The Folding Pathway of an FF domain: Characterization of an On-pathway Intermediate State Under Folding Conditions by 15N, 13Cα and 13C-methyl Relaxation Dispersion and 1H/2H-exchange NMR Spectroscopy

The FF domain from the human protein HYPA/FBP11 folds via a low-energy on-pathway intermediate (I). Elucidation of the structure of such folding intermediates and denatured states under conditions that favour folding are difficult tasks. Here, we investigated the millisecond time-scale equilibrium folding transition of the 71-residue four-helix bundle wild-type protein by 15N, 13Cα and methyl13C Carr-Purcell-Meiboom-Gill (CPMG) NMR relaxation dispersion experiments and by 1H/2H-exchange measurements. The relaxation data for the wild-type protein fitted a simple two-site exchange process between the folded state (F) and I. Destabilization of F in mutants A17G and Q19G allowed the detection of the unfolded state U by 15N CPMG relaxation dispersion. The dispersion data for these mutants fitted a three-site exchange scheme, U↔I↔F, with I populated higher than U. The kinetics and thermodynamics of the folding reaction were obtained via temperature and urea-dependent relaxation dispersion experiments, along with structural information on I from backbone 15N, 13Cα and side-chain methyl 13C chemical shifts, with further information from protection factors for the backbone amide groups from 1H/2H-exchange. Notably, helices H1–H3 are at least partially formed in I, while helix H4 is largely disordered. Chemical shift differences for the methyl 13C nuclei suggest a paucity of stable, native-like hydrophobic interactions in I. These data are consistent with Φ-analysis of the rate-limiting transition state between I and F. The combination of relaxation dispersion and Φ data can elucidate whole experimental folding pathways.