%0 Journal Article
%T Universal partitioning of the hierarchical fold network of 50-residue segments in proteins
%A Jun-ichi Ito
%A Yuki Sonobe
%A Kazuyoshi Ikeda
%A Kentaro Tomii
%A Junichi Higo
%J BMC Structural Biology
%D 2009
%I BioMed Central
%R 10.1186/1472-6807-9-34
%X The network was partitioned persistently into four regions for Kc ¡Ý 1000. This main partitioning is consistent with results of earlier studies, where similar partitioning was reported in classifying protein domain structures. Furthermore, the network was partitioned naturally into several dozens of sub-networks (i.e., communities). Therefore, intra-sub-network clusters were mutually connected with numerous links, although inter-sub-network ones were rarely done with few links. For Kc ¡Ý 1000, the major sub-networks were about 40; the contents of the major sub-networks were conserved. This sub-partitioning is a novel finding, suggesting that the network is structured hierarchically: Segments construct a cluster, clusters form a sub-network, and sub-networks constitute a region. Additionally, the network was characterized by non-power-law statistics, which is also a novel finding.Main findings are: (1) The universe of 50 residue segments found here was characterized by non-power-law statistics. Therefore, the universe differs from those ever reported for the protein domains. (2) The 50-residue segments were partitioned persistently and universally into some dozens (ca. 40) of major sub-networks, irrespective of the number of clusters. (3) These major sub-networks encompassed 90% of all segments. Consequently, the protein tertiary structure is constructed using the dozens of elements (sub-networks).Despite the vast number of amino-acid sequences, protein folds (or superfamilies) are quantitatively limited [1-4]. Consequently, protein fold classification is an important subject for elucidating the construction of protein tertiary structures. A key word to characterize protein folds is "hierarchy". Well-known databases ¨C SCOP [5] and CATH [6] ¨C have classified the tertiary structures of protein domains hierarchically. Similarly, a tree diagram was produced to classify the folds [7].Mapping the tertiary structures of full-length protein domains to a conformational space, a
%U http://www.biomedcentral.com/1472-6807/9/34