{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T18:56:15Z","timestamp":1785783375269,"version":"3.56.0"},"reference-count":85,"publisher":"National Academy of Sciences","issue":"19","license":[{"start":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T00:00:00Z","timestamp":1778198400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100015691","name":"HHS | NIH | NIAID | Division of Microbiology and Infectious Diseases","doi-asserted-by":"publisher","award":["AI R21183188"],"award-info":[{"award-number":["AI R21183188"]}],"id":[{"id":"10.13039\/100015691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["RAPID MCB-2032054"],"award-info":[{"award-number":["RAPID MCB-2032054"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"HHS | NIH | National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01 GM1151805"],"award-info":[{"award-number":["R01 GM1151805"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2026,5,12]]},"abstract":"<jats:p>The severe acute respiratory syndrome coronavirus 2 spike glycoprotein enables infection through a key conformational transition that exposes its receptor binding domain (RBD). Experimental evidence indicates that spike mutations, particularly the early D614G variant, alter the rate of this conformational shift, potentially increasing viral infectivity. We conducted extensive weighted ensemble simulations of the Ancestral, Delta, and Omicron BA.1 spike strains to investigate relationships between sequence mutations and RBD opening dynamics. We observe that Ancestral, Delta, and Omicron BA.1 spike RBDs open differently. Via dynamical network analysis, we identified two allosteric communication networks connecting all S1 domains: the established N2R linker and a newly investigated antiparallel R2N linker. In Delta and Omicron BA.1 variant spikes, RBD opening is facilitated by both linkers, while the Ancestral strain relies predominantly on the N2R linker. In the Ancestral spike, the D614-K854 salt bridge impedes allosteric communication through the R2N linker, whereas the loss of this salt bridge in all subsequent variants of concerns allows for increased local flexibility, thereby accelerating RBD opening. Hydrogen\u2013deuterium mass spectrometry experiments validate these altered dynamics in the D614 region. This study unveils a \u201chidden\u201d network, connecting the N-terminal domain to the RBD via the 614-proximal region, and the D614G mutation reshapes the fitness landscape of these critical viral glycoproteins.<\/jats:p>","DOI":"10.1073\/pnas.2504793123","type":"journal-article","created":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T09:47:13Z","timestamp":1778579233000},"update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":2,"title":["D614G reshapes allosteric networks and opening mechanisms of SARS-CoV-2 spikes"],"prefix":"10.1073","volume":"123","author":[{"given":"Fiona L.","family":"Kearns","sequence":"first","affiliation":[{"name":"Department of Molecular Biology, University of California San Diego","place":["La Jolla"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anthony T.","family":"Bogetti","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Pittsburgh","place":["Pittsburgh"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2681-8460","authenticated-orcid":false,"given":"Carla","family":"Calv\u00f3-Tusell","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, University of California San Diego","place":["La Jolla"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6929-7397","authenticated-orcid":false,"given":"Mac Kevin E.","family":"Braza","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Biochemistry, University of California San Diego","place":["La Jolla"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3581-1148","authenticated-orcid":false,"given":"Lorenzo","family":"Casalino","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, University of California San Diego","place":["La Jolla"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-9935-4039","authenticated-orcid":false,"given":"Amanda J.","family":"Gramm","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Pennsylvania State University","place":["University Park"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3782-2262","authenticated-orcid":false,"given":"Sean","family":"Braet","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Pennsylvania State University","place":["University Park"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mia A.","family":"Rosenfeld","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, University of California San Diego","place":["La Jolla"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harinda","family":"Rajapaksha","sequence":"additional","affiliation":[{"name":"Oracle for Research, Oracle Cloud","place":["Austin"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bryan","family":"Barker","sequence":"additional","affiliation":[{"name":"Oracle for Research, Oracle Cloud","place":["Austin"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8995-3067","authenticated-orcid":false,"given":"Ganesh","family":"Anand","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Pennsylvania