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 beta-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 x 10 ns) of simulations of the beta-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.
Khalid
Syma
S
Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
Bond
Peter J
PJ
Deol
Sundeep S
SS
Sansom
Mark S P
MS
D001419:Bacteria / Q000378:metabolism*; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry; D055592:Biophysical Phenomena; D001703:Biophysics; D002462:Cell Membrane / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D004134:Dimyristoylphosphatidylcholine / Q000737:chemistry; D004926:Escherichia coli / Q000378:metabolism; D007477:Ions; D008051:Lipid Bilayers / Q000737:chemistry; D008055:Lipids / Q000737:chemistry; D008954:Models, Biological; D008958:Models, Molecular; D008968:Molecular Conformation; D018272:Porins / Q000737:chemistry* / Q000502:physiology*; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D040901:Proteomics / Q000379:methods*; D011550:Pseudomonas aeruginosa / Q000378:metabolism*; D014867:Water / Q000737:chemistry
D001425:Bacterial Outer Membrane Proteins; D007477:Ions; D008051:Lipid Bilayers; D008055:Lipids; D018272:Porins; D014867:Water; D004134:Dimyristoylphosphatidylcholine