title: Disordered patterns in clustered Protein Data Bank and in eukaryotic and bacterial proteomes.
abstract: We have constructed the clustered Protein Data Bank and obtained clusters of chains of different identity inside each cluster, http://bioinfo.protres.ru/st_pdb/. We have compiled the largest database of disordered patterns (141) from the clustered PDB where identity between chains inside of a cluster is larger or equal to 75% (version of 28 June 2010) by using simple rules of selection. The results of these analyses would help to further our understanding of the physicochemical and structural determinants of intrinsically disordered regions that serve as molecular recognition elements. We have analyzed the occurrence of the selected patterns in 97 eukaryotic and in 26 bacterial proteomes. The disordered patterns appear more often in eukaryotic than in bacterial proteomes. The matrix of correlation coefficients between numbers of proteins where a disordered pattern from the library of 141 disordered patterns appears at least once in 9 kingdoms of eukaryota and 5 phyla of bacteria have been calculated. As a rule, the correlation coefficients are higher inside of the considered kingdom than between them. The patterns with the frequent occurrence in proteomes have low complexity (PPPPP, GGGGG, EEEED, HHHH, KKKKK, SSTSS, QQQQQP), and the type of patterns vary across different proteomes, http://bioinfo.protres.ru/fp/search_new_pattern.html.
authors.affiliation: Group of Bioinformatics, Institute of Protein Research Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
authors.forename: Michail Yu
authors.initials: MY
authors.lastname: Lobanov
authors.forename: Oxana V
authors.initials: OV
authors.lastname: Galzitskaya
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D030562:Databases, Protein; D005057:Eukaryotic Cells / Q000737:chemistry*; D008969:Molecular Sequence Data; D020543:Proteome; D017386:Sequence Homology, Amino Acid
chemical_list: D001426:Bacterial Proteins; D020543:Proteome
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