{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T11:03:27Z","timestamp":1785409407780,"version":"3.56.0"},"posted":{"date-parts":[[2026,1,7]]},"group-title":"Immunology","reference-count":72,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,1,7]],"date-time":"2026-01-07T00:00:00Z","timestamp":1767744000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"award":["R01AI127469"],"award-info":[{"award-number":["R01AI127469"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["U19AI159822"],"award-info":[{"award-number":["U19AI159822"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,1,7]]},"abstract":"<jats:title>Summary<\/jats:title>\n                <jats:p>The hepatitis C virus (HCV) envelope glycoprotein E1E2 heterodimer is the target of broadly neutralizing antibodies (bNAbs). Although prior studies have indicated that E1-dependent bNAbs are associated with spontaneous clearance of HCV, all E1-dependent human monoclonal antibodies (mAbs) have been isolated from individuals with chronic HCV infection. Here, we isolated E1-dependent bNAbs from an individual with high neutralizing antibody breadth who spontaneously cleared HCV, showing that these bNAbs bind to four distinct sites on E1E2. We also developed mAbClust, an algorithm that improves identification of accurate AlphaFold 3 (AF3) structure predictions of antigen-antibody complexes. We used AF3 and mAbClust to generate a high-confidence predicted structure of an E1-dependent bNAb in complex with E1E2, showing that this bNAb binds to a quaternary epitope spanning E1 and E2. This study identifies four neutralizing sites and a quaternary bNAb epitope associated with HCV control, which can guide HCV vaccine design. AF3 with mAbClust could have broad applications for accurate epitope mapping of antibodies.<\/jats:p>","DOI":"10.64898\/2026.01.06.698032","type":"posted-content","created":{"date-parts":[[2026,1,7]],"date-time":"2026-01-07T12:25:26Z","timestamp":1767788726000},"source":"Crossref","is-referenced-by-count":0,"title":["mAbClust with AlphaFold 3 avoids hallucinations to define a quaternary broadly neutralizing HCV epitope"],"prefix":"10.64898","author":[{"given":"Harry T.","family":"Paul","sequence":"first","affiliation":[{"name":"Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD. USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica L.","family":"Mimms","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD. USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hanna","family":"Aboueid","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD. USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Sanchez Buitrago","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD. USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liudmila","family":"Kulakova","sequence":"additional","affiliation":[{"name":"Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xander","family":"Wilcox","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katrina","family":"Kuhn","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD. USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hao","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric A.","family":"Toth","sequence":"additional","affiliation":[{"name":"Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicole","family":"Skinner","sequence":"additional","affiliation":[{"name":"The Abigail Wexner Research Institute at Nationwide Children\u2019s Hospital, Columbus, OH 43205, USA"},{"name":"Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH 43210, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew I.","family":"Flyak","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gilad","family":"Ofek","sequence":"additional","affiliation":[{"name":"Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA"},{"name":"Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"H. Benjamin","family":"Larman","sequence":"additional","affiliation":[{"name":"Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas R.","family":"Fuerst","sequence":"additional","affiliation":[{"name":"Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA"},{"name":"Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stuart C.","family":"Ray","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD. USA"},{"name":"Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea L.","family":"Cox","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD. USA"},{"name":"Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA"},{"name":"Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Justin R.","family":"Bailey","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD. USA"},{"name":"Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026010805500876000_2026.01.06.698032v1.1","unstructured":"Organization, W.H . (2024). Global hepatitis report 2024: action for access in low-and middle-income countries (World Health Organization)."