Identification of membrane spanning β strands in bacterial porins

Abstract

The membrane assembly of outer membrane proteins is more complex than that of transmembrane helical proteins owing to the intervention of many charged and polar residues in the membrane. Accordingly, the predictive accuracy of transmembrane β strands is considerably lower than that of transmembrane α helices. In this paper we develop a set of conformational parameters for membrane spanning β strands. We formulate an algorithm to predict the transmembrane β strands in the family of bacterial porins based on the conformational parameters and surrounding hydrophobicities of amino acid residues. A Fortran program has been developed which takes the amino acid sequence as the input file and gives the predicted transmembrane β strand as output. The present method predicts at an accuracy level of 82% for all the bacterial porins considered.