{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,8]],"date-time":"2026-02-08T03:41:31Z","timestamp":1770522091519,"version":"3.49.0"},"reference-count":112,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T00:00:00Z","timestamp":1770249600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Pendleton Laboratory Fund for Pediatric Infectious Disease Research"},{"name":"Manning Fund for COVID-19 Research at the University of Virginia"},{"DOI":"10.13039\/100008222","name":"Ivy Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100008222","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Coulter Foundation"},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01 AI176515"],"award-info":[{"award-number":["R01 AI176515"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"NIAID\u2013Duke University contract","doi-asserted-by":"publisher","award":["75N93025C00006"],"award-info":[{"award-number":["75N93025C00006"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"United States Department of Agriculture (USDA) National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["2025-67015-44993"],"award-info":[{"award-number":["2025-67015-44993"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"name":"University of Virginia Flow Cytometry Core Facility","award":["RRID:SCR_017829"],"award-info":[{"award-number":["RRID:SCR_017829"]}]},{"DOI":"10.13039\/100000054","name":"University of Virginia Comprehensive Cancer Center through the National Cancer Institute","doi-asserted-by":"publisher","award":["P30-CA044579"],"award-info":[{"award-number":["P30-CA044579"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Background: Killed Whole Cell Genome-Reduced Bacteria (KWC\/GRB), a versatile vaccine platform, can produce very low cost, thermostable, easily manufactured vaccines expressing complex immunogens that include potent immunomodulators. This system supports iterative optimization through a Design\u2013Build\u2013Test\u2013Learn (DBTL) workflow aimed at enhancing immunogenicity. We applied this approach to developing HIV-1 gp41 Membrane-Proximal External Region (MPER) vaccines using the scaffolded MPER antigen, 3AGJ, a recombinant heterologous protein engineered to mimic MPER structures recognized by broadly neutralizing monoclonal antibodies (bNAbs). Methods: Five KWC\/GRB vaccines expressing versions of 3AGJ were designed, including versions linked to immunomodulators and multimers of the immunogen. Display on the surface of the bacteria was evaluated by flow cytometry using the broadly neutralizing monoclonal antibody 2F5. Outbred HET3 mice were vaccinated intramuscularly, and MPER-specific antibody responses were assessed by ELISA and by the ability of the vaccines to induce neutralizing antibodies. Neutralization was measured against tier 1 and tier 2 HIV-1 pseudoviruses. Results: All five vaccines were strongly expressed on the bacterial surface and induced clear MPER-specific antibody responses in every mouse. About 33% of the animals showed detectable HIV-1 neutralization. Conclusions: These results demonstrate that a KWC\/GRB-based scaffold-MPER (3AGJ) vaccine can elicit HIV-1 neutralizing antibodies in a subset of animals. Although further optimization will be required to improve the consistency and magnitude of neutralizing responses, the findings provide an initial validation of the concept. There are many strategies that can be used to enhance and extend immune responses induced by KWC\/GRB vaccines that can be employed to yield improved anti-HIV-1 immune responses.<\/jats:p>","DOI":"10.3390\/v18020209","type":"journal-article","created":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T11:13:01Z","timestamp":1770289981000},"page":"209","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["HIV Membrane-Proximal External Region Scaffolded Immunogen as Killed Whole-Cell Genome-Reduced Vaccines"],"prefix":"10.3390","volume":"18","author":[{"given":"Juan Sebastian","family":"Quintero-Barbosa","sequence":"first","affiliation":[{"name":"Department of Pediatrics, University of Virginia, Charlottesville, VA 22908, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yufeng","family":"Song","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of Virginia, Charlottesville, VA 22908, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-9929-3185","authenticated-orcid":false,"given":"Frances","family":"Mehl","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of Virginia, Charlottesville, VA 22908, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5616-0877","authenticated-orcid":false,"given":"Shubham","family":"Mathur","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of Virginia, Charlottesville, VA 