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A computational docking study on the pH dependence of peptide binding to HLA-B27 sub-types differentially associated with ankylosing spondylitis

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dc.contributor.authorÖZBEK SARICA, PEMRA
dc.contributor.authorsSercinoglu, Onur; Ozcan, Gulin; Kabas, Zeynep Kutlu; Ozbek, Pemra
dc.date.accessioned2022-03-12T20:27:28Z
dc.date.available2022-03-12T20:27:28Z
dc.date.issued2016
dc.description.abstractA single amino acid difference (Asp116His), having a key role in a pathogenesis pathway, distinguishes HLA-B*27:05 and HLA-B*27:09 sub-types as associated and non-associated with ankylosing spondylitis, respectively. In this study, molecular docking simulations were carried out with the aim of comprehending the differences in the binding behavior of both alleles at varying pH conditions. A library of modeled peptides was formed upon single point mutations aiming to address the effect of 20 naturally occurring amino acids at the binding core peptide positions. For both alleles, computational docking was applied using Autodock 4.2. Obtained free energies of binding (FEB) were compared within the peptide library and between the alleles at varying pH conditions. The amino acid preferences of each position were studied enlightening the role of each on binding. The preferred amino acids for each position of pVIPR were found to be harmonious with experimental studies. Our results indicate that, as the pH is lowered, the capacity of HLA-B*27:05 to bind peptides in the library is largely lost. Hydrogen bonding analysis suggests that the interaction between the main anchor positions of pVIPR and their respective binding pocket residues are affected from the pH the most, causing an overall shift in the FEB profiles.
dc.identifier.doi10.1007/s10822-016-9934-z
dc.identifier.eissn1573-4951
dc.identifier.issn0920-654X
dc.identifier.pubmed27506766
dc.identifier.urihttps://hdl.handle.net/11424/233697
dc.identifier.wosWOS:000381982200006
dc.language.isoeng
dc.publisherSPRINGER
dc.relation.ispartofJOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
dc.rightsinfo:eu-repo/semantics/closedAccess
dc.subjectComputational molecular docking
dc.subjectAutodock 4.2
dc.subjectHLA docking
dc.subjectPeptide docking
dc.subjectHLA-B27
dc.subjectpH change
dc.subjectCross-presentation
dc.subjectMHC CLASS-I
dc.subjectHISTOCOMPATIBILITY COMPLEX-MOLECULES
dc.subjectCONTROLS PHAGOSOMAL PH
dc.subjectHLA CLASS-I
dc.subjectCROSS-PRESENTATION
dc.subjectDENDRITIC CELLS
dc.subjectEXOGENOUS ANTIGEN
dc.subjectSELF-PEPTIDE
dc.subjectPREDICTION
dc.subjectPROTEINS
dc.titleA computational docking study on the pH dependence of peptide binding to HLA-B27 sub-types differentially associated with ankylosing spondylitis
dc.typearticle
dspace.entity.typePublication
local.avesis.id7f2311b4-5c4a-4247-be7e-8de7965b2ab0
local.import.packageSS17
local.indexed.atWOS
local.indexed.atSCOPUS
local.indexed.atPUBMED
local.journal.numberofpages13
local.journal.quartileQ1
oaire.citation.endPage581
oaire.citation.issue7
oaire.citation.startPage569
oaire.citation.titleJOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
oaire.citation.volume30
relation.isAuthorOfPublication23dff805-7adb-4a47-9412-24e5d1012e63
relation.isAuthorOfPublication.latestForDiscovery23dff805-7adb-4a47-9412-24e5d1012e63

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