},{"key":"2026010805500876000_2026.01.06.698032v1.2","doi-asserted-by":"publisher","DOI":"10.1172\/JCI130720"},{"key":"2026010805500876000_2026.01.06.698032v1.3","doi-asserted-by":"publisher","DOI":"10.1002\/hep.27013"},{"key":"2026010805500876000_2026.01.06.698032v1.4","doi-asserted-by":"publisher","DOI":"10.1038\/s41577-025-01215-9"},{"key":"2026010805500876000_2026.01.06.698032v1.5","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jir835"},{"key":"2026010805500876000_2026.01.06.698032v1.6","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2023.1201033"},{"key":"2026010805500876000_2026.01.06.698032v1.7","doi-asserted-by":"publisher","DOI":"10.1172\/JCI160058"},{"key":"2026010805500876000_2026.01.06.698032v1.8","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-33035-z"},{"key":"2026010805500876000_2026.01.06.698032v1.9","doi-asserted-by":"publisher","DOI":"10.1016\/j.jhep.2020.01.005"},{"key":"2026010805500876000_2026.01.06.698032v1.10","doi-asserted-by":"publisher","DOI":"10.1016\/j.jim.2019.06.016"},{"key":"2026010805500876000_2026.01.06.698032v1.11","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1010179"},{"key":"2026010805500876000_2026.01.06.698032v1.12","doi-asserted-by":"publisher","DOI":"10.1182\/blood.V97.4.1023"},{"key":"2026010805500876000_2026.01.06.698032v1.13","doi-asserted-by":"publisher","DOI":"10.1172\/jci.insight.92872"},{"key":"2026010805500876000_2026.01.06.698032v1.14","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.53169"},{"key":"2026010805500876000_2026.01.06.698032v1.15","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.aav1882"},{"key":"2026010805500876000_2026.01.06.698032v1.16","doi-asserted-by":"publisher","DOI":"10.1002\/hep.28850"},{"key":"2026010805500876000_2026.01.06.698032v1.17","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0607026104"},{"key":"2026010805500876000_2026.01.06.698032v1.18","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2023.12.004"},{"key":"2026010805500876000_2026.01.06.698032v1.19","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2018.10.012"},{"key":"2026010805500876000_2026.01.06.698032v1.20","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.3009512"},{"key":"2026010805500876000_2026.01.06.698032v1.21","doi-asserted-by":"publisher","DOI":"10.1038\/nm1698"},{"key":"2026010805500876000_2026.01.06.698032v1.22","doi-asserted-by":"publisher","DOI":"10.4254\/wjh.v7.i6.831"},{"key":"2026010805500876000_2026.01.06.698032v1.23","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2021.10.005"},{"key":"2026010805500876000_2026.01.06.698032v1.24","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01440-12"},{"key":"2026010805500876000_2026.01.06.698032v1.25","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00248-09"},{"key":"2026010805500876000_2026.01.06.698032v1.26","doi-asserted-by":"publisher","DOI":"10.1172\/JCI78794"},{"key":"2026010805500876000_2026.01.06.698032v1.27","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2024.03.001"},{"key":"2026010805500876000_2026.01.06.698032v1.28","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2018.01194"},{"key":"2026010805500876000_2026.01.06.698032v1.29","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1012428"},{"key":"2026010805500876000_2026.01.06.698032v1.30","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abb5642"},{"key":"2026010805500876000_2026.01.06.698032v1.31","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.02070-18"},{"key":"2026010805500876000_2026.01.06.698032v1.32","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01872-07"},{"key":"2026010805500876000_2026.01.06.698032v1.33","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.78.13.7257-7263.2004"},{"key":"2026010805500876000_2026.01.06.698032v1.34","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1114927109"},{"key":"2026010805500876000_2026.01.06.698032v1.35","doi-asserted-by":"publisher","DOI":"10.1126\/science.abn9884"},{"key":"2026010805500876000_2026.01.06.698032v1.36","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-39659-z"},{"key":"2026010805500876000_2026.01.06.698032v1.37","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-024-07487-w"},{"key":"2026010805500876000_2026.01.06.698032v1.38","doi-asserted-by":"publisher","DOI":"10.1080\/19420862.2025.2545601"},{"key":"2026010805500876000_2026.01.06.698032v1.39","doi-asserted-by":"publisher","DOI":"10.1002\/pro.4865"},{"key":"2026010805500876000_2026.01.06.698032v1.40","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-023-02087-4"},{"key":"2026010805500876000_2026.01.06.698032v1.41","doi-asserted-by":"publisher","DOI":"10.1086\/428578"},{"key":"2026010805500876000_2026.01.06.698032v1.42","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2021.12.003"},{"key":"2026010805500876000_2026.01.06.698032v1.43","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2015149118"},{"key":"2026010805500876000_2026.01.06.698032v1.44","unstructured":"Metcalf, M.C. , Janus, B.M. , Jeong, S. , Law, M. , Mariuzza, R.A. , Toth, E.A. , Pierce, B.G. , Fuerst, T.R. , and Ofek, G . (2025). Structure of HCV E1E2 complex reveals intersection of the homodimer interface by neutralizing antibodies. Submitted."