Alignment of beta-barrels in (beta/alpha)8 proteins using hydrogen-bonding pattern.

A multiple alignment procedure for aligning the beta-sheet residues of the (beta/alpha)8-barrel structures is described. It uses a two-dimensional numbering scheme which is based on the covalent and hydrogen-bonding pattern of the beta-sheet. Two different scoring functions were used: one measured the sequence and topological similarity and the other the root-mean-square deviation of the coordinates of the matched residues. The procedure was applied to obtain multiple alignments of the beta-barrels of ten (beta/alpha)8-barrel proteins of known structure. Two kinds of alignments were derived: one in which the beta-strand numbering was preserved and another in which the beta-strands were allowed to be cyclically permuted. It is shown that-preservation of the beta-strand numbering corresponds to aligning only the layer structure of the beta-barrels. In order to obtain the optimal rotational alignment of the barrels as well, the beta-strands must be allowed to be renumbered. Although the 2-fold or 4-fold rotational symmetry of the beta-barrels makes it difficult to obtain unique rotational alignment of the barrels, the results of the alignment indicate that the beta-strands in the beta-barrel of enolase, xylose isomerase, taka-amylase, and possibly fructose biphosphate aldolase, must be cyclically permuted in order to be optimally aligned to those of the other proteins, which include triose phosphate isomerase, the alpha-subunit of tryptophan synthetase, flavocytochrome b2, ribulose-1, 5-biphosphate carboxylase/oxygenase, and glycolate oxidase.