22908, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-9261-6394","authenticated-orcid":false,"given":"Lauren","family":"Livingston","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of Virginia, Charlottesville, VA 22908, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3560-232X","authenticated-orcid":false,"given":"Peter D.","family":"Kwong","sequence":"additional","affiliation":[{"name":"Aaron Diamond AIDS Research Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA"},{"name":"Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA"},{"name":"Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8387-3952","authenticated-orcid":false,"given":"Xiaoying","family":"Shen","sequence":"additional","affiliation":[{"name":"Department of Surgery, Duke University, Durham, NC 27710, USA"},{"name":"Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David C.","family":"Montefiori","sequence":"additional","affiliation":[{"name":"Department of Surgery, Duke University, Durham, NC 27710, USA"},{"name":"Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Steven L.","family":"Zeichner","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of Virginia, Charlottesville, VA 22908, USA"},{"name":"Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2026,2,5]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"S5","DOI":"10.1038\/nm1209","article-title":"Vaccines: Past, Present and Future","volume":"11","author":"Plotkin","year":"2005","journal-title":"Nat. Med."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1615","DOI":"10.1093\/cid\/cis238","article-title":"Nomenclature for Immune Correlates of Protection After Vaccination","volume":"54","author":"Plotkin","year":"2012","journal-title":"Clin. Infect. Dis."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Greenwood, B. (2014). The Contribution of Vaccination to Global Health: Past, Present and Future. Philos. Trans. R. Soc. B Biol. Sci., 369.","DOI":"10.1098\/rstb.2013.0433"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1038\/nrd.2017.243","article-title":"mRNA Vaccines\u2014A New Era in Vaccinology","volume":"17","author":"Pardi","year":"2018","journal-title":"Nat. Rev. Drug Discov."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"6318","DOI":"10.1016\/j.vaccine.2023.09.007","article-title":"A Recombinant Chimeric Influenza Virus Vaccine Expressing the Consensus H3 Hemagglutinin Elicits Broad Hemagglutination Inhibition Antibodies against Divergent Swine H3N2 Influenza Viruses","volume":"41","author":"Yu","year":"2023","journal-title":"Vaccine"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1146\/annurev-med-042420-113212","article-title":"Whole Inactivated Virus and Protein-Based COVID-19 Vaccines","volume":"73","author":"Hotez","year":"2022","journal-title":"Annu. Rev. Med."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1016\/j.coviro.2011.08.002","article-title":"Influenza Virus Vaccines: Lessons from the 2009 H1N1 Pandemic","volume":"1","author":"Broadbent","year":"2011","journal-title":"Curr. Opin. Virol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"948","DOI":"10.1126\/science.abc5312","article-title":"A Strategic Approach to COVID-19 Vaccine R&D","volume":"368","author":"Corey","year":"2020","journal-title":"Science"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"17880","DOI":"10.1073\/pnas.1004728107","article-title":"Elicitation of Structure-Specific Antibodies by Epitope Scaffolds","volume":"107","author":"Ofek","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1116","DOI":"10.1016\/j.str.2010.06.010","article-title":"Computational Design of Epitope-Scaffolds Allows Induction of Antibodies Specific for a Poorly Immunogenic HIV Vaccine Epitope","volume":"18","author":"Correia","year":"2010","journal-title":"Structure"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Zhou, T., Zhu, J., Yang, Y., Gorman, J., Ofek, G., Srivatsan, S., Druz, A., Lees, C.R., Lu, G., and Soto, C. (2014). Transplanting Supersites of HIV-1 Vulnerability. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0099881"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Rujas, E., Leaman, D.P., Insausti, S., Ortigosa-Pascual, L., Zhang, L., Zwick, M.B., and Nieva, J.L. (2018). Functional Optimization of Broadly Neutralizing HIV-1 Antibody 10E8 by Promotion of Membrane Interactions. J. Virol., 92.","DOI":"10.1128\/JVI.02249-17"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Eslami, M., Fadaee Dowlat, B., Yaghmayee, S., Habibian, A., Keshavarzi, S., Oksenych, V., and Naderian, R. (2025). Next-Generation Vaccine Platforms: Integrating Synthetic Biology, Nanotechnology, and Systems Immunology for Improved Immunogenicity. Vaccines, 13.","DOI":"10.3390\/vaccines13060588"},{"key":"ref_14","unstructured":"Barrett, A., and Stanberry, L. (2009). Vaccines for Biodefense and Emerging and Neglected Diseases, Academic Press."