},{"key":"2026010805500876000_2026.01.06.698032v1.45","doi-asserted-by":"publisher","DOI":"10.3390\/v16050803"},{"key":"2026010805500876000_2026.01.06.698032v1.46","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth735"},{"key":"2026010805500876000_2026.01.06.698032v1.47","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2013.117"},{"key":"2026010805500876000_2026.01.06.698032v1.48","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01138-09"},{"key":"2026010805500876000_2026.01.06.698032v1.49","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2015.06.012"},{"key":"2026010805500876000_2026.01.06.698032v1.50","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.05959-11"},{"key":"2026010805500876000_2026.01.06.698032v1.51","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.02332-10"},{"key":"2026010805500876000_2026.01.06.698032v1.52","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2018.10.009"},{"key":"2026010805500876000_2026.01.06.698032v1.53","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1114927109"},{"key":"2026010805500876000_2026.01.06.698032v1.54","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2022.110859"},{"key":"2026010805500876000_2026.01.06.698032v1.55","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2009.02.080"},{"key":"2026010805500876000_2026.01.06.698032v1.56","doi-asserted-by":"publisher","DOI":"10.1002\/hep.31912"},{"key":"2026010805500876000_2026.01.06.698032v1.57","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofz076"},{"key":"2026010805500876000_2026.01.06.698032v1.58","doi-asserted-by":"publisher","DOI":"10.1099\/jgv.0.000608"},{"key":"2026010805500876000_2026.01.06.698032v1.59","doi-asserted-by":"publisher","DOI":"10.1002\/hep.28705"},{"key":"2026010805500876000_2026.01.06.698032v1.60","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.02518-14"},{"key":"2026010805500876000_2026.01.06.698032v1.61","doi-asserted-by":"publisher","DOI":"10.1002\/hep.27259"},{"key":"2026010805500876000_2026.01.06.698032v1.62","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btae586"},{"key":"2026010805500876000_2026.01.06.698032v1.63","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0161879"},{"key":"2026010805500876000_2026.01.06.698032v1.64","doi-asserted-by":"publisher","DOI":"10.5555\/3001460.3001507"},{"key":"2026010805500876000_2026.01.06.698032v1.65","doi-asserted-by":"crossref","unstructured":"Chen, F. , Nguyen, Y.T.K. , Lee, Y.-Z. , Giang, E. , Lau, S.C. , Koide, Y. , Hung, S.-H. , Ueno, L. , He, L. , Fuerst, T.R. , et al. (2025). The conserved bridging domain on HCV E1E2 glycoprotein complex is targeted by neutralizing antibodies from diverse lineages. Cold Spring Harbor Laboratory.","DOI":"10.1101\/2025.11.05.686883"},{"key":"2026010805500876000_2026.01.06.698032v1.66","doi-asserted-by":"publisher","DOI":"10.1016\/j.jim.2007.09.017"},{"key":"2026010805500876000_2026.01.06.698032v1.67","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-8976-8_30"},{"key":"2026010805500876000_2026.01.06.698032v1.68","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bth485"},{"key":"2026010805500876000_2026.01.06.698032v1.69","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkl970"},{"key":"2026010805500876000_2026.01.06.698032v1.70","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1994.1334"},{"key":"2026010805500876000_2026.01.06.698032v1.71","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2007.05.022"},{"key":"2026010805500876000_2026.01.06.698032v1.72","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.1146014"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.01.06.698032","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T13:50:17Z","timestamp":1767880217000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.01.06.698032"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,7]]},"references-count":72,"URL":"https:\/\/doi.org\/10.64898\/2026.01.06.698032","relation":{},"subject":[],"published":{"date-parts":[[2026,1,7]]},"subtype":"preprint"}}