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A detailed molecular understanding of this interaction is essential for elucidating the basis of peptide recognition and guiding antibody optimization. Here, molecular dynamics (MD) simulations combined with free energy perturbation (FEP) calculations were used to systematically investigate the effects of point mutations on both the fusion peptide and the antibody. Mutational analyses of key peptide residues showed that most substitutions reduce binding affinity, indicating that the native peptide sequence is finely optimized for recognition by VRC34.01. Decomposition of binding free energies further reveals that these effects are primarily driven by changes in van der Waals interactions associated with hydrophobic packing at the interface. In contrast, in silico mutagenesis of antibody interfacial residues identifies a small subset of affinity-enhancing mutations, including A33I, L96I and S93T. Structural analyses indicate that these mutations improve binding by optimizing local hydrophobic packing without altering the overall binding mode. These results provide a quantitative and structural framework for understanding fusion peptide recognition and highlight a general strategy for antibody affinity optimization through subtle interfacial packing refinement.<\/jats:p>","DOI":"10.1021\/acs.jpcb.6c03661","type":"journal-article","created":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T13:10:42Z","timestamp":1785849042000},"page":"7892-7900","source":"Crossref","is-referenced-by-count":1,"title":["In Silico Design\nof High-Affinity Antibody VRC34.01\nfor HIV-1 Fusion Peptide Recognition"],"prefix":"10.1021","volume":"130","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-8377-6945","authenticated-orcid":true,"given":"Mei","family":"Feng","sequence":"first","affiliation":[{"name":"Zhejiang University of Science and Technology , , ,","place":["Hangzhou, China, 310023"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nan","family":"Wang","sequence":"additional","affiliation":[{"name":"Zhejiang University of Science and Technology , , ,","place":["Hangzhou, China, 310023"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Song","sequence":"additional","affiliation":[{"name":"Zhejiang University , , ,","place":["Hangzhou, China, 310027"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-5083-1050","authenticated-orcid":true,"given":"Yan","family":"Wang","sequence":"additional","affiliation":[{"name":"Zhejiang University of Science and Technology , , ,","place":["Hangzhou, China, 310023"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1388-3458","authenticated-orcid":true,"given":"Tingting","family":"Sun","sequence":"additional","affiliation":[{"name":"Zhejiang University of Science and Technology , , ,","place":["Hangzhou, China, 310023"]},{"name":"Zhejiang Key Laboratory of Biomedical Intelligent Computing Technology , ,","place":["Hangzhou, China, 310008"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,7,27]]},"reference":[{"key":"2026080608124936800_cit1","doi-asserted-by":"publisher","first-page":"1805","DOI":"10.2174\/1381612043384448","article-title":"HIV-1 Gp41 as a Target for Viral Entry Inhibition","volume":"10","author":"Root","year":"2004","journal-title":"Curr. Pharm. Des."},{"key":"2026080608124936800_cit2","doi-asserted-by":"publisher","first-page":"2228","DOI":"10.1056\/NEJMra022812","article-title":"Novel Therapies Based on Mechanisms of HIV-1 Cell Entry","volume":"348","author":"Kilby","year":"2003","journal-title":"N. Engl. J. Med."},{"key":"2026080608124936800_cit3","doi-asserted-by":"publisher","first-page":"1234","DOI":"10.1016\/j.bbamem.2010.02.010","article-title":"Unravelling\nthe Molecular Basis of the Selectivity of the HIV-1 Fusion Inhibitor\nSifuvirtide Towards Phosphatidylcholine-Rich Rgid Membranes","volume":"1798","author":"Franquelim","year":"2010","journal-title":"Biochim. Biophys. Acta Gen. Subj."},{"key":"2026080608124936800_cit4","doi-asserted-by":"publisher","first-page":"878","DOI":"10.1016\/j.tim.2019.06.002","article-title":"Molecular\nMechanism of HIV-1 Entry","volume":"27","author":"Chen","year":"2019","journal-title":"Trends Microbiol."},{"key":"2026080608124936800_cit5","doi-asserted-by":"publisher","first-page":"857","DOI":"10.1038\/s41591-018-0042-6","article-title":"Epitope-based Vaccine\nDesign Yields Fusion Peptide-directed Antibodies that Neutralize Diverse\nStrains of HIV-1","volume":"24","author":"Xu","year":"2018","journal-title":"Nat. Med."