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Buck, P.O., Gomes, D.A., Beck, E., Kirson, N., Mattera, M., Carroll, S., Ultsch, B., Jayasundara, K., Uhart, M., and Garrison, L.P. (2024). New Vaccine Platforms\u2014Novel Dimensions of Economic and Societal Value and Their Measurement. Vaccines, 12.","DOI":"10.3390\/vaccines12030234"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/j.jconrel.2021.12.030","article-title":"Evolution of Drug Delivery Systems: From 1950 to 2020 and Beyond","volume":"342","author":"Park","year":"2022","journal-title":"J. Control. Release"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1038\/s41590-017-0007-9","article-title":"Emerging Viral Diseases from a Vaccinology Perspective: Preparing for the next Pandemic","volume":"19","author":"Graham","year":"2018","journal-title":"Nat. Immunol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1146\/annurev-immunol-041015-055515","article-title":"Broadly Neutralizing Antibodies to HIV and Their Role in Vaccine Design","volume":"34","author":"Burton","year":"2016","journal-title":"Annu. Rev. Immunol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1111\/imr.12484","article-title":"Identification and Specificity of Broadly Neutralizing Antibodies against HIV","volume":"275","author":"McCoy","year":"2017","journal-title":"Immunol. Rev."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"S45","DOI":"10.1038\/nm1213","article-title":"Mucosal Immunity and Vaccines","volume":"11","author":"Holmgren","year":"2005","journal-title":"Nat. Med."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1038\/nri3251","article-title":"Recent Progress in Mucosal Vaccine Development: Potential and Limitations","volume":"12","author":"Lycke","year":"2012","journal-title":"Nat. Rev. Immunol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1097\/QAD.0b013e328342ff11","article-title":"Anti-HIV-1 Antibodies 2F5 and 4E10 Interact Differently with Lipids to Bind Their Epitopes","volume":"25","author":"Franquelim","year":"2011","journal-title":"Aids"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"828","DOI":"10.1126\/science.aae0474","article-title":"Fusion Peptide of HIV-1 as a Site of Vulnerability to Neutralizing Antibody","volume":"352","author":"Kong","year":"2016","journal-title":"Science"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"856","DOI":"10.1126\/science.1187659","article-title":"Rational Design of Envelope Identifies Broadly Neutralizing Human Monoclonal Antibodies to HIV-1","volume":"329","author":"Wu","year":"2010","journal-title":"Science"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Irimia, A., Serra, A.M., Sarkar, A., Jacak, R., Kalyuzhniy, O., Sok, D., Saye-Francisco, K.L., Schiffner, T., Tingle, R., and Kubitz, M. (2017). Lipid Interactions and Angle of Approach to the HIV-1 Viral Membrane of Broadly Neutralizing Antibody 10E8: Insights for Vaccine and Therapeutic Design. PLoS Pathog., 13.","DOI":"10.1371\/journal.ppat.1006212"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1126\/science.1225416","article-title":"Broadly Neutralizing Antibodies Present New Prospects to Counter Highly Antigenically Diverse Viruses","volume":"337","author":"Burton","year":"2012","journal-title":"Science"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1007\/s11684-019-0721-9","article-title":"Broadly Neutralizing Antibodies and Vaccine Design against HIV-1 Infection","volume":"14","author":"Wang","year":"2020","journal-title":"Front. Med."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Williams, W.B., Wiehe, K., Saunders, K.O., and Haynes, B.F. (2021). Strategies for Induction of HIV-1 Envelope-Reactive Broadly Neutralizing Antibodies. J. Int. AIDS Soc., 24.","DOI":"10.1002\/jia2.25831"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Brouwer, P.J.M., Antanasijevic, A., Berndsen, Z., Yasmeen, A., Fiala, B., Bijl, T.P.L., Bontjer, I., Bale, J.B., Sheffler, W., and Allen, J.D. (2019). Enhancing and Shaping the Immunogenicity of Native-like HIV-1 Envelope Trimers with a Two-Component Protein Nanoparticle. Nat. Commun., 10.","DOI":"10.1038\/s41467-019-12080-1"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Ou, L., Kong, W.-P., Chuang, G.