Reversible protein phosphorylation is widely used by cells as a signaling mechanism. It regulates, directly or indirectly, most cellular processes. Protein kinases are the central coordinators of signaling, as they are the enzymes responsible for transferring a phosphate group from ATP to targeted protein substrates. Not surprising, perturbations in the action of kinases are associated with several human pathologies, including cancer. Understanding the molecular basis of kinase action and function is of critical importance for biomedical research. It requires knowledge of the kinase substrates, as well as comprehensive characterization of the dynamics and role of the phosphorylation events. Because many kinases are active in a cell and thousands of proteins are phosphorylated, the study of phosphorylation-mediated signaling pathways is challenging and powerful technologies are needed.
We have developed and applied quantitative mass spectrometry technologies for the phosphorylation analysis of protein complexes [1, 2], and for a global screen for in vivo kinase substrates [3, 4]. We are now expanding the use of these technologies to quantitatively characterize signaling dynamics at a proteome-wide scale.
DNA damage checkpoint signaling
In the presence of genotoxic stress, DNA damage checkpoint kinases (see Fig. 2) play a central role in coordinating an elaborate cellular response that involves processes such as DNA repair, DNA replication, cell cycle control and gene transcription. Understanding how the checkpoint kinases contribute to the maintenance of genomic integrity has important implications for cancer research and may provide the basis of rational treatment. We have identified an extensive network of targets of the DNA damage checkpoint kinases in the model organism S. cerevisiae (budding yeast) . A major challenge now is to understand the dynamic regulation of these targets.
We are using quantitative mass spectrometry to systematically characterize the intra-S-phase checkpoint signaling dynamics in yeast. Our goal is to understand how the checkpoint kinases maintain stability of the DNA replication fork, genomic integrity and cell viability.
1. Smolka, M.B., et al., Dynamic Changes in Protein-Protein Interaction and Protein Phosphorylation Probed with Amine-reactive Isotope Tag. Mol Cell Proteomics, 2005. 4(9): p. 1358-69.
2. Smolka, M.B., et al., An FHA domain-mediated protein interaction network of Rad53 reveals its role in polarized cell growth. J Cell Biol, 2006. 175(5): p. 743-53.
3. Smolka, M.B., et al., Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases. PNAS, 2007. 104(25): p. 10364-9.
4. Albuquerque, C.P.*, Smolka, M. B.* et al., A multidimensional chromatography technology for in-depth phosphoproteome analysis. Mol Cell Proteomics, 2008. (*Joint first authors).