Protein–small molecule interaction is vital in regulating protein functions and controlling various cellular processes. Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful methodology to study protein–small molecule interactions, however, to accurately probe the conformational dynamics of the protein upon small molecule binding, the HDX-MS experimental conditions should be carefully controlled and optimized. Here, the authors present the detailed continuous-labeling, bottom-up HDX-MS protocol for studying protein–small molecule interactions. They took a side-by-side HDX kinetics comparison of the Hsp90N protein with or without the treatment of small molecules (i.e., Radicicol, Geldanamycin) for displaying conformational changes induced by molecular interactions between Hsp90N and small molecules. Our sensitive and robust experimental protocol can facilitate the novice to quickly carry out the structural characterization of protein–small molecule interactions.

The work entitled “A hydrogen–deuterium exchange mass spectrometry-based protocol for protein-small molecule interaction analysis”was published on Biophysics Reports (published in Apr. 2023).
DOI: 10.52601/bpr.2023.230006