{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T01:37:22Z","timestamp":1778636242250,"version":"3.51.4"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,2,26]],"date-time":"2021-02-26T00:00:00Z","timestamp":1614297600000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000266","name":"UK Engineering and Physical Sciences Research Council","doi-asserted-by":"crossref","award":["EP\/N024796\/1"],"award-info":[{"award-number":["EP\/N024796\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,3,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>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\u2013bridge interactions and sidechain\u2013mainchain interactions. Two aspartic acid residues in partially buried salt-bridges (D290\u2013R273 and R355\u2013D398) 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.<\/jats:p>","DOI":"10.1093\/bib\/bbab056","type":"journal-article","created":{"date-parts":[[2021,2,3]],"date-time":"2021-02-03T23:04:18Z","timestamp":1612393458000},"page":"1499-1507","source":"Crossref","is-referenced-by-count":22,"title":["A model for pH coupling of the SARS-CoV-2 spike protein open\/closed equilibrium"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1302-0815","authenticated-orcid":false,"given":"Jim","family":"Warwicker","sequence":"first","affiliation":[{"name":"School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,2,25]]},"reference":[{"key":"2021032314364184000_ref1","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.virol.2017.12.015","article-title":"Physiological and molecular triggers for SARS-CoV membrane fusion and entry into host cells","volume":"517","author":"Millet","year":"2018","journal-title":"Virology"},{"key":"2021032314364184000_ref2","doi-asserted-by":"crossref","first-page":"15701","DOI":"10.1038\/s41598-018-34171-7","article-title":"Stabilized coronavirus spikes are resistant to conformational changes induced by receptor recognition or proteolysis","volume":"8","author":"Kirchdoerfer","year":"2018","journal-title":"Sci Rep"},{"key":"2021032314364184000_ref3","doi-asserted-by":"crossref","first-page":"1444","DOI":"10.1126\/science.abb2762","article-title":"Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2","volume":"367","author":"Yan","year":"2020","journal-title":"Science"},{"key":"2021032314364184000_ref4","doi-asserted-by":"crossref","first-page":"101212","DOI":"10.1016\/j.isci.2020.101212","article-title":"Proteolytic cleavage of the SARS-CoV-2 spike protein and the role of the novel S1\/S2 site","volume":"23","author":"Jaimes","year":"2020","journal-title":"iScience"},{"key":"2021032314364184000_ref5","doi-asserted-by":"crossref","first-page":"118541","DOI":"10.1016\/j.lfs.2020.118541","article-title":"Can endolysosomal deacidification and inhibition of autophagy prevent severe COVID-19?","volume":"262","author":"Morris","year":"2020","journal-title":"Life Sci"},{"key":"2021032314364184000_ref6","doi-asserted-by":"crossref","first-page":"109706","DOI":"10.1016\/j.cellsig.2020.109706","article-title":"Janus sword actions of chloroquine and hydroxychloroquine against COVID-19","volume":"73","author":"Chen","year":"2020","journal-title":"Cell Signal"},{"key":"2021032314364184000_ref7","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1038\/s41586-020-2333-6","article-title":"Structural transitions in influenza haemagglutinin at membrane fusion pH","volume":"583","author":"Benton","year":"2020","journal-title":"Nature"},{"key":"2021032314364184000_ref8","doi-asserted-by":"crossref","first-page":"D301","DOI":"10.1093\/nar\/gkl971","article-title":"The worldwide protein data Bank (wwPDB): ensuring a single, uniform archive of PDB data","volume":"35","author":"Berman","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2021032314364184000_ref9","doi-asserted-by":"crossref","first-page":"D282","DOI":"10.1093\/nar\/gkaa731","article-title":"CoV3D: a database of high resolution coronavirus protein structures","volume":"49","author":"Gowthaman","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2021032314364184000_ref10","doi-asserted-by":"crossref","first-page":"1586","DOI":"10.1126\/science.abd4251","article-title":"Distinct