Quantifying protein folding transition states with ΦT

A number of reaction coordinates have been proposed for reduced-dimensionality representations of a protein's folding free energy surface. We discuss in detail the entropic reaction coordinate Phi(T) = Delta Sdagger/DeltaS, recently introduced to quantify the conservation of mutations and the location of the folding transition state based on experimental temperature-tuning data. Numerical simulations illustrate the advantages as well as the limitations of Phi(T). Phi(T) can be determined from experiment, computation, and analytical theory; Phi(T) can also be used to investigate structurally localized perturbations of the free energy surface. However, Phi(T) is only a relative reaction cordinate; furthermore, proteins undergo cold denaturation at sufficiently low temperatures, and care must be taken in interpreting Phi(T) near the region where partial derivativeDeltaG/partial derivativeT = 0, particularly if the heat capacity change upon folding is small.