OmpF porin

Tieleman, D.P., Berendsen, H.J.C. A molecular dynamics study of the pores formed by E. coli OmpF porin in a fully hydrated POPE bilayer. Biophys. J., in print (1998). 

Typically, functional porins are homotrimers, which assemble from monomers and then integrate into the outer membrane. The general porins, water-filled diffusion pores, allow the passage of hydrophilic molecules up to a size of approximately 600 Daltons. They do not show particular substrate specificity, but display some selectivity for either anions or cations, and some discrimination with respect to the size of the solutes. The first published crystal structure of a bacterial porin was that of R. capsulatus [48]. Together with the atomic structures of two proteins from E. coli, the phosphate limitation-induced anion-selective PhoE porin and the osmotically regulated cation-selective OmpF porin, a common scheme was found [49]. Each monomer consists of 16 (3-strands spanning the outer membrane and forming a barrel-like structure. 

Thus, the important question of the secondary structure of the transmembrane elements can only be addressed with models and by structural comparison with other transmembrane proteins for which the structure has been resolved. Detailed information on the structure of transmembrane elements is available for the photoreaction center of Rhodopseudomonas viridis (review Deisenhofer and Michel, 1989), cytochrome c oxidase (Iwata et al., 1995) and the OmpF porin of E. coli (Cowan et al., 1992 Fig. 5.3), amongst others. In addition, high resolution electron microscopic investigations and X-ray studies of bacteriorhodopsin, a light-driven ion pump with seven transmembrane elements, have yielded valuable information on the structure and configuration of membrane-spaiming elements (Henderson et al., 1990 Kimura et al., 1997 Pebay-Peyrula et al., 1997 Fig. 5.4). With the successful crystallization of the photoreaction center of Rhodopseudomonas viridis, a membrane protein was displayed at atomic resolution for the first time (Deisenhofer et al., 1985). The membrane-... 

In contrast, the transmembrane domain of the bacterial OmpF porin is made up of P-elements. The P-elements, in this case, are not mostly made up of hydrophobic amino acids. 

Fig. 5.3. Structure of the OmpF porin of E. coli. The porin is a bacterial membrane protein with P-sheet structures as transmembrane elements. The structure of a monomer of the OmpF porin is shown. In total, 16 P-bands are configured in the form of a cylinder and form the waUs of a pore through which selective passage of ions takes place. LI—L8 are long loops, Tl,2,3 and T7,8 are short bends (T turn) that fink the P-sheets. According to Cowan et al. (1992), with per-...

Figure 8-20 MolScript ribbon drawings of the OmpF porin of E. coli. (A) View of the 340-residue monomer. (B) View of the trimer looking down the threefold axis. From Wa-tanabe et al3is From atomic coordinates of Cowan et al.3i9 (C) Molecular model of the constriction zone of the PhoE porin. Locations of key residues are shown, with positions of homologous residues in OmpF given in parentheses. Extracellular loops have been omitted. Constructed from coordinates of Cowan et al.349 by Samartzidou and Del-cour.342 Courtesy of Anne Delcour.

Figure 4.8 Single-channel traces of OmpF porin from Escherichia coli incorporated in a mercury-supported tethered bilayer lipid micromembrane immersed in aqueous 0.1 M KCI, at different applied potentials measured... 

Hitscherich, C., Kaplan, J., Allaman, M., Wiencek, J., and Loll, P. J. (2000). Static light scattering studies of OmpF porin imphcations for integral membrane protein crystallization, Protein, 9, 1559-1566. 

R. E. W. Hancock, S. W. Farmer, Z. S. Li, and K. Poole, Interaction of aminoglycosides with the outer membranes and purified lipopolysaccharide and OmpF porin of Escherichia coli, Antimicrob. Agents Chemother., 35 (1991) 1309-1314. 

Figure 17.5 Experimental methods to delivery a second reactant Y inside a X-containing vesicle. (1) Free (passive) diffusion ofY from outside to vesicle inside. (2) Fusion between two or more vesicles. (3) Microinjection of Y inside a giant vesicle. (4) Keeping the vesicles at the phase transition temperature (or by thermal cycles around T ). The permeability of lipid membranes is generally maximal at T - (5) Adding detergents at sublytic concentration, so that the membrane permeability is increased (especially for small solutes) without dramatic changes of membrane integrity. (6) Incorporation of pore-forming compounds in liposomes (a-hemolysin, OmpF porin,. ..)...

Figure 3 The OmpF porin channel (left) emhedded in an explicit POPC membrane, and (right) the corresponding top view of the OmpF. The L3 loop in the constriction zone of the three monomers is represented by the large shaded cylinder. The structure has been obtained from the protein database (lompf.pdb) and the plot has been rendered with...

Channel A Molecular Dynamics Simulation of OmpF Porin from Escherichia Coli in an Explicit Membrane with 1 M KCl Aqueous Salt Solution. 

Imaging the Electrostatic Potential of Transmembrane Channels Atomic Probe Microscopy of OmpF Porin. 

Dynamics Study of the Pores Formed by Escherichia coli OmpF Porin in a Fully Hydrated Palmitoyloleoylphosphatidylcholine Bilayer. 

F. A. Schabert, C. Henn, and A. Engel, Native Escherichia coU OmpF porin surfaces probed by atomic force microscopy. Science, 268,92-94 (199 53. 

Several studies that are in progress deal with transmembrane helices, small peptides bound to the surface of bilayers and larger integral membrane proteins suchs as OmpF porin from E. coli and we expect to see an increasing number of studies dealing with this type of lipid-protein interaction. 

Sen, K.., and Nikaido, H. (1991). Trimerization of an in vitro synthesized OmpF porin of Escherichia coli outer membrane. J. Biol. Chem. 266, 11295-11300. 

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