title: Scoring and identifying organism-specific functional patterns and putative phosphorylation sites in protein sequences using mutual information.
abstract: The co-variance of amino acid positions within a multiple alignment of 294 protein kinases from mammals, plants, and bacteria was studied. Applying mutual information (MI), characteristic amino acid sites have been identified markedly discriminating the different organisms. The relation of surface accessibility of these sites in the 3D structure of a kinase and their MI content is studied. We extended the method to score a predicted phosphorylation site of this highly conserved catalytic protein kinase region. Based on this score mammalian and plant protein kinases were grouped together apart from the bacterial kinases. Thus, the presented method allows us to analyse putative phosphorylation sites in the context of their organism-specific origin.
authors.affiliation: Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Golm 14476, Germany. weckwerth@mpimp-mpg.de
authors.forename: Wolfram
authors.initials: W
authors.lastname: Weckwerth
authors.forename: Joachim
authors.initials: J
authors.lastname: Selbig
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001419:Bacteria / Q000201:enzymology; D020134:Catalytic Domain; D017124:Conserved Sequence; D019143:Evolution, Molecular; D008322:Mammals; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010766:Phosphorylation; D010944:Plants / Q000201:enzymology; D011494:Protein Kinases / Q000737:chemistry* / Q000145:classification / Q000378:metabolism; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein / Q000379:methods*; D013045:Species Specificity
chemical_list: D011494:Protein Kinases