The Structure of the Major Transition State for Folding of an FF Domain from Experiment and Simulation

We have analysed the transition state of folding of the four-helix FF domain from HYPA/FBP11 by high-resolution experiment and simulation as part of a continuing effort to understand the principles of folding and the refinement of predictive methods. The major transition state for folding was subjected to a Φ-value analysis utilising 50 mutants. The transition state contained a nucleus for folding centred around the end of helix 1 (H1) and the beginning of helix 2 (H2). Secondary structure in this region was fully formed (Φ F=0.9–1) and tertiary interactions were well developed. Interactions in the distal part of the native structure were weak (Φ F=0–0.2). The hydrophobic core and other parts of the protein displayed intermediate Φ-values, suggesting that interactions coalesce as the end of H1 and beginning of H2 are in the process of being formed. The distribution of Φ-values resembled that of barnase, which folds via an intermediate, rather than that of CI2 which folds by a concerted nucleation–condensation mechanism. The overall picture of the transition state structure identified in molecular dynamics simulations is in qualitative agreement, with the turn connecting H1 and H2 being formed, a loosened core, and H4 partially unfolded and detached from the core. There are some differences in the details and interpretation of specific Φ-values.