State University","place":["University Park"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0590-483X","authenticated-orcid":false,"given":"Lillian T.","family":"Chong","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Pittsburgh","place":["Pittsburgh"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3422-805X","authenticated-orcid":false,"given":"Surl-Hee","family":"Ahn","sequence":"additional","affiliation":[{"name":"Department of Chemical Engineering, University of California Davis","place":["Davis"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9275-9553","authenticated-orcid":false,"given":"Rommie E.","family":"Amaro","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, University of California San Diego","place":["La Jolla"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2026,5,8]]},"reference":[{"key":"e_1_3_4_1_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-020-00468-6"},{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.02.058"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.abb2507"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-virology-110615-042301"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1002\/rmv.2507"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbrc.2020.10.012"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.abb7269"},{"key":"e_1_3_4_8_2","first-page":"162","article-title":"SARS-CoV-2 variant biology: Immune escape, transmission and fitness","volume":"21","author":"Carabelli A. M.","year":"2023","unstructured":"A. M. Carabelli , SARS-CoV-2 variant biology: Immune escape, transmission and fitness. Nat. Rev. Microbiol. 21, 162\u2013177 (2023), 10.1038\/s41579-022-00841-7.","journal-title":"Nat. Rev. Microbiol."},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.RA120.015303"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1093\/jb\/mvab041"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1063\/5.0137654"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41580-021-00418-x"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.26508\/lsa.202000786"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1021\/jacs.1c05435"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41401-020-0485-4"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41573-023-00672-y"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41423-023-01116-8"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.00376-24"},{"key":"e_1_3_4_19_2","doi-asserted-by":"publisher","DOI":"10.1038\/s44298-024-00043-3"},{"key":"e_1_3_4_20_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-50976-9"},{"key":"e_1_3_4_21_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2022.03.018"},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jinf.2024.106121"},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.06.043"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2895-3"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.09.032"},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-19808-4"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.65365"},{"key":"e_1_3_4_28_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.abf2303"},{"key":"e_1_3_4_29_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-21118-2"},{"key":"e_1_3_4_30_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijid.2020.10.033"},{"key":"e_1_3_4_31_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbc.2021.101238"},{"key":"e_1_3_4_32_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2020.11.012"},{"key":"e_1_3_4_33_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2022.11.025"},{"key":"e_1_3_4_34_2","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.abf0202"},{"key":"e_1_3_4_35_2","doi-asserted-by":"publisher","DOI":"10.1021\/acsomega.3c00944"},{"key":"e_1_3_4_36_2","doi-asserted-by":"crossref","unstructured":"M. McCallum Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants. Science 374 eabl8506 (2021).","DOI":"10.1101\/2021.08.11.455956"},{"key":"e_1_3_4_37_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.abl9463"},{"key":"e_1_3_4_38_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2213332120"},{"key":"e_1_3_4_39_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2021.06.006"},{"key":"e_1_3_4_40_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-28528-w"},{"key":"e_1_3_4_41_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ebiom.2023.104561"},{"key":"e_1_3_4_42_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-04266-9"},{"key":"e_1_3_4_43_2","doi-asserted-by":"publisher","DOI":"10.1515\/cclm-2021-1287"},{"key":"e_1_3_4_44_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmii.2022.03.007"},{"key":"e_1_3_4_45_2","doi-asserted-by":"publisher","DOI":"10.1002\/cbic.202200059"},{"key":"e_1_3_4_46_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(21)02758-6"},{"key":"e_1_3_4_47_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.2c00100"},{"key":"e_1_3_4_48_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.abn7760"},{"key":"e_1_3_4_49_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-32665-7"},{"key":"e_1_3_4_50_2","doi-asserted-by":"publisher","DOI":"10.1021\/acscentsci.0c01056"},{"key":"e_1_3_4_51_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2020.10.036"},{"key":"e_1_3_4_52_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41557-021-00758-3"},{"key":"e_1_3_4_53_2","doi-asserted-by":"crossref","unstructured":"L. T. Chong