ArticleJournal of structural biology2020
A graph-based approach identifies dynamic H-bond communication networks in spike protein S of SARS-CoV-2.
Article in Journal of structural biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 29 citations in OpenAlex.
- The protein-water H-bond network for bacterial response regulator REC domain activation.Journal of structural biology: X · 2026Article
- Graph-Based Analyses of Dynamic Water-Mediated Hydrogen-Bond Networks in Phosphatidylserine: Cholesterol Membranes.Biomolecules · 2023Article
- Protons taken hostage: Dynamic H-bond networks of the pH-sensing GPR68.Computational and structural biotechnology journal · 2023Article
- The Solvation of theInternational journal of molecular sciences · 2022Article
- Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2.Chemical reviews · 2022Review
- Structural insights in cell-type specific evolution of intra-host diversity by SARS-CoV-2.Nature communications · 2022Article
- Factors underlying asymmetric pore dynamics of disaggregase and microtubule-severing AAA+ machines.Biophysical journal · 2021Article
- Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants.PLoS computational biology · 2021Article
- Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease.Chemical science · 2021Article
- Proton-Binding Motifs of Membrane-Bound Proteins: From Bacteriorhodopsin to Spike Protein S.Frontiers in chemistry · 2021Article
- Phosphatidylglyerol Lipid Binding at the Active Site of an Intramembrane Protease.The Journal of membrane biology · 2020Review
- Tuning Proton Transfer Thermodynamics in SARS-Cov-2 Main Protease: Implications for Catalysis and Inhibitor Design.ChemRxiv : the preprint server for chemistry · 2020Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Corona virus spike protein S is a large homo-trimeric protein anchored in the membrane of the virion particle. Protein S binds to angiotensin-converting-enzyme 2, ACE2, of the host cell, followed by proteolysis of the spike protein, drastic protein conformational change with exposure of the fusion peptide of the virus, and entry of the virion into the host cell. The structural elements that govern conformational plasticity of the spike protein are largely unknown. Here, we present a methodology that relies upon graph and centrality analyses, augmented by bioinformatics, to identify and characterize large H-bond clusters in protein structures. We apply this methodology to protein S ectodomain and find that, in the closed conformation, the three protomers of protein S bring the same contribution to an extensive central network of H-bonds, and contribute symmetrically to a relatively large H-bond cluster at the receptor binding domain, and to a cluster near a protease cleavage site. Markedly different H-bonding at these three clusters in open and pre-fusion conformations suggest dynamic H-bond clusters could facilitate structural plasticity and selection of a protein S protomer for binding to the host receptor, and proteolytic cleavage. From analyses of spike protein sequences we identify patches of histidine and carboxylate groups that could be involved in transient proton binding.
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