title: Transmembrane protein models based on high-throughput molecular dynamics simulations with experimental constraints.
abstract: Elucidating the structure of transmembrane proteins domains with high-resolution methods is a difficult and sometimes impossible task. Here, we explain the method of combining a limited amount of experimental data with automated high-throughput molecular dynamics (MD) simulations of alpha-helical transmembrane bundles in an explicit lipid bilayer/water environment. The procedure uses a systematic conformational search of the helix rotation with experimentally constrained MDs simulations. The experimentally determined helix tilt and rotational angle of a labeled residue with site-specific infrared dichroism allows us to select a unique high-resolution model from a number of possible energy minima encountered in the systematic conformational search.
authors.affiliation: Department of Biological Sciences, University of Warwick, Coventry, UK.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Beevers
authors.forename: Andreas
authors.initials: A
authors.lastname: Kukol
mesh_terms: D003198:Computer Simulation; D007700:Kinetics; D008051:Lipid Bilayers / Q000737:chemistry / Q000378:metabolism; D008565:Membrane Proteins / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D014867:Water / Q000737:chemistry / Q000378:metabolism
chemical_list: D008051:Lipid Bilayers; D008565:Membrane Proteins; D014867:Water