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-Reference-Cited by-同舟云学术

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

Published:2024-05-02 Issue:19 Volume:128 Page:4696-4715
ISSN:1520-6106
Container-title:The Journal of Physical Chemistry B
language:en
Short-container-title:J. Phys. Chem. B

Author:

Raisinghani Nishank¹,Alshahrani Mohammed¹,Gupta Grace¹,Xiao Sian²^ORCID,Tao Peng²^ORCID,Verkhivker Gennady¹³^ORCID

Affiliation:

1. Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States

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

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

Funder

National Institute of Allergy and Infectious Diseases

National Institutes of Health

National Institute of General Medical Sciences

Publisher

American Chemical Society (ACS)

Link

https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.4c01341

Reference109 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

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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