Steve Smerdon

*Video coming soon*

Molecular recognition in the DNA-damage dependent phospho-interactome

Phosphorylation is one of the most widespread and important post-translational modifications found in human cells. Over 200,000 phosphosites have been annotated in the human proteome yet the functional significance of less than 10% is known. One of the most important is the generation of new binding sites for specific proteins or protein domains whereby phosphorylation acts as a highly regulated and reversible molecular 'switch' that signals the need for protein complex assembly. Several phospho-dependent binding proteins/modules have been identified over the last 20 years, including 14-3-3, FHA, BRCT-repeat, Polo-box, Mob, and PIH-N domains. All of these have been extensively characterised in the host laboratory but mainly with respect to the structural and functional basis of binding to specific biological target molecules. It is, nonetheless, clear that these represent only a small proportion of the entire spectrum of interactions mediated by these molecules in vivo.

Classical interaction screens by affinity-tag pull-down and mass spectrometry have, in some cases, been successful in revealing new interaction partners for a small subset of known phospho-interactor domains but often fail to detect weak or more transient interactions. One of the potential projects in the laboratory would seek to extend our catalogue of phospho-dependent interactions in the human response to DNA-damage, using a combined chemical biology, structural and mass spectrometry strategy to bypass some of the limitations of previous studies. This approach will exploit our accumulated expertise and understanding of the molecular basis of phospho-ligand binding to these domains to design structural variants that enable us to covalently capture phosphorylated interactors from DNA-damaged human cell cultures, thus increasing the signal-to-noise of downstream mass spectrometry identification procedures. Interesting candidate interactions would then be validated by a variety of biochemical, structural and cell-biological approaches as a basis for a more expansive study of the associated DDR signalling pathways in human cells. In principle, a similar approach could also be tailored to explore additional regulatory mechanisms such as allostery and interplay between phospho-dependent and phospho-independent interactions in specific systems currently of interest in the laboratory.

1. Hořejší, Z., Stach, L., Flower, T. G., Joshi, D., Flynn, H., Skehel, J. M., O'Reilly, N. J., Ogrodowicz, R. W., Smerdon, S. J. and Boulton, S. J. (2014)
Phosphorylation-dependent PIH1D1 interactions define substrate specificity of the R2TP cochaperone complex.
Cell Reports  7: 19-26. PubMed abstract

2. Rock, J. M., Lim, D., Stach, L., Ogrodowicz, R. W., Keck, J. M., Jones, M. H., Wong, C. C. L., Yates, J. R., Winey, M., Smerdon, S. J., Yaffe, M. B. and Amon, A. (2013)
Activation of the yeast hippo pathway by phosphorylation-dependent assembly of signaling complexes.
Science  340: 871-875. PubMed abstract

3. Lloyd, J., Chapman, J. R., Clapperton, J. A., Haire, L. F., Hartsuiker, E., Li, J., Carr, A. M., Jackson, S. P. and Smerdon, S. J. (2009)
A supramodular FHA/BRCT-repeat architecture mediates Nbs1 adaptor function in response to DNA damage.
Cell  139: 100-111. PubMed abstract

4. Stucki, M., Clapperton, J. A., Mohammad, D., Yaffe, M. B., Smerdon, S. J. and Jackson, S. P. (2005)
MDC1 directly binds phosphorylated histone H2AX to regulate cellular responses to DNA double-strand breaks.
Cell  123: 1213-1226. PubMed abstract

5. Clapperton, J. A., Manke, I. A., Lowery, D. M., Ho, T., Haire, L. F., Yaffe, M. B. and Smerdon, S. J. (2004)
Structure and mechanism of BRCA1 BRCT domain recognition of phosphorylated BACH1 with implications for cancer.
Nature Structural & Molecular Biology  11: 512-518. PubMed abstract