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Identification, classification, and analysis of beta‐bulges in proteins
Author(s) -
Chan A. W. Edith,
Hutchinson E. Gail,
Harris Daniel,
Thornton Janet M.
Publication year - 1993
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.5560021004
Subject(s) - beta sheet , beta (programming language) , twist , bulge , physics , crystallography , chemistry , protein structure , mathematics , astrophysics , geometry , nuclear magnetic resonance , stars , computer science , programming language
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.