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Proc Natl Acad Sci U S A. 2003 Jan 7;100(1):74-9. Epub 2002 Dec 26.

Structural basis and prediction of substrate specificity in protein serine/threonine kinases.

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1
Department of Biochemistry and Molecular Biology and Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia.

Abstract

The large number of protein kinases makes it impractical to determine their specificities and substrates experimentally. Using the available crystal structures, molecular modeling, and sequence analyses of kinases and substrates, we developed a set of rules governing the binding of a heptapeptide substrate motif (surrounding the phosphorylation site) to the kinase and implemented these rules in a web-interfaced program for automated prediction of optimal substrate peptides, taking only the amino acid sequence of a protein kinase as input. We show the utility of the method by analyzing yeast cell cycle control and DNA damage checkpoint pathways. Our method is the only available predictive method generally applicable for identifying possible substrate proteins for protein serinethreonine kinases and helps in silico construction of signaling pathways. The accuracy of prediction is comparable to the accuracy of data from systematic large-scale experimental approaches.

PMID:
12502784
PMCID:
PMC140887
DOI:
10.1073/pnas.0134224100
[Indexed for MEDLINE]
Free PMC Article
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