D. M. Zuckerman Weighted ensemble simulation: Advances in methods software and applications. Wiley Interdiscip. Rev. Comput. Mol. Sci. 15 e70055 (2025).","DOI":"10.1002\/wcms.70055"},{"key":"e_1_3_4_54_2","doi-asserted-by":"crossref","unstructured":"D. L. Lynch A. Pavlova Z. Fan J. C. Gumbart Weighted ensemble simulations reveal novel conformations and modulator effects in hepatitis B virus capsid assembly. J. Chem. Theory Comput. 21 12317\u201312327 (2025).","DOI":"10.1021\/acs.jctc.5c01197"},{"key":"e_1_3_4_55_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0006-3495(96)79552-8"},{"key":"e_1_3_4_56_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-biophys-070816-033834"},{"key":"e_1_3_4_57_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpca.0c10724"},{"key":"e_1_3_4_58_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.abb9983"},{"key":"e_1_3_4_59_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2022.03.028"},{"key":"e_1_3_4_60_2","doi-asserted-by":"publisher","DOI":"10.1021\/jacs.1c00556"},{"key":"e_1_3_4_61_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.abd5223"},{"key":"e_1_3_4_62_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2022.105855"},{"key":"e_1_3_4_63_2","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.ade5085"},{"key":"e_1_3_4_64_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2022.110729"},{"key":"e_1_3_4_65_2","doi-asserted-by":"publisher","DOI":"10.1021\/ct4008603"},{"key":"e_1_3_4_66_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41594-020-0468-7"},{"key":"e_1_3_4_67_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2100943118"},{"key":"e_1_3_4_68_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.8b00143"},{"key":"e_1_3_4_69_2","doi-asserted-by":"crossref","unstructured":"A. J. Gramm . SARS CoV-2 spike adopts distinct conformational ensembles in situ. bioRxiv [Preprint] (2025). https:\/\/doi.org\/10.1101\/2025.03.04.641425.","DOI":"10.1101\/2025.03.04.641425"},{"key":"e_1_3_4_70_2","doi-asserted-by":"publisher","DOI":"10.1021\/jacs.2c06148"},{"key":"e_1_3_4_71_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2020.11.001"},{"key":"e_1_3_4_72_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2022.167928"},{"key":"e_1_3_4_73_2","doi-asserted-by":"publisher","DOI":"10.1021\/ct5010615"},{"key":"e_1_3_4_74_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.3c01153"},{"key":"e_1_3_4_75_2","unstructured":"D. A. Case . Amber 2024 (University of California San Francisco 2024)."},{"key":"e_1_3_4_76_2","doi-asserted-by":"publisher","DOI":"10.1021\/ct400314y"},{"key":"e_1_3_4_77_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cpc.2012.09.022"},{"key":"e_1_3_4_78_2","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.23354"},{"key":"e_1_3_4_79_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4067"},{"key":"e_1_3_4_80_2","doi-asserted-by":"publisher","DOI":"10.1021\/ct900242e"},{"key":"e_1_3_4_81_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.RA120.016148"},{"key":"e_1_3_4_82_2","unstructured":"J. D. Russo WESTPA 2.0. GitHub. https:\/\/github.com\/westpa\/westpa. Accessed July 2020."},{"key":"e_1_3_4_83_2","unstructured":"D. A. Case Amber 18. University of California San Francisco 2018. https:\/\/ambermd.org. Accessed June 2020."},{"key":"e_1_3_4_84_2","doi-asserted-by":"publisher","DOI":"10.33011\/livecoms.1.2.10607"},{"key":"e_1_3_4_85_2","unstructured":"F. L. Kearns R.E. Amaro D614G_FOR_SHARING_amarolab.tar.gz. Amaro Lab. https:\/\/amarolab.ucsd.edu\/data.php#covid19. Deposited December 2025."}],"container-title":["Proceedings of the National Academy of Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pnas.org\/doi\/pdf\/10.1073\/pnas.2504793123","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pnas.org\/doi\/pdf\/10.1073\/pnas.2504793123","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,18]],"date-time":"2026-05-18T17:27:52Z","timestamp":1779125272000},"score":1,"resource":{"primary":{"URL":"https:\/\/pnas.org\/doi\/10.1073\/pnas.2504793123"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,8]]},"references-count":85,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2026,5,12]]}},"alternative-id":["10.1073\/pnas.2504793123"],"URL":"https:\/\/doi.org\/10.1073\/pnas.2504793123","relation":{},"ISSN":["0027-8424","1091-6490"],"issn-type":[{"value":"0027-8424","type":"print"},{"value":"1091-6490","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,8]]},"assertion":[{"value":"2025-03-18","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-02-27","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-05-08","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e2504793123"}}