title: Large scale characterization of the LC13 TCR and HLA-B8 structural landscape in reaction to 172 altered peptide ligands: a molecular dynamics simulation study.
abstract: The interplay between T cell receptors (TCRs) and peptides bound by major histocompatibility complexes (MHCs) is one of the most important interactions in the adaptive immune system. Several previous studies have computationally investigated their structural dynamics. On the basis of these simulations several structural and dynamical properties have been proposed as effectors of the immunogenicity. Here we present the results of a large scale Molecular Dynamics simulation study consisting of 100 ns simulations of 172 different complexes. These complexes consisted of all possible point mutations of the Epstein Barr Virus peptide FLRGRAYGL bound by HLA-B*08:01 and presented to the LC13 TCR. We compare the results of these 172 structural simulations with experimental immunogenicity data. We found that simulations with more immunogenic peptides and those with less immunogenic peptides are in fact highly similar and on average only minor differences in the hydrogen binding footprints, interface distances, and the relative orientation between the TCR chains are present. Thus our large scale data analysis shows that many previously suggested dynamical and structural properties of the TCR/peptide/MHC interface are unlikely to be conserved causal factors for peptide immunogenicity.
authors.affiliation: Department of Statistics, Protein Informatics Group, University of Oxford, Oxford, United Kingdom.
authors.forename: Bernhard
authors.initials: B
authors.lastname: Knapp
authors.affiliation: Department of Statistics, Protein Informatics Group, University of Oxford, Oxford, United Kingdom.
authors.forename: James
authors.initials: J
authors.lastname: Dunbar
authors.affiliation: Department of Statistics, Protein Informatics Group, University of Oxford, Oxford, United Kingdom.
authors.forename: Charlotte M
authors.initials: CM
authors.lastname: Deane
mesh_terms: D019295:Computational Biology; D015795:HLA-B8 Antigen / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D011948:Receptors, Antigen, T-Cell / Q000737:chemistry* / Q000378:metabolism
chemical_list: D015795:HLA-B8 Antigen; D010455:Peptides; D011948:Receptors, Antigen, T-Cell
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