Alignment of Beta-barrels in (β/α) 8 Proteins using Hydrogen-bonding Pattern

Abstract

A multiple alignment procedure for aligning the β-sheet residues of the (β/α) 8-barrel structures is described. It uses a two-dimensional numbering scheme which is based on the covalent and hydrogen-bonding pattern of the β-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 β-barrels often (β/α) 8-barrel proteins of known structure. Two kinds of alignments were derived: one in which the β-strand numbering was preserved and another in which the β-strands were allowed to be cyclically permuted. It is shown that preservation of the β-strands numbering corresponds to aligning only the layer structure of the β-barrels. In order to obtain the optimal rotational alignment of the barrels as well, the β-strands must be allowed to be renumbered. Although the 2-fold or 4-fold rotational symmetry of the β-barrels makes it difficult to obtain unique rotational alignment of the barrels, the results of the alignment indicate that the β-strands in the β-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 α-subunit of tryptophan synthetase, flavocytochrome b 2, ribulose-1,5-biphosphate carboxylase/oxygenase, and glycolate oxidase.