},{"key":"2026080608124936800_cit6","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1038\/nature13808","article-title":"Structure\nand Immune\nRecognition of Trimeric Pre-fusion HIV-1 Env","volume":"514","author":"Pancera","year":"2014","journal-title":"Nature"},{"key":"2026080608124936800_cit7","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1111\/imr.12507","article-title":"The HIV-1 Envelope\nGlycoprotein Structure: Nailing\nDown a Moving Target","volume":"275","author":"Ward","year":"2017","journal-title":"Immunol. Rev."},{"key":"2026080608124936800_cit8","doi-asserted-by":"publisher","first-page":"5752","DOI":"10.1128\/JVI.03187-14","article-title":"Structure and Dynamics of the Native HIV-1 Env Trimer","volume":"89","author":"Munro","year":"2015","journal-title":"J. Virol."},{"key":"2026080608124936800_cit9","doi-asserted-by":"publisher","first-page":"138","DOI":"10.1038\/nature13601","article-title":"Broad and Potent HIV-1 Neutralization by a Human Antibody\nthat Binds the Gp41\u2013Gp120 Interface","volume":"515","author":"Huang","year":"2014","journal-title":"Nature"},{"key":"2026080608124936800_cit10","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1016\/S0304-4157(00)00014-9","article-title":"Maturation of HIV Envelope\nGlycoprotein Precursors\nby Cellular Endoproteases","volume":"1469","author":"Moulard","year":"2000","journal-title":"Biochim. Biophys.\nActa Gen. Subj."},{"key":"2026080608124936800_cit11","doi-asserted-by":"publisher","first-page":"777","DOI":"10.1146\/annurev.biochem.70.1.777","article-title":"Mechanisms of Viral\nMembrane Fusion and Its Inhibition","volume":"70","author":"Eckert","year":"2001","journal-title":"Annu. Rev.\nBiochem."},{"key":"2026080608124936800_cit12","doi-asserted-by":"publisher","first-page":"828","DOI":"10.1126\/science.aae0474","article-title":"Fusion\nPeptide of HIV-1 as a Site of Vulnerability to Neutralizing Antibody","volume":"352","author":"Kong","year":"2016","journal-title":"Science"},{"key":"2026080608124936800_cit13","doi-asserted-by":"publisher","first-page":"763","DOI":"10.1038\/s41467-019-08738-5","article-title":"Capturing\nthe Inherent Structural\nDynamics of the HIV-1 Envelope Glycoprotein Fusion Peptide","volume":"10","author":"Kumar","year":"2019","journal-title":"Nat. Commun."},{"key":"2026080608124936800_cit14","doi-asserted-by":"publisher","first-page":"16199","DOI":"10.1038\/nmicrobiol.2016.199","article-title":"An HIV-1 Antibody from an Elite Neutralizer Implicates\nthe Fusion Peptide as a Site of Vulnerability","volume":"2","author":"van Gils","year":"2016","journal-title":"Nat. Microbiol."},{"key":"2026080608124936800_cit15","doi-asserted-by":"publisher","first-page":"873","DOI":"10.1016\/j.chom.2019.04.011","article-title":"Conformational Plasticity\nin the HIV-1 Fusion Peptide\nFacilitates Recognition by Broadly Neutralizing Antibodies","volume":"25","author":"Yuan","year":"2019","journal-title":"Cell Host Microbe"},{"key":"2026080608124936800_cit16","doi-asserted-by":"publisher","first-page":"7593","DOI":"10.1038\/s41467-023-42098-5","article-title":"Antibody-Directed Evolution Reveals a Mechanism for\nEnhanced Neutralization at the HIV-1 Fusion Peptide Site","volume":"14","author":"Banach","year":"2023","journal-title":"Nat. Commun."},{"key":"2026080608124936800_cit17","doi-asserted-by":"publisher","first-page":"12a","DOI":"10.1016\/j.bpj.2024.11.137","article-title":"Rational Engineering\nof HIV-1 Env to Enhance Recognition of Fusion Peptide in a Glycan-Dependent\nManner","volume":"124","author":"Thakur","year":"2025","journal-title":"Biophys. 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B"},{"key":"2026080608124936800_cit21","doi-asserted-by":"publisher","first-page":"111398","DOI":"10.1016\/j.foodhyd.2025.111398","article-title":"Enhancing\nProtein Interactions in Zein-\u03b2-Lactoglobulin Complexes by (\u2212)-Epigallocatechin-3-Gallate:\nExpanding the Potential of Molecular Glues in Food Application","volume":"167","author":"Jiao","year":"2025","journal-title":"Food Hydrocoll"},{"key":"2026080608124936800_cit22","doi-asserted-by":"publisher","first-page":"13110696","DOI":"10.1016\/j.foodhyd.2024.110696","article-title":"How the ovalbumin modulates the conformation\nof zein through protein-protein interactions","volume":"159","author":"Xie","year":"2025","journal-title":"Food Hydrocolloids"},{"key":"2026080608124936800_cit23","doi-asserted-by":"publisher","first-page":"15813","DOI":"10.1021\/jp805529z","article-title":"Single\nMutation Induced H3N2 Hemagglutinin Antibody\nNeutralization: a Free Energy Perturbation Study","volume":"112","author":"Zhou","year":"2008","journal-title":"J. Phys. Chem. B"},{"key":"2026080608124936800_cit24","doi-asserted-by":"publisher","first-page":"6709","DOI":"10.1021\/acs.jctc.6c00593","article-title":"Enhancing Relative\nBinding Free Energy Calculation\nwith Grand Canonical Monte Carlo, Water-swap Monte Carlo, Terminal-flip\nMonte Carlo and Replica Exchange Solute Tempering","volume":"22","author":"Hui","year":"2026","journal-title":"J. Chem. Theory Comput."