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OmpA: Gating and dynamics via molecular dynamics simulations

OmpA: Gating and dynamics via molecular dynamics simulations
OmpA: Gating and dynamics via molecular dynamics simulations
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 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.
outer membrane protein, ompA, molecular dynamics, homology model
0304-4165
1871-1880
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
Bond, Peter J.
08f46940-85e8-44c4-a368-d94342a10fd6
Carpenter, Timothy
b495994c-934e-4788-8f54-e4d47ddfeb1a
Sansom, Mark S.P.
ed30b4fc-bc73-4ad7-8c56-f51a67136e4e
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
Bond, Peter J.
08f46940-85e8-44c4-a368-d94342a10fd6
Carpenter, Timothy
b495994c-934e-4788-8f54-e4d47ddfeb1a
Sansom, Mark S.P.
ed30b4fc-bc73-4ad7-8c56-f51a67136e4e

Khalid, Syma, Bond, Peter J., Carpenter, Timothy and Sansom, Mark S.P. (2008) OmpA: Gating and dynamics via molecular dynamics simulations. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1778 (9), 1871-1880. (doi:10.1016/j.bbamem.2007.05.024).

Record type: Article

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 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.

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More information

Published date: September 2008
Keywords: outer membrane protein, ompA, molecular dynamics, homology model

Identifiers

Local EPrints ID: 149549
URI: http://eprints.soton.ac.uk/id/eprint/149549
ISSN: 0304-4165
PURE UUID: c6416348-b7b4-4489-9584-a84074f2d131
ORCID for Syma Khalid: ORCID iD orcid.org/0000-0002-3694-5044

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Date deposited: 30 Apr 2010 13:15
Last modified: 26 Nov 2019 01:43

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Contributors

Author: Syma Khalid ORCID iD
Author: Peter J. Bond
Author: Timothy Carpenter
Author: Mark S.P. Sansom

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