title: Cis-trans isomerization of the Epstein-Barr virus determinant peptide EENLLDFVRF after the DM1 TCR recognition of the HLA-B*4405/peptide complex.
abstract: The Epstein-Barr virus determinant peptide EENLLDFVRF shows high immunogenicity when presented by HLA-B*4405 allotype. This fact is accompanied by a cis-trans isomerization of the Leu5-Asp6 peptide bond upon TCR binding of the pMHC complex. Molecular dynamics simulations of pMHC/TCR structures, with the EENLLDFVRF peptide in cis and trans conformations have been employed in order to examine the structure and dynamics of the pMHC complex with such an unusual conformation. The results, based on MM-PBSA free energy computations as well as buried surface area analysis and interactions at the pMHC/TCR interface, indicate that the TCR binds preferably the pMHC complex with the Leu5-Asp6 peptide bond in cis conformation. It is the first time that this notable conformational feature of T-cell epitope is investigated.
authors.affiliation: Department of Economics, University of Ioannina, Ioannina, Greece. astavrak@cc.uoi.gr
authors.forename: Athanassios
authors.initials: A
authors.lastname: Stavrakoudis
mesh_terms: D019295:Computational Biology / Q000379:methods; D000939:Epitopes / Q000737:chemistry* / Q000276:immunology / Q000378:metabolism; D018984:Epitopes, T-Lymphocyte / Q000737:chemistry* / Q000276:immunology / Q000378:metabolism; D019309:Epstein-Barr Virus Nuclear Antigens / Q000737:chemistry* / Q000276:immunology / Q000378:metabolism; D015235:HLA-B Antigens / Q000737:chemistry* / Q000276:immunology / Q000378:metabolism; D006801:Humans; D007536:Isomerism; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry* / Q000276:immunology / Q000378:metabolism; D010446:Peptide Fragments / Q000737:chemistry* / Q000276:immunology / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D011948:Receptors, Antigen, T-Cell / Q000737:chemistry* / Q000276:immunology / Q000378:metabolism; D014764:Viral Proteins / Q000737:chemistry* / Q000276:immunology / Q000378:metabolism
chemical_list: D000939:Epitopes; D018984:Epitopes, T-Lymphocyte; D019309:Epstein-Barr Virus Nuclear Antigens; D015235:HLA-B Antigens; D009842:Oligopeptides; D010446:Peptide Fragments; D011948:Receptors, Antigen, T-Cell; D014764:Viral Proteins; C556584:glutamyl-glutamyl-asparagyl-leucyl-leucyl-aspartyl-phenylalanyl-valyl-arginyl-phenylalanine