conformational states of SARS-CoV-2 spike protein","volume":"369","author":"Cai","year":"2020","journal-title":"Science"},{"key":"2021032314364184000_ref11","doi-asserted-by":"crossref","first-page":"1295","DOI":"10.1016\/j.cell.2020.08.012","article-title":"Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding","volume":"182","author":"Starr","year":"2020","journal-title":"Cell"},{"key":"2021032314364184000_ref12","doi-asserted-by":"crossref","first-page":"65","DOI":"10.34172\/bi.2021.11","article-title":"A domain-based vaccine construct against SARS-CoV-2, the causative agent of COVID-19 pandemic: development of self-amplifying mRNA and peptide vaccines","volume":"11","author":"Pourseif","year":"2021","journal-title":"Bioimpacts"},{"key":"2021032314364184000_ref13","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1038\/s41586-020-2577-1","article-title":"Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing","volume":"586","author":"Riva","year":"2020","journal-title":"Nature"},{"key":"2021032314364184000_ref14","doi-asserted-by":"crossref","first-page":"3260","DOI":"10.1002\/prot.23189","article-title":"Progress in the prediction of pKa values in proteins","volume":"79","author":"Alexov","year":"2011","journal-title":"Proteins"},{"key":"2021032314364184000_ref15","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1006\/jmbi.1994.1301","article-title":"Prediction of pH-dependent properties of proteins","volume":"238","author":"Antosiewicz","year":"1994","journal-title":"J Mol Biol"},{"key":"2021032314364184000_ref16","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/bs.mie.2016.05.052","article-title":"Continuum electrostatics approaches to calculating pKas and ems in proteins","volume":"578","author":"Gunner","year":"2016","journal-title":"Methods Enzymol"},{"key":"2021032314364184000_ref17","doi-asserted-by":"crossref","first-page":"830","DOI":"10.1080\/08927022.2014.907492","article-title":"Recent development and application of constant pH molecular dynamics","volume":"40","author":"Chen","year":"2014","journal-title":"Mol Simulation"},{"key":"2021032314364184000_ref18","doi-asserted-by":"crossref","first-page":"2793","DOI":"10.1110\/ps.04785604","article-title":"Improved pKa calculations through flexibility based sampling of a water-dominated interaction scheme","volume":"13","author":"Warwicker","year":"2004","journal-title":"Protein Sci"},{"key":"2021032314364184000_ref19","doi-asserted-by":"crossref","first-page":"5112","DOI":"10.1093\/bioinformatics\/btaa646","article-title":"Protein-sol pKa: prediction of electrostatic frustration, with application to coronaviruses","volume":"36","author":"Hebditch","year":"2020","journal-title":"Bioinformatics"},{"key":"2021032314364184000_ref20","doi-asserted-by":"crossref","first-page":"1260","DOI":"10.1126\/science.abb2507","article-title":"Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation","volume":"367","author":"Wrapp","year":"2020","journal-title":"Science"},{"key":"2021032314364184000_ref21","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1016\/j.chom.2020.11.004","article-title":"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","volume":"28","author":"Zhou","year":"2020","journal-title":"Cell Host Microbe"},{"key":"2021032314364184000_ref22","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1016\/j.cell.2020.09.032","article-title":"Structural and functional analysis of the D614G SARS-CoV-2 spike protein variant","volume":"183","author":"Yurkovetskiy","year":"2020","journal-title":"Cell"},{"key":"2021032314364184000_ref23","doi-asserted-by":"publisher","DOI":"10.13.337980","article-title":"Structural impact on SARS-CoV-2 spike protein by D614G substitution","author":"Zhang","year":"2020","journal-title":"bioRxiv"},{"key":"2021032314364184000_ref24","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1126\/science.abd3255","article-title":"Free fatty acid binding pocket in the locked structure of SARS-CoV-2 spike protein","volume":"370","author":"Toelzer","year":"2020","journal-title":"Science"},{"key":"2021032314364184000_ref25","doi-asserted-by":"crossref","first-page":"934","DOI":"10.1038\/s41594-020-0478-5","article-title":"A