Gas phase conformations of biological molecules: the hydrogen/deuterium exchange mechanism

A model was developed to describe the deuterium uptake of gas phase polypeptide ions via H/D exchange with D₂O. Ab initio calculations established, for energetic reasons, that the exchange must take place via a “relay” mechanism involving both a charged site and a nearby basic site. Molecular dynamics simulations indicated that the D₂O molecule did not penetrate the core of the example peptide, protonated bradykinin (Bk+H)⁺, and hence the relay mechanism must occur on the peptide surface. Two factors were deemed to be important: (1) The surface accessibility of the charged sites and the basic sites and (2) the distances between them. An algorithm was developed that accounted for these features using the absolute exchange rate as a free parameter. Excellent agreement was obtained with experiment when equal weight was given to an ensemble of low energy conformations of (Bk+H)⁺, assumed to have a salt bridge primary structure. Single conformations, or other protonated forms, did not allow good agreement with experiment for any value of the absolute exchange rate constant.