%0 Journal Article
%T Protein-segment universe exhibiting transitions at intermediate segment length in conformational subspaces
%A Kazuyoshi Ikeda
%A Takatsugu Hirokawa
%A Junichi Higo
%A Kentaro Tomii
%J BMC Structural Biology
%D 2008
%I BioMed Central
%R 10.1186/1472-6807-8-37
%X Our statistical analyses of segment conformations and length revealed critical dual transitions in their conformational distribution with segments derived from all four structural classes. Dual transitions were identified with the intermediate phase between the short segments and domains. Consequently, protein segment universes were categorized. i) Short segments (10¨C22 residues) showed a distribution with a high frequency of secondary structure clusters. ii) Medium segments (23¨C26 residues) showed a distribution corresponding to an intermediate state of transitions. iii) Long segments (27¨C50 residues) showed a distribution converging on one huge cluster containing compact conformations with a smaller radius of gyration. This distribution reflects the protein structures' organization and protein domains' origin. Three major conformational components (radius of gyration, structural symmetry with respect to the N-terminal and C-terminal halves, and single-turn/two-turn structure) well define most of the segment universes. Furthermore, we identified several conformational components that were unique to each structural class. Those characteristics suggest that protein segment conformation is described by compositions of the three common structural variables with large contributions and specific structural variables with small contributions.The present results of the analyses of four protein structural classes show the universal role of three major components as segment conformational descriptors. The obtained perspectives of distribution changes related to the segment lengths using the three key components suggest both the adequacy and the possibility of further progress on the prediction strategies used in the recent de novo structure-prediction methods.Vast amounts of three-dimensional (3D) protein data from structural genomic studies and other individual efforts have been added to our knowledge, thereby enhancing our understanding of protein structures. To date, only
%U http://www.biomedcentral.com/1472-6807/8/37