Proteomic and Chemoproteomic Strategies to Interrogate Post-translational Modifications

Abstract

Protein activity is modulated by hundreds of post-translational modifications (PTMs). This thesis will describe the development and application of proteomic methods to study three chemically distinct PTMs. In the first project we describe the development of a proteomics platform to identify cysteine oxidation sites on interactors of the NADPH oxidase complex in response to EGF activation. The NADPH oxidases (Nox) are the source of H(2)O(2) which acts as a secondary messenger during EGFR activation. Known targets of Nox H(2)O(2) include phosphatases PTP1B and PTEN. Oxidation of the active site of PTP1B and PTEN temporarily inactivates their phosphatase activity which allows for EGF signal propagation. The platform involves combining TurboID with OxICAT to identify proteins which are oxidized by Nox2 in a spatially and temporally controlled manner. In the second project, our goal is to identify proteins which recognize two Met oxidation sites in actin known to play a role in regulating the transition between F and G actin. We utilized a peptide based photo-crosslinking approach to identify PFKL and HSP70s HSPA8 and HSPA1B as putative "readers" of oxidized or unoxidized methionine in actin respectively. Finally, protein citrullination is a enzyme catalyzed PTM where the guanidinium on arginine is converted into a urea by a family of enzymes called protein arginine deiminases. Aberrant citrullination is linked to many human diseases including rheumatoid arthritis. Therefore, proteomic methods to characterize citrullination can provide insights into disease pathophysiology. We describe the identification of novel protein targets of with a chemoselective biotin phenyl glyoxal probe, and the development of a label free proteomic method to identify sites of citrullination.