU1031-A:ARG1039; C:GLU1031-B:ARG1039, B:GLU1031-A:ARG1039, A:GLU1031-C:ARG1039), C:ASP574-A:LYS854, A:ASP574-B:LYS854, but we cannot find C:GLU773-A:LYS974. For the HBs, we only consider HBs around the residue GLY614 and find the wild-type has a HB ASP614.N2-ALA647.OD2 in chains B and C, respectively, and ASP614.N1-ALA647.OD1 in chain A, with the distance 3.2 Å, and the mutant has the same HBs but with shorter distances 2.78, 2.77, and 2.79 Å, respectively. For the secondary structure changes of segment SER605-VAL620 (around the residue at 614), we find the mutation D614G changed Turn into Coil at residue ASN616 and changed the side-chain orientation of the critical residue GLU619 (Fig. 8.1) – the superposition backbone RMSD value is 0.273619 Å.

Fig. 8.1 The secondary structure changes around the residue ASN616 for the 6vxx-close-D614Gmutant model

Around the residue at 614, the .π -.π stackings such as PHE318-TYR612, TYR695-TYR660, and PHE643-HID655 are still being kept in each chain of the mutant.

8.3.2 6vyb-Open-D614G-Mutant In Sect. 7.3.2 for the trimeric SARS-CoV-2 S wild-type 6vyb-open-model, our analyses of the MD trajectories data of 10 .μs confirm us:

330

8 Spike (S) Glycoprotein D614G Mutant

(4) SBs: – In each chain: ASP442-ARG509, ASP820-ARG815, ASP578-ARG328, ASP820-LYS811, ASP467-ARG454, ASP53-LYS195, ASP663-LYS310, GLU583-LYS535, ASP775-LYS733, GLU773-ARG1019, GLU340LYS356, ASP574-LYS557, ASP40-ARG44, GLU1031-ARG1039, ASP1084-LYS1086, ASP571-ARG567, ASP405-ARG403, GLU465ARG457, GLU191-ARG34 – Among chains: A:GLU1031-B:ARG1039, B:GLU1031-C:ARG1039, C:GLU1031-A:ARG1039 (with weak SBs A:GLU1031-B:LYS1038, B:GLU1031-A:LYS1038, C:GLU1031-A:LYS1038); C:ASP574-B: LYS854; B:GLU773-C:ARG1014 (5) HBs: – In each chain: B:ARG509.NE-B:ASP442.OD2 with occupancy rate 58.44% and B:ARG509.NH2-B:ASP442.OD1 with occupancy rate 51.62%. – Among chains: A:PHE43.N-B:PHE565.O with occupancy rate 51.38%, B:PHE43.N-C:PHE565.O with occupancy rate 54.01%, and C:PHE43.NA:PHE565.O with occupancy rate 54.37% – between side chains of PHE43 and PHE565, there are strong .π -.π stackings too. (6) .π -interactions: – 7 .π -cations: in each chain, TYR396-Arg.+ 355.NH2-PHE464, Lys.+ 1028.NZPHE1042, Lys.+ 278.NZ-PHE306, Arg.+ 44.NH2-HIS49, Arg.+ 466.NH2TRP353, Lys.+ 1073.NZ-PHE1075 – 17 .π -.π stackings: in each chain, TYR1110-PHE1075, PHE800-PHE898PHE802-PHE1052/PHE927, TYR660-TYR695, PHE92-TRP104 (2), PHE201-PHE106, PHE423-TRP353 (2), PHE377-TYR369, TRP436PHE374, PHE58-PHE275, TYR495-TYR453, PHE515-PHE392, PHE192TRP104 For the 6vyb-open-D614G-mutant, for the SBs, we find 119 SBs, where ASP442ARG509 is in A and C chains, respectively, GLU1031-ARG1039 exists not only among chains but also in each chain (C:GLU1031-C:ARG1039, B:GLU1031B:ARG1039, A:GLU1031-A:ARG1039; C:GLU1031-B:ARG1039, B:GLU1031A:ARG1039, A:GLU1031-C:ARG1039), and A:GLU1017-B:ARG1019, C:GLU1017-A:ARG1019, B:ASP745-A:ARG319, A:ASP745-C:ARG319, C:GLU702-A:LYS790, A:GLU702-B:LYS790, B:ASP985-A:LYS386, A:ASP1118-C:ARG1091, A:ASP198-C:LYS462, and A:ASP994-C:ARG995 exist among ABC chains. In each chain, the SBs ASP53-LYS195, ASP663-LYS310, GLU583-LYS535, ASP775-LYS733, GLU773-ARG1019 (C and A), GLU340LYS356 (C and A), ASP574-LYS557, ASP40-ARG44, ASP1084-LYS1086, ASP571-ARG567 (C and A), ASP405-ARG403, GLU465-ARG457 (A), and GLU191-ARG34 are still existing. For the HBs, we only consider HBs around the residue GLY614 and find the wild-type has a HB ASP614.N2-ALA647.OD2 in chains B and C, respectively, with distances 3.06 and 3.10 Å, respectively, and

8.4 Concluding Remarks

331

ASP614.N1-ALA647.OD1 in chain A with the distance 3.09 Åand the mutant has the same HBs but with shorter distances 2.83, 2.75, and 2.84 Å, respectively. For the secondary structure changes of segment SER605-VAL620 (around the residue at 614), we find the mutation D614G changed Coil + 3.10 -helix + Coil into Turn in segment ASN616-VAL620 and changed the side-chain orientation of the critical residue GLU619 (Fig. 8.2) – the superposition backbone RMSD value is 0.209914 Å.

Fig. 8.2 The secondary structure changes around the residue ASN616 in C chain for the 6vybopen-D614G-mutant model

Around the residue at 614, the .π -cation LYS.+ 1073.NZ-PHE1075 and the .π -.π stackings such as PHE318-TYR612, TYR695-TYR660, and PHE643-HID655 are still being kept in each chain of the mutant. In [155], we were told the two adjacent residues ASP614 and ASN616 point in opposite directions, unlikely sharing a meaningful interaction. In [105, 200, 215, 244, 261, 399], we were told there exists a HB A:ASP614-B:THR859 linking S1 and S2 of spike (6vsb.pdb), but we have not found it yet from 6vxx.pdb and 6vyb.pdb (Fig. 8.3). The mutation at 614 from charged residue ASP into the residue GLY (which has higher degree of freedom and is commonly associated with Turns in a protein secondary structure and sometimes acts as a helix or other structure breaker) should reduce the surface of electrostatic negative charges around segment 614–620. We illuminate the Poisson-Boltzmann electrostatic potential surface of segment 605– 620 of the 6vxx-model and the 6vyb-model in Fig. 8.4 (where we should also notice the difference at residue 607 for the two models).

8.4 Concluding Remarks In this brief chapter, we found that (compared with the wild-type) the D614G mutant has stronger hydrogen bonds between GLY614 and ALA647 in each monomer and changed the molecular structure at residue ASN616. Furthermore, research on the mutant is clearly needed. The PDB entry 6M17 has F chain CYS336-LEU518; we cut 6VXX.pdb and only keep CYS336-LEU518 segment, and for A, B, and C chains, the RMSDs from 6M17.pdb’s F chain are 65.715129, 95.341880, and 76.302272 Å, respectively. Hence, it is difficult to do molecular modeling for the D614G mutant in complex

332

8 Spike (S) Glycoprotein D614G Mutant

Fig. 8.3 No HB A:ASP-614-B:THR859 linking S1 and S2 of spike in 6vxx-model and 6vybmodel (as in 6vsb.pdb)

with the human ACE2 in the use of PDB entries 6M17 and 6VXX. However, seeing Fig. 8.5, because in the spike the residue LYS417 in the RBD spans 197 residues to the residue 614 and in three-dimensional (3D) space they distance to each other very far (for the 6vxx-close-D614G-mutant model, the distance between A:GLY614.C and A:LYS417.C is 62.35 Å, and for the 6vyb-open-D614G-mutant model, the distance between C:GLY614.C and C:LYS417.C is 62.60 Å), we still may say that the polar contact LYS417-ASP30 of Chap. 7 between SARS-CoV-2 S and human ACE2 should still exist for the SARS-CoV-2 D614G mutant in complex with human ACE2.

8.4.1 Confirmed from Some MD Datasets In [114], the data files contain structures of the D614G mutant and its (closed) wild-type at 500 ns from MD simulations of closed SARS-CoV-2 spike protein embedded in POPC membrane. Firstly, we use these datasets to identify structural

8.4 Concluding Remarks

333

Fig. 8.4 The Poisson-Boltzmann electrostatic potential surface of segment 605–620 of the 6vxxmodel and the 6vyb-model (up, 6vxx-model; down, 6vyb-model; left, wild-type; right, D614G mutant)

perturbations of the D614G mutant from its wild-type. Seeing Fig. 8.6, we know the mutation made some local structural perturbations: (i) for A chain at ASN616 and CYS617 Coil changed into Turn, (ii) for B chain at residue 614 Extended conformation/isolated Bridge changed into Turn and at GLU619 Turn changed into .α-Helix, and (iii) for C chain at VAL615 Turn changed into isolated Bridge and at THR618 .α-Helix changed into Coil. The D614G mutation made the wild-type lost HBs THR859.OG1-ASP614.OD1 [105, 200, 215, 244, 261, 399], SER591.OGASP614.O, and ARG847.NE-ASP614.OD2 (with SB B:ASP614-C:ARG847), but produced a new HB CYS851.N-GLY614.O (where the residue CYS851 is in the middle of residues ARG847 and THR859). Cino [75] presented two sets of 200 ns MD trajectories, respectively, for the wild-type and D614G prefusion spike proteins (6VSB.pdb, single RBD in the up conformation) with site-specific glycans. The SARS-CoV-2 spike protein resides on the exterior surface of the coronavirus and undergoes dramatic conformational changes upon host receptor binding. Figure 8.7 illuminates some structural pertur-

334

8 Spike (S) Glycoprotein D614G Mutant

Fig. 8.5 The polar contact LYS417-ASP30 of Chap. 7 between the SARS-CoV-2 spike and the human ACE2 will not be affected by the SARS-CoV-2 S D614G mutation

Fig. 8.6 The secondary structure changes around the residue ASN616 for the Saman Fatihi et al.’s D614G mutant and closed wild-type (replica 1 (WT1) and replica 2 (WT2)) models [114]

bations of the D614G mutant from its wild-type during 200 ns, where T is Turn, E is Extended conformation, B is isolated Bridge, H is .α-Helix, G is .310 -helix, I is .π -helix, and C is Coil. Let us see the MD performances of datasets [75]. By Figs. 8.8 and 8.9, we know the RMSD values for D614G rep1 seem to become stable, but for wild-type rep1, D614G rep2, and wild-type rep2, their RMSD values still intend to go up. Figure 8.10 seems to tell us that the RMSF variations of D614G mutant are less than those of its wild-type. By Table 8.1, we can confirm the conclusion we found in this chapter: the HB GLY614.N-ALA647.O of the D614G mutant becomes stronger than its wild-type, and we find that the D614G mutant has a new strong HB ALA845.NGLY614.O. From Table 8.1, we indeed can confirm D614G mutation made the lost of HBs THR859.OG1-ASP614.OD1/2 [105, 200, 215, 244, 261, 399] because of using 6vsb.pdb to build the models [75, 114]. We should also notice that the

Rep2

Rep1

GLY614.N-ALA647.O 66.18% ALA845.N-GLY614.O 32.35% GLY593.N-GLY614.O 18.63% SER591.OG-GLY614.O 7.35%

Spike D614G mutant GLY614.N-ALA647.O 66.01% LYS854.NZ-GLY614.O 2.96% ALA845.N-GLY614.O 43.84% SER591.OG-GLY614.O 0.99%

SER591.OG-ASP614.O 1.48%, SER591.OG-ASP614.OD2 0.99% THR859.OG1-ASP614.OD2 29.56%, THR859.OG1-ASP614.OD1 23.65% LYS854.NZ-ASP614.OD1 36.45%, LYS854.NZ-ASP614.OD2 24.14%, LYS854.NZ-ASP614.O 0.49% PHE592.N-ASP614.O 1.48% VAL860.N-ASP614.OD1 0.49% GLN613.NE2-ASP614.OD1 1.97% ASP614.N-GLN613.OE1 0.49%

THR859.OG1-ASP614.OD1 55.39%, THR859.OG1-ASP614.OD2 26.47% ARG847.NH2-ASP614.OD2 0.49%, ARG847.NH1-ASP614.O 0.49% GLN613.NE2-ASP614.OD2 0.49% ASP614.N-ALA647.O 24.14%

Spike WT ASP614.N-ALA647.O 44.61% LYS854.NZ-ASP614.O 0.98%, LYS854.NZ-ASP614.OD2 53.43%, LYS854.NZ-ASP614.OD1 19.61%

Table 8.1 The HBs at residue 614 (with occupancy rates) from the analyses of the 200 ns’ MD trajectory data of [75]

8.4 Concluding Remarks 335

336

8 Spike (S) Glycoprotein D614G Mutant

Fig. 8.7 The secondary structure changes around the residue ASN616 for Elio Cino’s 200 ns’ MD simulations rep1 and rep2 of D614G mutant and its wild-type, respectively [75]

8.4 Concluding Remarks

337

RMSD vs Frame: rep1.gro

RMSD vs Frame: rep1.gro

"rep1.gro:(protein) and name CA"

"rep1.gro:(protein) and name CA" 55

30 50

45 25

40

35

20

RMSD (Å)

30

RMSD (Å)

15 25

20

10 15

10 5

5

0

0 0

50

100

150

200

0

50

Frame

100

150

200

Frame

Fig. 8.8 The RMSD graphs of Elio Cino’s 200 ns’ MD simulations rep1 of D614G mutant and its wild-type

RMSD vs Frame: rep2.gro

RMSD vs Frame: rep2.gro 65 "rep2.gro:(protein) and name CA"

"rep2.gro:(protein) and name CA"

35

60

55

30 50

45 25

40

35

20

RMSD (Å)

RMSD (Å) 30

15 25

20 10 15

10 5

5

0

0 0

50

100

Frame

150

200

0

50

100

150

200

Frame

Fig. 8.9 The RMSD graphs of Elio Cino’s 200 ns’ MD simulations rep2 of D614G mutant and its wild-type

Fig. 8.10 The RMSF graphs of Elio Cino’s 200 ns’ MD simulations rep1 of D614G mutant and its wild-type and rep2 of D614G mutant and its wild-type (from up to down in turns), where for each graph, the y-axis (from up to down) is the MD running time from 0 to 200 ns and the x-axis (from left to right) is residue numbers from 27 to 1143

338

8 Spike (S) Glycoprotein D614G Mutant

Fig. 8.11 The SB ASP614.OD1/2-LYS854.NZ of Elio Cino’s 200 ns’ MD simulations rep1 and rep2 (from left to right) of spike wild-type

Fig. 8.12 The RMSF graphs of MD data of 6.5 .μs’ G-up, 8 .μs’ D-up, 6.5 .μs’ G-down, and 8 .μs’ D-down in [229] (from up to down in turns), where for each graph, the y-axis (from up to down) is the MD running time from 0 to 6.5 or 8 .μs and the x-axis (from left to right) is residue numbers from 14 to 1147

mutation made the SBs LYS854.NZ-ASP614.OD1/2 lost (Fig. 8.11), where the labels 0–5 are A:ASP614.OD1-A:LYS854.NZ, A:ASP614.OD2-A:LYS854.NZ, B:ASP614.OD2-B:LYS854.NZ, B:ASP614.OD1-B:LYS854.NZ, C:ASP614.OD2C:LYS854.NZ, and C:ASP614.OD1-C:LYS854.NZ in turns for rep1 and are A:ASP614.OD2-A:LYS854.NZ, A:ASP614.OD1-A:LYS854.NZ, B:ASP614.OD1B:LYS854.NZ, B:ASP614.OD2-B:LYS854.NZ, C:ASP614.OD2-C:LYS854.NZ, and C:ASP614.OD1-C:LYS854.NZ in turns for rep2. Mansbach et al. [229] reported that the SARS-CoV-2 spike variant D614G favors an open conformational state [229] and all their four sets of MD data level off at certain constant RMSD values. We optimized the four (the Mutant G_form-1up model (G-up), the Wild-type D_form-1up model (D-up), the Mutant G_form3down model (G-down), and the Wild-type D_form-3down model (D-down) ) homology models of [229] with RMSD values 2.823235, 2.757211, 2.769470, and 2.852602 Å, respectively, and get all their SBs listed in Tables 8.2 and 8.3, where the four models have 196, 180, 187, and 191 SBs and 559, 563, 543, and 574 HBs, respectively. At residue 614, the D614G mutation made the SB B:ASP614C:LYS854 (D-up and D-down) and the HBs THR859.OG1-ASP614.OD2 (D-up and D-down) and LYS854.NZ-ASP614.OD1 (D-up) of the wild-type lost. The MD data of 8 .μs for wild-type and 6.5 .μs for the variant can confirm our finding: the mutation made the HB GLY614.N-ALA647.O become stronger, GLY614.N-ALA647.O 56.06% (G-up), ASP614.N-ALA647.O 48.15% (D-up), GLY614.N-ALA647.O

8.4 Concluding Remarks

339

Fig. 8.13 The secondary structure changes around the residue ASN616 for MD simulations of D614G mutant G-up and G-down and its wild-type D-up and D-down [229]. Here, A, B, and C denote spike’s A, B, and C chains, respectively

340

8 Spike (S) Glycoprotein D614G Mutant

Fig. 8.14 The secondary structure changes around the residues ASN616 and G/D614 for the optimized G-up, D-up, G-down, and D-down models of [229], where A, B, and C are the three chains of the SARS-CoV-2 spike

58.46% (G-down), and ASP614.N-ALA647.O 56.79% (D-down), where 56.06% > 48.15% and 58.46% .> 56.79%. The MD data can also confirm the lost of SB B:ASP614-C:LYS854 and weak HBs LYS854.NZ-ASP614.OD2 7.41% (D-up), LYS854.NZ-ASP614.OD1 6.17% (D-up), LYS854.NZ-ASP614.OD2 8.64% (Ddown), and LYS854.NZ-ASP614.OD1 3.70% (D-down) by the D614G mutation. By the RMSF variations of the MD (Fig. 8.12), we can confirm the conclusion “the SARS-CoV-2 spike variant D614G favors an open conformational state” of [229]. Figure 8.13 illuminates some structural perturbations of the D614G mutant from its Wild-type during 8 or 6.5 .μs’ MD, where T is Turn, E is Extended conformation, B is isolated Bridge, H is .α-Helix, G is .310 -helix, I is .π -helix, and C is Coil. We can see a slight difference between Figs. 8.13 and 8.7; but we cannot find a rule of the local secondary-structure impact of the D614G mutation from the optimized G-up, D-up, G-down, and D-down models of [229] (Fig. 8.14).

.

D614G-mutant - 1 open (G-up) A:ASP1041-A:LYS1045 B:ASP1041-B:LYS1045 B:ASP1041-C:LYS786 C:ASP1041-C:LYS1045 A:ASP1084-A:LYS1086 A:ASP111-A:LYS113 B:ASP111-B:LYS113 A:ASP1118-C:ARG1091 C:ASP1118-A:ARG1091 C:ASP1118-B:ARG1091 B:ASP138-B:ARG21 B:ASP138-B:ARG78 C:ASP138-C:ARG78 A:ASP178-A:LYS187 B:ASP178-B:LYS182 C:ASP178-C:ARG102 A:ASP198-C:LYS462 B:ASP198-A:ARG357 B:ASP198-A:ARG466 C:ASP198-C:ARG983 A:ASP215-A:ARG214 B:ASP215-B:ARG214 C:ASP215-C:ARG214 A:ASP228-A:LYS202

Wild-type - 1 open (D-up) A:ASP1041-A:LYS1045 B:ASP1041-B:LYS1045 C:ASP1041-C:LYS1045 A:ASP1084-A:HIS1083 A:ASP1084-A:LYS1086 B:ASP1084-B:HIS1083 C:ASP1084-C:HIS1088 B:ASP111-B:LYS113 B:ASP1118-A:ARG1091 A:ASP138-A:LYS77 B:ASP138-B:ARG21 B:ASP138-B:ARG78 C:ASP138-C:ARG78 A:ASP178-A:LYS187 B:ASP198-B:LYS202 A:ASP215-A:ARG214 C:ASP215-C:ARG214 A:ASP228-A:LYS202 B:ASP228-B:LYS202 C:ASP228-C:LYS202 A:ASP253-A:ARG21 A:ASP287-A:LYS278 A:ASP290-A:ARG273 B:ASP290-B:ARG273

Table 8.2 The SBs of the optimized models of [229] D614G-mutant—all down (G-down) A:ASP1041-A:LYS1045 B:ASP1041-B:LYS1045 C:ASP1041-C:LYS1045 A:ASP1084-A:LYS1086 A:ASP111-A:LYS113 C:ASP1118-B:ARG1091 A:ASP138-A:LYS77 B:ASP138-B:ARG78 C:ASP138-C:ARG78 A:ASP178-A:LYS150 B:ASP178-B:ARG190 B:ASP178-B:LYS182 C:ASP178-C:LYS187 A:ASP215-A:ARG214 B:ASP215-B:ARG214 C:ASP215-C:ARG214 A:ASP228-C:ARG357 A:ASP228-A:LYS202 B:ASP228-B:LYS202 B:ASP228-B:LYS41 C:ASP228-C:LYS202 B:ASP253-B:ARG246 A:ASP290-A:ARG273 B:ASP290-B:ARG273

(continued)

Wild-type—all down (D-down) A:ASP1041-A:LYS1045 B:ASP1041-B:LYS1045 C:ASP1041-C:LYS1045 B:ASP1084-B:HIS1088 B:ASP1084-B:LYS1086 A:ASP111-A:LYS113 B:ASP111-B:LYS113 C:ASP111-C:LYS113 A:ASP1118-C:ARG1091 C:ASP1118-B:ARG1091 A:ASP1146-C:LYS1086 A:ASP138-A:LYS77 B:ASP138-B:ARG21 B:ASP138-B:ARG78 C:ASP138-C:ARG21 A:ASP178-A:LYS150 B:ASP178-B:LYS182 C:ASP178-C:LYS182 A:ASP198-A:LYS202 B:ASP198-A:LYS462 A:ASP215-A:ARG214 B:ASP215-B:ARG214 C:ASP215-C:ARG214 A:ASP228-A:LYS202

8.4 Concluding Remarks 341

D614G-mutant - 1 open (G-up) A:ASP228-A:LYS41 B:ASP228-B:LYS202 C:ASP228-C:LYS202 C:ASP228-C:LYS41 A:ASP253-A:ARG21 B:ASP253-B:ARG158 B:ASP287-B:LYS300 A:ASP290-A:ARG273 B:ASP290-B:ARG273 B:ASP290-B:ARG634 C:ASP290-C:ARG634 C:ASP294-C:LYS300 A:ASP389-A:LYS528 B:ASP389-B:LYS528 C:ASP389-C:LYS528 A:ASP398-A:ARG355 B:ASP398-B:ARG355 C:ASP398-C:ARG355 A:ASP40-A:ARG44 B:ASP40-B:ARG44 B:ASP40-B:LYS41 C:ASP40-A:ARG44 C:ASP40-B:ARG567 A:ASP405-A:ARG408 B:ASP405-B:ARG403

Table 8.2 (continued)

Wild-type - 1 open (D-up) B:ASP290-B:ARG634 C:ASP290-C:ARG634 C:ASP294-C:LYS300 C:ASP364-C:LYS528 A:ASP389-A:LYS528 C:ASP389-C:LYS386 B:ASP398-B:ARG355 C:ASP398-C:ARG355 A:ASP40-A:ARG44 B:ASP40-B:HIS49 C:ASP40-C:LYS202 A:ASP405-A:ARG403 A:ASP405-A:LYS417 B:ASP405-B:ARG403 C:ASP405-C:ARG403 A:ASP420-B:LYS386 B:ASP420-B:ARG457 A:ASP427-A:LYS424 B:ASP427-A:ARG408 C:ASP427-C:LYS424 B:ASP428-A:ARG403 B:ASP428-A:LYS417 A:ASP442-A:ARG346 B:ASP442-B:ARG509 C:ASP442-C:ARG509

D614G-mutant—all down (G-down) C:ASP290-C:ARG273 B:ASP294-B:LYS300 C:ASP294-C:LYS300 B:ASP389-B:LYS528 C:ASP389-A:ARG983 A:ASP398-A:ARG355 B:ASP398-B:ARG355 C:ASP398-C:ARG355 A:ASP40-A:ARG44 A:ASP40-A:LYS41 B:ASP40-B:ARG44 C:ASP40-C:ARG44 A:ASP405-A:ARG403 B:ASP405-B:ARG403 C:ASP405-C:ARG408 C:ASP405-C:LYS417 B:ASP420-B:LYS424 C:ASP420-A:LYS386 A:ASP427-A:LYS424 B:ASP427-B:LYS462 C:ASP427-C:LYS424 B:ASP428-B:LYS462 A:ASP442-A:ARG509 B:ASP442-B:ARG509 C:ASP442-C:ARG509

Wild-type—all down (D-down) A:ASP228-A:LYS41 B:ASP228-B:LYS202 B:ASP228-B:LYS41 C:ASP228-C:LYS202 A:ASP253-A:ARG158 B:ASP253-B:ARG246 A:ASP287-A:LYS278 B:ASP287-B:LYS278 A:ASP290-A:ARG273 B:ASP290-B:ARG273 C:ASP290-C:ARG634 A:ASP294-A:LYS300 A:ASP389-A:LYS528 C:ASP389-C:LYS386 A:ASP398-A:ARG355 B:ASP398-B:ARG355 C:ASP398-C:ARG355 A:ASP40-A:ARG44 B:ASP40-B:ARG44 C:ASP40-C:ARG44 A:ASP405-A:ARG408 B:ASP405-B:ARG408 B:ASP405-C:ARG408 C:ASP405-C:ARG403 B:ASP420-B:LYS417

342 8 Spike (S) Glycoprotein D614G Mutant

A:ASP420-A:LYS424 B:ASP420-B:LYS417 C:ASP420-C:LYS424 B:ASP427-B:LYS424 B:ASP428-A:ARG403 B:ASP442-B:ARG509 C:ASP442-C:ARG509 A:ASP467-A:ARG454 A:ASP467-A:ARG457 C:ASP467-C:ARG457 A:ASP53-A:LYS195 B:ASP53-B:LYS195 C:ASP53-C:LYS195 A:ASP568-B:LYS854 B:ASP568-C:LYS854 B:ASP571-C:ARG44 B:ASP571-B:ARG567 B:ASP571-C:HIS49 C:ASP571-C:ARG567 A:ASP574-A:LYS557 A:ASP574-B:LYS854 B:ASP574-B:LYS557 C:ASP574-C:LYS557 C:ASP574-A:LYS854 A:ASP578-A:ARG328 B:ASP578-B:ARG328

A:ASP467-A:ARG466 B:ASP467-B:ARG466 C:ASP467-C:ARG454 C:ASP467-C:ARG457 A:ASP53-A:LYS195 B:ASP53-B:LYS195 C:ASP53-C:LYS195 A:ASP568-B:LYS835 A:ASP568-B:LYS854 C:ASP568-A:LYS835 A:ASP571-B:ARG44 A:ASP571-A:ARG567 B:ASP571-C:ARG44 B:ASP571-C:LYS304 C:ASP571-A:ARG44 A:ASP574-A:LYS557 B:ASP574-B:LYS557 C:ASP574-C:LYS557 C:ASP574-A:LYS835 A:ASP578-A:ARG328 B:ASP578-B:ARG328 C:ASP578-C:ARG328 A:ASP586-A:LYS557 B:ASP586-B:LYS557 C:ASP586-C:LYS557 B:ASP614-C:LYS854

A:ASP467-A:ARG466 C:ASP467-C:ARG454 A:ASP53-A:LYS195 B:ASP53-B:LYS195 C:ASP53-C:LYS195 A:ASP568-B:LYS854 C:ASP568-A:LYS854 A:ASP571-B:ARG44 A:ASP571-A:ARG567 B:ASP571-C:ARG44 B:ASP571-B:ARG567 C:ASP571-A:ARG44 C:ASP571-C:ARG567 :AASP574-A:LYS557 A:ASP574-B:LYS854 B:ASP574-B:LYS557 C:ASP574-A:LYS854 A:ASP578-A:ARG328 B:ASP578-B:ARG328 C:ASP578-C:ARG328 A:ASP586-A:LYS557 B:ASP586-B:LYS557 A:ASP627-A:ARG634 B:ASP627-B:ARG634 C:ASP627-C:ARG634 A:ASP663-A:LYS310 (continued)

A:ASP427-A:LYS424 B:ASP427-B:LYS424 C:ASP427-C:LYS424 A:ASP442-A:ARG509 B:ASP442-B:ARG509 C:ASP442-C:ARG346 C:ASP442-C:ARG509 B:ASP467-C:LYS113 C:ASP467-C:ARG457 A:ASP53-A:LYS195 B:ASP53-B:LYS195 C:ASP53-C:LYS195 A:ASP568-B:LYS835 A:ASP568-B:LYS854 B:ASP568-C:LYS854 A:ASP571-B:ARG44 A:ASP571-A:ARG567 B:ASP571-C:ARG44 B:ASP571-B:ARG567 C:ASP571-A:ARG44 A:ASP574-A:LYS557 A:ASP574-B:LYS835 B:ASP574-C:LYS854 C:ASP574-C:LYS557 A:ASP578-A:ARG328 B:ASP578-B:ARG328

8.4 Concluding Remarks 343

D614G-mutant - 1 open (G-up) C:ASP578-C:ARG328 A:ASP586-A:LYS557 B:ASP586-B:LYS557 C:ASP586-C:LYS557 A:ASP627-A:ARG634 A:ASP663-A:LYS310 B:ASP663-B:LYS310 C:ASP663-C:LYS310 A:ASP737-C:ARG319 A:ASP745-C:ARG319 B:ASP745-A:ARG319 C:ASP745-B:ARG319 A:ASP775-A:LYS733 B:ASP775-B:LYS733 C:ASP775-C:LYS733 C:ASP80-C:ARG78 A:ASP808-A:LYS811 B:ASP808-B:LYS795 C:ASP808-C:LYS811 A:ASP820-A:ARG815 A:ASP820-A:LYS811 B:ASP820-B:ARG815

Table 8.2 (continued)

Wild-type - 1 open (D-up) A:ASP627-A:ARG634 A:ASP663-A:LYS310 B:ASP663-B:LYS310 C:ASP663-C:LYS310 B:ASP737-A:ARG319 A:ASP745-C:ARG319 C:ASP745-B:ARG319 A:ASP775-A:LYS733 B:ASP775-B:LYS733 C:ASP775-C:LYS733 B:ASP80-B:LYS77 C:ASP80-C:ARG78 A:ASP808-A:LYS795 B:ASP808-B:LYS811 C:ASP808-C:LYS795 A:ASP820-A:ARG815 A:ASP820-A:LYS811 B:ASP820-B:ARG815 C:ASP839-C:LYS835 B:ASP843-A:ARG646 C:ASP848-B:ARG646 A:ASP867-A:ARG815

D614G-mutant—all down (G-down) B:ASP663-B:LYS310 C:ASP663-C:LYS310 B:ASP745-A:ARG319 A:ASP775-A:LYS733 B:ASP775-B:LYS733 C:ASP775-C:LYS733 A:ASP796-A:LYS795 A:ASP80-A:LYS77 B:ASP80-B:ARG21 A:ASP808-A:LYS811 B:ASP808-B:LYS811 C:ASP808-C:LYS795 C:ASP808-C:LYS811 A:ASP820-A:ARG815 B:ASP820-B:ARG815 B:ASP820-B:LYS811 C:ASP820-C:ARG815 A:ASP839-A:LYS835 A:ASP843-A:LYS835 B:ASP843-A:ARG646 A:ASP848-C:ARG646 B:ASP848-B:ARG847

Wild-type—all down (D-down) C:ASP578-C:ARG328 A:ASP586-A:LYS557 C:ASP586-C:LYS557 B:ASP614-C:ARG847 A:ASP627-A:ARG634 B:ASP627-B:ARG634 A:ASP663-A:LYS310 B:ASP663-B:LYS310 C:ASP663-C:LYS310 B:ASP745-A:ARG319 C:ASP745-B:ARG319 A:ASP775-A:LYS733 B:ASP775-B:LYS733 C:ASP775-C:LYS733 A:ASP796-A:LYS795 A:ASP80-A:ARG21 A:ASP808-A:LYS811 B:ASP808-B:LYS811 C:ASP808-C:LYS811 A:ASP820-A:ARG815 B:ASP820-B:ARG815 C:ASP820-C:ARG815

344 8 Spike (S) Glycoprotein D614G Mutant

D614G-mutant - 1 open A:ASP830-A:LYS835 A:ASP839-C:ARG646 C:ASP839-B:ARG646 C:ASP839-C:LYS835 B:ASP843-A:ARG646 C:ASP843-B:ARG646 A:ASP848-C:LYS537 C:ASP848-C:ARG847 B:ASP867-B:LYS814 C:ASP867-C:ARG815 A:ASP936-A:LYS933 B:ASP936-B:LYS933 B:ASP950-B:LYS947 C:ASP950-C:LYS947 A:ASP979-A:ARG983 B:ASP979-A:ARG567 C:ASP979-C:ARG983 A:ASP985-C:LYS386 B:ASP985-A:LYS386 A:ASP994-C:ARG995 B:ASP994-A:ARG995 C:ASP994-B:ARG995 A:GLU1017-A:ARG1014 B:GLU1017-B:ARG1014

Wild-type - 1 open C:ASP867-C:ARG847 A:ASP936-A:LYS933 C:ASP936-C:LYS933 A:ASP950-A:LYS947 C:ASP950-C:LYS947 A:ASP979-C:ARG567 A:ASP979-C:HIS519 B:ASP979-B:ARG983 A:ASP985-C:LYS386 A:ASP994-C:ARG995 B:ASP994-A:ARG995 C:ASP994-B:ARG995 A:GLU1017-A:ARG1014 A:GLU1017-B:ARG1019 B:GLU1017-B:ARG1014 B:GLU1017-C:ARG1019 C:GLU1017-A:ARG1019 A:GLU1031-C:ARG1039 B:GLU1031-A:ARG1039 C:GLU1031-B:ARG1039 C:GLU1072-C:LYS1073 B:GLU1144-A:LYS1086 C:GLU1144-B:LYS1086 A:GLU132-A:LYS113

Table 8.3 The SBs of the optimized models of [229] (continuation) D614G-mutant—all down C:ASP848-C:ARG847 A:ASP867-A:ARG847 B:ASP867-B:ARG815 A:ASP88-C:LYS462 A:ASP936-A:LYS933 B:ASP936-B:LYS933 C:ASP950-C:LYS947 A:ASP979-A:ARG983 B:ASP979-B:ARG983 C:ASP979-C:ARG983 A:ASP985-C:LYS386 B:ASP985-A:LYS378 C:ASP985-B:LYS386 A:ASP994-C:ARG995 B:ASP994-A:ARG995 C:ASP994-B:ARG995 A:GLU1017-A:ARG1014 A:GLU1017-A:LYS947 B:GLU1017-B:ARG1014 B:GLU1017-C:ARG1019 C:GLU1017-A:ARG1019 B:GLU1031-A:ARG1039 C:GLU1031-C:ARG1039 C:GLU1072-C:LYS1073

(continued)

Wild-type—all down A:ASP839-A:ARG847 C:ASP839-C:LYS304 C:ASP839-C:LYS964 B:ASP843-B:ARG847 A:ASP867-A:ARG815 B:ASP867-B:ARG815 C:ASP867-C:ARG815 A:ASP936-A:LYS933 A:ASP950-A:LYS947 B:ASP950-B:LYS947 A:ASP979-C:ARG567 A:ASP985-C:LYS386 B:ASP985-A:LYS378 C:ASP985-B:LYS386 A:ASP994-C:ARG995 B:ASP994-A:ARG995 C:ASP994-B:ARG995 A:GLU1017-A:ARG1014 A:GLU1017-B:ARG1019 B:GLU1017-C:ARG1019 C:GLU1017-A:ARG1019 C:GLU1017-C:LYS947 B:GLU1031-A:ARG1039 C:GLU1031-B:ARG1039

8.4 Concluding Remarks 345

D614G-mutant - 1 open C:GLU1017-A:ARG1019 A:GLU1031-C:ARG1039 B:GLU1031-A:ARG1039 C:GLU1031-A:ARG1039 C:GLU1031-C:ARG1039 A:GLU1092-C:ARG1091 C:GLU1092-C:ARG1107 A:GLU1111-C:LYS1086 C:GLU132-C:LYS113 A:GLU154-A:ARG102 B:GLU154-B:ARG102 A:GLU156-A:ARG158 B:GLU156-B:ARG158 B:GLU156-B:ARG246 C:GLU156-C:ARG158 C:GLU156-C:ARG246 A:GLU169-C:ARG357 A:GLU169-A:LYS129 B:GLU169-B:LYS129 C:GLU169-B:ARG357 C:GLU169-C:LYS129 A:GLU180-A:LYS182 C:GLU180-C:LYS182 A:GLU191-A:ARG34 B:GLU191-B:ARG34

Table 8.3 (continued)

Wild-type - 1 open A:GLU154-A:LYS147 B:GLU154-B:ARG102 C:GLU154-C:ARG102 A:GLU156-A:ARG158 B:GLU156-B:ARG158 C:GLU156-C:ARG158 C:GLU156-C:ARG246 A:GLU169-A:LYS129 B:GLU169-B:LYS129 C:GLU169-C:LYS129 B:GLU180-B:LYS187 C:GLU180-C:LYS187 C:GLU180-C:LYS97 A:GLU191-A:ARG34 B:GLU191-B:ARG34 C:GLU191-C:ARG34 A:GLU224-A:LYS206 B:GLU224-B:LYS206 C:GLU224-C:LYS206 C:GLU281-C:LYS278 A:GLU340-A:LYS356 B:GLU406-B:LYS417 C:GLU406-C:ARG403 A:GLU465-A:ARG454 B:GLU465-B:ARG454

D614G-mutant—all down B:GLU1092-B:ARG1107 C:GLU1111-B:LYS1086 B:GLU132-A:ARG466 B:GLU132-B:LYS113 A:GLU156-A:ARG158 A:GLU156-A:ARG246 B:GLU156-B:ARG158 C:GLU156-C:ARG158 C:GLU156-C:ARG246 A:GLU169-A:LYS129 B:GLU169-B:LYS129 C:GLU169-C:LYS129 A:GLU180-A:LYS187 B:GLU180-B:LYS182 C:GLU180-C:LYS147 A:GLU191-A:ARG34 B:GLU191-B:ARG34 C:GLU191-C:ARG34 A:GLU224-A:LYS206 B:GLU224-B:LYS206 C:GLU224-C:LYS206 A:GLU281-C:LYS557 B:GLU281-B:LYS278 C:GLU324-C:LYS537 A:GLU406-A:LYS417

Wild-type—all down C:GLU1031-C:ARG1039 B:GLU1072-B:LYS1073 B:GLU1092-B:ARG1107 B:GLU1111-A:LYS1086 A:GLU154-A:ARG102 B:GLU154-B:ARG102 A:GLU156-A:ARG158 A:GLU169-A:LYS129 B:GLU169-B:LYS129 C:GLU169-C:LYS129 A:GLU180-A:LYS187 A:GLU180-A:LYS97 B:GLU180-B:LYS150 C:GLU180-C:LYS150 A:GLU191-A:ARG34 B:GLU191-B:ARG34 C:GLU191-C:ARG34 A:GLU224-A:LYS206 B:GLU224-B:LYS206 C:GLU224-C:LYS206 C:GLU281-C:LYS278 B:GLU324-B:LYS537 C:GLU324-C:LYS537 A:GLU406-A:ARG403 B:GLU406-B:ARG403

346 8 Spike (S) Glycoprotein D614G Mutant

C:GLU191-C:ARG34 A:GLU224-A:LYS206 B:GLU224-B:LYS206 C:GLU224-C:LYS206 A:GLU281-A:LYS278 B:GLU281-B:LYS835 C:GLU281-C:LYS278 C:GLU298-A:ARG765 C:GLU406-C:ARG403 A:GLU465-A:ARG457 A:GLU465-A:LYS462 C:GLU465-C:ARG457 A:GLU471-A:LYS458 B:GLU471-B:ARG457 C:GLU471-C:LYS458 A:GLU484-B:LYS378 B:GLU484-B:ARG403 B:GLU516-B:ARG355 B:GLU516-B:ARG466 A:GLU554-A:LYS535 B:GLU554-B:LYS535 C:GLU554-C:LYS535 A:GLU583-A:LYS535 B:GLU583-B:LYS535 C:GLU583-C:LYS535 B:GLU619-B:LYS537

C:GLU465-C:ARG457 C:GLU465-C:LYS462 C:GLU471-C:ARG454 A:GLU484-B:LYS378 A:GLU516-A:ARG357 B:GLU516-B:ARG357 C:GLU516-A:LYS41 A:GLU554-A:LYS535 B:GLU554-B:LYS535 C:GLU554-C:LYS535 A:GLU583-A:LYS535 B:GLU583-B:LYS535 C:GLU583-C:LYS535 C:GLU619-C:LYS537 C:GLU661-A:LYS786 A:GLU702-B:LYS790 B:GLU702-C:LYS790 C:GLU702-A:LYS790 A:GLU725-A:HIS1064 A:GLU725-A:LYS1028 B:GLU725-B:HIS1064 B:GLU725-B:LYS1028 C:GLU725-C:HIS1064 C:GLU725-C:LYS1028 B:GLU773-B:ARG1019 C:GLU773-C:ARG1019

B:GLU406-B:LYS417 C:GLU406-C:ARG403 C:GLU406-C:LYS417 A:GLU465-A:ARG457 A:GLU465-A:LYS462 C:GLU465-C:ARG457 A:GLU471-A:ARG454 A:GLU471-A:ARG457 B:GLU471-B:ARG454 B:GLU471-B:ARG457 A:GLU516-B:LYS202 B:GLU516-C:LYS41 A:GLU554-A:LYS535 B:GLU554-B:LYS535 C:GLU554-C:LYS535 A:GLU583-A:LYS558 B:GLU583-:BLYS535 B:GLU619-B:LYS537 C:GLU661-A:LYS786 A:GLU702-B:LYS790 B:GLU702-C:LYS790 C:GLU702-A:LYS790 A:GLU725-A:HIS1064 A:GLU725-A:LYS1028 B:GLU725-B:HIS1064 B:GLU725-B:LYS1028 (continued)

C:GLU406-C:LYS417 A:GLU465-A:ARG457 B:GLU465-B:LYS462 C:GLU465-C:LYS462 A:GLU471-A:LYS458 B:GLU471-B:ARG454 B:GLU471-B:ARG457 C:GLU471-C:LYS458 A:GLU484-A:LYS417 A:GLU516-B:LYS202 A:GLU516-B:LYS41 C:GLU516-A:ARG983 A:GLU554-A:LYS535 B:GLU554-B:LYS535 B:GLU554-B:LYS558 C:GLU554-C:LYS535 A:GLU583-A:LYS535 B:GLU583-B:LYS535 C:GLU583-C:ARG328 A:GLU619-A:LYS537 A:GLU661-B:LYS786 C:GLU661-A:LYS786 A:GLU702-B:LYS790 B:GLU702-C:LYS790 C:GLU702-A:LYS790 A:GLU725-A:HIS1064

8.4 Concluding Remarks 347

D614G-mutant - 1 open C:GLU619-A:ARG847 C:GLU661-A:LYS786 A:GLU702-B:LYS790 B:GLU702-C:LYS790 C:GLU702-A:LYS790 A:GLU725-A:HIS1064 A:GLU725-A:LYS1028 :GLU725-B:HIS1064 B:GLU725-B:LYS1028 C:GLU725-C:HIS1064 C:GLU725-C:LYS1028 A:GLU773-A:ARG1019 C:GLU773-C:ARG1019 A:GLU780-A:LYS776 B:GLU780-B:ARG1019 B:GLU780-B:LYS776 C:GLU780-C:LYS776 A:GLU868-A:LYS814 B:GLU868-B:LYS814 C:GLU868-C:LYS814 A:GLU96-A:ARG190 B:GLU96-B:ARG190 C:GLU96-C:ARG190 B:GLU988-A:LYS378

Table 8.3 (continued)

Wild-type - 1 open A:GLU780-A:ARG1019 A:GLU780-A:LYS776 C:GLU819-C:ARG815 B:GLU868-A:ARG646 A:GLU96-A:ARG190 B:GLU96-B:ARG190 C:GLU96-C:ARG190 B:GLU988-A:LYS378

D614G-mutant—all down C:GLU725-C:HIS1064 C:GLU725-C:LYS1028 A:GLU773-A:ARG1019 B:GLU773-B:LYS776 C:GLU773-C:ARG1019 A:GLU780-A:LYS776 B:GLU780-B:ARG1019 B:GLU780-B:LYS776 C:GLU780-C:LYS776 A:GLU868-A:ARG847 C:GLU868-C:LYS814 A:GLU96-A:ARG190 B:GLU96-B:ARG190 C:GLU96-C:ARG190 C:GLU990-B:ARG995

Wild-type—all down A:GLU725-A:LYS1028 B:GLU725-B:HIS1064 B:GLU725-B:LYS1028 C:GLU725-C:HIS1064 C:GLU725-C:LYS1028 A:GLU773-A:ARG1019 B:GLU773-B:ARG1019 C:GLU773-C:ARG1019 C:GLU773-C:LYS776 A:GLU780-A:LYS776 B:GLU780-B:LYS776 A:GLU868-A:LYS814 B:GLU868-A:ARG646 B:GLU868-B:LYS814 C:GLU868-C:LYS814 A:GLU96-A:ARG190 B:GLU96-B:ARG190 C:GLU96-C:ARG190 C:GLU990-B:ARG995

348 8 Spike (S) Glycoprotein D614G Mutant

Chapter 9

Spike (S) Glycoprotein N501Y Mutant

Abstract SARS-CoV-2 worldwide pandemic was once attributed to the mutations in the receptor-binding domain (RBD), the area that directly contacts human ACE2; one example is the variant N501Y in the RBD. The structural change may enhance the interaction between the spike protein and the ACE2 receptor of the host, increasing infectivity and increasing binding free energy. The studies of this chapter summarize the following structural bioinformatics for the SARS-CoV-2 N501Y mutant (where D/B chain is human ACE2 and F/E chain is spike RBD): (i). a salt bridge D:ASP39-F:LYS417 is between human ACE2 and spike RBD; (ii). at F:N501Y, there are two hydrogen bonds F:GLN506.NE2-F:TYR501.O and D:LYS353.NZ-F:TYR501.OH, and between ACE2 and RBD, there are hydrogen bonds F:GLN493.NE2-D:GLU44.OE2, D:LYS353.NZ-F:TYR501.OH, F:THR500.OG1-D:TYR50.OH, F:TYR449.OHD:ASP47.OD1, F:TYR489.OH-D:THR36.O, and F:TYR505.OH-D:GLU46.OE2 and E:GLN493.NE2-B:GLU35.OE2, E:GLN493.N/O-B:TYR453.O/N, and E:GLY502.H-B:LYS353.O; (iii). around F/E:N501Y, there are three hydrophobic interactions F:TYR501-D:TYR41, F:TYR501-D:LYS353, and B:LYS353E:GLY504 between spike RBD and human ACE2; (iv). at F:N501Y, there is a .π -.π stacking F:TYR501-D:TYR50 between spike RBD and human ACE2; and (v). the mutation N501Y changes GLY502 and GLN506 from Coil to Turn and changes VAL503-GLY504-TYR505 from .310 -helix to Turn. Keywords Optimized N501Y structures · Structural bioinformatics · Salt bridges · Polar contacts · Hydrophobic contacts and .π -interactions

9.1 Introduction SARS-CoV-2 worldwide pandemic was attributed to the mutations in the receptorbinding domain (RBD), the area that directly contacts human ACE2 [431]. Variant N501Y in the RBD had once emerged in a rapidly spreading lineage (B.1.1.7) in England. This variant is much more contagious than the original version (N501© The Author(s), under exclusive license to Springer Nature Switzerland AG 2023 J. Zhang, Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures, Springer Series in Biophysics 23, https://doi.org/10.1007/978-3-031-36773-1_9

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RBD). The structural change may enhance the interaction between the spike protein and the ACE2 receptor of the host, increasing infectivity [438] and increasing binding free energy [132, 174, 431]. It was found that this mutated version of RBD binds to human ACE2 about ten times more tightly than the native version (N501-RBD). This chapter is to optimize currently known N501Y structures and then present the structural bioinformatics such as the noncovalent interactions of hydrogen bonds (HBs), salt bridges (SBs), van der Waals (vdWs) contacts, hydrophobic (HYD) interactions, and .π-interactions (PIs) of the optimized N501Y structures. The performance of these structural bioinformatics is confirmed from some molecular dynamics (MD) simulations known currently. .μ-variant B.1.621 consists of E484K and N501Y mutations, where E484K mutation can help the variant running away from SARS-CoV-2 antibodies. .λ-variant is much like the .μ-variant.

9.2 The Homology Structure of N501Y Mutant Residue 501 is located on the viral RBD surface for cell entry and increases binding to the receptor ACE2. Thus, we had better choose 6m17.pdb. Openly accessible inpcrd and prmtop files of “wat_6m17_N501YboundREDUCED” were downloaded from [25]. From these two files, we generated a pdb file and removed the waters in it, adding TERs; then we input the pdb file into Maestro 10.1 (Academic Use Only) (https://www.schrodinger.com/maestro) to optimize it: “Edit.→Select Atoms.→All” and then “Tools.→Minimize.→Selected Atoms” (backbone RMSD value between the unoptimized and optimized models is 0.596831 Å). We denote the optimized model as the optimized-6m17-N501Y-mutant model in this chapter.

9.3 Structural Bioinformatics of N501Y Mutant 9.3.1 From the optimized-6m17-N501Y-mutant Model The noncovalent interactions of HBs, SBs, vdWs contacts, HYD interactions, and PIs are driving a protein to be able to perform its biological functions. In the below, we will find out the HBs, SBs, HYD interactions, and vdWs contacts of the optimized-6m17-N501Y-mutant model. All the SBs of the optimized-6m17-N501Y-mutant model can be seen in Table 9.1, where SB D:ASP39-F:LYS417 is between human ACE2 and spike RBD and SBs F:ASP405-F:ARG403, F:ASP442-F:ARG509, F:ASP467-F:ARG454, F:ASP467-F:ARG457, F:GLU340-F:LYS356, and F:GLU465-F:ARG457 are still within spike RBD as in Chap. 7.

9.3 Structural Bioinformatics of N501Y Mutant

351

Table 9.1 All the SBs of the optimized-6m17-N501Y-mutant model SB D:ASP39-F:LYS417 F:ASP389-F:LYS386 F:ASP405-F:ARG403 F:ASP427-F:LYS424 F:ASP442-F:ARG509 F:ASP467-F:ARG454 F:ASP467-F:ARG457 F:GLU340-F:LYS356 F:GLU465-F:ARG457 F:GLU465-F:LYS462 F:GLU471-F:LYS458 F:GLU516-F:ARG355 D:ASP47-D:LYS353 D:ASP207-D:ARG213 D:ASP210-D:ARG213 D:ASP210-D:ARG228 D:ASP215-D:LYS562 D:ASP335-D:LYS363 D:ASP355-D:ARG357 D:ASP494-D:LYS183 D:ASP499-D:ARG178 D:ASP499-D:LYS481 D:ASP509-D:LYS196 D:ASP597-D:LYS600 D:GLU31-D:LYS35 D:GLU44-D:LYS40 D:GLU46-D:ARG393 D:GLU119-D:LYS123 D:GLU175-D:HIS493 D:GLU190-D:ARG186 D:GLU190-D:LYS470 D:GLU191-D:ARG124 D:GLU198-D:LYS121 D:GLU206-D:ARG213 D:GLU217-D:ARG228 D:GLU236-D:LYS458 D:GLU240-D:LYS243 D:GLU241-D:ARG582 D:GLU310-D:ARG306

In N501Y mutant Human ACE2-spike RBD Within spike RBD Within spike RBD Within spike RBD Within spike RBD Within spike RBD Within spike RBD Within spike RBD Within spike RBD Within spike RBD Within spike RBD Within spike RBD Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2

In wild-type

Yes Yes Yes Yes Yes Yes

Yes Yes

Yes

Yes (continued)

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Table 9.1 (continued) SB D:GLU310-D:LYS313 D:GLU312-D:LYS309 D:GLU375-D:HIS378 D:GLU398-D:ARG514 D:GLU402-D:HIS374 D:GLU406-D:ARG518 D:GLU430-D:LYS419 D:GLU433-D:LYS288 D:GLU435-D:HIS540 D:GLU435-D:LYS541 D:GLU457-D:ARG460 D:GLU467-D:LYS465 D:GLU479-D:LYS475 D:GLU479-D:LYS476 D:GLU483-D:LYS476 D:GLU489-D:ARG482 D:GLU495-D:ARG186 D:GLU536-D:HIS535 D:GLU536-D:LYS416 D:GLU549-D:LYS534 D:GLU571-D:LYS577 D:GLU589-D:ARG582

In N501Y mutant Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2 Within human ACE2

In wild-type Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes

Yes

Regarding HBs, we find 2 HBs at residue N501Y, F:GLN506.NE2F:TYR501.O and D:LYS353.NZ-F:TYR501.OH (showing that the N501Y mutation enhanced the electrostatic interactions due to the formation of this strong HB; here, there are two HYD interactions at residue N501Y (Fig. 9.1 and Figs. 1C and 1E of [438]): F:TYR501-D:TYR41 (Y501 inserted into a cavity at the binding interface near Y41 of ACE2) and F:TYR501D:LYS353 HYD interactions [217]); 6 HBs between ACE2 and RBD, F:GLN493.NE2-D:GLU44.OE2, D:LYS353.NZ-F:TYR501.OH, F:THR500.OG1D:TYR50.OH, F:TYR449.OH-D:ASP47.OD1, F:TYR489.OH-D:THR36.O, and F:TYR505.OH-D:GLU46.OE2; 70 HBs within F chain spike RBD, F:ALA397.NF:LYS356.O, F:ARG355.NH1-F:SER514.OG, F:ARG355.NH2-F:GLU516.OE2, F:ARG357.NH1-F:ASN394.OD1, F:ARG403.NE-F:ASP405.OD1, F:ARG403. NH1-F:ASP405.OD2, F:ARG454.N-F:ASN422.OD1, F:ARG454.NH2-F:ASP467. O, F:ARG457.NE-F:ASP467.OD2, F:ARG457.NH2-F:GLU465.OE1, F:ARG509. NE-F:SER438.OG, F:ARG509.NH2-F:ASP442.OD2, F:ARG509.N-F:TRP436.O, F:ASN354.ND2-F:SER399.O, F:ASN437.ND2-F:GLN506.OE1, F:ASN439.NF:ASN437.OD1, F:ASN439.ND2-F:PRO499.O, F:ASN448.ND2-F:ASP442.O, F:ASN448.N-F:PHE497.O, F:ASN460.ND2-F:ASP420.OD2, F:ASN487.ND2-

9.3 Structural Bioinformatics of N501Y Mutant

353

F:ALA475.O, F:ASP405.OD1-F:ARG403.NE, F:CYS432.N-F:LEU513.O, F:GLN409.N-F:GLU406.O, F:GLN414.NE2-F:GLN414.O, F:GLN493.N-F: TYR453.O, F:GLN506.NE2-F:TYR501.O, F:GLU465.N-F:LYS462.O, F:GLU465. OE2-F:LYS462.NZ, F:GLU471.OE1-F:LYS458.NZ, F:GLU516.OE2-F:ARG355. NH2, F:GLY381.N-F:THR430.O, F:GLY416.N-F:ASP427.OD1, F:GLY416.NF:ASP420.OD1, F:ILE358.N-F:VAL395.O, F:ILE402.N-F:TYR508.O, F:ILE434. N-F:VAL511.O, F:LEU513.N-F:CYS432.O, F:LYS378.N-F:VAL433.O, F:LYS378. NZ-F:TYR380.OH, F:LYS386.NZ-F:ASP389.OD1, F:LYS386.NZ-F:LYS386.O, F:LYS417.N-F:GLN409.OE1, F:LYS417.NZ-F:LEU455.O, F:LYS424.NZF:ASP427.OD2, F:LYS424.NZ-F:LEU425.O, F:LYS444.NZ-F:ASP442.O, F:LYS458.NZ-F:GLU471.OE1, F:LYS462.N-F:GLU465.OE2, F:LYS462.NZF:GLU465.OE2, F:SER373.OG-F:SER371.OG, F:SER375.OG-F:ALA435.O, F:SER443.OG-F:ASN439.OD1, F:SER514.N-F:TYR396.O, F:SER514.OGF:GLU516.OE1, F:THR430.N-F:ASP428.O, F:TRP436.N-F:ARG509.O, F: TYR369.OH-F:THR385.OG1, F:TYR421.N-F:LYS417.O, F:TYR423.N-F:ILE418. O, F:TYR423.OH-F:ASP398.OD2, F:TYR451.OH-F:ASP442.OD1, F:TYR453.NF:GLN493.O, F:TYR473.N-F:TYR489.O, F:TYR495.OH-F:GLU406.OE1, F:TYR508.N-F:ILE402.O, F:VAL433.N-F:LYS378.O, F:VAL510.N-F:PHE400.O, F:VAL511.N-F:ILE434.O, and F:VAL512.N-F:ASP398.O; and 243 HBs within human ACE2.

Fig. 9.1 The N501Y mutation allows two hydrophobic interactions F:TYR501-D:TYR41 and F:TYR501-D:LYS353 between spike RBD and human ACE2 (orange color, hydrophobic; turquoise color, hydrophilic)

For .π -interactions, we find 10 .π -cations, F:TRP353-F:ARG466.NH2+, F: PHE464-F:ARG355.NH2+-F:TYR396, D:TRP57-D:ARG357.NH2+, D:TRP515D:ARG273.NH2+, D:PHE592-D:LYS596.NZ+, D:TYR497-D:LYS183.NZ+, D:TRP174-D:ARG178.NH2+-D:TRP271, and D:TRP478-D:LYS481.NZ+, and 3 .π -.π stackings F:PHE400-F:TYR423-F:TRP353-F:TYR423 within spike RBD, 1 .π -.π stacking F:TYR501-D:TYR50 between spike RBD and human ACE2 (the N501Y mutation allows an aromatic ring-ring interaction .π -.π stacking F:TYR501D:TYR50 and an additional HB F:TYR501.OH-D:LYS353.NZ2 (Fig. 4c of [213]) between the RBD and ACE2 – see Fig. 9.2), and 23 .π -.π stackings within human ACE2.

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Fig. 9.2 The N501Y mutation allows an aromatic ring-ring interaction .π -.π stacking F:TYR501D:TYR50 and an additional HB and vdWs contact F:TYR501.OH-D:LYS353.NZ between spike RBD and human ACE2 (left photo, wild-type; right two photos, N501Y mutant)

The mutation N501Y changes GLY502 and GLN506 from Coil to Turn and changes VAL503-GLY504-TYR505 from .310 -helix to Turn (Fig. 9.3).

Fig. 9.3 N501Y mutation changes GLY502 and GLN506 from Coil to Turn and changes VAL503GLY504-TYR505 from .310 -helix to Turn, where the residue number should minus 236

9.3.2 From MD Simulations The 500 ns’ MD simulation (based on 6M0J.pdb) of [117] showed that “the HB F:TYR501-D:LYS355 is not so pronounced and mainly the hydrophobic and .π -.π stackings of TYR501 increase the binding strength” (Fig. 2B of [117]). The 6 ns’ MD (based on 6M17.pdb) of [14] showed that (i) the N501Y mutation enhanced the electrostatic interactions due to the formation of a strong HB between F:T500 and D:D355 near the mutation site and (ii) SBs F:LYS417-D:ASP30, F:LYS458-D:GLU23, and F:ARG403-D:GLU37 contributed more than 40% of the total binding energies in the wild-type and the mutant. The 200 ns’ MD (based on 6VW1.pdb) of [217] showed that Y501 in the mutated spike RBD can be well-coordinated by Y41 and K353 in human ACE2 through

9.4 Concluding Remarks

355

hydrophobic interactions, which may increase the overall binding affinity of the spike RBD for human ACE2 by approximately 0.81 kcal/mol. The 100 ns’ MD of the N501Y_representative_structure in [431] found that there were also several RBD residues or residue clusters have significantly increased interactions with hACE2 after the N501Y mutation, such as Ser477 and Gln493 and its neighboring residues (Table 2 of [431]). From the optimized N501Y_representative_structure (backbone RMSD value between the unoptimized and optimized structures is 0.003439 Å), we get all the SBs with their HBs of the optimized N501Y_representative_structure listed in Table 9.2; a .π -.π stacking B:TYR41-E:TYR501 at RBD residue TYR501; HBs E:TYR501.NE:GLN498.O,E:GLN506.NE2-E:TYR501.O, and E:TYR501.OH-E:GLY496.O at RBD residue TYR501; HBs E:GLN493.NE2-B:GLU35.OE2, E:GLN493.N/OB:TYR453.O/N, and E:GLY502.H-B:LYS353.O between spike RBD and human ACE2; and a HYD B:LYS353-E:GLY504 between human ACE2 and spike RBD (Fig. 9.4).

