title: Molecular dynamics simulations of a membrane protein/amphipol complex.
abstract: Amphipathic polymers known as "amphipols" provide a highly stabilizing environment for handling membrane proteins in aqueous solutions. A8-35, an amphipol with a polyacrylate backbone and hydrophobic grafts, has been extensively characterized and widely employed for structural and functional studies of membrane proteins using biochemical and biophysical approaches. Given the sensitivity of membrane proteins to their environment, it is important to examine what effects amphipols may have on the structure and dynamics of the proteins they complex. Here we present the first molecular dynamics study of an amphipol-stabilized membrane protein, using Escherichia coli OmpX as a model. We begin by describing the structure of the complexes formed by supplementing OmpX with increasing amounts of A8-35, in order to determine how the amphipol interacts with the transmembrane and extramembrane surfaces of the protein. We then compare the dynamics of the protein in either A8-35, a detergent, or a lipid bilayer. We find that protein dynamics on all accessible length scales is restrained by A8-35, which provides a basis to understanding some of the stabilizing and functional effects of amphipols that have been experimentally observed.
authors.affiliation: Department of Physics, Brandeis University, 415 South Street, Waltham, MA, 02453, USA, perlm@brandeis.edu.
authors.forename: Jason D
authors.initials: JD
authors.lastname: Perlmutter
authors.forename: Jean-Luc
authors.initials: JL
authors.lastname: Popot
authors.forename: Jonathan N
authors.initials: JN
authors.lastname: Sachs
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D002462:Cell Membrane / Q000737:chemistry* / Q000648:ultrastructure*; D003198:Computer Simulation; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D006867:Hydrolases / Q000737:chemistry* / Q000648:ultrastructure*; D057927:Hydrophobic and Hydrophilic Interactions; D008051:Lipid Bilayers / Q000737:chemistry; D008954:Models, Biological; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D011108:Polymers / Q000737:chemistry*; D011437:Propylamines / Q000737:chemistry*; D011487:Protein Conformation; D012995:Solubility; D012996:Solutions; D013499:Surface Properties; D013501:Surface-Active Agents / Q000737:chemistry*; D014867:Water / Q000737:chemistry
chemical_list: D001425:Bacterial Outer Membrane Proteins; D029968:Escherichia coli Proteins; D008051:Lipid Bilayers; D011108:Polymers; D011437:Propylamines; D012996:Solutions; D013501:Surface-Active Agents; C499017:amphipol A8-35; D014867:Water; C482905:OmpX protein, E coli; D006867:Hydrolases