MISC

2005年5月

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

PROTEIN SCIENCE
  • K Ikeda
  • ,
  • K Tomii
  • ,
  • T Yokomizo
  • ,
  • D Mitomo
  • ,
  • K Maruyama
  • ,
  • S Suzuki
  • ,
  • J Higo

14
5
開始ページ
1253
終了ページ
1265
記述言語
英語
掲載種別
DOI
10.1110/ps.04956305
出版者・発行元
WILEY-BLACKWELL

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-alpha distances. Using principal component analysis (PCA) on the intrasegment C-alpha-C-alpha 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-alpha 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.

Web of Science ® 被引用回数 : 10

リンク情報
DOI
https://doi.org/10.1110/ps.04956305
Web of Science
https://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=JSTA_CEL&SrcApp=J_Gate_JST&DestLinkType=FullRecord&KeyUT=WOS:000228594900014&DestApp=WOS_CPL
ID情報
  • DOI : 10.1110/ps.04956305
  • ISSN : 0961-8368
  • eISSN : 1469-896X
  • Web of Science ID : WOS:000228594900014

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