{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T13:46:47Z","timestamp":1790776007190,"version":"4.1.0"},"reference-count":51,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2023,6,9]],"date-time":"2023-06-09T00:00:00Z","timestamp":1686268800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"U.S. National Institutes of Health","doi-asserted-by":"publisher","award":["AI107960"],"award-info":[{"award-number":["AI107960"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Adenovirus has strong therapeutic potential as an oncolytic virus and gene therapy vector. However, injecting human species C serotype 5 adenovirus, HAdv-C5, into the bloodstream leads to numerous interactions with plasma proteins that affect viral tropism and biodistribution, and can lead to potent immune responses and viral neutralization. The HAdv\/factor X (FX) interaction facilitates highly efficient liver transduction and protects virus particles from complement-mediated neutralization after intravenous delivery. Ablating the FX interaction site on the HAdv-C5 capsid leaves the virus susceptible to neutralization by natural IgM followed by activation of the complement cascade and covalent binding of complement components C4b and C3b to the viral capsid. Here we present structural models for IgM and complement components C1, C4b, and C3b in complex with HAdv-C5. Molecular dynamics simulations indicate that when C3b binds near the vertex, multiple stabilizing interactions can be formed between C3b, penton base, and fiber. These interactions may stabilize the vertex region of the capsid and prevent release of the virally encoded membrane lytic factor, protein VI, which is packaged inside of the viral capsid, thus effectively neutralizing the virus. In a situation where FX and IgM are competing for binding to the capsid, IgM may not be able to form a bent conformation in which most of its Fab arms interact with the capsid. Our structural modeling of the competitive interaction of FX and IgM with HAdv-C5 allows us to propose a mechanistic model for FX inhibition of IgM-mediated virus neutralization. According to this model, although IgM may bind to the capsid, in the presence of FX it will likely retain a planar conformation and thus be unable to promote activation of the complement cascade at the virus surface.<\/jats:p>","DOI":"10.3390\/v15061343","type":"journal-article","created":{"date-parts":[[2023,6,9]],"date-time":"2023-06-09T02:03:18Z","timestamp":1686276198000},"page":"1343","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Structural Model for Factor X Inhibition of IgM and Complement-Mediated Neutralization of Adenovirus"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1568-6936","authenticated-orcid":false,"given":"Nicole","family":"Wagner","sequence":"first","affiliation":[{"name":"Cleveland Center for Membrane and Structural Biology, Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8320-9007","authenticated-orcid":false,"given":"Dmitry M.","family":"Shayakhmetov","sequence":"additional","affiliation":[{"name":"Lowance Center for Human Immunology, Departments of Pediatrics and Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA"},{"name":"Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA"},{"name":"Discovery and Developmental Therapeutics Program, Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5980-4797","authenticated-orcid":false,"given":"Phoebe L.","family":"Stewart","sequence":"additional","affiliation":[{"name":"Cleveland Center for Membrane and Structural Biology, Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,6,9]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"e003255","DOI":"10.1136\/jitc-2021-003255","article-title":"Phase I, multicenter, open-label study of intravenous VCN-01 oncolytic adenovirus with or without nab-paclitaxel plus gemcitabine in patients with advanced solid tumors","volume":"10","author":"Alvarez","year":"2022","journal-title":"J. Immunother. Cancer"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"822","DOI":"10.1016\/j.ymthe.2020.09.001","article-title":"In Vivo HSC Gene Therapy Using a Bi-modular HDAd5\/35++ Vector Cures Sickle Cell Disease in a Mouse Model","volume":"29","author":"Li","year":"2021","journal-title":"Mol. Ther."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1186\/s13014-020-01593-5","article-title":"A phase 1 trial of the safety, tolerability and biological effects of intravenous Enadenotucirev, a novel oncolytic virus, in combination with chemoradiotherapy in locally advanced rectal cancer (CEDAR)","volume":"15","author":"Davis","year":"2020","journal-title":"Radiat. Oncol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/j.omtm.2023.03.008","article-title":"HDAd6\/35++\u2014A new helper-dependent adenovirus vector platform for in vivo transduction of hematopoietic stem cells","volume":"29","author":"Wang","year":"2023","journal-title":"Mol. Ther. Methods Clin. Dev."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"3449","DOI":"10.1002\/1873-3468.13649","article-title":"Interaction of adenovirus with antibodies, complement, and coagulation factors","volume":"593","author":"Allen","year":"2019","journal-title":"FEBS Lett."