Fast events in protein folding: Relaxation dynamics of secondary and tertiary structure in native apomyoglobin

We report the fast relaxation dynamics of “native” apomyoglobin (pH 5.3) following a 10-ns, laser-induced temperature jump. The structural dynamics are probed using time-resolved infrared spectroscopy. The infrared kinetics monitored within the amide I absorbance of the polypeptide backbone exhibit two distinct relaxation phases which have different spectral signatures and occur on very different time scales (ν = 1633 cm(−1), τ = 48 ns; ν = 1650 cm(−1), τ = 132 μs). We assign these two spectral components to discrete substructures in the protein: helical structure that is solvated (1633 cm(−1)) and native helix that is protected from solvation by interhelix tertiary interactions (1650 cm(−1)). Folding rate coefficients inferred from the observed relaxations at 60°C are k(f(solvated)) = (7 to 20) × 10(6) s(−1) and k(f(native)) = 3.6 × 10(3) s(−1), respectively. The faster rate is interpreted as the intrinsic rate of solvated helix formation, whereas the slower rate is interpreted as the rate of formation of tertiary contacts that determine a native helix. Thus, at 60°C helix formation precedes the formation of tertiary structure by over three orders of magnitude in this protein. Furthermore, the distinct thermodynamics and kinetics observed for the apomyoglobin substructures suggest that they fold independently, or quasi-independently. The observation of inhomogeneous folding for apomyoglobin is remarkable, given the relatively small size and structural simplicity of this protein.