Characterization of the outer membrane protein OprF of Pseudomonas aeruginosa in a lipopolysaccharide membrane by computer simulation

• Published in: Proteins, structure, function, and bioinformatics Vol. 74; no. 2; pp. 475 - 488
• Main Authors: Straatsma, T.P., Soares, T.A.
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 01.02.2009
• Subjects: Animals; Bacterial Outer Membrane Proteins - chemistry; Computer Simulation; Escherichia coli; lipopolysaccharide; Lipopolysaccharides - chemistry; Models, Biological; Models, Molecular; molecular dynamics simulation; OprF N-terminal domain; outer membrane protein; Protein Conformation; Protein Stability; Pseudomonas aeruginosa; Pseudomonas aeruginosa - chemistry; Static Electricity
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.22165

The N‐terminal domain of outer membrane protein OprF of Pseudomonas aeruginosa forms a membrane spanning eight‐stranded antiparallel β‐barrel domain that folds into a membrane channel with low conductance. The structure of this protein has been modeled after the crystal structure of the homologous protein OmpA of Escherichia coli. A number of molecular dynamics simulations have been carried out for the homology modeled structure of OprF in an explicit molecular model for the rough lipopolysaccharide (LPS) outer membrane of P. aeruginosa. The structural stability of the outer membrane model as a result of the strong electrostatic interactions compared with simple lipid bilayers is restricting both the conformational flexibility and the lateral diffusion of the porin in the membrane. Constricting side‐chain interactions within the pore are similar to those found in reported simulations of the protein in a solvated lipid bilayer membrane. Because of the strong interactions between the loop regions of OprF and functional groups in the saccharide core of the LPS, the entrance to the channel from the extracellular space is widened compared with the lipid bilayer simulations in which the loops are extruding in the solvent. The specific electrostatic signature of the LPS membrane, which results in a net intrinsic dipole across the membrane, is found to be altered by the presence of OprF, resulting in a small electrically positive patch at the position of the channel. Proteins 2009. © 2008 Wiley‐Liss, Inc.