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

Abstract

The N-terminal domain of outer membrane protein OprF of Pseudomonas aeruginosa forms a membrane spanning eight-stranded anti-parallel 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 to 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 to 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.

Role of the Native Outer-Membrane Environment on the Transporter BtuB

“…To better understand the local effects of the OM on embedded proteins, we developed an OM model suitable for MD simulations. The hydrophobic thickness and lateral diffusion rates of LPS in this OM model correspond reasonably well with previous simulations and experiments (7,11,38,39,42); however, the area per lipid/ LPS is~5-10% higher than that of a similar E. coli OM model (39), suggesting necessary changes for future iterations of our model. Finally, we carried out simulations of an OM transporter, BtuB, in a symmetric phospholipid bilayer and our model OM to characterize novel proteinmembrane interactions in the native environment.…”

“…The mean-square displacement was also determined for the LPS center of mass, which resulted in nearly identical diffusion values (data not shown). Root mean-square fluctuation (RMSF) values were calculated only for the C a atom of each amino acid (42) to remove rotamer conformation bias. A full summary of the aforementioned values for each system can be found in Table S2.…”

Identification of proteins involved in membrane fouling in membrane bioreactors (MBRs) treating municipal wastewater

“…Both OprF and OprD have β-barrel structures and are embedded in the outer cell membrane, which is comprised of lipopolysaccharide (LPS) (Biswas et al 2007;Staatsuma and Soares 2009). These proteins form channels for transporting substrates through the outer membrane and have considerably similar structures, properties, and functions.…”

Assembly and stability of Salmonella enterica ser. Typhi TolC protein in POPE and DMPE

“…On the issue of convergence, 5 ns is a short timescale in the biological world; membrane equilibration may require 20-40 ns of simulation time. However, we draw confidence from prior studies of 5-10 ns timescale that were shown to predict the general dynamics of studied protein [23,73]. Our subject protein has exhibited structural adaptation to the thinner DMPE membrane as a consequence of hydrophobic mismatch.…”