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-dim ensional numbering scheme which is based on the covalent and hydrogen- bonding pattern of the beta-sheet. Two different scoring functions wer e used: one measured the sequence and topological similarity and the o ther the root-mean-square deviation of the coordinates of the matched residues. The procedure was applied to obtain multiple alignments of t he beta-barrels often (beta/alpha)(8)-barrel proteins of known structu re. Two kinds of alignments were derived: one in which the beta-strand numbering was preserved and another in which the beta-strands were al lowed 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 alignm ent of the barrels as well, the beta-strands must be allowed to be ren umbered. Although the 2-fold or 4-fold rotational symmetry of the beta -barrels makes it difficult to obtain unique rotational alignment of t he barrels, the results of the alignment indicate that the beta-strand s in the beta-barrel of enolase, xylose isomerase, taka-amylase, and p ossibly fructose biphosphate aldolase, must be cyclically permuted in order to be optimally aligned to those of the other proteins, which in clude triose phosphate isomerase, the alpha-subunit of tryptophan synt hetase, flavocytochrome b(2), ribulose-1,5-biphosphate carboxylase/oxy genase, and glycolate oxidase.