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Visualization of conformational distribution of short to medium size segments in globular proteins and identification of local structural motifs

¹ Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan² School of Life Science, Tokyo University of Pharmacy and Life Science, Hachioji, Tokyo 192-0392, Japan³ Institute for Bioinformatics Research and Development (BIRD), Japan Science and Technology Corporation, Chiyoda-Ku, Tokyo 102-8666, Japan

(RECEIVED July 1, 2004; FINAL REVISION November 26, 2004; ACCEPTED December 3, 2004)

Analysis of the conformational distribution of polypeptide segments in a conformational space is the first step for understanding a principle of structural diversity of proteins. Here, we present a statistical analysis of protein local structures based on interatomic C distances. Using principal component analysis (PCA) on the intrasegment C–C atomic distances, the conformational space of protein segments, which we call the protein segment universe, has been visualized, and three essential coordinate axes, suitable for describing the universe, have been identified. Three essential axes specified radius of gyration, structural symmetry, and separation of hairpin structures from other structures. Among the segments of arbitrary length, 6–22 residues long, the conservation of those axes was uncovered. Further application of PCA to the two largest clusters in the universe revealed local structural motifs. Although some of motifs have already been reported, we identified a possibly novel strand motif. We also showed that a capping box, which is one of the helix capping motifs, was separated into independent subclusters based on the C geometry. Implications of the strand motif, which may play a role for protein–protein interaction, are discussed. The currently proposed method is useful for not only mapping the immense universe of protein structures but also identification of structural motifs.

Keywords: protein segment universe; structure classification; principal component analysis; local structural motif; helix capping

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.04956305.

Reprint requests to: Junichi Higo, School of Life Science, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan; e-mail: higo{at}ls.toyaku.ac.jp; fax: +81-426-76-5863.

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