-Y., Ghosh, M., Gulla, K., O\u2019Dell, S., Varriale, J., Barefoot, N., Changela, A., and Chao, C.W. (2020). Preclinical Development of a Fusion Peptide Conjugate as an HIV Vaccine Immunogen. Sci. Rep., 10.","DOI":"10.1038\/s41598-020-59711-y"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1038\/nature11544","article-title":"Broad and Potent Neutralization of HIV-1 by a Gp41-Specific Human Antibody","volume":"491","author":"Huang","year":"2012","journal-title":"Nature"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"van Gils, M.J., van den Kerkhof, T.L.G.M., Ozorowski, G., Cottrell, C.A., Sok, D., Pauthner, M., Pallesen, J., de Val, N., Yasmeen, A., and de Taeye, S.W. (2016). An HIV-1 Antibody from an Elite Neutralizer Implicates the Fusion Peptide as a Site of Vulnerability. Nat. Microbiol., 2.","DOI":"10.1038\/nmicrobiol.2016.199"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"2494","DOI":"10.1021\/acs.molpharmaceut.4c01341","article-title":"Distinctive Membrane Accommodation Traits Underpinning the Neutralization Activity of HIV-1 Antibody against MPER","volume":"22","author":"Domene","year":"2025","journal-title":"Mol. Pharm."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1016\/j.chom.2019.09.016","article-title":"Structural Basis for Broad HIV-1 Neutralization by the MPER-Specific Human Broadly Neutralizing Antibody LN01","volume":"26","author":"Pinto","year":"2019","journal-title":"Cell Host Microbe"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1038\/nature07352","article-title":"Challenges in the Development of an HIV-1 Vaccine","volume":"455","author":"Barouch","year":"2008","journal-title":"Nature"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1097\/COH.0b013e32833d17ac","article-title":"HIV Vaccines\u2014Lessons Learned and the Way Forward","volume":"5","author":"Kim","year":"2010","journal-title":"Curr. Opin. HIV AIDS"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1016\/j.cell.2019.06.030","article-title":"Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization","volume":"178","author":"Kong","year":"2019","journal-title":"Cell"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"596","DOI":"10.1007\/s13238-018-0534-7","article-title":"The Development of HIV Vaccines Targeting Gp41 Membrane-Proximal External Region (MPER): Challenges and Prospects","volume":"9","author":"Liu","year":"2018","journal-title":"Protein Cell"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"7214","DOI":"10.1016\/j.cell.2024.10.003","article-title":"Potent and Broad HIV-1 Neutralization in Fusion Peptide-Primed SHIV-Infected Macaques","volume":"187","author":"Wang","year":"2024","journal-title":"Cell"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Cheng, C., Xu, K., Kong, R., Chuang, G.-Y., Corrigan, A.R., Geng, H., Hill, K.R., Jafari, A.J., O\u2019Dell, S., and Ou, L. (2019). Consistent Elicitation of Cross-Clade HIV-Neutralizing Responses Achieved in Guinea Pigs after Fusion Peptide Priming by Repetitive Envelope Trimer Boosting. PLoS ONE, 14.","DOI":"10.1371\/journal.pone.0215163"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1111\/imr.12507","article-title":"The HIV-1 Envelope Glycoprotein Structure: Nailing down a Moving Target","volume":"275","author":"Ward","year":"2017","journal-title":"Immunol. Rev."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1016\/j.jmb.2011.10.003","article-title":"Computational Design of High-Affinity Epitope Scaffolds by Backbone Grafting of a Linear Epitope","volume":"415","author":"Azoitei","year":"2012","journal-title":"J. Mol. Biol."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Rantalainen, K., Berndsen, Z.T., Antanasijevic, A., Schiffner, T., Zhang, X., Lee, W.-H., Torres, J.L., Zhang, L., Irimia, A., and Copps, J. (2020). HIV-1 Envelope and MPER Antibody Structures in Lipid Assemblies. Cell Rep., 31.","DOI":"10.1016\/j.celrep.2020.107583"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"7147","DOI":"10.3168\/jds.2022-23219","article-title":"Evaluation of Immunogenicity of Enterobactin Conjugate Vaccine for the Control of Escherichia coli Mastitis in Dairy Cows","volume":"106","author":"Zeng","year":"2023","journal-title":"J. Dairy Sci."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1050","DOI":"10.1016\/S1473-3099(13)70273-1","article-title":"5 Year Efficacy of a Bivalent Killed Whole-Cell Oral Cholera Vaccine in Kolkata, India: A Cluster-Randomised, Double-Blind, Placebo-Controlled Trial","volume":"13","author":"Bhattacharya","year":"2013","journal-title":"Lancet Infect. Dis."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1056\/NEJMc1711583","article-title":"Single-Dose Cholera Vaccine in Response to an Outbreak in Zambia","volume":"378","author":"Ferreras","year":"2018","journal-title":"N. Engl. J. Med."