Modeling deuterium exchange behavior of ERK2 using pepsin mapping to probe secondary structure

Recently, mass spectrometry has been applied to studies of hydrogen exchange of backbone amides, allowing analysis of large proteins at physiological concentrations. Low resolution spatial information is obtained by digesting proteins after exchange into D2O, using electrospray ionization liquid chromatography/mass spectrometry (ESI-LC/MS) to measure deuteration by mass increases of resulting peptides. This study develops modeling paradigms to increase resolution, using the signal transduction kinase ERK2 as a prototype for larger, less stable proteins. In-exchange data for peptides were analyzed by nonlinear least squares and a maximum entropy method, distinguishing amides into fast, intermediate, slow, and nonexchanging classes. Analysis of completely nonexchanging or in-exchanging peptides and peptides with sequence overlaps showed that nonexchanging amides were generally hydrogen bonded and sterically constrained or buried > or = 2.2 A from the protein surface, while fast exchanging hydrogens were generally exposed at the protein surface. In order to more fully understand the intermediate and slow exchanging classes, an empirical model was developed by analyzing published exchange rates in cytochrome c. The model correlated protection factors with a combined dependency on surface accessibility, hydrogen bond length, and position of residues from alpha helix ends. Together with analysis of partial proteolytic products, the derived rules for exchange allowed modeling of exchange behavior of peptides. Substantial deviation from the predicted rates in some cases suggested a role for conformational freedom in regulating fast and intermediate exchanging amides.