Fig. 9.4 The hydrophobic contact B:LYS353-E:GLY504 between human ACE2 and spike RBD of the optimized N501Y_representative_structure

9.4 Concluding Remarks In summary, the studies of this chapter present the following structural bioinformatics for SARS-CoV-2 N501Y mutant (where D/B chain is human ACE2 and F/E chain is spike RBD): (i). a salt bridge D:ASP39-F:LYS417 is between human ACE2 and spike RBD; (ii). at F:N501Y, there are two hydrogen bonds F:GLN506.NE2-F:TYR501.O and D:LYS353.NZ-F:TYR501.OH, and between ACE2 and RBD, there are hydrogen bonds F:GLN493.NE2-D:GLU44.OE2, D:LYS353.NZ-F:TYR501.OH, F:THR500.OG1-D:TYR50.OH, F:TYR449.OHD:ASP47.OD1, F:TYR489.OH-D:THR36.O, and F:TYR505.OH-D:GLU46.OE2 and E:GLN493.NE2-B:GLU35.OE2, E:GLN493.N/O-B:TYR453.O/N, and E:GLY502.H-B:LYS353.O; (iii). around F/E:N501Y, there are three hydrophobic interactions F:TYR501-D:TYR41, F:TYR501-D:LYS353, and B:LYS353E:GLY504 between spike RBD and human ACE2; (iv). at F:N501Y, there is a .π -.π stacking F:TYR501-D:TYR50 between spike RBD and human ACE2; and (v). the mutation N501Y changes GLY502 and GLN506 from Coil to Turn and changes VAL503-GLY504-TYR505 from .310 -helix to Turn.

356

9 Spike (S) Glycoprotein N501Y Mutant

Table 9.2 All the SBs with their HBs of the optimized N501Y_representative_structure, where B is human ACE2 SER19-ASP615 and E is spike RBD CYS336-LEU518 SB B:ASP30-E:LYS417 E:ASP398-E:ARG355 E:ASP405-E:ARG403 E:ASP405-E:ARG408 E:ASP420-E:LYS424 E:ASP442-E:ARG509 E:ASP467-E:ARG454 E:ASP467-E:ARG457 E:GLU465-E:ARG466 E:GLU516-E:ARG357 B:GLU23-B:LYS26 B:GLU35-B:LYS31 B:GLU37-B:ARG393 B:GLU140-B:LYS131 B:GLU166-B:HIS493 B:GLU181-B:ARG177 B:GLU181-B:LYS470 B:GLU182-B:ARG115 B:GLU197-B:ARG192 B:GLU208-B:ARG219 B:GLU227-B:LYS458 B:GLU231-B:LYS234 B:GLU310-B:ARG306 B:GLU310-B:LYS313 B:GLU312-B:LYS309 B:GLU398-B:ARG514 B:GLU406-B:ARG518 B:GLU430-B:LYS416 B:GLU430-B:LYS541 B:GLU433-B:LYS288 B:GLU435-B:HIS540 B:GLU435-B:LYS541 B:GLU457-B:ARG460 B:GLU467-B:LYS465 B:GLU479-B:LYS476 B:GLU489-B:ARG482 B:GLU495-B:ARG177 B:GLU495-B:LYS475 B:GLU589-B:ARG582 B:GLU589-B:LYS596

HBs B:ASP30.OD2-E:LYS417.NZ E:ASP398.OD1-E:ARG355.NH1 E:ASP405.OD1-E:ARG403.NH1 E:ARG408.NH1-E:ASP405.OD1 E:ASP420.OD2-E:LYS424.NZ

E:GLU516.OE2-E:ARG357.NH2 B:GLU35.OE2-B:LYS31.NZ B:LYS131.NZ-B:GLU140.OE2 B:HIS493.NE2-B:GLU166.OE2 B:LYS470.NZ-B:GLU181.OE1 B:GLU182.OE1-B:ARG115.NH1, B:GLU182.OE2-B:ARG115.NE B:ARG192.NH1-B:GLU197.OE1, B:ARG192.NE-B:GLU197.OE2 B:GLU208.OE1-B:ARG219.NH1

B:GLU310.N-B:ARG306.O

B:ARG518.NH2-B:GLU406.OE2

B:HIS540.NE2-B:GLU435.OE2, B:GLU435.OE1-B:LYS541.NZ B:GLU435.OE1-B:LYS541.NZ B:LYS465.NZ-B:GLU467.OE2 B:LYS476.NZ-B:GLU479.OE1

(continued)

9.4 Concluding Remarks

357

Table 9.2 (continued) SB B:ASP38-B:LYS353 B:ASP111-B:LYS112 B:ASP198-B:ARG204 B:ASP201-B:ARG204 B:ASP201-B:ARG219 B:ASP216-B:LYS577 B:ASP225-B:HIS228 B:ASP355-B:ARG357 B:ASP335-B:LYS363 B:ASP367-B:LYS441 B:ASP382-B:HIS401 B:ASP431-B:LYS288 B:ASP494-B:LYS174 B:ASP499-B:ARG169 B:ASP499-B:LYS481 B:ASP509-B:LYS187 B:ASP597-B:LYS600

HBs B:LYS112.NZ-B:ASP111.OD2 B:ARG204.NH2-B:ASP198.OD1 B:ASP201.OD1-B:ARG219.NE B:LYS577.NZ-B:ASP216.O B:HIS228.NE2-B:ASP225.OD1 B:LYS363.NZ-B:ASP335.OD2

B:ASP431.OD2-B:LYS288.NZ

Chapter 10

Spike (S) Glycoprotein N165A and N234A Mutant

Abstract Casalino et al. (ACS Cent Sci 6:1722-1734, 2020) revealed an essential structural role of N-glycans at sites N165 and N234 in modulating the conformational dynamics of SARS-CoV-2 spike’s receptor-binding domain (RBD) and showed that deletion of the glycans through N165A and N234A mutations significantly reduces binding to ACE2 as a result of the RBD conformational shift toward the “down” state. We have not found any structural bioinformatics on salt bridges (SBs) in Casalino et al. (ACS Cent Sci 6:1722-1734, 2020); this chapter presents some SBs of the mutant and its wild-type. Basing on these SBs, we also furthermore studied the structural bioinformatics on hydrogen bonds (HBs) for the mutant and its wild-type. We can confirm the strong SBs GLU1031-ARG1039, ASP442-AEG509, ASP398-ARG355, GLU725-LYS1028, ASP53-LYS195, ASP775-LYS733, and ASP578-ASP328 and can confirm GLU1031-ARG1039, ASP442-AEG509, ASP398-ARG355, and ASP578-ASP328 are strong polar contacts. SBs GLU725-LYS1028, ASP53-LYS195, ASP775-LYS733 (with strong HB A/BS2:LYS733.NZ-A/BS2:ASP775.OD2), and ASP578-ARG328 (replica 6) are always 100% existing within A, B, and C chains, respectively, whether for the mutant or for the wild-type. We also find new strong HBs GLU1031-THR1027 and GLU725-PHE1062 are within each chain. However, we cannot say some differences between the 6vsb-open-N165A-and-N234A-mutant and its wild-type; this might be because the mutations N165A and N234A are changing the polar residue ASN into the strictly hydrophobic residue ALA and residues ASN and ALA are not charged residues. Keywords SARS-CoV-2 N165A and N234A mutant · Open “up” wild-type · Salt bridges analysis · Hydrogen bonds analysis · Comparisons of mutant and wild-type

© The Author(s), under exclusive license to Springer Nature Switzerland AG 2023 J. Zhang, Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures, Springer Series in Biophysics 23, https://doi.org/10.1007/978-3-031-36773-1_10

359

360

10 Spike (S) Glycoprotein N165A and N234A Mutant

10.1 Introduction The SARS-CoV-2 spike utilizes a glycan shield to thwart the host immune response. In [55], Casalino et al. [55] revealed an essential structural role of N-glycans at sites N165 and N234 in modulating the conformational dynamics of the spike’s receptorbinding domain (RBD), which is responsible for ACE2 recognition; and the authors showed that deletion of the glycans through N165A and N234A mutations significantly reduces binding to ACE2 as a result of the RBD conformational shift toward the “down” state. We have not found any structural bioinformatics on salt bridges (SBs) in [55]. This chapter will study the SBs of the mutant, compared with its wild-type, in the open “up” state.

10.2 Materials and Methods See [55] and its supporting information and Amaro Lab COVID-19 Data Sets at amarolab.ucsd.edu/covid19.php. The datasets are six replicas (where three are in 1000 ns and three are in 400 ns) of MD trajectories for full-length spike protein (with glycans) in the open state wild-type and N165A and N234A mutant, respectively. The models were built using the cryo-EM structure 6vsb.pdb as a reference. The spike has four chains: A (16–1273), RBD “UP,” B (16–1273), C (16–1273), and G (1–70); and segment names of ABC chains are AS1 (chain A, 16–685), RBD “UP,” AS2 (chain A, 686–1273), BS1 (chain B, 16–685), BS2 (chain B, 686–1273), CS1 (chain C, 16–685), and CS2 (chain C, 686–1273).

10.3 Results and Discussion Generally, we cannot see great differences of MD secondary structures between the mutant and the wild-type; but we see slight differences of MD secondary structures around the sites of mutations at residues 165 and 234 (Figs. 10.1 and 10.2, where the pink colors are .α-helices and the blue colors are .310 -helices). The MD RMSD performances are illuminated in Fig. 10.3, where the RMSD values are increasing from 0 to 45 Å during 1 .μs and within the last 100 ns the RMSD variations are within 5 Å. The MD RMSF performances are illuminated in Figs. 10.4 and 10.5. In Sect. 7.3.2, the 6VYB-spike-open-model structure and the 6VXX-AchainOptimized structure have SBs ASP820-ARG815, ASP578-ARG328, ASP820LYS811, ASP442-ARG509, ASP467-ARG454, ASP53-LYS195, ASP663LYS310, GLU583-LYS535, ASP775-LYS733, GLU773-ARG1019, GLU773ARG1014, GLU340-LYS356, ASP574-LYS557, ASP574-LYS854, ASP40ARG44, GLU1031-ARG1039, GLU1031-LYS1038, GLU725-LYS1028, ASP1084-

10.3 Results and Discussion

361

Fig. 10.1 The secondary structure changes around the residue 165 for A, B, and C chains (for each chain, the left is for the mutant, and the right is for the wild-type) of the 6vsb-open-N165Aand-N234A-mutant model (T, Turn; E, Extended conformation; B, isolated Bridge; H, .α-Helix; G, .310 -helix; I, .π -helix; C, Coil)

Fig. 10.2 The secondary structure changes around the residue 234 for A, B, and C chains (for each chain, the left is for the mutant, and the right is for the wild-type) of the 6vsb-open-N165Aand-N234A-mutant model (T, Turn; E, Extended conformation; B, isolated Bridge; H, .α-Helix; G, .310 -helix; I, .π -helix; C, Coil)

LYS1086, ASP571-ARG567, ASP405-ARG403, GLU465-ARG457, GLU191ARG34 ASP389-LYS528, ASP398-ARG355, GLU324-LYS537, GLU96-ARG190, and ASP228-LYS202. Our analyses of the MD datasets of [55] can confirm all the above SBs (Tables 10.1 and 10.2, where A, B, and C stand for the three chains

362

10 Spike (S) Glycoprotein N165A and N234A Mutant

Fig. 10.3 The RMSD-time (Å-ns) graphs for the six replicas’ MD data of [55] for the N165A and N234A mutant and the wild-type (the left graph is for the mutant, and the right graph is for the wild-type; series1 to series6 are for replicas 1–6, respectively)

Fig. 10.4 The RMSF graphs for the six replicas’ MD data of [55] for the N165A and N234A mutant and the wild-type (the up six graphs are for the mutant, and the down six graphs are for the wild-type; x-axis (from up to down), 0–100 ns (replicas 1–3) or 0–40 ns (replicas 4–6); y-axis, residue numbers 16–1273)

Fig. 10.5 The RMSF graphs around the mutation sites 165 and 234 for the six replicas’ MD data of [55] for the N165A and N234A mutant and the wild-type (the left six graphs are for the mutant, and the right six graphs are for the wild-type; up, for the mutation site at 165; down, for the mutation site at 234)

of the spike, “A” means the SB is within A chain, and “A-B” means the SB is within neither A chain nor B chain but between A chain and B chain) for both the N165A and N234A mutant and the wild-type. Tables 10.1 and 10.2 tell us that for these SBs, there is no great difference between the mutant and the wild-type; this

10.3 Results and Discussion

363

is because the mutations N165A and N234A are changing the polar residue ASN into the strictly hydrophobic residue ALA, where ASN and ALA are not charged residues. Figure 10.6 illuminates SBs between GLU1031 and ARG1039 of the mutant and the wild-type in the 12 MD replicas; for the mutant, SB GLU1031-ARG1039 is always maintained within A, B, and C, respectively, for all replicas (for replica 4, the mutant is with HBs BS2:ARG1039.NE-BS2:GLU1031.OE2 69.05% and CS2:ARG1039.NE-CS2:GLU1031.OE2 64.29%) and between C chain and B chain for replicas 3 and 6; for the wild-type, SB GLU1031-ARG1039 is always maintained within C chain for replicas 1 and 3–5; for the wild-type MD replica 2, during 0–680 ns, SB GLU1031-ARG1039 is maintained between C chain and B chain, and during 680–1000 ns, SB GLU1031-ARG1039 is maintained within C chain; and for the wild-type MD replica 6, SB GLU1031-ARG1039 is maintained between B chain and A chain and between C chain and B chain. All in all, SB GLU1031-ARG1039 is strongly maintained within or among A, B, and C chains of the spike in CH-CD regions; SB GLU1031-LYS1038 has similar property but is weaker than SB GLU1031-ARG1039. Let us see another two SBs ASP442-ARG509 and ASP398-ARG355 in the receptor-binding domain (RBD, 330–530) of spike. Figure 10.7 tells us SB ASP442ARG509 always exists within A chain and B chain, respectively (where for B chain, mutant replica 4, wild replica 5, and wild replica 3 are without the SB); in Table 10.3, the HBs between ASP442 and ARG509 are very strong. Figure 10.8 tells us SB ASP398-ARG355 always exists within C chain; within A chain, SB ASP398ARG355 always exists for the wild-type, but for the mutant, it is not always existing for MD replica 2 (120–710 ns) and 4 (0–120 ns). In Table 10.3, within C chain furin cleavage site S1 (CS1), the HBs between ASP398 and ARG355 are always strong. SBs GLU725-LYS1028, ASP53-LYS195, ASP775-LYS733 (with strong HB A/BS2:LYS733.NZ-A/BS2:ASP775.OD2 63.41%/62.38%/60.58%), and ASP578ARG328 (replica 6) are always 100% existing within A, B, and C chains, respectively, whether for the mutant or for the wild-type (Figs. 10.9, 10.10, 10.11, and 10.12), where residue LYS1028 is in the central helix (CH, 987–1034) region and ASP53-LYS195 are within the N-terminal domain (NTD, 16–291). Table 10.3 tells us HBs between ASP578 and ARG328 are strong (where ARG328 is in RBD), and we also find new strong HBs GLU1031-THR1027 and GLU725-PHE1062 are within each chain. We list, in Tables 10.4, 10.5, 10.6, and 10.7, all the HBs with more than 60% occupancy rates of the N165A and N234A mutant and its wildtype from the analyses of the 1 .μs’ (replicas 1–3) or 400 ns’ (replicas 4–6) MD trajectories of [55]. Around residues 165 and 234, the mutant has new HBs CS1:ALA163.N-CS1:GLU132.O 60.78% (replica 3), CS1:ALA163.NCS1:GLU132.O 71.43% (replica 6), CS1:VAL130.N-CS1:GLU169.OE2 66.67% (replica 1) (its wild-type has BS1:VAL130.N-BS1:PHE168.O 60.98% (replica 4)), and CS1:TYR396.OH-AS1:PRO230.O 64.36% (replica 1). At residue PHE238, it seems that the mutant has stronger HBs than its wild-type: the mutant has HBs BS1:LEU84.N-BS1:PHE238.O 61.39% (replica 1), BS1:LEU84.N-BS1:PHE238.O

364

10 Spike (S) Glycoprotein N165A and N234A Mutant

69.05% (replica 4), AS1:LEU84.N-AS1:PHE238.O 69.05% (replica 6), and BS1:LEU84.N-BS1:PHE238.O 61.9% (replica 6); but the wild-type only has HB AS1:LEU84.N-AS1:PHE238.O 60.98% (replica 1).

10.4 Concluding Remarks This chapter confirmed the SBs of Sect. 7.3.2 of the SARS-CoV-2 6VYBAchain-Optimized and 6VXX-Achain-Optimized structures. We can confirm the strong SBs GLU1031-ARG1039, ASP442-AEG509, ASP398-ARG355, GLU725LYS1028, ASP53-LYS195, ASP775-LYS733, and ASP578-ASP328 and can confirm GLU1031-ARG1039, ASP442-AEG509, ASP398-ARG355, and ASP578ASP328 are strong polar contacts. SBs GLU725-LYS1028, ASP53-LYS195, ASP775-LYS733 (with strong HB A/BS2:LYS733.NZ-A/BS2:ASP775.OD2), and ASP578-ARG328 (replica 6) are always 100% existing within A, B, and C chains, respectively, whether for the mutant or for the wild-type. We also find new strong HBs GLU1031-THR1027 and GLU725-PHE1062 are within each chain. However, we cannot say some differences between the 6vsb-open-N165A-and-N234A-mutant and its wild-type; this might be because the mutations N165A and N234A are changing the polar residue ASN into the strictly hydrophobic residue ALA and residues ASN and ALA are not charged residues. At last we show the SBs (Tables 10.8 and 10.9) and HBs (Table 10.10) of the 175 ns’ continuous MD trajectory of SARS-CoV-2 glycosylated spike opening [339], where we can confirm our findings above.

Supplementary Information

365

Supplementary Information

Fig. 10.6 The salt bridges between GLU1031 and ARG1039 of the mutant and the wild-type MD replicas 1–6 datasets [55] (left, mutant; right, wild-type; up to down, replica 1 to replica 6)

366

Fig. 10.6 (continued)

10 Spike (S) Glycoprotein N165A and N234A Mutant

Supplementary Information

367

Fig. 10.7 The salt bridges between ASP442 and ARG509 of the mutant and the wild-type MD replicas 1–6 datasets [55] (left, mutant; right, wild-type; up to down, replica 1 to replica 6), where for MD replica 6 within C chain of the wild-type, the SB is ASP442-ARG346 instead of ASP442ARG509

368

Fig. 10.7 (continued)

10 Spike (S) Glycoprotein N165A and N234A Mutant

Supplementary Information Table 10.1 Some SBs of the N165A and N234A mutant and its wild-type from the analyses of the 1 μs’ or 400 ns’ (6 replicas) MD trajectories of [55]

369 SBs

Rep.

SBs of mutant

SBs of wild-type

ASP820-ARG815

1

A, B, C

A, B, C

2

ASP820-LYS811

A, B, C A, B, C

A, B, C

A, B

A, C

5

A, B, C

A, B, C

6

A, B, C

A, B, C

1 2

B

3

A, B

4

B, C

5 6 ASP578-ARG328

ASP442-ARG509

ASP467-ARG454

1

ASP663-LYS310

GLU583-LYS535

GLU773-ARG1019

A, B, C

A, B, C

A, B, C

A, B, C

A, B, C

4

A, B, C

A, B, C

5

A, B, C

A, B, C

6

A, B, C

A, B, C

1

A, B, C

A, B, C

2

A, B, C

A, B, C

3

A, B, C

A, B, C

4

A, B, C

A, B, C

5

A, B, C

A, B, C

6

A, B, C

A, B

1

B, C

B, C

B, C

B, C

3

A, C

B, C

4

C

B, C

5

B, C

B, C

6

B, C

B, C

1

A, B, C

A, B, C

2

A, B, C

A, B, C

3

A, B, C

A, B, C

4

A, B, C

A, B, C

5

A, B, C

A, B, C

6

A, B, C

A, B, C

1

A, B, C

A, B, C

2

A, B, C

A, B, C

3

A, B, C

A, B, C

4

A, B, C

A, B, C

5

A, B, C

A, B, C

6

A, B

A, B, C

1

A, B, C

A, B, C

2

A, B, C

A, B, C

3

A, B, C

A, B, C

4

A, B, C

A, B, C

5

A, B, C

A, B, C

A, B, C

A, B, C

1

A, B, C

A, B, C

2

A, B, C

A, B, C

3

A, B, C

A, B, C

4

A, B, C

A, B, C

5

A, B, C

A, B, C

6

A, B, C

A, B, C

1

A, B, C

A, B, C

2

B, C

A, B, C

3

A, B, C

A, B, C

4

B

B

5 GLU773-ARG1014

A, B, C

B

2

6 ASP775-LYS733

B A

3

2

ASP53-LYS195

A, B, C

3 4

A, C

A, C

6

A

B

1

B-A

2

B-A

B-A

3

A-C

A-C

4

B-A

5

B-A

A-C, B-A

6

(continued)

370

10 Spike (S) Glycoprotein N165A and N234A Mutant

Table 10.1 (continued)

SBs

Rep.

SBs of mutant

SBs of wild-type

GLU340-LYS356

1

A, B, C

A, B, C

2

ASP574-LYS557

ASP574-LYS854

A, B, C

A, B, C

3

B,C

A, B, C

4

A, B, C

A, C

5

A, B, C

A, B, C

6

B, C

A, B, C

1

A, B, C

A, B, C

2

A, B, C

A, B, C

3

A, B, C

A, B, C

4

A, B, C

A, B, C

5

A, B, C

A, B, C

6

A, B, C

B, C

2

A-B, C-A

C

3

A

4

B-C

5

A-B, C-A

1

6 ASP40-ARG44

Table 10.2 Some SBs of the N165A and N234A mutant and its wild-type from the analyses of the 1 μs’ or 400 ns’ (6 replicas) MD trajectories of [55] (continuation)

C-A, B-C

1

A, B, C

A, B, C

2

A, B, C

A, B, C

3

A, B, C

A, B, C

4

A, C

A, B, C

5

A, B, C

A, B, C

6

A, B, C

A, B, C

SBs

Rep.

SBs of mutant

SBs of wild-type

GLU1031-ARG1039

1

A, B, C, A-B, A-C, B-A, C-B

A, B, C, A-B, A-C, B-A, C-B

2

A, B, C, A-C, B-A, C-B

A, B, C, A-B, A-C, B-A, C-B

3

A, B, C, A-C, B-A, C-B

A, B, C, A-C, B-A, C-B

4

GLU1031-LYS1038

A, B, C, B-A, C-B

A, B, C, A-C

5

A, B, C, A-B, A-C, B-A

A, B, C, A-B, B-A, C-B

6

A, B, C, A-C, B-A, B-C, C-B

A, C, A-C, B-A, C-B A, A-C, B-A

1

A, B-A, C-A

2

A, C-A

3

B

5

A, B-A, C-A A, B-A

4 C, A-C

6 GLU725-LYS1028

1

A, B, C

A, B, C

2

A, B, C

A, B, C

3

A, B, C

A, B, C

4

A, B, C

A, B, C

5 ASP1084-LYS1086

ASP571-ARG567

A, B, C

A, B, C

A, B, C

A, B, C

A, B, C

2

A, B, C

A, B, C

3

A, B

B, C

4

A, B, C

A, C

5

A, B, C

B, C

6

B, C

A, B, C

1

A, B, C

A, B, C

2

A, B, C

B, C

3

A, C

A, B, C

4

ASP405-ARG403

A, B, C

6 1

A, B, C

C

5

A, B, C

B, C

6

A, C

C

1

A, B, C

A, B, C

2

A, B, C

A, B, C

3

A, B, C

A, B, C

4

A, B, C

A, C

5

A, B, C

A, B

6

A, C

B, C

(continued)

Supplementary Information Table 10.2 (continued)

371 SBs

Rep.

SBs of mutant

SBs of wild-type

GLU465-ARG457

1

A, C

B, C

2

B, C

A, C

3

A, C

A, C

4

A

C

5

B

A, C

6

A, C

A, C

1

A, B, C

A, B, C

2

A, B

A, B, C

3

A, B, C

A, B, C

4

A, B, C

A, B, C

5

A, B, C

A, B, C

6

A, B, C

A, B, C

1

A, B, C

A, B, C

2

A, B, C

A, B, C

3

A, B, C

A, B, C

4

A, B, C

A, B, C

5

A, B, C

A, B, C

6

B, C

B, C

1

A, B, C

A, B, C

2

A, B, C

A, B, C

3

A, B, C

A, B, C

4

A, B, C

A, B, C

5

A, B, C

A, B, C

6

A, B, C

A, B, C

1

B, C

C

2

A

B, C

3

B, C

A, C

4

A

5

A

A

6

B, C

B, C

1

A

A

2

A

A

3

A

A

4

A

A

5

A

A

GLU191-ARG34

ASP389-LYS528

ASP398-ARG355

GLU324-LYS537

GLU96-ARG190

A

6 ASP228-LYS202

1

A, B

A, B

2

A, B

A, B, C

3

A, B

A, B

4

A, B

A, B

5

A, B

A, B

6

A, B

A, B, C

Wild

Mutant

AS1:TYR451.OH-AS1:ASP442.OD1 64.29% AS1:SER438.OG-AS1:ASP442.OD2 64.29%

BS2:SER1037.OG-BS2:GLU1031.OE2 66.67%

CS2:ARG1039.NE-CS2:GLU1031.OE2 64.29%

AS1:SER438.OG-AS1:ASP442.OD1 60.98%

AS2:GLU1031.N-AS2:THR1027.O 60.98%

AS1:PHE347.N-AS1:ASP442.OD2 60.98%

AS1:ARG509.NE-AS1:ASP442.OD1 75.61% BS1:ARG509.NH2-BS1:ASP442.OD1 63.41%

BS2:GLU1031.N-BS2:THR1027.O 68.29%

Rep6

BS1:ARG509.NH2-BS1:ASP442.OD2 65.85% AS1:ARG509.NE-AS1:ASP442.OD1 60.98%

CS2:GLU1031.N-CS2:THR1027.O 73.17%

CS2:SER1037.OG-CS2:GLU1031.OE1 60.98%

Rep5

BS1:ARG509.NH1-BS1:ASP442.OD1 78.05% AS1:ARG509.NE-AS1:ASP442.OD1 75.61% AS1:TYR451.OH-AS1:ASP442.OD2 65.85%

AS2:GLU1031.N-AS2:THR1027.O 64.36%

BS2:GLU1031.N-BS2:THR1027.O 70.73%

CS2:GLU1031.N-CS2:THR1027.O 63.41%

Rep3

Rep4

AS2:GLU1031.N-AS2:THR1027.O 61.39%

AS1:ARG509.NH2-AS1:ASP442.OD2 68.32% AS1:ARG509.NE-AS1:ASP442.OD1 62.38%

CS2:GLU1031.N-CS2:THR1027.O 64.36%

BS2:GLU1031.N-BS2:THR1027.O 62.38%

Rep2

BS1:ASN354.N-BS1:ASP398.OD2 68.29%

CS1:TYR423.OH-CS1:ASP398.OD2 68.29%

CS1:ARG355.NE-CS1:ASP398.OD1 85.37%

CS1:ARG355.NE-CS1:ASP398.OD2 60.98%

BS1:VAL512.N-BS1:ASP398.O 63.41%

AS1:VAL512.N-AS1:ASP398.O 65.85%

AS1:VAL512.N-AS1:ASP398.O 61.39%

BS1:VAL512.N-BS1:ASP398.O 63.37%

CS1:ARG355.NH2-CS1:ASP398.OD2 67.33%

CS1:ARG355.NE-CS1:ASP398.OD1 86.14%

CS1:ASP398.N-CS1:VAL512.O 60.4%

AS1:TYR451.OH-AS1:ASP442.OD1 66.34% AS1:ARG509.NE-AS1:ASP442.OD2 63.37%

BS1:VAL512.N-BS1:ASP398.O 66.34%

AS1:VAL512.N-AS1:ASP398.O 69.05%

AS1:VAL512.N-AS1:ASP398.O 70.73%

CS1:TYR423.OH-CS1:ASP398.OD2 73.17%

CS1:ARG355.NE-CS1:ASP398.OD1 75.61%

CS1:ARG355.NE-CS1:ASP398.OD1 61.9%

CS1:ASP398.N-CS1:VAL512.O 61.9%

BS1:VAL512.N-BS1:ASP398.O 64.29%

AS1:VAL512.N-AS1:ASP398.O 61.76%

AS1:SER438.OG-AS1:ASP442.OD2 71.29%

CS2:GLU1031.N-CS2:THR1027.O 66.67%

CS2:GLU1031.N-CS2:THR1027.O 61.39%

Rep6

Rep1

AS2:GLU1031.N-AS2:THR1027.O 82.93%

AS2:GLU1031.N-AS2:THR1027.O 61.9%

CS2:GLU1031.N-CS2:THR1027.O 64.29%

AS1:ARG509.NE-AS1:ASP442.OD2 80.95%

BS2:ARG1039.NE-BS2:GLU1031.OE2 69.05%

Rep5

Rep4

BS1:ARG509.NE-BS1:ASP442.OD2 66.67% BS1:ARG509.NH2-BS1:ASP442.OD1 61.76%

CS2:GLU1031.N-CS2:THR1027.O 68.63%

BS2:GLU1031.N-BS2:THR1027.O 63.73%

Rep3

CS1:ASP442.N-CS1:SER438.O 62.38%

CS1:ARG355.NH2-CS1:ASP398.OD2 61.39% AS1:VAL512.N-AS1:ASP398.O 61.39%

AS1:SER438.OG-AS1:ASP442.OD2 74.26%

AS2:GLU1031.N-AS2:THR1027.O 71.15%

ASP398-ARG355 CS1:ARG355.NE-CS1:ASP398.OD1 79.21%

AS1:ARG509.NH2-AS1:ASP442.OD1 65.35%

Rep2

ASP442-ARG509 AS1:ARG509.NE-AS1:ASP442.OD2 77.23%

BS2:GLU1031.N-BS2:THR1027.O 61.39%

Rep1

GLU1031-ARG1039

Table 10.3 The HBs of 7 strong SBs of the N165A and N234A mutant and its wild-type from the analyses of the 1 μs’ or 400 ns’ (6 replicas) MD trajectories of [55]

372 10 Spike (S) Glycoprotein N165A and N234A Mutant

Wild

Mutant

BS2:PHE1062.N-BS2:GLU725.O 60.78%

Rep3

Rep2

Rep6

Rep5

Rep4

Rep3

ASP578-ARG328

BS2:PHE1062.N-BS2:GLU725.O 70.73%

BS1:ARG328.NE-BS1:ASP578.OD1 60.98%

CS1:ASP578.N-CS1:GLU583.O 63.41%

CS1:ARG328.NH1-CS1:ASP578.OD2 70.73%

CS1:THR581.OG1-CS1:ASP578.OD1 85.37%

AS1:ASP578.N-AS1:GLU583.O 63.37%

AS1:ARG328.NE-AS1:ASP578.OD2 65.35%

BS1:ASP578.N-BS1:GLU583.O 60.4%

CS1:ASP578.N-CS1:GLU583.O 61.39%

AS1:ASP578.N-AS1:GLU583.O 63.37%

AS1:ASP578.N-AS1:GLU583.O 60.98%

CS1:ASP578.N-CS1:GLU583.O 68.29%

AS1:ASP578.N-AS1:GLU583.O 61.54%

CS1:ARG328.NH2-CS1:ASP578.OD2 64.36%

CS1:THR581.OG1-CS1:ASP578.OD2 74.26%

CS1:ARG328.NE-CS1:ASP578.OD1 76.24%

CS1:ARG328.NH2-CS1:ASP578.OD1 75.61%

AS2:LYS733.NZ-AS2:ASP775.OD2 63.41%

BS2:LYS733.NZ-BS2:ASP775.OD2 62.38%

BS2:LYS733.NZ-BS2:ASP775.OD2 60.58%

ASP775-LYS733

BS2:PHE1062.N-BS2:GLU725.O 73.17%

AS1:ARG273.N-AS1:ASP53.O 60.98%

CS1:ARG273.N-CS1:ASP53.O 60.98%

ASP53-LYS195

CS2:PHE1062.N-CS2:GLU725.O 68.29%

BS2:PHE1062.N-BS2:GLU725.O 60.4%

BS2:PHE1062.N-BS2:GLU725.O 66.67%

Rep6

Rep1

AS2:PHE1062.N-AS2:GLU725.O 65.85%

Rep5

Rep4

AS2:PHE1062.N-AS2:GLU725.O 75%

Rep2

GLU725-LYS1028

CS2:PHE1062.N-CS2:GLU725.O 63.37%

Rep1

Supplementary Information 373

374

10 Spike (S) Glycoprotein N165A and N234A Mutant

Fig. 10.8 The salt bridges between ASP398 and ARG355 of the mutant and the wild-type MD replicas 1–6 datasets [55] (left, mutant; right, wild-type; up to down, replica 1 to replica 6)

Supplementary Information

Fig. 10.8 (continued)

375

376

10 Spike (S) Glycoprotein N165A and N234A Mutant

Fig. 10.9 The salt bridges between GLU725 and LYS1028 of the mutant and the wild-type MD replicas 1–6 datasets [55] (left, mutant; right, wild-type; up to down, replica 1 to replica 6)

Supplementary Information

Fig. 10.9 (continued)

377

378

10 Spike (S) Glycoprotein N165A and N234A Mutant

Fig. 10.10 The salt bridges between ASP53 and LYS195 of the mutant and the wild-type MD replicas 1–6 datasets [55] (left, mutant; right, wild-type; up to down, replica 1 to replica 6)

Supplementary Information

Fig. 10.10 (continued)

379

380

10 Spike (S) Glycoprotein N165A and N234A Mutant

Fig. 10.11 The salt bridges between ASP775 and LYS733 of the mutant and the wild-type MD replicas 1–6 datasets [55] (left, mutant; right, wild-type; up to down, replica 1 to replica 6)

Supplementary Information

381

Fig. 10.11 (continued)

Fig. 10.12 The salt bridges between ASP578 and ARG328 of the mutant and the wild-type MD replica 6 datasets [55] (left, mutant; right, wild-type)

382

10 Spike (S) Glycoprotein N165A and N234A Mutant

Table 10.4 The HBs with more than 60% occupancy rates of the N165A and N234A mutant from the analyses of the 1 μs’ (replicas 1–3) MD trajectories of [55] Replica 1

Replica 2

Replica 3

CS1:ARG355.NE-CS1:ASP398.OD1 79.21%

AS1:LEU585.N-AS1:VAL576.O 79.81%

BS1:ARG457.N-BS1:ASP420.OD1 77.45%

CS1:LEU585.N-CS1:VAL576.O 78.22%

BS1:TYR91.N-BS1:GLY268.O 76.92%

CS2:SER1051.OG-CS2:HSE1064.ND1 76.47%

AS1:ARG509.NE-AS1:ASP442.OD2 77.23%

AS1:ARG683.NH1-AS2:ASP950.OD1 76.92%

CS1:TYR91.N-CS1:GLY268.O 74.51%

BS1:VAL511.N-BS1:ILE434.O 77.23%

AS2:PHE1062.N-AS2:GLU725.O 75%

AS1:VAL511.N-AS1:ILE434.O 74.51%

CS1:ARG328.NE-CS1:ASP578.OD1 76.24%

AS1:LEU277.N-AS1:HSE49.O 74.04%

BS1:PHE106.N-BS1:LEU117.O 74.51%

AS1:LEU118.N-AS1:LYS129.O 75.25%

BS1:VAL511.N-BS1:ILE434.O 73.08%

BS1:PHE43.N-AS1:PHE565.O 73.53%

CS1:LEU277.N-CS1:HSE49.O 74.26%

CS1:TYR380.N-CS1:GLY431.O 72.12%

AS1:LEU585.N-AS1:VAL576.O 73.53%

CS1:THR581.OG1-CS1:ASP578.OD2 74.26%

AS1:ARG34.NE-AS1:GLU191.OE1 72.12%

BS1:VAL511.N-BS1:ILE434.O 72.55%

AS1:SER438.OG-AS1:ASP442.OD2 74.26%

CS2:CYS1082.N-CS2:VAL1133.O 71.15%

BS1:ILE598.N-BS1:ALA609.O 71.57%

BS1:LEU118.N-BS1:LYS129.O 73.27%

AS2:GLU1031.N-AS2:THR1027.O 71.15%

BS1:LEU118.N-BS1:LYS129.O 70.59%

BS1:PHE43.N-AS1:PHE565.O 73.27%

AS1:TYR91.OH-AS1:GLU191.OE1 71.15%

AS1:LEU611.N-AS1:SER596.O 70.59%

BS1:ILE598.N-BS1:ALA609.O 72.28%

CS1:ILE598.N-CS1:ALA609.O 71.15%

BS2:TYR695.OH-BS1:GLU661.O 69.61%

AS1:LEU611.N-AS1:SER596.O 72.28%

AS2:MET902.N-AS2:PHE898.O 70.19%

AS1:TYR91.N-AS1:GLY268.O 69.61%

BS1:TYR91.N-BS1:GLY268.O 72.28%

CS2:THR1066.N-CS2:SER721.O 70.19%

BS1:TYR508.N-BS1:ILE402.O 69.61%

AS1:TYR91.N-AS1:GLY268.O 72.28%

AS1:TYR91.N-AS1:GLY268.O 70.19%

CS1:ILE598.N-CS1:ALA609.O 69.61%

AS2:SER1051.OG-AS2:HSE1064.ND1 72.28%

BS1:TRP64.N-BS1:ALA27.O 70.19%

CS2:THR1066.OG1-CS2:LYS1045.O 68.63%

AS2:ASN928.N-AS2:ALA924.O 71.29%

CS2:THR1066.OG1-CS2:LYS1045.O 69.23%

BS1:TYR266.N-BS1:ALA93.O 68.63%

AS1:LEU277.N-AS1:HSE49.O 70.3%

BS1:LEU118.N-BS1:LYS129.O 68.27%

CS2:GLU1031.N-CS2:THR1027.O 68.63%

BS1:TYR266.N-BS1:ALA93.O 70.3%

AS1:LEU611.N-AS1:SER596.O 67.31%

BS1:ARG454.N-BS1:ASN422.OD1 67.65%

AS1:LEU585.N-AS1:VAL576.O 70.3%

BS1:CYS336.N-BS1:VAL362.O 67.31%

BS1:LEU611.N-BS1:SER596.O 67.65%

BS1:VAL551.N-BS1:THR588.O 70.3%

AS1:LEU118.N-AS1:LYS129.O 67.31%

AS1:LEU277.N-AS1:HSE49.O 67.65%

CS2:SER1051.OG-CS2:HSE1064.ND1 69.31%

AS1:VAL511.N-AS1:ILE434.O 67.31%

AS1:GLN271.N-AS1:PHE55.O 67.65%

AS1:THR323.N-AS1:CYS538.O 69.31%

BS2:THR1077.OG1-BS2:PHE1095.O 66.35%

AS2:ASN928.N-AS2:ALA924.O 66.67%

AS1:PHE106.N-AS1:LEU117.O 69.31%

CS2:ASN928.N-CS2:ALA924.O 66.35%

CS1:LEU277.N-CS1:HSE49.O 66.67%

BS1:ILE434.N-BS1:VAL511.O 69.31%

BS2:THR883.OG1-BS2:ALA879.O 66.35%

BS2:THR1066.OG1-BS2:LYS1045.O 66.67%

BS2:SER1051.OG-BS2:HSE1064.ND1 68.32%

AS1:ILE598.N-AS1:ALA609.O 66.35%

BS1:ARG509.NE-BS1:ASP442.OD2 66.67%

BS1:ILE651.N-BS1:VAL610.O 68.32%

AS1:TYR37.OH-AS1:LEU54.O 66.35%

AS1:PHE543.N-AS1:LEU546.O 66.67%

CS1:TYR91.OH-CS1:GLU191.OE2 68.32%

BS1:ILE358.N-BS1:VAL395.O 66.35%

AS1:PHE106.N-AS1:LEU117.O 66.67%

AS2:LEU1063.N-AS2:PHE1052.O 68.32%

CS1:CYS671.N-CS2:TYR695.O 66.35%

CS1:TRP64.N-CS1:ALA27.O 66.67%

AS2:ALA879.N-AS2:SER875.O 67.33%

BS1:ILE598.N-BS1:ALA609.O 65.38%

CS2:CYS1082.N-CS2:VAL1133.O 65.69%

AS1:ILE587.N-AS1:ASP574.O 67.33%

CS1:LEU611.N-CS1:SER596.O 65.38%

CS2:ASN928.N-CS2:ALA924.O 65.69%

CS1:VAL511.N-CS1:ILE434.O 67.33%

AS2:ARG1019.NH1-AS2:ASN777.OD1 65.38%

BS2:GLN1054.N-BS2:VAL1061.O 65.69%

AS2:THR1066.OG1-AS2:LYS1045.O 66.34%

CS1:PHE275.N-CS1:THR51.O 65.38%

AS1:LEU650.N-AS1:PHE643.O 65.69%

BS1:TYR612.N-BS1:CYS649.O 66.34%

CS2:PHE1089.N-CS2:PHE1121.O 64.42%

BS1:VAL127.N-BS1:VAL120.O 65.69%

CS1:ILE587.N-CS1:ASP574.O 66.34%

BS1:PHE106.N-BS1:LEU117.O 64.42%

BS1:TYR37.OH-BS1:LEU54.O 65.69%

AS2:VAL1008.N-AS2:LEU1004.O 66.34%

CS1:VAL62.N-CS1:THR29.O 64.42%

AS1:TYR313.N-AS1:VAL597.O 65.69%

CS1:SER94.OG-CS1:ALA264.O 66.34%

BS2:THR1066.OG1-BS2:LYS1045.O 64.42%

BS2:ASN777.N-BS2:GLU773.O 64.71%

BS1:ARG44.NH2-BS1:ASP40.OD1 66.34%

AS1:ARG683.NH2-AS2:ASP950.OD2 64.42%

BS1:VAL551.N-BS1:THR588.O 64.71%

BS2:THR1077.OG1-BS2:PHE1095.O 65.35%

BS2:ASN777.N-BS2:GLU773.O 63.46%

CS1:TYR508.N-CS1:ILE402.O 64.71%

CS1:ILE128.N-CS1:TYR170.O 65.35%

CS1:LEU277.N-CS1:HSE49.O 63.46%

BS1:LEU585.N-BS1:VAL576.O 64.71%

CS1:LEU513.N-CS1:CYS432.O 65.35%

AS1:LYS202.N-AS1:LYS195.O 63.46%

AS1:LEU118.N-AS1:LYS129.O 64.71%

AS1:ARG509.NH2-AS1:ASP442.OD1 65.35%

AS1:PHE106.N-AS1:LEU117.O 63.46%

BS2:GLU1031.N-BS2:THR1027.O 63.73%

BS1:TYR380.N-BS1:GLY431.O 65.35%

AS2:SER1051.OG-AS2:HSE1064.ND1 62.5%

BS1:TYR313.OH-BS1:GLU309.O 63.73%

BS2:ALA879.N-BS2:SER875.O 64.36%

AS2:PHE1052.N-AS2:LEU1063.O 62.5%

BS1:TYR91.N-BS1:GLY268.O 63.73%

AS1:TYR612.N-AS1:CYS649.O 64.36%

AS2:ASN777.N-AS2:GLU773.O 62.5%

CS2:THR883.OG1-CS2:ALA879.O 63.73%

AS1:LEU229.N-AS1:PHE201.O 64.36%

AS2:HSD1088.N-AS2:ILE1081.O 62.5%

BS2:SER1051.OG-BS2:HSE1064.ND1 63.73%

AS2:TYR695.N-AS1:CYS671.O 64.36%

BS1:PHE194.N-BS1:VAL90.O 62.5%

BS1:ILE587.N-BS1:ASP574.O 63.73%

AS1:TYR37.OH-AS1:LEU54.O 64.36%

BS2:LEU1218.N-BS2:TRP1214.O 62.5%

BS1:CYS336.N-BS1:VAL362.O 63.73%

CS1:ARG328.NH2-CS1:ASP578.OD2 64.36%

CS2:ASN777.N-CS2:GLU773.O 62.5%

BS2:VAL1061.N-BS2:GLN1054.O 62.75%

AS1:ILE598.N-AS1:ALA609.O 64.36%

CS2:ARG1019.NH1-CS2:ASN777.OD1 62.5%

CS1:TYR37.OH-CS1:LEU54.O 62.75%

AS1:VAL433.N-AS1:LYS378.O 64.36%

AS2:THR1077.OG1-AS2:PHE1095.O 62.5%

BS2:THR1066.N-BS2:SER721.O 62.75%

CS1:TYR396.OH-AS1:PRO230.O 64.36%

CS2:THR883.OG1-CS2:ALA879.O 61.54%

AS2:THR1066.OG1-AS2:LYS1045.O 62.75%

BS2:THR1066.OG1-BS2:LYS1045.O 63.37%

BS1:TYR313.N-BS1:VAL597.O 61.54%

BS1:TYR612.N-BS1:CYS649.O 62.75%

CS2:PHE1062.N-CS2:GLU725.O 63.37%

BS1:LEU611.N-BS1:SER596.O 61.54%

BS1:ASN460.N-BS1:ASP420.OD2 62.75%

BS2:TYR695.OH-BS1:GLU661.O 63.37%

BS1:LEU585.N-BS1:VAL576.O 61.54%

BS2:VAL1096.N-BS2:PHE1103.O 62.75%

BS1:LEU650.N-BS1:PHE643.O 63.37%

BS1:TYR380.N-BS1:GLY431.O 61.54%

CS1:ARG44.NH2-CS1:ASP40.OD2 62.75%

BS1:LEU223.N-BS1:VAL36.O 63.37%

BS1:VAL127.N-BS1:VAL120.O 61.54%

BS1:LEU223.N-BS1:VAL36.O 62.75%

BS1:LEU585.N-BS1:VAL576.O 62.38%

CS1:VAL511.N-CS1:ILE434.O 61.54%

CS1:TYR380.N-CS1:GLY431.O 62.75%

BS1:TYR37.OH-BS1:LEU54.O 62.38%

AS1:TYR266.N-AS1:ALA93.O 61.54%

BS1:ARG44.NH2-BS1:ASP40.OD2 62.75%

BS1:VAL127.N-BS1:VAL120.O 62.38%

AS1:CYS336.N-AS1:VAL362.O 61.54%

AS1:LYS202.N-AS1:LYS195.O 61.76%

AS2:THR1077.OG1-AS2:PHE1095.O 62.38%

CS2:TYR1067.N-CS2:TYR1047.O 61.54%

BS1:ARG509.NH2-BS1:ASP442.OD1 61.76%

(continued)

Supplementary Information

383

Table 10.4 (continued) Replica 1

Replica 2

Replica 3

BS1:TYR313.OH-BS1:GLU309.O 62.38%

AS1:ASP578.N-AS1:GLU583.O 61.54%

AS1:VAL512.N-AS1:ASP398.O 61.76%

CS1:ASP442.N-CS1:SER438.O 62.38%

AS2:THR1066.OG1-AS2:LYS1045.O 60.58%

BS2:PHE1075.N-BS2:ILE712.O 61.76%

BS2:GLU1031.N-BS2:THR1027.O 61.39%

CS2:SER1051.OG-CS2:HSE1064.ND1 60.58%

AS1:VAL127.N-AS1:VAL120.O 61.76%

BS2:ASN777.N-BS2:GLU773.O 61.39%

BS2:LYS733.NZ-BS2:ASP775.OD2 60.58%

AS1:ILE598.N-AS1:ALA609.O 61.76%

AS1:PHE543.N-AS1:LEU546.O 61.39%

AS1:PHE275.N-AS1:THR51.O 60.58%

CS1:VAL551.N-CS1:THR588.O 61.76%

CS1:TYR91.N-CS1:GLY268.O 61.39%

CS1:TYR91.N-CS1:GLY268.O 60.58%

CS2:HSD1088.N-CS2:ILE1081.O 60.78%

BS1:LEU84.N-BS1:PHE238.O 61.39%

BS1:LYS202.N-BS1:LYS195.O 60.58%

BS2:PHE1062.N-BS2:GLU725.O 60.78%

CS1:ARG355.NH2-CS1:ASP398.OD2 61.39%

BS2:ILE742.N-BS2:CYS738.O 60.58%

CS1:PHE275.N-CS1:THR51.O 60.78%

BS2:THR1231.OG1-BS2:ILE1227.O 61.39%

CS1:GLN271.N-CS1:PHE55.O 60.58%

BS1:LEU117.N-BS1:PHE106.O 60.78%

CS2:THR1077.OG1-CS2:PHE1095.O 61.39%

CS1:VAL362.N-CS1:ASN334.O 60.58%

BS1:TYR396.N-BS1:SER514.O 60.78%

BS2:ASN928.N-BS2:ALA924.O 61.39%

CS2:VAL1096.N-CS2:PHE1103.O 60.58%

AS1:ILE434.N-AS1:VAL511.O 60.78%

BS1:ILE587.N-BS1:ASP574.O 61.39%

AS1:LEU189.N-AS1:THR208.O 60.58%

CS1:ALA163.N-CS1:GLU132.O 60.78%

AS1:VAL512.N-AS1:ASP398.O 61.39% CS1:LEU611.N-CS1:SER596.O 60.4% BS1:VAL362.N-BS1:ASN334.O 60.4% AS1:VAL511.N-AS1:ILE434.O 60.4% BS1:LEU277.N-BS1:HSE49.O 60.4% AS1:PHE92.N-AS1:PHE192.O 60.4% BS1:TYR396.N-BS1:SER514.O 60.4% BS1:PHE275.N-BS1:THR51.O 60.4%

Table 10.5 The HBs with more than 60% occupancy rates of the N165A and N234A mutant from the analyses of the 400 ns’ (replicas 4–6) MD trajectories of [55] Replica 4

Replica 5

Replica 6

AS1:LEU650.N-AS1:PHE643.O 85.71%

CS1:TYR91.N-CS1:GLY268.O 90.24%

CS1:ARG646.NE-CS1:ASP614.OD1 85.71%

CS1:TYR38.OH-CS1:GLY283.O 85.71%

AS2:GLU1031.N-AS2:THR1027.O 82.93%

BS1:LEU611.N-BS1:SER596.O 80.95%

BS1:LEU585.N-BS1:VAL576.O 83.33%

AS1:ARG683.NH1-AS2:ASP950.OD1 82.93%

AS1:TYR313.OH-AS1:GLU309.O 78.57%

CS1:TYR91.OH-CS1:GLU191.OE1 80.95%

BS2:THR1077.OG1-BS2:PHE1095.O 82.93%

AS1:ARG44.NH2-AS1:ASP40.OD1 78.57%

AS1:ARG34.NE-AS1:GLU191.OE1 80.95%

AS1:LEU277.N-AS1:HSE49.O 80.49%

AS1:ARG357.NH2-AS1:GLU516.OE1 78.57%

AS1:ARG509.NE-AS1:ASP442.OD2 80.95%

CS1:ILE434.N-CS1:VAL511.O 80.49%

CS2:SER1051.OG-CS2:HSE1064.ND1 76.19%

AS1:ARG683.NH2-AS2:ASP950.OD2 80.95%

AS1:PHE106.N-AS1:LEU117.O 78.05%

BS2:THR1066.OG1-BS2:LYS1045.O 76.19%

BS1:TYR91.N-BS1:GLY268.O 78.57%

AS1:LEU611.N-AS1:SER596.O 75.61%

BS1:LEU118.N-BS1:LYS129.O 76.19%

AS1:VAL511.N-AS1:ILE434.O 78.57%

CS1:ARG355.NE-CS1:ASP398.OD1 75.61%

AS1:LEU650.N-AS1:PHE643.O 73.81%

AS1:LEU277.N-AS1:HSE49.O 78.57%

CS1:TRP64.N-CS1:ALA27.O 75.61%

AS1:ILE598.N-AS1:ALA609.O 73.81%

AS2:THR887.OG1-AS2:SER884.O 76.19%

CS1:TYR380.N-CS1:GLY431.O 75.61%

AS1:TYR91.N-AS1:GLY268.O 73.81%

AS1:ARG683.NH1-AS2:ASP950.OD1 76.19%

CS2:THR1077.OG1-CS2:PHE1095.O 73.17%

BS1:PHE43.N-AS1:PHE565.O 73.81%

BS1:LEU611.N-BS1:SER596.O 76.19%

BS1:LEU585.N-BS1:VAL576.O 73.17%

AS1:VAL127.N-AS1:VAL120.O 73.81%

CS1:ARG646.NH2-CS1:ASP614.OD1 76.19%

BS1:VAL362.N-BS1:ASN334.O 73.17%

AS1:THR393.OG1-AS1:GLU516.OE1 73.81%

AS1:CYS336.N-AS1:VAL362.O 76.19%

AS1:CYS336.N-AS1:VAL362.O 73.17%

BS1:TYR508.N-BS1:ILE402.O 73.81%

BS1:VAL511.N-BS1:ILE434.O 76.19%

AS1:VAL551.N-AS1:THR588.O 73.17%

CS1:TYR508.N-CS1:ILE402.O 73.81%

BS1:VAL127.N-BS1:VAL120.O 76.19%

CS1:TYR423.OH-CS1:ASP398.OD2 73.17%

AS1:VAL511.N-AS1:ILE434.O 73.81%

CS2:SER1051.OG-CS2:HSE1064.ND1 73.81%

CS2:ASN928.N-CS2:ALA924.O 70.73%

AS1:PHE43.N-CS1:PHE565.O 73.81%

AS1:LEU611.N-AS1:SER596.O 73.81%

CS2:GLY885.N-CS2:GLY880.O 70.73%

CS2:VAL1068.N-CS2:THR719.O 71.43%

AS1:LEU585.N-AS1:VAL576.O 73.81%

CS2:TYR1067.N-CS2:TYR1047.O 70.73%

BS1:ILE598.N-BS1:ALA609.O 71.43%

CS1:TYR91.N-CS1:GLY268.O 73.81%

AS2:THR1066.OG1-AS2:LYS1045.O 70.73%

CS1:TYR91.N-CS1:GLY268.O 71.43%

CS1:TYR380.N-CS1:GLY431.O 73.81%

AS2:ASN777.N-AS2:GLU773.O 70.73%

CS1:ALA163.N-CS1:GLU132.O 71.43%

CS1:SER151.OG-CS1:TRP104.O 73.81%

CS1:LEU585.N-CS1:VAL576.O 70.73%

CS2:THR1066.OG1-CS2:LYS1045.O 69.05%

BS1:ILE128.N-BS1:TYR170.O 73.81%

BS1:TRP64.N-BS1:ALA27.O 70.73%

BS2:TYR695.OH-BS1:GLU661.O 69.05%

BS2:LEU1218.N-BS2:TRP1214.O 71.43%

BS1:PHE92.N-BS1:PHE192.O 70.73%

AS1:LEU611.N-AS1:SER596.O 69.05%

AS2:THR1066.N-AS2:SER721.O 71.43%

AS1:PHE194.N-AS1:VAL90.O 70.73%

BS1:TYR313.N-BS1:VAL597.O 69.05%

CS1:THR284.N-CS1:ASN280.OD1 71.43%

CS1:LEU513.N-CS1:CYS432.O 70.73%

BS1:TYR612.N-BS1:CYS649.O 69.05%

CS1:VAL551.N-CS1:THR588.O 71.43%

AS1:VAL512.N-AS1:ASP398.O 70.73%

AS1:ARG44.NH1-AS1:ASP40.OD2 69.05%

AS1:ARG34.NH2-AS1:GLU191.OE2 71.43%

CS2:PHE1089.N-CS2:PHE1121.O 70.73%

BS1:ILE587.N-BS1:ASP574.O 69.05%

AS1:TYR91.N-AS1:GLY268.O 71.43%

AS2:THR791.OG1-CS2:VAL705.O 70.73%

AS1:LEU84.N-AS1:PHE238.O 69.05%

CS1:VAL511.N-CS1:ILE434.O 71.43%

AS1:ARG685.NH2-AS2:ASP830.OD2 70.73%

AS1:LEU118.N-AS1:LYS129.O 69.05%

BS1:TYR380.N-BS1:GLY431.O 71.43%

CS1:VAL510.N-CS1:PHE400.O 70.73%

BS1:TYR266.N-BS1:ALA93.O 69.05%

AS1:PHE106.N-AS1:LEU117.O 71.43%

AS1:VAL511.N-AS1:ILE434.O 70.73%

BS1:LEU117.N-BS1:PHE106.O 69.05%

BS2:TYR1215.OH-CS2:ILE1210.O 69.05%

BS2:GLU1195.N-BS2:LYS1191.O 68.29%

BS1:CYS336.N-BS1:VAL362.O 69.05%

AS2:ASN928.N-AS2:ALA924.O 69.05%

AS2:HSD1088.N-AS2:ILE1081.O 68.29%

AS1:VAL512.N-AS1:ASP398.O 69.05%

AS2:THR1066.OG1-AS2:LYS1045.O 69.05%

AS1:TYR313.OH-AS1:GLU309.O 68.29%

BS1:TYR91.OH-BS1:GLU191.OE2 69.05%

AS2:SER1051.OG-AS2:HSE1064.ND1 69.05%

BS1:PHE43.N-AS1:PHE565.O 68.29%

BS1:ILE434.N-BS1:VAL511.O 69.05%

(continued)