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1007\/s00253-005-0227-z","article-title":"Autodisplay: Efficient Bacterial Surface Display of Recombinant Proteins","volume":"69","author":"Jose","year":"2006","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1016\/S0966-842X(98)01318-3","article-title":"The Great Escape: Structure and Function of the Autotransporter Proteins","volume":"6","author":"Henderson","year":"1998","journal-title":"Trends Microbiol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"692","DOI":"10.1128\/MMBR.68.4.692-744.2004","article-title":"Type V Protein Secretion Pathway: The Autotransporter Story","volume":"68","author":"Henderson","year":"2004","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1038\/nrmicro2733","article-title":"From Self Sufficiency to Dependence: Mechanisms and Factors Important for Autotransporter Biogenesis","volume":"10","author":"Leyton","year":"2012","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1539","DOI":"10.1111\/j.1365-2958.1992.tb00875.x","article-title":"AIDA-I, the Adhesin Involved in Diffuse Adherence of the Diarrhoeagenic Escherichia coli Strain 2787 (O126:H27), Is Synthesized via a Precursor Molecule","volume":"6","author":"Benz","year":"1992","journal-title":"Mol. Microbiol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"5400","DOI":"10.1128\/JB.00164-06","article-title":"Trimeric Autotransporters Require Trimerization of the Passenger Domain for Stability and Adhesive Activity","volume":"188","author":"Cotter","year":"2006","journal-title":"J. Bacteriol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"2297","DOI":"10.1038\/sj.emboj.7601132","article-title":"Structure of the Outer Membrane Translocator Domain of the Haemophilus Influenzae Hia Trimeric Autotransporter","volume":"25","author":"Meng","year":"2006","journal-title":"EMBO J."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"14679","DOI":"10.1074\/jbc.M311496200","article-title":"The Haemophilus Influenzae Hia Autotransporter Contains an Unusually Short Trimeric Translocator Domain","volume":"279","author":"Surana","year":"2004","journal-title":"J. Biol. Chem."},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Maeda, D.L.N.F., Tian, D., Yu, H., Dar, N., Rajasekaran, V., Meng, S., Mahsoub, H.M., Sooryanarain, H., Wang, B., and Heffron, C.L. (2021). Killed Whole-Genome Reduced-Bacteria Surface-Expressed Coronavirus Fusion Peptide Vaccines Protect against Disease in a Porcine Model. Proc. Natl. Acad. Sci. USA, 118.","DOI":"10.1073\/pnas.2025622118"},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Quintero-Barbosa, J.S., Song, Y., Mehl, F., Mathur, S., Livingston, L., Shen, X., Montefiori, D.C., Tan, J., and Zeichner, S.L. (2025). Engineering Enhanced Immunogenicity of Surface-Displayed Immunogens in a Killed Whole-Cell Genome-Reduced Bacterial Vaccine Platform Using Class I Viral Fusion Peptides. Vaccines, 14.","DOI":"10.3390\/vaccines14010014"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"1625","DOI":"10.4049\/jimmunol.164.3.1625","article-title":"Linear PADRE T Helper Epitope and Carbohydrate B Cell Epitope Conjugates Induce Specific High Titer IgG Antibody Responses1","volume":"164","author":"Alexander","year":"2000","journal-title":"J. Immunol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1016\/S0264-410X(97)00186-2","article-title":"Potent Immunogenic Short Linear Peptide Constructs Composed of B Cell Epitopes and Pan DR T Helper Epitopes (PADRE) for Antibody Responses in Vivo","volume":"15","author":"Alexander","year":"1997","journal-title":"Vaccine"},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Lu, Y., and Swartz, J.R. (2016). Functional Properties of Flagellin as a Stimulator of Innate Immunity. Sci. Rep., 6.","DOI":"10.1038\/srep18379"},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Sharma, P., Levy, O., and Dowling, D.J. (2020). The TLR5 Agonist Flagellin Shapes Phenotypical and Functional Activation of Lung Mucosal Antigen Presenting Cells in Neonatal Mice. Front. Immunol., 11.","DOI":"10.3389\/fimmu.2020.00171"},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Rady, H.F., Dai, G., Huang, W., Shellito, J.E., and Ramsay, A.J. (2016). Flagellin Encoded in Gene-Based Vector Vaccines Is a Route-Dependent Immune Adjuvant. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0148701"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"5667","DOI":"10.1074\/jbc.M307759200","article-title":"Identification of Conserved Domains in Salmonella Muenchen Flagellin That Are Essential for Its Ability to Activate TLR5 and to Induce an Inflammatory Response in Vitro","volume":"279","author":"Murthy","year":"2004","journal-title":"J. Biol. Chem."