Although DNA sequences encode proteins with unique folded structures, the number of genes in an organism does not solely determine the biological complexity. Covalent post-translational modifications modulate the activity of cellular proteins and expand the amino acid code from 20 amino acids to several hundred different building blocks. Each modification uniquely alters protein function, such as targeting to the lipid membrane (prenylation, palmitoylation) or regulation of protein structure or function (acetylation, methylation, phosphorylation). This vast array of modifications means that understanding the function and regulation of a protein in a cell includes identification of post-translation processing steps. Numerous human diseases have been linked to post-translational modifications, and inhibitors of enzymes that catalyze these modifications are attractive targets for developing new drugs to treat an array of diseases.

The Fierke lab investigates the specificity and biological function of two medically important classes of post-translational modifications, lipidation and acetylation and the enzymes that catalyze these reactions: protein farnesyltransferase (FTase), protein geranylgeranyltransferase type I (GGTase-I), and histone deacetylases (HDACs). Enzymes that catalyze post-translational modifications face similar molecular recognition challenges; they must recognize and efficiently modify a range of protein substrates in the midst of a larger number of non-substrate proteins, making identification of the in vivo substrates an important and difficult task. For both the prenyltransferases and HDAC8 we have examined the substrate selectivity and have developed rules for molecular recognition, including computational algorithms. Based on these data we have proposed that several hundred proteins are prenylated and validated these as substrates by in vivo analysis. Similarly, for HDAC8 we have identified highly reactive peptide substrates using both computational and biological approaches as well as demonstrating increased reactivity with protein substrates. Furthermore, we have analyzed regulation of the activity and specificity of HDAC8 by phosphorylation and Zn/Fe metal switching. These data provide insight into the biological substrates and function of HDAC8.