Identifying Dysregulated Protein Activities Using Activity-Based Proteomics

Abstract

Activity-based protein profiling (ABPP) is a chemical proteomic technique that allows for selective labeling, visualization, and enrichment of the subset of active enzymes in a complex proteome. Given the dominant role of posttranslational modifications in regulating protein function in vivo, ABPP provides a direct readout of activity that is not attained through traditional proteomic methods. The first application of chemical proteomics in C. elegans was used to identify dysregulated serine hydrolase and cysteine-mediated protein activities in the long-lived daf-2 mutant, revealing LBP-3, K02D7.1, and C23H4.2 as novel regulators of lifespan and dauer formation. The tools of ABPP were also utilized in studying protein interactions at the host-pathogen interface of V. cholerae infection, discovering four pathogen-secreted proteases that alter the biochemical composition of the host, decrease the activity of host serine hydrolases, and inhibit bacterial binding by a host-secreted lectin. Lastly, ABPP was used to study the targets of protein arginine deiminases (PADs) using a citrulline-specific activity-based probe (ABP), highlighting its utility in detecting biologically relevant PAD substrates as well as identifying mRNA processing factors as previously unknown targets of PAD. Taken together, these studies demonstrate the ability of ABPP to discover novel protein regulators of physiological and pathological processes.