title: Making connections between ultrafast protein folding kinetics and molecular dynamics simulations.
abstract: Determining the rate of forming the truly folded conformation of ultrafast folding proteins is an important issue for both experiments and simulations. The double-norleucine mutant of the 35-residue villin subdomain is the focus of recent computer simulations with atomistic molecular dynamics because it is currently the fastest folding protein. The folding kinetics of this protein have been measured in laser temperature-jump experiments using tryptophan fluorescence as a probe of overall folding. The conclusion from the simulations, however, is that the rate determined by fluorescence is significantly larger than the rate of overall folding. We have therefore employed an independent experimental method to determine the folding rate. The decay of the tryptophan triplet-state in photoselection experiments was used to monitor the change in the unfolded population for a sequence of the villin subdomain with one amino acid difference from that of the laser temperature-jump experiments, but with almost identical equilibrium properties. Folding times obtained in a two-state analysis of the results from the two methods at denaturant concentrations varying from 1.5-6.0 M guanidinium chloride are in excellent agreement, with an average difference of only 20%. Polynomial extrapolation of all the data to zero denaturant yields a folding time of 220 (+100,-70) ns at 283 K, suggesting that under these conditions the barrier between folded and unfolded states has effectively disappeared--the so-called "downhill scenario."
authors: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.
authors: Troy
authors: T
authors: Cellmer
authors: Marco
authors: M
authors: Buscaglia
authors: Eric R
authors: ER
authors: Henry
authors: James
authors: J
authors: Hofrichter
authors: William A
authors: WA
authors: Eaton
mesh_terms: D018360:Crystallography, X-Ray; D005453:Fluorescence; D007700:Kinetics; D008840:Microfilament Proteins / Q000737:chemistry* / Q000235:genetics; D056004:Molecular Dynamics Simulation; D009154:Mutation; D009646:Norleucine / Q000737:chemistry / Q000235:genetics; D017510:Protein Folding; D017434:Protein Structure, Tertiary / Q000235:genetics; D013696:Temperature; D014364:Tryptophan / Q000737:chemistry / Q000235:genetics
chemical_list: D008840:Microfilament Proteins; C026615:villin; D009646:Norleucine; D014364:Tryptophan