IDENTIFICATION OF MEMBRANE-SPANNING BETA-STRAND IN BACTERIAL PORINS

The membrane assembly of outer membrane proteins is more complex than that of transmembrane helical proteins owing to the intervention of ma ny charged and polar residues in the membrane. Accordingly, the predic tive accuracy of transmembrane beta strands is considerably lower than that of transmembrane alpha helices. In this paper we develop a set o f conformational parameters for membrane spanning beta strands. We for mulate an algorithm to predict the transmembrane beta strands in the f amily of bacterial porins based on the conformational parameters and s urrounding hydrophobicities of amino acid residues, A Fortran program has been developed which takes the amino acid sequence as the input fi le and gives the predicted transmembrane beta strand as output. The pr esent method predicts at an accuracy level of 82% for all the bacteria l porins considered.