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Modeling and simulations of a bacterial outer membrane protein: OprF from Pseudomonas aeruginosa

Modeling and simulations of a bacterial outer membrane protein: OprF from Pseudomonas aeruginosa
Modeling and simulations of a bacterial outer membrane protein: OprF from Pseudomonas aeruginosa
OprF is a major outer membrane protein from Pseudomonas aeruginosa, a homolog of OmpA from Escherichia coli. The N-terminal domains of both proteins have been demonstrated to form low conductance channels in lipid bilayers. Homology models, consisting of an eight-stranded -barrel, of the N-terminal domain OprF have been constructed based on the crystal structure of the corresponding domain from E. coli OmpA. OprF homology models have been evaluated via a set (6 × 10 ns) of simulations of the -barrel embedded within a solvated dimyristoyl-phosphatidylcholine (DMPC) bilayer. The conformational stability of the models is similar to that of the crystal structure of OmpA in comparable simulations. There is a degree of water penetration into the pore-like center of the OprF barrel. The presence of an acidic/basic (E8/K121) side-chain interaction within the OprF barrel may form a gate able to close/open a central pore. Lipid-protein interactions within the simulations were analyzed and revealed that aromatic side-chains (Trp, Tyr) of OprF interact with lipid headgroups. Overall, the behavior of the OprF model in simulations supports the suggestion that this molecule is comparable to OmpA. The simulations help to explain the mechanism of formation of low conductance pores within the outer membrane.
dimyristoyl-phosphatidylcholine, outer membrane proteins, molecular dynamics, OmpA N-terminal domain, homology model
0887-3585
6-15
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
Bond, Peter J.
08f46940-85e8-44c4-a368-d94342a10fd6
Deol, Sundeep S.
d45d1bcd-9065-4b44-99c5-a0c33d70c368
Sansom, Mark S.P.
ed30b4fc-bc73-4ad7-8c56-f51a67136e4e
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
Bond, Peter J.
08f46940-85e8-44c4-a368-d94342a10fd6
Deol, Sundeep S.
d45d1bcd-9065-4b44-99c5-a0c33d70c368
Sansom, Mark S.P.
ed30b4fc-bc73-4ad7-8c56-f51a67136e4e

Khalid, Syma, Bond, Peter J., Deol, Sundeep S. and Sansom, Mark S.P. (2006) Modeling and simulations of a bacterial outer membrane protein: OprF from Pseudomonas aeruginosa. Proteins: Structure, Function, and Bioinformatics, 63 (1), 6-15. (doi:10.1002/prot.20845).

Record type: Article

Abstract

OprF is a major outer membrane protein from Pseudomonas aeruginosa, a homolog of OmpA from Escherichia coli. The N-terminal domains of both proteins have been demonstrated to form low conductance channels in lipid bilayers. Homology models, consisting of an eight-stranded -barrel, of the N-terminal domain OprF have been constructed based on the crystal structure of the corresponding domain from E. coli OmpA. OprF homology models have been evaluated via a set (6 × 10 ns) of simulations of the -barrel embedded within a solvated dimyristoyl-phosphatidylcholine (DMPC) bilayer. The conformational stability of the models is similar to that of the crystal structure of OmpA in comparable simulations. There is a degree of water penetration into the pore-like center of the OprF barrel. The presence of an acidic/basic (E8/K121) side-chain interaction within the OprF barrel may form a gate able to close/open a central pore. Lipid-protein interactions within the simulations were analyzed and revealed that aromatic side-chains (Trp, Tyr) of OprF interact with lipid headgroups. Overall, the behavior of the OprF model in simulations supports the suggestion that this molecule is comparable to OmpA. The simulations help to explain the mechanism of formation of low conductance pores within the outer membrane.

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Published date: 1 April 2006
Keywords: dimyristoyl-phosphatidylcholine, outer membrane proteins, molecular dynamics, OmpA N-terminal domain, homology model

Identifiers

Local EPrints ID: 48165
URI: http://eprints.soton.ac.uk/id/eprint/48165
ISSN: 0887-3585
PURE UUID: d375471a-ab68-462c-bd7e-08e8bd3eb620
ORCID for Syma Khalid: ORCID iD orcid.org/0000-0002-3694-5044

Catalogue record

Date deposited: 31 Aug 2007
Last modified: 17 Dec 2019 01:44

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