Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations

Experimentally, protein engineering and φ-value analysis is the method of choice to characterize the structure in folding transition state ensemble (TSE) of any protein. Combining experimental φ values and computer simulations has led to a deeper understanding of how proteins fold. In this report, we construct the TSE of chymotrypsin inhibitor 2 from published φ values. Importantly, we verify, by means of multiple independent simulations, that the conformations in the TSE have a probability of ≈0.5 to reach the native state rapidly, so the TSE consists of true transition states. This finding validates the use of transition state theory underlying all φ-value analyses. Also, we present a method to dissect and study the TSE by generating conformations that have a disrupted α-helix (α-disrupted states) or disordered β-strands 3 and 4 (β-disrupted states). Surprisingly, the α-disrupted states have a stronger tendency to fold than the β-disrupted states, despite the higher φ values for the α-helix in the TSE. We give a plausible explanation for this result and discuss its implications on protein folding and design. Our study shows that, by using both experiments and computer simulations, we can gain many insights into protein folding.