Identification, classification, and analysis of beta‐bulges in proteins

Abstract

A β-bulge is a region of irregularity in a β-sheet involving two β-strands. It usually involves two or more residues in the bulged strand opposite to a single residue on the adjacent strand. These irregularities in β-sheets were identified and classified automatically, extending the definition of β-bulges given by Richardson et al. (Richardson, J.S., Getzoff, E.D., & Richardson, D.C., 1978, Proc. Natl. Acad. Sci. USA 75, 2574–2578). A set of 182 protein chains (170 proteins) was used, and a total of 362 bulges were extracted. Five types of β-bulges were found: classic, G1, wide, bent, and special. Their characteristic amino acid preferences were found for most classes of bulges. Basically, bulges occur frequently in proteins; on average there are more than two bulges per protein. In general, β-bulges produce two main changes in the structure of a β-sheet: (1) disrupt the normal alternation of side-chain direction; (2) accentuate the twist of the sheet, altering the direction of the surrounding strands.