title: Geometric analysis of alloreactive HLA α-helices.
abstract: Molecular dynamics (MD) is a valuable tool for the investigation of functional elements in biomolecules, providing information on dynamic properties and processes. Previous work by our group has characterized static geometric properties of the two MHC α-helices comprising the peptide binding region recognized by T cells. We build upon this work and used several spline models to approximate the overall shape of MHC α-helices. We applied this technique to a series of MD simulations of alloreactive MHC molecules that allowed us to capture the dynamics of MHC α-helices' steric configurations. Here, we discuss the variability of spline models underlying the geometric analysis with varying polynomial degrees of the splines.
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.identifier: 0000-0002-5743-5166
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: Rudolf
authors.initials: R
authors.lastname: Karch
authors.affiliation: Institute for Nuclear Research and Nuclear Energy (INRNE), Bulgarian Academy of Sciences 72, Tzarigradsko Chaussee, Sofia 1784, Bulgaria.
authors.forename: Nevena
authors.identifier: 0000-0002-2372-2319
authors.initials: N
authors.lastname: Ilieva
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
mesh_terms: D006680:HLA Antigens / Q000737:chemistry*; D006801:Humans; D056004:Molecular Dynamics Simulation; D017433:Protein Structure, Secondary
chemical_list: D006680:HLA Antigens