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1016\/j.chom.2019.02.016","article-title":"Complement C4 Prevents Viral Infection through Capsid Inactivation","volume":"25","author":"Bottermann","year":"2019","journal-title":"Cell Host Microbe"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1016\/j.chom.2019.03.010","article-title":"Complement Seals a Virus to Block Infection","volume":"25","author":"Smith","year":"2019","journal-title":"Cell Host Microbe"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1992","DOI":"10.1128\/JVI.79.4.1992-2000.2005","article-title":"Adenovirus protein VI mediates membrane disruption following capsid disassembly","volume":"79","author":"Wiethoff","year":"2005","journal-title":"J. Virol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"108351","DOI":"10.1016\/j.clim.2020.108351","article-title":"Interactions of viruses and the humoral innate immune response","volume":"212","author":"Maloney","year":"2020","journal-title":"Clin. Immunol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1016\/0167-5699(86)90168-4","article-title":"Immunoglobulin flexibility in complement activation","volume":"7","author":"Feinstein","year":"1986","journal-title":"Immunol. Today"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1016\/j.pharmthera.2016.11.014","article-title":"Complement: A primer for the coming therapeutic revolution","volume":"172","author":"Barnum","year":"2017","journal-title":"Pharmacol. Ther."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"S5","DOI":"10.1002\/ajh.26855","article-title":"Complement biology for hematologists","volume":"98","author":"Duval","year":"2023","journal-title":"Am. J. Hematol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1206","DOI":"10.4049\/jimmunol.152.3.1206","article-title":"Mapping of amino acid residues in the C mu 3 domain of mouse IgM important in macromolecular assembly and complement-dependent cytolysis","volume":"152","author":"Arya","year":"1994","journal-title":"J. Immunol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"11900","DOI":"10.1073\/pnas.1901841116","article-title":"Insights into IgM-mediated complement activation based on in situ structures of IgM-C1-C4b","volume":"116","author":"Sharp","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"101627","DOI":"10.1016\/j.smim.2022.101627","article-title":"Complement component C3: A structural perspective and potential therapeutic implications","volume":"59","author":"Geisbrecht","year":"2022","journal-title":"Semin. Immunol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1054","DOI":"10.1073\/pnas.79.4.1054","article-title":"Third component of human complement: Localization of the internal thiolester bond","volume":"79","author":"Thomas","year":"1982","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"602277","DOI":"10.3389\/fimmu.2021.602277","article-title":"Hijacking Factor H for Complement Immune Evasion","volume":"12","author":"Moore","year":"2021","journal-title":"Front. Immunol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"7478","DOI":"10.1128\/JVI.79.12.7478-7491.2005","article-title":"Adenovirus binding to blood factors results in liver cell infection and hepatotoxicity","volume":"79","author":"Shayakhmetov","year":"2005","journal-title":"J. Virol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1126\/science.1226625","article-title":"Coagulation factor X activates innate immunity to human species C adenovirus","volume":"338","author":"Doronin","year":"2012","journal-title":"Science"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"5483","DOI":"10.1073\/pnas.0711757105","article-title":"Adenovirus serotype 5 hexon is critical for virus infection of hepatocytes in vivo","volume":"105","author":"Kalyuzhniy","year":"2008","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1016\/j.cell.2008.01.016","article-title":"Adenovirus serotype 5 hexon mediates liver gene transfer","volume":"132","author":"Waddington","year":"2008","journal-title":"Cell"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1038\/nm.3107","article-title":"Coagulation factor X shields adenovirus type 5 from attack by natural antibodies and complement","volume":"19","author":"Xu","year":"2013","journal-title":"Nat. Med."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1038\/gt.2016.32","article-title":"The relevance of coagulation factor X protection of adenoviruses in human sera","volume":"23","author":"Duffy","year":"2016","journal-title":"Gene Ther."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"eabc6659","DOI":"10.1126\/scitranslmed.abc6659","article-title":"Systemic cancer therapy with engineered adenovirus that evades innate immunity","volume":"12","author":"Atasheva","year":"2020","journal-title":"Sci. Transl. Med."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"e00850-17","DOI":"10.1128\/JVI.00850-17","article-title":"Atomic Structures of Minor Proteins VI and VII in Human Adenovirus","volume":"91","author":"Dai","year":"2017","journal-title":"J. Virol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1002\/pro.3943","article-title":"UCSF ChimeraX: Structure visualization for researchers, educators, and developers","volume":"30","author":"Pettersen","year":"2021","journal-title":"Protein Sci."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"W296","DOI":"10.1093\/nar\/gky427","article-title":"SWISS-MODEL: Homology modelling of protein structures and complexes","volume":"46","author":"Waterhouse","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1038\/44880","article-title":"A triple beta-spiral in the adenovirus fibre shaft reveals a new structural motif for a fibrous protein","volume":"401","author":"Mitraki","year":"1999","journal-title":"Nature"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera\u2014A visualization system for exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J. Comput. Chem."