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

• Published in: Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2006-04, Vol.63 (1), p.6-15
• Main Authors: Khalid, Syma, Bond, Peter J., Deol, Sundeep S., Sansom, Mark S. P.
• Format: Article
• Language: English
• Subjects: Bacteria - metabolism; Bacterial Outer Membrane Proteins - chemistry; Biophysical Phenomena; Biophysics; Cell Membrane - metabolism; Computational Biology - methods; Computer Simulation; Crystallography, X-Ray; dimyristoyl-phosphatidylcholine; Dimyristoylphosphatidylcholine - chemistry; Escherichia coli; Escherichia coli - metabolism; homology model; Ions; Lipid Bilayers - chemistry; Lipids - chemistry; Models, Biological; Models, Molecular; Molecular Conformation; molecular dynamics; OmpA N-terminal domain; outer membrane proteins; Porins - chemistry; Porins - physiology; Protein Binding; Protein Conformation; Protein Structure, Tertiary; Proteomics - methods; Pseudomonas aeruginosa; Pseudomonas aeruginosa - metabolism; Water - chemistry
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.20845

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 β‐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 β‐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. Proteins 2006. © 2006 Wiley‐Liss, Inc.