384

10 Spike (S) Glycoprotein N165A and N234A Mutant

Table 10.5 (continued) Replica 4

Replica 5

Replica 6

BS2:ARG1039.NE-BS2:GLU1031.OE2 69.05%

BS1:VAL511.N-BS1:ILE434.O 68.29%

AS2:THR716.OG1-AS2:GLN1071.O 69.05%

AS2:VAL729.N-AS2:HSD1058.O 69.05%

AS1:ILE434.N-AS1:VAL511.O 68.29%

AS2:THR1231.OG1-AS2:ILE1227.O 66.67%

CS1:ARG646.NE-CS1:ASP614.OD2 69.05%

AS2:MET902.N-AS2:PHE898.O 68.29%

CS2:HSD1088.N-CS2:ILE1081.O 66.67%

BS1:LEU277.N-BS1:HSE49.O 69.05%

AS1:TYR91.N-AS1:GLY268.O 68.29%

AS2:THR1077.OG1-AS2:PHE1095.O 66.67%

CS1:ARG34.NH1-CS1:GLU191.OE1 69.05%

CS1:ASP578.N-CS1:GLU583.O 68.29%

AS2:TYR1067.N-AS2:TYR1047.O 66.67%

CS1:HSD69.N-CS1:PHE79.O 69.05%

AS1:PHE92.N-AS1:PHE192.O 68.29%

CS2:GLU1031.N-CS2:THR1027.O 66.67%

BS1:LEU84.N-BS1:PHE238.O 69.05%

AS2:SER1051.OG-AS2:HSE1064.ND1 68.29%

BS2:PHE1062.N-BS2:GLU725.O 66.67%

BS1:ILE119.N-BS1:TRP104.O 69.05%

CS1:ARG454.NE-CS1:ASP467.OD1 68.29%

BS2:ASP737.N-BS2:GLY857.O 66.67%

BS1:PHE106.N-BS1:LEU117.O 69.05%

AS2:ILE1221.N-AS2:TRP1217.O 65.85%

AS1:TYR266.N-AS1:ALA93.O 66.67%

BS1:CYS336.N-BS1:VAL362.O 69.05%

AS2:CYS1082.N-AS2:VAL1133.O 65.85%

AS1:VAL576.N-AS1:LEU585.O 66.67%

CS2:CYS1082.N-CS2:VAL1133.O 69.05%

CS2:PHE1075.N-CS2:ILE712.O 65.85%

CS1:TYR37.OH-CS1:LEU54.O 66.67%

CS2:ARG1039.NH1-AS2:SER1030.OG 69.05%

AS2:PHE1062.N-AS2:GLU725.O 65.85%

BS1:ILE326.N-BS1:ASN540.O 66.67%

AS1:TYR612.N-AS1:CYS649.O 69.05%

BS1:CYS671.N-BS2:TYR695.O 65.85%

CS1:TYR380.N-CS1:GLY431.O 66.67%

AS2:PHE1089.N-AS2:PHE1121.O 69.05%

AS2:ARG1019.NH1-AS2:ASN777.OD1 65.85%

BS1:VAL433.N-BS1:LYS378.O 66.67%

AS2:CYS1082.N-AS2:VAL1133.O 66.67%

AS1:LEU585.N-AS1:VAL576.O 65.85%

BS2:VAL1096.N-BS2:PHE1103.O 66.67%

AS2:MET902.N-AS2:PHE898.O 66.67%

AS1:TYR91.OH-AS1:GLU191.OE1 65.85%

CS1:VAL551.N-CS1:THR588.O 66.67%

BS2:THR1066.OG1-BS2:LYS1045.O 66.67%

AS1:TYR37.OH-AS1:LEU54.O 65.85%

CS1:ARG44.NH2-CS1:ASP40.OD2 66.67%

BS2:SER1037.OG-BS2:GLU1031.OE2 66.67%

AS1:LEU229.N-AS1:PHE201.O 65.85%

BS1:TYR91.N-BS1:GLY268.O 66.67%

BS2:TYR695.N-BS1:CYS671.O 66.67%

BS1:TYR380.N-BS1:GLY431.O 65.85%

AS2:THR883.OG1-AS2:ALA879.O 66.67%

AS1:TYR313.OH-AS1:GLU309.O 66.67%

BS1:CYS336.N-BS1:VAL362.O 65.85%

AS2:ASN777.N-AS2:GLU773.O 66.67%

CS1:LEU277.N-CS1:HSE49.O 66.67%

BS1:LEU118.N-BS1:LYS129.O 65.85%

BS2:ILE742.N-BS2:CYS738.O 66.67%

AS1:GLN271.N-AS1:PHE55.O 66.67%

AS1:LEU118.N-AS1:LYS129.O 65.85%

BS2:THR1077.OG1-BS2:PHE1095.O 64.29%

CS1:TYR269.OH-CS1:PRO85.O 66.67%

CS2:PHE1052.N-CS2:LEU1063.O 65.85%

CS2:ASN777.N-CS2:GLU773.O 64.29%

AS1:LEU241.N-AS1:GLY103.O 66.67%

AS1:ARG319.NH1-AS1:CYS590.O 65.85%

AS1:TYR313.N-AS1:VAL597.O 64.29%

CS1:VAL433.N-CS1:LYS378.O 66.67%

BS1:LYS202.N-BS1:LYS195.O 65.85%

AS1:PHE275.N-AS1:THR51.O 64.29%

CS1:VAL130.N-CS1:GLU169.OE2 66.67%

CS1:VAL362.N-CS1:ASN334.O 65.85%

CS1:ASN536.N-CS1:LEU552.O 64.29%

AS1:VAL551.N-AS1:THR588.O 66.67%

CS1:CYS671.N-CS2:TYR695.O 65.85%

AS1:PHE192.N-AS1:PHE92.O 64.29%

CS1:LEU585.N-CS1:VAL576.O 66.67%

AS1:PHE392.N-AS1:VAL524.O 65.85%

BS1:ARG44.NH2-BS1:ASP40.OD2 64.29%

BS1:VAL433.N-BS1:LYS378.O 66.67%

BS2:THR1238.OG1-BS2:LEU1234.O 63.41%

BS1:LEU585.N-BS1:VAL576.O 64.29%

BS1:LEU560.N-BS1:GLN563.OE1 66.67%

CS2:CYS1082.N-CS2:VAL1133.O 63.41%

AS1:LEU241.N-AS1:GLY103.O 64.29%

AS2:TYR1067.N-AS2:TYR1047.O 64.29%

BS2:VAL1096.N-BS2:PHE1103.O 63.41%

BS1:LEU223.N-BS1:VAL36.O 64.29%

AS2:ALA879.N-AS2:SER875.O 64.29%

AS2:PHE1075.N-AS2:ILE712.O 63.41%

CS1:VAL362.N-CS1:ASN334.O 64.29%

CS2:ARG1039.NE-CS2:GLU1031.OE2 64.29%

CS2:SER884.OG-CS2:LEU894.O 63.41%

AS1:PHE392.N-AS1:VAL524.O 64.29%

CS2:ILE788.N-BS2:ALA701.O 64.29%

CS2:THR883.OG1-CS2:ALA879.O 63.41%

BS1:VAL511.N-BS1:ILE434.O 64.29%

CS2:GLU1031.N-CS2:THR1027.O 64.29%

BS2:THR1066.N-BS2:SER721.O 63.41%

BS2:SER1051.OG-BS2:HSE1064.ND1 64.29%

CS2:TYR695.OH-CS1:GLU661.O 64.29%

AS2:PHE1052.N-AS2:LEU1063.O 63.41%

BS2:ALA879.N-BS2:SER875.O 64.29%

BS2:VAL729.N-BS2:HSD1058.O 64.29%

BS1:TYR612.N-BS1:CYS649.O 63.41%

BS1:LEU277.N-BS1:HSE49.O 64.29%

AS2:ASN777.N-AS2:GLU773.O 64.29%

CS1:GLN271.N-CS1:PHE55.O 63.41%

AS1:PHE92.N-AS1:PHE192.O 64.29%

BS1:PHE92.N-BS1:PHE192.O 64.29%

AS1:GLN271.N-AS1:PHE55.O 63.41%

CS1:LYS202.N-CS1:LYS195.O 64.29%

BS1:LEU118.N-BS1:LYS129.O 64.29%

CS1:PHE65.N-CS1:TYR265.O 63.41%

AS1:ILE128.N-AS1:TYR170.O 64.29%

AS1:LEU118.N-AS1:LYS129.O 64.29%

CS1:LYS202.N-CS1:LYS195.O 63.41%

AS1:TYR396.N-AS1:SER514.O 64.29%

BS2:CYP1241.N-BS2:CYS1236.O 64.29%

BS1:ILE358.N-BS1:VAL395.O 63.41%

AS2:MET1229.N-AS2:ILE1225.O 61.9%

CS1:ILE587.N-CS1:ASP574.O 64.29%

BS2:PHE802.N-BS2:LYS795.O 63.41%

AS2:PHE1089.N-AS2:PHE1121.O 61.9%

CS1:SER555.OG-CS1:ASP586.OD2 64.29%

CS1:TYR37.OH-CS1:LEU54.O 63.41%

AS2:LEU1034.N-AS2:MET1029.O 61.9%

BS1:ILE434.N-BS1:VAL511.O 64.29%

BS2:TYR695.OH-BS1:SER673.O 63.41%

BS2:ASN928.N-BS2:ALA924.O 61.9%

BS1:VAL512.N-BS1:ASP398.O 64.29%

CS2:ASP737.N-CS2:GLY857.O 63.41%

BS2:LEU1034.N-BS2:MET1029.O 61.9%

AS1:TYR451.OH-AS1:ASP442.OD1 64.29%

BS1:TYR91.N-BS1:GLY268.O 63.41%

CS2:LEU1063.N-CS2:PHE1052.O 61.9%

AS1:SER438.OG-AS1:ASP442.OD2 64.29%

CS1:LEU611.N-CS1:SER596.O 63.41%

BS2:GLN1054.N-BS2:VAL1061.O 61.9%

BS2:GLU1195.N-BS2:LYS1191.O 61.9%

BS1:CYS617.N-BS1:GLN644.OE1 63.41%

CS1:ALA668.N-AS2:PRO863.O 61.9%

AS2:VAL1096.N-AS2:PHE1103.O 61.9%

AS2:ASN928.N-AS2:ALA924.O 60.98%

AS1:CYS671.N-AS2:TYR695.O 61.9%

CS2:ALA879.N-CS2:SER875.O 61.9%

BS2:TYR1067.N-BS2:TYR1047.O 60.98%

CS1:ARG646.NH2-CS1:ASP614.OD2 61.9%

AS2:GLU1031.N-AS2:THR1027.O 61.9%

CS2:THR1066.N-CS2:SER721.O 60.98%

AS1:LEU277.N-AS1:HSE49.O 61.9%

AS2:ARG1019.NH1-AS2:ASN777.OD1 61.9%

AS2:THR883.OG1-AS2:ALA879.O 60.98%

CS2:ILE997.N-CS2:ILE993.O 61.9%

BS1:TYR313.N-BS1:VAL597.O 61.9%

AS2:ALA879.N-AS2:SER875.O 60.98%

AS1:PHE543.N-AS1:LEU546.O 61.9%

CS1:TYR313.N-CS1:VAL597.O 61.9%

CS2:LEU938.N-CS2:ILE934.O 60.98%

BS1:PHE92.N-BS1:PHE192.O 61.9%

AS2:SER1003.OG-AS2:GLY999.O 61.9%

CS1:TYR313.OH-CS1:GLU309.O 60.98%

BS1:LYS202.N-BS1:LYS195.O 61.9%

AS1:ARG567.NE-AS1:ASP571.OD2 61.9%

BS1:ILE598.N-BS1:ALA609.O 60.98%

BS1:TRP64.N-BS1:ALA27.O 61.9%

AS1:TYR266.N-AS1:ALA93.O 61.9%

AS1:ILE598.N-AS1:ALA609.O 60.98%

BS1:LEU84.N-BS1:PHE238.O 61.9%

BS1:ILE358.N-BS1:VAL395.O 61.9%

BS2:VAL1008.N-BS2:LEU1004.O 60.98%

CS2:THR1077.OG1-CS2:PHE1095.O 61.9%

AS1:ILE128.N-AS1:TYR170.O 61.9%

CS1:LEU277.N-CS1:HSE49.O 60.98%

BS2:VAL1061.N-BS2:GLN1054.O 61.9%

BS1:LEU117.N-BS1:PHE106.O 61.9%

CS1:ARG273.N-CS1:ASP53.O 60.98%

AS2:ALA1022.N-AS2:ILE1018.O 61.9%

CS1:ASP398.N-CS1:VAL512.O 61.9%

AS1:ARG34.NH2-AS1:GLU191.OE2 60.98%

AS1:PHE318.N-AS1:GLY593.O 61.9%

CS1:ARG355.NE-CS1:ASP398.OD1 61.9%

AS1:ARG44.NH2-AS1:ASP40.OD2 60.98%

BS1:TYR37.OH-BS1:LEU54.O 61.9%

CS1:VAL362.N-CS1:ASN334.O 61.9%

AS1:THR323.N-AS1:CYS538.O 60.98%

CS2:SER875.OG-CS2:ALA871.O 61.9%

CS1:CYS336.N-CS1:VAL362.O 61.9%

CS1:TYR269.OH-CS1:PRO85.O 60.98%

CS2:VAL729.N-CS2:HSD1058.O 61.9%

(continued)

Supplementary Information

385

Table 10.5 (continued) Replica 4

Replica 5

Replica 6

AS1:ILE434.N-AS1:VAL511.O 61.9%

BS1:ILE119.N-BS1:TRP104.O 60.98%

CS1:VAL597.N-CS1:TYR313.O 61.9%

BS2:VAL1104.N-BS2:GLN1113.O 61.9%

CS1:GLN493.N-CS1:TYR453.O 60.98%

CS1:PHE92.N-CS1:PHE192.O 61.9%

CS2:ASN928.N-CS2:ALA924.O 61.9%

AS2:VAL1096.N-AS2:PHE1103.O 60.98%

AS1:GLN493.N-AS1:TYR453.O 61.9%

BS1:ILE598.N-BS1:ALA609.O 61.9%

CS2:HSE1064.N-CS2:THR723.O 60.98%

CS1:LEU513.N-CS1:CYS432.O 61.9%

AS1:LEU189.N-AS1:THR208.O 61.9%

CS1:VAL511.N-CS1:ILE434.O 60.98%

BS2:ASN928.N-BS2:ALA924.O 61.9%

BS2:THR883.OG1-BS2:ALA879.O 60.98%

BS1:THR299.OG1-BS1:PRO295.O 61.9%

BS1:LEU611.N-BS1:SER596.O 60.98%

CS1:THR523.OG1-CS1:THR393.O 61.9%

AS1:ASP578.N-AS1:GLU583.O 60.98% BS1:PHE194.N-BS1:VAL90.O 60.98%

Table 10.6 The HBs with more than 60% occupancy rates of the wild-type from the analyses of the 1 μs’ (replicas 1–3) MD trajectories of [55] Replica 1

Replica 2

Replica 3

CS2:TYR695.OH-CS1:GLU661.O 77.23%

CS1:ARG355.NE-CS1:ASP398.OD1 86.14%

BS2:TYR695.OH-BS1:GLU661.O 78.22%

CS1:ASP420.N-CS1:GLY416.O 73.27%

AS1:ILE598.N-AS1:ALA609.O 80.2%

BS1:PHE43.N-AS1:PHE565.O 77.23%

BS1:ARG44.NH2-BS1:ASP40.OD2 73.27%

CS1:TYR351.OH-CS1:ASP467.OD2 78.22%

BS1:LEU118.N-BS1:LYS129.O 77.23%

BS2:SER1051.OG-BS2:HSE1064.ND1 72.28%

AS1:TYR37.OH-AS1:LEU54.O 76.24%

AS1:LEU277.N-AS1:HSE49.O 74.26%

CS2:SER1051.OG-CS2:HSE1064.ND1 72.28%

BS1:ARG567.NH2-CS2:ASP979.OD1 76.24%

BS1:TYR91.OH-BS1:GLU191.OE1 74.26%

AS1:LEU611.N-AS1:SER596.O 72.28%

BS2:TYR695.OH-BS1:GLU661.O 74.26%

CS1:TYR91.N-CS1:GLY268.O 74.26%

BS1:LYS202.N-BS1:LYS195.O 72.28%

BS2:SER1051.OG-BS2:HSE1064.ND1 73.27%

AS1:LEU118.N-AS1:LYS129.O 74.26%

BS1:ILE598.N-BS1:ALA609.O 71.29%

CS1:VAL511.N-CS1:ILE434.O 73.27%

BS1:VAL511.N-BS1:ILE434.O 74.26%

BS1:TYR91.N-BS1:GLY268.O 71.29%

BS1:ILE598.N-BS1:ALA609.O 72.28%

AS1:VAL511.N-AS1:ILE434.O 73.27%

AS1:PHE543.N-AS1:LEU546.O 71.29%

AS1:VAL127.N-AS1:VAL120.O 72.28%

BS2:SER1051.OG-BS2:HSE1064.ND1 73.27%

CS1:SER151.OG-CS1:TRP104.O 71.29%

BS1:LEU118.N-BS1:LYS129.O 72.28%

BS1:ILE598.N-BS1:ALA609.O 71.29%

CS1:ARG454.N-CS1:ASN422.OD1 71.29%

AS1:LEU513.N-AS1:CYS432.O 72.28%

BS1:LEU277.N-BS1:HSE49.O 70.3%

BS1:LEU611.N-BS1:SER596.O 71.29%

AS1:PHE43.N-CS1:PHE565.O 71.29%

BS1:LEU611.N-BS1:SER596.O 70.3%

AS1:SER438.OG-AS1:ASP442.OD2 71.29%

CS1:LEU585.N-CS1:VAL576.O 71.29%

CS1:VAL511.N-CS1:ILE434.O 70.3%

AS1:TYR37.OH-AS1:LEU54.O 70.3%

BS1:LEU611.N-BS1:SER596.O 71.29%

CS1:ILE598.N-CS1:ALA609.O 69.31%

CS1:VAL511.N-CS1:ILE434.O 70.3%

CS1:TYR37.OH-CS1:LEU54.O 71.29%

BS1:TYR508.N-BS1:ILE402.O 69.31%

BS2:TYR695.OH-BS1:GLU661.O 69.31%

CS1:PHE275.N-CS1:THR51.O 70.3%

AS1:TYR91.N-AS1:GLY268.O 67.33%

CS1:LEU277.N-CS1:HSE49.O 69.31%

BS1:ARG403.NH2-BS1:ASP405.OD2 70.3%

BS2:THR1066.OG1-BS2:LYS1045.O 67.33%

BS1:PHE43.N-AS1:PHE565.O 69.31%

BS2:THR1066.OG1-BS2:LYS1045.O 70.3%

CS1:TYR313.OH-CS1:GLU309.O 67.33%

CS2:THR883.OG1-CS2:ALA879.O 69.31%

CS2:SER1051.OG-CS2:HSE1064.ND1 70.3%

CS1:LEU585.N-CS1:VAL576.O 67.33%

AS1:VAL551.N-AS1:THR588.O 68.32%

AS1:ARG158.NE-AS1:GLU156.OE1 70.3%

AS1:PHE106.N-AS1:LEU117.O 66.34%

AS1:PHE43.N-CS1:PHE565.O 68.32%

BS2:VAL1008.N-BS2:LEU1004.O 69.31%

AS2:SER1051.OG-AS2:HSE1064.ND1 66.34%

BS1:TYR37.OH-BS1:LEU54.O 68.32%

BS1:ARG457.N-BS1:ASP420.OD1 69.31%

AS1:ILE598.N-AS1:ALA609.O 66.34%

BS1:TYR380.N-BS1:GLY431.O 68.32%

CS1:ARG408.NH1-BS1:ASP405.OD1 69.31%

BS2:ILE742.N-BS2:CYS738.O 66.34%

AS1:LEU118.N-AS1:LYS129.O 68.32%

CS2:THR1066.N-CS2:SER721.O 68.32%

CS2:CYS1082.N-CS2:VAL1133.O 66.34%

BS1:SER673.OG-BS1:ASP663.OD1 68.32%

BS1:TRP64.N-BS1:ALA27.O 68.32%

BS2:THR1066.N-BS2:SER721.O 65.35%

BS1:VAL511.N-BS1:ILE434.O 68.32%

AS1:TYR91.N-AS1:GLY268.O 68.32%

AS1:ILE651.N-AS1:VAL610.O 65.35%

AS2:ASN928.N-AS2:ALA924.O 67.33%

AS2:ASN777.N-AS2:GLU773.O 68.32%

BS1:PHE106.N-BS1:LEU117.O 65.35%

AS1:ILE598.N-AS1:ALA609.O 67.33%

AS1:LEU277.N-AS1:HSE49.O 68.32%

AS2:THR1066.OG1-AS2:LYS1045.O 65.35%

AS1:ILE651.N-AS1:VAL610.O 67.33%

AS1:ARG509.NH2-AS1:ASP442.OD2 68.32%

CS2:SER1051.OG-CS2:HSE1064.ND1 65.35%

CS2:TYR1067.N-CS2:TYR1047.O 67.33%

AS1:VAL511.N-AS1:ILE434.O 67.33%

AS1:LEU611.N-AS1:SER596.O 65.35%

AS2:ASN777.N-AS2:GLU773.O 67.33%

BS1:ILE128.N-BS1:TYR170.O 67.33%

CS1:VAL551.N-CS1:THR588.O 65.35%

AS1:VAL511.N-AS1:ILE434.O 67.33%

CS1:ARG355.NH2-CS1:ASP398.OD2 67.33%

BS1:ARG34.NH2-BS1:GLU191.OE2 65.35%

AS1:TYR451.OH-AS1:ASP442.OD1 66.34%

CS1:SER366.OG-CS1:ASP364.OD2 67.33%

AS2:THR1066.N-AS2:SER721.O 64.36%

AS2:SER1051.OG-AS2:HSE1064.ND1 66.34%

AS1:LEU611.N-AS1:SER596.O 67.33%

AS2:GLU1031.N-AS2:THR1027.O 64.36%

AS1:LEU277.N-AS1:HSE49.O 66.34%

CS1:ARG34.NH2-CS1:GLU191.OE1 67.33%

AS1:TYR380.N-AS1:GLY431.O 64.36%

CS1:LEU585.N-CS1:VAL576.O 66.34%

CS2:ALA879.N-CS2:SER875.O 66.34%

AS1:LEU585.N-AS1:VAL576.O 64.36%

AS1:PHE65.N-AS1:TYR265.O 66.34%

CS2:THR1066.OG1-CS2:LYS1045.O 66.34%

BS1:LEU585.N-BS1:VAL576.O 64.36%

BS1:VAL512.N-BS1:ASP398.O 66.34%

CS2:ASN777.N-CS2:GLU773.O 66.34%

BS1:ARG34.NE-BS1:GLU191.OE1 64.36%

AS2:ALA879.N-AS2:SER875.O 66.34%

AS1:LEU585.N-AS1:VAL576.O 66.34%

CS2:THR1066.OG1-CS2:LYS1045.O 63.37%

BS2:THR883.OG1-BS2:ALA879.O 65.35%

AS1:LEU118.N-AS1:LYS129.O 66.34%

BS2:ILE997.N-BS2:ILE993.O 63.37%

CS2:ILE923.N-CS2:ASN919.O 64.36%

AS1:TYR313.N-AS1:VAL597.O 65.35%

CS1:TRP64.N-CS1:ALA27.O 63.37%

BS1:LEU118.N-BS1:LYS129.O 64.36%

CS1:TYR91.OH-CS1:GLU191.OE2 65.35%

AS1:ASP578.N-AS1:GLU583.O 63.37%

BS2:CYS1082.N-BS2:VAL1133.O 64.36%

AS1:ILE128.N-AS1:TYR170.O 65.35%

CS1:VAL510.N-CS1:PHE400.O 63.37%

BS1:TYR612.N-BS1:CYS649.O 64.36%

BS1:CYS336.N-BS1:VAL362.O 65.35%

CS1:LEU277.N-CS1:HSE49.O 63.37%

(continued)

386

10 Spike (S) Glycoprotein N165A and N234A Mutant

Table 10.6 (continued) Replica 1

Replica 2

Replica 3

CS2:THR1077.OG1-CS2:PHE1095.O 64.36%

AS1:ARG328.NE-AS1:ASP578.OD2 65.35%

AS1:PHE65.N-AS1:TYR265.O 63.37%

AS1:ARG44.NH2-AS1:ASP40.OD2 63.37%

CS1:ARG34.NE-CS1:GLU191.OE2 65.35%

AS2:THR1077.OG1-AS2:PHE1095.O 63.37%

AS1:TYR91.N-AS1:GLY268.O 63.37%

CS2:GLU1031.N-CS2:THR1027.O 64.36%

BS2:LYS733.NZ-BS2:ASP775.OD2 62.38%

AS1:ILE434.N-AS1:VAL511.O 63.37%

AS2:VAL1008.N-AS2:LEU1004.O 64.36%

CS1:SER596.N-CS1:LEU611.O 62.38%

AS1:TYR508.N-AS1:ILE402.O 63.37%

AS1:PHE275.N-AS1:THR51.O 64.36%

AS1:TYR37.OH-AS1:LEU54.O 62.38%

CS1:TYR313.OH-CS1:GLU309.O 63.37%

CS1:PHE543.N-CS1:LEU546.O 64.36%

BS1:PHE543.N-BS1:LEU546.O 62.38%

AS1:ASP578.N-AS1:GLU583.O 63.37%

BS1:VAL362.N-BS1:ASN334.O 64.36%

CS1:LYS202.N-CS1:LYS195.O 62.38%

BS2:ALA1022.N-BS2:ILE1018.O 63.37%

AS2:THR1066.OG1-AS2:LYS1045.O 64.36%

CS1:VAL433.N-CS1:LYS378.O 62.38%

AS1:ARG509.NE-AS1:ASP442.OD2 63.37%

AS1:PHE106.N-AS1:LEU117.O 64.36%

BS2:THR1077.OG1-BS2:PHE1095.O 62.38%

AS1:LYS202.N-AS1:LYS195.O 62.38%

CS1:TYR313.N-CS1:VAL597.O 63.37%

AS2:ALA879.N-AS2:SER875.O 62.38%

BS1:VAL127.N-BS1:VAL120.O 62.38%

BS1:ILE358.N-BS1:VAL395.O 63.37%

AS2:PHE1052.N-AS2:LEU1063.O 62.38%

BS1:CYS336.N-BS1:VAL362.O 62.38%

BS1:VAL512.N-BS1:ASP398.O 63.37%

BS1:TYR380.N-BS1:GLY431.O 62.38%

AS1:PHE106.N-AS1:LEU117.O 62.38%

AS1:ILE434.N-AS1:VAL511.O 63.37%

CS1:ILE434.N-CS1:VAL511.O 62.38%

BS2:ALA879.N-BS2:SER875.O 62.38%

BS1:TYR91.N-BS1:GLY268.O 63.37%

AS2:TYR1067.N-AS2:TYR1047.O 61.39%

BS1:LEU277.N-BS1:HSE49.O 62.38%

BS2:ILE693.N-BS1:SER673.O 63.37%

BS1:TYR612.N-BS1:CYS649.O 61.39%

CS2:GLU1031.N-CS2:THR1027.O 61.39%

BS1:ARG567.NH1-CS2:ASP979.OD2 63.37%

BS1:TYR37.OH-BS1:LEU54.O 61.39%

CS2:ASN777.N-CS2:GLU773.O 61.39%

BS2:THR1077.OG1-BS2:PHE1095.O 62.38%

BS1:PHE275.N-BS1:THR51.O 61.39%

BS1:ILE651.N-BS1:VAL610.O 61.39%

BS2:TYR1067.N-BS2:TYR1047.O 62.38%

CS1:ARG102.N-CS1:LEU241.O 61.39%

CS1:ILE587.N-CS1:ASP574.O 61.39%

BS2:THR883.OG1-BS2:ALA879.O 62.38%

AS1:GLY381.N-CS1:PHE490.O 61.39%

CS1:ASP578.N-CS1:GLU583.O 61.39%

BS2:GLU1031.N-BS2:THR1027.O 62.38%

BS2:THR1231.OG1-BS2:ILE1227.O 60.4%

CS2:LEU1063.N-CS2:PHE1052.O 61.39%

BS1:VAL267.N-BS1:THR63.O 62.38%

CS2:HSD1088.N-CS2:ILE1081.O 60.4%

AS1:LEU585.N-AS1:VAL576.O 61.39%

BS1:TYR313.OH-BS1:GLU309.O 62.38%

CS2:ASN928.N-CS2:ALA924.O 60.4%

BS1:PHE106.N-BS1:LEU117.O 61.39%

BS1:VAL551.N-BS1:THR588.O 62.38%

AS1:TYR313.N-AS1:VAL597.O 60.4%

BS2:VAL1096.N-BS2:PHE1103.O 61.39%

BS1:VAL433.N-BS1:LYS378.O 62.38%

AS1:VAL551.N-AS1:THR588.O 60.4%

BS2:ASN928.N-BS2:ALA924.O 61.39%

BS1:ARG102.N-BS1:LEU241.O 62.38%

BS1:VAL62.N-BS1:THR29.O 60.4%

AS1:PHE92.N-AS1:PHE192.O 61.39%

AS1:ARG509.NE-AS1:ASP442.OD1 62.38%

AS1:GLN493.N-AS1:TYR453.O 60.4%

BS2:THR1066.N-BS2:SER721.O 60.4%

AS2:VAL1096.N-AS2:PHE1103.O 61.39%

BS2:LEU1063.N-BS2:PHE1052.O 60.4%

CS1:TYR269.OH-CS1:PRO85.O 60.4%

AS2:GLU1031.N-AS2:THR1027.O 61.39%

AS2:LEU1063.N-AS2:PHE1052.O 60.4%

AS2:VAL1096.N-AS2:PHE1103.O 60.4%

AS1:VAL512.N-AS1:ASP398.O 61.39%

CS1:TYR313.N-CS1:VAL597.O 60.4%

BS1:ASP578.N-BS1:GLU583.O 60.4%

CS2:VAL1096.N-CS2:PHE1103.O 61.39%

CS1:ILE128.N-CS1:TYR170.O 60.4%

CS1:PHE92.N-CS1:PHE192.O 60.4%

BS1:LEU277.N-BS1:HSE49.O 61.39%

BS1:LYS202.N-BS1:LYS195.O 60.4%

CS1:ASP398.N-CS1:VAL512.O 60.4%

CS2:SER974.OG-CS2:ASP979.OD2 61.39%

CS2:LEU1063.N-CS2:PHE1052.O 60.4%

BS1:GLN271.N-BS1:PHE55.O 60.4%

BS1:ARG454.N-BS1:ASN422.OD1 61.39%

CS1:TYR91.OH-CS1:GLU191.OE1 60.4%

BS1:TYR380.N-BS1:GLY431.O 61.39%

BS1:ARG44.NH2-BS1:ASP40.OD2 60.4%

CS1:LEU513.N-CS1:CYS432.O 61.39% BS2:ILE997.N-BS2:ILE993.O 61.39% AS1:ILE587.N-AS1:ASP574.O 60.4% AS1:THR323.N-AS1:CYS538.O 60.4% BS2:THR1238.OG1-BS2:LEU1234.O 60.4% AS2:TYR1067.N-AS2:TYR1047.O 60.4% CS1:TYR313.OH-CS1:GLU309.O 60.4% CS1:LEU277.N-CS1:HSE49.O 60.4% BS2:ILE1232.N-BS2:VAL1228.O 60.4% AS2:CYS1082.N-AS2:VAL1133.O 60.4% BS2:PHE1062.N-BS2:GLU725.O 60.4% BS1:TYR269.OH-BS1:PRO85.O 60.4%

Supplementary Information

387

Table 10.7 The HBs with more than 60% occupancy rates of the wild-type from the analyses of the 400 ns’ (replicas 4–6) MD trajectories of [55] Replica 4

Replica 5

Replica 6

CS1:THR581.OG1-CS1:ASP578.OD1 85.37%

BS2:TYR695.OH-BS1:GLU661.O 82.93%

CS1:ARG355.NE-CS1:ASP398.OD1 85.37%

CS1:SER316.OG-AS2:ASP737.OD2 82.93%

BS1:PHE43.N-AS1:PHE565.O 82.93%

AS1:VAL127.N-AS1:VAL120.O 80.49%

AS1:VAL511.N-AS1:ILE434.O 82.93%

BS2:SER1051.OG-BS2:HSE1064.ND1 78.05%

CS2:SER1051.OG-CS2:HSE1064.ND1 78.05%

BS2:TYR695.OH-BS1:GLU661.O 80.49%

BS1:LEU118.N-BS1:LYS129.O 78.05%

CS1:TYR351.OH-CS1:ASP467.OD2 78.05%

CS2:SER974.OG-CS2:ASP979.OD1 78.05%

CS1:TYR91.OH-CS1:GLU191.OE2 75.61%

AS1:THR323.N-AS1:CYS538.O 75.61%

BS1:ARG509.NH1-BS1:ASP442.OD1 78.05%

AS1:PHE106.N-AS1:LEU117.O 75.61%

BS1:PHE43.N-AS1:PHE565.O 75.61%

AS1:ILE598.N-AS1:ALA609.O 75.61%

BS1:GLN493.N-BS1:TYR453.O 75.61%

CS1:TYR37.OH-CS1:LEU54.O 75.61%

BS1:ILE598.N-BS1:ALA609.O 75.61%

BS2:ASN928.N-BS2:ALA924.O 73.17%

AS1:VAL510.N-AS1:PHE400.O 75.61%

AS1:LEU277.N-AS1:HSE49.O 75.61%

AS2:THR1066.OG1-AS2:LYS1045.O 73.17%

AS1:ARG509.NE-AS1:ASP442.OD1 75.61%

CS1:ARG328.NH2-CS1:ASP578.OD1 75.61%

AS1:TYR313.OH-AS1:GLU309.O 73.17%

CS1:ILE128.N-CS1:TYR170.O 75.61%

AS2:THR1077.OG1-AS2:PHE1095.O 75.61%

BS1:TYR37.OH-BS1:LEU54.O 73.17%

AS2:VAL1096.N-AS2:PHE1103.O 73.17%

BS1:ARG44.NH2-BS1:ASP40.OD2 75.61%

AS1:TYR396.N-AS1:SER514.O 73.17%

CS2:THR1066.OG1-CS2:LYS1045.O 73.17%

AS1:ARG509.NE-AS1:ASP442.OD1 75.61%

AS1:VAL511.N-AS1:ILE434.O 73.17%

CS2:GLU1031.N-CS2:THR1027.O 73.17%

BS2:HSD1088.N-BS2:ILE1081.O 73.17%

CS2:PHE1089.N-CS2:PHE1121.O 73.17%

AS1:ILE651.N-AS1:VAL610.O 73.17%

BS2:TYR1067.N-BS2:TYR1047.O 73.17%

CS1:LEU585.N-CS1:VAL576.O 73.17%

AS1:LEU585.N-AS1:VAL576.O 73.17%

BS2:PHE1062.N-BS2:GLU725.O 73.17%

BS2:THR1077.OG1-BS2:PHE1095.O 70.73%

CS1:LEU585.N-CS1:VAL576.O 73.17%

BS2:ILE693.N-BS1:SER673.O 73.17%

AS1:PHE92.N-AS1:PHE192.O 70.73%

BS2:PHE1062.N-BS2:GLU725.O 70.73%

CS1:LEU585.N-CS1:VAL576.O 73.17%

CS1:TYR91.N-CS1:GLY268.O 70.73%

AS1:PHE275.N-AS1:THR51.O 70.73%

BS1:ARG567.NH2-CS2:ASP979.OD2 73.17%

AS1:CYS336.N-AS1:VAL362.O 70.73%

BS1:VAL62.N-BS1:THR29.O 70.73%

AS1:TYR508.N-AS1:ILE402.O 73.17%

BS1:CYS336.N-BS1:VAL362.O 70.73%

AS1:TYR91.N-AS1:GLY268.O 70.73%

BS2:CYS1082.N-BS2:VAL1133.O 70.73%

BS2:THR1066.OG1-BS2:LYS1045.O 68.29%

BS1:ARG567.NH2-CS2:ASP979.OD1 70.73%

CS2:PHE1089.N-CS2:PHE1121.O 70.73%

CS2:THR1066.OG1-CS2:LYS1045.O 68.29%

BS1:TYR269.OH-BS1:PRO85.O 70.73%

AS2:GLU918.N-AS2:ASN914.O 70.73%

AS1:ARG44.NH2-AS1:ASP40.OD2 68.29%

CS1:VAL511.N-CS1:ILE434.O 70.73%

BS2:GLU1031.N-BS2:THR1027.O 70.73%

AS1:TYR37.OH-AS1:LEU54.O 68.29%

AS1:VAL511.N-AS1:ILE434.O 70.73%

AS2:VAL729.N-AS2:HSD1058.O 70.73%

AS1:PHE65.N-AS1:TYR265.O 68.29%

AS1:TYR91.OH-AS1:GLU191.OE1 70.73%

CS1:GLN613.N-CS1:GLY594.O 70.73%

AS1:LYS77.NZ-AS1:ASP138.OD1 68.29%

BS1:ARG567.NH1-CS2:ASP979.OD2 70.73%

BS1:PHE43.N-AS1:PHE565.O 70.73%

CS1:TYR396.N-CS1:SER514.O 68.29%

BS2:ALA1022.N-BS2:ILE1018.O 70.73%

AS1:THR323.N-AS1:CYS538.O 70.73%

CS1:ILE434.N-CS1:VAL511.O 68.29%

AS2:GLU918.N-AS2:ASN914.O 68.29%

BS1:GLN271.N-BS1:PHE55.O 70.73%

AS1:TYR508.N-AS1:ILE402.O 68.29%

BS2:GLU1031.N-BS2:THR1027.O 68.29%

BS1:TYR266.N-BS1:ALA93.O 70.73%

AS1:LEU650.N-AS1:PHE643.O 68.29%

AS2:ALA879.N-AS2:SER875.O 68.29%

BS1:VAL511.N-BS1:ILE434.O 70.73%

CS1:VAL511.N-CS1:ILE434.O 68.29%

BS2:TYR695.OH-BS1:GLU661.O 68.29%

BS2:GLN1036.NE2-BS2:HSE1048.O 70.73%

BS1:LEU611.N-BS1:SER596.O 68.29%

CS2:ASN777.N-CS2:GLU773.O 68.29%

BS1:VAL551.N-BS1:THR588.O 70.73%

CS1:TRP64.N-CS1:ALA27.O 68.29%

AS1:LEU650.N-AS1:PHE643.O 68.29%

AS1:TYR91.N-AS1:GLY268.O 70.73%

CS2:ASN928.N-CS2:ALA924.O 65.85%

BS1:LEU650.N-BS1:PHE643.O 68.29%

BS1:LEU585.N-BS1:VAL576.O 70.73%

AS2:ALA879.N-AS2:SER875.O 65.85%

BS1:ILE598.N-BS1:ALA609.O 68.29%

CS1:ARG328.NH1-CS1:ASP578.OD2 70.73%

BS2:ARG1019.NH1-BS2:ASN777.OD1 65.85%

AS1:LEU277.N-AS1:HSE49.O 68.29%

CS1:ARG457.NH2-CS1:GLU465.OE1 70.73%

AS1:LEU611.N-AS1:SER596.O 65.85%

AS1:PHE43.N-CS1:PHE565.O 68.29%

AS1:PHE592.N-AS1:PHE318.O 70.73%

BS1:TYR612.N-BS1:CYS649.O 65.85%

AS1:PHE192.N-AS1:PHE92.O 68.29%

CS2:PHE1062.N-CS2:GLU725.O 68.29%

AS1:ILE587.N-AS1:ASP574.O 65.85%

BS1:TYR266.N-BS1:ALA93.O 68.29%

AS2:ARG1019.NH1-AS2:ASN777.OD1 68.29%

AS2:ILE997.N-AS2:ILE993.O 65.85%

BS1:VAL267.N-BS1:THR63.O 68.29%

BS1:LEU277.N-BS1:HSE49.O 68.29%

AS1:ARG44.NH1-AS1:ASP40.OD1 65.85%

AS1:LEU118.N-AS1:LYS129.O 68.29%

AS1:VAL267.N-AS1:THR63.O 68.29%

CS1:LEU223.N-CS1:VAL36.O 65.85%

AS1:ILE358.N-AS1:VAL395.O 68.29%

AS1:PHE43.N-CS1:PHE565.O 68.29%

BS1:TRP64.N-BS1:ALA27.O 65.85%

AS1:ALA397.N-AS1:LYS356.O 68.29%

AS1:PHE65.N-AS1:TYR265.O 68.29%

BS1:PHE106.N-BS1:LEU117.O 65.85%

BS1:LEU611.N-BS1:SER596.O 68.29%

CS1:VAL62.N-CS1:THR29.O 68.29%

CS1:TYR380.N-CS1:GLY431.O 65.85%

CS1:TYR423.OH-CS1:ASP398.OD2 68.29%

CS1:TYR91.OH-CS1:GLU191.OE1 68.29%

AS1:VAL120.N-AS1:VAL127.O 65.85%

BS1:ASN354.N-BS1:ASP398.OD2 68.29%

AS1:LYS202.N-AS1:LYS195.O 68.29%

BS1:VAL362.N-BS1:ASN334.O 65.85%

AS2:ASN960.N-AS2:ALA956.O 68.29%

CS1:ASP420.N-CS1:GLY416.O 68.29%

CS1:TYR489.OH-AS1:GLY381.O 65.85%

CS1:TYR91.N-CS1:GLY268.O 68.29%

BS1:ILE434.N-BS1:VAL511.O 68.29%

AS1:VAL512.N-AS1:ASP398.O 65.85%

CS2:ILE923.N-CS2:ASN919.O 65.85%

CS1:ARG454.N-CS1:ASN422.OD1 68.29%

BS1:TYR508.N-BS1:ILE402.O 65.85%

BS2:MET902.N-BS2:PHE898.O 65.85%

AS1:TYR313.N-AS1:VAL597.O 68.29%

BS2:THR1066.N-BS2:SER721.O 65.85%

CS2:ALA879.N-CS2:SER875.O 65.85%

CS1:TYR269.OH-CS1:PRO85.O 68.29%

BS2:MET697.N-BS1:GLY669.O 65.85%

CS2:LEU938.N-CS2:ILE934.O 65.85%

CS2:THR716.OG1-CS2:GLN1071.O 65.85%

AS1:VAL362.N-AS1:ASN334.O 65.85%

BS2:ILE693.N-BS1:SER673.O 65.85%

BS1:LEU611.N-BS1:SER596.O 65.85%

AS2:GLU918.N-AS2:ASN914.O 65.85%

CS1:LEU611.N-CS1:SER596.O 65.85%

BS1:LYS202.N-BS1:LYS195.O 65.85%

BS1:LEU277.N-BS1:HSE49.O 65.85%

BS1:VAL551.N-BS1:THR588.O 65.85%

CS1:VAL511.N-CS1:ILE434.O 65.85%

BS1:TYR91.N-BS1:GLY268.O 65.85%

AS1:TYR37.OH-AS1:LEU54.O 65.85%

BS1:ARG509.NH2-BS1:ASP442.OD2 65.85%

BS2:THR1238.OG1-BS2:LEU1234.O 63.41%

BS1:PHE194.N-BS1:VAL90.O 65.85%

CS2:SER1051.OG-CS2:HSE1064.ND1 65.85%

BS2:TYR1067.N-BS2:TYR1047.O 63.41%

BS1:ILE128.N-BS1:TYR170.O 65.85%

CS2:HSE1064.N-CS2:THR723.O 65.85%

BS2:ALA879.N-BS2:SER875.O 63.41%

BS1:PHE106.N-BS1:LEU117.O 65.85%

(continued)

388

10 Spike (S) Glycoprotein N165A and N234A Mutant

Table 10.7 (continued) Replica 4

Replica 5

Replica 6

AS1:ILE587.N-AS1:ASP574.O 65.85%

BS1:TYR313.N-BS1:VAL597.O 63.41%

CS1:ARG457.NH2-CS1:ASP467.OD1 65.85%

CS1:PHE92.N-CS1:PHE192.O 65.85%

AS2:ASN960.N-AS2:ALA956.O 63.41%

BS1:ARG246.NH2-BS1:ASP80.OD2 65.85%

CS1:LEU277.N-CS1:HSE49.O 65.85%

CS1:LEU611.N-CS1:SER596.O 63.41%

AS1:ARG158.NE-AS1:GLU156.OE1 65.85%

AS1:TYR451.OH-AS1:ASP442.OD2 65.85%

AS1:VAL551.N-AS1:THR588.O 63.41%

AS2:VAL729.N-AS2:HSD1058.O 65.85%

BS2:THR1077.OG1-BS2:PHE1095.O 63.41%

BS1:ASP568.N-BS1:THR572.O 63.41%

CS2:GLN957.N-CS2:ASN953.O 65.85%

CS2:MET902.N-CS2:PHE898.O 63.41%

AS1:PHE543.N-AS1:LEU546.O 63.41%

CS1:ILE598.N-CS1:ALA609.O 65.85%

CS2:GLU1031.N-CS2:THR1027.O 63.41%

CS1:LYS202.N-CS1:LYS195.O 63.41%

AS1:GLN271.N-AS1:PHE55.O 65.85%

AS1:PHE643.N-AS1:LEU650.O 63.41%

AS1:THR523.OG1-AS1:THR393.O 63.41%

BS1:VAL511.N-BS1:ILE434.O 65.85%

BS1:TYR37.OH-BS1:LEU54.O 63.41%

AS1:LEU118.N-AS1:LYS129.O 63.41%

CS1:ILE434.N-CS1:VAL511.O 65.85%

CS1:TYR37.OH-CS1:LEU54.O 63.41%

BS1:VAL512.N-BS1:ASP398.O 63.41%

AS2:LEU1218.N-AS2:TRP1214.O 63.41%

AS1:LEU229.N-AS1:PHE201.O 63.41%

BS1:ARG457.N-BS1:ASP420.OD1 63.41%

AS2:ILE1216.N-AS2:LYS1211.O 63.41%

AS1:VAL127.N-AS1:VAL120.O 63.41%

AS1:ILE434.N-AS1:VAL511.O 63.41%

CS2:ASN1173.N-CS2:ILE1169.O 63.41%

AS1:LEU118.N-AS1:LYS129.O 63.41%

AS2:VAL1096.N-AS2:PHE1103.O 63.41%

BS2:THR883.OG1-BS2:ALA879.O 63.41%

AS1:ILE358.N-AS1:VAL395.O 63.41%

AS2:THR1066.N-AS2:SER721.O 63.41%

AS2:SER1051.OG-AS2:HSE1064.ND1 63.41%

CS1:ILE358.N-CS1:VAL395.O 63.41%

BS2:VAL729.N-BS2:HSD1058.O 63.41%

BS2:ALA1026.N-BS2:ALA1022.O 63.41%

CS1:ALA397.N-CS1:LYS356.O 63.41%

AS1:LEU585.N-AS1:VAL576.O 63.41%

BS1:SER673.OG-BS1:ASP663.OD2 63.41%

CS1:GLN493.N-CS1:TYR453.O 63.41%

CS1:LEU277.N-CS1:HSE49.O 63.41%

AS2:LYS733.NZ-AS2:ASP775.OD2 63.41%

CS2:ASN928.N-CS2:ALA924.O 63.41%

BS1:TYR396.N-BS1:SER514.O 63.41%

CS1:VAL597.N-CS1:TYR313.O 63.41%

AS2:ASN777.N-AS2:GLU773.O 63.41%

AS1:THR572.OG1-BS2:ASP848.OD2 63.41%

CS1:TRP64.N-CS1:ALA27.O 63.41%

AS1:PHE59.N-AS1:PHE32.O 63.41%

AS2:GLN1005.N-AS2:LEU1001.O 63.41%

BS1:ALA363.N-BS1:CYS525.O 63.41%

CS1:ASP578.N-CS1:GLU583.O 63.41%

CS2:THR1077.OG1-CS2:PHE1095.O 60.98%

BS1:LEU244.N-BS1:PRO139.O 63.41%

AS2:THR883.OG1-AS2:ALA879.O 63.41%

CS2:THR1105.OG1-CS2:GLN1106.O 60.98%

BS1:ARG78.NH2-BS1:ASP80.OD1 63.41%

CS2:SER1055.OG-CS2:GLU819.OE1 63.41%

CS2:SER1037.OG-CS2:GLU1031.OE1 60.98%

BS1:ARG78.NE-BS1:ASP80.OD2 63.41%

CS1:LYS202.N-CS1:LYS195.O 63.41%

BS2:GLN1054.N-BS2:VAL1061.O 60.98%

AS1:LEU513.N-AS1:CYS432.O 63.41%

AS2:ASN1023.N-AS2:ARG1019.O 63.41%

AS2:VAL729.N-AS2:HSD1058.O 60.98%

AS2:THR1231.OG1-AS2:ILE1227.O 63.41%

CS2:THR1231.OG1-CS2:ILE1227.O 60.98%

BS1:ILE598.N-BS1:ALA609.O 60.98%

AS2:THR1066.N-AS2:SER721.O 63.41%

CS2:THR1077.OG1-CS2:PHE1095.O 60.98%

CS1:TYR313.OH-CS1:GLU309.O 60.98%

AS2:ASN777.N-AS2:GLU773.O 63.41%

CS2:THR791.OG1-CS2:PRO807.O 60.98%

AS1:VAL62.N-AS1:THR29.O 60.98%

BS2:VAL1008.N-BS2:LEU1004.O 63.41%

BS1:ILE651.N-BS1:VAL610.O 60.98%

BS1:VAL539.N-BS1:GLY550.O 60.98%

BS1:ARG509.NH2-BS1:ASP442.OD1 63.41%

BS2:ARG1000.NH1-BS2:ILE742.O 60.98%

CS1:VAL62.N-CS1:THR29.O 60.98%

AS1:THR208.N-AS1:LEU189.O 63.41%

AS1:TYR37.OH-AS1:LEU54.O 60.98%

BS1:PHE92.N-BS1:PHE192.O 60.98%

BS1:LEU585.N-BS1:VAL576.O 63.41%

AS1:PHE92.N-AS1:PHE192.O 60.98%

CS1:PHE194.N-CS1:VAL90.O 60.98%

AS2:THR883.OG1-AS2:ALA879.O 63.41%

AS1:LEU84.N-AS1:PHE238.O 60.98%

AS1:LEU229.N-AS1:PHE201.O 60.98%

BS1:ILE434.N-BS1:VAL511.O 63.41%

BS2:THR1027.OG1-BS2:ASN1023.O 60.98%

AS1:TYR380.N-AS1:GLY431.O 60.98%

AS2:PHE1075.N-AS2:ILE712.O 60.98%

AS1:VAL551.N-AS1:THR588.O 60.98%

AS1:TYR495.OH-AS1:VAL401.O 60.98%

CS2:THR1066.N-CS2:SER721.O 60.98%

BS1:TYR91.N-BS1:GLY268.O 60.98%

AS2:THR716.OG1-AS2:GLN1071.O 60.98%

AS2:GLU1031.N-AS2:THR1027.O 60.98%

CS1:TYR266.N-CS1:ALA93.O 60.98%

CS2:SER1051.OG-CS2:HSE1064.ND1 60.98%

BS2:LEU1063.N-BS2:PHE1052.O 60.98%

BS1:TYR380.N-BS1:GLY431.O 60.98%

CS2:GLN1011.N-CS2:TYR1007.O 60.98%

AS2:LEU938.N-AS2:ILE934.O 60.98%

CS1:ASN121.N-CS1:SER155.O 60.98%

CS1:TYR37.OH-CS1:LEU54.O 60.98%

BS2:ASN777.N-BS2:GLU773.O 60.98%

BS1:GLN493.N-BS1:TYR453.O 60.98%

CS1:TYR269.OH-CS1:PRO85.O 60.98%

AS1:LEU611.N-AS1:SER596.O 60.98%

CS2:THR1066.OG1-CS2:LYS1045.O 60.98%

BS2:THR1231.OG1-BS2:ILE1227.O 60.98%

AS1:VAL610.N-AS1:ILE651.O 60.98%

BS2:ASP737.N-BS2:GLY857.O 60.98%

BS2:VAL1068.N-BS2:THR719.O 60.98%

CS1:SER596.N-CS1:LEU611.O 60.98%

AS2:ASN928.N-AS2:ALA924.O 60.98%

AS2:LEU822.N-AS2:ILE818.O 60.98%

BS1:ARG319.NH1-BS1:ASN317.OD1, CS1:VAL551.N-CS1:THR588.O 60.98%

AS2:SER1051.OG-AS2:HSE1064.ND1 60.98%

CS2:ARG847.NH1-BS1:ASP568.OD2 60.98%

AS1:ARG273.N-AS1:ASP53.O, CS1:PHE543.N-CS1:LEU546.O 60.98%

BS1:VAL130.N-BS1:PHE168.O 60.98%

CS1:VAL551.N-CS1:THR588.O 60.98%

AS1:ILE128.N-AS1:TYR170.O, BS1:CYS336.N-BS1:VAL362.O 60.98%

BS1:PHE65.N-BS1:TYR265.O 60.98%

BS1:LYS202.N-BS1:LYS195.O 60.98%

CS1:ARG454.N-CS1:ASN422.OD1, BS1:SER443.OG-BS1:TYR495.O 60.98%

AS1:ARG44.NH2-AS1:ASP40.OD1 60.98%

AS1:ARG509.NE-AS1:ASP442.OD1 60.98%

AS2:THR1077.OG1-AS2:PHE1095.O, BS1:CYS649.N-BS1:TYR612.O 60.98%

BS2:CYS1082.N-BS2:VAL1133.O 60.98%

AS1:PHE58.N-AS1:ASP290.OD1, CS1:TYR279.N-CS1:VAL47.O 60.98%

BS1:LEU585.N-BS1:VAL576.O 60.98%

BS1:TYR91.N-BS1:GLY268.O, CS2:ASP1153.N-CS2:PHE1148.O 60.98%

BS1:ARG328.NE-BS1:ASP578.OD1 60.98%

AS2:TYR695.OH-AS1:SER673.O, AS2:CYS760.N-AS2:TYR756.O 60.98%

BS1:VAL511.N-BS1:ILE434.O 60.98%

AS1:PHE106.N-AS1:LEU117.O, AS1:SER438.OG-AS1:ASP442.OD1 60.98%

CS1:ARG355.NE-CS1:ASP398.OD2 60.98%

BS1:LEU118.N-BS1:LYS129.O, AS1:PHE347.N-AS1:ASP442.OD2 60.98%

Supplementary Information

389

Table 10.8 The 20 SBs (Sect. 7.3.2) of the wild-type from the analyses of the 175 ns’ continuous MD trajectory of SARS-CoV-2 glycosylated spike opening [339] ASP820-ARG815

A:ASP820-A:ARG815, B:ASP820-B:ARG815, C:ASP820-C:ARG815

ASP820-LYS811

A:ASP820-A:LYS811, C:ASP820-C:LYS811

ASP578-ARG328

A:ASP578-A:ARG328, B:ASP578-B:ARG328, C:ASP578-C:ARG328

ASP467-ARG454

A:ASP467-A:ARG454, C:ASP467-C:ARG454 C:ASP467-C:LYS458

ASP53-LYS195

A:ASP53-A:LYS195, B:ASP53-B:LYS195, C:ASP53-C:LYS195

ASP663-LYS310

A:ASP663-A:LYS310, B:ASP663-B:LYS310, C:ASP663-C:LYS310 B:ASP663-B:ARG683 B:ASP663-B:ARG685

GLU583-LYS535

A:GLU583-A:LYS535, B:GLU583-B:LYS535, C:GLU583-C:LYS535 A:GLU583-A:ARG328 A:GLU583-A:LYS558, C:GLU583-C:LYS558

ASP775-LYS733

A:ASP775-A:LYS733, B:ASP775-B:LYS733, C:ASP775-C:LYS733

GLU773-ARG1019

A:GLU773-A:ARG1019, B:GLU773-B:ARG1019 B:GLU773-B:LYS776, C:GLU773-C:LYS776 B:GLU773-A:LYS947

GLU340-LYS356

A:GLU340-A:LYS356, B:GLU340-B:LYS356, C:GLU340-C:LYS356

ASP574-LYS557

A:ASP574-A:LYS557, B:ASP574-B:LYS557, C:ASP574-C:LYS557 A:ASP574-B:LYS854, B:ASP574-C:LYS854, C:ASP574-A:LYS854 C:ASP574-A:ARG847

ASP40-ARG44

A:ASP40-A:ARG44, B:ASP40-B:ARG44, C:ASP40-C:ARG44

GLU725-HIS1064

A:GLU725-A:LYS1028, B:GLU725-B:LYS1028, C:GLU725-C:LYS1028

ASP1084-LYS1086

A:ASP1084-A:LYS1086, B:ASP1084-B:LYS1086, C:ASP1084-C:LYS1086

ASP571-ARG567

A:ASP571-A:ARG567, B:ASP571-B:ARG567 B:ASP571-C:LYS964 C:ASP571-A:ARG44

ASP405-ARG403

A:ASP405-A:ARG408, B:ASP405-B:ARG408, B:ASP405-C:ARG408, C:ASP405-A:ARG408 A:ASP405-A:LYS417 B:ASP405-C:LYS378

GLU465-ARG457

A:GLU465-A:LYS462, B:GLU465-B:LYS462, C:GLU465-C:LYS462

GLU191-ARG34

A:GLU191-A:ARG34, B:GLU191-B:ARG34, C:GLU191-C:ARG34

GLU1031-ARG1039

A:GLU1031-A:ARG1039, B:GLU1031-B:ARG1039, C:GLU1031-C:ARG1039 A:GLU1031-C:ARG1039, C:GLU1031-A:ARG1039, B:GLU1031-A:ARG1039, C:GLU1031-B:ARG1039

ASP405-ARG403

A:ASP405-A:ARG408, B:ASP405-B:ARG408, B:ASP405-C:ARG408, C:ASP405-A:ARG408 A:ASP405-A:LYS417 B:ASP405-C:LYS378

ASP574-LYS854

A:ASP574-B:LYS854, B:ASP574-C:LYS854, C:ASP574-A:LYS854

ASP442-ARG509

A:ASP442-A:ARG509, B:ASP442-B:ARG509, C:ASP442-C:ARG509 B:ASP442-B:ARG346, C:ASP442-C:ARG346

ASP398-ARG355

A:ASP398-A:ARG355, B:ASP398-B:ARG355, C:ASP398-C:ARG355

CS1:LYS558.NZ-CS1:GLU583.OE1 10.40%

AS2:LYS733.NZ-AS2:ASP775.OD2 24.86%, AS2:LYS733.NZ-AS2:ASP775.OD1 20.81%,

GLU583-LYS558

ASP775-LYS733

CS2:LYS776.NZ-CS2:GLU773.OE2 10.40%

BS1:LYS356.NZ-BS1:GLU340.OE1 17.34%

AS2:LYS854.NZ-CS1:ASP574.OD1 16.76%, BS2:LYS854.NZ-AS1:ASP574.OD2 39.31%

AS2:ARG847.NH2-CS1:ASP574.OD2 12.72%

AS1:ARG44.NH2-AS1:ASP40.OD1 67.05%, AS1:ARG44.NH1-AS1:ASP40.OD2 56.65%, AS1:ARG44.NH2-AS1:ASP40.OD2 11.56%, AS1:ARG44.NH1-AS1:ASP40.OD1 10.98%

GLU773-LYS776

GLU340-LYS356

ASP574-LYS854

ASP574-ARG847

ASP40-ARG44

CS1:ARG44.NH2-CS1:ASP40.OD2 77.46%, CS1:ARG44.NH1-CS1:ASP40.OD1 56.07%

BS1:ARG44.NH2-BS1:ASP40.OD2 74.57%, BS1:ARG44.NH1-BS1:ASP40.OD1 60.12%,

AS2:ARG1019.NE-AS2:GLU773.OE2 34.68%, AS2:ARG1019.NH2-AS2:GLU773.OE1 32.95%, AS2:ARG1019.NE-AS2:GLU773.OE1 30.64%, AS2:ARG1019.NH2-AS2:GLU773.OE2 26.01%

GLU773-ARG1019

CS2:LYS733.NZ-CS2:ASP775.OD2 40.46%, CS2:LYS733.NZ-CS2:ASP775.OD1 10.40%

BS2:LYS733.NZ-BS2:ASP775.OD1 32.95%, BS2:LYS733.NZ-BS2:ASP775.OD2 19.65%,

BS1:ARG683.NH2-BS1:ASP663.OD2 15.03%, BS1:ARG683.NH1-BS1:ASP663.OD1 13.87%

ASP663-ARG683

CS1:LYS310.NZ-CS1:ASP663.OD2 43.93%

BS1:LYS310.NZ-BS1:ASP663.OD2 18.50%, BS1:LYS310.NZ-BS1:ASP663.OD1 10.40%,

AS1:LYS310.NZ-AS1:ASP663.OD1 20.23%, AS1:LYS310.NZ-AS1:ASP663.OD2 18.50%,

CS1:LYS195.NZ-CS1:ASP53.OD1 16.18%, CS1:LYS195.NZ-CS1:ASP53.OD2 12.72%

BS1:LYS195.NZ-BS1:ASP53.OD1 13.29%,

AS1:LYS195.NZ-AS1:ASP53.OD1 15.03%,

ASP663-LYS310

CS1:LYS458.NZ-CS1:ASP467.OD2 31.79%, CS1:LYS458.NZ-CS1:ASP467.OD1 22.54%

ASP53-LYS195

CS1:ARG454.NH1-CS1:ASP467.OD1 42.20%

AS1:ARG454.NH2-AS1:ASP467.OD2 21.97%, AS1:ARG454.NH2-AS1:ASP467.OD1 17.92%, AS1:ARG454.NH1-AS1:ASP467.OD2 16.18%, AS1:ARG454.NH1-AS1:ASP467.OD1 15.03%

CS1:ARG328.NH1-CS1:ASP578.OD2 27.75%, CS1:ARG328.NH1-CS1:ASP578.OD1 24.86%, CS1:ARG328.NH2-CS1:ASP578.OD1 11.56%

ASP467-LYS458

ASP467-ARG454

BS1:ARG328.NH1-BS1:ASP578.OD2 26.01%, BS1:ARG328.NH1-BS1:ASP578.OD1 31.21%,

AS1:ARG328.NH1-AS1:ASP578.OD2 34.68%, AS1:ARG328.NH1-AS1:ASP578.OD1 16.18%,

CS2:ARG815.NE-CS2:ASP820.OD1 16.76%, CS2:ARG815.NE-CS2:ASP820.OD2 13.29%, CS2:ARG815.NH2-CS2:ASP820.OD1 10.40%

BS2:ARG815.NE-BS2:ASP820.OD1 34.10%, BS2:ARG815.NE-BS2:ASP820.OD2 23.70%,

AS2:ARG815.NH1-AS2:ASP820.OD2 12.14%,

ASP820-ARG815

ASP578-ARG328

HBs of the SB

SB

Table 10.9 HBs of the 20 SBs (Sect. 7.3.2) of the wild-type from the analyses of the 175 ns’ continuous MD trajectory of SARS-CoV-2 glycosylated spike (where AS1 is (chain A, 16–685), AS2 is (chain A, 686–1140), BS1 is (chain B, 16–685), BS2 is (chain B, 686–1140), CS1 is (chain C, 16–685), and CS2 is (chain C, 686–1140)) opening [339]

