Phi Value Analysis - Example: Barnase

Example: Barnase

Alan Fersht pioneered the phi value analysis method by first applying it to the small bacterial protein barnase. In conjunction with molecular dynamics simulations, the analysis illustrated that, at least for this protein, the transition state between folding and unfolding is the same in both reaction directions and more closely resembled the native state. Phi values were found to vary considerably with the location of the mutation, with some regions of the protein yielding values near 0 and others yielding values near 1. The distribution of phi values over the protein agrees well with the simulated unfolding transition state in all but one helix, later identified as folding semi-independently and forming native-like contacts with the remainder of the protein only after the complete transition state has been reached. Such variations in the folding rate within a protein present another challenge in interpreting phi values, since the transition state structure cannot be determined experimentally. Folding and unfolding simulations, though computationally expensive, can provide valuable structural information that complements phi value results.