},{"key":"2026080608124936800_cit25","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1021\/ct700301q","article-title":"GROMACS 4: Algorithms\nfor Highly Efficient, Load-Balanced, and Scalable Molecular Simulation","volume":"4","author":"Hess","year":"2008","journal-title":"J. Chem. Theory Comput."},{"key":"2026080608124936800_cit26","doi-asserted-by":"publisher","first-page":"134110","DOI":"10.1063\/5.0018516","article-title":"Heterogeneous Parallelization\nand Acceleration of Molecular Dynamics Simulations in GROMACS","volume":"153","author":"Pa\u0301ll","year":"2020","journal-title":"J. Chem. Phys."},{"key":"2026080608124936800_cit27","doi-asserted-by":"publisher","first-page":"3586","DOI":"10.1021\/jp973084f","article-title":"All-Atom Empirical\nPotential for Molecular Modeling\nand Dynamics Studies of Proteins","volume":"102","author":"MacKerell","year":"1998","journal-title":"J. Phys. Chem.\nB"},{"key":"2026080608124936800_cit28","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1063\/1.445869","article-title":"Comparison\nof Simple Potential Functions for Simulating Liquid Water","volume":"79","author":"Jorgensen","year":"1983","journal-title":"J. Chem. Phys."},{"key":"2026080608124936800_cit29","doi-asserted-by":"publisher","first-page":"1165","DOI":"10.1007\/s10118-026-3568-y","article-title":"Length-dependent\nNanopore Transport and Surface-induced\nUnfolding of Polyglutamine Chains","volume":"44","author":"Feng","year":"2026","journal-title":"Chin. J.\nPolym. Sci."},{"key":"2026080608124936800_cit30","doi-asserted-by":"publisher","first-page":"131356","DOI":"10.1016\/j.ijbiomac.2024.131356","article-title":"In Silico Design of\nHigh-affinity Antigenic Peptides for HLA-B44","volume":"267","author":"Feng","year":"2024","journal-title":"Int. J. Biol. Macromol."},{"key":"2026080608124936800_cit31","doi-asserted-by":"publisher","first-page":"6107","DOI":"10.1039\/D0SC06946A","article-title":"Molecular\nMechanism of Secreted Amyloid-\u03b2 Precursor Protein in Binding\nand Modulating GABA(B)R1a","volume":"12","author":"Feng","year":"2021","journal-title":"Chem. Sci."},{"key":"2026080608124936800_cit32","doi-asserted-by":"publisher","first-page":"10089","DOI":"10.1063\/1.464397","article-title":"Particle Mesh Ewald: An N log (N)\nMethod for Ewald Sums in Large Systems","volume":"98","author":"Darden","year":"1993","journal-title":"J. Chem.\nPhys."},{"key":"2026080608124936800_cit33","doi-asserted-by":"publisher","first-page":"1463","DOI":"10.1002\/(sici)1096-987x(199709)18:12&lt;1463::aid-jcc4&gt;3.0.co;2-h","article-title":"A Linear Constraint\nSolver for Molecular Simulations","volume":"18","author":"Hess","year":"1997","journal-title":"J. Comput.\nChem."},{"key":"2026080608124936800_cit34","doi-asserted-by":"publisher","first-page":"014101","DOI":"10.1063\/1.2408420","article-title":"Canonical\nSampling Through Velocity\nRescaling","volume":"126","author":"Bussi","year":"2007","journal-title":"J. Chem. Phys."},{"key":"2026080608124936800_cit35","doi-asserted-by":"publisher","first-page":"5727","DOI":"10.1021\/acs.jctc.9b00548","article-title":"Insights\nInto Membrane Protein-Lipid Interactions from Free Energy Calculations","volume":"15","author":"Corey","year":"2019","journal-title":"J. Chem. Theory Comput."},{"key":"2026080608124936800_cit36","doi-asserted-by":"publisher","first-page":"715","DOI":"10.1002\/jcc.26036","article-title":"Alchemical\nGrid Dock (AlGDock): Binding Free Energy Calculations between Flexible\nLigands and Rigid Receptors","volume":"41","author":"Minh","year":"2020","journal-title":"J. Comput. Chem."},{"key":"2026080608124936800_cit37","doi-asserted-by":"publisher","first-page":"3794","DOI":"10.1021\/acs.jcim.9b00362","article-title":"Computing Relative Binding Affinity\nof Ligands to Receptor: An Effective Hybrid Single-Dual-Topology Free-Energy\nPerturbation Approach in NAMD","volume":"59","author":"Jiang","year":"2019","journal-title":"J. Chem. Inf.\nModel."