390 10 Spike (S) Glycoprotein N165A and N234A Mutant

AS1:ARG509.NE-AS1:ASP442.OD2 78.03%, AS1:ARG509.NH2-AS1:ASP442.OD1 49.13%,

ASP398-ARG355

AS2:LYS854.NZ-CS1:ASP574.OD1 16.76%, BS2:LYS854.NZ-AS1:ASP574.OD2 39.31%

ASP442-ARG509

CS1:ARG355.NH1-CS1:ASP398.OD2 25.43%, CS1:ARG355.NH1-CS1:ASP398.OD1 17.92%, CS1:ARG355.NH2-CS1:ASP398.OD1 14.45%, CS1:ARG355.NH2-CS1:ASP398.OD2 12.72%

BS1:ARG355.NH1-BS1:ASP398.OD2 41.04%, BS1:ARG355.NH1-BS1:ASP398.OD1 35.84%,

AS1:ARG355.NH1-AS1:ASP398.OD2 69.94%, AS1:ARG355.NH1-AS1:ASP398.OD1 10.40%,

CS1:ARG509.NE-CS1:ASP442.OD2 75.72%, CS1:ARG509.NH2-CS1:ASP442.OD1 60.12%

BS1:ARG509.NE-BS1:ASP442.OD1 50.87%, BS1:ARG509.NH2-BS1:ASP442.OD2 36.99%, BS1:ARG509.NH2-BS1:ASP442.OD1 14.45%, BS1:ARG509.NE-BS1:ASP442.OD2 13.87%,

AS1:LYS417.NZ-AS1:ASP405.OD2 23.12%, AS1:LYS417.NZ-AS1:ASP405.OD1 11.56%

ASP574-LYS854

CS1:ARG408.NH1-BS1:ASP405.OD2 17.34%, CS1:ARG408.NH2-BS1:ASP405.OD1 15.03%, CS1:ARG408.NH1-BS1:ASP405.OD1 14.45%, CS1:ARG408.NE-BS1:ASP405.OD2 10.98%

AS1:ARG408.NH1-CS1:ASP405.OD1 13.29%

AS1:ARG408.NH2-AS1:ASP405.OD1 25.43%, AS1:ARG408.NH2-AS1:ASP405.OD2 14.45%,

CS2:ARG1039.NE-AS2:GLU1031.OE1 24.28%, CS2:ARG1039.NE-AS2:GLU1031.OE2 13.29%

AS2:ARG1039.NH2-CS2:GLU1031.OE1 30.06%, AS2:ARG1039.NH2-CS2:GLU1031.OE2 21.39%,

AS2:ARG1039.NE-BS2:GLU1031.OE2 23.12%, AS2:ARG1039.NH2-BS2:GLU1031.OE2 20.81%,

CS2:ARG1039.NH1-CS2:GLU1031.OE1 15.61%,

BS2:ARG1039.NE-BS2:GLU1031.OE1 82.66%, BS2:ARG1039.NH2-BS2:GLU1031.OE2 52.60%,

AS2:ARG1039.NH1-AS2:GLU1031.OE2 12.72%,

CS1:ARG34.NH1-CS1:GLU191.OE1 38.73%

ASP405-LYS417

ASP405-ARG408

GLU1031-ARG1039

AS1:ARG34.NH1-AS1:GLU191.OE2 35.84%,

BS1:ARG34.NE-BS1:GLU191.OE1 79.19%, BS1:ARG34.NH2-BS1:GLU191.OE2 76.88%,

AS1:LYS417.NZ-AS1:ASP405.OD2 23.12%, AS1:LYS417.NZ-AS1:ASP405.OD1 11.56%

GLU191-ARG34

CS1:ARG567.NH1-CS1:ASP571.O 14.45%

AS1:ARG567.NH1-AS1:ASP571.O 23.70%,

CS2:LYS1028.NZ-CS2:GLU725.OE2 21.39%, CS2:LYS1028.NZ-CS2:GLU725.OE1 16.18%

BS2:LYS1028.NZ-BS2:GLU725.OE2 21.97%, BS2:LYS1028.NZ-BS2:GLU725.OE1 15.03%,

AS2:LYS1028.NZ-AS2:GLU725.OE2 29.48%, AS2:LYS1028.NZ-AS2:GLU725.OE1 23.12%,

ASP405-LYS417

ASP571-ARG567

GLU725-LYS1028

Supplementary Information 391

392 Table 10.10 The HBs with more than 66% occupancy rates of the wild-type from the analyses of the 175 ns’ continuous MD trajectory of SARS-CoV-2 glycosylated spike (where AS1 is (chain A, 16–685), AS2 is (chain A, 686–1140), BS1 is (chain B, 16–685), BS2 is (chain B, 686–1140), CS1 is (chain C, 16–685), and CS2 is (chain C, 686–1140)) opening [339]

10 Spike (S) Glycoprotein N165A and N234A Mutant HBs: BS2:ARG1039.NE-BS2:GLU1031.OE1 82.66% AS1:SER366.OG-AS1:ASP364.OD1 80.35% BS1:ARG34.NE-BS1:GLU191.OE1 79.19% AS1:ARG509.NE-AS1:ASP442.OD2 78.03% CS1:ARG44.NH2-CS1:ASP40.OD2 77.46% BS1:ARG34.NH2-BS1:GLU191.OE2 76.88% BS1:THR393.OG1-BS1:GLU516.OE1 76.88% BS1:TYR37.OH-BS1:LEU54.O 76.30% CS1:ILE101.N-CS1:GLU96.OE1 76.30% CS1:ILE100.N-CS1:GLU96.OE1 76.30% AS2:SER1051.OG-AS2:HSE1064.ND1 75.72% AS1:LEU229.N-AS1:PHE201.O 75.72% CS1:ARG509.NE-CS1:ASP442.OD2 75.72% BS2:SER1051.OG-BS2:HSE1064.ND1 75.14% BS1:TYR396.OH-BS1:GLU516.OE2 75.14% BS1:ARG44.NH2-BS1:ASP40.OD2 74.57% AS1:TYR37.OH-AS1:LEU54.O 74.57% CS1:LEU611.N-CS1:SER596.O 74.57% AS1:LEU611.N-AS1:SER596.O 73.99% CS1:TYR37.OH-CS1:LEU54.O 73.99% CS1:SER438.OG-CS1:ASP442.OD2 73.99% AS2:THR883.OG1-AS2:ALA879.O 73.41% AS1:SER221.OG-AS1:GLU191.OE1 72.83% BS1:TYR91.N-BS1:GLY268.O 72.25% CS1:TYR451.OH-CS1:ASP442.OD1 72.25% AS2:ASN777.N-AS2:GLU773.O 72.25% BS2:THR883.OG1-BS2:ALA879.O 72.25% CS1:SER673.OG-CS1:ASP663.OD1 71.68% CS1:ILE598.N-CS1:ALA609.O 71.68% BS1:VAL511.N-BS1:ILE434.O 71.68% AS2:THR1066.OG1-AS2:LYS1045.O 71.10% BS1:LEU611.N-BS1:SER596.O 70.52% BS1:LEU277.N-BS1:HSE49.O 70.52% CS1:LEU277.N-CS1:HSE49.O 70.52% BS1:LEU585.N-BS1:VAL576.O 70.52% AS1:ARG190.NE-AS1:GLU96.OE1 70.52% BS1:ILE651.N-BS1:VAL610.O 70.52% AS1:VAL511.N-AS1:ILE434.O 70.52% BS1:PHE106.N-BS1:LEU117.O 69.94% AS1:ARG355.NH1-AS1:ASP398.OD2 69.94% BS2:TYR695.OH-BS1:GLU661.O 69.94% BS1:ILE598.N-BS1:ALA609.O 69.94% CS1:TYR91.N-CS1:GLY268.O 69.94% CS2:TYR695.OH-CS1:GLU661.O 69.36% AS1:ILE651.N-AS1:VAL610.O 69.36% BS1:LEU242.N-BS1:PRO139.O 69.36% AS1:TYR91.N-AS1:GLY268.O 68.79% AS1:LYS202.N-AS1:LYS195.O 68.79% CS1:VAL512.N-CS1:ASP398.O 68.79% AS1:LEU585.N-AS1:VAL576.O 68.21% BS1:THR114.OG1-BS1:ASP111.OD1 68.21% CS1:TRP64.N-CS1:ALA27.O 68.21% CS1:VAL511.N-CS1:ILE434.O 68.21% AS1:ILE598.N-AS1:ALA609.O 67.63% BS2:THR1077.OG1-BS2:PHE1095.O67.05% CS1:ILE651.N-CS1:VAL610.O 67.05% AS1:ARG44.NH2-AS1:ASP40.OD1 67.05% AS1:ILE434.N-AS1:VAL511.O 67.05% BS1:VAL512.N-BS1:ASP398.O 67.05% AS1:TYR508.N-AS1:ILE402.O 67.05% AS2:GLU918.N-AS2:ASN914.O 66.47% BS2:SER1037.OG-BS2:GLU1031.OE1 66.47% CS1:LYS202.N-CS1:LYS195.O 66.47% CS1:LEU118.N-CS1:LYS129.O 66.47% BS1:ASN121.N-BS1:ARG102.O66.47% AS2:VAL1096.N-AS2:PHE1103.O 66.47%

Chapter 11

SARS (SARS-CoV-1)

Abstract Coronavirus SARS-CoV-2 spike (S) glycoproteins promote entry into cells and are the main target of antibodies and inhibitors. Angiotensin-converting enzyme 2 (ACE2) is the cellular receptor for SARS-CoV-2 and is an antiviral drug target against SARS-CoV-2. In Chap. 7, we found a strong polar contact LYS417ASP30 between the receptor-binding domain (RBD) of SARS-CoV-2 S and the human ACE2, keeping during 10 .μs of molecular dynamics (MD) simulations. Is this polar contact “unique” for SARS-CoV-2 or “common” for all coronavirus (such as SARS, MERS, etc.)? This chapter is to answer this question. The answer is that the strong polar contact LYS417-ASP30 is uniquely existing during 10 .μs only for SARS-CoV-2, but not for all coronavirus—this might be an important clue against COVID-19. As by-products, we found a strong salt bridge (with weak hydrogen bonds) GLU329-ARG426 and a strong hydrogen bond ASP355.OD2-THR486.OG1 (with occupancy rate 64.01%) between human ACE2 and SARS-CoV-1 S RBD. Keywords CoV · SARS-CoV-2 S RBD · SARS-CoV-1 RBD · MERS RBD · Human ACE2 · Polar contact LYS417-ASP30

11.1 Introduction “Coronavirus” (CoV) is an umbrella term for a family virus that shares similar properties. Some coronaviruses have been behind concerning disease outbreaks, namely, SARS (i.e., SARS-CoV-1), MERS, and SARS-CoV-2. The SARS-CoV-2 “severe acute respiratory syndrome (SARS) coronavirus 2” is the disease at the center of our current global health crisis of COVID-19. Coronavirus spike (S) glycoproteins promote entry into cells and are the main target of antibodies. The angiotensin-converting enzyme (ACE)-related carboxypeptidase, ACE2, is a type I integral membrane protein of 805 amino acids that contains 1 HEXXH + E zincbinding consensus sequence, and it has been implicated in the regulation of heart function and also as a functional receptor for coronavirus such as SARS and SARSCoV-2 [359]. SARS-CoV-2 and SARS recognize the same ACE2 in humans. The © The Author(s), under exclusive license to Springer Nature Switzerland AG 2023 J. Zhang, Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures, Springer Series in Biophysics 23, https://doi.org/10.1007/978-3-031-36773-1_11

393

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11 SARS (SARS-CoV-1)

structure of SARS RBD complexed with ACE2 is the one with PDB entry 2AJF. This brief chapter is to do molecular dynamics (MD) computations of this structure to confirm the polar contact LYS417-ASP30 is unique for SARS-CoV-2 or common for all coronavirus (such as SARS, MERS, etc.) too.

11.2 Materials and Methods The MD materials and methods can be seen from [321]: MD trajectory was initiated from ACE2 in complex with the RBD of spike protein from SARS-CoV-1 (PDB entry 2AJF). AE chains of 2AJF.pdb are used, where A chain aa SER19ASP615 is human ACE2 and E chain aa CYS323-GLU502 is RBD of SARS-CoV-1 S. “The simulations used the Amber ff99SB-ILDN force field for proteins, the CHARMM TIP3P model for water, and the generalized Amber force field for glycosylated asparagine. The C- and A- peptide termini, including those exposed due to missing loops in the published structural models, are capped with amide and acetyl groups respectively. The system was neutralized and salted with NaCl, with a final concentration of 0.15 M. The interval between frames is 1.2 ns. The simulations were conducted at 310 K in the NPT ensemble.” The MD trajectory can be downloaded under the Creative Commons Attribution 4.0 International Public License from [321], and the data ID is DESRES-ANTON-10875755 (2AJF.pdb). We denote the model as the 2AJF model. In the below, (i) firstly, AE chains of 2AJF.pdb will be optimized into a much more stable transition state—the hybrid strategy [405] of mathematical optimization’s neighboring different (local search) algorithms is used in the optimization; (ii) secondly, we will present some important structural bioinformatics from the structure optimized; and (iii) we then prove the structural bioinformatics of (ii) from the analyses of the MD data of [321]. The noncovalent interactions of hydrogen bonds (HBs), salt bridges (SBs), van der Waals (vdWs) contacts, and hydrophobic (HYD) interactions are driving a protein to be able to perform its biological functions. This chapter will find out the HBs, SBs, HYD interactions, and vdWs contacts of each model from the large MD trajectory data and evaluate the reliability of the MD trajectory data.

11.3 New Structural Bioinformatics We optimized the AE chains of 2AJF.pdb and got an optimized structure (denoted as 2AJF-AEchains-Optimized ) with 2.102410 Å of RMSD value from its original structure. For the 2AJF-AEchains-Optimized structure, we found 1 SB A:GLU329E:ARG426 between A chain and E chain, 2 SBs E:ASP429-E:ARG495 and E:ASP385-E:ARG342 in E chain, and 17 SBs in A chain, A:ASP201-A:ARG219, A:GLU208-A:ARG219, A:GLU37-A:ARG393, A:GLU457-A:ARG460, A:ASP509-A:LYS187,

11.3 New Structural Bioinformatics

395

A:GLU406-A:HIS374, A:ASP355-A:ARG357, A:ASP431-A:LYS288, A:GLU435-A:HIS540, A:GLU310-A:ARG306, A:GLU402-A:HIS378 (GLU402-HIS374), A:GLU435-A:LYS541, A:GLU402-A:HIS374, A:ASP597-A:LYS600, A:GLU182-A:ARG115 (here, GLU189LYS112 of Chap. 7 was replaced), A:GLU227-A:LYS458, and A:ASP543-A:HIS417 (here,

GLU495-ARG177 and GLU181-ARG177 of Chap. 7 were lost); 87 HBs; 10 π -cations E:LYS323.N-E:PHE325, E:TYR383-E:ARG342.NH2-E:PHE451, E:ARG453.NH2-

.

E:TRP340, A:ARG357.NH2-A:TYR48, A:ARG273.NH2-A:TYR515, A:ARG169.NH2A:TRP165, A:ARG204.NH2-A:TRP461 (2), and A:LYS174.NZ-A:TYR497; 28 .π -.π stackings E:TYR202-E:TYR196, E:PHE460-E:HIS445, E:TYR410-E:TRP340 (2), E:TYR484E:TYR41, E:TRP69-E:PHE40, A:TYR255-A:HIS265 (2), A:TRP459-A:TRP477-A:TRP478 (2), A:PHE504-A:HIS505-A:PHE512/A:TYR515, A:TYR48-A:TRP349 (2), A:TYR497-A:HIS493, A:PHE523-A:TYR587-A:PHE588, A:TYR385-A:TYR381, A:TYR217-A:TRP566, A:PHE400A:PHE525, A:PHE315-A:PHE314-A:HIS373-A:PHE369, A:PHE327-A:TRP328 (2), and A:TYR127-A:TRP168; and its Poison-Boltzmann electrostatic potential surface,

hydrophobic/hydrophilic surface, secondary structure, SASA, etc.; we know that E chain (i.e., RBD of spike) has high Psi degrees and low Phi degrees. For the 10 .μs MD simulation trajectory data [321], there are 8335 frames with frame interval 1.2 ns. From the 8335 frames, we got 189 SBs and 4696 HBs (we list the HBs with more than 50% occupancy rates during the 10 .μs’ MD simulations (Figs. 11.2 and 11.3) for the 2AJF-model in Table 11.6). We can confirm a strong polar contact E:ASP429-E:ARG495 in chain E (i.e., the RBD of spike) (Fig. 11.3) (HBs E:ARG495.NE-E:ASP429.OD2 is with 56.12% occupancy rate, and E:ARG495.NH2-E:ASP429.OD1 is with 51.34% occupancy rate); the strong SBs ASP431-LYS288 (with HBs LYS288.NZ-ASP431.OD2 (15.87%) and LYS288.NZ-ASP431.OD1 (15.60%)—where in the bracket are the HB occupancy rates), ASP509-LYS187 (with HBs LYS187.NZ-ASP509.OD1 (18.21%) and LYS187.NZ-ASP509.OD2 (12.86%)), GLU435-LYS541 (with HBs LYS541.NZ-GLU435.OE1 (12.97%) and LYS541.NZGLU435.OE2 (12.37%)), ASP201-ARG219 (with HBs ARG219.NE-ASP201.OD2 (26.55%), ARG219.NH2-ASP201.OD1 (23.78%), ARG219.NE-ASP201.OD1 (13.32%), ARG219.NH2ASP201.OD2 (10.39%), and ARG219.NE-ASP201.CG (0.05%)), GLU182-ARG115 (with HBs ARG115.NH1-GLU182.OE1 (22.27%), ARG115.NH1-GLU182.OE2 (21.55%), ARG115.NEGLU182.OE2 (20.02%), and ARG115.NE-GLU182.OE1 (19.53%)), ASP355-ARG357 (with HBs ARG357.NH1-ASP355.OD2 (64.24%) and ARG357.NE-ASP355.OD1 (57.47%)), ASP597LYS600 (with HBs LYS600.NZ-ASP597.OD1 (11.97%) and LYS600.NZ-ASP597.OD2 (11.66%)), and GLU227-LYS458 in chain A (i.e., human ACE2) (Fig. 11.3); and a

strong SB A:GLU329-E:ARG426 between chain A and chain E (but with weak HBs E:ARG426.NH2-A:GLU329.OE1 (6.42%), E:ARG426.NH2-A:GLU329.OE2 (6.23%), E:ARG426.NH1-A:GLU329.OE2 (4.27%), and E:ARG426.NH1-

396

11 SARS (SARS-CoV-1)

A:GLU329.OE1 (4.01%)) of the 2AJF-AEchains-Optimized model; we illuminate some important SBs in Fig. 11.1, where we know the SB A:GLU329-E:ARG426 is very strong and A:GLU23-E:LYS465 and A:GLU37-E:LYS390 are very weak (HBs E:LYS465.NZ-A:GLU23.OE2, E:LYS465.NZ-A:GLU23.OE1, E:LYS390.NZA:GLU37.OE1, and E:LYS390.NZ-A:GLU37.OE2 are also very weak with low occupancy rates 0.17%, 0.13%, 0.32%, and 0.28%, respectively). In Chap. 7, we found at GLU329 of human ACE2, there is a very strong polar contact linking to the residue ARG439 of SARS-CoV-2 S RBD—where the structure of 6VW1.pdb was determined based on SARS’ template so that we found the polar contact GLU329-ARG439. At position 417 for SARS-CoV-1 is a strictly hydrophobic residue MET417 (2AJF.pdb). For SARS-CoV-1, we cannot find a strong polar contact at 417 of spike RBD linking to ASP30 of human ACE2.For MERS-CoV, its host binding to is the DPP4 receptor, not the ACE2; thus, here, we cannot do a comparison for the ACE2 between MERS-CoV-1 and SARS-CoV-2. For SARSCoV-1, from Table 11.6, we found a strong HB E:THR486.OG1-A:ASP355.OD2 with occupancy rate 64.01% during the whole 10 .μs of MD.

For the MD, during the 10 .μs starting from about the 2450th frame, RMSD values (Fig. 11.2) equilibrate around 4.2 Å, and the whole RMSD values of 8335 frames (whose frame interval is 1.2 ns) vary within about 2 Å—this implies to us the MD is very reliable; larger RMSF values (Fig. 11.2) are mainly at segments 129–139, 336–346, 371–381, and 461–471 and the C-terminal around residue 609. The secondary structure developments have no significant changes in 10 .μs, but the segments 77–82, 146–147, 171–175, 249–252, 275–281, 332–342, 422–431, 492–509, and 607–615 of human ACE2 and the segments 323–334, 345–358, 367– 382, and 418–501 of the spike have changes during the 10 .μs of MD (Figs. 11.4 and 11.2).

11.3 New Structural Bioinformatics

397

Fig. 11.1 Important SBs A:GLU329-E:ARG426, AGLU23-ELYS465, AGLU37-ELYS390, etc. of the 2AJF model between the SARS-CoV-1 spike and the human ACE2 confirmed by MD data in [321]

Fig. 11.2 The RMSD and RMSF performances of the MD of the 2AJF model for SARS-CoV-1

11.3.1 SARS-CoV-1 Spike in Folding@home We got the SARS-CoV-1 spike (trimer, 5x58.pdb) 741 .μs’ MD free data of Folding@home (https://foldingathome.org/) from website https://osf.io/fs2yv/file [439]. The spike trimer has AB chains (ARG18-ARG667, SER668-VAL1104), CD chains (ARG18-ARG667, SER668-VAL1104), and EF chains (ARG18ARG667, SER668-VAL1104). In the optimized AB chains, i.e., the spike monomer, we found .π -cations B:TRP868-B:ARG887.NH2+-B:TRP868, B:ARG1021.NH2+B:PHE1024-B:LYS1010.NZ+, A:ARG453.NH2+-A:TRP340, A:LYS221.NZ+-A:PHE193, A:PHE59-A:LYS188.NZ+-A:TYR195, A:ARG183.NH2+-A:HIS181, and A:ARG207.NH2+A:HIS70 and .π -.π stackings B:TRP868-B:TYR886-B:TRP868, B:TYR771-B:PHE870, B:PHE784-B:PHE779, B:PHE1034-B:PHE784-B:PHE880-B:PHE782-B:PHE909, A:TRP423A:PHE361-A:PHE329, A:TYR646-B:TYR677, A:TYR440-A:TYR481-A:PHE483, A:TRP340A:TYR410-A:TRP340, A:PHE89-A:TRP101-A:PHE185, A:HIS70-A:PHE253-A:HIS33, and A:PHE22-A:PHE76-A:TRP245. The optimized trimer has the following SBs:

◦ B:ASP1023-B:LYS1027, D:ASP1023-D:LYS1027, F:ASP1023-F:LYS1027 ◦ B:ASP1100-F:ARG1073, D:ASP1100-B:ARG1073, F:ASP1100-D:ARG1073

. .

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11 SARS (SARS-CoV-1)

E:ASP134-E:ARG232 A:ASP171-A:LYS175, C:ASP171-C:LYS175, E:ASP171-E:LYS175 A:ASP191-A:LYS190, C:ASP191-C:LYS190, E:ASP191-E:LYS190 C:ASP267-C:LYS265 A:ASP277-A:ARG620, C:ASP277-C:ARG620, E:ASP277-E:ARG620 A:ASP376-A:LYS373, A:ASP376-A:LYS514, C:ASP376-C:LYS514, E:ASP376-E:LYS514 A:ASP385-A:ARG342, C:ASP385-C:ARG342, E:ASP385-E:ARG342 A:ASP392-A:ARG395, C:ASP392-C:LYS390, E:ASP392-E:ARG395, A:ASP393-A:LYS390, E:ASP393-E:LYS390 C:ASP407-C:LYS411, E:ASP407-E:LYS411, E:ASP407-E:LYS447 A:ASP414-A:LYS411 A:ASP415-C:LYS190, C:ASP415-E:LYS190, E:ASP415-A:LYS190 A:ASP429-A:ARG495, C:ASP429-C:ARG495, E:ASP429-E:ARG495 A:ASP44-A:ARG48, C:ASP44-C:ARG48, E:ASP44-E:ARG48 A:ASP454-A:ARG441, C:ASP454-C:ARG441, E:ASP454-E:ARG441, A:ASP454-A:ARG444, C:ASP454-C:ARG444, E:ASP454-E:ARG444 A:ASP463-A:LYS465, C:ASP463-C:LYS465, E:ASP463-E:LYS465 A:ASP480-A:LYS439, C:ASP480-C:LYS439, E:ASP480-E:LYS439 A:ASP50-A:LYS265, E:ASP50-E:LYS265 A:ASP554-D:LYS836, C:ASP554-F:LYS836, E:ASP554-B:LYS836 A:ASP557-D:ARG982, C:ASP557-F:ARG982, E:ASP557-B:ARG982 A:ASP560-A:LYS543, C:ASP560-C:LYS543, E:ASP560-E:LYS543, A:ASP560-D:LYS836 A:ASP57-A:LYS188, C:ASP57-C:LYS188, E:ASP57-E:LYS188 A:ASP649-A:LYS297, C:ASP649-C:LYS297, E:ASP649-E:LYS297 B:ASP757-B:ARG761, D:ASP757-D:ARG761, F:ASP757-F:ARG761 B:ASP790-B:LYS777, D:ASP790-D:LYS777, F:ASP790-F:LYS777 B:ASP802-B:ARG797 D:ASP802-D:LYS793, F:ASP802-F:LYS793 F:ASP812-F:LYS817 F:ASP825-F:ARG829 B:ASP830-B:ARG829, D:ASP830-D:ARG829 D:ASP849-D:ARG797, F:ASP849-F:ARG797 A:ASP85-A:LYS84, C:ASP85-A:ARG449, E:ASP85-C:ARG449 B:ASP850-B:LYS796, D:ASP850-D:ARG797, D:ASP850-D:LYS796, F:ASP850-F:ARG797, F:ASP850-F:LYS796 B:ASP932-B:LYS929, D:ASP932-D:LYS929, F:ASP932-F:LYS929 B:ASP961-B:ARG965, D:ASP961-D:ARG965, F:ASP961-F:ARG965 B:ASP976-F:ARG977, D:ASP976-B:ARG977, F:ASP976-D:ARG977 B:GLU1013-B:ARG1021, B:GLU1013-F:ARG1021, D:GLU1013-B:ARG1021, D:GLU1013-D:ARG1021, F:GLU1013-D:ARG1021, F:GLU1013-F:ARG1021 D:GLU1054-D:ARG1055 B:GLU1066-B:HIS1065, D:GLU1066-D:HIS1065, F:GLU1066-F:HIS1065 B:GLU1074-B:ARG1089, D:GLU1074-D:ARG1089, F:GLU1074-F:ARG1089

11.3 New Structural Bioinformatics

◦ ◦ .◦ .◦ .◦ .◦ .◦ .◦ .◦ .◦ .◦ . .

◦ ◦ .◦ .◦ .◦ .◦ . .

399

E:GLU162-E:ARG126 A:GLU174-A:LYS142, C:GLU174-C:LYS142, E:GLU174-E:LYS142 A:GLU184-A:ARG38, C:GLU184-C:ARG38, E:GLU184-E:ARG38 A:GLU268-E:ARG544, C:GLU268-A:ARG544, E:GLU268-C:ARG544 A:GLU294-A:LYS287, C:GLU294-C:LYS287, E:GLU294-E:LYS287 A:GLU327-A:LYS343, C:GLU327-C:LYS343, E:GLU327-E:LYS343 A:GLU502-C:LYS221, C:GLU502-E:LYS221, E:GLU502-A:LYS221 A:GLU593-A:ARG667 A:GLU640-F:LYS672 A:GLU647-D:LYS768, C:GLU647-F:LYS768, E:GLU647-B:LYS768 B:GLU707-B:LYS1010, D:GLU707-D:LYS1010, F:GLU707-F:LYS1010, F:GLU707-F:HIS1046 B:GLU730-B:LYS968, D:GLU730-D:LYS968, F:GLU730-F:LYS968 B:GLU755-B:ARG1001, D:GLU755-D:ARG1001, F:GLU755-F:ARG1001 B:GLU762-B:ARG758, F:GLU762-F:ARG758, F:GLU762-F:ARG761 B:GLU900-F:LYS1068, D:GLU900-B:LYS1068, F:GLU900-D:LYS1068 A:GLU93-A:ARG99, C:GLU93-C:ARG99, E:GLU93-E:ARG99 B:GLU999-D:ARG1001, D:GLU999-F:ARG1001, F:GLU999-B:ARG1001.

The HBs of MD of 5x58 SARS-CoV-1 spike trimer with occupancy rates .≥30% during the 741 .μs’ MD are listed in Tables 11.1 and 11.2.

11.3.2 HCoV-NL63 Spike in Folding@home SARS-CoV-1 caused an outbreak in 2003 with a high case fatality rate but has not become a pandemic. NL63 was discovered in the following year and continues to spread around the globe but is substantially less lethal than either SARS virus [381]. Human coronavirus 229E and OC43 are another two human coronaviruses. We got the HCoV-NL63 spike (trimer) 651 .μs’ MD free data of Folding@home (https://foldingathome.org/) from website https://osf.io/fs2yv/file [439]. The trimer has ABC chains; in each chain, there are 1202 residues ALA23PHE1224. In the optimized A chain, we get .π -cations ARG1204.NH2+-TYR1153, ARG1105.NH2+-PHE1108-LYS1094.NZ+, ARG870.NH2+-PHE878, ALA23.N+TYR204, LYS311.NZ+-PHE342, and LYS390.NZ+-TYR587 and .π -.π stackings PHE840-PHE835, PHE848-PHE950-TYR851, HIS71-TYR176, TYR893-

400

11 SARS (SARS-CoV-1)

TYR910, PHE230-TRP235, TYR298-PHE402-PHE142, PHE317-PHE384, TRP600-PHE552-TRP600, PHE560-TYR473, PHE493-TRP541-TRP585-HIS586, and TRP541-TRP585-TRP541. The optimized trimer has the following SBs: ◦ ◦ .◦ .◦ .◦ . .

◦ ◦ .◦ .◦ .◦ .◦ . .

◦ ◦ .◦ .◦ .◦ . .

◦ ◦ .◦ .◦ .◦ .◦ .◦ .◦ . .

◦

.

◦ ◦ .◦ .◦ . .

◦ ◦ .◦ .◦ .◦ . .

A:ASP1048-B:LYS629, B:ASP1048-C:LYS629, C:ASP1048-A:LYS629 A:ASP1051-B:LYS556, B:ASP1051-C:LYS556, C:ASP1051-A:LYS556 A:ASP1150-A:ARG1204, B:ASP1150-B:ARG1204, C:ASP1150-C:ARG1204 A:ASP1167-A:ARG1172, B:ASP1167-B:ARG1172, C:ASP1167-C:ARG1172 A:ASP1188-B:ARG1158, B:ASP1188-C:ARG1158, C:ASP1188-A:ARG1158, A:ASP1188-A:ARG1182, B:ASP1188-B:ARG1182, C:ASP1188-C:ARG1182 A:ASP125-A:LYS107, B:ASP125-B:LYS107, C:ASP125-C:LYS107 A:ASP223-A:ARG225, B:ASP223-B:ARG225, C:ASP223-C:ARG225 A:ASP393-A:LYS390, B:ASP393-B:LYS390, C:ASP393-C:LYS390 A:ASP411-A:LYS311, B:ASP411-B:LYS311, C:ASP411-C:LYS311 A:ASP422-A:ARG250, B:ASP422-B:ARG250, C:ASP422-C:ARG250 A:ASP439-A:ARG225, B:ASP439-B:ARG225, C:ASP439-C:ARG225, A:ASP439-A:ARG256, B:ASP439-B:ARG256, C:ASP439-C:ARG256 A:ASP466-C:ARG799, C:ASP466-B:ARG799 A:ASP484-A:ARG525, B:ASP484-B:ARG525, C:ASP484-C:ARG525 A:ASP634-A:LYS562, B:ASP634-B:LYS562, C:ASP634-C:LYS562 A:ASP682-A:ARG702, B:ASP682-B:ARG702, C:ASP682-C:ARG702 A:ASP816-A:ARG819, B:ASP816-B:ARG819, C:ASP816-C:ARG819, A:ASP816-A:LYS812, B:ASP816-B:LYS812, C:ASP816-C:LYS812 A:ASP828-A:ARG1088, B:ASP828-B:ARG1088, C:ASP828-C:ARG1088 A:ASP83-A:LYS167, B:ASP83-B:LYS167, C:ASP83-C:LYS167 A:ASP850-A:LYS973, B:ASP850-B:LYS973, C:ASP850-C:LYS973 B:ASP875-B:ARG870 A:ASP892-A:LYS894, B:ASP892-B:LYS894, C:ASP892-C:LYS894 C:ASP922-C:ARG925 A:GLU1002-A:ARG748, B:GLU1002-B:ARG748, C:GLU1002-C:ARG748 A:GLU1083-A:LYS1080, B:GLU1083-B:LYS1080, C:GLU1083-C:LYS1080, A:GLU1083-C:ARG1089 A:GLU1097-A:ARG1105, A:GLU1097-B:ARG1105, B:GLU1097-B: ARG1105, B:GLU1097-C:ARG1105, C:GLU1097-A:ARG1105, C:GLU1097C:ARG1105 A:GLU1223-A:LYS1219, B:GLU1223-B:LYS1219, C:GLU1223-C:LYS1219 A:GLU375-A:ARG297, B:GLU375-B:ARG297, C:GLU375-C:ARG297 A:GLU398-A:LYS318, B:GLU398-B:LYS318, C:GLU398-C:LYS318 A:GLU448-A:ARG250, B:GLU448-B:ARG250, C:GLU448-C:ARG250, A:GLU448-C:LYS801, B:GLU448-A:LYS801, C:GLU448-B:LYS801 A:GLU471-A:LYS629, B:GLU471-B:LYS629, C:GLU471-C:LYS629 A:GLU582-A:LYS546, B:GLU582-B:LYS546, C:GLU582-C:LYS546 A:GLU602-C:ARG1049, B:GLU602-A:ARG1049, C:GLU602-B:ARG1049 A:GLU618-A:ARG617, B:GLU618-B:ARG617, C:GLU618-C:ARG617 A:GLU700-A:ARG702, B:GLU700-B:ARG702, C:GLU700-C:ARG702

Supplementary Information

401

◦ A:GLU776-A:HIS1130, B:GLU776-B:HIS1130, C:GLU776-C:HIS1130, A:GLU776-A:LYS1094, B:GLU776-B:LYS1094, C:GLU776-C:LYS1094 .◦ A:GLU825-A:ARG1085, B:GLU825-B:ARG1085, C:GLU825-C:ARG1085, A:GLU825-A:ARG1088, B:GLU825-B:ARG1088, C:GLU825-C:ARG1088 .◦ A:GLU924-A:ARG746 .◦ A:GLU94-A:ARG72, B:GLU94-B:ARG72, C:GLU94-C:ARG72. .

The HBs of MD of HCoV-NL63 spike trimer with occupancy rates .≥30% during the 651 .μs’ MD are listed in Tables 11.3, 11.4, and 11.5.

11.4 Concluding Remarks In Chap. 7, we found a strong polar contact LYS417-ASP30 between the RBD of SARS-CoV-2 S and the human ACE2, keeping during 10 .μs of MD. Is this polar contact “unique” for SARS-CoV-2 or “common” for all coronavirus (such as SARS, MERS, etc.)? This chapter answered this question. The answer is: the strong polar contact LYS417-ASP30 is uniquely existing during 10 .μs only for SARS-CoV-2, but not for all coronavirus such as SARS and MERS. As by-products, we found a strong SB (with weak HBs) GLU329-ARG426 and a strong HB ASP355.OD2THR486.OG1 (with occupancy rate 64.01%) between the human ACE2 and the RBD of SARS-CoV-1 S (Table 11.6).

Supplementary Information

402

11 SARS (SARS-CoV-1)

Fig. 11.3 Some strong SBs of the 2AJF model confirmed by MD trajectory data in [321]

Supplementary Information

403

Fig. 11.4 The secondary structure developments of the MD of the 2AJF model for SARS-CoV-1 (where the frame interval is 12 ns)

404

Fig. 11.4 (continued)

11 SARS (SARS-CoV-1)

D:SER701.N-D:VAL1050.O 54.10%

B:SER703.N-B:THR1048.O 54.10%

F:GLN756.NE2-F:ILE752.O 54.10%

F:THR991.OG1-F:GLN987.O 54.10%

C:ILE573.N-C:ASP560.O 54.10%

A:VAL525.N-A:GLY536.O 54.10%

C:VAL124.N-C:ILE117.O 54.10%

D:VAL1076.N-D:THR1087.O 54.10%

F:VAL1076.N-F:THR1087.O 54.10%

C:ASP429.N-C:THR425.O 54.10%

F:GLU1013.N-F:THR1009.O 54.10%

D:THR921.OG1-D:GLN917.O 54.10%

D:THR988.OG1-D:GLN984.O 54.10%

E:TYR88.N-E:GLY255.O 54.10%

A:ILE115.N-A:ARG126.O 54.10%

D:VAL1078.N-D:PHE1085.O 52.46%

B:THR863.OG1-B:LEU859.O 52.46%

B:THR760.OG1-B:GLN756.O 52.46%

F:VAL675.N-E:SER659.O 52.46%

B:VAL675.N-A:SER659.O 52.46%

E:VAL290.N-E:LEU286.O 52.46%

A:ALA237.N-A:PHE138.O 52.46%

E:ALA237.N-E:PHE138.O 52.46%

C:TYR438.OH-C:ASP429.OD1 52.46%

E:ASP267.N-E:THR271.O 52.46%

A:GLY552.N-A:SER561.O 52.46%

E:VAL642.N-F:ALA676.O 52.46%

F:THR980.N-F:ASP976.O 52.46%

C:ALA237.N-C:PHE138.O 52.46%

A:ILE116.N-A:TRP101.O 52.46%

B:THR865.OG1-B:SER861.O 50.82%

B:GLU1013.N-B:THR1009.O 50.82%

D:MET770.N-B:ALA683.O 50.82%

B:SER798.N-B:GLU801.OE1 50.82%

E:LYS287.N-E:LEU283.O 50.82%

D:VAL945.N-D:LEU941.O 50.82%

D:ARG982.NH1-D:ILE724.O 50.82%

A:ASP564.N-A:GLU569.O 50.82%

E:ILE125.N-E:TYR163.O 50.82%

D:THR922.OG1-D:GLU918.O 50.82%

A:VAL497.N-A:LEU421.O 81.97%

F:VAL990.N-F:LEU986.O 80.33%

B:VAL1043.N-B:GLN1036.O 80.33%

F:VAL1043.N-F:GLN1036.O 73.77%

E:VAL124.N-E:ILE117.O 73.77%

E:VAL497.N-E:LEU421.O 73.77%

B:VAL860.N-B:THR856.O 72.13%

C:VAL254.N-C:THR67.O 72.13%

A:TYR41.OH-A:LEU58.O 70.49%

F:THR865.OG1-F:SER861.O 68.85%

F:VAL860.N-F:THR856.O 68.85%

F:THR856.OG1-F:GLU801.OE2 68.85%

A:ASP267.N-A:THR271.O 68.85%

A:VAL124.N-A:ILE117.O 68.85%

C:VAL498.N-C:ASP385.O 68.85%

C:VAL497.N-C:LEU421.O 68.85%

D:VAL1043.N-D:GLN1036.O 67.21%

E:VAL496.N-E:PHE387.O 67.21%

E:VAL254.N-E:THR67.O 67.21%

E:VAL498.N-E:ASP385.O 67.21%

F:SER798.N-F:GLU801.OE1 65.57%

D:VAL711.N-D:HIS1040.O 65.57%

B:VAL990.N-B:LEU986.O 65.57%

A:VAL537.N-A:SER574.O 65.57%

C:VAL537.N-C:SER574.O 65.57%

A:VAL102.N-A:ARG232.O 65.57%

A:VAL114.N-A:PHE103.O 65.57%

B:VAL1050.N-B:SER701.O 65.57%

D:VAL1050.N-D:SER701.O 65.57%

F:ILE979.N-F:ILE975.O 63.93%

B:VAL711.N-B:HIS1040.O 63.93%

D:VAL990.N-D:LEU986.O 63.93%

D:THR865.OG1-D:SER861.O 63.93%

F:GLN1018.NE2-F:HIS1030.O 62.30%

F:ALA1004.N-F:ILE1000.O 62.30%

D:ALA1004.N-D:ILE1000.O 62.30%

E:PHE47.N-C:PHE551.O 62.30%

A:VAL254.N-A:THR67.O 62.30%

E:VAL102.N-E:ARG232.O 62.30%

A:VAL498.N-A:ASP385.O 62.30%

A:SER279.OG-A:ASP277.OD2 44.26%

D:ILE1000.N-D:ARG996.O 44.26%

F:THR760.OG1-F:GLN756.O 44.26%

B:VAL1042.N-B:MET709.O 44.26%

C:SER113.N-C:CYS128.O 44.26%

A:ALA127.N-A:PHE161.O 44.26%

C:VAL420.N-C:LYS365.O 44.26%

C:LYS142.N-C:SER239.O 44.26%

E:ILE573.N-E:ASP560.O 44.26%

D:SER717.N-D:THR841.O 44.26%

F:ILE1000.N-F:ARG996.O 44.26%

B:TYR677.OH-A:GLU647.O 44.26%

D:THR856.OG1-D:GLU801.OE2 44.26%

D:GLU1013.N-D:THR1009.O 44.26%

B:SER1052.N-B:ASN699.O 44.26%

F:PHE1057.N-F:ILE694.O 44.26%

E:ASP429.N-E:THR425.O 45.90%

E:CYS635.N-E:GLN599.O 45.90%

F:TYR677.OH-E:GLU647.O 45.90%

A:PHE460.N-A:TYR475.O 45.90%

E:THR229.N-E:GLY104.O 45.90%

C:ILE116.N-C:TRP101.O 45.90%

C:LEU194.N-C:LEU222.O 45.90%

F:SER750.N-F:ASN746.O 45.90%

B:PHE1044.N-B:GLU707.O 45.90%

C:ASP385.N-C:VAL498.O 45.90%

A:CYS133.N-A:ILE152.O 45.90%

A:VAL140.N-A:ALA237.O 45.90%

A:LYS258.N-A:PHE59.O 45.90%

E:TYR88.OH-E:GLU184.OE2 45.90%

E:ASP572.N-E:THR539.O 45.90%

F:PHE1044.N-F:GLU707.O 45.90%

D:SER798.N-D:GLU801.OE1 45.90%

B:THR1048.N-B:SER703.O 45.90%

B:VAL1047.N-B:MET1032.O 45.90%

E:VAL66.N-E:HIS33.O 45.90%

A:PHE262.N-A:THR55.O 45.90%

C:THR608.OG1-C:THR604.O 45.90%

D:ALA1008.N-D:ALA1004.O 45.90%

B:TYR1049.N-B:TYR1029.O 45.90%

Table 11.1 The HBs of MD of 5x58 SARS-CoV-1 spike trimer with occupancy rates ≥30% during the 741 μs’ MD

(continued)

A:GLU93.N-A:HIS181.O 40.98%

C:PHE47.N-A:PHE551.O 40.98%

A:LEU571.N-A:VAL562.O 40.98%

B:THR980.N-B:ASP976.O 40.98%

D:THR991.OG1-D:GLN987.O 40.98%

D:ALA676.N-C:GLU640.O 40.98%

D:GLN931.N-D:LEU927.O 40.98%

F:VAL1042.N-F:MET709.O 40.98%

F:MET770.N-D:ALA683.O 40.98%

D:PHE909.N-D:ILE905.O 40.98%

D:PHE1085.N-D:VAL1078.O 40.98%

D:ILE1086.N-D:GLN1095.O 40.98%

C:ILE81.N-C:PHE231.O 42.62%

A:GLU184.N-A:GLY199.O 42.62%

E:SER607.OG-E:CYS603.O 42.62%

E:VAL314.N-E:ASN528.O 42.62%

A:ILE203.N-A:LYS180.O 42.62%

D:GLN984.N-D:THR980.O 42.62%

E:TYR266.N-E:THR51.O 42.62%

A:LYS287.N-A:LEU283.O 42.62%

D:GLN936.N-D:ASP932.O 42.62%

C:GLU184.N-C:GLY199.O 42.62%

C:VAL276.N-C:MET263.O 42.62%

A:TYR266.N-A:THR51.O 42.62%

F:SER861.N-F:ALA857.O 42.62%

F:GLN883.NE2-F:THR863.O 42.62%

E:GLU131.N-E:ASN155.O 42.62%

A:PHE47.N-E:PHE551.O 42.62%

C:MET263.N-C:VAL276.O 42.62%

A:SER289.OG-A:GLU285.O 42.62%

C:LYS287.N-C:LEU283.O 42.62%

E:CYS657.N-F:TYR677.O 42.62%

D:THR1048.N-D:SER703.O 42.62%

C:ARG495.NH2-C:ASP429.OD1 42.62%

E:ILE116.N-E:TRP101.O 42.62%

A:LYS142.N-A:SER239.O 42.62%

C:TYR195.N-C:LYS188.O 42.62%

F:GLN987.N-F:LEU983.O 42.62%

B:ARG747.N-B:THR743.O 42.62%

A:CYS657.N-B:TYR677.O 42.62%

Supplementary Information 405

D:THR863.OG1-D:LEU859.O 50.82%

C:VAL307.N-C:GLN614.O 50.82%

A:SER461.N-A:LYS465.O 50.82%

E:CYS133.N-E:ILE152.O 50.82%

F:SER798.OG-F:GLN1036.OE1 50.82%

D:SER798.OG-D:GLN1036.OE1 49.18%

B:TYR723.N-B:ASP719.O 49.18%

C:TYR266.N-C:THR51.O 49.18%

E:VAL562.N-E:LEU571.O 49.18%

B:LEU735.N-B:CYS731.O 49.18%

A:TYR88.N-A:GLY255.O 49.18%

A:VAL97.N-A:GLU93.OE1 49.18%

C:ALA127.N-C:PHE161.O 49.18%

D:LEU966.N-D:ILE962.O 49.18%

A:SER141.N-A:THR146.O 49.18%

C:SER141.N-C:THR146.O 49.18%

E:SER113.N-E:CYS128.O 49.18%

C:SER461.N-C:LYS465.O 49.18%

C:GLU131.N-C:ASN155.O 49.18%

E:THR425.OG1-E:ASP429.OD2 49.18%

B:MET770.N-F:ALA683.O 47.54%

C:VAL290.N-C:LEU286.O 62.30%

C:VAL114.N-C:PHE103.O 62.30%

B:GLN756.NE2-B:ILE752.O 60.66%

C:ASP572.N-C:THR539.O 60.66%

F:VAL1078.N-F:PHE1085.O 59.02%

F:GLN931.N-F:LEU927.O 59.02%

F:VAL945.N-F:LEU941.O 59.02%

E:VAL537.N-E:SER574.O 59.02%

E:VAL114.N-E:PHE103.O 59.02%

B:VAL1078.N-B:PHE1085.O 59.02%

B:SER701.N-B:VAL1050.O 57.38%

B:THR856.OG1-B:GLU801.OE2 57.38%

F:ALA1037.N-F:GLU801.OE2 57.38%

B:ALA1004.N-B:ILE1000.O 57.38%

F:ASN759.N-F:GLU755.O 57.38%

A:VAL642.N-B:ALA676.O 57.38%

A:ASP572.N-A:THR539.O 57.38%

B:ILE979.N-B:ILE975.O 57.38%

E:ILE115.N-E:ARG126.O 57.38%

C:VAL642.N-D:ALA676.O 57.38%

B:VAL945.N-B:LEU941.O 57.38%

A:PHE231.N-A:ILE81.O 47.54%

A:SER113.N-A:CYS128.O 47.54%

A:VAL66.N-A:HIS33.O 55.74%

A:GLU131.N-A:ASN155.O 55.74%

A:GLN546.N-A:GLN549.OE1 47.54%

E:VAL98.N-E:GLU93.OE1 47.54%

B:LEU966.N-B:ILE962.O 47.54%

E:TYR438.OH-E:ASP429.OD1 55.74%

B:ILE1000.N-B:ARG996.O 55.74%

A:VAL496.N-A:PHE387.O 55.74%

D:GLN1036.NE2-D:PRO1035.O 47.54%

B:THR922.OG1-B:GLU918.O 47.54%

E:ASP564.N-E:GLU569.O 55.74%

D:ILE979.N-D:ILE975.O 55.74%

C:ASP564.N-C:GLU569.O 47.54%

A:VAL98.N-A:GLU93.OE2 47.54%

C:PHE262.N-C:THR55.O 55.74%

C:VAL525.N-C:GLY536.O 55.74%

A:THR608.OG1-A:THR604.O 47.54%

F:SER1019.OG-F:GLU1013.OE1 50.82%

D:VAL675.N-C:SER659.O 62.30%

D:LEU735.N-D:CYS731.O 47.54%

C:LEU499.N-C:CYS419.O 50.82%

C:VAL496.N-C:PHE387.O 62.30%

F:THR863.OG1-F:LEU859.O 55.74%

E:VAL420.N-E:LYS365.O 50.82%

F:VAL711.N-F:HIS1040.O 62.30%

D:GLN987.N-D:LEU983.O 55.74%

E:VAL140.N-E:ALA237.O 50.82%

F:VAL1050.N-F:SER701.O 62.30%

B:ALA1037.N-B:GLU801.OE2 47.54%

E:PHE262.N-E:THR55.O 50.82%

C:TYR88.N-C:GLY255.O 62.30%

D:TYR677.OH-C:GLU647.O 47.54%

B:THR988.OG1-B:GLN984.O 50.82%

C:ASP267.N-C:THR271.O 62.30%

C:VAL66.N-C:HIS33.O 57.38%

C:CYS657.N-D:TYR677.O 50.82%

A:VAL290.N-A:LEU286.O 62.30%

F:GLN1036.NE2-F:PRO1035.O 57.38%

D:VAL1042.N-D:MET709.O 50.82%

D:VAL860.N-D:THR856.O 62.30%

Table 11.1 (continued)

C:SER289.OG-C:GLU285.O 47.54%

A:VAL596.N-A:ILE584.O 47.54%

E:SER141.N-E:THR146.O 47.54%

E:VAL97.N-E:GLU93.OE1 47.54%

C:VAL98.N-C:GLU93.OE1 47.54%

F:THR943.OG1-F:GLN939.O 47.54%

F:GLN1018.NE2-F:ARG887.O 47.54%

A:ASP429.N-A:THR425.O 47.54%

D:GLN993.N-D:TYR989.O 44.26%

F:SER1003.OG-F:GLU999.O 44.26%

D:VAL1047.N-D:MET1032.O 44.26%

F:VAL1047.N-F:MET1032.O 44.26%

C:PHE89.N-C:PHE185.O 44.26%

F:ILE1086.N-F:GLN1095.O 44.26%

C:ASP154.N-C:GLU131.O 44.26%

F:LEU966.N-F:ILE962.O 44.26%

C:LEU216.N-C:VAL40.O 44.26%

A:ILE573.N-A:ASP560.O 44.26%

F:THR921.OG1-F:GLN917.O 44.26%

D:SER703.N-D:THR1048.O 44.26%

F:SER1052.N-F:ASN699.O 44.26%

E:ARG495.NH2-E:ASP429.OD1 44.26%

E:ASP385.N-E:VAL498.O 44.26%

E:LEU499.N-E:CYS419.O 44.26%

C:THR229.N-C:GLY104.O 44.26%

C:PHE231.N-C:ILE81.O 44.26%

E:ASP560.N-E:GLY552.O 40.98%

E:PHE231.N-E:ILE81.O 40.98%

E:ILE203.N-E:LYS180.O 40.98%

E:VAL606.N-E:ASN602.O 40.98%

C:ILE584.N-C:VAL596.O 40.98%

D:ALA997.N-D:GLN993.O 40.98%

B:ILE913.N-B:PHE909.O 40.98%

A:ILE428.N-A:THR425.O 40.98%

E:ALA91.N-E:ARG183.O 40.98%

C:ARG495.NE-C:ASP429.OD2 40.98%

C:VAL97.N-C:GLU93.OE1 40.98%

A:ILE584.N-A:VAL596.O 40.98%

B:SER750.N-B:ASN746.O 40.98%

B:SER717.N-B:THR841.O 40.98%

B:ALA906.N-B:GLN902.O 40.98%

B:THR1059.OG1-B:PHE1077.O 40.98%

C:THR425.OG1-C:ASP429.OD2 40.98%

A:LEU499.N-A:CYS419.O 40.98%

A:VAL420.N-A:LYS365.O 40.98%

E:LEU194.N-E:LEU222.O 40.98%

C:PHE187.N-C:ILE87.O 40.98%

406 11 SARS (SARS-CoV-1)

E:CYS278.N-E:THR261.O 31.15% E:SER279.OG-E:ASP277.OD1 31.15% A:ASP560.N-A:GLY552.O 31.15% D:THR980.N-D:ASP976.O 31.15%

A:ILE219.N-A:VAL196.O 34.43% A:LEU194.N-A:LEU222.O 34.43% A:ILE125.N-A:TYR163.O 34.43% A:ASN409.ND2-A:ILE405.O 34.43%

B:THR943.N-B:GLN939.O 37.70%

D:THR943.OG1-D:GLN939.O 37.70%

A:LEU216.N-A:VAL40.O 37.70%

C:VAL98.N-C:GLU93.OE2 37.70%

E:THR425.N-E:PRO493.O 37.70%

B:ILE694.N-B:PHE1057.O 37.70%

D:ILE694.N-D:PHE1057.O 37.70%

C:ILE115.N-C:ARG126.O 39.34%

C:GLN492.NE2-C:THR487.O 39.34%

D:ALA906.N-D:GLN902.O 39.34%

D:MET884.N-D:PHE880.O 39.34%

F:PHE909.N-F:ILE905.O 39.34%

F:SER703.N-F:THR1048.O 39.34%

D:SER1012.N-D:ALA1008.O 37.70%

E:ASN119.N-E:ASN122.O 37.70%

D:GLN883.NE2-D:THR863.O 37.70%

C:VAL606.N-C:ASN602.O 37.70%

E:TYR41.OH-E:LEU58.O 39.34%

E:ILE81.N-E:PHE231.O 39.34%

A:GLY104.N-A:ASN230.O 39.34%

A:THR425.N-A:PRO493.O 37.70%

C:THR92.N-C:ALA251.O 39.34%

A:PHE187.N-A:ILE87.O 39.34%

E:LEU636.N-E:PHE629.O 37.70%

B:ALA695.N-D:GLN877.O 37.70%

E:SER289.OG-E:GLU285.O 39.34%

E:SER461.N-E:LYS465.O 37.70%

E:ALA384.N-E:LYS343.O 37.70%

C:VAL596.N-C:ILE584.O 39.34%

F:THR988.OG1-F:GLN984.O 39.34%

C:SER370.N-F:ARG965.O 37.70%

B:ALA1008.N-B:ALA1004.O 39.34%

B:THR991.OG1-B:GLN987.O 39.34%

E:TRP101.N-E:ILE116.O 37.70%

B:GLN1036.NE2-B:PRO1035.O 37.70%

D:THR922.N-D:GLU918.O 37.70%

C:THR71.N-C:ALA250.O 39.34%

A:MET151.N-A:PHE137.O 39.34%

F:VAL767.N-F:PHE764.O 39.34%

A:ILE621.N-A:GLN280.O 34.43%

D:PHE1057.N-D:ILE694.O 37.70%

E:PHE253.N-E:ALA90.O 39.34%

E:VAL596.N-E:ILE584.O 37.70%

B:ILE696.N-B:ARG1055.O 37.70%

A:LEU182.N-A:GLN201.O 39.34%

E:GLU184.N-E:GLY199.O 37.70%

C:VAL140.N-C:ALA237.O 37.70%

E:GLY552.N-E:SER561.O 39.34%

A:ALA384.N-A:LYS343.O 39.34%

B:PHE1057.N-B:ILE694.O 31.15%

F:GLN992.N-F:THR988.O 34.43% E:ILE621.N-E:GLN280.O 34.43%

A:SER370.N-D:ARG965.O 37.70%

F:GLN993.N-F:TYR989.O 39.34%

D:ILE696.N-D:ARG1055.O 39.34%

C:ASN435.ND2-C:ASP429.O 31.15%

D:SER750.N-D:ASN746.O 34.43%

E:LEU571.N-E:VAL562.O 37.70%

F:THR922.OG1-F:GLU918.O 39.34%

B:ILE905.N-B:ASN901.O 34.43%

C:TYR383.N-C:SER500.O 34.43%

A:ASN118.N-A:ARG99.O 34.43%

E:THR148.N-E:ALA139.O 34.43%

C:ASN189.N-C:ASP85.O 34.43%

A:VAL186.N-A:TYR197.O 34.43%

B:SER964.OG-B:ASN960.O 34.43%

C:LYS258.N-C:PHE59.O 34.43%

A:VAL562.N-A:LEU571.O 34.43%

C:LEU571.N-C:VAL562.O 34.43%

C:VAL562.N-C:LEU571.O 34.43%

A:LEU264.N-A:TYR53.O 34.43%

F:ALA1007.N-F:SER1003.O 34.43%

D:ILE916.N-D:ALA912.O 34.43%

D:GLN1018.NE2-D:HIS1030.O 34.43%

B:VAL1076.N-B:THR1087.O 34.43%

F:PHE1085.N-F:VAL1078.O 34.43%

(continued)

B:VAL897.N-B:THR894.O 31.15%

A:ARG441.N-A:ASN409.OD1 31.15%

E:TYR383.N-E:SER500.O 31.15%

E:ASN189.N-E:ASP85.O 31.15%

C:PHE253.N-C:ALA90.O 31.15%

B:THR980.OG1-B:ASP976.O 31.15%

D:THR988.N-D:GLN984.O 31.15%

F:THR988.N-F:GLN984.O 31.15%

A:VAL606.N-A:ASN602.O 31.15%

A:SER607.OG-A:CYS603.O 31.15%

F:TYR677.N-E:CYS657.O 31.15%

D:LEU1045.N-D:PHE1034.O 31.15%

D:SER1052.N-D:ASN699.O 31.15%

B:PHE888.N-B:MET884.O 31.15%

A:VAL389.N-A:TYR494.O 31.15%

C:PHE460.N-C:TYR475.O 31.15%

A:TYR367.N-A:GLY418.O 31.15%

E:TYR195.N-E:LYS188.O 31.15%

E:LEU222.N-E:LEU194.O 31.15%

E:GLY255.N-E:TYR88.O 31.15%

A:LYS265.N-A:ASP274.O 37.70%

F:LYS1010.N-F:LEU1006.O 39.34%

C:ASN479.N-C:TYR440.O 34.43%

D:LYS1010.N-D:LEU1006.O 37.70%

B:THR943.OG1-B:GLN939.O 37.70%

F:ILE913.N-F:PHE909.O 39.34%

B:LEU840.N-B:ASN838.OD1 31.15%

A:SER582.N-A:TYR598.O 31.15%

B:GLN992.N-B:THR988.O 31.15%

F:GLN939.N-F:ASN935.O 31.15%

B:LEU843.N-B:LYS715.O 31.15%

D:THR1048.OG1-D:LYS1027.O 39.34%

E:VAL98.N-E:GLU93.OE2 34.43%

E:LYS258.N-E:PHE59.O 34.43%

A:GLY68.N-A:THR31.O 34.43%

F:ILE724.N-F:CYS720.O 34.43%

C:SER607.OG-C:CYS603.O 34.43%

F:ALA754.N-F:SER750.O 31.15%

A:VAL583.N-A:TYR300.O 37.70%

A:TYR383.N-A:SER500.O 39.34%

D:ALA1037.N-D:GLU801.OE2 31.15%

D:ILE975.N-D:ALA971.O 39.34%

F:SER717.N-F:THR841.O 34.43% B:THR988.N-B:GLN984.O 34.43%

F:ARG761.N-F:ASP757.O 37.70%

B:GLN993.N-B:TYR989.O 37.70%

B:THR921.OG1-B:GLN917.O 31.15%

D:GLY862.N-D:ALA858.O 31.15%

F:VAL897.N-F:THR894.O 31.15%

F:THR1059.OG1-F:PHE1077.O 31.15%

F:THR1059.OG1-F:PHE1077.O 31.15%

E:LEU182.N-E:GLN201.O 39.34%

E:VAL583.N-E:TYR300.O 34.43%

B:ARG761.N-B:ASP757.O 34.43%

D:SER919.OG-D:GLN915.O 34.43%

F:GLY867.N-F:GLY862.O 34.43%

F:GLY867.N-F:GLY862.O 34.43%

E:PHE187.N-E:ILE87.O 39.34%

D:GLU900.N-D:ASN896.O 37.70%

D:HIS1046.N-D:THR705.O 37.70%

B:PHE1085.N-B:VAL1078.O 37.70%

E:MET263.N-E:VAL276.O 39.34%

E:VAL276.N-E:MET263.O 39.34%

B:TYR1070.N-B:ILE1063.O 37.70%

D:LEU983.N-D:ILE979.O 39.34%

B:TYR1070.N-B:ILE1063.O 37.70%

E:LYS265.N-E:ASP274.O 39.34%

E:LYS265.N-E:ASP274.O 39.34%

Table 11.2 The HBs of MD 5x58 SARS-CoV-1 spike trimer with occupancy rates ≥30% during the 741 μs’ MD (continuation)

