{"paper_id":"0673a618-8e22-45f1-ac24-8cffa73fdf08","body_text":"Conformational trajectory of the HIV-1 fusion peptide during CD4-induced envelope opening | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Biological Sciences - Article Conformational trajectory of the HIV-1 fusion peptide during CD4-induced envelope opening Priyamvada Acharya, Bhishem Thakur, Revansiddha Katte, Wang Xu, and 5 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5090208/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 17 May, 2025 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Abstract The hydrophobic fusion peptide (FP), a critical component of the HIV-1 entry machinery, is located at the N terminal stretch of the envelope (Env) gp41 subunit 1-3 . The receptor-binding gp120 subunit of Env forms a heterodimer with gp41 and assembles into a trimer, in which FP is accessible for antibody binding 3 . Env conformational changes or “opening” that follow receptor binding result in FP relocating to a newly formed interprotomer pocket at the gp41-gp120 interface where it is sterically inaccessible to antibody 4 . The mechanistic steps connecting the entry-related transition of antibody accessible-to-inaccessible FP configurations remain unresolved. Here, using SOSIP-stabilized Env ectodomains 5 , we visualized atomic-level details of a functional entry intermediate, where partially open Env was bound to receptor CD4, co-receptor mimetic antibody 17b, and FP-targeting antibody VRC34.01, demonstrating that FP remains antibody accessible despite substantial receptor-induced Env opening. We determined a series of structures delineating stepwise opening of Env from its closed state to a newly resolved intermediate and defining downstream re-organizations of the gp120-gp41 interface that ultimately resulted in FP burial in an antibody-inaccessible configuration. Our studies improve our understanding of HIV-1 entry and provide information on entry-related conformation reorganization of a key site of HIV vulnerability to neutralizing antibody. Biological sciences/Structural biology/Electron microscopy/Cryoelectron microscopy Health sciences/Diseases/Infectious diseases/HIV infections Health sciences/Medical research/Translational research Full Text Additional Declarations There is NO Competing Interest. Supplementary Files TableS1.xlsx Table S1 FPpaperSupplementfigures14Sept2024.pdf Supplementary Materials Cite Share Download PDF Status: Published Journal Publication published 17 May, 2025 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {\"props\":{\"pageProps\":{\"initialData\":{\"identity\":\"rs-5090208\",\"acceptedTermsAndConditions\":true,\"allowDirectSubmit\":false,\"archivedVersions\":[],\"articleType\":\"Biological Sciences - Article\",\"associatedPublications\":[],\"authors\":[{\"id\":358987552,\"identity\":\"84c3bd21-697d-4c30-ac82-4946e7b7c599\",\"order_by\":0,\"name\":\"Priyamvada Acharya\",\"email\":\"data:image/png;base64,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\",\"orcid\":\"https://orcid.org/0000-0002-0089-277X\",\"institution\":\"Duke University\",\"correspondingAuthor\":true,\"prefix\":\"\",\"firstName\":\"Priyamvada\",\"middleName\":\"\",\"lastName\":\"Acharya\",\"suffix\":\"\"},{\"id\":358987553,\"identity\":\"6d82a275-3d11-4904-b35d-2fc7fa9598a4\",\"order_by\":1,\"name\":\"Bhishem