Ensemble modulation as an origin of denaturant-independent hydrogen exchange in proteins

Native state hydrogen exchange (HX) has become a powerful tool for the analysis of conformational states that exist under native conditions. However, the interpretation of HX data in terms of conformational fluctuations is still controversial. In particular, it has been shown that many residues display exchange behavior that is independent of denaturant concentration. It has been postulated that this lack of denaturant dependence results from local fluctuations that do not expose appreciable amounts of buried surface area. Here, we use a general thermodynamic description of HX to explore the different possibilities for this behavior. We find that the denaturant dependence seen in HX experiments under native conditions is not a de facto indication of the amount of surface area exposure required for exchange. Instead, this behavior results from the relatively homogenous character of the conformational ensemble that exists under native conditions and the non-specific nature of denaturant effects. Furthermore, a comparison of the HX behavior from a stabilized mutant of Staphylococcal nuclease (SNase) with that predicted for the wild-type SNase from the COREX algorithm suggests that denaturant-independent exchange of many residues is consistent with significant (∼10 %) surface area exposure for this protein.