Supplementary Information 407

E:ASN435.N-E:PHE483.O 34.43% D:ILE724.N-D:CYS720.O 34.43% A:PHE83.N-A:THR229.O 34.43% C:LEU222.N-C:LEU194.O 34.43% E:ARG441.N-E:ASN409.OD1 34.43% D:SER861.N-D:ALA857.O 34.43% F:GLN984.N-F:THR980.O 34.43% D:THR943.N-D:GLN939.O 34.43% A:TYR163.N-A:ILE125.O 34.43% E:ARG495.NE-E:ASP429.OD2 34.43% B:GLN987.N-B:LEU983.O 34.43% D:TYR1070.N-D:ILE1063.O 32.79% B:GLN1018.NE2-B:HIS1030.O 32.79% F:TYR1049.N-F:TYR1029.O 32.79% D:ASN759.N-D:GLU755.O 32.79% D:THR980.OG1-D:ASP976.O 32.79% E:PHE83.N-E:THR229.O 32.79% D:ALA885.N-D:ALA881.O 32.79% D:TYR1049.N-D:TYR1029.O 32.79% B:SER1019.OG-B:GLU1013.OE1 32.79%

D:THR1059.OG1-D:PHE1077.O 36.07%

F:ILE905.N-F:ASN901.O 36.07%

F:MET884.N-F:PHE880.O 36.07%

F:ALA912.N-F:GLN908.O 36.07%

F:ALA1008.N-F:ALA1004.O 36.07%

B:ASN759.N-B:GLU755.O 36.07%

F:ALA676.N-E:GLU640.O 36.07%

F:VAL934.N-F:LEU930.O 36.07%

D:TYR723.N-D:ASP719.O 36.07%

A:MET263.N-A:VAL276.O 36.07%

E:GLU93.N-E:HIS181.O 36.07%

E:LYS198.N-E:LYS217.O 36.07%

B:THR705.N-B:HIS1046.O 36.07%

F:THR1048.N-F:SER703.O 36.07%

B:HIS1046.N-B:THR705.O 36.07%

B:SER798.OG-B:GLN1036.OE1 36.07%

B:VAL934.N-B:LEU930.O 36.07%

C:ILE652.N-C:ILE656.O 36.07%

A:ILE117.N-A:VAL124.O 36.07%

A:ASP154.N-A:GLU131.O 36.07%

D:VAL897.N-D:THR894.O 36.07%

F:ALA906.N-F:GLN902.O 36.07%

E:LYS142.N-E:SER239.O 39.34%

C:TYR41.OH-C:LEU58.O 39.34%

C:GLN546.N-C:GLN549.OE1 34.43%

F:LEU983.N-F:ILE979.O 34.43%

B:ALA676.N-A:GLU640.O 34.43%

B:ILE1086.N-B:GLN1095.O 36.07%

C:ASN230.N-C:GLY104.O 39.34%

F:SER701.N-F:VAL1050.O 34.43%

F:THR980.OG1-F:ASP976.O 37.70%

D:VAL808.N-D:LEU804.O 39.34%

A:THR229.N-A:GLY104.O 39.34%

Table 11.2 (continued)

C:TYR197.N-C:VAL186.O 31.15%

B:GLN931.N-B:LEU927.O 31.15%

C:SER353.OG-C:ASP351.OD1 31.15%

E:ALA127.N-E:PHE161.O 31.15%

A:CYS128.N-A:SER113.O 31.15%

B:THR841.N-B:SER717.O 31.15%

E:ILE584.N-E:VAL596.O 31.15%

D:PHE1044.N-D:GLU707.O 31.15%

A:THR487.OG1-A:TYR484.O 31.15%

D:PHE888.N-D:MET884.O 31.15%

D:SER964.OG-D:ASN960.O 31.15%

E:THR92.N-E:ALA251.O 31.15%

C:ILE203.N-C:LYS180.O 31.15%

F:ASP719.N-F:GLY839.O 31.15%

B:ASN942.N-B:ALA938.O 31.15%

B:LEU1045.N-B:PHE1034.O 31.15%

A:ARG495.NH2-A:ASP429.OD1 31.15%

C:CYS128.N-C:SER113.O 31.15%

D:ASP967.N-A:SER370.OG 31.15%

A:ASN189.N-A:ASP85.O 31.15%

A:VAL314.N-A:ASN528.O 31.15%

A:SER64.OG-A:PRO61.O 31.15%

D:THR760.OG1-D:GLN756.O 31.15%

D:ILE905.N-D:ASN901.O 31.15%

408 11 SARS (SARS-CoV-1)

F:THR991.N-F:GLN987.O 31.15%

C:ALA284.N-C:ASN281.OD1 32.79% C:VAL102.N-C:ARG232.O 32.79% E:ASP154.N-E:GLU131.O 32.79% E:ILE428.N-E:THR425.O 32.79% C:ILE428.N-C:THR425.O 32.79% B:LYS1010.N-B:LEU1006.O 32.79% F:LEU843.N-F:LYS715.O 32.79% D:THR991.N-D:GLN987.O 32.79% E:LEU264.N-E:TYR53.O 32.79% E:PHE103.N-E:VAL114.O 32.79% C:VAL382.N-C:ILE345.O 32.79% F:HIS1046.N-F:THR705.O 32.79% E:THR608.OG1-E:THR604.O 32.79%

A:THR567.OG1-A:ASP564.OD1 36.07%

E:SER370.N-B:ARG965.O 36.07%

E:CYS128.N-E:SER113.O 36.07%

C:CYS133.N-C:ILE152.O 36.07%

E:SER35.N-E:SER64.O 36.07%

A:GLN549.N-A:GLN546.O 36.07%

A:TYR440.N-A:ASN479.O 36.07%

D:LEU843.N-D:LYS715.O 36.07%

A:TRP101.N-A:ILE116.O 36.07%

A:PHE103.N-A:VAL114.O 36.07%

B:ALA1007.N-B:SER1003.O 36.07%

C:ASN435.N-C:PHE483.O 36.07%

B:SER861.OG-B:ALA857.O 36.07%

B:ASP719.N-B:GLY839.O 32.79%

F:THR841.N-F:SER717.O 32.79%

A:ARG342.NE-A:ASP385.OD1 32.79%

A:VAL98.N-A:GLU93.OE1 32.79%

C:GLY552.N-C:SER561.O 32.79%

F:ILE752.N-F:ALA748.O 32.79%

C:HIS181.N-C:GLU93.O 32.79%

A:ILE81.N-A:PHE231.O 32.79%

C:SER292.N-C:LYS287.O 32.79%

C:VAL581.N-C:THR302.O 32.79%

F:ASN1080.N-F:SER1083.O 32.79%

A:ASN119.N-A:ASN122.O 32.79%

F:LEU735.N-F:CYS731.O 32.79%

A:VAL394.N-A:LYS390.O 31.15%

B:TYR677.N-A:CYS657.O 32.79%

A:ALA284.N-A:ASN281.OD1 36.07%

Supplementary Information 409

B:VAL593.N-B:LEU581.O 63.93%

B:PHE326.N-B:ILE315.O 63.93%

A:VAL314.N-A:ASN403.O 63.93%

B:VAL609.N-B:PHE522.O 63.93%

C:TYR437.OH-C:LEU255.O 63.93%

A:ASN285.ND2-A:ILE39.O 63.93%

A:THR41.OG1-A:ILE217.O 63.93%

B:ILE640.N-B:THR676.O 63.93%

A:VAL675.N-A:LEU662.O 63.93%

C:VAL675.N-C:LEU662.O 63.93%

B:SER26.N-B:GLN29.OE1 63.93%

C:THR930.N-C:MET926.O 63.93%

C:SER932.OG-C:MET928.O 63.93%

C:VAL1149.N-C:TYR1153.O 63.93%

B:VAL517.N-B:ILE566.O 63.93%

B:VAL1059.N-B:ALA1055.O 63.93%

C:VAL1007.N-C:ALA1003.O 63.93%

A:ILE632.N-A:TYR635.O 62.30%

B:VAL194.N-B:THR38.O 62.30%

A:VAL427.N-A:GLY247.O 62.30%

C:LEU1127.N-C:ASN1120.O 62.30%

B:SER932.OG-B:MET928.O 62.30%

B:ILE983.N-B:PHE979.O 62.30%

A:ILE983.N-A:PHE979.O 62.30%

C:VAL362.N-C:SER355.O 62.30%

C:THR584.OG1-C:SER589.O 62.30%

A:VAL32.N-A:MET27.O 62.30%

B:ALA1055.N-B:ASP1051.O 60.66%

B:TYR437.OH-B:LEU255.O 60.66%

B:VAL686.N-B:GLY457.O 60.66%

B:GLN1015.N-B:LEU1011.O 60.66%

A:VAL1059.N-A:ALA1055.O 60.66%

B:VAL1132.N-B:SER772.O 85.25%

A:VAL1132.N-A:SER772.O 85.25%

C:VAL425.N-C:SER249.O 81.97%

B:VAL425.N-B:SER249.O 80.33%

C:VAL378.N-C:MET296.O 78.69%

B:VAL162.N-B:GLU147.O 78.69%

A:VAL162.N-A:GLU147.O 78.69%

A:VAL1084.N-A:LYS1080.O 78.69%

C:VAL1132.N-C:SER772.O 78.69%

A:VAL598.N-A:CYS577.O 77.05%

B:VAL378.N-B:MET296.O 77.05%

B:VAL192.N-B:VAL40.O 77.05%

A:VAL1074.N-A:LEU1070.O 77.05%

C:VAL786.N-C:MET915.O 77.05%

C:VAL829.N-C:GLU825.O 77.05%

B:VAL1185.N-B:ASP1188.OD2 77.05%

A:VAL366.N-A:CYS351.O 75.41%

A:VAL316.N-A:ASN401.O 75.41%

C:VAL987.N-C:ILE983.O 75.41%

A:VAL1185.N-A:ASP1188.OD2 75.41%

A:VAL1141.N-A:LEU763.O 75.41%

B:VAL1074.N-B:LEU1070.O 73.77%

A:VAL686.N-A:GLY457.O 73.77%

A:VAL829.N-A:GLU825.O 73.77%

C:GLU1097.N-C:GLN1093.O 73.77%

C:VAL1141.N-C:LEU763.O 73.77%

A:VAL378.N-A:MET296.O 73.77%

B:VAL149.N-B:PHE160.O 73.77%

C:THR41.OG1-C:ILE217.O 72.13%

B:VAL1141.N-B:LEU763.O 72.13%

C:VAL1173.N-C:ARG1182.O 72.13%

B:VAL1173.N-B:ARG1182.O 72.13%

C:PHE326.N-C:ILE315.O 57.38%

A:ASP1150.N-A:ILE1202.O 57.38%

B:VAL1190.N-B:VAL1156.O 57.38%

B:VAL32.N-B:MET27.O 57.38%

B:VAL598.N-B:CYS577.O 57.38%

A:VAL1149.N-A:TYR1153.O 57.38%

A:SER978.OG-A:ILE974.O 57.38%

C:HIS1130.N-C:GLN774.O 57.38%

C:GLN1015.N-C:LEU1011.O 57.38%

C:LEU77.N-C:ILE89.O 57.38%

C:VAL173.N-C:SER56.O 57.38%

B:VAL717.N-B:ALA694.O 57.38%

B:LEU151.N-B:ARG158.O 57.38%

B:ILE674.N-B:ARG642.O 57.38%

C:VAL194.N-C:THR38.O 57.38%

C:MET296.N-C:VAL378.O 57.38%

A:PHE326.N-A:ILE315.O 57.38%

C:VAL598.N-C:CYS577.O 59.02%

C:VAL609.N-C:PHE522.O 59.02%

C:ILE983.N-C:PHE979.O 59.02%

A:ARG1088.NH1-A:ILE780.O 59.02%

C:VAL717.N-C:ALA694.O 59.02%

B:VAL293.N-B:PHE275.O 59.02%

A:TYR1155.N-A:ILE1147.O 59.02%

B:ALA1091.N-B:SER1087.O 59.02%

A:VAL173.N-A:SER56.O 59.02%

B:VAL786.N-B:MET915.O 59.02%

A:LYS444.N-A:SER440.O 59.02%

A:THR196.OG1-A:PRO33.O 59.02%

B:MET296.N-B:VAL378.O 59.02%

A:VAL609.N-A:PHE522.O 59.02%

C:VAL316.N-C:ASN401.O 59.02%

Table 11.3 The HBs of MD of HCoV-NL63 spike trimer with occupancy rates ≥30% during the 651 μs’ MD B:VAL202.N-B:THR195.O 54.10%

A:VAL91.N-A:PHE75.O 52.46%

C:LYS107.N-C:ASP125.O 52.46%

C:LEU151.N-C:ARG158.O 52.46%

C:VAL32.N-C:MET27.O 52.46%

B:VAL421.N-B:GLN253.O 52.46%

A:ILE376.N-A:TYR298.O 52.46%

A:PHE352.N-A:TYR327.O 52.46%

A:LEU1134.N-A:THR770.O 52.46%

B:VAL101.N-B:PHE132.O 52.46%

B:VAL91.N-B:PHE75.O 52.46%

C:CYS737.N-C:SER741.O 52.46%

A:VAL717.N-A:ALA694.O 52.46%

B:VAL186.N-B:GLY62.O 52.46%

A:ASN625.N-A:ILE641.O 52.46%

C:VAL423.N-C:LEU251.O 52.46%

C:ASN285.ND2-C:ILE39.O 52.46%

B:LEU238.N-B:GLN253.OE1 52.46%

B:LYS564.N-B:SER601.O 52.46%

B:LEU581.N-B:GLY594.O 52.46%

C:ALA1091.N-C:SER1087.O 54.10%

B:SER249.N-B:VAL425.O 54.10%

C:VAL1018.N-C:ILE1014.O 54.10%

A:VAL793.N-A:CYS789.O 54.10%

B:TYR792.OH-B:ARG1066.O 54.10%

A:GLN433.N-A:ASN426.O 54.10%

C:THR1209.OG1-C:GLU1206.O 54.10%

B:VAL745.N-B:ASN733.O 54.10%

A:THR102.N-A:THR92.O 54.10%

B:VAL173.N-B:SER56.O 54.10%

C:LEU171.N-C:TYR58.O 54.10%

A:LEU151.N-A:ARG158.O 54.10%

410 11 SARS (SARS-CoV-1)

C:VAL91.N-C:PHE75.O 52.46%

A:VAL415.N-A:TRP261.O 52.46%

B:GLY735.N-B:ILE743.O 50.82% A:PHE1128.N-A:GLU776.O 50.82%

C:TYR298.N-C:ILE376.O 54.10% C:VAL377.N-C:TYR385.O 54.10% C:ASN285.N-C:LEU260.O 54.10% C:VAL474.N-C:ASN631.O 54.10% A:VAL194.N-A:THR38.O 54.10% B:PHE673.N-B:PHE664.O 54.10%

C:ALA583.N-C:THR591.O 65.57%

C:ILE632.N-C:TYR635.O 65.57%

A:ILE674.N-A:ARG642.O 65.57%

B:VAL829.N-B:GLU825.O 65.57%

A:VAL192.N-A:VAL40.O 65.57%

A:ILE736.N-A:MET729.O 50.82%

C:ARG1182.NH2-C:ASP1188.OD1 50.82%

C:LEU257.N-C:GLY224.O 50.82%

B:VAL362.N-B:SER355.O 50.82%

C:SER767.N-C:ASP1137.O 50.82%

A:MET928.N-A:GLU924.O 50.82%

B:THR196.N-B:SER36.O 50.82% C:VAL793.N-C:CYS789.O 50.82%

B:VAL314.N-B:ASN403.O 54.10%

C:ILE640.N-C:THR676.O 65.57%

B:ARG1088.NH1-B:ILE780.O 65.57%

C:VAL192.N-C:VAL40.O 65.57%

C:VAL1084.N-C:LYS1080.O 50.82% A:ILE357.N-A:THR360.O 50.82%

B:THR584.OG1-B:SER589.O 54.10%

B:ILE376.N-B:TYR298.O 50.82% C:TRP261.N-C:VAL415.O 50.82% C:SER172.N-C:ALA76.O 50.82%

B:HIS1130.N-B:GLN774.O 55.74% C:VAL517.N-C:ILE566.O 55.74%

A:VAL1173.N-A:ARG1182.O 67.21%

B:THR1209.OG1-B:GLU1206.O 67.21%

B:ILE1211.N-B:LEU1207.O 50.82% A:VAL377.N-A:TYR385.O 50.82%

A:VAL728.N-A:ILE736.O 55.74% C:THR1008.OG1-C:ILE1004.O 55.74%

C:ARG1088.NH1-C:ILE780.O 67.21%

B:VAL987.N-B:ILE983.O 67.21%

C:VAL427.N-C:GLY247.O 65.57%

C:ASN959.N-C:GLN955.O 50.82% C:VAL1163.N-C:THR1174.O 50.82%

A:VAL517.N-A:ILE566.O 55.74% B:MET695.N-B:GLN683.O 55.74%

A:VAL149.N-A:PHE160.O 67.21%

C:ILE674.N-C:ARG642.O 50.82% A:GLN774.N-A:HIS1130.O 50.82%

A:SER932.OG-A:MET928.O 55.74% B:GLU1097.N-B:GLN1093.O 55.74%

A:TYR437.OH-A:LEU255.O 67.21%

B:ILE632.N-B:TYR635.O 67.21%

A:VAL786.N-A:MET915.O 67.21%

C:VAL421.N-C:GLN253.O 50.82% B:LEU804.N-B:CYS800.O 50.82%

C:VAL728.N-C:ILE736.O 55.74% B:THR930.N-B:MET926.O 55.74%

C:VAL1074.N-C:LEU1070.O 68.85%

C:VAL366.N-C:CYS351.O 67.21%

B:TYR298.N-B:ILE376.O 50.82% A:ASN285.N-A:LEU260.O 50.82%

A:TYR716.OH-A:GLY740.O 55.74% C:THR102.N-C:THR92.O 55.74%

A:VAL362.N-A:SER355.O 68.85%

A:ASN387.N-A:GLU375.O 68.85%

B:ILE340.N-B:LYS311.O 52.46% B:ALA583.N-B:THR591.O 50.82%

C:ASN625.N-C:ILE641.O 55.74% B:ASN625.N-B:ILE641.O 55.74% B:THR196.OG1-B:PRO33.O 55.74%

C:VAL162.N-C:GLU147.O 68.85%

A:VAL1190.N-A:VAL1156.O 68.85%

B:VAL675.N-B:LEU662.O 68.85%

B:THR92.OG1-B:SER73.O 52.46% A:LEU1133.N-A:THR1113.O 52.46%

A:MET296.N-A:VAL378.O 55.74% C:THR196.OG1-C:PRO33.O 55.74%

B:VAL316.N-B:ASN401.O 68.85%

C:VAL1059.N-C:ALA1055.O 68.85%

A:VAL1018.N-A:ILE1014.O 52.46%

C:VAL593.N-C:LEU581.O 55.74% B:PHE352.N-B:TYR327.O 55.74%

B:VAL1149.N-B:TYR1153.O 60.66%

B:VAL728.N-B:ILE736.O 60.66%

A:VAL421.N-A:GLN253.O 70.49%

B:VAL366.N-B:CYS351.O 68.85%

A:LYS564.N-A:SER601.O 52.46% C:VAL882.N-C:PHE878.O 52.46%

A:HIS78.N-A:LYS170.O 57.38% B:ILE1192.N-B:GLY1154.O 57.38%

B:VAL1018.N-B:ILE1014.O 60.66%

A:GLU1097.N-A:GLN1093.O 60.66%

A:VAL182.N-A:ILE66.O 70.49%

C:VAL1185.N-C:ASP1188.OD2 70.49%

B:SER978.OG-B:ILE974.O 52.46% C:VAL1190.N-C:VAL1156.O 52.46%

C:VAL149.N-C:PHE160.O 57.38% B:ARG150.N-B:THR143.O 57.38%

B:VAL1084.N-B:LYS1080.O 60.66%

A:VAL1163.N-A:THR1174.O 60.66%

A:VAL425.N-A:SER249.O 70.49%

A:VAL987.N-A:ILE983.O 70.49%

A:ALA1091.N-A:SER1087.O 52.46% C:SER978.OG-C:ILE974.O 52.46%

A:TYR298.N-A:ILE376.O 57.38% A:LEU238.N-A:GLN253.OE1 57.38%

B:ASN285.ND2-B:ILE39.O 60.66%

C:VAL686.N-C:GLY457.O 60.66%

C:VAL182.N-C:ILE66.O 72.13%

B:VAL182.N-B:ILE66.O 72.13%

Supplementary Information 411

A:LEU257.N-A:GLY224.O 45.90%

C:SER36.OG-C:ASP34.O 45.90%

C:MET695.N-C:GLN683.O 45.90%

A:SER184.OG-A:HIS47.O 45.90%

B:SER184.OG-B:HIS47.O 45.90%

C:TYR687.N-C:SER690.O 45.90%

A:GLN706.N-A:SER718.O 45.90%

B:TYR687.N-B:SER690.O 45.90%

C:TYR716.OH-C:GLY740.O 45.90%

A:LEU77.N-A:ILE89.O 45.90%

A:ILE780.N-A:ASP1124.O 45.90%

A:HIS1130.N-A:GLN774.O 45.90%

C:LYS564.N-C:SER601.O 45.90%

B:THR791.OG1-B:ASP788.OD1 45.90%

B:LYS444.N-B:SER440.O 45.90%

B:LYS104.N-B:TYR90.O 45.90%

A:ILE1192.N-A:GLY1154.O 45.90%

C:VAL202.N-C:THR195.O 45.90%

A:PHE673.N-A:PHE664.O 45.90%

C:SER145.N-C:THR148.O 45.90%

C:VAL856.N-C:LEU853.O 45.90%

B:CYS567.N-B:THR599.O 45.90%

A:TYR391.N-A:PHE384.O 45.90%

C:GLU815.N-C:CYS811.O 45.90%

C:PHE487.N-C:ARG525.O 44.26%

C:LEU581.N-C:GLY594.O 44.26%

B:PHE579.N-B:LEU596.O 44.26%

C:ALA416.N-C:ARG297.O 44.26%

A:TRP261.N-A:VAL415.O 44.26%

A:THR1029.OG1-A:LEU1025.O 44.26%

A:ARG150.N-A:THR143.O 44.26%

B:VAL684.N-B:TYR459.O 44.26%

A:LEU171.N-A:TYR58.O 44.26%

A:TYR90.N-A:LYS104.O 44.26%

A:GLN1015.N-A:LEU1011.O 44.26%

C:PHE1128.N-C:GLU776.O 44.26%

C:PHE563.N-C:ILE606.O 49.18%

A:VAL474.N-A:ASN631.O 49.18%

C:GLN433.N-C:ASN426.O 49.18%

A:ASN193.N-A:THR205.O 49.18%

B:VAL40.N-B:VAL192.O 49.18%

A:SER26.N-A:GLN29.OE1 49.18%

A:SER172.N-A:ALA76.O 49.18%

A:VAL882.N-A:PHE878.O 49.18%

C:MET926.N-C:ASP922.O 49.18%

B:LEU1127.N-B:ASN1120.O 49.18%

A:GLN1092.N-A:ARG1088.O 49.18%

A:LEU1127.N-A:ASN1120.O 49.18%

A:THR1131.N-A:PHE1116.O 49.18%

C:LYS1139.N-C:ILE765.O 49.18%

B:TYR1155.N-B:ILE1147.O 49.18%

C:VAL400.N-C:VAL273.O 49.18%

B:VAL474.N-B:ASN631.O 49.18%

C:ASN193.N-C:THR205.O 49.18%

C:SER249.N-C:VAL425.O 49.18%

A:ALA685.N-A:GLY693.O 49.18%

C:THR483.OG1-C:THR519.OG1 49.18%

A:VAL40.N-A:VAL192.O 49.18%

A:MET695.N-A:GLN683.O 49.18%

A:VAL593.N-A:LEU581.O 49.18%

A:ASN354.N-A:LEU325.O 47.54%

A:LEU581.N-A:GLY594.O 47.54%

C:CYS567.N-C:THR599.O 47.54%

B:ASN387.N-B:GLU375.O 47.54%

B:THR419.N-B:ARG256.O 47.54%

B:THR41.OG1-B:ILE217.O 47.54%

A:VAL202.N-A:THR195.O 47.54%

C:SER184.OG-C:HIS47.O 47.54%

A:TYR65.N-A:LEU140.O 47.54%

C:LEU820.N-C:ASP816.O 47.54%

B:PHE1128.N-B:GLU776.O 47.54%

C:ILE1211.N-C:LEU1207.O 47.54%

A:LEU300.N-A:ARG374.O 40.98%

B:ARG380.N-B:ASP294.O 40.98%

A:ILE1211.N-A:LEU1207.O 40.98%

C:CYS1148.N-C:VAL1200.O 40.98%

A:CYS1148.N-A:VAL1200.O 40.98%

B:VAL1163.N-B:THR1174.O 40.98%

B:ARG1176.N-B:ASN1161.O 40.98%

A:SER841.OG-A:SER837.O 40.98%

A:LYS1100.N-A:ILE1095.O 40.98%

C:MET928.N-C:GLU924.O 40.98%

A:ILE743.N-A:GLY735.O 40.98%

A:TYR687.N-A:SER690.O 40.98%

C:TYR65.N-C:LEU140.O 40.98%

A:ALA908.N-A:ASP904.O 40.98%

C:ARG150.N-C:THR143.O 40.98%

A:SER428.N-A:ASN431.O 40.98%

B:VAL273.N-B:VAL400.O 40.98%

A:ILE524.N-A:ASN558.OD1 40.98%

B:LYS318.N-B:ALA399.O 40.98%

A:THR584.OG1-A:SER589.O 40.98%

B:TYR90.N-B:LYS104.O 42.62%

A:SER249.N-A:VAL425.O 42.62%

C:ASN354.N-C:LEU325.O 42.62%

B:ARG1105.NH1-B:GLU1097.OE1 42.62%

A:CYS351.N-A:GLY367.O 42.62%

C:ALA988.N-C:ASN984.O 42.62%

C:GLN1092.N-C:ARG1088.O 42.62%

C:HIS78.N-C:LYS170.O 42.62%

A:ILE640.N-A:THR676.O 42.62%

B:GLN1092.N-B:ARG1088.O 42.62%

A:LEU103.N-A:LEU130.O 42.62%

A:PHE49.N-A:PHE183.O 42.62%

A:THR791.OG1-A:ASP788.OD2 42.62%

C:CYS800.N-C:ASN797.OD1 42.62%

B:ASN285.N-B:LEU260.O 42.62%

B:TRP261.N-B:VAL415.O 42.62%

Table 11.4 The HBs of MD of HCoV-NL63 spike trimer with occupancy rates ≥30% during the 651 μs’ MD (continuation 1)

A:ILE606.N-A:PHE563.O 39.34%

B:SER772.N-B:VAL1132.O 39.34%

C:PHE840.N-C:ASP836.O 39.34%

A:ASN1096.N-A:GLN1092.O 39.34%

C:THR92.OG1-C:SER73.O 39.34%

A:PHE64.N-A:SER184.O 39.34%

B:GLU815.N-B:CYS811.O 39.34%

C:SER26.OG-C:TYR154.O 39.34%

C:THR628.N-C:GLY639.O 39.34%

A:THR419.N-A:ARG256.O 39.34%

B:GLY608.N-B:GLN561.O 39.34%

C:PHE352.N-C:TYR327.O 39.34%

B:ASP1150.N-B:ILE1202.O 39.34%

A:THR1209.N-A:GLU1206.O 39.34%

A:ARG1172.N-A:TYR1165.O 39.34%

B:SER841.OG-B:SER837.O 39.34%

B:ALA988.N-B:ASN984.O 39.34%

A:GLY735.N-A:ILE743.O 39.34%

B:LEU77.N-B:ILE89.O 39.34%

B:TYR716.N-B:LEU709.O 39.34%

A:SER26.OG-A:TYR154.O 39.34%

A:SER36.OG-A:ASP34.O 39.34%

C:VAL415.N-C:TRP261.O 39.34%

B:ASN1012.N-B:THR1008.O 39.34%

B:TYR716.OH-B:GLY740.O 39.34%

C:ILE692.N-C:ALA685.O 39.34%

C:VAL684.N-C:TYR459.O 39.34%

C:PHE673.N-C:PHE664.O 39.34%

C:SER219.OG-C:GLY31.O 39.34%

A:ILE1063.N-A:VAL1059.O 39.34%

C:ILE39.N-C:ASN285.OD1 39.34%

A:ALA416.N-A:ARG297.O 39.34%

C:GLY608.N-C:GLN561.O 39.34%

B:TYR391.OH-B:ILE368.O 39.34%

A:GLU582.N-A:TYR544.O 39.34%

C:GLU582.N-C:TYR544.O 39.34%

412 11 SARS (SARS-CoV-1)

C:LEU709.N-C:TYR716.O 37.70% C:ILE105.N-C:VAL128.O 37.70%

C:SER879.N-C:ASP875.O 40.98% B:VAL400.N-B:VAL273.O 40.98%

C:THR195.N-C:ASN203.O 37.70% C:ASN426.N-C:ASN434.O 37.70%

A:VAL293.N-A:PHE275.O 44.26%

A:LEU30.N-A:SER26.O 44.26%

C:THR599.N-C:CYS567.O 42.62%

C:ILE340.N-C:LYS311.O 42.62%

A:VAL101.N-A:PHE132.O 45.90%

A:SER100.N-A:GLU94.O 45.90%

B:THR102.N-B:THR92.O 45.90%

A:THR930.N-A:MET926.O 45.90%

C:ASN1071.N-C:LEU1067.O 37.70% B:CYS737.N-B:SER741.O 37.70% A:LYS1094.N-A:LEU1090.O 37.70%

A:ARG1182.NH1-A:ASP1188.OD2 42.62%

B:ILE1147.N-B:TYR1155.O 42.62%

C:TYR391.OH-C:ILE368.O 42.62%

C:CYS351.N-C:GLY367.O 45.90%

A:CYS567.N-A:THR599.O 45.90%

B:ALA416.N-B:ARG297.O 45.90%

A:TYR385.N-A:VAL377.O 37.70% B:ARG297.N-B:ALA416.O 37.70% C:LEU1067.N-C:ILE1063.O 37.70%

A:SER145.N-A:THR148.O 42.62%

B:SER821.OG-B:ALA817.O 42.62%

B:LEU103.N-B:LEU130.O 42.62%

A:THR1209.OG1-A:GLU1206.O 45.90%

C:PHE579.N-C:LEU596.O 45.90%

B:GLU582.N-B:TYR544.O 45.90%

A:ILE340.N-A:LYS311.O 37.70%

B:THR405.N-B:SER312.O 37.70%

B:THR239.OG1-B:SER242.O 42.62%

B:ASN193.N-B:THR205.O 42.62%

B:ASN959.N-B:GLN955.O 45.90%

C:ARG1182.NH1-C:ASP1188.OD2 45.90%

C:LYS1100.N-C:ILE1095.O 37.70% B:ILE1115.N-B:THR1131.O 37.70%

A:ALA379.N-A:GLN383.O 42.62%

C:ALA1055.N-C:ASP1051.O 42.62%

B:LYS1094.N-B:LEU1090.O 45.90%

B:LEU1133.N-B:THR1113.O 45.90%

C:THR1006.OG1-C:GLU1002.O 37.70%

B:ILE353.N-B:THR364.O 37.70%

C:PHE317.N-C:VAL324.O 37.70%

A:THR1220.OG1-A:ASP1216.O 37.70%

B:MET926.N-B:ASP922.O 40.98%

B:LYS107.N-B:ASP125.O 44.26%

C:THR1136.N-C:ASN768.O 44.26%

C:ILE736.N-C:MET729.O 45.90%

C:THR826.OG1-C:ALA822.O 45.90%

B:LEU1134.N-B:THR770.O 37.70% B:ILE765.N-B:LYS1139.O 37.70% B:ARG1158.N-B:ASP1188.O 37.70%

B:PHE75.N-B:VAL91.O 40.98% B:SER767.N-B:ASP1137.O 40.98% B:SER26.OG-B:TYR154.O 40.98%

A:LYS1139.N-A:ILE765.O 44.26%

A:VAL186.N-A:GLY62.O 44.26%

C:THR826.N-C:ALA822.O 44.26%

C:SER821.OG-C:ALA817.O 45.90%

B:HIS78.N-B:LYS170.O 45.90%

C:LYS104.N-C:TYR90.O 37.70% B:ILE743.N-B:GLY735.O 37.70%

C:LEU251.N-C:VAL423.O 40.98% C:SER26.N-C:GLN29.OE1 40.98%

C:THR258.N-C:PHE417.O 37.70%

C:TYR90.N-C:LYS104.O 45.90%

C:ILE743.N-C:GLY735.O 44.26%

B:THR1006.OG1-B:GLU1002.O 44.26%

C:VAL1077.N-C:PHE1073.O 45.90%

B:PHE49.N-B:PHE183.O 45.90%

B:VAL427.N-B:GLY247.O 44.26%

B:LEU1067.N-B:ILE1063.O 44.26%

B:LEU662.N-B:TYR654.O 37.70% B:SER644.OG-A:LEU900.O 37.70%

B:LEU424.N-B:LEU436.O 40.98% C:ALA908.N-C:ASP904.O 40.98%

B:VAL377.N-B:TYR385.O 44.26%

B:SER428.N-B:ASN431.O 44.26%

B:PHE317.N-B:VAL324.O 47.54%

B:GLN433.N-B:ASN426.O 47.54%

C:VAL314.N-C:ASN403.O 45.90%

B:VAL423.N-B:LEU251.O 37.70%

C:ILE376.N-C:TYR298.O 40.98% A:VAL423.N-A:LEU251.O 40.98%

A:PHE487.N-A:ARG525.O 44.26%

C:ARG380.N-C:ASP294.O 44.26%

C:THR791.OG1-C:ASP788.OD2 47.54%

A:CYS737.N-A:SER741.O 47.54%

A:TYR391.OH-A:ILE368.O 45.90%

C:VAL324.N-C:PHE317.O 37.70% B:TYR391.N-B:PHE384.O 37.70% C:LEU1050.N-C:ILE1046.O 37.70%

C:LEU1133.N-C:THR1113.O 40.98% B:ILE606.N-B:PHE563.O 40.98% A:GLY608.N-A:GLN561.O 40.98%

C:ILE1192.N-C:GLY1154.O 44.26%

B:CYS1148.N-B:VAL1200.O 44.26%

C:ASP1150.N-C:ILE1202.O 44.26%

A:SER830.OG-A:THR826.O 47.54%

B:THR488.N-B:SER508.O 47.54%

C:LYS318.N-C:ALA399.O 47.54%

C:TYR544.N-C:GLU582.O 39.34%

C:TYR792.N-C:ASP788.O 39.34%

B:VAL1077.N-B:PHE1073.O 40.98% A:VAL881.N-A:LEU877.O 40.98%

B:GLN964.NE2-B:ALA962.O 44.26%

C:GLN964.N-C:ASN959.OD1 44.26%

C:VAL186.N-C:GLY62.O 47.54%

C:GLY735.N-C:ILE743.O 47.54%

B:LEU171.N-B:TYR58.O 39.34% A:LYS104.N-A:TYR90.O 39.34%

C:VAL40.N-C:VAL192.O 40.98% C:LYS444.N-C:SER440.O 40.98%

B:MET928.N-B:GLU924.O 44.26%

B:GLN774.N-B:HIS1130.O 44.26%

A:ALA583.N-A:THR591.O 47.54%

B:LEU300.N-B:ARG374.O 47.54%

Supplementary Information 413

B:VAL324.N-B:PHE317.O 34.43%

C:ILE524.N-C:ASN558.OD1 34.43%

C:LYS1094.N-C:LEU1090.O 37.70%

C:ILE765.N-C:LYS1139.O 37.70%

C:SER492.N-C:GLN504.O 31.15%

C:ALA977.N-C:LYS973.O 32.79%

B:SER492.N-B:GLN504.O 31.15%

B:TYR654.N-B:GLY663.O 31.15%

C:SER1121.N-C:GLU874.OE1 31.15% A:THR1064.OG1-A:ASP1060.O 31.15% C:LEU30.N-C:SER26.O 31.15% B:VAL1017.N-B:LYS1013.O 31.15% B:LYS1100.N-B:ILE1095.O 31.15%

A:THR791.OG1-A:ASP788.OD1 32.79% C:GLU825.N-C:SER821.O 32.79% A:ASN1096.ND2-A:GLN1092.O 32.79% B:ARG1182.NH1-B:ASP1188.OD2 32.79%

A:ARG1182.NH2-A:ASP1188.OD1 34.43%

C:SER355.N-C:VAL362.O 34.43%

B:THR599.N-B:CYS567.O 34.43%

B:PHE563.N-B:ILE606.O 34.43%

C:SER428.N-C:ASN431.O 36.07%

A:LEU804.N-A:CYS800.O 36.07%

C:VAL190.N-C:GLY42.O 36.07%

A:VAL684.N-A:TYR459.O 36.07%

C:ILE867.N-C:GLU924.OE1 31.15% A:SER1075.N-A:ASN1071.O 31.15%

A:VAL1200.N-A:GLY1146.O 32.79% B:VAL415.N-B:TRP261.O 32.79% C:THR1064.OG1-C:ASP1060.O 32.79%

B:ARG374.N-B:ASN387.OD1 34.43%

A:TYR792.N-A:ASP788.O 34.43%

B:ILE692.N-B:ALA685.O 34.43%

A:ILE692.N-A:ALA685.O 36.07%

B:ALA685.N-B:GLY693.O 36.07%

B:LEU824.N-B:LEU820.O 36.07%

A:CYS447.N-A:GLU443.O 31.15% B:SER172.N-B:ALA76.O 31.15%

C:TYR1155.N-C:ILE1147.O 32.79% B:ILE1063.N-B:VAL1059.O 32.79%

B:SER871.N-B:GLU874.OE1 34.43%

A:GLN964.N-A:ASN959.OD1 34.43%

B:PHE236.N-B:GLU375.OE1 36.07%

C:GLN253.N-C:VAL421.O 36.07%

B:VAL404.N-B:LEU266.O 31.15% A:GLU375.N-A:ASN387.OD1 31.15%

B:ILE736.N-B:MET729.O 32.79% B:SER871.N-B:GLU874.OE2 32.79% C:SER841.OG-C:SER837.O 32.79%

A:ALA76.N-A:SER172.O 34.43%

C:TYR777.OH-C:PRO1123.O 34.43%

B:THR1008.OG1-B:ILE1004.O 34.43%

C:TYR391.N-C:PHE384.O 36.07%

C:ILE606.N-C:PHE563.O 36.07%

C:LEU238.N-C:GLN253.OE1 36.07%

B:SER764.N-A:GLY941.O 31.15%

B:GLY869.N-B:GLN859.O 31.15% B:ASN985.N-B:LYS981.O 31.15%

C:TYR58.N-C:LEU171.O 32.79% A:THR826.N-A:ALA822.O 32.79%

B:THR791.OG1-B:ASP788.OD2 34.43%

C:ALA685.N-C:GLY693.O 34.43%

C:VAL273.N-C:VAL400.O 36.07%

C:SER523.OG-C:VAL609.O 36.07%

B:ASP1051.N-C:PRO551.O 31.15% C:THR696.OG1-C:ASP682.OD1 31.15%

C:THR897.OG1-A:ALA697.O 32.79% B:TYR65.N-B:LEU140.O 32.79%

B:ILE39.N-B:ASN285.OD1 34.43%

B:CYS794.N-B:ALA790.O 34.43%

C:ASN529.N-C:ALA489.O 36.07%

A:LEU394.N-A:GLY382.O 36.07%

A:SER1121.OG-A:GLU874.OE1 31.15% B:GLU398.N-B:LYS318.O 31.15%

B:HIS197.N-B:ARG200.O 32.79%

A:ALA1055.N-A:ASP1051.O 34.43%

A:THR239.OG1-A:SER242.O 34.43%

C:THR770.N-C:LEU1134.O 37.70%

C:LEU509.N-C:ASN512.O 36.07%

A:SER1030.N-A:ASN1026.O 32.79%

B:LEU1078.N-B:VAL1074.O 31.15%

A:ARG642.N-A:ILE674.O 32.79% A:ASN426.N-A:ASN434.O 32.79%

B:LEU394.N-B:GLY382.O 34.43%

B:ILE524.N-B:ASN558.OD1 34.43%

C:TYR716.N-C:LEU709.O 37.70%

A:SER658.OG-C:GLN909.OE1 37.70%

C:LEU300.N-C:ARG374.O 31.15% A:ARG250.NH2-A:ASP422.OD1 31.15%

C:ILE357.N-C:THR360.O 32.79%

B:THR319.N-B:TYR322.O 31.15%

A:SER355.OG-A:ASP323.O 32.79%

C:ARG1158.N-C:ASP1188.O 32.79% B:THR1220.OG1-B:ASP1216.O 32.79%

A:TYR777.OH-A:PRO1123.O 36.07%

C:PHE417.N-C:CYS259.O 36.07%

B:ASN354.N-B:LEU325.O 34.43%

A:TYR716.N-A:LEU709.O 37.70%

A:VAL1017.N-A:LYS1013.O 37.70%

B:PHE64.N-B:SER184.O 37.70%

C:LEU130.N-C:LEU103.O 31.15% B:THR1006.N-B:GLU1002.O 31.15%

C:THR1131.N-C:PHE1116.O 32.79% C:ILE1115.N-C:THR1131.O 32.79%

B:SER656.N-B:ASN660.O 36.07%

C:LEU394.N-C:GLY382.O 36.07%

A:ARG380.N-A:ASP294.O 37.70%

A:TYR58.N-A:LEU171.O 37.70%

A:LEU954.N-A:PHE950.O 31.15%

A:SER492.N-A:GLN504.O 37.70%

A:LYS665.N-A:ILE652.O 31.15%

B:SER989.OG-B:ASN985.O 32.79% A:SER871.N-A:GLU874.OE1 32.79%

C:GLN774.N-C:HIS1130.O 36.07%

C:ALA379.N-C:GLN383.O 36.07%

A:HIS1005.N-A:ALA1001.O 37.70%

Table 11.5 The HBs of MD of HCoV-NL63 spike trimer with occupancy rates ≥30% during the 651 μs’ MD (continuation 2)

414 11 SARS (SARS-CoV-1)

B:LEU709.N-B:TYR716.O 32.79% A:ILE397.N-A:ARG380.O 32.79% B:SER895.OG-B:ASP892.OD2 32.79% A:TYR88.N-A:CYS106.O 32.79%

C:LEU824.N-C:LEU820.O 32.79% B:GLN683.NE2-B:SER460.OG 32.79%

A:TYR633.N-A:VAL474.O 31.15% C:ALA1068.N-C:THR1064.O 31.15% B:SER741.OG-B:ASP739.OD1 31.15% B:SER830.OG-B:THR826.O 31.15% C:ALA976.N-C:GLN972.O 31.15% A:ALA977.N-A:LYS973.O 31.15%

A:THR826.OG1-A:ALA822.O 34.43% B:SER1121.OG-B:GLU874.OE1 34.43% C:SER871.N-C:GLU874.OE2 34.43% A:SER767.N-A:ASP1137.O 34.43% A:ALA956.N-A:LEU952.O 34.43% C:THR405.N-C:SER312.O 34.43% B:LEU257.N-B:GLY224.O 34.43% B:LEU251.N-B:VAL423.O 34.43% B:VAL793.N-B:CYS789.O 34.43% A:SER772.N-A:VAL1132.O 34.43% C:ILE353.N-C:THR364.O 34.43% C:ILE1063.N-C:VAL1059.O 34.43% C:HIS197.N-C:ARG200.O 34.43% C:ALA76.N-C:SER172.O 34.43% A:LYS107.N-A:ASP125.O 34.43% B:PHE840.N-B:ASP836.O 34.43% A:THR760.OG1-A:THR1198.O 34.43% C:THR488.N-C:SER508.O 34.43% A:GLN253.N-A:VAL421.O 34.43% B:GLN253.N-B:VAL421.O 34.43% B:GLN706.N-B:SER718.O 34.43% B:LEU820.N-B:ASP816.O 34.43% A:PHE579.N-A:LEU596.O 34.43% B:ALA379.N-B:GLN383.O 34.43% B:GLN683.N-B:MET695.O 34.43% B:LEU130.N-B:LEU103.O 34.43% B:VAL881.N-B:LEU877.O 34.43% C:ASN401.N-C:VAL316.O 34.43% C:TYR526.OH-C:ILE543.O 32.79% B:ILE397.N-B:ARG380.O 32.79% B:THR628.N-B:GLY639.O 32.79% C:LEU662.N-C:TYR654.O 32.79% A:LYS812.N-A:THR808.O 32.79% A:ALA60.N-A:THR169.O 32.79% A:THR696.N-A:TYR715.O 32.79% A:VAL1077.N-A:PHE1073.O 32.79% C:LEU103.N-C:LEU130.O 32.79% C:ARG1085.NE-C:GLU825.OE2 32.79% A:THR1008.OG1-A:ILE1004.O 32.79% A:LEU1126.N-A:LEU778.O 32.79%

A:ARG1088.N-A:VAL1084.O 36.07%

B:SER1121.OG-B:GLU874.OE2 36.07%

B:ASP875.N-B:SER871.O 36.07%

A:ARG1105.NH1-A:GLU1097.OE1 36.07%

B:THR770.N-B:LEU1134.O 36.07%

A:THR1136.N-A:ASN768.O 36.07%

C:ILE1147.N-C:TYR1155.O 36.07%

C:LEU596.N-C:PHE579.O 36.07%

B:TYR597.N-B:SER569.O 36.07%

A:LEU596.N-A:PHE579.O 36.07%

A:SER656.N-A:ASN660.O 36.07%

B:SER1030.N-B:ASN1026.O 36.07%

B:ALA908.N-B:ASP904.O 36.07%

C:PHE64.N-C:SER184.O 36.07%

C:HIS152.N-C:GLY141.O 36.07%

A:ILE105.N-A:VAL128.O 36.07%

B:ILE105.N-B:VAL128.O 36.07%

A:THR92.OG1-A:SER73.O 36.07%

B:ILE780.N-B:ASP1124.O 36.07%

C:LEU1126.N-C:LEU778.O 36.07%

C:SER1121.OG-C:GLU874.OE1 36.07%

A:SER871.N-A:GLU874.OE2 36.07%

A:THR488.N-A:SER508.O 36.07%

B:LEU596.N-B:PHE579.O 36.07%

C:ASN387.N-C:GLU375.O 36.07%

A:HIS197.N-A:ARG200.O 36.07%

B:THR195.N-B:ASN203.O 36.07%

C:TYR792.OH-C:ARG1066.O 36.07%

C:VAL101.N-C:PHE132.O 36.07%

C:ILE780.N-C:ASP1124.O 36.07%

B:ILE1009.N-B:HIS1005.O 36.07%

A:MET926.N-A:ASP922.O 36.07%

B:VAL993.N-B:SER989.O 36.07%

A:SER1121.OG-A:GLU874.OE2 36.07%

C:ILE1118.N-C:LEU1129.O 36.07%

A:ILE1147.N-A:TYR1155.O 36.07%

B:TYR544.N-B:GLU582.O 36.07%

A:ILE353.N-A:THR364.O 36.07%

B:THR1029.N-B:LEU1025.O 36.07%

B:ILE66.N-B:VAL182.O 36.07%

A:ARG225.NH2-A:GLU443.OE2 31.15%

A:THR196.N-A:SER36.O 31.15%

B:SER547.OG-A:ASP1051.OD2 31.15%

A:ASN959.N-A:GLN955.O 31.15%

B:ALA976.N-B:GLN972.O 31.15%

A:ILE1118.N-A:LEU1129.O 31.15%

A:ASN1120.N-A:LEU1127.O 31.15%

A:VAL1007.N-A:ALA1003.O 31.15%

B:SER100.N-B:GLU94.O 31.15%

C:ILE66.N-C:VAL182.O 31.15%

C:THR791.OG1-C:ASP788.OD1 31.15%

B:ARG225.NH2-B:GLU443.OE1 31.15%

A:ASN666.N-A:ASN671.O 31.15%

B:PHE568.N-B:VAL515.O 31.15%

A:LYS318.N-A:ALA399.O 31.15%

C:PHE568.N-C:VAL515.O 31.15%

C:ARG1176.N-C:ASN1161.O 31.15%

B:ILE1118.N-B:LEU1129.O 31.15%

C:ALA99.N-C:GLU134.O 31.15%

B:ILE357.N-B:THR360.O 31.15%

C:ASN506.N-C:THR490.O 31.15%

C:VAL881.N-C:LEU877.O 32.79%

A:LEU424.N-A:LEU436.O 32.79%

A:THR258.N-A:PHE417.O 32.79%

B:LYS1139.N-B:ILE765.O 32.79%

A:THR770.N-A:LEU1134.O 32.79%

A:PHE840.N-A:ASP836.O 32.79%

B:SER329.N-B:TYR350.O 32.79%

C:ARG642.N-C:ILE674.O 32.79%

C:ILE89.N-C:LEU77.O 34.43%

B:TYR777.OH-B:PRO1123.O 36.07% A:SER329.N-A:TYR350.O 31.15%

Supplementary Information 415

416 Table 11.6 The HBs with more than 50% occupancy rates during the 10 μs’ MD simulations for the 2AJF model of [321]

11 SARS (SARS-CoV-1) Donor

Acceptor

Occupancy

A:THR229.OG1

A:ASP225.O

67.99%

A:ARG357.NH1

A:ASP355.OD2

64.24%

E:THR486.OG1

A:ASP355.OD2

64.01%

A:THR282.OG1

A:LEU278.O

62.63%

A:THR567.OG1

A:TYR215.O

60.17%

E:ARG441.N

E:ASN409.OD1

59.90%

A:TYR237.OH

A:VAL485.O

58.87%

A:SER331.OG

A:PHE327.O

58.87%

A:HIS241.N

A:TYR237.O

58.79%

A:ARG357.NE

A:ASP355.OD1

57.47%

A:TYR127.OH

A:SER502.O

57.05%

A:PHE464.N

A:ARG460.O

56.40%

E:THR425.OG1

E:ASP429.OD2

56.15%

E:ARG495.NE

E:ASP429.OD2

56.12%

A:SER317.OG

A:LYS313.O

55.86%

A:TRP461.N

A:GLU457.O

55.76%

E:TYR438.OH

E:ASP429.OD1

55.49%

A:THR129.OG1

A:THR125.O

55.06%

E:VAL420.N

E:LYS365.O

54.18%

A:THR371.OG1

A:ASP367.O

54.05%

A:THR125.OG1

A:ASN121.O

53.52%

A:LEU359.N

A:THR347.O

53.49%

A:GLU375.N

A:THR371.O

52.67%

A:THR122.OG1

A:THR118.O

52.65%

A:TYR516.OH

A:THR229.OG1

52.12%

E:ARG495.NH2

E:ASP429.OD1

51.34%

A:MET383.N

A:ILE379.O

50.92%

A:GLU238.N

A:LYS234.O

50.69%

A:THR27.OG1

A:GLU23.O

50.57%

Chapter 12

MERS-Coronavirus (MERS)

Abstract This chapter briefly presents some structural bioinformatics about MERS-CoV binding with human ACE2. We find in the middle of interactions there are several hydrogen bonds and salt bridges linking the monomeric MERSCoV spike and the human ACE2 and hydrophobic core linking the beginning several residues of human ACE2 and the residues GLU513, PRO515, and VAL555 of the spike. Keywords CoV · MERS-CoV · Monomeric spike · Binding human ACE2 · Optimization and MD studies

12.1 Introduction Coronaviruses belong to the Beta genus. Middle East respiratory syndrome (MERS) is a viral respiratory disease caused by a novel coronavirus (Middle East respiratory syndrome coronavirus or MERS-CoV) that was first identified in Saudi Arabia in 2012. Although most of human cases of MERS-CoV infections have been attributed to human-to-human infections in healthcare settings, current scientific evidence suggests that dromedary camels are a major reservoir host for MERS-CoV and an animal source of MERS infection in humans. However, the exact role of dromedaries in the transmission of the virus and the exact route(s) of transmission are unknown. The emergence and persistence of MERS-CoV, almost one decade by now, highlight the need for the rapid development of effective interventions against this highly pathogenic coronavirus (CoV). Structural MD studies related to MERSCoV infection process are limited. Our structural bioinformatics presented in this chapter should be useful to the interventions against MERS-CoV.

© The Author(s), under exclusive license to Springer Nature Switzerland AG 2023 J. Zhang, Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures, Springer Series in Biophysics 23, https://doi.org/10.1007/978-3-031-36773-1_12

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418

12 MERS-Coronavirus (MERS)

12.2 Materials and Methods 5x5c.pdb is the prefusion structure of MERS-CoV spike glycoprotein [396], the structure has ABC chains, and each chain has residues TYR18-ALA1206; in the structure, there are two states of the RBD with receptor-binding region either buried (lying state) or exposed (standing state) – demonstrating an inherently flexible RBD readily recognized by the receptor. A MERS-human ACE2 binding model was built by Rynkiewicz et al. at website https://people.rit.edu/gabsbi. The model has two chains: A chain aa SER1-ASP597 is the human ACE2, and B chain aa VAL598LEU805 is the MERS-CoV spike monomer aa VAL381-LEU588. This chapter is to optimize this model and then present some basic structural bioinformatics for MERS binding human ACE2.

12.3 New Structural Bioinformatics We optimized the model with RMSD value 0.559261 Å. In the optimized model, there are seven .π -cations TYR197-LYS559.NZ+, TYR261-LYS423.NZ+, PHE574LYS578.NZ+, TRP147-ARG151.NH2+, TRP284-ARG288.NH2+, TYR497-ARG255.NH2+, and TRP443-ARG186.NH2+ in A chain and three .π -.π stackings TYR686-PHE616, PHE621PHE602, and PHE788-PHE635 in B chain. Tables 12.1 and 12.2 listed all the HBs and

SBs of the optimized model; the HB A:ASP12.OD2-B:LYS719.NZ and the SB A:ASP12-B:LYS719 link A chain and B chain of the model optimized (Fig. 12.1); there are also another two HBs A:LYS13.NZ-B:GLY755.O and B:LYS719.NZA:THR9.OG1 linking AB chains (Fig. 12.1). We also find there is a hydrophobic core/hole between B chain and A chain constructed by residues VAL772-PRO732GLU730 of B chain spike and residues SER1-GLU5-THR9 of A chain human ACE2 (Fig. 12.1). In order to agree with the residue numbers of 5x5c.pdb, we should subtract 217 from B chain residue numbers.

Fig. 12.1 There is a hydrophobic core/hole between B chain and A chain constructed by residues VAL772-PRO732-GLU730 of B chain MERS spike monomer and residues SER1-GLU5-THR9 of A chain human ACE2. The HBs A:ASP12.OD2-B:LYS719.NZ-A:THR9.OG1, B:GLY755.OA:LYS13.NZ, and SB A:ASP12-B:LYS719 are in the middle of the contacts between B chain and A chain

During viral membrane fusion with the cell membrane, the virus spike S2 protein arranges in a coiled coil with its HR2 domain packed into a deep groove on HR1. The MD of MERS-CoV is done in [164]; the MD simulations were carried out for MERS-CoV heptad repeat domains (HRs, PDB entries 4MOD and 4NJL) HR

12.4 Concluding Remarks

419

trimer, S2 monomer, and S2 trimer. Fluctuation of HR residue positions revealed major changes in the C-terminal of HR2 and the linker coil between HR1 and HR2 in both monomer and trimer [164]. Hydrophobic residues at the a and d positions of HR helices stabilize the whole system [164]. In [7], the author explored structural dynamics of the MERS-CoV receptor DPP4 and mutant DPP4 receptors. Mouse DPP4 (mDPP4) receptor is not a functional receptor for MERS-CoV, while human DPP4 (hDPP4) is. The variability of DPP4 receptors against MERS-CoV is not fully investigated, especially conformational and structural differences. Therefore, investigating the conformational differences of the DPP4 receptors can aid in developing new small animal models for MERSCoV vaccines and antiviral agent evaluation. In [7], the author used MD simulations and docking techniques to investigate these structural differences in DPP4 receptors, and results showed chimeric mouse mDPP4 (cmDPP4) has a similar compact conformation as the wild-type hDPP4 based on the structural analysis. Interestingly, a single THR288ALA mutation induced a relaxed conformation in chimeric 2 hDPP4 (c2hDPP4) and chimeric 2 mDPP4 (c2mDPP4) [7]; in addition to its significant effect on the DPP4 flexibility, the THR288 residue is known for its critical function in MERS-CoV RBD interaction. Moreover, MERS-CoV RBD adopts a “standing” conformation when docked to hDPP4 and cmDPP4 in blade IV and V regions [7].

12.4 Concluding Remarks We optimized a model of MERS-CoV monomeric spike binding with human ACE2. In the optimized model, we found seven .π -cations TYR197-LYS559.NZ+, TYR261LYS423.NZ+, PHE574-LYS578.NZ+, TRP147-ARG151.NH2+, TRP284-ARG288.NH2+, TYR497-ARG255.NH2+, and TRP443-ARG186.NH2+ in human ACE2 and three .π -.π stackings TYR686-PHE616, PHE621-PHE602, and PHE788-PHE635 in the MERS spike;

the HB A:ASP12.OD2-B:LYS719.NZ and the SB A:ASP12-B:LYS719 link A chain human ACE2 and B chain MERS spike of the model optimized; there are also another two HBs A:LYS13.NZ-B:GLY755.O and B:LYS719.NZ-A:THR9.OG1 linking AB chains; we also found there is a hydrophobic core/hole between B chain and A chain constructed by residues VAL772-PRO732-GLU730 of B chain spike and residues SER1-GLU5-THR9 of A chain human ACE2. Brief reviews on MDs of MERS-CoV spike HR, S2 [164] and MERS-CoV receptor DPP4 [7] are done in this chapter.