},{"key":"ref_63","doi-asserted-by":"crossref","unstructured":"Diaz-Dinamarca, D.A., Manzo, R.A., Soto, D.A., Avenda\u00f1o-Valenzuela, M.J., Bastias, D.N., Soto, P.I., Escobar, D.F., Vasquez-Saez, V., Carri\u00f3n, F., and Pizarro-Ortega, M.S. (2020). Surface Immunogenic Protein of Streptococcus Group B Is an Agonist of Toll-Like Receptors 2 and 4 and a Potential Immune Adjuvant. Vaccines, 8.","DOI":"10.3390\/vaccines8010029"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"12501","DOI":"10.1128\/JVI.02097-15","article-title":"Bispecific Antibodies Targeting Different Epitopes on the HIV-1 Envelope Exhibit Broad and Potent Neutralization","volume":"89","author":"Asokan","year":"2015","journal-title":"J. Virol."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"5761","DOI":"10.1016\/j.vaccine.2012.06.086","article-title":"Development of VAX128, a Recombinant Hemagglutinin (HA) Influenza-Flagellin Fusion Vaccine with Improved Safety and Immune Response","volume":"30","author":"Taylor","year":"2012","journal-title":"Vaccine"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1146\/annurev-immunol-030409-101243","article-title":"Control of Immunity by the TNFR-Related Molecule OX40 (CD134)","volume":"28","author":"Croft","year":"2010","journal-title":"Annu. Rev. Immunol."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1007\/s11095-008-9767-0","article-title":"Insertion of the Designed Helical Linker Led to Increased Expression of Tf-Based Fusion Proteins","volume":"26","author":"Amet","year":"2009","journal-title":"Pharm. Res."},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Jeong, W.H., Lee, H., Song, D.H., Eom, J.-H., Kim, S.C., Lee, H.-S., Lee, H., and Lee, J.-O. (2016). Connecting Two Proteins Using a Fusion Alpha Helix Stabilized by a Chemical Cross Linker. Nat. Commun., 7.","DOI":"10.1038\/ncomms11031"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"1357","DOI":"10.1016\/j.addr.2012.09.039","article-title":"Fusion Protein Linkers: Property, Design and Functionality","volume":"65","author":"Chen","year":"2013","journal-title":"Adv. Drug Deliv. Rev."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly Accurate Protein Structure Prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1002\/pro.3235","article-title":"UCSF ChimeraX: Meeting Modern Challenges in Visualization and Analysis","volume":"27","author":"Goddard","year":"2018","journal-title":"Protein Sci."},{"key":"ref_72","doi-asserted-by":"crossref","unstructured":"Meng, E.C., Goddard, T.D., Pettersen, E.F., Couch, G.S., Pearson, Z.J., Morris, J.H., and Ferrin, T.E. (2023). UCSF ChimeraX: Tools for Structure Building and Analysis. Protein Sci., 32.","DOI":"10.1002\/pro.4792"},{"key":"ref_73","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_74","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1111\/j.1365-2958.2004.04386.x","article-title":"Cell Size and Nucleoid Organization of Engineered Escherichia coli Cells with a Reduced Genome","volume":"55","author":"Hashimoto","year":"2005","journal-title":"Mol. Microbiol."},{"key":"ref_75","doi-asserted-by":"crossref","unstructured":"Kato, J., and Hashimoto, M. (2007). Construction of Consecutive Deletions of the Escherichia coli Chromosome. Mol. Syst. Biol., 3.","DOI":"10.1038\/msb4100174"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"1439","DOI":"10.1128\/JVI.02108-09","article-title":"Tiered Categorization of a Diverse Panel of HIV-1 Env Pseudoviruses for Assessment of Neutralizing Antibodies","volume":"84","author":"Seaman","year":"2010","journal-title":"J. Virol."},{"key":"ref_77","doi-asserted-by":"crossref","unstructured":"Prasad, V.R., and Kalpana, G.V. (2009). Measuring HIV Neutralization in a Luciferase Reporter Gene Assay. HIV Protocols, Humana Press.","DOI":"10.1007\/978-1-59745-170-3"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"10108","DOI":"10.1128\/JVI.79.16.10108-10125.2005","article-title":"Human Immunodeficiency Virus Type 1 Env Clones from Acute and Early Subtype B Infections for Standardized Assessments of Vaccine-Elicited Neutralizing Antibodies","volume":"79","author":"Li","year":"2005","journal-title":"J. Virol."},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"Kamdem Toukam, D., Tenbusch, M., Stang, A., Temchura, V., Storcksdieck Genannt Bonsmann, M., Grewe, B., Koch, S., Meyerhans, A., Nchinda, G., and Kaptue, L. (2012). Targeting Antibody Responses to the Membrane Proximal External Region of the Envelope Glycoprotein of Human Immunodeficiency Virus. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0038068"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"1991","DOI":"10.1007\/s10439-019-02398-8","article-title":"An Engineered Biomimetic MPER Peptide Vaccine Induces Weakly HIV Neutralizing Antibodies in Mice","volume":"48","author":"Shao","year":"2020","journal-title":"Ann. Biomed. Eng."