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Assessing Peptide Binding to MHC II: An Accurate Semiempirical Quantum Mechanics Based Proposal

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dc.creatorOrtiz-Mahecha C.A.spa
dc.creatorBohórquez H.J.spa
dc.creatorAgudelo W.A.spa
dc.creatorPatarroyo M.A.spa
dc.creatorPatarroyo M.E.spa
dc.creatorSuárez C.F.spa
dc.date.accessioned2020-05-25T23:55:59Z
dc.date.available2020-05-25T23:55:59Z
dc.date.created2019spa
dc.description.abstractEstimating peptide-major histocompatibility complex (pMHC) binding using structural computational methods has an impact on understanding overall immune function triggering adaptive immune responses in MHC class II molecules. We developed a strategy for optimizing pMHC structure interacting with water molecules and for calculating the binding energy of receptor + ligand systems, such as HLA-DR1 + HA, HLA-DR1 + CLIP, HLA-DR2 + MBP, and HLA-DR3 + CLIP, as well as a monosubstitution panel. Taking pMHC's structural properties, we assumed that ?H ? -T?S would generate a linear model for estimating relative free energy change, using three semiempirical quantum methods (PM6, PM7, and FMO-SCC-DFTB3) along with the implicit solvent models, and considering proteins in neutral and charged states. Likewise, we confirmed our approach's effectiveness in calculating binding energies having high correlation with experimental data and low root-mean-square error ( less than 2 kcal/mol). All in all, our pipeline differentiates weak from strong peptide binders as a reliable method for studying pMHC interactions. © 2019 American Chemical Society.eng
dc.format.mimetypeapplication/pdf
dc.identifier.doihttps://doi.org/10.1021/acs.jcim.9b00672
dc.identifier.issn1549960X
dc.identifier.issn15499596
dc.identifier.urihttps://repository.urosario.edu.co/handle/10336/22284
dc.language.isoengspa
dc.publisherAmerican Chemical Societyspa
dc.relation.citationEndPage5160
dc.relation.citationIssueNo. 12
dc.relation.citationStartPage5148
dc.relation.citationTitleJournal of Chemical Information and Modeling
dc.relation.citationVolumeVol. 59
dc.relation.ispartofJournal of Chemical Information and Modeling, ISSN:1549960X, 15499596, Vol.59, No.12 (2019); pp. 5148-5160spa
dc.relation.urihttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85076244262&doi=10.1021%2facs.jcim.9b00672&partnerID=40&md5=cec6d248113953a4e898865e102576f4spa
dc.rights.accesRightsinfo:eu-repo/semantics/openAccess
dc.rights.accesoAbierto (Texto Completo)spa
dc.source.instnameinstname:Universidad del Rosariospa
dc.source.reponamereponame:Repositorio Institucional EdocURspa
dc.subject.keywordBindersspa
dc.subject.keywordFree energyspa
dc.subject.keywordMean square errorspa
dc.subject.keywordMoleculesspa
dc.subject.keywordPeptidesspa
dc.subject.keywordQuantum theoryspa
dc.subject.keywordAdaptive immune responsespa
dc.subject.keywordImmune functionspa
dc.subject.keywordImplicit solvent modelspa
dc.subject.keywordMajor histocompatibility complexspa
dc.subject.keywordRelative free energyspa
dc.subject.keywordReliable methodsspa
dc.subject.keywordRoot mean square errorsspa
dc.subject.keywordSemi-empirical quantum mechanicsspa
dc.subject.keywordBinding energyspa
dc.titleAssessing Peptide Binding to MHC II: An Accurate Semiempirical Quantum Mechanics Based Proposalspa
dc.typearticleeng
dc.type.hasVersioninfo:eu-repo/semantics/publishedVersion
dc.type.spaArtículospa
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