title: OmpA: gating and dynamics via molecular dynamics simulations.
abstract: Outer membrane proteins (OMPs) of Gram-negative bacteria have a variety of functions including passive transport, active transport, catalysis, pathogenesis and signal transduction. Whilst the structures of approximately 25 OMPs are currently known, there is relatively little known about their dynamics in different environments. The outer membrane protein, OmpA from Escherichia coli has been studied extensively in different environments both experimentally and computationally, and thus provides an ideal test case for the study of the dynamics and environmental interactions of outer membrane proteins. We review molecular dynamics simulations of OmpA and its homologues in a variety of different environments and discuss possible mechanisms of pore gating. The transmembrane domain of E. coli OmpA shows subtle differences in dynamics and interactions between a detergent micelle and a lipid bilayer environment. Simulations of the crystallographic unit cell reveal a micelle-like network of detergent molecules interacting with the protein monomers. Simulation and modelling studies emphasise the role of an electrostatic-switch mechanism in the pore-gating mechanism. Simulation studies have been extended to comparative models of OmpA homologues from Pseudomonas aeruginosa (OprF) and Pasteurella multocida (PmOmpA), the latter model including the periplasmic C-terminal domain.
authors.affiliation: Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
authors.forename: Syma
authors.initials: S
authors.lastname: Khalid
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Bond
authors.forename: Timothy
authors.initials: T
authors.lastname: Carpenter
authors.forename: Mark S P
authors.initials: MS
authors.lastname: Sansom
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry / Q000378:metabolism* / Q000502:physiology*; D003198:Computer Simulation; D004926:Escherichia coli; D015640:Ion Channel Gating / Q000502:physiology*; D007700:Kinetics; D008954:Models, Biological; D008958:Models, Molecular; D016979:Pasteurella multocida; D011487:Protein Conformation; D011550:Pseudomonas aeruginosa; D017385:Sequence Homology; D055672:Static Electricity
chemical_list: D001425:Bacterial Outer Membrane Proteins; C078167:OMPA outer membrane proteins