Ionization of D571 Is Coupled with SARS-CoV-2 Spike Up/Down Equilibrium Revealing the pH-Dependent Allosteric Mechanism of Receptor-Binding Domains
pmid: 35736566
Ionization of D571 Is Coupled with SARS-CoV-2 Spike Up/Down Equilibrium Revealing the pH-Dependent Allosteric Mechanism of Receptor-Binding Domains
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.
- New York University United States
- East China Normal University China (People's Republic of)
- China Pharmaceutical University China (People's Republic of)
- New York University Shanghai China (People's Republic of)
Protein Domains, SARS-CoV-2, Spike Glycoprotein, Coronavirus, COVID-19, Humans, Angiotensin-Converting Enzyme 2, Hydrogen-Ion Concentration, Molecular Dynamics Simulation, Protein Binding
Protein Domains, SARS-CoV-2, Spike Glycoprotein, Coronavirus, COVID-19, Humans, Angiotensin-Converting Enzyme 2, Hydrogen-Ion Concentration, Molecular Dynamics Simulation, Protein Binding
2 Research products, page 1 of 1
- 2020IsRelatedTo
- 2020IsRelatedTo
citations This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).6 popularity This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.Top 10% influence This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).Average impulse This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.Top 10%
