Structure of the hydrophobic core in the transition state for folding of chymotrypsin inhibitor 2: a critical test of the protein engineering method of analysis.

Chymotrypsin inhibitor 2 (CI2) unfolds and refolds according to a simple two-state kinetic mechanism. The single rate-determining transition state may thus be studied by kinetics of both unfolding and refolding. This has allowed the direct testing of some facets of the protein engineering procedure (phi-value analysis). The structure of the hydrophobic core of CI2 in the transition state was analyzed from kinetic and thermodynamic measurements of guanidinium chloride-induced unfolding of 11 mutants and of their rates of refolding. In all cases, the strengths of the interactions measured from refolding kinetics in water are in excellent agreement with those measured from unfolding kinetics in guanidinium chloride solutions and extrapolated to zero molar denaturant. Changes in the free energies of unfolding on mutation, as well as other equilibrium properties calculated from the rate constants, are also in excellent agreement with those measured directly from equilibrium studies. These data provide further evidence for application of the principle of microscopic reversibility to aspects of protein folding in the presence of denaturant and the validity of extrapolation to the absence of denaturant. The edges of the hydrophobic core of CI2 are significantly weakened in the transition state, and, in many cases, the interactions are totally lost. The center of the core remains partially intact; the interaction energy is lowered by about 50%.(ABSTRACT TRUNCATED AT 250 WORDS)