Ynamide Coupling Reagent for the Chemical Cross-Linking of Proteins in Live Cells

Chemicalcross-linking of proteins coupled with massspectrometryanalysis (CXMS) is a powerful method for the study of protein structureand protein-protein interactions (PPIs). However, the chemicalprobes used in the CXMS are limited to bidentate reactive warheads,and the available zero-length cross-linkers are restricted to 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride/N-hydroxysuccinimide (EDC/NHS)and 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride(DMTMM). To alleviate this issue, an efficient coupling reagent, sulfonylynamide, was developed as a new zero-length cross-linker that canconnect high-abundance carboxyl residues (D/E) with lysine (K) toform amide bonds in the absence of any catalyst. Significant improvementin the cross-linking efficiency and specificity in comparison withtraditional EDC/NHS was achieved with model proteins, which includesinter- and intramolecular conjugations. The cross-linked structureswere validated by X-ray crystallography. Importantly, this couplingreagent can be successfully used to capture interacting proteins inthe whole proteome and can be a useful reagent for probing potentialprotein-protein interactions in situ.

Automated summary

Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) is a powerful method for studying protein structure and protein-protein interactions (PPIs). However, the available chemical probes and zero-length cross-linkers are limited. To overcome this, researchers developed a new coupling reagent, sulfonyl amide, which efficiently connects carboxyl residues (D/E) with lysine (K) to form amide bonds without any catalyst. This new reagent showed significant improvement in cross-linking efficiency and specificity compared to traditional methods.