Many of the targets of protein kinases include other protein kinases, and these enzymes can sequentially regulate each other in complex signaling networks. Of the 23, 000 proteins encoded by the human genome, two-thirds have already been demonstrated to be phosphorylated at over 93,000 phosphosites. Serine (S), threonine (T) and tyrosine (Y) represent the three amino acid residues most commonly targeted by these protein kinases. Protein kinases transfer the gamma phosphate of ATP to hydroxyl (-OH) groups found on amino acids in substrate proteins. Protein phosphorylation catalyzed by protein kinases is the predominant mode of reversible post-translational control of proteins in eukaryotic cells. Therefore, it is critical to map and track cell signaling networks with high precision in humans for diagnostic and therapeutic purposes. Defective cell signaling, which can arise from gene mutation or toxic stimuli, has been linked to over 400 human diseases, including cancer, diabetes, autoimmunity, and neurological disorders. The ability of cells to perceive and correctly respond to their micro-environment is essential for growth, development, homeostasis, defense, and reproduction for tissue repair. Integrated cell signaling pathways contribute to complex communications networks that govern basic and specialized cellular activities. ConclusionsĪpplication of this improved kinase substrate prediction algorithm to the primary structures of over 23, 000 proteins encoded by the human genome has permitted the identification of about 650, 000 putative phosphosites, which are posted on the open source PhosphoNET website ( ). Furthermore for many of the better known kinases, the predicted optimal phosphosite sequences were more accurate than the consensus phosphosite sequences inferred by simple alignment of the phosphosites of known kinase substrates.

Comparison of our predicted matrices with experimentally-derived matrices from about 9,000 known kinase-phosphosite substrate pairs revealed a high degree of concordance with the established preferences of about 150 well studied protein kinases. This represents a marked advancement over existing methods such as those used in NetPhorest (179 kinases in 76 groups) and NetworKIN (123 kinases), which consider only positive determinants for kinase substrate prediction. The presented method predicts 488 different kinase catalytic domain substrate specificity matrices in 478 typical and 4 atypical human kinases that rely on both positive and negative determinants for scoring individual phosphosites for their suitability as kinase substrates.

Here, we have focused on identification of kinase-substrate interactions through prediction of the phosphorylation site specificity from knowledge of the primary amino acid sequence of the catalytic domain of each kinase. The major components of intracellular signaling networks are protein kinases and protein phosphatases, which catalyze the reversible phosphorylation of proteins.

Therefore, there is high impetus to define the composition and architecture of cellular communications networks in humans. Defective signal transduction underlies many pathologies, including cancer, diabetes, autoimmunity and about 400 other human diseases. Complex intracellular signaling networks monitor diverse environmental inputs to evoke appropriate and coordinated effector responses.

Kinases with known consensus sequences