Chemoproteomic profiling and discovery of protein electrophiles in human cells

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...

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Bibliographic Details
Published in:Nature chemistry 2017-03, Vol.9 (3), p.234-243
Main Authors: Matthews, Megan L, He, Lin, Horning, Benjamin D, Olson, Erika J, Correia, Bruno E, Yates, 3rd, John R, Dawson, Philip E, Cravatt, Benjamin F
Format: Article
Language:English
Subjects:
Adenosylmethionine Decarboxylase - chemistry
Adenosylmethionine Decarboxylase - metabolism
Amino acids
Amino Acids - chemistry
Amino Acids - metabolism
Cell Survival
Chemistry
Fluorescent Dyes - chemistry
HEK293 Cells
Humans
Hydrazines - chemistry
Metabolism
Methionine - chemistry
Methionine - metabolism
Molecular Structure
Nerve Tissue Proteins - chemistry
Nerve Tissue Proteins - metabolism
Oxidation
Proteins
Proteomics
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Summary: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.
ISSN:1755-4330
1755-4349
DOI:10.1038/nchem.2645