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 Psi 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 Phi analysis. We present here a combination of these two procedures for defining the structure of the TS of ubiquitin, a small alpha/beta 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 Phi and Psi values were used as ensemble-averaged structural restraints to determine an ensemble of structures representing the TS of ubiquitin. Although the available Psi 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 Phi 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.