Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variant Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms-Reference-Cited by-同舟云学术

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Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variant Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms

Published:2023-08-07 Issue:16 Volume:63 Page:5272-5296
ISSN:1549-9596
Container-title:Journal of Chemical Information and Modeling
language:en
Short-container-title:J. Chem. Inf. Model.

Author:

Xiao Sian¹^ORCID,Alshahrani Mohammed²,Gupta Grace²,Tao Peng¹^ORCID,Verkhivker Gennady²³^ORCID

Affiliation:

1. Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States

2. Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States

3. Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States

Funder

Kay Family Foundation

National Institute of General Medical Sciences

Publisher

American Chemical Society (ACS)

Subject

Library and Information Sciences,Computer Science Applications,General Chemical Engineering,General Chemistry

Link

https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.3c00778

Reference145 articles.

1. Characterization of the receptor-binding domain (RBD) of 2019 novel coronavirus: implication for development of RBD protein as a viral attachment inhibitor and vaccine

2. Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2

3. Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

4. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

5. Distinct conformational states of SARS-CoV-2 spike protein

Cited by 12 articles. 订阅此论文施引文献订阅此论文施引文献，注册后可以免费订阅5篇论文的施引文献，订阅后可以查看论文全部施引文献

1. AlphaFold2 Modeling and Molecular Dynamics Simulations of the Conformational Ensembles for the SARS-CoV-2 Spike Omicron JN.1, KP.2 and KP.3 Variants: Mutational Profiling of Binding Energetics Reveals Epistatic Drivers of the ACE2 Affinity and Escape Hotspots of Antibody Resistance;Viruses;2024-09-13

2. Atomistic Prediction of Structures, Conformational Ensembles and Binding Energetics for the SARS-CoV-2 Spike JN.1, KP.2 and KP.3 Variants Using AlphaFold2 and Molecular Dynamics Simulations: Mutational Profiling and Binding Free Energy Analysis Reveal Epistatic Hotspots of the ACE2 Affinity and Immune Escape;2024-07-10

3. AlphaFold2 Predictions of Conformational Ensembles and Atomistic Simulations of the SARS-CoV-2 Spike XBB Lineages Reveal Epistatic Couplings between Convergent Mutational Hotspots that Control ACE2 Affinity;The Journal of Physical Chemistry B;2024-05-02

4. Ensemble-Based Mutational Profiling and Network Analysis of the SARS-CoV-2 Spike Omicron XBB Lineages for Interactions with the ACE2 Receptor and Antibodies: Cooperation of Binding Hotspots in Mediating Epistatic Couplings Underlies Binding Mechanism and Immune Escape;International Journal of Molecular Sciences;2024-04-12

5. Predicting Functional Conformational Ensembles and Binding Mechanisms of Convergent Evolution for SARS-CoV-2 Spike Omicron Variants Using AlphaFold2 Sequence Scanning Adaptations and Molecular Dynamics Simulations;2024-04-03

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