Protein phosphorylation is the most common reversible post-translational modification in eukaryotes, yet signaling networks comprising protein kinases, their regulators, and their substrates are only partially elucidated. The overall goals of the proposed project are to build a comprehensive collection of consensus phosphorylation motifs for the entire collection of protein kinases encoded in the human genome using arrayed positional scanning peptide libraries, and integrate this data into web-accessible tools that are currently available to the entire biomedical community. The resulting dataset of protein kinase specificity motifs and informatics tools will: (1) allow functional annotation of a large number of proteins whose phosphorylation sites already have been, or currently are, being mapped in high-throughput phosphoproteomic mass- spectrometry experiments and datasets that have been previously funded by the NIH by now identifying the relevant kinase and signaling pathways responsible for these modifications;(2) allow the identification of new protein kinase substrates relevant to human health and disease and place them within the context of specific signal transduction pathways;and (3) provide a general set of kinase tools useful for structural and drug inhibitor studies and for the therapeutic targeting of specific signaling pathways implicated in human disease. To illustrate the utility of our approach, we will investigate predicted substrates of protein kinases in the Hippo signaling pathway, a conserved tumor suppressor pathway important in regulating cell proliferation, differentiation and survival. This project will serve to increase our fundamental understanding of how specificity is achieved by protein kinases, will identify critical connections in signaling networks, and will provide a general resource for researchers studying signal transduction and protein phosphorylation.

Public Health Relevance

Protein kinases play key roles in human disease and are important targets for some anti-cancer drugs. In this research, we are using high-throughput methods to analyze the function of every human kinase. This work will help in determining which kinases will be effective drug targets, and will provide resources to assist in kinase-targeted drug discovery.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Molecular and Integrative Signal Transduction Study Section (MIST)
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Dunsmore, Sarah
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Yale University
Schools of Medicine
New Haven
United States
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Marholz, Laura J; Zeringo, Nicholas A; Lou, Hua Jane et al. (2018) In Silico Design and in Vitro Characterization of Universal Tyrosine Kinase Peptide Substrates. Biochemistry 57:1847-1851
Creixell, Pau; Pandey, Jai P; Palmeri, Antonio et al. (2018) Hierarchical Organization Endows the Kinase Domain with Regulatory Plasticity. Cell Syst 7:371-383.e4
Miller, Chad J; Turk, Benjamin E (2018) Homing in: Mechanisms of Substrate Targeting by Protein Kinases. Trends Biochem Sci 43:380-394
Jeschke, Grace R; Lou, Hua Jane; Weise, Keith et al. (2018) Substrate priming enhances phosphorylation by the budding yeast kinases Kin1 and Kin2. J Biol Chem 293:18353-18364
Hymel, David; Grant, Robert A; Tsuji, Kohei et al. (2018) Histidine N(?)-cyclized macrocycles as a new genre of polo-like kinase 1 polo-box domain-binding inhibitors. Bioorg Med Chem Lett 28:3202-3205
Suarez-Lopez, Lucia; Sriram, Ganapathy; Kong, Yi Wen et al. (2018) MK2 contributes to tumor progression by promoting M2 macrophage polarization and tumor angiogenesis. Proc Natl Acad Sci U S A 115:E4236-E4244
Cobbaut, Mathias; Derua, Rita; Döppler, Heike et al. (2017) Differential regulation of PKD isoforms in oxidative stress conditions through phosphorylation of a conserved Tyr in the P+1 loop. Sci Rep 7:887
Chen, Catherine; Nimlamool, Wutigri; Miller, Chad J et al. (2017) Rational Redesign of a Functional Protein Kinase-Substrate Interaction. ACS Chem Biol 12:1194-1198
Goldberg, Allison B; Cho, Eunice; Miller, Chad J et al. (2017) Identification of a Substrate-selective Exosite within the Metalloproteinase Anthrax Lethal Factor. J Biol Chem 292:814-825
Mathea, Sebastian; Abdul Azeez, Kamal R; Salah, Eidarus et al. (2016) Structure of the Human Protein Kinase ZAK in Complex with Vemurafenib. ACS Chem Biol 11:1595-602

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