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A multidomain outer membrane protein from Pasteurella multocida: Modelling and simulation studies of PmOmpA

A multidomain outer membrane protein from Pasteurella multocida: Modelling and simulation studies of PmOmpA
A multidomain outer membrane protein from Pasteurella multocida: Modelling and simulation studies of PmOmpA
PmOmpA is a two-domain outer membrane protein from Pasteurella multocida. The N-terminal domain of PmOmpA is a homologue of the transmembrane ?-barrel domain of OmpA from Escherichia coli, whilst the C-terminal domain of PmOmpA is a homologue of the extra-membrane Neisseria meningitidis RmpM C-terminal domain. This enables a model of a complete two domain PmOmpA to be constructed and its conformational dynamics explored via MD simulations of the protein embedded within two different phospholipid bilayers (DMPC and DMPE). The conformational stability of the transmembrane ?-barrel is similar to that of a homology model of OprF from Pseudomonas aeruginosa in bilayer simulations. There is a degree of water penetration into the interior of the ?-barrel, suggestive of a possible transmembrane pore. Although the PmOmpA model is stable over 20 ns simulations, retaining its secondary structure and fold integrity throughout, substantial flexibility is observed in a short linker region between the N- and the C-terminal domains. At low ionic strength, the C-terminal domain moves to interact electrostatically with the lipid bilayer headgroups. This study demonstrates that computational approaches may be applied to more complex, multi-domain outer membrane proteins, rather than just to transmembrane ?-barrels, opening the possibility of in silico proteomics approaches to such proteins.
0304-4165
2831-2840
Carpenter, Timothy
b495994c-934e-4788-8f54-e4d47ddfeb1a
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
Sansom, Mark S.P.
ed30b4fc-bc73-4ad7-8c56-f51a67136e4e
Carpenter, Timothy
b495994c-934e-4788-8f54-e4d47ddfeb1a
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
Sansom, Mark S.P.
ed30b4fc-bc73-4ad7-8c56-f51a67136e4e

Carpenter, Timothy, Khalid, Syma and Sansom, Mark S.P. (2007) A multidomain outer membrane protein from Pasteurella multocida: Modelling and simulation studies of PmOmpA. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1768 (11), 2831-2840. (doi:10.1016/j.bbamem.2007.07.025).

Record type: Article

Abstract

PmOmpA is a two-domain outer membrane protein from Pasteurella multocida. The N-terminal domain of PmOmpA is a homologue of the transmembrane ?-barrel domain of OmpA from Escherichia coli, whilst the C-terminal domain of PmOmpA is a homologue of the extra-membrane Neisseria meningitidis RmpM C-terminal domain. This enables a model of a complete two domain PmOmpA to be constructed and its conformational dynamics explored via MD simulations of the protein embedded within two different phospholipid bilayers (DMPC and DMPE). The conformational stability of the transmembrane ?-barrel is similar to that of a homology model of OprF from Pseudomonas aeruginosa in bilayer simulations. There is a degree of water penetration into the interior of the ?-barrel, suggestive of a possible transmembrane pore. Although the PmOmpA model is stable over 20 ns simulations, retaining its secondary structure and fold integrity throughout, substantial flexibility is observed in a short linker region between the N- and the C-terminal domains. At low ionic strength, the C-terminal domain moves to interact electrostatically with the lipid bilayer headgroups. This study demonstrates that computational approaches may be applied to more complex, multi-domain outer membrane proteins, rather than just to transmembrane ?-barrels, opening the possibility of in silico proteomics approaches to such proteins.

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More information

Published date: November 2007

Identifiers

Local EPrints ID: 149569
URI: http://eprints.soton.ac.uk/id/eprint/149569
ISSN: 0304-4165
PURE UUID: 563e2628-d4eb-4102-baf9-9f582368e8da
ORCID for Syma Khalid: ORCID iD orcid.org/0000-0002-3694-5044

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Date deposited: 03 Jun 2010 13:57
Last modified: 14 Mar 2024 02:53

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Contributors

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

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