},{"key":"2026080608124936800_cit38","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1007\/978-1-0716-1209-5_12","article-title":"Free Energy\nCalculations for Protein-Ligand Binding Prediction","volume":"2266","author":"Jespers","year":"2021","journal-title":"Methods Mol. Biol."},{"key":"2026080608124936800_cit39","doi-asserted-by":"publisher","first-page":"168640","DOI":"10.1016\/j.jmb.2024.168640","article-title":"Robust Prediction\nof Relative Binding Energies for Protein-Protein Complex Mutations\nUsing Free Energy Perturbation Calculations","volume":"436","author":"Sampson","year":"2024","journal-title":"J. Mol. Biol."},{"key":"2026080608124936800_cit40","doi-asserted-by":"publisher","first-page":"8486","DOI":"10.1073\/pnas.1913242117","article-title":"In Silico Design and\nValidation of High-Affinity RNA Aptamers Targeting\nEpithelial Cellular Adhesion Molecule Dimers","volume":"117","author":"Bell","year":"2020","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2026080608124936800_cit41","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2214430120","article-title":"A Mutagenesis Study of Autoantigen\nOptimization for Potential T1D Vaccine Design","volume":"120","author":"Song","year":"2023","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2026080608124936800_cit42","doi-asserted-by":"publisher","first-page":"3715","DOI":"10.1038\/s41467-023-39410-8","article-title":"Mutagenesis and Structural\nStudies Reveal the Basis for the Specific Binding of SARS-CoV-2 SL3\nRNA Element with Human TIA1 Protein","volume":"14","author":"Zhang","year":"2023","journal-title":"Nat. Commun."},{"key":"2026080608124936800_cit43","doi-asserted-by":"publisher","first-page":"1654","DOI":"10.1002\/jcc.21274","article-title":"Free Energy Simulations\nReveal a\nDouble Mutant Avian H5N1 Virus Hemagglutinin with Altered Receptor\nBinding Specificity","volume":"30","author":"Das","year":"2009","journal-title":"J. Comput. Chem."},{"key":"2026080608124936800_cit44","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1006\/jmbi.1994.1430","article-title":"Decomposition of the Free Energy of a System in Terms\nof Specific Interactions-Implications for Theoretical and Experimental\nStudies","volume":"240","author":"Mark","year":"1994","journal-title":"J. Mol. Biol."},{"key":"2026080608124936800_cit45","doi-asserted-by":"publisher","first-page":"801","DOI":"10.1006\/jmbi.1995.0656","article-title":"The Meaning of Component Analysis: Decomposition of\nthe Free Energy in Terms of Specific Interactions","volume":"254","author":"Boresch","year":"1995","journal-title":"J. Mol. Biol."},{"key":"2026080608124936800_cit46","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1006\/jmbi.1995.0600","article-title":"Decomposition of\nInteraction Free Energies in Proteins\nand Other Complex Systems","volume":"254","author":"Brady","year":"1995","journal-title":"J. Mol. Biol."},{"key":"2026080608124936800_cit47","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1007\/s00214-007-0264-z","article-title":"Do All Pieces\nMake\na Whole? Thiele Cumulants and the Free Energy Decomposition","volume":"117","author":"Bren","year":"2007","journal-title":"Theor. Chem. Acc."},{"key":"2026080608124936800_cit48","doi-asserted-by":"publisher","first-page":"18569","DOI":"10.1039\/C9CP02909E","article-title":"Exploration\nof HIV-1 fusion peptide\u2013antibody VRC34.01 binding reveals fundamental\nneutralization sites","volume":"21","author":"Feng","year":"2019","journal-title":"Phys. Chem. Chem. Phys."}],"container-title":["The Journal of Physical\nChemistry B"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jpcb.6c03661","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jpcbfk\/article-pdf\/130\/31\/7892\/66288051\/acs.jpcb.6c03661.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jpcbfk\/article-pdf\/130\/31\/7892\/66288051\/acs.jpcb.6c03661.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T12:25:24Z","timestamp":1786019124000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jpcbfk\/article\/130\/31\/7892\/5234427\/In-Silico-Design-of-High-Affinity-Antibody-VRC34"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,27]]},"references-count":48,"journal-issue":{"issue":"31","published-online":{"date-parts":[[2026,7,27]]},"published-print":{"date-parts":[[2026,8,6]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jpcb.6c03661","relation":{},"ISSN":["1520-6106","1520-5207"],"issn-type":[{"value":"1520-6106","type":"print"},{"value":"1520-5207","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,27]]}}}