Reverse-Polarity Activity-Based Protein Profiling
de novo PTM discovery
Reverse-polarity activity-based protein profiling (RP-ABPP) is a chemical proteomics approach that uses clickable, nucleophilic hydrazine probes to capture and identify protein-bound electrophiles in cells. The RP-ABPP approach is used to characterize the structure and function of reactive electrophilic PTMs and the proteins that harbor them, which may uncover unknown or novel functions of proteins in an endogenous setting. RP-ABPP has demonstrated utility as a versatile method to monitor metabolic regulation of electrophilic cofactors, as was done with the pyruvoyl cofactor in S-adenosyl-L- methionine decarboxylase (AMD1) and discover novel types of electrophilic modifications on proteins in human cells, as was done with the glyoxylyl modification on secernin-3 (SCRN3). These cofactors cannot be predicted by sequence and as such this area is relatively undeveloped. RP-ABPP is the only global unbiased approach to discover these electrophiles. Here, the utility of these experiments is described and a detailed protocol is provided for de novo discovery, quantitation, and global profiling of electrophilic functionality of proteins through the use of nitrogenous nucleophilic probes deployed directly to living cells in culture.