UMass Chan Medical School Faculty Publications


Proximity-Dependent Labeling of Cysteines

UMMS Affiliation

Department of Biochemistry and Molecular Pharmacology; Program in Chemical Biology; Mass Spectrometry Facility; Thompson Lab

Publication Date


Document Type



Amino Acids, Peptides, and Proteins | Biochemistry, Biophysics, and Structural Biology | Chemistry | Enzymes and Coenzymes


Mapping protein-protein interactions is crucial for understanding various signaling pathways in living cells, and developing new techniques for this purpose has attracted significant interest. Classic methods (e.g., the yeast two-hybrid) have been supplanted by more sophisticated chemical approaches that label proximal proteins (e.g., BioID, APEX). Herein we describe a proximity-based approach that uniquely labels cysteines. Our approach exploits the nicotinamide N-methyltransferase (NNMT)-catalyzed methylation of an alkyne-substituted 4-chloropyridine (SS6). Upon methylation of the pyridinium nitrogen, this latent electrophile diffuses out of the active site and labels proximal proteins on short time scales ( < /=5 min). We validated this approach by identifying known (and novel) interacting partners of protein arginine deiminase 2 (PAD2) and pyruvate dehydrogenase kinase 1 (PDK1). To our knowledge, this technology uniquely exploits a suicide substrate to label proximal cysteines in live cells.


Calcium, Protein identification, Peptides and proteins, Monomers, Labeling

DOI of Published Version



Sen S, Sultana N, Shaffer SA, Thompson PR. Proximity-Dependent Labeling of Cysteines. J Am Chem Soc. 2021 Nov 24;143(46):19257-19261. doi: 10.1021/jacs.1c07069. Epub 2021 Nov 11. PMID: 34762412. Link to article on publisher's site

Related Resources

Link to Article in PubMed

Journal/Book/Conference Title

Journal of the American Chemical Society

PubMed ID