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Diversity of functions of proteins with internal symmetry in spatial arrangement of secondary structural elements

Published online by Cambridge University Press:  01 June 1999

KENGO KINOSHITA ,
AKINORI KIDERA  and
NOBUHIRO GO
KENGO KINOSHITA
Affiliation:
Division of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
AKINORI KIDERA
Affiliation:
Division of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
NOBUHIRO GO
Affiliation:
Division of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
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Abstract

We carry out a systematic analysis of the correlation between similarity of protein three-dimensional structures and their evolutionary relationships. The structural similarity is quantitatively identified by an all-against-all comparison of the spatial arrangement of secondary structural elements in nonredundant 967 representative proteins, and the evolutionary relationship is judged according to the definition of superfamily in the SCOP database. We find the following symmetry rule: a protein pair that has similar folds but belong to different superfamilies has (with a very rare exception) certain internal symmetry in its common similar folds. Possible reasons behind the symmetry rule are discussed.

Keywords

evolution of proteinspatial arrangement of secondary structural elementssymmetry of protein foldsthree-dimensional structure comparison
Type
Research Article
Information
Protein Science , Volume 8 , Issue 6 , June 1999 , pp. 1210 - 1217
Copyright
© 1999 The Protein Society

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