Folding patterns of porin and bacteriorhodopsin.

Abstract

Porin spans the outer membrane of Escheichia coli with most of the protein embedded within the membrane. It lacks pronounced hydrophobic domains and consists predominantly of ,3-pleated sheet. These observations require the acommodation of polar and ionizable residues in an environment that has a low dielectric constant. Owing to a currently limited understanding of the constraints governing membrane protein structure, a miinimal approach to structure prediction is proposed that identifies segments causing polypeptides to reverse their direction (turn identification). The application of this procedure avoids hydrophobicity parameters and yields a model of porin which is in good agreement with all experimental data available. The presence of polar and ionizable residues within membrane boundaries implies a dense (saturating) network of hydrogen bond donor and acceptor groups. Application to a paradigm of hydrophobic membrane proteins, bacteriorhodopsin, reveals a pattern consistent with its a-helical folding. The postulated structure includes significantly more polar residues in the membrane domain than have been assumed previously, suggesting that there are also hydrogen bonding networks in bacteriorhodopsin. Extensive networks permeating protein interior and surfaces would explain the extraordinary stability and the tight interactions between functional units in the formation of crystaline arrays of both proteins.

Two‐dimensional structure of the Opc invasin from Neisseria meningitidis

“…1), the protein spans the membrane 10 times, exposing five hydrophilic loops (L1-L5) to the cell surface and the N-terminus plus four turns (Ta-Td) to the periplasm. Minor discrepancies with the criteria used are that the hydrophobic side of strands 1 (counting from the N-terminus), 4, 6 and 7 contain five slightly hydrophilic residues (T 14 , S 18 , T 94 , S 147 , and S 159 ), and the criteria of Paul and Rosenbusch (1985) did not predict turn Ta but did predict a turn (H 13 -D 15 ) within strand 1. Thr (and more rarely Ser) has been found on the non-polar side of the transmembrane strands of porins (Weiss et al, 1991;Cowan et al, 1992) and turn prediction is not absolute with the current algorithms (Paul and Rosenbusch, 1985).…”

Alignment and structure prediction of divergent protein families: periplasmic and outer membrane proteins of bacterial efflux pumps

“…Further, when a simple threshold was applied to the combination function, such that continuous regions of more than six residues with values >0.65 are predicted to be TM b-strand, this resulted in correct assignment of 77 % of the residues from maltoporin (see Figure 10(a)), 73 % for OmpF, and 78 % for R. blastica porin. The average prediction accuracy of 76 % for these three protein families is higher than that of other described methods (Paul & Rosenbusch, 1985;Stoorvogel et al, 1991;Vogel & Ja È hnig, 1986;Gromiha et al 1997;Gromiha & Ponnuswamy, 1993). The only computational methods reporting equal or higher accuracy (of which we are aware) either include the test protein in the training procedure (Ponnuswamy & Gromiha, 1993) or use only a single test protein which has signi®cant sequence similarity to one of the training proteins (E-value 9 e À10 by BLAST search of PDB; Gromiha et al, 1997).…”

Nucleotide sequence of the gene encoding the 11‐kDa subunit of the ubiquinol – cytochrome‐c oxidoreductase in Saccharomyces cerevisiae

“…Four of the turns are also predicted by the algorithm described by Paul and Rosenbusch [45], which successfully allows turn identification in the membrane proteins bacteriorhodopsin and porin. The fact that the 11-kDa protein is potentially capable of forming a structure similar to that found in pore-forming membrane proteins, like the E. coli OmpA protein and porin [45,461 could mean that it too fulfils a pore-forming role within the ubiquinolcytochrome-c oxidoreductase. As yet, little is known about the function of this subunit in the complex, apart from the fact that it is closely associated with both cytochrome b and the 14-kDa subunit VII of the complex [4].…”