Premium
Barrel structures in proteins: Automatic identification and classification including a sequence analysis of TIM barrels
Author(s) -
Nagano Nozomi,
Gail HUTCHINSON E.,
Thornton Janet M.
Publication year - 1999
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 - 10.1110/ps.8.10.2072
Subject(s) - barrel (horology) , triosephosphate isomerase , antiparallel (mathematics) , protein structure , sequence (biology) , chemistry , crystallography , biophysics , biology , biochemistry , physics , enzyme , materials science , quantum mechanics , magnetic field , composite material
Automated methods for identifying and characterizing regular β‐barrels from coordinate data have been developed to analyze and classify various kinds of barrel structures based on geometric parameters such as the barrel strand number ( n ) and shear number ( S ). In total, we find 1,316 barrels in the January 1998 release of Protein Data Bank. Of 1,316 barrels, 1,277 barrels had an even shear number, corresponding to 50 nonhomologous families. The (βα) 8 triose phosphate isomerase (TIM) barrel ( n = 8, S = 8) fold has the largest number of apparently nonhomologous entries, 16, although the trypsin like antiparallel ( n = 6, S = 8) barrels (representing only three families) are the most common with 527 barrels. Of all the protein families that exhibit barrel structures, 68% are found to be various kinds of enzymes, the remainder being binding proteins and transport membrane proteins. In addition, the layers of side chains, which form the cores of barrels with S = n and S = 2 n , are also analyzed. More sophisticated methods were developed for detecting TIM barrels specifically, including consideration of the amino acid propensities for the side chains that form the layers. We found that the residues on the outside of the eight stranded parallel β‐barrel, buried by the α‐helices, are much more hydrophobic than the residues inside the barrel.