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Journal of the American Chemical Society. 2021 Aug 4;143(30):11349-11360. doi: 10.1021/jacs.1c00556 Q115.62025

Free Energy Landscapes from SARS-CoV-2 Spike Glycoprotein Simulations Suggest that RBD Opening Can Be Modulated via Interactions in an Allosteric Pocket

针对SARS-CoV-2刺突糖蛋白的模拟表明,作用于别构袋中的相互作用可以调节RBD开启状态——自由能量景观分析法 翻译改进

Lucy Fallon  1  2, Kellon A A Belfon  1  2, Lauren Raguette  1  2, Yuzhang Wang  1  2, Darya Stepanenko  1  3, Abbigayle Cuomo  2, Jose Guerra  4, Stephanie Budhan  2, Sarah Varghese  5, Christopher P Corbo  6, Robert C Rizzo  1  3, Carlos Simmerling  1  2

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作者单位

  • 1 Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States.
  • 2 Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States.
  • 3 Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, United States.
  • 4 Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794, United States.
  • 5 Undergraduate Program in Biology, Stony Brook University, Stony Brook, New York 11794, United States.
  • 6 Graduate Program in Molecular and Cellular Pharmacology, Stony Brook University, Stony Brook, New York 11794, United States.
  • DOI: 10.1021/jacs.1c00556 PMID: 34270232

    摘要 Ai翻译

    The SARS-CoV-2 coronavirus is an enveloped, positive-sense single-stranded RNA virus that is responsible for the COVID-19 pandemic. The spike is a class I viral fusion glycoprotein that extends from the viral surface and is responsible for viral entry into the host cell and is the primary target of neutralizing antibodies. The receptor binding domain (RBD) of the spike samples multiple conformations in a compromise between evading immune recognition and searching for the host-cell surface receptor. Using atomistic simulations of the glycosylated wild-type spike in the closed and 1-up RBD conformations, we map the free energy landscape for RBD opening and identify interactions in an allosteric pocket that influence RBD dynamics. The results provide an explanation for experimental observation of increased antibody binding for a clinical variant with a substitution in this pocket. Our results also suggest the possibility of allosteric targeting of the RBD equilibrium to favor open states via binding of small molecules to the hinge pocket. In addition to potential value as experimental probes to quantify RBD conformational heterogeneity, small molecules that modulate the RBD equilibrium could help explore the relationship between RBD opening and S1 shedding.

    Keywords:sars-cov-2 spike glycoprotein; free energy landscapes; allosteric pocket

    Copyright © Journal of the American Chemical Society. 中文内容为AI机器翻译,仅供参考!

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    期刊名:Journal of the american chemical society

    缩写:J AM CHEM SOC

    ISSN:0002-7863

    e-ISSN:1520-5126

    IF/分区:15.6/Q1

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    Free Energy Landscapes from SARS-CoV-2 Spike Glycoprotein Simulations Suggest that RBD Opening Can Be Modulated via Interactions in an Allosteric Pocket