A:SER52.OG-A:GLY48.O

A:LEU438.N-A:PHE434.O

A:ASP579.OD1-A:LYS582.NZ

A:CYS512.N-A:GLN508.O

A:ARG151.NE-A:ASP481.OD1

A:ARG151.NH1-A:ASP481.OD2

A:GLN58.N-A:PHE54.O

A:GLN58.NE2-A:GLU57.OE2

A:ARG255.N-A:ASP251.OD2

A:ARG288.N-A:ASP285.OD1

A:LYS229.NZ-A:LEU263.O

A:THR100.OG1-A:LYS96.O

A:THR37.OG1-A:ASN40.OD1

A:LYS457.NZ-A:GLU461.OE2

A:GLU220.N-A:LYS216.O

A:GLU292.OE2-A:LYS295.NZ

A:GLU294.OE1-A:LYS291.NZ

A:ASN103.ND2-A:ASN99.O

A:ASN116.N-A:GLU122.O

A:ASN116.ND2-A:GLU122.OE1

A:THR478.OG1-A:ASP476.OD2 A:THR501.OG1-A:TYR497.O

A:LYS94.NZ-A:GLU171.OE1 A:MET105.N-A:ILE101.O

A:LYS96.NZ-A:ASP93.OD2

A:TRP253.N-A:ASP251.OD1

A:TRP145.N-A:ASN141.O

A:THR9.OG1-A:GLU5.O

A:THR549.OG1-A:TYR197.O

A:LYS578.NZ-A:GLU571.OE2 A:LYS582.NZ-A:ASP579.OD1 A:LYS8.NZ-A:GLU5.OE2

A:GLU164.OE2-A:ARG97.NE

A:GLU179.N-A:ASP183.OD2

A:GLU214.OE2-A:ARG564.NH2

A:ARG564.NH2-A:GLU214.OE2

A:THR478.N-A:ASP476.OD2

A:THR435.OG1-A:THR431.O

A:THR396.OG1-A:SER393.O

A:THR344.OG1-A:LEU315.O

A:ARG97.NE-A:GLU164.OE2

A:LYS578.N-A:PHE574.O

A:LYS523.NZ-A:GLU417.OE2

A:LYS516.NZ-A:ALA514.O

A:LYS423.NZ-A:ILE273.O

A:ARG97.NH1-A:GLU164.OE1

A:GLU164.N-A:PRO160.O

A:GLU164.OE1-A:ARG97.NH1

A:ARG564.NH1-A:ASN562.OD1

A:ARG564.NH1-A:GLU214.OE1

A:GLU163.N-A:ARG159.O

A:GLU163.OE1-A:ARG159.NE

A:THR347.OG1-A:ASP350.OD2 A:THR353.OG1-A:ASP349.O

A:LYS447.NZ-A:GLU179.OE1 A:LYS457.N-A:GLU477.OE2

A:GLU148.N-A:LEU144.O

A:GLU153.N-A:SER149.O

A:ARG464.NH1-A:THR590.O

A:ARG464.NH2-A:GLU471.OE2

A:ARG500.N-A:ARG496.O

A:THR347.N-A:ASP350.OD2

A:LYS440.N-A:TYR436.O

A:GLU122.N-A:ASN119.O

A:GLU142.N-A:ASP139.OD2

A:ARG375.NH2-A:ALA368.O

A:ARG464.N-A:TRP460.O

A:ARG541.NE-A:ASN538.O

A:THR306.OG1-A:GLY336.O A:THR329.N-A:LEU341.O A:THR34.OG1-A:TRP30.O

A:LYS345.NZ-A:ASP317.OD2 A:LYS398.NZ-A:ASP525.O A:LYS423.NZ-A:ASP274.OD2

A:GLN580.N-A:TRP576.O

A:GLN580.NE2-A:ASP579.OD2

A:GLN63.NE2-A:ASN85.OD1

A:ARG339.NE-A:ASP337.OD1

A:THR276.OG1-A:ASP274.OD1

A:THR276.N-A:ASP274.OD1

A:THR264.N-A:LEU260.O

A:THR211.N-A:ASP207.O

A:THR107.OG1-A:ASN103.O

A:THR107.N-A:ASN103.O

A:THR104.OG1-A:THR100.O

A:LYS345.N-A:ASP350.OD1

A:LYS335.NZ-A:ASP20.OD1

A:LYS335.N-A:GLU19.OE2

A:LYS295.NZ-A:GLU292.OE2

A:LYS291.NZ-A:GLU294.OE1

A:LYS270.NZ-A:GLU415.OE1

A:LYS270.NZ-A:ASP413.OD2

A:ARG339.NH1-A:ASP337.OD2

A:ARG339.N-A:TRP331.O

A:GLN454.NE2-A:ASP453.OD2

A:GLN504.N-A:ARG500.O

A:ARG201.NH1-A:GLU190.OE1

A:ARG201.NH2-A:ASP183.OD2

A:GLN370.NE2-A:ARG541.O

A:GLN411.NE2-A:ASP413.OD1

A:ARG186.NH2-A:ASP180.OD1

A:ARG201.NE-A:ASP183.OD1

A:GLN362.NE2-A:PRO303.O

A:GLN370.N-A:TYR367.O

A:ARG174.NH2-A:GLU179.O

A:ARG186.N-A:GLY182.O

A:SER593.OG-A:TRP592.O

A:SER589.OG-A:ASP591.OD2

A:LYS216.N-A:PHE212.O

A:LYS169.NZ-A:ASP491.OD2

A:GLN307.NE2-A:GLU311.OE1

A:GLN322.NE2-A:THR34.O

A:ARG159.NH1-A:LYS452.O

A:ARG159.NH2-A:GLU477.OE1

A:SER527.OG-A:ASP525.OD2 A:SER529.OG-A:GLU531.OE1 A:SER589.N-A:ILE241.O

A:LYS13.NZ-A:GLU17.OE2 A:LYS13.NZ-B:GLY755.O A:LYS169.N-A:TYR165.O

A:GLN24.N-A:ASP20.O

A:GLN24.NE2-A:ASP20.OD2

A:GLN287.N-A:ASP285.OD2

A:ARG159.NE-A:GLU163.OE1

A:SER527.N-A:ASP525.OD2

A:SER407.OG-A:ASP409.OD1

A:LEU79.N-A:VAL75.O

A:LEU374.N-A:PRO371.O

A:ARG159.NH1-A:GLU163.OE2

A:ARG151.NH2-A:TRP147.O

A:SER493.OG-A:GLU380.OE2

A:LEU421.N-A:GLU417.O

A:ASP49.N-A:ASN45.O

A:ASP491.OD2-A:LYS169.NZ

A:ARG143.NH1-A:ALA135.O

A:SER393.OG-A:GLN508.OE1 A:SER402.OG-A:LYS398.O

A:ARG143.NH1-A:SER137.O

A:LEU341.N-A:THR329.O A:LEU352.N-A:MET348.O

A:ASP413.OD2-A:LYS270.NZ

A:ASP481.OD1-A:ARG151.NE

A:ALA510.N-A:GLN506.O

A:SER391.OG-A:GLU388.O

A:ALA7.N-A:ILE3.O

A:LEU27.N-A:TYR23.O

A:SER299.OG-A:PHE296.O

A:ASP207.N-A:GLN203.O

A:ASP274.OD2-A:LYS423.NZ

A:ALA246.N-A:VAL470.O

A:ALA278.N-A:ASP277.OD1

A:LEU244.N-A:GLY468.O

A:SER152.OG-A:GLU148.OE2 A:SER26.N-A:PHE22.O

A:ALA224.N-A:GLU220.O

A:ILE418.N-A:ASN414.O A:ILE428.N-A:GLN424.O

A:ASP12.OD2-B:LYS719.NZ

A:ASP20.OD1-A:LYS335.NZ

A:ALA18.N-A:PHE14.O

Table 12.1 The HBs of the optimized MERS ACE2 binding model A:TYR479.OH-A:GLU148.OE2

B:LEU660.N-B:LEU619.O

B:LEU619.N-B:LEU660.O

B:ILE790.N-B:CYS695.O

B:ILE717.N-B:ASN685.OD1

B:ILE697.N-B:PHE788.O

B:ILE659.N-B:THR791.O

B:ILE650.N-B:SER646.O

B:HIS703.NE2-B:GLU782.OE1

B:GLY789.N-B:ASP661.O

B:GLY787.N-B:PHE663.O

B:GLY775.N-B:ASP756.O

B:GLU766.OE1-B:LYS760.NZ

B:GLU599.OE2-B:LYS630.NZ

B:GLU599.OE1-B:LYS804.NZ

B:GLN793.N-B:SER657.O

B:GLN733.N-B:CYS720.O

B:GLN688.NE2-B:CYS695.O

B:GLN612.NE2-B:THR750.OG1

B:CYS695.N-B:ILE790.O

B:ASP661.OD2-B:ARG618.NE

B:ASP661.N-B:GLY789.O

B:ASN718.ND2-B:SER776.OG

B:ASN692.ND2-B:SER689.OG

B:ASN638.N-B:LEU698.O

B:ASN625.ND2-B:PRO803.O

B:ARG722.NH2-B:GLY767.O

B:ARG722.NE-B:LEU724.O

B:ARG618.NH2-B:ASP661.OD1

B:ARG618.NE-B:ASP661.OD2

B:ALA773.N-B:TYR758.O

B:ALA699.N-B:MET786.O

A:VAL469.N-A:LYS463.O

A:VAL321.N-A:ASN320.OD1

A:VAL226.N-A:LEU222.O

A:VAL194.N-A:ASP198.OD1

A:TYR569.OH-A:GLN424.OE1

A:TYR503.N-A:THR499.O

A:TYR498.OH-A:VAL208.O

A:TYR497.OH-A:GLU384.OE1

B:PHE788.N-B:ILE697.O

B:TYR758.N-B:ALA773.O

B:TYR740.OH-B:PHE616.O

B:TYR716.N-B:SER776.O

B:TYR714.OH-B:THR781.OG1

B:TYR714.N-B:VAL778.O

B:TYR686.OH-B:ASP661.OD1

B:TYR665.OH-B:MET669.O

B:TYR665.N-B:GLN785.O

B:TYR662.OH-B:PRO604.O

B:TYR662.N-B:LYS617.O

B:TYR626.OH-B:ALA651.O

B:TYR614.OH-B:PRO748.O

B:TRP752.N-B:ASP756.OD2

B:THR791.N-B:ILE659.O

B:THR781.OG1-B:GLN783.O

B:THR777.OG1-B:ASP754.OD2

B:THR707.OG1-B:LEU606.O

B:THR700.OG1-B:ASN638.OD1

B:THR700.N-B:SER636.O

B:THR694.OG1-B:GLN688.OE1

B:THR694.N-B:SER643.O

B:THR641.N-B:LEU696.O

B:THR609.OG1-B:THR709.OG1

B:SER776.N-B:TYR716.O

B:SER763.OG-B:GLU766.OE2

B:SER763.N-B:GLU766.OE2

B:SER745.OG-B:PRO742.O

B:SER725.N-B:ASP727.OD2

B:SER682.OG-B:SER677.OG

B:SER677.OG-B:SER674.O

B:SER671.OG-B:ASP672.OD2

B:SER664.N-B:PRO611.O

B:SER656.OG-B:GLY795.O

B:SER652.OG-B:ALA648.O

B:SER643.N-B:THR694.O

B:SER636.N-B:THR700.O

B:SER633.N-B:THR629.O

B:SER603.OG-B:ASP601.OD1

B:SER603.N-B:ASP601.OD1

420 12 MERS-Coronavirus (MERS)

A:TRP548.NE1-A:TYR189.O A:TYR165.OH-A:ASP491.OD1 A:TYR178.N-A:ALA173.O

A:PHE267.N-A:ASN419.OD1 A:PHE290.N-A:ALA286.O A:TYR199.OH-A:ASP207.OD2

A:ILE403.N-A:HIS399.O

A:ASP12.N-A:LYS8.O

A:TYR436.OH-A:GLU209.OE2

A:SER149.N-A:TRP145.O

A:TYR367.N-A:TYR363.O A:TYR367.OH-A:ASP364.OD1

A:SER137.OG-A:GLU142.OE1

A:SER110.OG-A:SER106.O

A:ILE289.N-A:ASP285.O

A:ILE36.N-A:LYS323.O

A:ASN72.N-A:GLU4.OE2

A:TYR261.N-A:THR258.O A:TYR261.OH-A:ASN272.OD1

A:PHE570.N-A:LEU566.O A:PHE574.N-A:PHE570.O

A:HIS399.ND1-A:ASP525.OD1

A:ILE101.N-A:ARG97.O

A:ASN568.ND2-A:GLU509.OE2

A:ASN581.N-A:LEU577.O

A:ASN85.ND2-A:ASN176.OD1

A:TYR225.N-A:HIS221.O A:TYR23.OH-A:ASP337.OD2

A:PHE537.N-A:GLY533.O A:PHE54.N-A:LYS50.O

A:HIS223.N-A:TYR219.O

A:HIS223.NE2-A:GLY468.O

A:ASN560.ND2-A:ASP207.OD1

A:ASN568.N-A:ARG564.O

A:TYR219.OH-A:VAL467.O

A:PHE446.N-A:ARG442.O A:PHE507.N-A:TYR503.O

A:HIS16.ND1-A:ASP12.O

A:HIS210.N-A:GLU206.O

A:ASN490.ND2-A:PHE486.O

A:ASN554.ND2-A:LEU550.O

A:TYR197.OH-A:GLU553.OE1

A:PHE420.N-A:THR416.O

A:GLY196.N-A:ASP198.OD2

A:GLY254.N-A:ASP251.OD1

A:GLY334.N-A:ASP332.OD1

A:ASN419.N-A:GLU415.O

A:ASN419.ND2-A:PHE267.O

A:ASN45.N-A:VAL41.O

A:TRP592.NE1-A:ASP597.OD1

A:PHE14.N-A:PHE10.O A:PHE256.N-A:ASP251.OD2

A:GLU5.OE2-A:LYS8.NZ

A:GLU571.N-A:LEU567.O

A:ASN31.N-A:LEU27.O

A:ASN33.N-A:SER29.O

B:LEU762.N-B:GLY769.O

A:TRP331.N-A:ARG339.O A:TRP443.N-A:GLU439.O

A:MET365.N-A:ILE361.O A:MET437.N-A:PRO433.O

A:GLU471.N-A:GLU471.OE1

A:GLU471.OE2-A:ARG464.NH2

A:ASN170.ND2-A:VAL166.O

A:ASN232.ND2-A:ALA228.O

B:LEU705.N-B:PRO702.O

A:TRP30.N-A:SER26.O A:TRP310.NE1-A:GLU294.OE2

A:MET342.N-A:MET314.O A:MET348.N-A:THR276.OG1

A:GLU380.N-A:ASP188.OD2

A:GLU461.N-A:LYS457.O

A:ASN136.ND2-A:GLU132.OE2

B:LEU667.N-B:GLN785.OE1

B:PHE621.N-B:LEU658.O

B:MET786.N-B:ALA699.O

B:LYS804.NZ-B:GLU599.OE1

B:LYS760.NZ-B:GLU766.OE1

B:LYS760.N-B:LEU771.O

B:LYS719.NZ-A:THR9.OG1

B:LYS719.NZ-A:ASP12.OD2

B:LYS713.NZ-B:TRP752.O

B:LYS710.NZ-B:GLU782.O

B:LYS670.NZ-B:ASP639.OD1

B:LYS630.NZ-B:GLU599.OE2

B:LYS630.N-B:ASN627.OD1

B:LYS617.NZ-B:TYR662.OH

B:LYS617.NZ-B:THR609.O

B:LEU771.N-B:LYS760.O

B:LEU698.N-B:ASP639.O

B:LEU696.N-B:THR641.O

A:ASN15.N-A:LEU11.O

A:TRP257.NE1-A:GLY254.O A:TRP284.N-A:MET279.O

A:MET134.N-A:LEU130.O A:MET305.N-A:GLU294.OE2

A:GLU357.N-A:THR353.O

A:GLU38.N-A:GLU38.OE2

A:ASN119.ND2-A:GLU122.OE1

A:ASN136.N-A:GLU132.O

B:TYR758.OH-B:ASP756.OD2

B:VAL772.N-B:SER721.O

B:VAL751.N-B:SER715.OG

B:VAL735.N-B:GLN683.O

B:VAL701.N-B:LEU784.O

B:TYR794.OH-B:GLN644.OE1

12.4 Concluding Remarks 421

422 Table 12.2 The SBs of the optimized MERS ACE2 binding model

12 MERS-Coronavirus (MERS) In A chain

In B chain

Linking A-B chains

ASP20-LYS335

ASP639-LYS670

A:ASP12-B:LYS719

ASP93-LYS96

ASP661-ARG618

ASP180-ARG186

GLU599-LYS630

ASP183-ARG201

GLU599-LYS804

ASP188-LYS544

GLU753-LYS713

ASP274-LYS423

GLU766-LYS760

ASP317-LYS345

GLU782-HIS703

ASP337-ARG339

GLU782-LYS710

ASP364-HIS383 ASP413-LYS270 ASP481-ARG151 ASP491-LYS169 ASP525-HIS399 ASP579-LYS582 GLU4-LYS8 GLU5-LYS8 GLU17-LYS13 GLU19-ARG375 GLU163-ARG159 GLU164-ARG97 GLU171-LYS94 GLU179-LYS447 GLU190-ARG201 GLU209-LYS440 GLU214-ARG564 GLU220-HIS221 GLU292-ARG288 GLU292-LYS295 GLU294-LYS291 GLU357-HIS360 GLU380-ARG496 GLU384-HIS356 GLU388-ARG500 GLU412-LYS401 GLU415-LYS270 GLU417-HIS522 GLU417-LYS523 GLU439-ARG442 GLU461-LYS457 GLU465-LYS216 GLU471-ARG464 GLU477-ARG159 GLU531-LYS516 GLU571-LYS578

Chapter 13

Human ACE2, Human IL6, Human IL6R, and Human nAChRs

Abstract SARS-CoV-2, the virus causing the COVID-19 global pandemic, encodes for a trimeric spike glycoprotein that contains a receptor-binding domain (RBD) that binds favorably to the ACE2 (angiotensin-converting enzyme 2) receptor present on the surface of human host cell. There is some early evidence that human interleukin 6 (human IL6) can be used as an inflammatory marker for severe COVID-19 infection with poor prognosis. Human IL6R is the IL6 receptor that has been shown to interact with IL6 and ciliary neurotrophic factor. This short chapter is to study human ACE2, human IL6, and human IL6R from optimization and molecular dynamics (MD) point of view to present some basic structural bioinformatics of them. The studies are fundamentally important in the fight against SARS-CoV-2. Human .α4β2-, .α7-, and .αβγ δ-nAChRs binding SARS-CoV-2 spike Y674-R685 region are also studied in this chapter. Keywords COVID-19 · Human ACE2 · Human IL6 · Human IL6R · Molecular structure optimization and molecular dynamics (MD) studies

13.1 Introduction SARS-CoV-2, the virus causing the COVID-19 global pandemic, encodes for a trimeric spike glycoprotein that contains a receptor-binding domain (RBD) that binds favorably to the ACE2 (angiotensin-converting enzyme 2) receptor present on the surface of human throat cells and lung epithelial cells. The receptor-binding motif (S438-Q506 region) of SARS-CoV-2 spike is known to bind to ACE2. This binding creates a fusion between the human cell membrane and the spike protein, allowing the viral genetic material to be replicated within the human host cell. Therefore, understanding the interaction of the spike with ACE2 at the cell surface is fundamentally important in the fight against SARS-CoV-2. There is some early evidence that interleukin 6 (IL6) can be used as an inflammatory marker for severe COVID-19 infection with poor prognosis, in the content of the wider coronavirus pandemic. IL6 is responsible for stimulating acute phase protein synthesis. It © The Author(s), under exclusive license to Springer Nature Switzerland AG 2023 J. Zhang, Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures, Springer Series in Biophysics 23, https://doi.org/10.1007/978-3-031-36773-1_13

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13 Human ACE2, Human IL6, Human IL6R, and Human nAChRs

supports the growth of B cells and is antagonistic to regulatory T cells. Human IL6R is the IL6 receptor that has been shown to interact with IL6 and ciliary neurotrophic factor. Human IL6R is a protein complex consisting of an IL6 receptor subunit (IL6R) and interleukin 6 signal transducer glycoprotein 130. This brief chapter is to introduce some basic structural bioinformatics of human ACE2, human IL6, and human IL6R through our optimization and MD technologies.

13.2 Materials and Methods We got the human ACE2 monomer (6LZG.pdb, aa SER19-ALA614) 664 .μs, human IL6 monomer (1ALU.pdb, aa LEU19-MET184) 1593 .μs, and human IL6R monomer (1N26.pdb, aa LEU1-SER299) 196 .μs’ MD free datasets of Folding@home (foldingathome.org) from website osf.io/fs2yv/file [439]. We firstly optimized the three structures of human-ACE2-6LZG-model, human-IL6-1ALUmodel, and human-IL6-1ALU-model; from the optimized models, we get some basic structural bioinformatics such as .π -interactions, SBs, HBs, the PoissonBoltzmann electrostatic potential surfaces, the Ramachandran plot diagram, and the hydrophobic surface. Furthermore, we confirm these bioinformatics by the analysis of these open MD trajectories of [439].

13.3 New Structural Bioinformatics 13.3.1 Human ACE2 Monomer For the human-ACE2-6LZG-model (6LZG.pdb, aa SER19-ALA614, 75787 atoms) optimized, we get 7 .π -cations LYS288.NZ.+ -PHE285, LYS596.NZ.+ -PHE592, ARG357.NH2.+ -TRP48, ARG273.NH2.+ -TYR515, ARG204.NH2.+ -TRP461, ARG169.NH2.+ TRP165, and HIS493.ND1.+ -TYR497 and 24 .π -.π stackings TYR217-TRP566, TRP349TRP48-TRP349, TYR196-TYR202, TYR385-TYR381, PHE464-TYR199, TRP328-PHE327TRP328, PHE390-PHE40, TRP409-TRP477-TRP478, TRP477-TRP478, TYR497-HIS493, TRP566-TYR217, PHE504-HIS505-TYR515-PHE512, TYR255-TYR158-HIS265, TYR243TRP594, PHE588-TYR587, HIS417-PHE314-PHE315, and PHE314-HIS373. Segments TRP168-ARG169, TRP202-TRP203-ARG204, TRP459-ARG460-TRP461, ARG514-TYR515TYR516, and TYR587-PHE588 have strong SASA characters. Figure 13.1 illuminates

the Poisson-Boltzmann electrostatic potential surface (EPS), Ramachandran plot diagram, and hydrophobic surface of the optimized human-ACE2-6LZG-model, where we may see large areas of red-colored negative charges on the EPS. For the MD, we may see in Fig. 13.2 that the .α-helix in segment PRO492LEU503 unfolds into 3.10 -helix and turns during 664 .μs’ MD (Tables 13.1 and 13.2).

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425

Fig. 13.1 The Poisson-Boltzmann electrostatic potential surfaces, Ramachandran plot diagram, and hydrophobic surface of the optimized human-ACE2-6LZG-model

Fig. 13.2 Secondary structure of the human-ACE2-6LZG-model during 664 .μs’ MD

During the MD, the SBs GLU197-ARG204 and GLU589-LYS596 do not exist, but replaced by ASP427-LYS288, ASP427-LYS419, and GLU589ARG582, respectively; but the SBs ASP38-LYS353, ASP201-ARG219, ASP335-LYS363, ASP382-HIS401, ASP431-LYS288, ASP509-LYS187, ASP543-LYS416, ASP597-LYS600, GLU35-LYS31, GLU37-ARG393, GLU166-HIS493, GLU181-ARG177, GLU181-LYS470, GLU189-LYS112, GLU208-ARG219, GLU227-LYS458, GLU231-LYS234, GLU310-ARG306, GLU310-LYS313, GLU312-LYS309, GLU398-ARG514, GLU406-ARG518, GLU430-LYS541, GLU433-LYS288, GLU435-HIS540, GLU435-LYS541, GLU457-ARG460, GLU467-LYS465, GLU479-LYS476, and GLU549-LYS534 are strong. The SBs ASP201-ARG219, ASP597LYS600, GLU181-ARG177, GLU208-ARG219, GLU231-LYS234, GLU310-ARG306, GLU310-LYS313, GLU312-LYS309, GLU457-ARG460, GLU467-LYS465, GLU479-LYS476, and GLU549-LYS534 span several residues, respectively. We illuminate the SBs GLU435-LYS541, ASP509-LYS187, GLU166-HIS493, GLU189-LYS112, GLU406-ARG518, GLU435-HIS540, GLU37-ARG393, GLU181-LYS470, GLU227-LYS458, GLU398-ARG514, GLU430-LYS541, ASP38-LYS353, ASP382-HIS401, ASP431-LYS288, ASP543-LYS416, GLU433-LYS288, and GLU549-LYS534 spanning a large number of residues in Fig. 13.7.

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13 Human ACE2, Human IL6, Human IL6R, and Human nAChRs

Table 13.1 All the SBs in the optimized human-ACE2-6LZG-model and in the 664 .μs’ MD Opt-SBs

664 .μs-MD-SBs

ASP111-ARG115

ASP111-ARG115, ASP111-LYS112, ASP111-LYS114, ASP111-LYS74

ASP198-ARG204

ASP136-LYS341

ASP201-ARG219

ASP198-ARG204, ASP198-LYS465

ASP206-LYS562

ASP201-ARG204, ASP201-ARG219

ASP30-HIS34

ASP206-ARG514, ASP206-LYS562

ASP335-LYS363

ASP213-LYS577

ASP355-ARG357

ASP225-HIS228

ASP382-HIS401

ASP269-ARG273

ASP38-LYS353

ASP292-LYS288, ASP292-LYS441

ASP431-LYS288

ASP295-LYS288

ASP494-LYS174

ASP303-ARG306, ASP303-LYS309

ASP499-HIS493

ASP30-HIS34

ASP509-LYS187

ASP335-LYS341, ASP335-LYS363

ASP543-LYS416

ASP350-ARG357, ASP350-ARG393, ASP350-LYS353

ASP597-LYS600

ASP355-ARG357, ASP355-LYS353

GLU166-HIS493

ASP367-HIS345, ASP367-LYS363, ASP367-LYS441

GLU181-ARG177

ASP368-LYS363

GLU181-LYS470

ASP382-ARG393, ASP382-HIS378, ASP382-HIS401, ASP382-LYS353, ASP382-LYS562

GLU189-LYS112

ASP38-LYS353

GLU197-ARG204 X

ASP427-LYS288, ASP427-LYS419

GLU208-ARG219

ASP431-LYS288, ASP431-LYS419

GLU227-LYS458

ASP471-ARG177, ASP471-LYS475

GLU22-LYS26

ASP494-ARG177, ASP494-LYS174, ASP494-LYS475

GLU231-LYS234

ASP499-ARG169, ASP499-HIS493, ASP499-LYS481

GLU310-ARG306

ASP509-ARG460, ASP509-LYS187

GLU310-LYS313

ASP543-LYS416

GLU312-LYS309

ASP597-LYS600

GLU35-LYS31

ASP609-ARG482

GLU37-ARG393

ASP67-LYS114, ASP67-LYS68

GLU398-ARG514

GLU110-LYS114, GLU110-LYS74

GLU402-ARG514

GLU140-LYS131, GLU140-LYS341, GLU140-LYS363

GLU402-ARG518

GLU145-ARG273, GLU145-HIS505, GLU145-LYS363

GLU406-ARG518

GLU150-LYS363

GLU430-LYS541

GLU166-ARG169, GLU166-HIS493

GLU433-LYS288

GLU171-LYS131

GLU435-HIS540

GLU171-LYS174

GLU435-LYS541

GLU181-ARG177, GLU181-LYS470

GLU457-ARG460

GLU182-ARG115

GLU467-LYS465

GLU189-ARG192, GLU189-LYS112

GLU479-LYS475

X GLU197-ARG219, GLU197-LYS465

GLU479-LYS476

GLU208-ARG219, GLU208-HIS195, GLU208-LYS94

GLU483-LYS476

GLU224-HIS228

GLU489-ARG482

GLU227-LYS458

GLU495-ARG177

GLU22-LYS26

GLU527-ARG582

GLU231-LYS234

GLU549-LYS534

GLU232-ARG582, GLU232-HIS228

GLU564-ARG559

GLU238-LYS234

GLU589-LYS596 X

GLU23-LYS26 GLU310-ARG306, GLU310-LYS309, GLU310-LYS313 GLU312-LYS309, GLU312-LYS313 GLU329-LYS309, GLU329-LYS353 GLU35-HIS34, GLU35-LYS31 GLU375-HIS374, GLU375-HIS378 GLU37-ARG393, GLU37-LYS353 GLU398-ARG514, GLU398-ARG518, GLU398-HIS401, GLU398-LYS562 GLU402-ARG514, GLU402-ARG518, GLU402-HIS374, GLU402-HIS378, GLU402-HIS401 GLU406-ARG518, GLU406-HIS374 GLU430-LYS288, GLU430-LYS416, GLU430-LYS419, GLU430-LYS541 GLU433-LYS247, GLU433-LYS288 GLU435-HIS540, GLU435-LYS288, GLU435-LYS416, GLU435-LYS419, GLU435-LYS541

(continued)

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427

Table 13.1 (continued) Opt-SBs

664 .μs-MD-SBs GLU457-ARG460 GLU467-ARG192, GLU467-LYS465 GLU479-ARG482, GLU479-LYS475, GLU479-LYS476 GLU483-ARG482 GLU489-ARG169, GLU489-ARG482, GLU489-HIS493, GLU489-LYS481 GLU495-ARG177, GLU495-HIS493, GLU495-LYS174, GLU495-LYS470, GLU495-LYS475 GLU527-ARG582 GLU536-LYS541 GLU549-LYS534, GLU549-LYS553 GLU564-ARG559, GLU564-LYS562 GLU56-LYS131 GLU571-LYS577 X GLU589-ARG582 GLU75-LYS74

Table 13.2 Some polar contacts GLU166-HIS493, GLU227-LYS458, GLU189-LYS112, GLU181-LYS470, GLU398-ARG514, GLU435-LYS541, ASP509-LYS187, GLU406ARG518, GLU37-ARG393, and GLU435-HIS540 of the human-ACE2-6LZG-model GLU166-HIS493

HIS493.NE2-GLU166.OE1 17.56%, HIS493.NE2-GLU166.OE2 20.36%, TYR497.OH-GLU166.OE1 7.39%, TYR497.OH-GLU166.OE2 4.99%

GLU227-LYS458

LYS458.NZ-GLU227.OE2 13.77%, LYS458.NZ-GLU227.OE1 9.78%, TYR454.OH-GLU227.OE2 12.18%, TYR454.OH-GLU227.OE1 9.18%

GLU189-LYS112

LYS112.NZ-GLU189.OE2 11.58%, LYS112.NZ-GLU189.OE1 10.38%

GLU181-LYS470

LYS470.NZ-GLU181.OE2 12.38%, LYS470.NZ-GLU181.OE1 9.58%

GLU398-ARG514

GLU398.N-ASP206.OD1 15.57%, GLU398.N-ASP206.OD2 15.37%, ARG514.NH1-GLU398.OE1 8.78%, ARG514.NH1-GLU398.OE2 8.58%, SER511.OG-GLU398.OE1 6.39%, SER511.OG-GLU398.OE2 6.79%

GLU435-LYS541

LYS541.NZ-GLU435.OE2 7.98%, LYS541.NZ-GLU435.OE1 6.59%, HIS540.NE2-GLU435.OE1 6.79%, HIS540.NE2-GLU435.OE2 6.59%

ASP509-LYS187

LYS187.NZ-ASP509.OD2 7.39%, LYS187.NZ-ASP509.OD1 6.99%, TYR183.OH-ASP509.OD1 17.76%, TYR183.OH-ASP509.OD2 13.57%, TRP203.NE1-ASP509.O 6.79%, TYR199.OH-ASP509.OD2 6.79%, TYR199.OH-ASP509.OD1 6.59%

GLU406-ARG518

ARG518.NE-GLU406.OE1 7.39%, ARG518.NE-GLU406.OE2 6.19%, ARG518.NH1-GLU406.OE2 5.39%, GLN522.NE2-GLU406.O 9.58%, HIS374.ND1-GLU406.OE2 8.18%, HIS374.ND1-GLU406.OE1 6.19%

GLU37-ARG393

ARG393.NH1-GLU37.OE1 7.78%, ARG393.NH2-GLU37.OE2 7.39%, ARG393.NH1-GLU37.OE2 6.99%, ARG393.NH2-GLU37.OE1 5.99%

GLU435-HIS540

HIS540.NE2-GLU435.OE1 6.79%, HIS540.NE2-GLU435.OE2 6.59%, LYS541.NZ-GLU435.OE2 7.98%, LYS541.NZ-GLU435.OE1 6.59%

The HBs with occupancy rates .≥5% during 664 .μs’ MD are listed in Tables 13.3 and 13.4. Some very interesting SBs with stronger HBs such as GLU166-HIS493, GLU227-LYS458, GLU189-LYS112, GLU181-LYS470, GLU398-ARG514, GLU435-LYS541, ASP509-LYS187, GLU406-ARG518, GLU37-ARG393, and GLU435-HIS540 are listed in

Table 13.2.

13.3.2 Human IL6 Monomer There is some early evidence that interleukin 6 (IL6) can be used as an inflammatory marker for severe COVID-19 infection with poor prognosis, in the content of the wider coronavirus pandemic. IL6 is responsible for stimulating acute phase protein synthesis. It supports the growth of B cells and is antagonistic to regulatory T cells. SBs and HBs of the optimized human-IL6-1ALU-model are listed in Tables 13.5 and 13.6. SBs GLU110-ARG113, GLU80-LYS129, GLU95-LYS120, ASP160-ARG104, ASP26-ARG30, ASP71-LYS70, ASP71-LYS86, GLU42-LYS46, and GLU51-

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13 Human ACE2, Human IL6, Human IL6R, and Human nAChRs

Fig. 13.3 Secondary structure of the human-IL6-1ALU-model during 1593 .μs’ MD

Fig. 13.4 The Poisson-Boltzmann electrostatic potential surfaces of the optimized human-IL61ALU-model

ARG40 of human-IL6-1ALU-model during 1593 .μs’ MD are illuminated in Fig. 13.8. The SB GLU110-ARG113 is with stronger HBs ARG113.NH2-GLU110.OE1 14.33%, ARG113.NH2-GLU110.OE2 12.65%, ARG113.NE-GLU110.OE2 8.39%, ARG113.NEGLU110.OE1 8.39%, and ALA114.N-GLU110.O 14.99% during the 1593 .μs’ MD.

During the 1593 .μs’ MD, we should also notice the stronger HBs between ARG182 and ASP26, ARG182.NE-ASP26.OD1 14.81%, ARG182.NE-ASP26.OD2 13.19%, ARG182.NH2-ASP26.OD1 13.07%, and ARG182.NH2-ASP26.OD2 12.77%, and the stronger HBs between SER47 and ASP160: SER47.OG-ASP160.OD2 15.95% and SER47.OGASP160.OD1 14.33%.

During the 1593 .μs’ MD, the secondary structures of the human-IL6-1ALUmodel are not variable largely (Fig. 13.3). But we should notice the PoissonBoltzmann electrostatic potential surfaces of the optimized human-IL6-1ALUmodel have large areas of positive charges (blue colored in Fig. 13.4).

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429

Table 13.3 The HBs (with occupancy rates .≥5%) of the human-ACE2-6LZG-model during 664 .μs’ MD VAL316.N-GLU312.O 78.24%

LYS458.N-TYR454.O 34.93%

TYR279.OH-ASN437.OD1 24.95%

SER317.N-LYS313.O 18.96%

VAL244.N-LEU240.O 76.85%

SER77.N-LEU73.O 34.73%

LEU570.N-TRP566.O 24.95%

TYR237.N-ILE233.O 18.76%

VAL487.N-LYS481.O 66.87%

ALA569.N-PRO565.O 34.53%

THR434.OG1-ASP431.OD1 24.95%

SER77.OG-LEU73.O 18.76%

VAL574.N-LEU570.O 66.27%

LEU186.N-GLU182.O 34.33%

THR118.N-LYS114.O 24.75%

ALA99.N-LEU95.O 18.56%

GLU197.N-ASP201.OD1 65.47%

THR362.OG1-LEU333.O 33.93%

SER43.N-LEU39.O 24.35%

VAL172.N-TRP168.O 18.56%

VAL93.N-ASN90.OD1 63.87%

GLU238.N-LYS234.O 33.33%

SER502.OG-CYS498.O 24.35%

MET376.N-ALA372.O 18.56%

TRP461.N-GLU457.O 62.67%

GLN76.N-PHE72.O 33.33%

ARG460.NH2-GLU457.OE2 24.35%

MET462.N-LYS458.O 18.36%

VAL488.N-LEU262.O 61.28%

HIS373.ND1-PHE369.O 33.33%

GLN531.N-GLU527.O 24.35%

LYS465.N-TRP461.O 18.16%

VAL209.N-TYR217.O 61.28%

ARG161.N-ASP157.O 33.13%

TYR252.OH-LEU156.O 24.15%

LYS309.N-GLN305.O 18.16%

GLU483.N-GLU479.O 60.48%

GLN98.N-LYS94.O 32.73%

GLN89.N-GLU22.OE1 24.15%

GLU406.N-GLU402.O 18.16%

HIS241.N-TYR237.O 59.88%

LYS481.N-TRP477.O 32.34%

ALA246.N-ALA242.O 24.15%

ARG582.N-ASN580.OD1 17.96%

LYS476.N-GLN472.O 59.68%

ILE54.N-LYS341.O 32.14%

ASN121.N-ASN117.O 23.95%

ARG518.N-ARG514.O 17.96%

SER607.N-ILE259.O 59.08%

ARG192.NE-GLU197.O 31.94%

TRP168.NE1-SER502.O 23.95%

GLN96.NE2-THR92.O 17.96%

THR449.OG1-ARG273.O 57.09%

SER124.N-LEU120.O 31.94%

TRP48.N-SER44.O 23.95%

ASN63.N-VAL59.O 17.96%

THR282.OG1-LEU278.O 54.49%

HIS374.N-LEU370.O 31.94%

ILE421.N-HIS417.O 23.75%

THR434.OG1-ASP431.OD2 17.76%

SER155.OG-ILE151.O 54.29%

ALA25.N-ILE21.O 31.74%

ILE513.N-GLU457.OE1 23.55%

THR371.N-ASP367.O 17.76%

THR517.N-ILE513.O 53.69%

TYR215.OH-GLU571.OE2 31.54%

THR52.OG1-TRP48.O 23.35%

TYR183.OH-ASP509.OD1 17.76%

SER113.OG-SER109.O 52.69%

ARG219.NE-ASP201.OD2 31.54%

GLN102.N-GLN98.O 23.35%

MET332.N-ILE358.O 17.76%

TYR521.N-THR517.O 51.70%

ASN51.ND2-SER47.O 31.34%

GLU310.N-ARG306.O 23.15%

ASP299.N-ASP295.O 17.56%

THR229.OG1-ASP225.O 51.30%

TRP566.NE1-TYR207.O 31.34%

LEU370.N-MET366.O 23.15%

GLU312.N-PHE308.O 17.56%

SER47.OG-SER43.O 51.30%

TYR215.OH-GLU571.OE1 31.34%

THR453.N-THR449.O 22.95%

GLN96.N-THR92.O 17.56%

VAL132.N-LEU142.O 51.10%

ILE436.N-ASN432.O 30.94%

ASN117.N-SER113.O 22.95%

GLU435.N-ASP431.O 17.56%

VAL226.N-LEU222.O 50.70%

LYS187.N-TYR183.O 30.74%

TYR217.OH-ASP225.OD2 22.95%

HIS493.NE2-GLU166.OE1 17.56%

LEU95.N-LEU91.O 50.50%

HIS535.N-CYS530.O 30.74%

GLU457.N-THR453.O 22.95%

ARG460.NH2-GLU457.OE1 17.37%

THR453.OG1-THR449.O 49.90%

VAL447.N-ALA443.O 30.74%

GLN442.N-PHE438.O 22.95%

ASN149.N-LEU144.O 17.17%

MET123.N-ILE119.O 49.50%

THR496.OG1-ASP494.OD1 30.74%

ILE358.N-SER331.OG 22.75%

LEU554.N-ALA550.O 17.17%

GLU375.N-THR371.O 48.90%

LEU97.N-VAL93.O 30.74%

GLN300.N-ALA296.O 22.75%

SER47.N-SER43.O 17.17%

HIS378.N-HIS374.O 48.30%

THR78.OG1-LYS74.O 30.34%

GLN221.N-SER218.O 22.75%

ARG245.NH2-GLY260.O 17.17%

THR567.OG1-TYR215.O 47.90%

ILE446.N-GLN442.O 29.74%

ALA80.N-GLN76.O 22.75%

ARG357.N-TRP349.O 16.97%

VAL283.N-TYR279.O 47.70%

SER545.OG-ASP543.OD2 29.74%

MET62.N-ASN58.O 22.55%

ARG219.NH2-GLU208.OE1 16.97%

THR517.OG1-ILE513.O 47.31%

PHE40.N-ALA36.O 29.54%

TRP302.NE1-GLN300.OE1 22.36%

TYR454.N-LEU450.O 16.97%

ALA36.N-PHE32.O 46.91%

LEU439.N-GLU435.O 29.34%

ARG161.NH1-SER155.O 22.36%

MET360.N-MET332.O 16.77%

LEU148.N-LEU143.O 46.71%

LYS74.N-SER70.O 29.14%

THR445.OG1-LYS441.O 22.36%

GLN380.NE2-MET376.O 16.77%

THR129.OG1-THR125.O 45.71%

LEU116.N-LYS112.O 28.74%

GLU231.N-GLU227.O 22.36%

TRP459.N-MET455.O 16.77%

VAL506.N-LEU503.O 45.51%

THR496.OG1-ASP494.OD2 28.54%

SER502.OG-ASP499.O 22.16%

ASN49.N-LEU45.O 16.77%

MET480.N-LYS476.O 45.51%

TRP163.N-ASN159.O 28.54%

LYS114.N-GLU110.O 22.16%

LYS596.N-PHE592.O 16.57%

SER411.OG-ILE407.O 43.51%

LEU73.N-TRP69.O 28.34%

GLN42.N-ASP38.O 22.16%

ASN586.N-ARG582.O 16.37%

SER218.N-GLN221.OE1 43.51%

GLN89.N-GLU22.OE2 28.14%

ASP67.N-ASN63.O 21.96%

LEU558.N-LEU554.O 16.37%

ARG245.N-HIS241.O 43.31%

LEU359.N-THR347.O 28.14%

LYS26.N-GLU22.O 21.96%

ARG219.NH1-ASP201.OD1 16.37%

VAL298.N-THR294.O 42.32%

LEU29.N-ALA25.O 27.94%

ASP225.N-GLN221.O 21.76%

LEU391.N-ASN33.OD1 16.37%

TYR183.N-LEU179.O 42.12%

LEU120.N-LEU116.O 27.94%

TYR217.N-VAL209.O 21.76%

LEU45.N-TYR41.O 16.37%

LEU440.N-ILE436.O 41.92%

LEU320.N-PHE315.O 27.94%

ALA153.N-ASN149.O 21.56%

LEU278.N-TRP275.O 16.37%

TRP477.NE1-ASP499.OD2 41.92%

ARG169.NH1-MET270.O 27.74%

ALA65.N-ASN61.O 21.56%

GLU479.N-LYS475.O 16.17%

THR122.OG1-THR118.O 41.72%

SER167.OG-TRP163.O 27.74%

ASN572.N-LEU568.O 21.56%

TYR243.OH-THR282.O 16.17%

SER128.OG-SER124.O 41.72%

ARG115.N-ASP111.O 27.54%

ARG460.NH2-TYR510.O 21.36%

PHE28.N-GLN24.O 16.17%

TYR237.OH-VAL485.O 41.52%

VAL59.N-THR55.O 27.54%

MET249.N-ARG245.O 21.16%

GLN522.N-ARG518.O 16.17%

ALA372.N-ASP368.O 41.32%

LEU456.N-PHE452.O 27.54%

ILE513.N-GLU457.OE2 21.16%

SER170.OG-GLU166.O 16.17%

PHE464.N-ARG460.O 41.12%

ASN51.N-SER47.O 27.35%

TRP302.N-MET297.O 20.96%

LEU418.N-THR414.O 15.97%

VAL343.N-ASN51.O 40.92%

ILE151.N-GLY147.O 27.35%

GLN524.NE2-ASN578.O 20.96%

GLU402.N-GLU398.O 15.77%

THR27.OG1-GLU23.O 40.72%

SER113.N-SER109.O 27.35%

ASN58.ND2-ASN53.O 20.76%

ARG482.N-TRP478.O 15.77%

ILE119.N-ARG115.O 40.52%

ASN599.N-LEU595.O 27.15%

ARG161.NH2-LEU267.O 20.76%

LEU450.N-ILE446.O 15.77%

THR593.OG1-GLU589.O 40.12%

THR371.OG1-ASP367.O 27.15%

GLN526.N-GLN522.O 20.56%

SER317.OG-LYS313.O 15.77%

THR125.OG1-ASN121.O 39.72%

ALA71.N-ASP67.O 27.15%

LYS94.N-ASN90.O 20.56%

ARG219.NH2-GLU208.OE2 15.57%

LEU444.N-LEU440.O 39.72%

SER44.N-PHE40.O 27.15%

HIS493.NE2-GLU166.OE2 20.36%

GLU398.N-ASP206.OD1 15.57%

TYR516.OH-THR229.OG1 39.52%

ILE126.N-THR122.O 26.95%

ALA46.N-GLN42.O 20.36%

GLN472.N-PRO469.O 15.57%

LEU262.N-GLY486.O 39.32%

THR414.OG1-SER411.O 26.95%

MET455.N-PRO451.O 20.16%

LYS476.NZ-GLU479.OE1 15.57%

LEU595.N-LEU591.O 39.12%

ALA242.N-GLU238.O 26.75%

GLU75.N-ALA71.O 20.16%

ARG192.N-ASN188.O 15.37%

GLN101.NE2-ALA80.O 38.92%

ASN64.N-GLN60.O 26.75%

GLU467.N-MET462.O 20.16%

LYS313.NZ-GLU310.OE2 15.37%

VAL184.N-TYR180.O 38.72%

PHE592.N-PHE588.O 26.75%

THR593.N-GLU589.O 19.96%

GLN175.N-GLU171.O 15.37%

PHE525.N-TYR521.O 37.92%

SER545.OG-ASP543.OD1 26.55%

GLN60.N-GLU56.O 19.96%

GLU329.N-GLN325.O 15.37%

ILE484.N-MET480.O 37.52%

HIS401.N-ASN397.O 26.55%

PHE315.N-ALA311.O 19.96%

LYS313.NZ-GLU310.OE1 15.37%

TYR180.N-LEU176.O 37.13%

TYR217.OH-ASP225.OD1 26.35%

ASP382.N-HIS378.O 19.76%

GLU398.N-ASP206.OD2 15.37%

ALA443.N-LEU439.O 36.73%

GLU181.N-ARG177.O 26.15%

LEU410.N-GLU406.O 19.76%

ALA164.N-GLU160.O 15.17%

(continued)

430

13 Human ACE2, Human IL6, Human IL6R, and Human nAChRs

Table 13.3 (continued) ILE379.N-GLU375.O 36.53%

HIS241.NE2-GLY486.O 26.15%

SER411.N-ILE407.O 19.56%

SER331.OG-PHE327.O 36.53%

THR229.N-ASP225.O 26.15%

LYS247.N-TYR243.O 19.36%

VAL318.N-PHE314.O 36.53%

MET152.N-LEU148.O 25.95%

PHE400.N-ASN397.OD1 15.17%

VAL463.N-TRP459.O 19.36%

CYS530.N-GLN526.O 36.13%

SER420.N-LYS416.O 25.95%

LEU424.N-LEU418.O 19.16%

GLU166.N-LEU162.O 35.93%

ASN33.N-LEU29.O 25.75%

ARG115.NH1-GLU182.OE2 19.16%

SER70.N-GLY66.O 35.13%

TYR252.N-LEU248.O 25.75%

ARG115.NH1-GLU182.OE1 19.16%

TRP349.N-ARG357.O 25.35%

Table 13.4 The HBs (with occupancy rates .≥5%) of the human-ACE2-6LZG-model during 664 .μs’ MD (continuation) LEU248.N-VAL244.O 14.97%

TYR587.N-PRO583.O 10.98%

ARG393.NE-GLN388.O 7.98%

GLY260.N-SER257.O 6.39%

THR519.OG1-TYR515.O 14.97%

ALA386.N-ASP382.O 10.98%

TYR207.OH-THR517.OG1 7.98%

SER511.OG-GLU398.OE1 6.39%

VAL185.N-GLU181.O 14.97%

SER44.OG-PHE40.O 10.98%

VAL364.N-ASP368.OD2 7.98%

HIS493.ND1-GLU489.OE1 6.39%

SER70.OG-GLY66.O 14.97%

SER128.N-SER124.O 10.78%

PHE72.N-LYS68.O 7.98%

THR20.OG1-GLU23.OE1 6.39%

LYS476.NZ-GLU479.OE2 14.97%

GLN598.N-TRP594.O 10.78%

THR347.OG1-PRO346.O 7.98%

VAL212.N-ASP216.OD1 6.19%

ARG460.N-LEU456.O 14.97%

SER170.N-GLU166.O 10.78%

LYS541.NZ-GLU435.OE2 7.98%

HIS401.NE2-HIS378.O 6.19%

HIS228.N-GLU224.O 14.77%

SER545.N-ASP543.OD1 10.78%

ARG161.NE-HIS265.O 7.98%

GLU227.N-ILE223.O 6.19%

GLU160.N-ASP157.OD2 14.57%

GLN340.NE2-THR52.O 10.78%

SER155.OG-GLU160.OE1 7.78%

ARG518.NE-GLU406.OE2 6.19%

ALA412.N-MET408.O 14.57%

THR347.N-LEU359.O 10.78%

ARG393.NH1-GLU37.OE1 7.78%

LYS441.NZ-ILE291.O 6.19%

ARG204.N-GLY200.O 14.57%

VAL107.N-GLY104.O 10.58%

LEU162.N-TYR158.O 7.78%

HIS374.ND1-GLU406.OE1 6.19%

ALA191.N-LYS187.O 14.57%

HIS378.ND1-GLU375.OE2 10.58%

ASP201.N-ASP198.OD2 7.78%

GLN552.NE2-THR548.O 6.19%

TYR202.N-ASP198.O 14.37%

ARG245.NH2-GLY605.O 10.58%

THR118.OG1-LYS114.O 7.58%

ARG393.NH2-GLU37.OE1 5.99%

ARG115.NE-GLU182.OE2 14.37%

ARG482.NH1-THR608.O 10.58%

GLU433.N-ASP431.OD1 7.58%

SER155.OG-GLU160.OE2 5.99%

ALA533.N-LEU529.O 14.37%

HIS34.N-ASP30.O 10.38%

SER331.N-PHE327.O 7.58%

TYR196.OH-GLN102.OE1 5.99%

ALA193.N-GLU189.O 14.37%

SER124.OG-LEU120.O 10.38%

ARG518.NE-GLU406.OE1 7.39%

ILE259.N-SER257.OG 5.99%

GLN60.NE2-GLU56.O 14.37%

GLN81.NE2-SER77.O 10.38%

ASN137.N-ASN134.OD1 7.39%

ARG177.NE-GLU181.OE2 5.79%

GLU37.N-ASN33.O 14.37%

MET82.N-LEU79.O 10.38%

ASP295.N-ASP292.OD2 7.39%

LEU392.N-PRO389.O 5.79% ARG357.NE-ASP355.OD2 5.79%

ARG115.NE-GLU182.OE1 14.17%

LYS112.NZ-GLU189.OE1 10.38%

TYR497.OH-GLU166.OE1 7.39%

GLN552.N-THR548.O 14.17%

THR414.OG1-CYS542.O 10.38%

LYS187.NZ-ASP509.OD2 7.39%

LYS234.NZ-GLU231.OE2 5.79%

PHE32.N-PHE28.O 14.17%

THR496.N-ASP494.OD2 10.18%

ASN194.ND2-MET190.O 7.39%

LYS600.NZ-ASP597.OD2 5.79%

GLN380.NE2-PRO321.O 14.17%

GLN388.N-TYR385.O 10.18%

ARG393.NH2-GLU37.OE2 7.39%

PHE588.N-LEU584.O 5.79%

TRP478.N-MET474.O 13.97%

TYR199.N-ASN188.OD1 10.18%

LYS553.N-GLU549.O 7.39%

ALA403.N-GLY399.O 5.79%

ASN188.N-VAL184.O 13.97%

THR365.OG1-ASP368.OD1 10.18%

ASN154.ND2-GLU150.O 7.39%

PHE512.N-GLU457.OE2 5.79%

THR362.N-LEU333.O 13.97%

SER167.N-TRP163.O 10.18%

GLN175.NE2-GLU171.O 7.19%

ALA403.N-PHE400.O 5.79%

LYS458.NZ-GLU227.OE2 13.77%

LYS68.N-ASN64.O 9.98%

ARG357.NH1-ASP355.OD1 7.19%

SER547.OG-GLU549.OE2 5.59%

HIS535.NE2-PRO538.O 13.77%

VAL404.N-PHE400.O 9.98%

THR129.N-THR125.O 7.19%

SER511.OG-GLU457.OE2 5.59%

GLU160.N-ASP157.OD1 13.77%

TYR587.OH-GLN442.OE1 9.98%

ARG169.NH2-TRP165.O 7.19%

ASN33.ND2-LEU29.O 5.59%

ARG161.NH2-ASN277.OD1 13.77%

SER43.OG-LEU39.O 9.98%

ARG357.NH1-ASP355.OD2 7.19%

GLN531.NE2-GLU527.O 5.59%

GLU527.N-PHE523.O 13.57%

ILE407.N-ALA403.O 9.98%

VAL364.N-ASP368.OD1 7.19%

SER507.OG-ALA501.O 5.39%

TYR183.OH-ASP509.OD2 13.57%

PHE369.N-THR365.O 9.98%

ASN330.N-GLY326.O 7.19%

SER155.N-MET152.O 5.39%

SER563.OG-GLU564.OE1 13.57%

LYS458.NZ-GLU227.OE1 9.78%

ARG393.N-PRO389.O 7.19%

THR362.N-THR334.O 5.39%

VAL573.N-ALA569.O 13.57%

ALA311.N-ILE307.O 9.78%

LEU266.N-PRO263.O 7.19%

SER409.OG-GLU406.OE1 5.39%

LEU240.N-LEU236.O 13.17%

SER545.N-ASP543.OD2 9.78%

THR129.OG1-ILE126.O 7.19%

TYR497.N-ASP494.O 5.39%

GLU571.N-THR567.O 13.17%

LYS577.NZ-GLY214.O 9.58%

GLY66.N-MET62.O 7.19%

SER602.N-ASN599.O 5.39%

LYS419.NZ-PHE428.O 12.97%

LEU100.N-GLN96.O 9.58%

GLN139.NE2-ASN137.OD1 7.19%

ARG518.NH1-GLU406.OE2 5.39%

LEU39.N-GLU35.O 12.97%

HIS378.ND1-GLU375.OE1 9.58%

LEU560.N-MET557.O 6.99%

GLU589.N-ASN586.O 5.39%

GLU35.N-LYS31.O 12.97%

GLN522.NE2-GLU406.O 9.58%

LYS475.NZ-ASP471.OD2 6.99%

THR294.N-ASP292.OD2 5.19%

MET190.N-LEU186.O 12.77%

ASP30.N-LYS26.O 9.58%

ARG393.NH1-GLU37.OE2 6.99%

ASN194.ND2-GLN102.O 5.19%

ASP136.N-ASN134.OD1 12.77%

CYS542.N-LEU539.O 9.58%

GLU182.N-PRO178.O 6.99%

ARG306.NE-GLU310.OE2 5.19%

THR496.N-ASP494.OD1 12.77%

LYS470.NZ-GLU181.OE1 9.58%

LYS187.NZ-ASP509.OD1 6.99%

ARG357.NE-ASP355.OD1 5.19%

LYS419.N-PRO415.O 12.77%

LEU529.N-PHE525.O 9.58%

SER611.OG-ALA614.OXT 6.99%

ILE307.N-ASP303.O 5.19%

GLN101.N-LEU97.O 12.77%

ASN61.N-GLU57.O 9.38%

ALA528.N-GLN524.O 6.99%

ASN437.ND2-GLU433.O 4.99%

GLN305.N-ASP303.OD1 12.57%

ASN397.ND2-ASP206.O 9.38%

GLN300.NE2-LEU423.O 6.99%

ASN154.N-GLU150.O 4.99%

SER563.OG-GLU564.OE2 12.57%

LEU79.N-GLU75.O 9.38%

THR294.OG1-ASP292.OD1 6.79%

THR434.N-ASP431.OD2 4.99%

LYS470.NZ-GLU181.OE2 12.38%

MET383.N-ILE379.O 9.18%

TRP203.NE1-ASP509.O 6.79%

LYS600.NZ-ASP597.OD1 4.99%

TYR127.N-MET123.O 12.38%

TYR454.OH-GLU227.OE1 9.18%

TYR279.N-THR276.O 6.79%

TYR497.OH-GLU166.OE2 4.99%

TYR454.OH-GLU227.OE2 12.18%

THR434.OG1-GLN429.O 9.18%

ASN578.ND2-ASP225.OD1 6.79%

THR125.N-ASN121.O 4.99%

PHE555.N-GLY551.O 12.18%

THR347.OG1-HIS345.O 8.98%

ARG273.N-ASP269.OD1 6.79%

GLU22.N-SER19.O 4.99%

ASN90.N-GLU22.OE2 12.18%

THR52.N-TRP48.O 8.98%

ARG219.N-GLU208.OE1 6.79%

ARG177.NE-GLU181.OE1 4.99%

SER511.OG-GLU457.OE1 12.18%

GLU433.N-ASP431.OD2 8.98%

TYR279.OH-ASN437.O 6.79%

LYS309.NZ-GLU312.OE2 4.99%

ASN90.N-GLU22.OE1 12.18%

LYS481.NZ-ASP499.OD2 8.98%

SER44.OG-ASP350.O 6.79%

ALA532.N-ALA528.O 4.99%

TRP459.NE1-TRP473.O 11.98%

ASN149.ND2-ASP269.OD1 8.98%

LYS541.N-PRO538.O 6.79%

THR20.OG1-GLU23.OE2 4.99%

LYS313.N-LYS309.O 11.98%

LYS441.N-ASN437.O 8.78%

ARG559.N-PHE555.O 6.79%

LEU503.N-PRO500.O 4.99%

(continued)

13.3 New Structural Bioinformatics

431

Table 13.4 (continued) GLN305.N-ASP303.OD2 11.98%

TYR381.OH-LEU560.O 8.78%

SER511.OG-GLU398.OE2 6.79%

GLN524.N-LEU520.O 11.78%

VAL212.N-ASP216.OD2 8.78%

HIS540.NE2-GLU435.OE1 6.79%

MET366.N-THR294.OG1 11.78%

HIS195.N-ALA191.O 8.78%

TRP271.NE1-SER502.O 4.99%

TYR199.OH-ASP509.OD2 6.79%

LEU351.N-ASP355.O 11.58%

TRP165.N-ARG161.O 8.78%

MET270.N-ASN149.OD1 6.59%

LYS112.NZ-GLU189.OE2 11.58%

TRP477.NE1-ASP499.OD1 8.78%

LYS541.NZ-GLU435.OE1 6.59%

MET557.N-LYS553.O 11.58%

GLY130.N-ILE126.O 8.78%

HIS540.NE2-GLU435.OE2 6.59%

GLU189.N-VAL185.O 11.58%

LEU142.N-VAL132.O 8.78%

TYR199.OH-ASP509.OD1 6.59%

GLN300.NE2-GLY422.O 11.38%

ARG514.NH1-GLU398.OE1 8.78%

SER563.OG-GLN388.OE1 6.59%

ASN556.N-GLN552.O 11.38%

THR27.N-GLU23.O 8.58%

ARG219.N-GLU208.OE2 6.59%

GLN24.N-THR20.O 11.38%

GLN526.NE2-SER411.OG 8.58%

HIS493.ND1-GLU489.OE2 6.59%

ASN149.ND2-ASP269.OD2 11.38%

MET297.N-VAL293.O 8.58%

GLU208.N-GLY205.O 6.59%

TYR243.N-HIS239.O 11.38%

TYR385.N-TYR381.O 8.58%

HIS239.N-PRO235.O 6.59%

ARG169.NE-ASP499.OD1 11.38%

LYS465.NZ-GLU467.OE2 8.58%

LYS465.NZ-GLU467.OE1 6.59%

ASN599.ND2-HIS239.ND1 11.18%

ASN188.ND2-PHE464.O 8.58%

PHE512.N-GLU457.OE1 6.39%

THR365.OG1-ASP368.OD2 11.18%

ARG514.NH1-GLU398.OE2 8.58%

GLU564.N-GLY561.O 6.39%

THR282.N-LEU278.O 11.18%

GLN81.NE2-GLN101.O 8.58%

ASP295.N-ASP292.OD1 6.39%

LYS31.N-THR27.O 11.18%

ARG273.N-ASP269.OD2 8.38%

ASN546.ND2-ALA533.O 6.39%

v SER547.N-ILE544.O 11.18%

ASP355.N-GLY352.O 8.38%

ARG460.NH1-VAL506.O 6.39%

THR122.N-THR118.O 11.18%

SER77.OG-LEU100.O 8.38%

PHE523.N-THR519.O 6.39%

TYR127.OH-SER502.O 11.18%

ASN437.N-GLU433.O 8.38%

THR276.OG1-THR445.OG1 6.39%

THR294.OG1-ASP292.OD2 8.38%

ASN580.N-GLN524.OE1 6.39%

HIS374.ND1-GLU406.OE2 8.18%

THR519.N-TYR515.O 6.39%

THR449.OG1-THR445.O 8.18%

TYR50.N-ALA46.O 6.39%

PHE390.N-ASN33.OD1 8.18%

LYS234.NZ-GLU231.OE1 6.39%

Table 13.5 All the SBs in the optimized human-IL6-1ALU-model and in the 1593 .μs’ MD Opt-SBs

1593 .μs-MD-SBs

ASP160-ARG104

ASP134-LYS120, ASP134-LYS128, ASP134-LYS131, ASP134-LYS86

ASP26-ARG30

ASP160-ARG104, ASP160-ARG40, ASP160-HIS164, ASP160-LYS46, ASP160-LYS54

ASP71-LYS70, ASP71-LYS86

ASP26-ARG182, ASP26-ARG24, ASP26-ARG30, ASP26-LYS27

GLU110-ARG113

ASP34-ARG30

GLU172-LYS171

ASP71-LYS66, ASP71-LYS70, ASP71-LYS86

GLU42-LYS46

GLU106-ARG104, GLU106-LYS46

GLU51-ARG40

GLU109-ARG113

GLU80-LYS129

GLU110-ARG113, GLU110-LYS41

GLU95-LYS120

GLU172-ARG168, GLU172-ARG179, GLU172-LYS171, GLU172-LYS54, GLU172-LYS66, GLU172-LYS70 GLU23-ARG182, GLU23-ARG24, GLU23-ARG30, GLU23-LYS128, GLU23-LYS129, GLU23-LYS27 GLU42-LYS41, GLU42-LYS46 GLU51-ARG168, GLU51-ARG40, GLU51-HIS164, GLU51-LYS171, GLU51-LYS54 GLU55-ARG168, GLU55-ARG179, GLU55-ARG40, GLU55-HIS164, GLU55-LYS171, GLU55-LYS54, GLU55-LYS66 GLU59-ARG168, GLU59-ARG40, GLU59-HIS164, GLU59-LYS150, GLU59-LYS54, GLU59-LYS66 GLU69-ARG179, GLU69-ARG182, GLU69-LYS66, GLU69-LYS70, GLU69-LYS86 GLU80-ARG182, GLU80-LYS128, GLU80-LYS129, GLU80-LYS131, GLU80-LYS70 GLU81-LYS128, GLU81-LYS129, GLU81-LYS131 GLU93-LYS150, GLU93-LYS66, GLU93-LYS70 GLU95-LYS120 GLU99-ARG113, GLU99-LYS120

13.3.3 Human IL6R Monomer IL6R is the IL6 receptor which has been shown to interact with IL6 and ciliary neurotrophic factor. The IL6 receptor is a protein complex consisting of an IL6 receptor subunit (IL6R) and interleukin 6 signal transducer glycoprotein 130. Few .π-interactions ARG274.NH2.+ -TRP284, ARG237.NH2.+ -TRP287, LYS105.NZ.+ -PHE103, TRP214-HIS261-TRP214, TRP219-PHE234-TRP219, and PHE155-TYR148 are in the human-IL6R-1N26-model optimized. The optimized human-IL6R-1N26-model has six .β-sheets and one helix (listed in Table 13.7 and illuminated in Fig. 13.5 during the 196 .μs’ MD). The Poisson-Boltzmann

432

13 Human ACE2, Human IL6, Human IL6R, and Human nAChRs

Fig. 13.5 Secondary structure of the human-IL6R-1N26-model during 196 .μs’ MD

Fig. 13.6 The Poisson-Boltzmann electrostatic potential surfaces of the optimized human-IL6R1N26-model

electrostatic potential surfaces of the optimized human-IL6R-1N26-model shows us there are large blue-colored positive charges (Fig. 13.6). As all the SBs and HBs in the humanACE2-6LZG-model and humanIL61ALU-model (Figs. 13.7 and 13.8), all the SBs and HBs in the optimized human-IL6R-1N26-model and in the 196 .μs’ MD are listed in Tables 13.8 and 13.9. SBs ASP35-ARG79, ASP198-LYS105, GLU114-LYS154, GLU235ARG274, GLU241-ARG268, GLU290-ARG239, ASP71-LYS45, ASP141-ARG4, and ASP221-HIS256 are illuminated in Fig. 13.9.

