Porins

Despite all the shortcomings listed above, full particle classical MD can be considered mature [84]. Even when all shortcomings will be overcome, we can now clearly delineate the limits for application. These are mainly in the size of the system and the length of the possible simulation. With the rapidly growing cheap computer memory shear size by itself is hardly a limitation several tens of thousands of particles can be handled routinely (for example, we report a simulation of a porin trimer protein embedded in a phospholipid membrane in aqueous environment with almost 70,000 particles [85] see also the contribution of K. Schulten in this symposium) and a million particles could be handled should that be desired. 

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). 

Many small molecules can penetrate the outer ced membrane by diffusion through channels created by outer-membrane proteins caded porins. 

Porin channels are impHcated in the transport of cephalosporins because ceds deficient in porins are much more impermeable than are ceds that are rich in porins. The porins appear to function as a molecular sieve, adowing molecules of relatively low molecular weight to gain access to the periplasmic space by passive diffusion. In enterobacteria, a clear correlation exists between porin quantity and cephalosporin resistance, suggesting that the outer membrane is the sole barrier to permeabdity. However, such a relationship is not clearly defined for Pseudomonas aeruginosa where additional barriers may be involved (139,144,146). 

Despite considerable efforts very few membrane proteins have yielded crystals that diffract x-rays to high resolution. In fact, only about a dozen such proteins are currently known, among which are porins (which are outer membrane proteins from bacteria), the enzymes cytochrome c oxidase and prostaglandin synthase, and the light-harvesting complexes and photosynthetic reaction centers involved in photosynthesis. In contrast, many other membrane proteins have yielded small crystals that diffract poorly, or not at all, using conventional x-ray sources. However, using the most advanced synchrotron sources (see Chapter 18) it is now possible to determine x-ray structures from protein crystals as small as 20 pm wide which will permit more membrane protein structures to be elucidated. 

This enigma was resolved in 1990 when the x-ray structure of an outer membrane protein, porin, showed that the transmembrane regions were p... 

The first x-ray structure of a porin was determined by the group of Georg Schulz and Wolfram Welte at Ereiburg University, Germany, who succeeded in growing crystals of a porin from Rhodobacter capsulatus that diffracted to 1.8 A resolution. Since then the x-ray structures of several other porin molecules have been determined and found to be very similar to the R. capsulatus porin despite having no significant sequence identity. 

Each subunit of the trimeric porin molecule from R. capsulatus folds into a 16-stranded up and down antiparallel P barrel in which all p strands form... 

The complete porin molecule is a stable trimer of three identical subunits, three each with a functional channel (Figure 12.8). About one-third of the... 

Fi re 12.8 Schematic diagram of the trimerlc porin molecule viewed from the extracellular space. Blue regions illustrate the walls of the three porin barrels, the loop regions that constrict the channel are red and the calcium atoms are orange. 

Cowan, S.W. Bacterial porins lessons from three high-resolution structures. Curr. Opin. Struct. Biol. 

Garavito, R.M., Rosenbusch, J.R Isolation and crystallization of bacterial porin. Methods Enzymol. 

Nikaido, H. Porins and specific diffusion channels in bacterial outer membranes. J. Biol. Chem. 269 3905-3908, 1994. 

Cowan, S.W., et al. Crystal structures explain functional properties of two E. coli porins. Nature 358 727-733, 1992. 

Structural basis for sugar translocation through malto-porin channels at 3.1 A resolution. Science 267 512-514, 1995. 

Weiss, M.S., et al. Molecular architecture and electrostatic properties of a bacterial porin. Science 254 1627-1630, 1991. 

Each porin molecule has three channels Ion channels combine ion selectivity with high levels of ion conductance The K+ channel is a tetrameric molecule with one ion pore in the interface between the four subunits... 

The amino acid compositions and sequences of the /3-strands in porin proteins are novel. Polar and nonpolar residues alternate along the /3-strands, with polar residues facing the central pore or cavity of the barrel and nonpolar residues facing out from the barrel where they can interact with the hydrophobic lipid milieu of the membrane. The smallest diameter of the porin channel is about 5 A. Thus, a maltodextrin polymer (composed of two or more glucose units) must pass through the porin in an extended conformation (like a spaghetti strand). 

Porin and Bacterial Source Pore Diameter (nm) Mj. Exclusion Limit... 

Source Adapted, from Benz, R., 1984. Sti ucture and selecdvity of porin channels. Current Topics in Membrane TrawsjiJorf 21 199-219 and Benz, R., 1988. Sti ucture and function of porins from Gram-negative bacteria. Annual Review of Microbiology 42 359-393. 

FIGURE 10.28 A model for the arrangement of the porin PhoE in the outer membrane of E. coli. The transmembrane segments are strands of /3-sheet. 

FIGURE 10.29 Three-dimensional recon-strnction of porin from Rhodohacter capsulatus. Drawings of (a) side view of porin monomer showing /3-sheet strnctnre. (b) Top view and (c) nearly top view of porin trimer. 

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