Thakur\",\"email\":\"\",\"orcid\":\"\",\"institution\":\"Duke University\",\"correspondingAuthor\":false,\"prefix\":\"\",\"firstName\":\"Bhishem\",\"middleName\":\"\",\"lastName\":\"Thakur\",\"suffix\":\"\"},{\"id\":358987554,\"identity\":\"22eaeae0-c66d-4d58-8a18-a3e69879c0ba\",\"order_by\":2,\"name\":\"Revansiddha Katte\",\"email\":\"\",\"orcid\":\"\",\"institution\":\"University of Texas at Tyler Health Science Center\",\"correspondingAuthor\":false,\"prefix\":\"\",\"firstName\":\"Revansiddha\",\"middleName\":\"\",\"lastName\":\"Katte\",\"suffix\":\"\"},{\"id\":358987555,\"identity\":\"b35c09df-326b-474d-987d-a16bc6d6b13e\",\"order_by\":3,\"name\":\"Wang Xu\",\"email\":\"\",\"orcid\":\"https://orcid.org/0000-0003-4452-9240\",\"institution\":\"University of Texas at Tyler Health Science Center\",\"correspondingAuthor\":false,\"prefix\":\"\",\"firstName\":\"Wang\",\"middleName\":\"\",\"lastName\":\"Xu\",\"suffix\":\"\"},{\"id\":358987556,\"identity\":\"62ca400d-c49d-42f4-8458-41c585966a01\",\"order_by\":4,\"name\":\"Katarzyna Janowska\",\"email\":\"\",\"orcid\":\"\",\"institution\":\"Duke Human Vaccine Institute\",\"correspondingAuthor\":false,\"prefix\":\"\",\"firstName\":\"Katarzyna\",\"middleName\":\"\",\"lastName\":\"Janowska\",\"suffix\":\"\"},{\"id\":358987557,\"identity\":\"b60f1c4e-b3f2-4f25-bf77-7b5bde6b2057\",\"order_by\":5,\"name\":\"Salam Sammour\",\"email\":\"\",\"orcid\":\"\",\"institution\":\"Duke Human Vaccine Institute\",\"correspondingAuthor\":false,\"prefix\":\"\",\"firstName\":\"Salam\",\"middleName\":\"\",\"lastName\":\"Sammour\",\"suffix\":\"\"},{\"id\":358987558,\"identity\":\"242d6b48-53a7-47ce-bcf7-873788f34df3\",\"order_by\":6,\"name\":\"Rory Henderson\",\"email\":\"\",\"orcid\":\"https://orcid.org/0000-0002-4301-6382\",\"institution\":\"Duke Human Vaccine Institute; Department of Medicine; Department of Immunology, Duke University\",\"correspondingAuthor\":false,\"prefix\":\"\",\"firstName\":\"Rory\",\"middleName\":\"\",\"lastName\":\"Henderson\",\"suffix\":\"\"},{\"id\":358987559,\"identity\":\"0cef3d52-185e-4d9b-870c-41b2a3753fdb\",\"order_by\":7,\"name\":\"Maolin Lu\",\"email\":\"\",\"orcid\":\"\",\"institution\":\"Duke University\",\"correspondingAuthor\":false,\"prefix\":\"\",\"firstName\":\"Maolin\",\"middleName\":\"\",\"lastName\":\"Lu\",\"suffix\":\"\"},{\"id\":358987560,\"identity\":\"837c3494-4815-4d93-afca-c28b9cb2908c\",\"order_by\":8,\"name\":\"Peter Kwong\",\"email\":\"\",\"orcid\":\"\",\"institution\":\"Columbia University\",\"correspondingAuthor\":false,\"prefix\":\"\",\"firstName\":\"Peter\",\"middleName\":\"\",\"lastName\":\"Kwong\",\"suffix\":\"\"}],\"badges\":[],\"createdAt\":\"2024-09-14 17:40:13\",\"currentVersionCode\":1,\"declarations\":\"\",\"doi\":\"10.21203/rs.3.rs-5090208/v1\",\"doiUrl\":\"https://doi.org/10.21203/rs.3.rs-5090208/v1\",\"draftVersion\":[],\"editorialEvents\":[{\"content\":\"https://doi.org/10.1038/s41467-025-59721-2\",\"type\":\"published\",\"date\":\"2025-05-17T04:00:00+00:00\"}],\"editorialNote\":\"\",\"failedWorkflow\":false,\"files\":[{\"id\":82974122,\"identity\":\"f429aa1b-3b71-4809-aafe-220feaa12db3\",\"added_by\":\"auto\",\"created_at\":\"2025-05-18 07:06:53\",\"extension\":\"pdf\",\"order_by\":1,\"title\":\"\",\"display\":\"\",\"copyAsset\":false,\"role\":\"manuscript-pdf\",\"size\":18377040,\"visible\":true,\"origin\":\"\",\"legend\":\"Article