Quantifying protein folding transition states with Φ_T

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 Φ_T = Δ S^†/ΔS, 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 Φ_T · Φ_T can be determined from experiment, computation, and analytical theory; Φ_T can also be used to investigate structurally localized perturbations of the free energy surface. However, Φ_T is only a relative reaction cordinate; furthermore, proteins undergo cold denaturation at sufficiently low temperatures, and care must be taken in interpreting Φ_T near the region where ∂ ΔG/∂T = 0, particularly if the heat capacity change upon folding is small.