OmpA: gating and dynamics via molecular dynamics simulations

Biochim Biophys Acta. 2008 Sep;1778(9):1871-80. doi: 10.1016/j.bbamem.2007.05.024. Epub 2007 Jun 2.

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Bacterial Outer Membrane Proteins / chemistry
  • Bacterial Outer Membrane Proteins / metabolism*
  • Bacterial Outer Membrane Proteins / physiology*
  • Computer Simulation*
  • Escherichia coli
  • Ion Channel Gating / physiology*
  • Kinetics
  • Models, Biological
  • Models, Molecular
  • Pasteurella multocida
  • Protein Conformation
  • Pseudomonas aeruginosa
  • Sequence Homology
  • Static Electricity

Substances

  • Bacterial Outer Membrane Proteins
  • OMPA outer membrane proteins