File\",\"description\":\"\",\"filename\":\"FPtrajectory14Sept2024TextFigures.pdf\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-5090208/v1_covered_161b1c81-6638-4f12-b1d3-a32f437c38a7.pdf\"},{\"id\":68324704,\"identity\":\"c9e98bce-8429-4d49-9bd3-1d43e1536b6c\",\"added_by\":\"auto\",\"created_at\":\"2024-11-06 05:41:33\",\"extension\":\"xlsx\",\"order_by\":1,\"title\":\"\",\"display\":\"\",\"copyAsset\":false,\"role\":\"supplement\",\"size\":11629,\"visible\":true,\"origin\":\"\",\"legend\":\"Table S1\",\"description\":\"\",\"filename\":\"TableS1.xlsx\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-5090208/v1/0621bec133ea36066b85e8c4.xlsx\"},{\"id\":68324705,\"identity\":\"1d5d5072-e55b-47d2-b82c-946446a2aa82\",\"added_by\":\"auto\",\"created_at\":\"2024-11-06 05:41:33\",\"extension\":\"pdf\",\"order_by\":2,\"title\":\"\",\"display\":\"\",\"copyAsset\":false,\"role\":\"supplement\",\"size\":13631314,\"visible\":true,\"origin\":\"\",\"legend\":\"Supplementary Materials\",\"description\":\"\",\"filename\":\"FPpaperSupplementfigures14Sept2024.pdf\",\"url\":\"https://assets-eu.researchsquare.com/files/rs-5090208/v1/11be425fad5917eae28dec5c.pdf\"}],\"financialInterests\":\"There is \\u003cb\\u003eNO\\u003c/b\\u003e Competing Interest.\",\"formattedTitle\":\"Conformational trajectory of the HIV-1 fusion peptide during CD4-induced envelope opening\",\"fulltext\":[],\"fulltextSource\":\"\",\"fullText\":\"\",\"funders\":[],\"hasAdminPriorityOnWorkflow\":false,\"hasManuscriptDocX\":false,\"hasOptedInToPreprint\":true,\"hasPassedJournalQc\":\"\",\"hasAnyPriority\":true,\"hideJournal\":false,\"highlight\":\"\",\"institution\":\"\",\"isAcceptedByJournal\":true,\"isAuthorSuppliedPdf\":true,\"isDeskRejected\":\"\",\"isHiddenFromSearch\":false,\"isInQc\":false,\"isInWorkflow\":false,\"isPdf\":true,\"isPdfUpToDate\":true,\"isWithdrawnOrRetracted\":false,\"journal\":{\"display\":true,\"email\":\"info@researchsquare.com\",\"identity\":\"nature-portfolio\",\"isNatureJournal\":true,\"hasQc\":false,\"allowDirectSubmit\":false,\"externalIdentity\":\"\",\"sideBox\":\"\",\"snPcode\":\"\",\"submissionUrl\":\"\",\"title\":\"Nature Portfolio\",\"twitterHandle\":\"\",\"acdcEnabled\":false,\"dfaEnabled\":false,\"editorialSystem\":\"ejp\",\"reportingPortfolio\":\"\",\"inReviewEnabled\":true,\"inReviewRevisionsEnabled\":false},\"keywords\":\"\",\"lastPublishedDoi\":\"10.21203/rs.3.rs-5090208/v1\",\"lastPublishedDoiUrl\":\"https://doi.org/10.21203/rs.3.rs-5090208/v1\",\"license\":{\"name\":\"CC BY 4.0\",\"url\":\"https://creativecommons.org/licenses/by/4.0/\"},\"manuscriptAbstract\":\"The hydrophobic fusion peptide (FP), a critical component of the HIV-1 entry machinery, is located at the N terminal stretch of the envelope (Env) gp41 subunit\\u003csup\\u003e1-3\\u003c/sup\\u003e. The receptor-binding gp120 subunit of Env forms a heterodimer with gp41 and assembles into a trimer, in which FP is accessible for antibody binding\\u003csup\\u003e3\\u003c/sup\\u003e. Env conformational changes or “opening” that follow receptor binding result in FP relocating to a newly formed interprotomer pocket at the gp41-gp120 interface where it is sterically inaccessible to antibody\\u003csup\\u003e4\\u003c/sup\\u003e. The mechanistic steps connecting the entry-related transition of antibody accessible-to-inaccessible FP