Abstract
Protein kinases control cellular decision processes by phosphorylating specific substrates. Thousands of in vivo phosphorylation sites have been identified, mostly by proteome-wide mapping. However, systematically matching these sites to specific kinases is presently infeasible, due to limited specificity of consensus motifs, and the influence of contextual factors, such as protein scaffolds, localization, and expression, on cellular substrate specificity. We have developed an approach (NetworKIN) that augments motif-based predictions with the network context of kinases and phosphoproteins. The latter provides 60%-80% of the computational capability to assign in vivo substrate specificity. NetworKIN pinpoints kinases responsible for specific phosphorylations and yields a 2.5-fold improvement in the accuracy with which phosphorylation networks can be constructed. Applying this approach to DNA damage signaling, we show that 53BP1 and Rad50 are phosphorylated by CDK1 and ATM, respectively. We describe a scalable strategy to evaluate predictions, which suggests that BCLAF1 is a GSK-3 substrate.
Publication types
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Research Support, N.I.H., Extramural
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Research Support, Non-U.S. Gov't
MeSH terms
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Acid Anhydride Hydrolases
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Ataxia Telangiectasia Mutated Proteins
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Binding Sites / genetics
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CDC2 Protein Kinase / genetics
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CDC2 Protein Kinase / metabolism
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Cell Cycle Proteins / genetics
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Cell Cycle Proteins / metabolism
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Computational Biology / methods*
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DNA Damage / genetics
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DNA Repair Enzymes / genetics
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DNA Repair Enzymes / metabolism
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DNA-Binding Proteins / genetics
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DNA-Binding Proteins / metabolism
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Glycogen Synthase Kinase 3 / genetics
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Glycogen Synthase Kinase 3 / metabolism
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Humans
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Intracellular Signaling Peptides and Proteins / genetics
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Intracellular Signaling Peptides and Proteins / metabolism
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Phosphoproteins / metabolism*
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Phosphorylation
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Protein Kinases / genetics
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Protein Kinases / metabolism*
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Protein Serine-Threonine Kinases / genetics
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Protein Serine-Threonine Kinases / metabolism
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Proteomics / methods*
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Repressor Proteins / genetics
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Repressor Proteins / metabolism
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Signal Transduction / physiology
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Software*
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Transcription Factors / genetics
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Transcription Factors / metabolism
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Tumor Suppressor Proteins / genetics
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Tumor Suppressor Proteins / metabolism
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Tumor Suppressor p53-Binding Protein 1
Substances
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BCLAF1 protein, human
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Cell Cycle Proteins
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DNA-Binding Proteins
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Intracellular Signaling Peptides and Proteins
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Phosphoproteins
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Repressor Proteins
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TP53BP1 protein, human
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Transcription Factors
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Tumor Suppressor Proteins
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Tumor Suppressor p53-Binding Protein 1
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Protein Kinases
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ATM protein, human
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Ataxia Telangiectasia Mutated Proteins
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Protein Serine-Threonine Kinases
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CDC2 Protein Kinase
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Glycogen Synthase Kinase 3
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Acid Anhydride Hydrolases
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RAD50 protein, human
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DNA Repair Enzymes