13.3.4 Human α4β2-, α7-, and αβγ δ-nAChR It is reported in [252] that the Y674-R685 (YQTQTNSPRRAR) peptide of SARSCoV-2 spike exhibits favorable binding affinity to nicotinic acetylcholine receptors (nAChRs). In [252], there is a possible binding of the Y674-R685 region to three

13.3 New Structural Bioinformatics

433

Table 13.6 The HBs (with occupancy rates .≥5%) of the human-IL6-1ALU-model during 1593 .μs’ MD Opt-HBs

1593 .μs-MD-HBs

ALA130.N-LEU126.O

VAL121.N-MET117.O 64.27%

ALA114.N-GLU110.O 14.99%

ALA145.N-PRO141.O

VAL115.N-GLN111.O 64.21%

LYS27.N-GLU23.O 14.93%

ALA58.N-GLU59.OE1

THR163.OG1-GLN159.O 60.79%

ARG182.NE-ASP26.OD1 14.81%

ALA68.N-ASP71.OD2

SER118.N-ALA114.O 55.22%

LYS171.N-LEU167.O 14.57%

ARG113.N-GLU109.O

VAL85.N-GLU81.O 51.86%

GLN102.N-LEU98.O 14.51%

ARG113.NH1-GLU110.OE2

ILE29.N-ILE25.O 47.12%

LYS41.N-SER37.O 14.45%

ARG168.NH2-GLU51.O

ILE123.N-THR119.O 46.82%

THR142.OG1-ASP140.OD1 14.45%

ARG168.NH2-SER53.O

ILE166.N-THR162.O 44.84%

GLN116.NE2-GLU99.OE1 14.45%

ARG182.NH2-ARG179.O

SER176.N-GLU172.O 43.94%

SER47.OG-ASP160.OD1 14.33%

ARG24.NH2-SER21.OG

SER177.OG-PHE173.O 42.93%

ARG113.NH2-GLU110.OE1 14.33%

ARG30.NE-ASP26.OD1

LEU181.N-SER177.O 42.51%

ASN144.N-ASP140.O 14.33%

ARG30.NH2-ASP26.OD2

SER169.N-LEU165.O 41.61%

LEU147.N-THR143.O 14.27%

ARG40.N-ILE36.O

ILE36.N-ILE32.O 39.69%

ALA130.N-LEU126.O 13.79%

ARG40.NH1-GLU51.OE2

THR119.OG1-VAL115.O 39.21%

LYS150.N-SER146.O 13.55%

ARG40.NH2-GLU51.OE1

LEU33.N-ILE29.O 36.03%

ARG179.N-GLN175.O 13.43%

ASN103.ND2-GLU99.O

GLN127.N-ILE123.O 35.37%

THR137.OG1-LEU133.O 13.25%

ASN61.N-ALA58.O

SER37.OG-LEU33.O 33.99%

ARG182.NE-ASP26.OD2 13.19%

ASN79.ND2-GLU81.OE2

GLN175.N-LYS171.O 33.57%

ARG182.NH2-ASP26.OD1 13.07%

ASP160.N-GLN156.O

PHE170.N-ILE166.O 33.45%

HIS164.N-ASP160.O 12.95%

ASP26.N-SER22.O

THR43.OG1-LEU39.O 33.45%

ARG182.NH2-ASP26.OD2 12.77%

ASP26.OD2-ARG30.NH2

GLU172.N-ARG168.O 32.85%

ARG113.NH2-GLU110.OE2 12.65%

ASP34.N-ARG30.O

SER176.OG-GLU172.O 31.95%

LYS86.N-THR82.O 12.59%

CYS44.N-ARG40.O

LEU174.N-PHE170.O 30.76%

TYR100.OH-GLN159.OE1 12.59%

GLN102.NE2-GLU109.OE2

LEU84.N-GLU80.O 29.80%

CYS83.N-ASN79.O 12.53%

GLN116.N-ALA112.O

THR162.OG1-LEU158.O 29.26%

SER177.N-PHE173.O 12.29%

GLN127.N-ILE123.O

CYS44.N-ARG40.O 29.02%

LEU158.N-ASN155.OD1 12.29%

GLN175.N-LYS171.O

THR89.N-VAL85.O 28.30%

ARG30.N-ASP26.O 11.99%

GLU110.OE2-ARG113.NH1

ALA112.N-SER108.O 27.34%

ALA153.N-THR149.O 11.81%

GLU172.OE2-LYS171.NZ

ARG113.N-GLU109.O 27.28%

GLN116.NE2-GLU99.OE2 11.75%

GLU42.OE2-LYS46.NZ

LEU167.N-THR163.O 27.16%

SER108.N-GLU42.OE2 11.21%

GLU51.OE1-ARG40.NH2

ILE88.N-LEU84.O 26.62%

TYR100.N-VAL96.O 11.15%

GLU51.OE2-ARG40.NH1

MET117.N-ARG113.O 25.72%

ARG182.N-LEU178.O 10.85%

GLU55.N-GLU55.OE2

THR149.OG1-ALA145.O 25.06%

GLU106.N-GLU42.OE2 10.67%

GLU59.N-GLU59.OE1

LEU92.N-ILE88.O 23.98%

LEU165.N-MET161.O 10.37%

GLU93.N-THR89.O

THR162.OG1-GLN154.OE1 23.98%

SER47.OG-THR43.O 10.01%

GLU99.N-GLU95.O

ASN79.N-GLY72.O 23.68%

ASN103.N-GLU99.O 9.83%

GLY72.N-GLU69.O

GLN116.N-ALA112.O 23.68%

LYS46.N-GLU42.O 9.83%

GLY90.N-LYS86.O

GLN159.N-ASN155.O 23.44%

MET161.N-TRP157.O 9.77%

HIS164.N-ASP160.O

LEU91.N-ILE87.O 23.08%

SER108.N-GLU42.OE1 9.65%

ILE123.N-THR119.O

SER108.OG-GLU42.OE2 22.60%

GLU106.N-GLU42.OE1 9.47%

ILE36.N-ILE32.O

SER108.OG-GLU42.OE1 22.54%

LEU39.N-GLY35.O 9.35%

LEU122.N-SER118.O

ASP26.N-SER22.O 22.36%

GLN159.NE2-LEU151.O 9.29%

LEU126.N-LEU122.O

ARG168.N-HIS164.O 21.88%

SER107.N-GLU42.OE2 9.23%

LEU148.N-ASN144.O

GLN124.N-LYS120.O 21.64%

GLN183.N-ALA180.O 8.99%

LEU174.N-PHE170.O

SER169.OG-LEU165.O 21.22%

THR20.OG1-GLU23.OE2 8.87%

LEU178.N-LEU174.O

THR162.N-LEU158.O 21.10%

GLN102.NE2-LEU98.O 8.81%

LEU181.N-SER177.O

GLN152.N-LEU148.O 20.92%

SER118.OG-ALA114.O 8.75%

LEU57.N-LYS54.O

GLU42.N-ALA38.O 20.68%

SER53.OG-GLU51.OE2 8.75%

LEU84.N-GLU80.O

LEU178.N-LEU174.O 20.50%

THR20.N-GLU23.OE2 8.69%

LYS120.NZ-GLU95.OE1

ALA145.N-PRO141.O 20.38%

PHE94.N-GLY90.O 8.57%

LYS129.N-LEU126.O

GLU99.N-GLU95.O 20.08%

ARG113.NE-GLU110.OE2 8.39%

LYS129.NZ-MET184.OXT

ASP34.N-ARG30.O 19.96%

ARG113.NE-GLU110.OE1 8.39%

LYS129.NZ-GLU80.OE1

GLN159.NE2-GLN154.O 19.78%

LEU19.N-GLU23.OE2 8.39%

LYS171.NZ-GLU172.OE2

THR143.OG1-ASP140.OD2 19.72%

SER107.N-GLU42.OE1 8.27%

LYS27.N-GLU23.O

SER146.N-THR142.O 19.42%

THR143.N-ASP140.OD2 8.03%

LYS46.N-THR43.O

LYS120.N-GLN116.O 19.36%

MET184.N-LEU181.O 8.03%

LYS46.NZ-GLU42.OE2

ALA180.N-SER176.O 19.18%

LEU122.N-SER118.O 8.03%

LYS70.NZ-ASP71.OD1

GLN28.NE2-SER118.O 19.06%

ASP71.N-ALA68.O 7.97%

LYS86.N-THR82.O

THR149.N-ALA145.O 19.00%

SER52.N-ASN48.O 7.79%

LYS86.NZ-LYS66.O

THR163.N-GLN159.O 18.82%

ALA68.N-ASP71.OD1 7.61%

LYS86.NZ-ASP71.OD2

THR143.OG1-ASP140.OD1 18.65%

THR143.N-ASP140.OD1 7.55%

PHE105.N-LEU101.O

PHE173.N-SER169.O 18.29%

ASP160.N-GLN156.O 7.49%

(continued)

434

13 Human ACE2, Human IL6, Human IL6R, and Human nAChRs

Table 13.6 (continued) Opt-HBs

1593 .μs-MD-HBs

PHE170.N-ILE166.O

LEU151.N-LEU147.O 18.17%

LEU19.N-GLU23.OE1 7.49%

PHE173.N-SER169.O

LEU148.N-ASN144.O 17.93%

THR20.OG1-GLU23.OE1 7.25%

SER108.OG-GLU42.OE1

SER146.OG-THR142.O 17.93%

SER53.OG-MET49.O 7.13%

SER118.OG-ALA114.O

THR82.N-ASN79.OD1 17.69%

ALA38.N-ASP34.O 7.13%

SER146.OG-THR142.O

PHE105.N-LEU101.O 17.45%

SER53.OG-GLU51.OE1 7.07%

SER169.N-LEU165.O

THR43.N-LEU39.O 17.03%

SER37.N-LEU33.O 7.01%

SER176.OG-GLU172.O

GLN102.NE2-GLN116.OE1 16.67%

LEU98.N-PHE94.O 6.83%

SER177.N-PHE173.O

ILE25.N-SER21.O 16.37%

THR20.N-GLU23.OE1 6.77%

SER177.OG-PHE173.O

THR142.OG1-ASP140.OD2 15.95%

ILE32.N-GLN28.O 6.41%

SER47.N-THR43.O

SER47.OG-ASP160.OD2 15.95%

ARG30.NE-ASP26.OD2 6.18%

SER47.OG-THR43.OG1

ARG40.N-ILE36.O 15.77%

ARG104.NH1-GLN156.OE1 5.88%

SER53.OG-GLU55.OE1

LEU126.N-LEU122.O 15.71%

THR142.N-ASP140.OD2 5.88%

THR142.N-ASP140.OD1

GLU42.N-LEU39.O 15.47%

LYS46.NZ-GLU42.OE2 5.82%

THR142.OG1-ASP140.OD1

GLU93.N-THR89.O 15.41%

ASN103.ND2-GLU99.O 5.76%

THR143.N-ASP140.OD2

SER47.N-THR43.O 15.41%

ALA68.N-ASP71.OD2 5.76%

THR143.OG1-ASP140.OD2

ILE87.N-CYS83.O 15.29%

ARG104.N-TYR100.O 5.76%

THR149.N-ALA145.O

GLN116.NE2-GLU95.O 5.64%

THR149.OG1-ALA145.O

ARG30.NE-ASP26.OD1 5.16%

SER53.N-GLU51.OE2 5.58%

THR162.OG1-LEU158.O

THR82.OG1-ASP71.O 5.16%

GLN152.NE2-LEU148.O 5.46%

THR20.N-GLU23.OE1

SER76.OG-GLU69.OE2 5.16%

GLN28.N-ARG24.O 5.40%

THR20.OG1-GLU23.OE1

ARG113.NH2-GLU109.OE2 5.10%

ARG113.NH1-GLN102.OE1 5.34%

THR82.N-ASN79.OD1

ARG113.NH1-GLU109.OE2 5.10%

THR142.N-ASP140.OD1 5.28%

THR82.OG1-ASP71.O

THR82.OG1-ASN79.OD1 5.10%

SER53.N-GLU51.OE1 5.28%

THR89.N-VAL85.O

LYS120.NZ-GLU95.OE2 5.04%

GLN116.NE2-GLU95.OE2 5.28%

TYR100.N-VAL96.O

GLN154.NE2-LEU151.O 5.04%

ARG113.NH1-GLU109.OE1 5.28%

VAL115.N-GLN111.O

PHE125.N-VAL121.O 5.04%

LYS46.NZ-GLU42.OE1 5.22%

Table 13.7 The optimized human-IL6R-1N26-model has six .β-sheets and one helix

Sheet1-strand1_1

aa VAL15-SER18

Sheet1-strand1_2

aa THR38-ARG44

Sheet1-strand1_3

aa SER53-MET58

Sheet1-strand1_4

aa GLY73-TYR78

Sheet1-strand1_5

aa THR86-VAL91;

Sheet2-strand2_1

aa THR25-THR27

Sheet2-strand2_2

aa ARG61-LEU63;

Sheet3-strand3_1

aa SER101-PHE103

Sheet3-strand3_2

aa VAL111-TRP115

Sheet3-strand3_3

aa CYS146-SER149

Sheet3-strand3_4

aa LYS154-LEU159;

Sheet4-strand4_1

aa LYS126-PHE134

Sheet4-strand4_2

aa GLU140-PRO145

Sheet4-strand4_3

aa PHE168-ALA176

Sheet4-strand4_4

aa SER181-PHE183

Sheet4-strand4_5

aa GLN187-GLN190;

Sheet5-strand5_1

aa ALA201-ALA207

Sheet5-strand5_2

aa LEU215-GLN220

Sheet5-strand5_3

aa HIS257-ILE260;

Sheet6-strand6_1

aa LEU232-ALA240

Sheet6-strand6_2

aa THR247-MET250

Sheet6-strand6_3

aa HIS269-GLU277

Sheet6-strand6_4

aa ALA291-GLY293;

Helix_3_10

aa LEU69-ASP71

nAChRs: the human .α4β2 and .α7 subtypes and the muscle-like .αβγ δ receptor from Tetronarce californica; we denote them as .α4β2-complex, .α7-complex, and .αβγ δ-complex. The Y674-R685 peptide contains a PRRA motif, a four-residue insertion not found in other SARS-like coronaviruses (in 6VSB.pdb, the Y674R685 loop is entirely missing, whereas in 6VXX.pdb, only three residues Y674, Q675, and T676 were solved); this peptide is at the S1/S2 site (i.e., between R685 and S686) of SARS-CoV-2 spike. The peptide G381-K386 in the S1 subunit in the spike protein has also been hypothesized to interact with nAChRs, but

13.3 New Structural Bioinformatics

435

Table 13.8 All the SBs in the optimized human-IL6R-1N26-model and in the 196 .μs’ MD Opt-SBs

196 .μs-MD-SBs

ASP141-ARG132, ASP141-ARG4

ASP141-ARG132, ASP141-ARG4, ASP141-ARG5

ASP165-LYS133

ASP165-LYS133

ASP198-LYS105

ASP198-HIS223, ASP198-LYS105

ASP221-HIS256

ASP221-ARG231, ASP221-HIS256

ASP35-ARG79

ASP22-ARG65

ASP71-LYS45

ASP253-ARG231, ASP253-ARG233, ASP253-LYS252

GLU10-ARG5

ASP262-ARG213, ASP262-HIS269

GLU114-LYS154

ASP35-ARG79, ASP35-ARG82

GLU235-ARG274

ASP71-ARG44, ASP71-ARG65, ASP71-HIS51, ASP71-HIS88, ASP71-LYS45

GLU241-ARG268

GLU10-ARG13, GLU10-ARG4, GLU10-ARG5, GLU10-LYS126

GLU290-ARG239

GLU114-LYS154

GLU32-ARG79

GLU140-ARG132, GLU140-LYS133

GLU96-ARG118

GLU163-ARG104

GLU97-LYS182

GLU235-ARG274, GLU235-LYS252 GLU241-ARG239, GLU241-ARG242, GLU241-ARG268 GLU278-ARG231, GLU278-ARG233 GLU283-LYS105, GLU283-LYS185 GLU286-LYS105 GLU290-ARG239, GLU290-LYS244 GLU298-ARG210, GLU298-ARG213, GLU298-ARG268 GLU32-ARG60, GLU32-ARG79, GLU32-ARG82 GLU34-ARG60, GLU34-ARG61, GLU34-ARG79, GLU34-ARG82 GLU96-ARG118, GLU96-LYS182 GLU97-LYS182, GLU97-LYS185

glycosylation makes this unlikely. We optimized the three models and got their RMSD values 0.505718, 0.528214, and 0.468340 Å compared with the three models of [252]. The three .α4β2-, .α7-, and .αβγ δ-nAChR models (downloaded from covid.molssi.org/simulations) are built on 6UWZ.pdb, where its AD chains are the acetylcholine receptor subunit .α, B chain is the acetylcholine receptor subunit .δ, C chain is the acetylcholine receptor subunit .β, and E chain is the acetylcholine receptor subunit .γ ; our structural bioinformatics on the bindings is listed in Table 13.10, where spike’s two peptides YQTQTNSPRRAR are labeled with residue numbers 1912–1935, 1866–1889, and 1949–1972 for .α4β2, .α7, and .αβγ δ complex models, respectively, and the HBs within the peptide adopt extended conformations in the .α4β2 and .α7 complexes. All the nAChR residues that interact with the spike peptide 674YQTQTNSPRRAR685 (F chain and G chain) are as follows: ◦ .α4β2 F chain: D:TYR1339 (where there is a .π-cation linking to spike’s ARG682.NH2+), D:GLU1340 (where there exists a SB linking to spike’s residue ARG683), D:CYS1341, D:TYR1346, E:MET1559, E:SER1561, E:THR1582, E:PHE1642, E:SER1691, E:ASP1693, E:ASP1694 G chain: A:ARG188, A:LYS189, A:TYR190, A:GLU191, A:CYS192, A:TYR197, B:MET410, B:SER412, B:TRP431, B:LYS537, B:PHE493, B:SER538, B:SER542, B:LEU543, B:ASP544, B:ASP545 .◦ .α7 F chain: C:TRP1268, C:SER1269, C:TYR1270, C:ARG1305, C:PHE1306, C:TYR1307, C:GLU1308, C:CYS1309, C:TYR1314, E:SER1528, E:TRP1547, .

SER122.OG-ASP92.OD2 23.88%

VAL217.N-CYS258.O 66.17%

LYS133.NZ-ASP165.OD2

LYS154.NZ-GLU114.OE2

ALA8.N-GLU10.OE1

ARG104.NH1-SER109.O

VAL112.N-PHE103.O 52.74%

GLN272.NE2-SER288.O 50.75% CYS28.N-ARG60.O 49.75%

SER122.OG-ASP92.OD1

SER149.N-LYS154.O

ARG5.NH1-GLU10.OE2

ARG60.NH1-VAL31.O

VAL131.N-PHE142.O 51.74%

ARG274.N-GLU235.O 21.39%

GLY191.N-SER167.O 16.92%

ILE170.N-ARG132.O 47.76%

SER184.N-MET173.O 16.42% ARG118.N-GLU96.OE1 15.92% LYS154.NZ-GLU114.OE2 15.92%

LYS154.NZ-GLU114.OE1 15.42% GLN9.N-THR124.O 15.42%

CYS174.N-VAL128.O 40.30% GLU144.N-LEU129.O 38.81%

SER285.OG-GLU286.O

SER288.N-LEU273.O

SER50.OG-LYS45.O

SER76.OG-THR86.OG1

GLN190.NE2-SER166.O

GLN196.N-ARG104.O

GLN272.N-ARG237.O

GLN272.NE2-SER288.O

CYS77.N-GLY85.O 38.81%

VAL24.N-LEU64.O 40.30%

ARG239.NH2-GLU290.OE2 15.42%

LEU16.N-HIS88.O 15.92%

PHE189.N-TYR169.O 15.92%

ARG104.NH1-SER109.O 42.29% LYS182.N-VAL175.O 40.80% SER216.N-THR206.O 40.80%

SER224.OG-ASP198.OD2

SER243.N-ALA240.O

SER285.N-ALA275.O

VAL67.N-ASP22.O 15.92%

GLN147.N-SER156.O

PHE155.N-TRP115.O 43.28%

SER156.OG-GLU114.OE2 16.42%

LEU89.N-GLY73.O 16.42%

GLN276.N-ARG233.O 16.42%

SER119.N-GLU96.OE2 16.42%

SER172.N-LEU130.O 16.42%

GLN187.N-VAL171.O

CYS28.N-ARG60.O

SER149.N-LYS154.O 42.79%

SER18.OG-ASP22.OD2

SER216.N-THR206.O

CYS157.N-CYS113.O

CYS174.N-VAL128.O

LEU129.N-GLU144.O 44.28% ARG237.N-GLN272.O 44.28%

SER178.OG-ASP92.OD2

SER184.OG-LYS185.O

ASP71.OD1-LYS45.NZ

SER288.OG-PRO289.O 44.78%

LEU26.N-LEU62.O 46.77%

THR204.N-THR218.O 46.77%

CYS113.N-CYS157.O

SER177.OG-VAL93.O

SER178.N-ASP92.OD2

ASP198.OD1-LYS105.NZ

ASP35.OD2-ARG79.NH2

SER172.OG-SER184.OG

SER177.N-GLY180.O

ASN74.N-ARG44.O

ASP165.OD2-LYS133.NZ

GLN281.N-GLU277.OE2 17.41% TYR238.OH-ASP262.OD1 17.41% GLU241.N-ARG268.O 16.92%

TYR238.N-THR247.O 48.76% SER156.N-GLN147.O 48.26%

SER152.OG-SER149.OG

SER156.N-GLN147.O

SER167.OG-ASP165.OD1

ARG79.NH2-ASP35.OD2

ASN110.ND2-GLN158.OE1

VAL208.N-TRP214.O 17.91%

ARG44.N-ASN74.O 18.41%

LEU43.N-SER53.O 18.91%

LYS133.N-GLU140.O 18.91%

HIS269.N-GLY293.O 18.91%

ARG239.NH2-GLU290.OE1 19.40%

GLY293.N-HIS269.O 19.40%

GLY59.N-ALA37.O 20.40%

PHE103.N-VAL112.O 20.40%

ASN202.ND2-GLN220.OE1

ALA275.N-SER285.OG 50.75%

TYR169.N-PHE189.O 51.74%

PHE279.N-GLU277.OE2

SER101.N-GLU114.O

ARG268.NH2-GLU241.OE1

VAL175.N-LYS182.O 52.24%

SER72.OG-GLN68.O 52.74%

ARG233.N-GLN276.O 52.74%

VAL39.N-GLY57.O 55.72%

ARG44.N-ASN74.O

PHE142.N-VAL131.O

PHE155.N-TRP115.O

ARG239.NH2-GLU290.OE2

ARG268.NE-GLU241.OE2

PHE103.N-VAL112.O

PHE134.N-PHE168.O

ARG239.N-VAL270.O

VAL128.N-CYS174.O 53.73%

LYS45.NZ-ASP71.OD1

LYS45.NZ-HIS70.O

ARG233.N-GLN276.O

ARG237.N-GLN272.O

ARG239.NE-GLU290.OE1

CYS102.N-GLN187.OE1 23.38% THR125.N-SER122.O 23.38% ALA201.N-GLN220.O 22.89%

SER285.N-ALA275.O 63.68% ILE260.N-LEU215.O 62.69% LEU130.N-SER172.O 61.69%

LYS182.N-VAL175.O

LYS182.NZ-GLU97.OE1

LYS185.NZ-GLN99.OE1

ARG118.N-GLU96.OE2

SER119.OG-GLU96.OE2 23.88%

PHE142.N-VAL131.O 24.38%

VAL42.N-SER76.O 65.17%

VAL171.N-GLN187.O 75.12%

ARG231.N-GLU278.OE1

ARG104.NH2-PRO162.O

SER177.N-GLY180.O 23.88%

VAL270.N-ARG239.O 68.16%

LYS126.N-ALA176.O

LYS126.NZ-LEU123.O

ALA275.N-SER285.OG

GLN187.N-VAL171.O 24.88% SER119.OG-GLU96.OE1 24.88%

ALA37.N-ASP35.OD1

SER285.OG-GLU286.O 79.10% VAL271.N-ALA291.O 75.12%

LYS105.NZ-ASP198.OD1

ALA176.N-LYS126.O

196 .μs-MD-HBs

LEU90.N-LEU16.O

ALA160.N-GLU144.OE2

Opt-HBs

Table 13.9 The HBs (with occupancy rates .≥5%) of the human-IL6R-1N26-model during 196 .μs’ MD THR124.OG1-ASP92.OD2 10.95%

(continued)

ARG79.NH1-ASP35.OD1 8.46%

ARG268.NH2-GLU241.OE1 8.46%

TRP115.N-PHE155.O 8.46%

SER167.N-ASP165.OD2 8.46%

ARG231.NH2-GLU278.OE1 8.46%

ARG79.NH2-ASP35.OD1 8.46%

ARG79.N-PRO83.O 8.46%

LYS105.NZ-ASP198.OD1 8.46%

TRP225.NE1-TYR230.O 8.96%

SER76.OG-THR86.OG1 8.96%

ARG79.NH1-ASP35.OD2 8.96%

PHE168.N-PHE134.O 8.96%

ARG118.N-GLU96.OE2 9.45%

VAL179.N-ASP92.OD2 9.45%

THR124.OG1-SER177.OG 9.45%

SER265.OG-GLU298.OE1 9.45%

ARG268.NH2-GLU241.OE2 9.45%

GLN135.N-SER137.O 9.95%

ARG231.NE-GLU278.OE1 9.95%

PHE279.N-GLU277.OE2 9.95%

SER181.OG-CYS6.O 9.95%

LYS182.NZ-PRO95.O 9.95%

CYS146.N-ALA127.O 9.95%

GLN9.NE2-LEU123.O 9.95%

SER177.OG-ASP92.OD1 9.95%

ARG274.NH2-GLU235.OE1 9.95%

GLN276.NE2-GLY282.O 10.45%

TYR78.N-HIS40.O 10.45%

GLN99.NE2-GLU97.O 10.45%

PHE279.N-GLU277.OE1 10.45%

SER167.N-ASP165.OD1 10.45%

GLY21.N-VAL67.O 10.45%

THR125.OG1-SER122.O 10.95%

GLU283.N-LEU195.O 10.95%

ALA291.N-VAL271.O 10.95%

GLU235.N-ARG274.O 10.95%

436 13 Human ACE2, Human IL6, Human IL6R, and Human nAChRs

THR125.OG1-SER122.OG

THR204.N-THR218.O

THR206.N-SER216.O

TRP225.N-PRO222.O

TRP225.NE1-TYR230.O

TRP249.N-LEU236.O

TRP287.N-GLU286.OE1

TRP41.N-TRP55.O

TRP55.N-TRP41.O

TYR148.OH-GLN153.OE1

TYR169.N-PHE189.O

TYR169.OH-ALA160.O

TYR230.OH-GLU163.OE2

TYR238.OH-ASP262.OD2

TYR75.N-VAL87.O

VAL112.N-PHE103.O

VAL131.N-PHE142.O

VAL171.N-GLN187.O

VAL175.N-LYS182.O

VAL217.N-CYS258.O

VAL251.N-PHE234.O

VAL270.N-ARG239.O

VAL271.N-ALA291.O

VAL39.N-GLY57.O

VAL42.N-SER76.O

VAL87.N-TYR75.O

VAL91.N-SER72.OG

GLN281.N-GLU277.OE1

GLN281.NE2-GLU163.OE1

GLN68.NE2-SER66.O

GLU10.OE2-ARG5.NH1

GLU114.N-SER101.O

GLU140.N-LYS133.O

GLU151.N-GLU151.OE2

GLU235.N-ARG274.O

GLU241.N-ARG268.O

GLU241.OE1-ARG268.NH2

GLU241.OE2-ARG268.NE

GLU290.OE2-ARG239.NH2

GLU32.N-GLU32.OE2

GLU34.N-GLU34.OE2

GLU97.OE1-LYS182.NZ

GLY164.N-GLU163.OE1

GLY21.N-VAL67.O

GLY280.N-GLU277.OE1

GLY293.N-HIS269.O

GLY57.N-VAL39.O

GLY59.N-ALA37.O

GLY73.N-LEU89.O

HIS256.NE2-ASP221.OD2

HIS269.N-GLY293.O

HIS269.NE2-TRP264.O

ILE170.N-ARG132.O

196 .μs-MD-HBs

HIS88.N-GLY14.O 5.47% ARG231.N-GLU278.OE1 5.47%

LEU64.N-VAL24.O

LEU89.N-GLY73.O

ARG231.NH2-GLU278.OE2 5.97% TRP214.N-ASN211.OD1 5.97%

THR124.OG1-SER178.OG 5.97%

ASP35.N-GLU32.O 5.97%

LEU273.N-SER288.OG

GLU278.N-ARG231.O 11.44%

LEU215.N-ILE260.O

SER72.N-GLN68.O 5.97%

LEU43.N-SER53.O

ARG104.NE-ILE194.O 11.44%

LEU19.N-ASP22.OD2

LEU1.N-ASP141.OD2 5.97%

ALA37.N-ASP35.OD2 5.97%

SER18.N-LEU90.O 11.44%

LEU16.N-HIS88.O

SER101.OG-LEU100.O 5.97%

LEU267.N-TRP264.O 5.97%

SER109.OG-SER106.O 5.97%

SER177.OG-VAL93.O 6.47%

GLN99.NE2-GLU97.OE2 6.47%

GLY85.N-CYS77.O 6.47%

GLN255.NE2-HIS257.O 6.47%

GLN99.NE2-GLU97.OE1 6.47%

GLN281.NE2-GLU277.OE1 6.97%

ARG231.N-GLU278.OE2 6.97%

GLY280.N-GLU277.O 6.97%

ILE194.N-GLN190.O 6.97%

ALA37.N-ASP35.OD1 6.97%

GLN196.N-LYS105.O 6.97%

LEU236.N-TRP249.O 6.97%

LYS105.NZ-ASP198.OD2 7.46%

ARG104.NH2-PRO162.O 7.46%

SER66.N-ASP22.O 7.46%

HIS257.NE2-SER216.OG 7.46%

VAL251.N-PHE234.O 7.46%

SER177.OG-ASP92.OD2 7.46%

ARG213.NE-ALA263.O 7.46%

THR125.OG1-SER122.OG 7.46%

GLN9.N-SER177.O 7.46%

VAL179.N-ASP92.OD1 7.96%

GLN187.NE2-LEU100.O 7.96%

ALA139.N-LYS133.O 7.96%

ARG239.N-VAL270.O 7.96%

SER243.N-ALA240.O 7.96%

GLN220.N-ALA201.O 8.46%

LEU236.N-TRP249.O

ARG231.NE-GLU278.OE2 11.44%

LEU130.N-SER172.O

SER178.OG-ASP92.OD1 11.44%

ASN202.ND2-GLN220.OE1 11.94%

GLN281.NE2-GLU277.OE2 11.94%

GLY57.N-VAL39.O 11.94%

GLU114.N-SER101.O 11.94%

LEU215.N-ILE260.O 11.94%

HIS40.N-TYR78.O 11.94%

LEU159.N-VAL111.O 12.44%

ARG268.NE-GLU241.OE1 12.44%

GLN281.N-GLU277.OE1 12.44%

THR124.OG1-ASP92.OD1 12.94%

ARG237.NH2-GLN272.OE1 12.94%

TRP55.N-TRP41.O 13.43%

SER156.OG-GLU114.OE1 13.43%

ASP92.N-SER18.O 13.43%

SER265.OG-GLU298.OE2 13.43%

GLN196.NE2-TRP284.O 13.93%

SER178.OG-ASP92.OD2 13.93%

TYR238.OH-ASP262.OD2 13.93%

THR86.OG1-SER76.OG 13.93%

THR120.OG1-GLN153.OE1 13.93%

TYR148.OH-GLN150.OE1 13.93%

ARG132.N-ILE170.O 13.93%

ARG268.NE-GLU241.OE2 14.43%

SER18.OG-LEU90.O 14.43%

ARG274.NH2-GLU235.OE2 14.43%

CYS258.N-VAL217.O 14.93%

TYR75.N-VAL87.O 14.93%

SER119.N-GLU96.OE1 14.93%

ARG213.N-ASN211.OD1 11.44%

MET173.N-SER184.OG 25.37%

SER224.OG-ASP198.OD1 25.87%

GLN272.N-ARG237.O 25.87%

SER122.OG-ASP92.OD1 26.87%

THR206.N-SER216.O 27.36%

PHE134.N-PHE168.O 27.36%

GLN147.N-SER156.O 27.86%

THR218.N-THR204.O 28.36%

SER224.OG-ASP198.OD2 28.86%

SER184.OG-LYS185.O 29.85%

TRP249.N-LEU236.O 30.35%

GLN190.NE2-SER166.O 30.35%

ALA176.N-LYS126.O 30.35%

CYS113.N-CYS157.O 31.34%

TRP41.N-TRP55.O 32.84%

VAL111.N-LEU159.O 33.33%

VAL87.N-TYR75.O 33.83%

SER76.N-VAL42.O 33.83%

SER167.OG-ASP165.OD2 34.33%

LEU62.N-LEU26.O 34.33%

LEU273.N-SER288.OG 34.83%

SER167.OG-ASP165.OD1 34.83%

LEU64.N-VAL24.O 34.83%

SER288.N-LEU273.O 35.32%

LYS126.N-ALA176.O 37.31%

GLN196.N-ARG104.O 37.81%

CYS157.N-CYS113.O 38.31%

LEU90.N-LEU16.O 38.31%

THR247.N-TYR238.O 38.81%

LEU129.N-GLU144.O

ILE260.N-LEU215.O

THR124.OG1-ASP92.OD2

GLN276.N-ARG233.O

GLN276.NE2-GLY282.O

Opt-HBs

Table 13.9 (continued)

13.3 New Structural Bioinformatics 437

438

13 Human ACE2, Human IL6, Human IL6R, and Human nAChRs

Table 13.10 The HBs and SBs of the three nicotinic acetylcholine receptors (nAChRs) linking to the spike peptide YQTQTNSPRRAR .α4β2

.α7

.αβγ δ

F:ALA1922.N-D:GLU1340.OE2

G:ALA1888.N-A:GLU189.OE1

F:ASN1954.ND2-B:ASP543.OD1

D:GLU1340-F:ARG1921

G:ASN1883.ND2-B:ASP537.OD2

B:ASP543-F:ARG1958

G:ALA1934.N-A:GLU191.OE2

D:ARG1305.NH1-F:GLN1867.OE1

A:TYR190.OH-F:GLN1950.OE1

F:ARG1874.NH1-F:GLN1869.OE1

G:TYR1961.N-E:ASP1730.OD2

F:GLN1869.NE2-F:THR1868.OG1

G:GLN1962.NE2-E:ASP1733.OD2

F:THR1951.N-B:ASP558.OD2 G:GLN1925.NE2-B:ASP544.OD2 G:THR1926.N-B:ASP544.OD1 F:GLN1915.NE2-F:THR1914.O

E:GLU1720-G:ARG1970

G:GLN1925.N-G:THR1928.OG1 G:GLN1964.NE2-G:THR1963.OG1

E:GLN1549, E:GLN1609, E:GLN1651, E:MET1652, E:ASP1656, E:SER1658, E:GLY1659 G chain: A:TRP149, A:SER150, A:PHE187, A:TYR188, A:GLU189, A:CYS190, A:TYR195, B:SER409, B:GLN430, B:GLN490, B:ASP537, B:SER539, B:GLY540 .◦ .αβγ δ F chain: A:VAL88, A:TYR189, A:TYR190, A:THR191, A:CYS192, A:TYR198, B:THR416, B:TRP435, B:ASP437, B:LEU499, B:MET541, B:THR542, B:ASP543 (where there exists a SB linking to spike’s residue ARG683), B:THR544, B:ILE545, B:ILE552, B:ILE556, B:ASP558, B:PRO559, B:GLU560 G chain: D:TRP1326, D:VAL1365, D:TYR1366, D:TYR1367, D:THR1368, D:CYS1369, D:TYR1375, E:LYS1590, E:THR1592, E:TYR1667, E:TRP1611, E:GLU1613, E:GLN1615, E:TYR1673, E:GLU1719, E:GLU1720 (where there exists a SB linking to spike’s residue ARG683), E:HID1728, E:ASP1730, E:GLU1732, E:ASP1733 We can see the chains which bind F-chain YQTQTNSPRRAR are DE-chains, CE-chains, and AB-chains of .α4β2, .α7, and .αβγ δ models, respectively, and the chains which bind G-chain YQTQTNSPRRAR are AB-chains, AB-chains, and DEchains of .α4β2, .α7, and .αβγ δ models, respectively (Table 13.10 too). In addition to the observation of [252], we not only find the G-chain YQTQTNSPRRAR Y674R685 penetrates deeply into the binding pocket of .α7 but also find it penetrates deeply into the binding pocket of .αβγ δ.

13.4 Concluding Remarks This chapter studies the three models human-ACE2-6LZG-model, human-IL61ALU-model, and human-IL6-1ALU-model for the fighting against SARS-CoV-2. The human-ACE2-6LZG-model has strong polar contacts GLU166-HIS493, GLU227-LYS458, GLU189-LYS112, GLU181-LYS470, GLU398-ARG514, GLU435-LYS541, ASP509-LYS187, GLU406-ARG518, GLU37-ARG393, and GLU435-HIS540 during the long MD simulation, and a large variable segment PRO492-LEU503 unfolds from .α-helix into 3.10 -helix and turns, and the model

13.4 Concluding Remarks

439

Fig. 13.7 The SBs GLU435-LYS541, ASP509-LYS187, GLU166-HIS493, GLU189-LYS112, GLU406-ARG518, GLU435-HIS540, GLU37-ARG393, GLU181-LYS470, GLU227-LYS458, GLU398-ARG514, GLU430-LYS541, ASP38-LYS353, ASP382-HIS401, ASP431-LYS288, ASP543-LYS416, GLU433-LYS288, and GLU549-LYS534 spanning a large number of residues of the human-ACE2-6LZG-model during the 664 μs’ MD

440

Fig. 13.7 (continued)

13 Human ACE2, Human IL6, Human IL6R, and Human nAChRs

13.4 Concluding Remarks

441

Fig. 13.8 The SBs GLU110-ARG113, GLU80-LYS129, GLU95-LYS120, ASP160-ARG104, ASP26-ARG30, ASP71-LYS70, ASP71-LYS86, GLU42-LYS46, and GLU51-ARG40 of the human-IL6-1ALU-model during the 1593 μs’ MD

442

13 Human ACE2, Human IL6, Human IL6R, and Human nAChRs

Fig. 13.9 The SBs ASP35-ARG79, ASP198-LYS105, GLU114-LYS154, GLU235-ARG274, GLU241-ARG268, GLU290-ARG239, ASP71-LYS45, ASP141-ARG4, and ASP221-HIS256 of the human-IL6R-1N26-model during the 196 μs’ MD

13.4 Concluding Remarks

443

has large areas of negative charges of Poisson-Boltzmann electrostatic potential surfaces. The human-IL6-1ALU-model has strong SBs GLU110-ARG113, GLU80LYS129, GLU95-LYS120, ASP160-ARG104, ASP26-ARG30, ASP71-LYS70, ASP71-LYS86, GLU42-LYS46, and GLU51-ARG40 during the long MD simulation; during the long MD, we should also notice the stronger HBs between ARG182 and ASP26, ARG182.NE-ASP26.OD1 14.81%, ARG182.NE-ASP26.OD2 13.19%, ARG182.NH2-ASP26.OD1 13.07%, and ARG182.NH2-ASP26.OD2 12.77%, and the stronger HBs between SER47 and ASP160: SER47.OG-ASP160.OD2 15.95% and SER47.OG-ASP160.OD1 14.33%; the Poisson-Boltzmann electrostatic potential surfaces of the optimized human-IL6-1ALU-model have large areas of positive charges. The optimized human-IL6R-1N26-model has six .α-sheets and one 3.10 -helix; the Poisson-Boltzmann electrostatic potential surfaces of the optimized human-IL6R-1N26-model have large positive charges; SBs ASP35-ARG79, ASP198-LYS105, GLU114-LYS154, GLU235-ARG274, GLU241-ARG268, GLU290-ARG239, ASP71-LYS45, ASP141-ARG4, and ASP221-HIS256 are important to maintain the structural stability of the human-IL6R-1N26-model. Human .α4β2-, .α7-, and .αβγ δ-nAChRs binding SARS-CoV-2 spike Y674-R685 region are also studied in this chapter.

Chapter 14

PLpro Binding with 12 Compounds

Abstract The papain-like protease (PLpro), a component of the large, multidomain protein NSP3, is a cysteine protease essential for the replication of coronaviruses and thus a potential target for antivirals. This chapter confirms a binding site consisting of .α-helices 5 and 8 and the strands 1, 2, 3, 4, and 7 of .β-sheet-4 of PLpro monomer. Keywords MD and optimization studies · SARS-CoV-2 PLpro · PLpro-binding site · Top compounds · Drug designing or discovery

14.1 Introduction The papain-like protease (PLpro), a component of the large, multi-domain protein NSP3, is a cysteine protease essential for the replication of coronaviruses and thus a potential target for antivirals. In [321], it is suggested that the Gly165-Gly273 pocket could be potentially exploited as an interaction site for small-molecule inhibitors and 12 compounds were presented in [321]. This chapter is to optimize and then MD-study these 12 compounds.

14.2 Materials and Methods The 5- or 2-microsecond simulation MD trajectories in [321] of PLpro bound to 12 rationally designed inhibitors will be used in this chapter. We denote the datasets as the following 12 models: Model1-DESRES-ANTON-11730054T1-08, Model2-DESRES-ANTON-11730063-T1-04, Model3-DESRES-ANTON11730068, Model4-DESRES-ANTON-11738401-T1-05, Model5-DESRESANTON-11738463-T1-06, Model6-DESRES-ANTON-11738465-T2-01, Model7DESRES-ANTON-11738466-T1-07, Model8-DESRES-ANTON-12330576-T111, Model9-DESRES-ANTON-12330880-T2-02, Model10-DESRES-ANTON12346144, Model11-DESRES-ANTON-12346145-T1-10, and Model12-DESRESANTON-12346146-T1-09. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2023 J. Zhang, Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures, Springer Series in Biophysics 23, https://doi.org/10.1007/978-3-031-36773-1_14

445

446

14 PLpro Binding with 12 Compounds

14.3 Results and Discussions Seeing Fig. 14.1, Table 14.1, and Fig. 14.2, we may know the binding residues are in regions aa 110–113, aa 158–168, residue 209, aa 246–249, aa 265–274, and aa 302–303, i.e., .α-helices 5 and 8 and the strands 1, 2, 3, 4, and 7 of .β-sheet-4. In this binding site, there are SBs ASP287-HIS273 (with HBs ASP287.N-HIS290.O 44.00% 1, 43.40% 2, 42.80% 4, 48.20% 5, 40.80% 6, 48.60% 7, 45.00% 8, 43.00% 9, 41.00% 10, 47.00% 11, and 43.50% 12: Tables 14.2, 14.3, 14.4, and 14.5), GLU264-ARG285 (with HBs ARG285.NE-GLU264.OE2 31.40% 1, NEOE1 35.50% 2, NE-OE2 29.20% 5, NH2-OE1 32.00% 6, NE-OE1 28.80% 7, NH2-OE2 31.50% 10, and NH2-OE2 31.00% 12: Tables 14.2, 14.3, 14.4, and 14.5), ASP165-ARG167, GLU162-LYS158 (with HB LYS158.NZ-LEU163.O 31.50% 11: Tables 14.2, 14.3, 14.4, and 14.5), GLU168-LYS158, and GLU168-ARG167 to maintain its structural stability.

Fig. 14.1 The ligands’ interaction diagrams for the 12 optimized models

Table 14.1 The HBs with more than 30% occupancy rates from the analyses of the 100 .μs’ MD trajectory data of [321] The model

Residues in the binding site

Model1-DESRES-ANTON-11730054-T1-08-optimized

163, 164, 165, 167, 168, 248, 249, 265, 267, 268, 269, 270, 271, 274, 302, 317

Model2-DESRES-ANTON-11730063-T1-04-optimized

158, 163, 164, 165, 167, 168, 209, 248, 249, 265, 267, 268, 269, 270, 274, 317

Model3-DESRES-ANTON-11730068-optimized

163, 164, 165, 166, 167, 168, 209, 246, 247, 248, 249, 265, 268, 269, 270, 271, 272, 274, 302, 303, 317

Model4-DESRES-ANTON-11738401-T1-05-optimized

163, 164, 165 168, 248, 249, 265, 267, 268, 269, 270, 271, 272, 274, 302, 317

Model5-DESRES-ANTON-11738463-T1-06-optimized

110, 113, 163, 164, 165, 167, 168, 209, 248, 249, 265, 267, 268, 269, 270, 272, 274, 302, 317

Model6-DESRES-ANTON-11738465-T2-01-optimized

110, 112, 113, 163, 164, 165, 167, 168, 248, 249, 265, 267, 268, 269, 270, 272, 273, 274, 317

Model7-DESRES-ANTON-11738466-T1-07-optimized

110, 112, 113, 163, 164, 165, 167, 168, 249, 265, 268, 269, 270, 272, 274, 302, 317

Model8-DESRES-ANTON-12330576-T1-11-optimized

110, 112, 113, 163, 164, 165, 168, 209, 247, 248, 249, 267, 268, 269, 270, 272, 273, 274, 302, 317

Model9-DESRES-ANTON-12330880-T2-02-optimized

110, 112, 113, 163, 164, 165, 167, 168, 248, 249, 265, 267, 268, 269, 270, 272, 273, 274, 302, 317

v Model10-DESRES-ANTON-12346144-optimized

158, 163, 164, 165, 168, 248, 249, 265, 267, 268, 269, 270, 274, 302, 317

Model11-DESRES-ANTON-12346145-T1-10-optimized

158, 163, 164, 165, 248, 249, 265, 269, 270, 274, 302, 317

Model12-DESRES-ANTON-12346146-T1-09-optimized

158, 163, 164, 165, 167, 168, 209, 248, 249, 265, 268, 269, 270, 271, 274, 302, 317

14.3 Results and Discussions

447

For the PLpro monomer, it is interesting to see the positively charged HIS, LYS, and ARG residues such as HIS+192, LYS+191, LYS+196, ARG+229, LYS+218, LYS+293, HIS+290, LYS+95, LYS+93, HIS+48, LYS+46, and LYS+44 are distributed onto the boundary of the Poisson-Boltzmann electrostatic potential surface (Fig. 14.3 with blue colors). For the 5 or 2 .μs’ MDs of the 12 PLpro monomer models, seeing the MD secondary structures and RMSF performance in Fig. 14.4, we may know the 3.10 helices 1 and 9 and the 5th strand of .β-sheet-3 have secondary structure changes during the MD and the N-terminal residues before .α-helix-3 (including .β-sheet-1 with five strands, .α-helix-1, and .α-helix-2) have larger RMSF values.

Fig. 14.2 The .α-helices’ and .β-sheets’ 3D structure of the PLpro monomer model, where the circle including .α-helices 5 and 8 and the strands 1, 2, 3, 4, and 7 of .β-sheet-4 is the binding site for the 12 ligands

Fig. 14.3 The Poisson-Boltzmann electrostatic potential surface diagram for the PLpro monomer model

448

14 PLpro Binding with 12 Compounds

14.4 Concluding Remarks The papain-like protease (PLpro), a component of the large, multi-domain protein NSP3, is a cysteine protease essential for the replication of coronaviruses and thus a potential target for antivirals. This chapter confirms a binding site consisting of .α-helices 5 and 8 and the strands 1, 2, 3, 4, and 7 of .β-sheet-4 of PLpro monomer. The binding site residues are aa 110, 112, 113, 58, 163, 164, 165, 167, 168, 209, 246, 247, 248, 249, 265, 267, 268, 269, 270, 271, 272, 273, 274, 302, and 303 of PLpro.

