Biochemical characterization of the epigenomic markers

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The repertoire of proteins that make up a proteome can be two to three orders of magnitude higher than the number of genes in its genome. This paradox, which is largely due to the myriad of posttranslational modifications (PTMs) deposited on protein backbones and/or side chains, expands the complexity of the cellular machinery and fine-tune biological pathways by altering the intrinsic biochemical properties of the modified proteins. Such modifications include, but are not restricted to, phosphorylation, acetylation, methylation, ubiquitinylation and sumoylation. The biological consequences of the signal will vary depending on the covalent alteration, the underlying chemistry and the type of residue that will be modified. Despite great progress in the development of proteomic and genomic tools, the biochemical and functional roles of enzymes that attach acetyl, methyl or phosphate groups have remained elusive. My laboratory employs X-ray crystallography and steady-steady-state kinetics to characterize covalent modifying enzymes. Our long-term goals are to elucidate the fundamental basis underlying the recognition and modification of a family of proteins that are central to DNA scaffolding, namely the histone proteins. Histone covalent modifications are critical for controlling DNA compaction and thereby a flurry of cellular processes. Being central to all eukaryotic organisms, determination of the mechanistic details eliciting histone modifications will provide a working model to uncover biological pathways controlled by each covalent modification. In this proposal, we will elucidate the mechanisms by which two histone methyltransferases selectively recognize unique residues on one histone tail and determine the consensus motifs recognized by these proteins. In a whole, the information retrieved by our research program will 1) provide the overall 3D-shape of histone modifying enzymes, 2) elucidate the atomic details of the driving forces central for the activity of post-transcriptional modifying enzymes and 3) determine the key binding interfaces of an enzyme conferring specificity for a given protein substrate.