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Nat Chem. 2017 Mar;9(3):234-243. doi: 10.1038/nchem.2645. Epub 2016 Oct 31.

Chemoproteomic profiling and discovery of protein electrophiles in human cells.

Author information

1
Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA.
2
Bioinformatics Solutions Inc., Waterloo, Ontario N2L 6J2, Canada.
3
Chemistry and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
4
École polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland.

Abstract

Activity-based protein profiling (ABPP) serves as a chemical proteomic platform to discover and characterize functional amino acids in proteins on the basis of their enhanced reactivity towards small-molecule probes. This approach, to date, has mainly targeted nucleophilic functional groups, such as the side chains of serine and cysteine, using electrophilic probes. Here we show that 'reverse-polarity' (RP)-ABPP using clickable, nucleophilic hydrazine probes can capture and identify protein-bound electrophiles in cells. Using this approach, we demonstrate that the pyruvoyl cofactor of S-adenosyl-L-methionine decarboxylase (AMD1) is dynamically controlled by intracellular methionine concentrations. We also identify a heretofore unknown modification-an N-terminally bound glyoxylyl group-in the poorly characterized protein secernin-3. RP-ABPP thus provides a versatile method to monitor the metabolic regulation of electrophilic cofactors and discover novel types of electrophilic modifications on proteins in human cells.

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