},{"key":"ref_81","doi-asserted-by":"crossref","unstructured":"Buzon, V., Natrajan, G., Schibli, D., Campelo, F., Kozlov, M.M., and Weissenhorn, W. (2010). Crystal Structure of HIV-1 Gp41 Including Both Fusion Peptide and Membrane Proximal External Regions. PLoS Pathog., 6.","DOI":"10.1371\/journal.ppat.1000880"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1038\/nature13808","article-title":"Structure and Immune Recognition of Trimeric Pre-Fusion HIV-1 Env","volume":"514","author":"Pancera","year":"2014","journal-title":"Nature"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"1391","DOI":"10.1073\/pnas.1309842111","article-title":"Structure of an HIV-1\u2013Neutralizing Antibody Target, the Lipid-Bound Gp41 Envelope Membrane Proximal Region Trimer","volume":"111","author":"Reardon","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1016\/j.immuni.2019.02.008","article-title":"Longitudinal Analysis Reveals Early Development of Three MPER-Directed Neutralizing Antibody Lineages from an HIV-1-Infected Individual","volume":"50","author":"Krebs","year":"2019","journal-title":"Immunity"},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1038\/s41590-024-01833-w","article-title":"Vaccination Induces Broadly Neutralizing Antibody Precursors to HIV Gp41","volume":"25","author":"Schiffner","year":"2024","journal-title":"Nat. Immunol."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"1083","DOI":"10.1038\/s41590-024-01844-7","article-title":"Affinity Gaps among B Cells in Germinal Centers Drive the Selection of MPER Precursors","volume":"25","author":"Ray","year":"2024","journal-title":"Nat. Immunol."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1038\/nri2868","article-title":"Vaccine Delivery: A Matter of Size, Geometry, Kinetics and Molecular Patterns","volume":"10","author":"Bachmann","year":"2010","journal-title":"Nat. Rev. Immunol."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"2425","DOI":"10.1016\/j.immuni.2023.08.011","article-title":"Multivalent Antigen Display on Nanoparticle Immunogens Increases B Cell Clonotype Diversity and Neutralization Breadth to Pneumoviruses","volume":"56","author":"Ols","year":"2023","journal-title":"Immunity"},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.coi.2020.01.007","article-title":"Shaping Humoral Immunity to Vaccines through Antigen-Displaying Nanoparticles","volume":"65","author":"Irvine","year":"2020","journal-title":"Curr. Opin. Immunol."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1146\/annurev-immunol-020711-075032","article-title":"Germinal Centers","volume":"30","author":"Victora","year":"2012","journal-title":"Annu. Rev. Immunol."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1016\/j.immuni.2016.09.001","article-title":"Germinal Center B Cell Dynamics","volume":"45","author":"Mesin","year":"2016","journal-title":"Immunity"},{"key":"ref_92","doi-asserted-by":"crossref","unstructured":"Kelly, H.G., Tan, H.-X., Juno, J.A., Esterbauer, R., Ju, Y., Jiang, W., Wimmer, V.C., Duckworth, B.C., Groom, J.R., and Caruso, F. (2020). Self-Assembling Influenza Nanoparticle Vaccines Drive Extended Germinal Center Activity and Memory B Cell Maturation. JCI Insight, 5.","DOI":"10.1172\/jci.insight.136653"},{"key":"ref_93","doi-asserted-by":"crossref","unstructured":"Ursin, R.L., Dhakal, S., Liu, H., Jayaraman, S., Park, H.-S., Powell, H.R., Sherer, M.L., Littlefield, K.E., Fink, A.L., and Ma, Z. (2022). Greater Breadth of Vaccine-Induced Immunity in Females than Males Is Mediated by Increased Antibody Diversity in Germinal Center B Cells. mBio, 13.","DOI":"10.1128\/mbio.01839-22"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"1702","DOI":"10.1016\/j.cell.2015.11.056","article-title":"Immunogenicity of Stabilized HIV-1 Envelope Trimers with Reduced Exposure of Non-Neutralizing Epitopes","volume":"163","author":"Ozorowski","year":"2015","journal-title":"Cell"},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1038\/s41590-018-0235-7","article-title":"Recent Progress in Broadly Neutralizing Antibodies to HIV","volume":"19","author":"Sok","year":"2018","journal-title":"Nat. Immunol."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1021\/bi00895a027","article-title":"Variations in Affinities of Antibodies during the Immune Response*","volume":"3","author":"Eisen","year":"1964","journal-title":"Biochemistry"},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1038\/nrd4529","article-title":"Advances in the Development of Influenza Virus Vaccines","volume":"14","author":"Krammer","year":"2015","journal-title":"Nat. Rev. Drug Discov."