Detecting remote homologues using scoring matrices calculated from the estimation of amino acid substitution rates of beta-barrel membrane proteins.

Beta-barrel membrane proteins (MP) are found in Gram-negative bacteria, mitochondria and chloroplasts. They play important roles in metabolism of bacteria, where they are involved in transport of solutes in and out of the cell. Beta-barrel proteins may also act as proteases, lipases and may be important for cell-cell adhesion. Currently, there are about 30 non-redundant solved structures of beta-barrels. Although the number of b-barrel folds is fairly small, it is possible to expand the amount of available structural information by homology modeling using existing structures as templates. The scope of structure prediction may be widened by finding remote homologues of the existing structures. To improve the sensitivity of the database searches and the quality of sequence alignments, we first study evolutionary history of transmembrane segments of 7 beta-barrel membrane proteins by estimating substitution rates with a Bayesian Monte Carlo approach. Next, we calculate amino acid substitution matrices, beta-barrel Transmembrane scoring Matrices (bbTM), specifically tuned for TM regions, which can be used to detect remote homologues. We then test bbTM matrices by comparing their performance with membrane-protein derived scoring matrices PHAT and SLIM. Our results demonstrate that bbTM matrices have higher selectivity towards transmembrane beta-barrel proteins and may be used with higher confidence in database searches for remote homologues of this class of proteins.