title: Early relaxation dynamics in the LC 13 T cell receptor in reaction to 172 altered peptide ligands: a molecular dynamics simulation study.
abstract: The interaction between the T cell receptor and the major histocompatibility complex is one of the most important events in adaptive immunology. Although several different models for the activation process of the T cell via the T cell receptor have been proposed, it could not be shown that a structural mechanism, which discriminates between peptides of different immunogenicity levels, exists within the T cell receptor. In this study, we performed systematic molecular dynamics simulations of 172 closely related altered peptide ligands in the same T cell receptor/major histocompatibility complex system. Statistical evaluations yielded significant differences in the initial relaxation process between sets of peptides at four different immunogenicity levels.
authors.affiliation: Center for Medical Statistics, Informatics and Intelligent Systems, Section for Biosimulation and Bioinformatics, Medical University of Vienna, Vienna, Austria. bernhard.knapp@meduniwien.ac.at
authors.forename: Bernhard
authors.initials: B
authors.lastname: Knapp
authors.forename: Georg
authors.initials: G
authors.lastname: Dorffner
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Schreiner
mesh_terms: D001665:Binding Sites; D006801:Humans; D008024:Ligands; D008285:Major Histocompatibility Complex / Q000276:immunology*; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry* / Q000276:immunology; D011485:Protein Binding; D011948:Receptors, Antigen, T-Cell / Q000737:chemistry* / Q000276:immunology; D013816:Thermodynamics
chemical_list: D008024:Ligands; D010455:Peptides; D011948:Receptors, Antigen, T-Cell