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"1636","DOI":"10.1016\/j.cell.2019.11.003","article-title":"High-Throughput Mapping of B Cell Receptor Sequences to Antigen Specificity","volume":"179","author":"Setliff","year":"2019","journal-title":"Cell"},{"key":"ref_99","doi-asserted-by":"crossref","unstructured":"Conti, S., Kaczorowski, K.J., Song, G., Porter, K., Andrabi, R., Burton, D.R., Chakraborty, A.K., and Karplus, M. (2021). Design of Immunogens to Elicit Broadly Neutralizing Antibodies against HIV Targeting the CD4 Binding Site. Proc. Natl. Acad. Sci. USA, 118.","DOI":"10.1073\/pnas.2018338118"},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1038\/s41586-018-0344-3","article-title":"The Outer Membrane Is an Essential Load-Bearing Element in Gram-Negative Bacteria","volume":"559","author":"Rojas","year":"2018","journal-title":"Nature"},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"109","DOI":"10.3109\/1040841X.2013.804032","article-title":"Autotransporter-Based Cell Surface Display in Gram-Negative Bacteria","volume":"41","author":"Nicolay","year":"2015","journal-title":"Crit. Rev. Microbiol."},{"key":"ref_102","doi-asserted-by":"crossref","unstructured":"Guenaga, J., Dosenovic, P., Ofek, G., Baker, D., Schief, W.R., Kwong, P.D., Karlsson Hedestam, G.B., and Wyatt, R.T. (2011). Heterologous Epitope-Scaffold Prime: Boosting Immuno-Focuses B Cell Responses to the HIV-1 Gp41 2F5 Neutralization Determinant. PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0016074"},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"3380","DOI":"10.1128\/JVI.03473-14","article-title":"A Native-Like SOSIP.664 Trimer Based on an HIV-1 Subtype B env gene","volume":"89","author":"Pugach","year":"2015","journal-title":"J. Virol."},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"11265","DOI":"10.1128\/JVI.01359-09","article-title":"Broad HIV-1 Neutralization Mediated by Plasma Antibodies against the Gp41 Membrane Proximal External Region","volume":"83","author":"Gray","year":"2009","journal-title":"J. Virol."},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1038\/s41591-018-0042-6","article-title":"Epitope-Based Vaccine Design Yields Fusion Peptide-Directed Antibodies That Neutralize Diverse Strains of HIV-1","volume":"24","author":"Xu","year":"2018","journal-title":"Nat. Med."},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1038\/nri2526","article-title":"The Role of TNF Superfamily Members in T-Cell Function and Diseases","volume":"9","author":"Croft","year":"2009","journal-title":"Nat. Rev. Immunol."},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1146\/annurev.immunol.23.021704.115839","article-title":"TNF\/TNFR family members in costimulation of T cell responses","volume":"23","author":"Watts","year":"2005","journal-title":"Annu. Rev. Immunol."},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1016\/j.chom.2020.01.027","article-title":"VRC34-Antibody Lineage Development Reveals How a Required Rare Mutation Shapes the Maturation of a Broad HIV-Neutralizing Lineage","volume":"27","author":"Shen","year":"2020","journal-title":"Cell Host Microbe"},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1074\/jbc.M112.424432","article-title":"Designing a Soluble near Full-Length HIV-1 Gp41 Trimer","volume":"288","author":"Gao","year":"2013","journal-title":"J. Biol. Chem."},{"key":"ref_110","doi-asserted-by":"crossref","unstructured":"Krebs, S.J., McBurney, S.P., Kovarik, D.N., Waddell, C.D., Jaworski, J.P., Sutton, W.F., Gomes, M.M., Trovato, M., Waagmeester, G., and Barnett, S.J. (2014). Multimeric Scaffolds Displaying the HIV-1 Envelope MPER Induce MPER-Specific Antibodies and Cross-Neutralizing Antibodies When Co-Immunized with Gp160 DNA. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0113463"},{"key":"ref_111","doi-asserted-by":"crossref","unstructured":"Meuskens, I., Saragliadis, A., Leo, J.C., and Linke, D. (2019). Type V Secretion Systems: An Overview of Passenger Domain Functions. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.01163"},{"key":"ref_112","doi-asserted-by":"crossref","unstructured":"van Ulsen, P., Zinner, K.M., Jong, W.S.P., and Luirink, J. (2018). On Display: Autotransporter Secretion and Application. FEMS Microbiol. Lett., 365.","DOI":"10.1093\/femsle\/fny165"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/2\/209\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,7]],"date-time":"2026-02-07T05:19:01Z","timestamp":1770441541000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/2\/209"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2,5]]},"references-count":112,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2026,2]]}},"alternative-id":["v18020209"],"URL":"https:\/\/doi.org\/10.3390\/v18020209","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2,5]]}}}