Ultrafast Folding of α3D: A de novo Designed Three-Helix Bundle Protein

Here, we describe the folding/unfolding kinetics of α3D, a small designed three-helix bundle. Both IR temperature jump and ultrafast fluorescence mixing methods reveal a single-exponential process consistent with a minimal folding time of$3.2 \pm 1.2\>\mu s$(at ≈50° C), indicating that a protein can fold on the 1- to 5-μ s time scale. Furthermore, the single-exponential nature of the relaxation indicates that the prefactor for transition state (TS)-folding models is probably$\geq\!1\>(\mu s)^{-1}$for a protein of this size and topology. Molecular dynamics simulations and IR spectroscopy provide a molecular rationale for the rapid, single-exponential folding of this protein. α3Dshows a significant bias toward local helical structure in the thermally denatured state. The molecular dynamics-simulated TS ensemble is highly heterogeneous and dynamic, allowing access to the TS via multiple pathways.