The beta bulge: a common small unit of nonrepetitive protein structure.

Abstract

A beta bulge is a region between two consecutive beta-type hydrogen bonds which includes two residues (positions 1 and 2) on one strand opposite a single residue (position x) on the other strand. Compared to regular beta structure, a beta bulge puts the usual alternation of side-chain direction out of register on one of the strands, introduces a slight bend in the beta sheet, and locally accentuates the usual right-handed strand twist. Almost all beta bulges are between antiparallel strands, usually between a narrow rather than a wide pair of hydrogen bonds. Ninety-one examples are listed. The two commonest types are the "classic" beta bulge, with position 1 in approximately alpha-helical conformation, and the "G1" beta bulge, with a required glycine at position 1 in approximately left-handed alpha-helical conformation, G1 bulges almost always occur in combination with a type II tight turn. The functional roles of beta bulges probably include compensating for the effects of a single-residue insertion or deletion within beta structure and providing the strong local twist required for form closed beta barrel structures.