title: Identification, classification, and analysis of beta-bulges in proteins.
abstract: A beta-bulge is a region of irregularity in a beta-sheet involving two beta-strands. It usually involves two or more residues in the bulged strand opposite to a single residue on the adjacent strand. These irregularities in beta-sheets were identified and classified automatically, extending the definition of beta-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 beta-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, beta-bulges produce two main changes in the structure of a beta-sheet: (1) disrupt the normal alternation of side-chain direction; (2) accentuate the twist of the sheet, altering the direction of the surrounding strands.
authors.affiliation: Department of Biochemistry and Molecular Biology, University College, London, United Kingdom.
authors.forename: A W
authors.initials: AW
authors.lastname: Chan
authors.forename: E G
authors.initials: EG
authors.lastname: Hutchinson
authors.forename: D
authors.initials: D
authors.lastname: Harris
authors.forename: J M
authors.initials: JM
authors.lastname: Thornton
mesh_terms: D000595:Amino Acid Sequence; D016282:Aspartic Acid Endopeptidases / Q000737:chemistry; D006860:Hydrogen Bonding; D007136:Immunoglobulins / Q000737:chemistry; D008969:Molecular Sequence Data; D011392:Proline / Q000737:chemistry; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000145:classification; D017386:Sequence Homology, Amino Acid
chemical_list: D007136:Immunoglobulins; D011506:Proteins; D011392:Proline; D016282:Aspartic Acid Endopeptidases