Hydrogen/deuterium exchange connected with mass spectrometry is increasingly applied for the interrogation of protein conformation, mapping protein dynamics, identification of protein-ligand interaction sites, and allosteric conformation changes. The dynamics of protein changes is determined with the m/z value of deuterated and non-deuterated protein or percentage of deuterium incorporation for the digested peptides. Hydrogen/deuterium exchange data are processed with selected software and finally quaternary structure of protein is visualized showing how different protein and ligand chains hook up with each other. Obtained results can help understand how protein interacts with its ligand and elucidate the role of this complex in a living organism. Utilization of this method is demonstrated by the amyloid-beta peptide aggregation associated with Alzheimer's disease; determination of the structure toxin-co-regulated pili Vibrio cholerae in connection with its pathogenesis or revelation of binding sites on Mouse double minute 2 homolog complex with small molecule Nutlin-3 which is important for elucidation of drug effects in cancer research.

Keywords: mass spectrometry; protein-protein interaction