Determination of the Transition State Ensemble for the Folding of Ubiquitin from a Combination of Phi and Psi Analyses

Protein engineering techniques have emerged as powerful tools for characterizing transition states (TSs) for protein folding. Recently, the Si analysis, in which double-histidine mutations create the possibility of reversible crosslinking in the native state, has been proposed as an additional approach to the well-established F analysis. We present here a combination of these two procedures for defining the structure of the TS of ubiquitin, a small a/ protein that has been used extensively as a model system for both experimental and computational studies of the protein-folding process. We performed a series of molecular dynamics simulations in which F and S values were used as ensemble-averaged structural restraints to determine an ensemble of structures representing the TS of ubiquitin. Although the available values for ubiquitin did not, by themselves, generate well-defined TS ensembles, the inclusion of the restricted set of zero or unity values, but not fractional ones, provided useful complementary information to the F analysis. Our results show that the TS of ubiquitin is formed by a relatively narrow ensemble of structures exhibiting an overall native-like topology in which the N-terminal and C-terminal regions are in close proximity.