configurations remain unresolved. Here, using SOSIP-stabilized Env ectodomains\\u003csup\\u003e5\\u003c/sup\\u003e, we visualized atomic-level details of a functional entry intermediate, where partially open Env was bound to receptor CD4, co-receptor mimetic antibody 17b, and FP-targeting antibody VRC34.01, demonstrating that FP remains antibody accessible despite substantial receptor-induced Env opening. We determined a series of structures delineating stepwise opening of Env from its closed state to a newly resolved intermediate and defining downstream re-organizations of the gp120-gp41 interface that ultimately resulted in FP burial in an antibody-inaccessible configuration. Our studies improve our understanding of HIV-1 entry and provide information on entry-related conformation reorganization of a key site of HIV vulnerability to neutralizing antibody.\",\"manuscriptTitle\":\"Conformational trajectory of the HIV-1 fusion peptide during CD4-induced envelope opening\",\"msid\":\"\",\"msnumber\":\"\",\"nonDraftVersions\":[{\"code\":1,\"date\":\"2024-11-06 05:41:28\",\"doi\":\"10.21203/rs.3.rs-5090208/v1\",\"editorialEvents\":[],\"status\":\"published\",\"journal\":{\"display\":true,\"email\":\"info@researchsquare.com\",\"identity\":\"nature-communications\",\"isNatureJournal\":true,\"hasQc\":false,\"allowDirectSubmit\":false,\"externalIdentity\":\"NCOMMS\",\"sideBox\":\"Learn more about [Nature Communications](http://www.nature.com/ncomms/)\",\"snPcode\":\"\",\"submissionUrl\":\"https://mts-ncomms.nature.com/\",\"title\":\"Nature Communications\",\"twitterHandle\":\"\",\"acdcEnabled\":true,\"dfaEnabled\":true,\"editorialSystem\":\"ejp\",\"reportingPortfolio\":\"Nature Communications\",\"inReviewEnabled\":true,\"inReviewRevisionsEnabled\":false}}],\"origin\":\"\",\"ownerIdentity\":\"b387397f-fe34-47b3-8875-c70ca70b8abd\",\"owner\":[],\"postedDate\":\"November 6th, 2024\",\"published\":true,\"recentEditorialEvents\":[],\"rejectedJournal\":[],\"revision\":\"\",\"amendment\":\"\",\"status\":\"published-in-journal\",\"subjectAreas\":[{\"id\":38196444,\"name\":\"Biological sciences/Structural biology/Electron microscopy/Cryoelectron microscopy\"},{\"id\":38196445,\"name\":\"Health sciences/Diseases/Infectious diseases/HIV infections\"},{\"id\":38196446,\"name\":\"Health sciences/Medical research/Translational research\"}],\"tags\":[],\"updatedAt\":\"2025-05-18T07:06:34+00:00\",\"versionOfRecord\":{\"articleIdentity\":\"rs-5090208\",\"link\":\"https://doi.org/10.1038/s41467-025-59721-2\",\"journal\":{\"identity\":\"nature-communications\",\"isVorOnly\":false,\"title\":\"Nature Communications\"},\"publishedOn\":\"2025-05-17 04:00:00\",\"publishedOnDateReadable\":\"May 17th, 2025\"},\"versionCreatedAt\":\"2024-11-06 05:41:28\",\"video\":\"\",\"vorDoi\":\"10.1038/s41467-025-59721-2\",\"vorDoiUrl\":\"https://doi.org/10.1038/s41467-025-59721-2\",\"workflowStages\":[]},\"version\":\"v1\",\"identity\":\"rs-5090208\",\"journalConfig\":\"researchsquare\"},\"__N_SSP\":true},\"page\":\"/article/[identity]/[[...version]]\",\"query\":{\"redirect\":\"/article/rs-5090208\",\"identity\":\"rs-5090208\",\"version\":[\"v1\"]},\"buildId\":\"8U1c8b4HqxoKbykW_rLl7\",\"isFallback\":false,\"isExperimentalCompile\":false,\"dynamicIds\":[84888],\"gssp\":true,\"scriptLoader\":[]}","source_license":"CC-BY-4.0","license_restricted":false}