Fig. 14.4 The MD secondary structures and RMSF graphs for the PLpro monomer model

Model numbers

1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 with HBs ASP287.N-HIS290.O 44% 1, 43.4% 2, 42.8% 4, 48.2% 5, 40.8% 6, 48.6% 7, 45% 8, 43% 9, 41% 10, 47% 11, 43.5% 12

1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12

1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12

1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12

1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 with HBs ARG285.NE-GLU264.OE2 31.4% 1, NE-OE1 35.5% 2, NE-OE2 29.2% 5, NH2-OE1 32% 6, NE-OE1 28.8% 7, NH2-OE2 31.5% 10, NH2-OE2 31% 12

1, 3, 4, 7, 9, 10, 11

8

2, 4, 5, 6, 7, 10, 11, 12

1, 2, 6, 7, 9, 11, 12

3, 5

5

1, 3, 5, 6, 8, 9, 10, 12

1, 2, 3, 4, 5, 6, 7, 9, 12

2, 3, 4, 7, 9, 11

1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12

1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12

3, 5, 7

4, 8

1, 2, 3, 4, 5, 9, 11, 12

1, 2, 4, 5, 6, 7, 8, 9, 10, 12

3, 4, 6, 7, 8, 9, 10, 11, 12

1, 4, 8, 10, 11

3, 6, 9, 10, 12

1, 4, 5, 6, 7, 9, 12 with HB LYS158.NZ-LEU163.O 31.5% 11

3, 10, 11

1, 5, 8, 9, 11, 12

8

9, 11, 12

1, 2, 5, 6, 7, 8, 9, 11, 12

2, 3, 5, 8, 9, 11, 12

4

2, 9

5

1, 3, 9

SBs

ASP287-HIS273

ASP77-ARG83

GLU239-LYS183

GLU251-LYS298

GLU264-ARG285

ASP230-LYS191

ASP230-ARG229

ASP38-LYS92

GLU125-LYS307

GLU125-LYS127

GLU125-ARG141

GLU281-LYS293

GLU296-LYS253

GLU78-ARG66

ASP144-ARG139

ASP215-LYS218

ASP109-HIS90

ASP109-LYS93

ASP165-ARG167

ASP287-ARG285

ASP41-LYS44

ASP63-ARG66

GLU135-ARG139

GLU162-LYS158

GLU168-LYS158

GLU168-ARG167

GLU180-LYS127

GLU281-LYS280

GLU2-LYS4

GLU52-LYS7

GLU52-LYS4

GLU68-HIS18

GLU296-LYS253

GLU308-LYS218

Table 14.2 The SBs of the optimized models [321]:

14.4 Concluding Remarks 449

450

14 PLpro Binding with 12 Compounds

Table 14.3 The HBs with more than 30% occupancy rates from the analyses of the 5 .μs’ MD trajectory data of [321] Model1-optimized

Model2-optimized

Model3-optimized

Model4-optimized

MET244.N-VAL206.O 73.00%

TYR155.N-LEU151.O 73.00%

MET245.N-VAL304.O 73.00%

LEU118.N-LEU114.O 69.40%

TYR155.N-LEU151.O 67.60%

PHE56.N-PHE9.O 68.60%

TYR265.OH-ASN268.O 70.80%

TYR73.OH-VAL12.O 68.40%

ILE286.N-HIS276.O 67.40%

LEU118.N-LEU114.O 68.20%

MET244.N-VAL206.O 69.80%

PHE56.N-PHE9.O 68.40%

PHE56.N-PHE9.O 66.80%

MET245.N-VAL304.O 68.00%

LEU174.N-MET170.O 69.80%

TYR155.N-LEU151.O 66.60%

LEU200.N-ARG184.O 66.00%

TYR84.OH-ASN147.OD1 68.00%

PHE56.N-PHE9.O 66.60%

TYR265.OH-ASN268.O 66.40%

MET245.N-VAL304.O 63.40%

LEU200.N-ARG184.O 65.60%

TYR84.N-PHE80.O 66.40%

ILE286.N-HIS276.O 66.20%

LYS106.N-LYS95.O 62.40%

TYR73.OH-VAL12.O 65.00%

PHE32.N-TYR28.O 64.80%

MET244.N-VAL206.O 65.00%

PHE305.N-CYS261.O 61.80%

ILE286.N-HIS276.O 64.80%

TYR155.N-LEU151.O 64.60%

LEU200.N-ARG184.O 63.80%

MET170.N-VAL166.O 60.80%

PHE305.N-CYS261.O 63.40%

LEU200.N-ARG184.O 63.80%

MET245.N-VAL304.O 63.80%

TYR265.OH-ASN268.O 60.60%

MET170.N-VAL166.O 63.00%

PHE305.N-CYS261.O 62.20%

PHE305.N-CYS261.O 62.40%

PHE32.N-TYR28.O 60.00%

MET244.N-VAL206.O 62.60%

TYR73.OH-VAL12.O 61.20%

LYS106.N-LYS95.O 62.20%

TYR84.N-PHE80.O 57.80%

ALA140.N-ALA136.O 62.00%

TYR84.OH-ASN147.OD1 59.00%

GLU135.N-PRO131.O 61.20%

MET85.N-LEU81.O 55.60%

PHE32.N-TYR28.O 58.00%

LEU121.N-VAL117.O 58.80%

TYR84.OH-ASN147.OD1 61.00%

LEU121.N-VAL117.O 54.80%

ARG184.NE-GLN238.OE1 57.60%

LYS106.N-LYS95.O 58.80%

PHE32.N-TYR28.O 61.00%

LEU118.N-LEU114.O 54.40%

TYR84.N-PHE80.O 57.60%

GLN238.NE2-ALA205.O 58.80%

GLN238.NE2-ALA205.O 57.80%

ASN187.N-TYR234.O 53.80%

VAL8.N-GLN20.O 57.40%

LEU118.N-LEU114.O 58.60%

TYR84.N-PHE80.O 57.80%

THR169.OG1-ASP165.O 53.80%

LYS106.N-LYS95.O 56.40%

ARG184.NE-GLN238.OE1 57.40%

ALA140.N-ALA136.O 57.20%

v VAL8.N-GLN20.O 52.80%

LEU174.N-MET170.O 55.80%

THR302.OG1-ASP303.OD2 57.00%

MET170.N-VAL166.O 56.40%

LEU174.N-MET170.O 52.40%

LEU119.N-SER115.O 55.60%

PHE128.N-GLN134.OE1 55.20%

THR302.N-ASN263.O 55.20%

GLN20.N-VAL8.O 51.60%

THR302.N-ASN263.O 55.20%

LYS307.N-THR258.O 55.00%

VAL8.N-GLN20.O 54.60%

ARG141.N-TYR137.O 51.20%

GLU135.N-PRO131.O 54.60%

ARG141.N-TYR137.O 54.20%

GLU264.N-THR275.O 54.40%

THR35.OG1-GLY33.O 51.00%

LEU88.N-TYR84.O 53.60%

ARG285.N-THR292.O 54.00%

ARG285.N-THR292.O 53.20%

TYR73.OH-VAL12.O 50.60%

ILE152.N-PHE148.O 53.20%

ILE286.N-HIS276.O 54.00%

GLY220.N-ASN216.O 52.80%

ASN263.N-ASP303.O 50.00%

VAL99.N-LEU102.O 52.00%

ALA140.N-ALA136.O 53.40%

LEU121.N-VAL117.O 52.40%

LEU88.N-TYR84.O 49.80%

GLN238.NE2-ALA205.O 51.60%

THR35.OG1-GLY33.O 53.40%

LEU119.N-SER115.O 51.60%

ARG184.NE-GLN238.OE1 49.80%

ASN187.N-TYR234.O 51.20%

LEU88.N-TYR84.O 52.40%

ASN187.N-TYR234.O 50.60%

LEU119.N-SER115.O 49.80%

LEU124.N-ALA120.O 50.00%

GLN20.N-VAL8.O 51.80%

ILE152.N-PHE148.O 50.40%

PHE128.N-GLN134.OE1 49.20%

SER104.N-PRO97.O 49.80%

VAL8.N-GLN20.O 51.60%

ARG184.NE-GLN238.OE1 50.00%

GLN238.NE2-ALA205.O 48.60%

THR35.OG1-GLY33.O 49.80%

GLN122.NE2-LEU118.O 51.20%

VAL99.N-LEU102.O 49.60%

GLU264.N-THR275.O 48.60%

PHE128.N-GLN134.OE1 49.80%

ILE223.N-ALA231.O 50.20%

MET85.N-LEU81.O 49.60%

SER104.N-PRO97.O 48.40%

TYR284.N-THR278.O 49.40%

ILE277.N-ALA262.O 50.00%

THR103.N-GLN122.OE1 49.40%

ARG285.N-THR292.O 48.40%

GLN122.NE2-THR103.O 49.20%

VAL304.N-MET245.O 50.00%

PHE128.N-GLN134.OE1 49.40%

VAL221.N-GLN233.O 48.40%

GLU264.N-THR275.O 49.00%

LEU119.N-SER115.O 49.60%

GLN122.NE2-THR103.O 49.20%

VAL304.N-MET245.O 47.40%

MET85.N-LEU81.O 48.80%

MET170.N-VAL166.O 48.80%

TYR284.N-THR278.O 49.00%

TYR155.OH-TYR73.O 46.60%

THR103.N-GLN122.OE1 48.60%

GLN233.N-VAL221.O 48.20%

THR91.N-ALA87.O 49.00%

MET24.N-LYS4.O 46.40%

ASN178.N-LYS127.O 48.40%

MET85.N-LEU81.O 47.80%

LEU174.N-MET170.O 48.80%

THR302.N-ASN263.O 46.40%

GLN20.N-VAL8.O 48.20%

THR278.N-TYR284.O 47.20%

VAL304.N-MET245.O 48.60%

GLY220.N-ASN216.O 46.40%

THR169.OG1-ASP165.O 47.60%

LEU260.N-PHE305.O 47.20%

GLN122.NE2-LEU118.O 48.60%

TYR265.N-PRO300.O 46.20%

THR91.N-ALA87.O 47.20%

VAL99.N-LEU102.O 47.20%

LEU88.N-TYR84.O 48.20%

VAL189.N-THR232.O 46.00%

ARG285.N-THR292.O 47.00%

THR169.N-ASP165.O 46.00%

THR35.OG1-GLY33.O 47.40%

GLN122.NE2-LEU118.O 45.80%

GLY220.N-ASN216.O 46.80%

TYR284.N-THR278.O 46.00%

LEU260.N-PHE305.O 46.60%

TYR284.N-THR278.O 45.60%

TYR155.OH-TYR73.O 46.60%

VAL189.N-THR232.O 45.80%

GLN20.N-VAL8.O 45.20%

ASN178.N-LYS127.O 45.00%

THR171.OG1-ARG167.O 46.60%

ASN187.N-TYR234.O 45.60%

ILE277.N-ALA262.O 45.20%

ALA140.N-ALA136.O 44.60%

LEU151.N-ASN147.O 45.80%

TYR265.N-PRO300.O 44.80%

ASN129.N-HIS176.O 44.80%

VAL185.N-GLN237.O 44.60%

MET24.N-LYS4.O 45.60%

SER104.N-PRO97.O 44.60%

TYR155.OH-TYR73.O 44.80%

ILE277.N-ALA262.O 44.20%

ALA132.N-TYR72.O 45.60%

LEU37.N-ALA40.O 44.60%

ALA132.N-TYR72.O 44.80%

ASP287.N-HIS290.O 44.00%

THR198.N-LEU186.O 45.20%

TYR208.OH-GLN233.OE1 44.60%

PHE70.N-ARG66.O 43.80%

VAL189.N-THR232.O 44.40%

THR302.N-ASN263.O 44.20%

VAL189.N-THR232.O 44.00%

TYR306.OH-LEU212.O 43.80%

GLN122.NE2-LEU118.O 44.20%

ILE152.N-PHE148.O 44.00%

VAL188.N-LYS196.O 43.80%

TYR265.N-PRO300.O 44.20%

VAL188.N-LYS196.O 43.60%

TYR36.N-PHE57.O 44.20%

GLY53.N-LYS7.O 43.60%

SER104.N-PRO97.O 43.20%

LEU260.N-PHE305.O 43.40%

ARG66.N-ASP62.O 44.00%

THR91.N-ALA87.O 43.60%

ASP287.N-HIS290.O 42.80%

VAL99.N-LEU102.O 42.40%

ASP287.N-HIS290.O 43.40%

GLN238.NE2-SER240.OG 42.80%

GLY53.N-LYS7.O 42.60%

LEU186.N-THR198.O 42.20%

VAL221.N-GLN233.O 43.40%

ALA136.N-ALA132.O 42.80%

THR171.OG1-ARG167.O 42.60%

ASN111.ND2-LYS106.O 42.20%

ILE277.N-ALA262.O 43.20%

TYR73.N-ALA69.O 41.40%

THR169.OG1-ASP165.O 42.20%

LEU151.N-ASN147.O 41.00%

TYR306.OH-LEU212.O 43.20%

MET24.N-LYS4.O 41.40%

PHE70.N-ARG66.O 41.80%

GLN233.N-VAL221.O 41.00%

VAL188.N-LYS196.O 43.20%

THR35.N-THR43.OG1 41.00%

MET24.N-LYS4.O 41.60%

ILE223.N-ALA231.O 40.60%

THR35.N-THR43.OG1 43.20%

GLY210.N-SER246.O 40.20%

ILE223.N-ALA231.O 41.00%

GLY53.N-LYS7.O 40.60%

VAL304.N-MET245.O 43.00%

ASN129.N-HIS176.O 40.20%

GLN233.N-VAL221.O 40.80%

TYR73.N-ALA69.O 40.40%

LEU37.N-ALA40.O 42.60%

THR103.N-GLN122.OE1 40.00%

THR11.OG1-ASN16.O 40.40%

THR103.N-GLN122.OE1 40.40%

LEU121.N-VAL117.O 42.40%

TYR155.OH-TYR73.O 39.60%

VAL221.N-GLN233.O 40.00%

THR11.OG1-ASN16.O 40.40%

ASN129.N-HIS176.O 42.40%

VAL185.N-GLN237.O 39.40%

TYR137.N-LEU133.O 40.00%

PHE57.N-TYR36.O 40.00%

GLN233.N-VAL221.O 42.20%

ASN178.N-LYS127.O 39.40%

THR278.N-TYR284.O 40.00%

THR91.N-ALA87.O 39.80%

VAL185.N-GLN237.O 42.00%

THR11.OG1-ASN16.O 39.40%

GLU239.N-LYS183.O 40.00%

THR171.OG1-ARG167.O 39.60%

LEU260.N-PHE305.O 42.00%

PHE70.N-ARG66.O 39.20%

THR198.N-LEU186.O 39.60%

GLU135.N-PRO131.O 39.00%

ASN16.N-ASP13.OD1 41.60%

TYR36.N-PHE57.O 38.40%

LEU151.N-ASN147.O 39.40%

(continued)

14.4 Concluding Remarks

451

Table 14.3 (continued) Model1-optimized

Model2-optimized

Model3-optimized

Model4-optimized

LEU37.N-ALA40.O 38.60%

THR11.OG1-ASN16.O 41.60%

VAL188.N-LYS196.O 38.40%

TYR306.OH-LEU212.O 39.20%

LEU173.N-THR169.O 38.60%

LYS307.N-THR258.O 41.60%

ARG66.N-ASP62.O 38.00%

LEU37.N-ALA40.O 39.00%

THR198.N-LEU186.O 37.80%

LEU186.N-THR198.O 41.20%

THR103.OG1-ALA140.O 37.80%

ARG66.N-ASP62.O 38.80%

THR278.N-TYR284.O 37.40%

ILE223.N-ALA231.O 41.20%

ASN16.N-ASP13.OD1 37.60%

LEU173.N-THR169.O 38.40%

GLN122.NE2-THR103.O 37.40%

GLY53.N-LYS7.O 40.20%

GLY220.N-ASN216.O 37.20%

CYS149.N-ALA145.O 37.80%

MET207.N-VAL203.O 37.40%

PHE70.N-ARG66.O 39.40%

VAL221.N-GLN233.O 37.00%

TYR36.N-PHE57.O 37.60%

ASN129.N-HIS176.O 37.20%

TYR265.OH-ASN268.O 39.20%

GLN122.NE2-THR103.O 36.80%

MET207.N-VAL203.O 37.20%

THR35.N-THR43.OG1 37.00%

SER156.OG-ILE152.O 38.80%

LEU124.N-ALA120.O 36.60%

ARG141.N-TYR137.O 37.00%

TYR297.OH-GLU264.OE1 36.60%

TYR137.N-LEU133.O 38.20%

TYR297.OH-GLU264.OE1 36.20%

TYR73.N-ALA69.O 37.00%

ARG66.N-ASP62.O 36.20%

GLN238.NE2-SER240.OG 37.80%

GLN134.N-ALA130.O 36.00%

ASN111.ND2-LYS106.O 36.40%

SER246.OG-ASP303.OD1 36.00%

MET207.N-VAL203.O 37.80%

TYR306.OH-LEU212.O 36.00%

THR35.N-THR43.OG1 36.00%

ALA136.N-ALA132.O 36.00%

TYR265.N-PRO300.O 37.60%

GLU135.N-PRO131.O 35.80%

TYR297.OH-GLU264.OE2 36.00%

LYS307.N-THR258.O 35.80%

LEU173.N-THR169.O 36.60%

ASP23.N-GLN31.OE1 35.80%

VAL185.N-GLN237.O 36.00%

TYR36.N-PHE57.O 35.60%

CYS149.N-ALA145.O 35.40%

THR198.N-LEU186.O 35.60%

LEU186.N-THR198.O 35.80%

ILE152.N-PHE148.O 35.40%

GLY210.N-SER246.O 35.20%

SER86.N-GLY82.O 35.60%

SER156.OG-ILE152.O 35.40%

LYS280.N-THR282.O 35.40%

PHE9.N-LYS54.O 35.00%

TYR297.OH-GLU264.OE2 35.40%

HIS51.N-HIS48.O 35.20%

SER86.N-GLY82.O 34.60%

SER67.N-ASP63.O 35.00%

HIS51.N-HIS48.O 35.20%

SER67.N-ASP63.O 35.00%

THR275.N-GLU264.O 34.40%

TYR297.OH-GLU264.OE1 34.80%

SER156.OG-ILE152.O 35.00%

LEU81.N-ASP77.O 34.40%

GLN134.N-ALA130.O 34.40%

ASN111.ND2-LYS106.O 34.80%

VAL22.N-ILE6.O 35.00%

VAL22.N-ILE6.O 34.20%

GLY210.N-SER246.O 34.00%

ARG141.N-TYR137.O 34.60%

SER246.OG-ASP303.OD1 35.00%

SER86.N-GLY82.O 34.00%

ASN263.ND2-ASP303.OD2 33.60%

ASP23.N-GLN31.OE1 34.20%

PHE57.N-TYR36.O 34.80%

LYS307.N-THR258.O 34.00%

ASN16.N-ASP13.OD1 33.40%

THR292.N-ARG285.O 34.20%

ASN111.ND2-LYS106.O 34.80%

ASN16.N-ASP13.OD2 34.00%

PHE9.N-LYS54.O 33.40%

THR278.N-TYR284.O 33.60%

TYR234.N-ASN187.O 34.20%

THR292.N-ARG285.O 33.80%

TYR297.OH-GLU264.OE2 33.40%

THR10.N-HIS18.O 33.60%

THR10.N-HIS18.O 33.80%

ALA247.N-THR302.O 33.80%

HIS51.N-HIS48.O 33.00%

ALA247.N-THR302.O 33.40%

LEU151.N-ASN147.O 32.80%

ALA120.N-SER116.O 33.40%

VAL22.N-ILE6.O 32.40%

GLU239.N-LYS183.O 33.40%

TYR28.OH-HIS51.ND1 32.40%

LYS92.N-LEU88.O 33.40%

SER67.N-ASP63.O 31.80%

TYR28.OH-HIS51.ND1 33.20%

THR169.OG1-ASP165.O 32.20%

TYR297.OH-GLU264.OE1 33.20%

THR103.OG1-ALA140.O 31.80%

PHE57.N-TYR36.O 33.20%

LEU235.N-LEU217.O 32.00%

SER246.OG-ASP303.OD2 33.20%

THR10.N-HIS18.O 31.60%

ARG184.N-LEU200.O 32.60%

MET207.N-VAL203.O 32.00%

ASN178.N-LYS127.O 32.80%

ALA132.N-TYR72.O 31.60%

LYS92.N-LEU88.O 32.40%

ASN110.ND2-GLY161.O 31.60%

THR10.N-HIS18.O 32.80%

ARG184.N-LEU200.O 31.60%

VAL22.N-ILE6.O 32.20%

PHE9.N-LYS54.O 31.60%

GLY210.N-SER246.O 32.20%

ARG285.NE-GLU264.OE2 31.40%

SER246.OG-ASP303.OD2 31.60%

SER25.N-ASP23.OD2 31.20%

PHE9.N-LYS54.O 32.00%

GLU239.N-LYS183.O 31.40%

TYR73.N-ALA69.O 31.20%

CYS149.N-ALA145.O 30.80%

LEU124.N-ALA120.O 31.80%

LEU124.N-ALA120.O 31.40%

TYR297.OH-GLU264.OE2 31.20%

SER67.N-ASP63.O 30.80%

ASN16.N-ASP13.OD1 31.60%

SER156.N-ILE152.O 31.20%

LEU235.N-LEU217.O 30.80%

TYR137.N-LEU133.O 30.20%

GLN238.NE2-SER240.OG 31.20%

ASP23.N-GLN31.OE1 31.20%

ASN89.N-MET85.O 30.60%

ARG184.N-LEU200.O 30.20%

ARG184.N-LEU200.O 31.20%

LYS92.N-LEU88.O 30.80%

ASN263.ND2-ASP303.OD1 29.80%

LEU186.N-THR198.O 29.80%

LEU254.N-TYR297.O 31.00%

TYR28.OH-HIS51.ND1 30.20%

SER86.N-GLY82.O 29.60%

THR292.N-ARG285.O 29.80%

THR169.N-ASP165.O 30.60%

ALA247.N-THR302.O 30.20%

LYS280.N-THR282.O 29.40%

MET294.N-LEU283.O 29.60%

PHE57.N-TYR36.O 30.40%

ALA231.N-ILE223.O 30.00%

HIS51.N-HIS48.O 29.40%

SER156.N-ILE152.O 29.60%

TYR28.OH-HIS51.ND1 29.80%

452

14 PLpro Binding with 12 Compounds

Table 14.4 The HBs with more than 30% occupancy rates from the analyses of the 5 (for Model5optimized to Model7-optimized) or 2 (for Model8-optimized) .μs’ MD trajectory data of [321] Model5-optimized

Model6-optimized

Model7-optimized

Model8-optimized

THR302.N-ASN263.O 72.80%

PHE56.N-PHE9.O 66.80%

MET244.N-VAL206.O 72.40%

TYR155.N-LEU151.O 77.50%

TYR155.N-LEU151.O 70.40%

PHE305.N-CYS261.O 66.60%

LEU200.N-ARG184.O 70.20%

PHE56.N-PHE9.O 72.50%

ILE286.N-HIS276.O 68.20%

MET244.N-VAL206.O 65.20%

TYR155.N-LEU151.O 70.00%

LEU200.N-ARG184.O 70.50%

GLU264.N-THR275.O 67.80%

LEU200.N-ARG184.O 64.00%

ILE286.N-HIS276.O 69.20%

MET244.N-VAL206.O 69.00%

MET244.N-VAL206.O 67.40%

TYR155.N-LEU151.O 63.40%

PHE56.N-PHE9.O 63.80%

PHE305.N-CYS261.O 68.50%

ASN263.ND2-ASP303.OD2 67.20%

PHE32.N-TYR28.O 62.40%

ARG184.NE-GLN238.OE1 62.80%

TYR155.OH-TYR73.O 65.00%

LEU200.N-ARG184.O 65.80%

MET170.N-VAL166.O 61.00%

PHE32.N-TYR28.O 60.40%

LEU118.N-LEU114.O 64.00%

ASN263.N-ASP303.O 65.60%

MET245.N-VAL304.O 60.00%

LEU118.N-LEU114.O 59.20%

MET245.N-VAL304.O 64.00%

SER246.OG-ASP303.OD1 63.00%

VAL8.N-GLN20.O 58.20%

LEU174.N-MET170.O 58.80%

ILE286.N-HIS276.O 62.50%

TYR265.OH-ASN268.O 62.40%

ARG184.NE-GLN238.OE1 57.00%

TYR84.N-PHE80.O 58.40%

PHE32.N-TYR28.O 60.00%

LEU118.N-LEU114.O 62.00%

LYS106.N-LYS95.O 56.80%

GLN238.NE2-ALA205.O 57.80%

GLN238.NE2-ALA205.O 59.50%

PHE56.N-PHE9.O 61.00%

ILE286.N-HIS276.O 55.60%

MET245.N-VAL304.O 57.00%

TYR84.N-PHE80.O 59.50%

MET245.N-VAL304.O 60.80%

LEU118.N-LEU114.O 55.20%

THR35.OG1-GLY33.O 57.00%

SER246.OG-ASP303.OD1 59.50%

TYR84.OH-ASN147.OD1 60.20%

LEU121.N-VAL117.O 55.20%

TYR155.OH-TYR73.O 56.40%

MET170.N-VAL166.O 58.50%

TYR84.N-PHE80.O 60.00%

MET85.N-LEU81.O 54.80%

PHE305.N-CYS261.O 56.40%

VAL8.N-GLN20.O 57.50%

PHE305.N-CYS261.O 60.00%

TYR84.N-PHE80.O 54.40%

THR302.N-ASN263.O 55.80%

ARG184.NE-GLN238.OE1 57.00%

LYS106.N-LYS95.O 59.60%

GLN238.NE2-ALA205.O 53.80%

LYS106.N-LYS95.O 55.00%

LEU174.N-MET170.O 56.50%

MET170.N-VAL166.O 58.20%

THR35.OG1-GLY33.O 52.80%

MET170.N-VAL166.O 54.80%

TYR73.OH-VAL12.O 55.00%

THR302.OG1-ALA247.O 56.60%

SER104.N-PRO97.O 52.60%

GLU264.N-THR275.O 53.20%

PHE128.N-GLN134.OE1 54.50%

ASN187.N-TYR234.O 56.00%

THR302.N-ASN263.O 52.20%

MET85.N-LEU81.O 53.00%

GLN238.NE2-SER240.OG 54.00%

GLN238.NE2-ALA205.O 55.60%

GLN233.N-VAL221.O 52.00%

LEU119.N-SER115.O 52.40%

ALA140.N-ALA136.O 53.50%

PHE128.N-GLN134.OE1 55.20%

LEU88.N-TYR84.O 50.80%

ASN187.N-TYR234.O 52.40%

LYS106.N-LYS95.O 53.50%

PHE32.N-TYR28.O 55.00%

TYR284.N-THR278.O 50.60%

GLY220.N-ASN216.O 52.20%

VAL99.N-LEU102.O 52.50%

LEU174.N-MET170.O 54.40%

ILE223.N-ALA231.O 50.40%

VAL8.N-GLN20.O 52.00%

LEU119.N-SER115.O 52.50%

ALA140.N-ALA136.O 54.40%

PHE128.N-GLN134.OE1 50.20%

ARG141.N-TYR137.O 52.00%

ILE152.N-PHE148.O 52.50%

VAL8.N-GLN20.O 54.00%

ARG285.N-THR292.O 50.20%

LEU88.N-TYR84.O 51.80%

GLN233.N-VAL221.O 51.50%

ARG184.NE-GLN238.OE1 53.60%

LEU260.N-PHE305.O 50.00%

TYR265.N-PRO300.O 51.60%

TYR208.OH-GLN233.OE1 50.50%

VAL99.N-LEU102.O 53.40%

LEU119.N-SER115.O 50.00%

PHE128.N-GLN134.OE1 50.60%

VAL189.N-THR232.O 50.50%

THR103.N-GLN122.OE1 52.60%

GLN20.N-VAL8.O 48.80%

LEU121.N-VAL117.O 50.60%

GLN20.N-VAL8.O 49.50%

GLU135.N-PRO131.O 52.00%

GLU264.N-THR275.O 48.80%

THR169.OG1-ASP165.O 49.80%

MET85.N-LEU81.O 49.50%

LEU88.N-TYR84.O 51.80%

THR169.OG1-ASP165.O 48.40%

ASP287.N-HIS290.O 48.60%

ARG285.N-THR292.O 49.50%

MET85.N-LEU81.O 51.40%

ARG141.N-TYR137.O 48.20%

ILE277.N-ALA262.O 48.20%

LEU88.N-TYR84.O 49.50%

THR35.OG1-GLY33.O 51.00%

ALA140.N-ALA136.O 48.00%

VAL188.N-LYS196.O 47.80%

THR169.OG1-ASP165.O 49.00%

TYR265.N-PRO300.O 50.80%

LEU174.N-MET170.O 47.60%

ALA140.N-ALA136.O 47.80%

THR103.N-GLN122.OE1 48.50%

ILE152.N-PHE148.O 50.80%

TYR84.OH-ASN147.OD1 47.60%

TYR73.OH-VAL12.O 47.60%

ASN129.N-HIS176.O 48.50%

ASN16.N-ASP13.OD2 50.40%

VAL189.N-THR232.O 46.60%

MET24.N-LYS4.O 47.20%

ASN178.N-LYS127.O 48.50%

LEU119.N-SER115.O 49.60%

TYR208.OH-GLN233.OE1 46.40%

SER104.N-PRO97.O 46.60%

VAL304.N-MET245.O 48.00%

GLN20.N-VAL8.O 49.00%

GLN122.NE2-LEU118.O 45.60%

GLN122.NE2-LEU118.O 46.60%

GLY53.N-LYS7.O 47.50%

VAL188.N-LYS196.O 48.40%

LYS307.N-THR258.O 45.60%

VAL304.N-MET245.O 46.40%

LEU121.N-VAL117.O 47.50%

SER104.N-PRO97.O 48.20%

LEU37.N-ALA40.O 44.20%

TYR284.N-THR278.O 46.20%

GLU135.N-PRO131.O 47.00%

ASP287.N-HIS290.O 48.20%

MET24.N-LYS4.O 43.40%

GLN20.N-VAL8.O 45.00%

TYR265.N-PRO300.O 47.00%

GLY220.N-ASN216.O 47.80%

ASN187.N-TYR234.O 43.00%

THR103.N-GLN122.OE1 45.00%

GLN122.NE2-LEU118.O 46.50%

ILE277.N-ALA262.O 47.60%

VAL99.N-LEU102.O 42.60%

LEU37.N-ALA40.O 45.00%

LEU151.N-ASN147.O 46.50%

ASN178.N-LYS127.O 47.00%

ILE277.N-ALA262.O 42.60%

GLY53.N-LYS7.O 44.20%

TYR306.OH-LEU212.O 46.50%

THR169.OG1-ASP165.O 47.00%

GLN238.NE2-SER240.OG 42.60%

ILE223.N-ALA231.O 44.20%

TYR284.N-THR278.O 45.50%

TYR155.OH-TYR73.O 47.00%

PHE70.N-ARG66.O 42.40%

LEU260.N-PHE305.O 44.00%

ARG66.N-ASP62.O 45.00%

LEU37.N-ALA40.O 46.80%

GLY53.N-LYS7.O 42.20%

GLN238.NE2-SER240.OG 44.00%

ASP287.N-HIS290.O 45.00%

VAL304.N-MET245.O 46.20%

THR35.N-THR43.OG1 41.80%

TYR306.OH-LEU212.O 43.80%

THR302.N-ASN263.O 45.00%

ILE223.N-ALA231.O 45.80%

THR91.N-ALA87.O 41.80%

GLN233.N-VAL221.O 43.80%

GLU264.N-THR275.O 44.50%

TYR284.N-THR278.O 45.60%

TYR265.OH-ASN268.O 41.80%

ILE152.N-PHE148.O 43.40%

THR35.OG1-GLY33.O 44.50%

VAL189.N-THR232.O 45.60%

THR278.N-TYR284.O 41.60%

ASN263.N-ASP303.O 43.40%

LEU260.N-PHE305.O 44.50%

ALA132.N-TYR72.O 45.60%

TYR155.OH-TYR73.O 41.60%

ASN178.N-LYS127.O 42.20%

ARG141.N-TYR137.O 44.00%

MET24.N-LYS4.O 45.20%

TYR306.OH-LEU212.O 41.40%

TYR73.N-ALA69.O 41.80%

ILE223.N-ALA231.O 44.00%

LEU121.N-VAL117.O 45.20%

TYR265.N-PRO300.O 41.40%

VAL189.N-THR232.O 41.40%

MET24.N-LYS4.O 43.50%

GLN122.NE2-LEU118.O 45.00%

TYR73.OH-VAL12.O 41.20%

LEU151.N-ASN147.O 40.80%

ALA247.N-THR302.O 43.00%

SER116.OG-ASN263.OD1 44.80%

TYR297.OH-GLU264.OE2 41.20%

VAL185.N-GLN237.O 40.40%

LEU37.N-ALA40.O 42.50%

ARG285.N-THR292.O 44.80%

ASP287.N-HIS290.O 40.80%

THR278.N-TYR284.O 40.20%

THR302.OG1-ASP303.OD2 42.50%

LEU260.N-PHE305.O 44.40%

ASN129.N-HIS176.O 40.80%

ASN129.N-HIS176.O 40.00%

SER104.N-PRO97.O 42.50%

VAL185.N-GLN237.O 42.80%

TYR73.N-ALA69.O 40.60%

THR91.N-ALA87.O 39.80%

ALA231.N-ILE223.O 42.50%

GLN233.N-VAL221.O 42.60%

VAL185.N-GLN237.O 40.40%

VAL99.N-LEU102.O 39.40%

TYR265.OH-ASN268.O 42.00%

ASN129.N-HIS176.O 42.60%

THR103.N-GLN122.OE1 40.00%

THR11.OG1-ASN16.O 39.00%

ILE277.N-ALA262.O 42.00%

THR198.N-LEU186.O 42.40%

THR11.OG1-ASN16.O 40.00%

ARG285.N-THR292.O 38.40%

ASN111.N-ALA108.O 41.50%

THR35.N-THR43.OG1 42.40%

TYR36.N-PHE57.O 39.60%

LEU173.N-THR169.O 38.20%

VAL185.N-GLN237.O 40.50%

TYR306.OH-LEU212.O 42.40%

THR103.OG1-ALA140.O 39.00%

TYR36.N-PHE57.O 38.20%

THR278.N-TYR284.O 40.00%

(continued)

14.4 Concluding Remarks

453

Table 14.4 (continued) Model5-optimized

Model6-optimized

Model7-optimized

Model8-optimized

GLN122.NE2-THR103.O 42.40%

LYS280.N-THR282.O 38.80%

THR198.N-LEU186.O 38.00%

ASN187.N-TYR234.O 40.00%

THR171.OG1-ARG167.O 42.20%

VAL304.N-MET245.O 38.60%

GLU135.N-PRO131.O 37.40%

SER86.N-GLY82.O 40.00%

THR169.N-ASP165.O 41.60%

MET207.N-VAL203.O 38.20%

ARG66.N-ASP62.O 37.40%

ALA120.N-SER116.O 39.50%

THR91.N-ALA87.O 41.40%

GLU135.N-PRO131.O 38.00%

TYR297.OH-GLU264.OE1 37.00%

TYR137.N-LEU133.O 39.00%

LEU151.N-ASN147.O 41.40%

GLY220.N-ASN216.O 38.00%

VAL221.N-GLN233.O 37.00%

TYR234.N-ASN187.O 39.00%

ARG141.N-TYR137.O 40.20%

ASP23.N-GLN31.OE1 37.80%

PHE57.N-TYR36.O 36.60%

GLN122.NE2-THR103.O 38.50%

ALA120.N-SER116.O 40.20%

THR198.N-LEU186.O 37.80%

THR35.N-THR43.OG1 36.60%

LYS92.N-LEU88.O 38.50%

LEU173.N-THR169.O 40.00%

TYR234.N-ASN187.O 37.60%

SER86.N-GLY82.O 36.60%

TYR73.N-ALA69.O 38.00%

GLN238.NE2-SER240.OG 39.60%

VAL188.N-LYS196.O 37.40%

SER116.OG-ASN263.OD1 36.20%

GLY210.N-SER246.O 37.50%

ARG66.N-ASP62.O 38.60%

GLY210.N-SER246.O 37.40%

PHE70.N-ARG66.O 35.60%

THR11.OG1-ASN16.O 37.50%

SER156.OG-ILE152.O 38.60%

ALA136.N-ALA132.O 37.40%

GLN122.NE2-THR103.O 35.60%

ASP23.N-GLN31.OE1 37.50%

THR278.N-TYR284.O 38.00%

GLN134.N-ALA130.O 37.20%

SER67.N-ASP63.O 35.60%

THR10.N-HIS18.O 37.50%

GLY210.N-SER246.O 38.00%

ARG66.N-ASP62.O 37.20%

TYR297.OH-GLU264.OE2 35.40%

THR171.OG1-ARG167.O 37.00%

VAL221.N-GLN233.O 37.80%

LEU151.N-ASN147.O 36.40%

PHE9.N-LYS54.O 35.20%

SER67.N-ASP63.O 36.50%

TYR36.N-PHE57.O 37.40%

ILE152.N-PHE148.O 36.40%

GLN134.N-ALA130.O 34.80%

GLU168.N-ASP165.OD2 36.00%

PHE57.N-TYR36.O 37.20%

THR10.N-HIS18.O 36.20%

LEU235.N-LEU217.O 34.60%

SER240.OG-GLU308.O 36.00%

TYR137.N-LEU133.O 37.20%

LEU186.N-THR198.O 36.20%

TYR84.OH-ASN147.OD1 34.60%

TYR36.N-PHE57.O 35.50%

LEU186.N-THR198.O 37.20%

GLN122.NE2-THR103.O 35.40%

LEU186.N-THR198.O 34.40%

SER156.OG-ILE152.O 35.50%

GLY53.N-LYS7.O 37.20%

VAL22.N-ILE6.O 35.20%

LYS92.N-LEU88.O 34.00%

THR35.N-THR43.OG1 35.50%

PHE70.N-ARG66.O 36.40%

SER67.N-ASP63.O 34.80%

VAL22.N-ILE6.O 33.80%

PHE70.N-ARG66.O 35.50%

LYS92.N-LEU88.O 35.80%

THR171.OG1-ARG167.O 34.20%

GLY210.N-SER246.O 33.80%

ASN263.ND2-ASP303.OD2 35.50%

THR11.OG1-ASN16.O 35.60%

VAL221.N-GLN233.O 34.20%

ASN89.N-MET85.O 33.40%

GLY220.N-ASN216.O 35.00%

TYR252.N-GLY299.O 34.60%

ASN178.N-LYS127.O 33.40%

SER246.OG-ASP303.OD1 33.20%

ASN111.ND2-LYS106.O 35.00%

THR10.N-HIS18.O 34.00%

HIS51.N-HIS48.O 33.20%

CYS149.N-ALA145.O 33.20%

CYS149.N-ALA145.O 35.00%

LEU124.N-ALA120.O 34.00%

ALA231.N-ILE223.O 33.00%

HIS51.N-HIS48.O 33.00%

TYR28.OH-HIS51.ND1 34.50%

LEU235.N-LEU217.O 33.80%

ASN263.N-ASP303.O 32.80%

ALA132.N-TYR72.O 32.20%

MET207.N-VAL203.O 34.50%

ASP23.N-GLN31.OE1 33.80%

TYR28.OH-HIS51.ND1 32.80%

ASN263.ND2-ASP303.OD2 32.00%

VAL221.N-GLN233.O 34.00%

CYS149.N-ALA145.O 33.40%

ALA132.N-TYR72.O 32.80%

ASN16.N-ASP13.OD2 32.00%

THR198.N-LEU186.O 34.00%

TYR73.N-ALA69.O 33.20%

LEU173.N-THR169.O 32.40%

HIS18.N-THR10.O 31.80%

PHE57.N-TYR36.O 34.00%

TYR297.OH-GLU264.OE1 33.00%

ASN16.N-ASP13.OD2 32.40%

TYR137.N-LEU133.O 31.80%

ARG184.N-LEU200.O 33.50%

VAL22.N-ILE6.O 33.00%

ARG285.NH2-GLU264.OE1 32.00%

ARG184.N-LEU200.O 31.60%

LEU186.N-THR198.O 33.50%

HIS51.N-HIS48.O 32.40%

CYS149.N-ALA145.O 31.60%

THR103.OG1-ALA140.O 31.20%

TYR297.OH-GLU264.OE1 33.50%

TYR306.N-VAL243.O 32.00%

SER156.N-ILE152.O 31.60%

ASN111.ND2-LYS106.O 31.00%

TYR297.OH-GLU264.OE2 33.00%

ALA231.N-ILE223.O 31.80%

THR171.N-ARG167.O 30.60%

ASN16.N-ASP13.OD1 30.60%

LYS307.N-THR258.O 33.00%

SER86.N-GLY82.O 31.00%

ASN111.ND2-LYS106.O 30.60%

TYR306.N-VAL243.O 30.60%

LEU235.N-LEU217.O 32.50%

MET207.N-VAL203.O 30.80%

ALA154.N-ALA150.O 30.60%

THR171.OG1-ARG167.O 30.20%

ALA154.N-ALA150.O 32.50%

THR171.N-ARG167.O 30.80%

ASN89.N-MET85.O 30.40%

THR10.N-HIS18.O 30.20%

SER25.N-ASP23.OD2 32.50%

HIS18.N-THR10.O 30.20%

SER86.N-GLY82.O 30.40%

SER156.OG-ILE152.O 29.60%

VAL22.N-ILE6.O 32.00%

ARG184.N-LEU200.O 30.00%

ASN16.N-ASP13.OD1 30.20%

SER156.N-ILE152.O 29.40%

THR91.OG1-ALA146.O 32.00%

PHE9.N-LYS54.O 30.00%

ALA247.N-THR302.O 30.00%

VAL243.N-TYR306.O 29.40%

ASN16.N-ASP13.OD2 31.50%

GLU239.N-LYS183.O 30.00%

TYR297.OH-GLU264.OE1 30.00%

ALA136.N-ALA132.O 29.20%

MET294.N-LEU283.O 31.00%

ASN16.ND2-ASP13.OD1 29.80%

LEU124.N-ALA120.O 29.80%

LYS307.N-THR258.O 29.20%

THR292.N-ARG285.O 30.50%

THR275.N-GLU264.O 29.80%

PHE9.N-LYS54.O 29.00%

THR91.OG1-ALA146.O 29.00%

GLU168.N-ASP165.OD1 30.50%

TYR297.OH-GLU264.OE2 29.60%

GLU239.N-LYS183.O 29.00%

MET207.N-VAL203.O 29.00%

SER104.OG-GLY288.O 30.50%

ASN89.N-MET85.O 29.60%

ARG184.N-LEU200.O 29.00%

TYR28.OH-HIS51.ND1 28.80%

LYS158.N-LEU153.O 30.00%

ARG285.NE-GLU264.OE2 29.20%

SER25.N-ASP23.OD1 29.00%

ARG285.NE-GLU264.OE1 28.80%

LYS183.N-GLU239.O 30.00%

454

14 PLpro Binding with 12 Compounds

Table 14.5 The HBs with more than 30% occupancy rates from the analyses of the 2 .μs’ MD trajectory data of [321] Model9-optimized

Model10-optimized

Model11-optimized

Model12-optimized

TYR84.N-PHE80.O 70.00%

TYR155.N-LEU151.O 71.50%

LEU118.N-LEU114.O 70.50%

LEU200.N-ARG184.O 68.50%

LEU200.N-ARG184.O 69.00%

PHE56.N-PHE9.O 71.00%

LEU200.N-ARG184.O 68.50%

TYR84.N-PHE80.O 68.50%

TYR155.N-LEU151.O 67.00%

MET245.N-VAL304.O 69.50%

MET244.N-VAL206.O 68.00%

TYR155.N-LEU151.O 67.50%

MET244.N-VAL206.O 66.00%

PHE305.N-CYS261.O 68.00%

MET245.N-VAL304.O 68.00%

MET245.N-VAL304.O 66.00%

MET245.N-VAL304.O 65.00%

TYR265.OH-ASN268.O 68.00%

PHE32.N-TYR28.O 66.00%

PHE56.N-PHE9.O 65.00%

LYS106.N-LYS95.O 64.50%

LEU118.N-LEU114.O 65.00%

ILE286.N-HIS276.O 66.00%

TYR84.OH-ASN147.OD1 63.50%

TYR73.OH-VAL12.O 62.50%

MET170.N-VAL166.O 65.00%

ARG184.NE-GLN238.OE1 64.00%

MET244.N-VAL206.O 62.50%

LEU174.N-MET170.O 62.50%

MET244.N-VAL206.O 64.00%

MET170.N-VAL166.O 63.50%

ILE286.N-HIS276.O 62.00%

ILE286.N-HIS276.O 62.00%

PHE32.N-TYR28.O 63.00%

THR302.N-ASN263.O 63.50%

LEU118.N-LEU114.O 61.00%

TYR84.OH-ASN147.OD1 62.00%

LEU200.N-ARG184.O 62.00%

TYR155.N-LEU151.O 62.50%

GLN238.NE2-ALA205.O 60.50%

PHE56.N-PHE9.O 59.00%

LYS106.N-LYS95.O 62.00%

PHE56.N-PHE9.O 61.00%

PHE32.N-TYR28.O 60.50%

ARG184.NE-GLN238.OE1 58.50%

ALA140.N-ALA136.O 59.50%

PHE305.N-CYS261.O 61.00%

LYS106.N-LYS95.O 60.00%

VAL8.N-GLN20.O 58.00%

ILE286.N-HIS276.O 59.00%

LEU121.N-VAL117.O 58.00%

THR103.N-GLN122.OE1 59.50%

LEU119.N-SER115.O 57.00%

VAL8.N-GLN20.O 57.50%

LYS106.N-LYS95.O 58.00%

TYR265.OH-ASN268.O 59.50%

PHE305.N-CYS261.O 57.00%

LYS307.N-THR258.O 57.00%

TYR155.OH-TYR73.O 56.50%

VAL8.N-GLN20.O 59.00%

PHE32.N-TYR28.O 56.00%

ARG184.NE-GLN238.OE1 56.50%

THR35.OG1-GLY33.O 55.00%

ASN16.N-ASP13.OD1 58.00%

LEU121.N-VAL117.O 55.50%

LEU119.N-SER115.O 56.00%

ASN263.N-ASP303.O 54.50%

LEU88.N-TYR84.O 57.00%

ASN178.N-LYS127.O 55.00%

GLN238.NE2-ALA205.O 56.00%

THR169.OG1-ASP165.O 54.00%

ALA140.N-ALA136.O 57.00%

THR169.OG1-ASP165.O 53.50%

PHE128.N-GLN134.OE1 55.50%

TYR73.OH-VAL12.O 53.00%

MET170.N-VAL166.O 56.50%

LYS307.N-THR258.O 53.50%

SER246.OG-ASP303.OD1 55.50%

TYR84.N-PHE80.O 52.50%

LEU119.N-SER115.O 55.00%

MET170.N-VAL166.O 53.50%

TYR84.N-PHE80.O 54.00%

ARG285.N-THR292.O 52.00%

ARG184.NE-GLN238.OE1 54.50%

THR35.OG1-GLY33.O 52.50%

TYR73.OH-VAL12.O 54.00%

LEU88.N-TYR84.O 51.50%

THR302.N-ASN263.O 54.00%

ARG141.N-TYR137.O 52.50%

TYR155.OH-TYR73.O 53.50%

VAL189.N-THR232.O 51.50%

LEU174.N-MET170.O 53.50%

GLN233.N-VAL221.O 52.00%

LEU174.N-MET170.O 53.00%

MET85.N-LEU81.O 51.00%

GLU264.N-THR275.O 53.50%

PHE128.N-GLN134.OE1 51.50%

THR35.OG1-GLY33.O 53.00%

GLN233.N-VAL221.O 51.00%

VAL304.N-MET245.O 53.50%

ILE223.N-ALA231.O 51.00%

ARG285.N-THR292.O 52.00%

GLN238.NE2-ALA205.O 50.50%

MET85.N-LEU81.O 53.00%

TYR208.OH-GLN233.OE1 51.00%

THR103.N-GLN122.OE1 51.50%

VAL8.N-GLN20.O 49.50%

PHE128.N-GLN134.OE1 53.00%

TYR284.N-THR278.O 50.50%

ASN187.N-TYR234.O 51.50%

THR103.N-GLN122.OE1 49.50%

PHE305.N-CYS261.O 52.00%

GLN238.NE2-ALA205.O 50.50%

VAL99.N-LEU102.O 50.50%

ILE152.N-PHE148.O 49.50%

TYR284.N-THR278.O 50.50%

LEU118.N-LEU114.O 50.50%

MET85.N-LEU81.O 50.00%

PHE70.N-ARG66.O 49.00%

ASN187.N-TYR234.O 50.00%

MET85.N-LEU81.O 50.50%

LEU260.N-PHE305.O 50.00%

LEU119.N-SER115.O 48.50%

GLN233.N-VAL221.O 49.00%

TYR155.OH-TYR73.O 50.00%

TYR284.N-THR278.O 49.50%

MET24.N-LYS4.O 48.00%

LEU260.N-PHE305.O 49.00%

THR302.N-ASN263.O 49.00%

GLN122.NE2-LEU118.O 49.00%

ILE277.N-ALA262.O 48.00%

THR35.OG1-GLY33.O 48.00%

THR103.N-GLN122.OE1 48.50%

LEU151.N-ASN147.O 48.50%

ASP287.N-HIS290.O 47.00%

GLY220.N-ASN216.O 48.00%

ILE152.N-PHE148.O 48.50%

VAL185.N-GLN237.O 47.50%

LEU174.N-MET170.O 46.50%

TYR155.OH-TYR73.O 48.00%

VAL304.N-MET245.O 48.50%

GLU264.N-THR275.O 47.50%

TYR284.N-THR278.O 46.50%

ASN263.N-ASP303.O 48.00%

LEU88.N-TYR84.O 48.50%

GLN20.N-VAL8.O 47.50%

ASN129.N-HIS176.O 46.00%

VAL185.N-GLN237.O 48.00%

ASN187.N-TYR234.O 48.00%

ILE152.N-PHE148.O 47.50%

GLU264.N-THR275.O 45.50%

ASN129.N-HIS176.O 47.50%

ARG285.N-THR292.O 47.50%

SER104.N-PRO97.O 47.00%

SER104.N-PRO97.O 45.00%

SER104.N-PRO97.O 47.00%

GLN20.N-VAL8.O 47.00%

LEU88.N-TYR84.O 47.00%

GLN20.N-VAL8.O 45.00%

LYS307.N-THR258.O 47.00%

VAL99.N-LEU102.O 46.50%

VAL188.N-LYS196.O 47.00%

ARG141.N-TYR137.O 44.50%

THR169.OG1-ASP165.O 46.50%

ALA140.N-ALA136.O 45.50%

THR302.N-ASN263.O 46.00%

PHE128.N-GLN134.OE1 44.00%

LEU121.N-VAL117.O 46.50%

SER104.N-PRO97.O 45.50%

TYR265.N-PRO300.O 46.00%

LEU173.N-THR169.O 44.00%

GLN20.N-VAL8.O 46.00%

GLN238.NE2-SER240.OG 45.50%

VAL304.N-MET245.O 46.00%

TYR73.N-ALA69.O 43.00%

VAL188.N-LYS196.O 45.00%

ILE277.N-ALA262.O 45.00%

VAL189.N-THR232.O 45.50%

VAL185.N-GLN237.O 43.00%

ARG141.N-TYR137.O 45.00%

MET24.N-LYS4.O 44.50%

GLU135.N-PRO131.O 45.50%

TYR306.OH-LEU212.O 43.00%

GLN122.NE2-LEU118.O 45.00%

VAL185.N-GLN237.O 44.50%

ASN129.N-HIS176.O 45.00%

GLN122.NE2-LEU118.O 43.00%

GLN238.NE2-SER240.OG 45.00%

GLY53.N-LYS7.O 43.50%

ILE223.N-ALA231.O 44.00%

THR278.N-TYR284.O 43.00%

ARG285.N-THR292.O 44.00%

VAL189.N-THR232.O 43.50%

MET24.N-LYS4.O 44.00%

LEU260.N-PHE305.O 42.50%

ASP287.N-HIS290.O 43.50%

LEU37.N-ALA40.O 43.50%

ASN111.ND2-LYS106.O 44.00%

TYR234.N-ASN187.O 42.50%

LEU151.N-ASN147.O 43.00%

THR91.N-ALA87.O 43.50%

THR171.OG1-ARG167.O 43.50%

TYR265.N-PRO300.O 42.50%

ASN111.N-ALA108.O 43.00%

ASP287.N-HIS290.O 43.00%

TYR306.OH-LEU212.O 43.50%

VAL99.N-LEU102.O 42.50%

ILE223.N-ALA231.O 43.00%

GLU264.N-THR275.O 43.00%

PHE57.N-TYR36.O 43.00%

VAL304.N-MET245.O 42.50%

VAL189.N-THR232.O 41.00%

GLN122.NE2-LEU118.O 43.00%

GLY220.N-ASN216.O 43.00%

PHE57.N-TYR36.O 42.50%

GLN122.NE2-THR103.O 41.00%

TYR234.N-ASN187.O 42.50%

THR278.N-TYR284.O 42.00%

TYR84.OH-ASN147.OD1 42.50%

THR35.N-THR43.OG1 41.00%

TYR73.N-ALA69.O 42.50%

ASN16.N-ASP13.OD2 42.00%

ASN16.N-ASP13.OD1 42.00%

VAL221.N-GLN233.O 41.00%

TYR36.N-PHE57.O 42.50%

GLY53.N-LYS7.O 41.50%

ALA140.N-ALA136.O 42.00%

THR171.OG1-ARG167.O 40.50%

LEU260.N-PHE305.O 42.50%

ILE277.N-ALA262.O 41.50%

LEU37.N-ALA40.O 42.00%

VAL99.N-LEU102.O 40.50%

THR11.OG1-ASN16.O 42.00%

GLN233.N-VAL221.O 41.50%

THR35.N-THR43.OG1 41.50%

MET24.N-LYS4.O 39.50%

ALA136.N-ALA132.O 40.50%

ASP287.N-HIS290.O 41.00%

GLY220.N-ASN216.O 41.00%

TYR265.N-PRO300.O 39.50%

SER86.N-GLY82.O 40.00%

THR169.OG1-ASP165.O 41.00%

ALA132.N-TYR72.O 41.00%

TYR73.N-ALA69.O 39.00%

ASN129.N-HIS176.O 39.50%

GLN122.NE2-THR103.O 40.50%

LEU151.N-ASN147.O 41.00%

TYR36.N-PHE57.O 38.50%

PHE57.N-TYR36.O 39.50%

THR198.N-LEU186.O 40.50%

TYR265.OH-ASN268.O 41.00%

MET207.N-VAL203.O 38.50%

ASP23.N-GLN31.OE1 39.00%

VAL221.N-GLN233.O 40.50%

ILE223.N-ALA231.O 40.50%

LEU186.N-THR198.O 38.50%

(continued)

14.4 Concluding Remarks

455

Table 14.5 (continued) Model9-optimized

Model10-optimized

Model11-optimized

Model12-optimized

ARG184.N-LEU200.O 38.50%

LEU121.N-VAL117.O 40.00%

GLU135.N-PRO131.O 40.00%

THR91.N-ALA87.O 38.50%

VAL188.N-LYS196.O 38.00%

THR11.OG1-ASN16.O 39.50%

SER86.N-GLY82.O 40.00%

ILE152.N-PHE148.O 38.00%

ARG66.N-ASP62.O 37.50%

THR35.N-THR43.OG1 39.00%

THR10.N-HIS18.O 40.00%

THR198.N-LEU186.O 38.00%

LYS280.N-THR282.O 37.50%

TYR36.N-PHE57.O 39.00%

VAL221.N-GLN233.O 39.50%

LYS92.N-LEU88.O 37.50%

THR278.N-TYR284.O 37.50%

LEU37.N-ALA40.O 39.00%

THR91.N-ALA87.O 39.50%

LEU37.N-ALA40.O 36.00%

SER246.OG-ASP303.OD2 37.50%

LEU173.N-THR169.O 39.00%

THR198.N-LEU186.O 39.00%

ASN111.ND2-LYS106.O 35.50%

THR198.N-LEU186.O 37.00%

ARG141.N-TYR137.O 38.50%

SER246.OG-ASP303.OD2 39.00%

THR169.N-ASP165.O 35.50%

TYR297.OH-GLU264.OE1 36.50%

ARG66.N-ASP62.O 38.00%

GLN122.NE2-THR103.O 38.50%

ARG285.NE-GLU264.OE1 35.50%

VAL221.N-GLN233.O 36.50%

ALA120.N-SER116.O 38.00%

GLY210.N-SER246.O 38.00%

ASP23.N-GLN31.OE1 35.00%

TYR297.OH-GLU264.OE2 36.50%

MET207.N-VAL203.O 38.00%

GLY53.N-LYS7.O 38.00%

ARG184.N-LEU200.O 35.00%

GLY210.N-SER246.O 36.50%

SER156.OG-ILE152.O 38.00%

GLN238.NE2-SER240.OG 37.50%

THR11.OG1-ASN16.O 34.50%

HIS51.N-HIS48.O 35.50%

GLN238.NE2-SER240.OG 38.00%

GLN134.N-ALA130.O 37.50%

GLU135.N-PRO131.O 34.50%

ASN111.N-ALA108.O 35.50%

ALA247.N-THR302.O 37.50%

ASN263.ND2-ASP303.OD1 37.50%

ILE277.N-ALA262.O 34.50%

TYR265.N-PRO300.O 35.50%

TYR297.OH-GLU264.OE1 37.50%

LYS92.N-LEU88.O 37.00%

GLY210.N-SER246.O 34.50%

MET207.N-VAL203.O 35.00%

TYR84.OH-ASN147.OD1 37.50%

ARG66.N-ASP62.O 36.50%

ASN16.ND2-ASP13.OD2 34.50%

VAL22.N-ILE6.O 34.50%

ASN178.N-LYS127.O 36.50%

THR91.OG1-ALA146.O 36.50%

ARG66.N-ASP62.O 34.00%

TYR137.N-LEU133.O 34.50%

TYR73.N-ALA69.O 36.00%

THR275.N-GLU264.O 36.50%

THR91.OG1-ALA146.O 34.00%

THR35.N-THR43.OG1 34.50%

THR91.N-ALA87.O 36.00%

TYR297.OH-GLU264.OE1 36.50%

SER156.N-ILE152.O 34.00%

GLN122.NE2-THR103.O 34.50%

ARG184.N-LEU200.O 35.50%

TYR208.OH-GLN233.OE1 36.50%

HIS51.N-HIS48.O 34.00%

LYS158.N-LEU153.O 34.50%

SER86.N-GLY82.O 35.50%

SER67.N-ASP63.O 36.00%

TYR252.N-GLY299.O 34.00%

PHE70.N-ARG66.O 34.00%

ASP23.N-GLN31.OE1 35.50%

TYR36.N-PHE57.O 35.50%

CYS149.N-ALA145.O 33.50%

GLU168.N-ASP165.OD1 33.50%

LYS92.N-LEU88.O 35.00%

TYR297.OH-GLU264.OE2 35.00%

SER116.OG-ASN263.OD1 33.50%

THR10.N-HIS18.O 33.00%

ALA132.N-TYR72.O 35.00%

VAL22.N-ILE6.O 35.00%

ALA132.N-TYR72.O 33.00%

GLN134.N-ALA130.O 33.00%

ASN89.N-MET85.O 34.50%

LYS307.N-THR258.O 35.00%

TYR297.OH-GLU264.OE2 33.00%

GLU135.N-PRO131.O 33.00%

THR292.N-ARG285.O 34.50%

THR302.OG1-ALA247.O 35.00%

THR278.N-TYR284.O 33.00%

PHE9.N-LYS54.O 32.50%

PHE70.N-ARG66.O 34.50%

ASN187.N-TYR234.O 34.00%

SER246.OG-ASP303.OD1 33.00%

THR171.OG1-ARG167.O 32.50%

LEU186.N-THR198.O 34.00%

ASN111.ND2-LYS106.O 34.00%

VAL22.N-ILE6.O 33.00%

SER67.N-ASP63.O 32.00%

PHE9.N-LYS54.O 34.00%

HIS51.N-HIS48.O 33.50%

GLU239.N-LYS183.O 32.00%

TYR28.OH-HIS51.ND1 32.00%

TYR137.N-LEU133.O 33.50%

CYS149.N-ALA145.O 33.00%

PHE70.N-ARG66.O 32.00%

THR302.OG1-ASP303.OD1 32.00%

LEU124.N-ALA120.O 33.50%

MET207.N-VAL203.O 33.00%

TYR306.OH-LEU212.O 32.00%

ALA120.N-SER116.O 31.50%

SER67.N-ASP63.O 33.00%

LYS183.N-GLU239.O 33.00%

TYR297.OH-GLU264.OE1 32.00%

CYS149.N-ALA145.O 31.50%

TYR28.OH-HIS51.ND1 32.50%

ALA231.N-ILE223.O 32.50%

THR10.N-HIS18.O 32.00%

LEU186.N-THR198.O 31.50%

VAL22.N-ILE6.O 32.50%

VAL188.N-LYS196.O 32.50%

ARG83.NE-SER79.OG 32.00%

ARG83.NE-SER79.OG 31.50%

LYS280.N-THR282.O 32.00%

LEU186.N-THR198.O 32.50%

GLY53.N-LYS7.O 31.50%

SER156.OG-ILE152.O 31.50%

ARG285.NH2-GLU264.OE2 31.50%

ASP23.N-GLN31.OE1 32.00%

PHE9.N-LYS54.O 31.50%

ASN16.N-ASP13.OD2 31.00%

TYR252.N-GLY299.O 31.00%

TYR137.N-LEU133.O 32.00%

TYR28.OH-HIS51.ND1 31.00%

SER156.N-ILE152.O 31.00%

SER25.N-ASP23.OD1 30.50%

LYS158.NZ-LEU163.O 31.50%

ARG285.NH2-GLU264.OE2 31.00%

ALA231.N-ILE223.O 31.00%

ASN263.ND2-ASP303.OD2 30.50%

THR171.OG1-ARG167.O 31.00%

LEU254.N-TYR297.O 30.50%

LEU235.N-LEU217.O 31.00%

HIS51.N-HIS48.O 30.50%

GLU168.N-ASP165.OD2 30.50%

LEU173.N-THR169.O 30.50%

LEU173.N-THR169.O 30.50%

LEU235.N-LEU217.O 30.50%

THR292.N-ARG285.O 30.50%

SER156.OG-ILE152.O 30.50%

SER240.OG-GLU308.O 30.50%

TYR297.OH-GLU264.OE2 30.00%

TYR72.OH-GLU135.OE2 29.50%

ASN110.ND2-GLY161.O 30.50%

ASN89.N-MET85.O 30.50%

VAL42.N-THR35.O 30.00%

SER104.OG-GLY288.O 29.50%

ASN263.ND2-ASP303.OD2 30.00%

LEU151.N-ASN147.O 30.00%

THR10.N-HIS18.O 30.00%

SER25.N-ASP23.OD1 29.50%

SER67.N-ASP63.O 30.00%

LYS183.N-GLU239.O 30.00%

LYS183.N-GLU239.O 30.00%

MET294.N-LEU283.O 29.50%

TYR306.N-VAL243.O 29.50%

Chapter 15

3CLpro Binding with N3/Lopinavir/Ritonavir

Abstract This brief chapter is to do molecular dynamics (MD) studies on SARSCoV-2 3CLpro binding with three inhibitors N3, lopinavir, and ritonavir, respectively, and to do optimization studies on SARS-CoV-2 Mpro binding with top 100 compounds, respectively. Here, we present a note of results of studies: the catalytic dyad (HIS41 and CYS145) residues and the strong polar contact ARG40-ASP187 , etc. are always constructing a binding cavity for the inhibitors/compounds. SARSCoV-2 3CLpro is an attractive drug target against COVID-19; the note of structural bioinformatics presented by this brief chapter might be useful or helpful to drug designers. Keywords MD and optimization studies · SARS-CoV-2 3CLpro · 3CLpro-binding site · Top 100 compounds · Drug designing or discovery

15.1 Introduction SARS-CoV-2 3C-like protease (3CLpro) or called main protease (Mpro) is a key coronavirus enzyme (which plays a pivotal role in mediating viral replication and transcription) for the maturation of viral particles and an attractive drug target against COVID-19. In Sect. 2.3.2 of Chap. 2, we did MD studies on SARS-CoV2 3CLpro dimer (with unliganded active site/without ligand – we denoted as the 6Y84-dimer model and the 6LU7-dimer model ), without any binding. This chapter is doing MD and optimization studies on some bindings of SARS-CoV-2 3CLpro with inhibitors (such as N3, lopinavir, and ritonavir) and with top 100 drugs.

© The Author(s), under exclusive license to Springer Nature Switzerland AG 2023 J. Zhang, Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures, Springer Series in Biophysics 23, https://doi.org/10.1007/978-3-031-36773-1_15

457

458

15 3CLpro Binding with N3/Lopinavir/Ritonavir

15.2 Materials and Methods 15.2.1 N3 at the Binding Pocket of SARS-CoV-2 Mpro “Data includes all of the trajectories (1000) of classical all-atom MD simulations of inhibitor N3 at the binding pocket of SARS-CoV2 main protease target (PDB ID: 6LU7). In order to decrease the size of the file only protein and ligand trajectories were provided. Simulation has been performed with Desmond. Proteinligand complexes were obtained from RCSB PDB (PDB ID: 6LU7). Complex was placed in the cubic boxes with explicit TIP3P water models that have 10.0 Å thickness from surfaces of protein. The system is neutralized by adding counter ions, and salt solution of 0.15M NaCl was also used to adjust the concentration of the systems. The long-range electrostatic interactions were calculated by the particle mesh Ewald method. A cut-off radius of 9.0 Å was used for both van der Waals and Coulombic interactions. The temperature was set as 310 K initially, and NoseHoover thermostat was used for adjustment. Martyna-Tobias-Klein protocol was employed to control the pressure, which was set at 1.01325 bar. The time-step was assigned as 2.0 fs. The default values were used for minimization and equilibration steps, and finally 100 ns production run was performed for the simulations” [102] – we denote as the N3-model.

15.2.2 Lopinavir at the Binding Pocket of SARS-CoV-2 Mpro “Data includes all of the trajectories (2000) of classical all-atom MD simulations of Lopinavir at the binding pocket of SARS-CoV-2 main protease target. In order to decrease the size of the file, only protein and ligand trajectories were provided. Simulation has been performed with Desmond. Protein-ligand complexes were obtained by Glide/SP docking program. Complex was placed in the cubic boxes with explicit TIP3P water models that have 10.0 Å thickness from surfaces of protein. The system is neutralized by adding counter ions, and salt solution of 0.15M NaCl was also used to adjust the concentration of the systems. The long-range electrostatic interactions were calculated by the particle mesh Ewald method. A cut-off radius of 9.0 Å was used for both van der Waals and Coulombic interactions. The temperature was set as 310 K initially, and Nose-Hoover thermostat was used for adjustment. Martyna-Tobias-Klein protocol was employed to control the pressure, which was set at 1.01325 bar. The time-step was assigned as 2.0 fs. The default values were used for minimization and equilibration steps, and finally 500 ns production run was performed for the simulations” [103] – we denote as the Lopinavir-model.

15.2 Materials and Methods

459

15.2.3 Ritonavir at the Binding Pocket of SARS-CoV-2 Mpro “Data includes all of the trajectories (2000) of classical all-atom MD simulations of Ritonavir at the binding pocket of SARS-CoV2 main protease target. In order to decrease the size of the file only protein and ligand trajectories were provided. Simulation has been performed with Desmond. Protein-ligand complexes were obtained by Glide/SP docking program. Complex was placed in the cubic boxes with explicit TIP3P water models that have 10.0 Å thickness from surfaces of protein. The system is neutralized by adding counter ions, and salt solution of 0.15M NaCl was also used to adjust the concentration of the systems. The long-range electrostatic interactions were calculated by the particle mesh Ewald method. A cut-off radius of 9.0 Å was used for both van der Waals and Coulombic interactions. The temperature was set as 310 K initially, and Nose-Hoover thermostat was used for adjustment. Martyna-Tobias-Klein protocol was employed to control the pressure, which was set at 1.01325 bar. The time-step was assigned as 2.0 fs. The default values were used for minimization and equilibration steps, and finally 500 ns production run was performed for the simulation” [104] – we denote as the Ritonavir-model.

15.2.4 Top 100 Drugs Binding with SARS-CoV-2 Mpro “7922 compounds were downloaded from NPC database (https://tripod.nih.gov/ npc/). In order to eliminate the non-specific binders, some criteria including molecular weight, between 100–1000 g/mol; number of rotatable bonds, .