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Ionization of D571 Is Coupled with SARS-CoV-2 Spike Up/Down Equilibrium Revealing the pH-Dependent Allosteric Mechanism of Receptor-Binding Domains.
Li, Tong; Yu, Lan; Sun, Jingfang; Liu, Jinfeng; He, Xiao.
  • Li T; School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
  • Yu L; School of Science, China Pharmaceutical University, Nanjing 210009, China.
  • Sun J; School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
  • Liu J; School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
  • He X; Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.
J Phys Chem B ; 126(26): 4828-4839, 2022 07 07.
Article in English | MEDLINE | ID: covidwho-1900410
ABSTRACT
As a type I viral fusion protein, SARS-CoV-2 spike undergoes a pH-dependent switch to mediate the endosomal positioning of the receptor-binding domain to facilitate viral entry into cells and immune evasion. Gaps in our knowledge concerning the conformational transitions and key intramolecular motivations have hampered the development of effective therapeutics against the virus. To clarify the pH-sensitive elements on spike-gating the receptor-binding domain (RBD) opening and understand the details of the RBD opening transition, we performed microsecond-time scale constant pH molecular dynamics simulations in this study. We identified the deeply buried D571 with a clear pKa shift, suggesting a potential pH sensor, and showed the coupling of ionization of D571 with spike RBD-up/down equilibrium. We also computed the free-energy landscape for RBD opening and identified the crucial interactions that influence RBD dynamics. The atomic-level characterization of the pH-dependent spike activation mechanism provided herein offers new insights for a better understanding of the fundamental mechanisms of SARS-CoV-2 viral entry and infection and hence supports the discovery of novel therapeutics for COVID-19.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Limits: Humans Language: English Journal: J Phys Chem B Journal subject: Chemistry Year: 2022 Document Type: Article Affiliation country: Acs.jpcb.2c02365

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Limits: Humans Language: English Journal: J Phys Chem B Journal subject: Chemistry Year: 2022 Document Type: Article Affiliation country: Acs.jpcb.2c02365