A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causative agent of the coronavirus disease 2019 (COVID-19) pandemic, is thought to release its RNA genome at either the cell surface or within endosomes, the balance being dependent on spike protein stability, and the complement of receptors, co-receptors and proteases. To investigate possible mediators of pH-dependence, pKa calculations have been made on a set of structures for spike protein ectodomain and fragments from SARS-CoV-2 and other coronaviruses. Dominating a heat map of the aggregated predictions, three histidine residues in S2 are consistently predicted as destabilizing in pre-fusion (all three) and post-fusion (two of the three) structures. Other predicted features include the more moderate energetics of surface salt–bridge interactions and sidechain–mainchain interactions. Two aspartic acid residues in partially buried salt-bridges (D290–R273 and R355–D398) have pKas that are calculated to be elevated and destabilizing in more open forms of the spike trimer. These aspartic acids are most stabilized in a tightly closed conformation that has been observed when linoleic acid is bound, and which also affects the interactions of D614. The D614G mutation is known to modulate the balance of closed to open trimer. It is suggested that D398 in particular contributes to a pH-dependence of the open/closed equilibrium, potentially coupled to the effects of linoleic acid binding and D614G mutation, and possibly also A570D mutation. These observations are discussed in the context of SARS-CoV-2 infection, mutagenesis studies, and other human coronaviruses.

[1]  Xavier Robert,et al.  Deciphering key features in protein structures with the new ENDscript server , 2014, Nucleic Acids Res..

[2]  G. Leung,et al.  Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020 , 2021, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[3]  A. Mulholland,et al.  Free fatty acid binding pocket in the locked structure of SARS-CoV-2 spike protein , 2020, Science.

[4]  Spike Glycoprotein and Host Cell Determinants of SARS-CoV-2 Entry and Cytopathic Effects , 2020, Journal of Virology.

[5]  Jim Warwicker,et al.  Protein-sol pKa: prediction of electrostatic frustration, with application to coronaviruses , 2020, Bioinform..

[6]  Qiang Zhou,et al.  Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2 , 2020, Science.

[7]  G. Whittaker,et al.  Proteolytic Cleavage of the SARS-CoV-2 Spike Protein and the Role of the Novel S1/S2 Site , 2020, iScience.

[8]  Yongfei Cai,et al.  Structural impact on SARS-CoV-2 spike protein by D614G substitution , 2020, bioRxiv.

[9]  Simon C. Potter,et al.  The EMBL-EBI search and sequence analysis tools APIs in 2019 , 2019, Nucleic Acids Res..

[10]  B. Graham,et al.  Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation , 2020, Science.

[11]  D. Higgins,et al.  Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.

[12]  Nathan A. Baker,et al.  Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins. , 2016, Methods in enzymology.

[13]  G. Whittaker,et al.  Physiological and molecular triggers for SARS-CoV membrane fusion and entry into host cells , 2017, Virology.

[14]  Pardis C Sabeti,et al.  Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant , 2020, Cell.

[15]  Sarah L. Williams,et al.  Progress in the prediction of pKa values in proteins , 2011, Proteins.

[16]  Jim Warwicker,et al.  Improved pKa calculations through flexibility based sampling of a water‐dominated interaction scheme , 2004, Protein science : a publication of the Protein Society.

[17]  Peter B Rosenthal,et al.  Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion , 2020, Nature.

[18]  M. Maes,et al.  Can endolysosomal deacidification and inhibition of autophagy prevent severe COVID-19? , 2020, Life Sciences.

[19]  N. Guex,et al.  SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling , 1997, Electrophoresis.

[20]  Eytan Ruppin,et al.  Discovery of SARS-CoV-2 Antivirals through Large-scale Drug Repositioning , 2020, Nature.

[21]  A thermostable, closed SARS-CoV-2 spike protein trimer , 2020, Nature Structural & Molecular Biology.

[22]  Jared Adolf-Bryfogle,et al.  CoV3D: a database of high resolution coronavirus protein structures , 2020, Nucleic Acids Res..

[23]  B. Haynes,et al.  Cold sensitivity of the SARS-CoV-2 spike ectodomain , 2020, Nature Structural & Molecular Biology.

[24]  Haruki Nakamura,et al.  The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data , 2006, Nucleic Acids Res..

[25]  Daniel Wrapp,et al.  Stabilized coronavirus spikes are resistant to conformational changes induced by receptor recognition or proteolysis , 2018, Scientific Reports.

[26]  R. Friesner,et al.  Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains , 2020, Cell Host & Microbe.

[27]  Wei Chen,et al.  Recent development and application of constant pH molecular dynamics , 2014, Molecular simulation.

[28]  M. Gilson,et al.  Prediction of pH-dependent properties of proteins. , 1994, Journal of molecular biology.

[29]  The UniProt Consortium,et al.  UniProt: a worldwide hub of protein knowledge , 2018, Nucleic Acids Res..

[30]  J. Geiger,et al.  Janus sword actions of chloroquine and hydroxychloroquine against COVID-19 , 2020, Cellular Signalling.

[31]  S. Rawson,et al.  Distinct conformational states of SARS-CoV-2 spike protein , 2020, Science.

[32]  Douglas E. V. Pires,et al.  Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource , 2020, Nature Genetics.

[33]  T. Ideker,et al.  Functional Landscape of SARS-CoV-2 Cellular Restriction , 2020, bioRxiv.

[34]  B. Haynes,et al.  D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction , 2020, Cell Reports.

[35]  J. Skehel,et al.  Structural transitions in influenza haemagglutinin at membrane fusion pH , 2020, Nature.

[36]  Pardis C Sabeti,et al.  Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant , 2020, bioRxiv.

[37]  Sepideh Parvizpour,et al.  A domain-based vaccine construct against SARS-CoV-2, the causative agent of COVID-19 pandemic: development of self-amplifying mRNA and peptide vaccines , 2020, BioImpacts : BI.