Journal
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
Volume 1768, Issue 11, Pages 2831-2840Publisher
ELSEVIER SCIENCE BV
DOI: 10.1016/j.bbamem.2007.07.025
Keywords
outer membrane protein; OmpA; molecular dynamics; homology model; RmpM; OprF
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Funding
- Biotechnology and Biological Sciences Research Council [B19456, BEP17032, BBS/B/16011] Funding Source: Medline
- Wellcome Trust Funding Source: Medline
- Biotechnology and Biological Sciences Research Council [B19456, BEP17032, BBS/B/16011] Funding Source: researchfish
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PmOmpA is a two-domain outer membrane protein from Pasteurella multocida. The N-terminal domain of PmOmpA is a homologue of the transmembrane beta-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 beta-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 beta-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, multidomain outer membrane proteins, rather than just to transmembrane beta-barrels, opening the possibility of in silico proteomics approaches to such proteins. (c) 2007 Elsevier B.V. All rights reserved.
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