thermostable, closed SARS-CoV-2 spike protein trimer","volume":"27","author":"Xiong","year":"2020","journal-title":"Nat Struct Mol Biol"},{"key":"2021032314364184000_ref26","doi-asserted-by":"crossref","first-page":"108630","DOI":"10.1016\/j.celrep.2020.108630","article-title":"D614G mutation alters SARS-CoV-2 spike conformation and enhances protease cleavage at the S1\/S2 junction","volume":"34","author":"Gobeil","year":"2021","journal-title":"Cell Rep"},{"key":"2021032314364184000_ref27","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1038\/s41586-020-2772-0","article-title":"Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion","volume":"588","author":"Benton","year":"2020","journal-title":"Nature"},{"key":"2021032314364184000_ref28","doi-asserted-by":"crossref","first-page":"2002106","DOI":"10.2807\/1560-7917.ES.2020.26.1.2002106","article-title":"Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020","volume":"26","author":"Leung","year":"2021","journal-title":"Euro Surveill"},{"key":"2021032314364184000_ref29","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1038\/s41588-020-0693-3","article-title":"Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource","volume":"52","author":"Portelli","year":"2020","journal-title":"Nat Genet"},{"key":"2021032314364184000_ref30","doi-asserted-by":"publisher","DOI":"10.1038\/s41594-020-00547-5","article-title":"Cold sensitivity of the SARS-CoV-2 spike ectodomain","author":"Edwards","year":"2021","journal-title":"Nat Struct Mol Biol"},{"key":"2021032314364184000_ref31","doi-asserted-by":"publisher","DOI":"10.1101\/2020.09.29.319566","article-title":"Functional landscape of SARS-CoV-2 cellular restriction","author":"Martin-Sancho","year":"2020","journal-title":"bioRxiv"},{"key":"2021032314364184000_ref32","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.02304-20","article-title":"Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects","author":"Nguyen","year":"2020","journal-title":"J Virol"},{"key":"2021032314364184000_ref33","doi-asserted-by":"crossref","first-page":"D506","DOI":"10.1093\/nar\/gky1049","article-title":"UniProt: a worldwide hub of protein knowledge","volume":"47","author":"UniProt","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2021032314364184000_ref34","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1038\/msb.2011.75","article-title":"Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal omega","volume":"7","author":"Sievers","year":"2011","journal-title":"Mol Syst Biol"},{"key":"2021032314364184000_ref35","doi-asserted-by":"crossref","first-page":"W636","DOI":"10.1093\/nar\/gkz268","article-title":"The EMBL-EBI search and sequence analysis tools APIs in 2019","volume":"47","author":"Madeira","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2021032314364184000_ref36","doi-asserted-by":"crossref","first-page":"W320","DOI":"10.1093\/nar\/gku316","article-title":"Deciphering key features in protein structures with the new ENDscript server","volume":"42","author":"Robert","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2021032314364184000_ref37","doi-asserted-by":"crossref","first-page":"2714","DOI":"10.1002\/elps.1150181505","article-title":"SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling","volume":"18","author":"Guex","year":"1997","journal-title":"Electrophoresis"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/22\/2\/1499\/36654668\/bbab056.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/22\/2\/1499\/36654668\/bbab056.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,3,23]],"date-time":"2021-03-23T11:05:54Z","timestamp":1616497554000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/22\/2\/1499\/6149292"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,2,25]]},"references-count":37,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2021,2,25]]},"published-print":{"date-parts":[[2021,3,22]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbab056","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.10.31.363176","asserted-by":"object"}]},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,3]]},"published":{"date-parts":[[2021,2,25]]}}}