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1016\/j.jmb.2010.11.043","article-title":"Model of the trimeric fiber and its interactions with the pentameric penton base of human adenovirus by cryo-electron microscopy","volume":"406","author":"Liu","year":"2011","journal-title":"J. Mol. Biol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"10183","DOI":"10.1073\/pnas.1300547110","article-title":"High-resolution structures of the IgM Fc domains reveal principles of its hexamer formation","volume":"110","author":"Muller","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"5399","DOI":"10.1073\/pnas.97.10.5399","article-title":"Crystal structure of a Staphylococcus aureus protein A domain complexed with the Fab fragment of a human IgM antibody: Structural basis for recognition of B-cell receptors and superantigen activity","volume":"97","author":"Graille","year":"2000","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"986","DOI":"10.1073\/pnas.1616998114","article-title":"Structure and activation of C1, the complex initiating the classical pathway of the complement cascade","volume":"114","author":"Mortensen","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"768","DOI":"10.1073\/pnas.1718709115","article-title":"Structure of the C1r-C1s interaction of the C1 complex of complement activation","volume":"115","author":"Almitairi","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1093\/emboj\/21.3.231","article-title":"The crystal structure of the zymogen catalytic domain of complement protease C1r reveals that a disruptive mechanical stress is required to trigger activation of the C1 complex","volume":"21","author":"Lacroix","year":"2002","journal-title":"EMBO J."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"15821","DOI":"10.1074\/jbc.M113.464545","article-title":"A molecular switch governs the interaction between the human complement protease C1s and its substrate, complement C4","volume":"288","author":"Perry","year":"2013","journal-title":"J. Biol. Chem."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1006","DOI":"10.1107\/S2059798316012201","article-title":"Re-evaluation of low-resolution crystal structures via interactive molecular-dynamics flexible fitting (iMDFF): A case study in complement C4","volume":"72","author":"Croll","year":"2016","journal-title":"Acta Crystallogr. D Struct. Biol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1133","DOI":"10.15252\/embj.201593673","article-title":"Regulators of complement activity mediate inhibitory mechanisms through a common C3b-binding mode","volume":"35","author":"Forneris","year":"2016","journal-title":"EMBO J."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"606","DOI":"10.1038\/emboj.2010.341","article-title":"Substrate recognition by complement convertases revealed in the C5-cobra venom factor complex","volume":"30","author":"Laursen","year":"2011","journal-title":"EMBO J."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1042\/bj1930115","article-title":"The covalent-binding reaction of complement component C3","volume":"193","author":"Sim","year":"1981","journal-title":"Biochem. J."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1190","DOI":"10.1016\/S0006-3495(02)75476-3","article-title":"Structure and dynamics of zymogen human blood coagulation factor X","volume":"82","author":"Venkateswarlu","year":"2002","journal-title":"Biophys. J."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"044130","DOI":"10.1063\/5.0014475","article-title":"Scalable molecular dynamics on CPU and GPU architectures with NAMD","volume":"153","author":"Phillips","year":"2020","journal-title":"J. Chem. Phys."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1545","DOI":"10.1002\/jcc.21287","article-title":"CHARMM: The biomolecular simulation program","volume":"30","author":"Brooks","year":"2009","journal-title":"J. Comput. Chem."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: Visual molecular dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. Mol. Graph."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"W554","DOI":"10.1093\/nar\/gky381","article-title":"gRINN: A tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations","volume":"46","author":"Sercinoglu","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"12049","DOI":"10.1128\/JVI.01652-06","article-title":"Visualization of alpha-helices in a 6-angstrom resolution cryoelectron microscopy structure of adenovirus allows refinement of capsid protein assignments","volume":"80","author":"Saban","year":"2006","journal-title":"J. Virol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1002\/pro.5560060201","article-title":"The internal thioester and the covalent binding properties of the complement proteins C3 and C4","volume":"6","author":"Law","year":"1997","journal-title":"Protein Sci."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"5488","DOI":"10.4049\/jimmunol.1500087","article-title":"Structural Basis for the Function of Complement Component C4 within the Classical and Lectin Pathways of Complement","volume":"194","author":"Mortensen","year":"2015","journal-title":"J. Immunol."},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Emerson, C.C., and Stewart, P.L. (2021). Structure-Based Modeling of Complement C4 Mediated Neutralization of Adenovirus. Viruses, 13.","DOI":"10.3390\/v13010111"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"11491","DOI":"10.1128\/JVI.01214-09","article-title":"Cryo-electron microscopy structure of an adenovirus-integrin complex indicates conformational changes in both penton base and integrin","volume":"83","author":"Lindert","year":"2009","journal-title":"J. Virol."},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Flatt, J.W., Kim, R., Smith, J.G., Nemerow, G.R., and Stewart, P.L. (2013). An intrinsically disordered region of the adenovirus capsid is implicated in neutralization by human alpha defensin 5. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0061571"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/15\/6\/1343\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T19:51:23Z","timestamp":1760125883000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/15\/6\/1343"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,6,9]]},"references-count":51,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2023,6]]}},"alternative-id":["v15061343"],"URL":"https:\/\/doi.org\/10.3390\/v15061343","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,6,9]]}}}