Profiles from structure based sequence alignment of porins can identify ß stranded integral membrane proteins

Introduction Integral membrane protein structures constitute less than 2% of protein structures in the Protein Data Bank (PDB) (Bernstein et al., 1977). The known membrane protein structures can be divided into two structural classes: α helical and β stranded proteins. The β stranded membrane proteins form β barrel structures of which porins are type members. Porins are general diffusion, pore-forming proteins which are present in the outer membrane of Gram-negative bacteria. They exist as homotrimers on the outer membrane and form the majority of outer membrane proteins. The basic structural motif of the porins, the βbarrel that forms the transmembrane core, is formed of 16 β strands in general-diffusion porins and 18 β strands in sugar-specific porins (Schulz, 1996). Earlier Gibbs sampler techniques have been used to detect motifs in bacterial membrane proteins (Neuwald et al., 1995) and to identify transmembrane β-strand regions in mitochondrial pore proteins (Mannella et al., 1996). We have used the profiles made from structurally conserved regions (SCR) of porins as a potential tool to identify or discriminate β stranded integral membrane proteins.