An Analysis of the Amino Acid Clustering Pattern in (α/β)8 Barrel Proteins

1573-4943

Amino acid clusters ; data base analysis ; physicochemical ; secondary structure ; tertiary structure ; TIM barrel

Springer Online Journal Archives 1860-2000

Chemistry and Pharmacology

Abstract The (α/β)8 barrel proteins, in spite of having a common fold, do not show any sequence similarity. In order to understand the factors which are responsible for maintaining the common fold, the three-dimensional structures of 36 (α/β)8 barrel proteins are analyzed for the presence of identical amino acid clusters or physicochemically similar clusters. The results reveal 14 identical amino acid clusters and a large number of physicochemically similar clusters. Further analysis of the similar clusters points to the conservation of secondary structures, the presence of pairs of residues occupying topologically equivalent secondary structures, and the presence of certain key residues which may play a vital role in directing and stabilizing the (α/β)8 barrel fold.

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