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The occupancy of the FA site by linoleic acid (LA) reduces infectivity by \u2018locking\u2019 the spike in a less infectious conformation. Here, we use dynamical-nonequilibrium molecular dynamics (D-NEMD) simulations to compare the allosteric responses of spike variants to LA removal. D-NEMD simulations show that the FA site is coupled to other functional regions of the protein, e.g. the receptor-binding motif (RBM), N-terminal domain (NTD), furin cleavage site, and regions surrounding the fusion peptide. D-NEMD simulations also identify the allosteric networks connecting the FA site to these functional regions. The comparison between the wild-type spike and four variants (Alpha, Delta, Delta plus, and Omicron BA.1) shows that the variants differ significantly in their responses to LA removal. The allosteric connections to the FA site on Alpha are generally similar to those on the wild-type protein, with the exception of the RBM and the S71\u2013R78 region, which show a weaker link to the FA site. In contrast, Omicron is the most different variant, exhibiting significant differences in the RBM, NTD, V622\u2013L629, and furin cleavage site. These differences in the allosteric modulation may be of functional relevance, potentially affecting transmissibility and virulence. Experimental comparison of the effects of LA on SARS-CoV-2 variants, including emerging variants, is warranted.<\/jats:p>","DOI":"10.1093\/jmcb\/mjad021","type":"journal-article","created":{"date-parts":[[2023,10,10]],"date-time":"2023-10-10T10:57:44Z","timestamp":1696935464000},"source":"Crossref","is-referenced-by-count":17,"title":["SARS-CoV-2 spike variants differ in their allosteric responses to linoleic acid"],"prefix":"10.1093","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8753-4950","authenticated-orcid":false,"given":"A Sofia F","family":"Oliveira","sequence":"first","affiliation":[{"name":"School of Chemistry, Centre for Computational Chemistry, University of Bristol , Bristol BS8 1TS , UK"},{"name":"School of Chemistry, University of Bristol , Bristol BS8 1TS , UK"},{"name":"School of Biochemistry, University of Bristol , Bristol BS8 1TD , UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1240-8463","authenticated-orcid":false,"given":"Deborah K","family":"Shoemark","sequence":"additional","affiliation":[{"name":"School of Biochemistry, University of Bristol , Bristol BS8 1TD , UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1136-4008","authenticated-orcid":false,"given":"Andrew D","family":"Davidson","sequence":"additional","affiliation":[{"name":"School of Cellular and Molecular Medicine, University of Bristol, University Walk , Bristol BS8 1TD , UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7518-9045","authenticated-orcid":false,"given":"Imre","family":"Berger","sequence":"additional","affiliation":[{"name":"School of Chemistry, University of Bristol , Bristol BS8 1TS , UK"},{"name":"School of Biochemistry, University of Bristol , Bristol BS8 1TD , UK"},{"name":"School of Chemistry, Max Planck Bristol Centre for Minimal Biology, Bristol BS8 1TS , UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1516-9760","authenticated-orcid":false,"given":"Christiane","family":"Schaffitzel","sequence":"additional","affiliation":[{"name":"School of Biochemistry, University of Bristol , Bristol BS8 1TD , UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1015-4567","authenticated-orcid":false,"given":"Adrian J","family":"Mulholland","sequence":"additional","affiliation":[{"name":"School of Chemistry, Centre for Computational Chemistry, University of Bristol , Bristol BS8 1TS , UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,3,29]]},"reference":[{"key":"2023101010565930300_bib1","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1002\/prot.25776","article-title":"F508del disturbs the dynamics of the nucleotide binding domains of CFTR before and after ATP hydrolysis","volume":"88","author":"Abreu","year":"2020","journal-title":"Proteins"},{"key":"2023101010565930300_bib2","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1109\/MCSE.2020.3024155","article-title":"Biomolecular simulations in the time of COVID19, and after","volume":"22","author":"Amaro","year":"2020","journal-title":"Comput. 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