title: Relative Movements of Domains in Large Molecules of the Immune System.
abstract: Molecular dynamics was used to simulate large molecules of the immune system (major histocompatibility complex class I, presented epitope, T-cell receptor, and a CD8 coreceptor.) To characterize the relative orientation and movements of domains local coordinate systems (based on principal component analysis) were generated and directional cosines and Euler angles were computed. As a most interesting result, we found that the presence of the coreceptor seems to influence the dynamics within the protein complex, in particular the relative movements of the two α-helices, Gα1 and Gα2.
authors.affiliation: Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Schreiner
authors.affiliation: Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria.
authors.forename: Rudolf
authors.initials: R
authors.lastname: Karch
authors.affiliation: Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria.
authors.forename: Reiner
authors.initials: R
authors.lastname: Ribarics
authors.affiliation: Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria.
authors.forename: Michael
authors.initials: M
authors.lastname: Cibena
authors.affiliation: Institute of Information and Communication Technologies (IICT), Bulgarian Academy of Sciences, 25 A, Acad. G. Bonchev Street, 1113 Sofia, Bulgaria.
authors.forename: Nevena
authors.initials: N
authors.lastname: Ilieva
mesh_terms: D001665:Binding Sites; D016827:CD8 Antigens / Q000737:chemistry* / Q000276:immunology; D015796:HLA-B27 Antigen / Q000737:chemistry* / Q000276:immunology; D006801:Humans; D054992:Immunological Synapses / Q000737:chemistry / Q000276:immunology; D016018:Least-Squares Analysis; D056004:Molecular Dynamics Simulation; D009154:Mutation; D010455:Peptides / Q000737:chemistry* / Q000276:immunology; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D017433:Protein Structure, Secondary; D016693:Receptors, Antigen, T-Cell, alpha-beta / Q000737:chemistry* / Q000276:immunology; D040681:Structural Homology, Protein; D001613:beta 2-Microglobulin / Q000737:chemistry* / Q000276:immunology
chemical_list: D016827:CD8 Antigens; C409469:CD8 antigen, alpha chain; C090660:HLA-B protein, human; D015796:HLA-B27 Antigen; D010455:Peptides; D016693:Receptors, Antigen, T-Cell, alpha-beta; D001613:beta 2-Microglobulin