An extensive set of equilibrium and kinetic data was analyzed for an ultra-fast folding protein - the villin sub-domain. The equilibrium data consist of the excess heat capacity, tryptophan fluorescence quantum yield, and natural circular-dichroism spectrum as a function of temperature, while the kinetic data consist of time courses of the quantum yield from nanosecond-laser temperature-jump experiments. The data are well fit with three kinds of models - a three-state chemical-kinetics model, a physical-kinetics model, and an Ising-like theoretical model that considers 105 possible conformations (microstates). In both the physical-kinetics and theoretical models folding is described as diffusion on a one-dimensional free-energy surface. In the physical-kinetics model the reaction coordinate is unspecified, while in the theoretical model order parameters, either the fraction of native contacts or the number of native residues, are used as reaction coordinates. The validity of these two reaction coordinates is demonstrated from calculation of the splitting probability from the rate matrix of the master equation for all 105 microstates. The analysis of the data on site-directed mutants using the chemical-kinetics model provides information on the structure of the transition-state ensemble; the physical-kinetics model allows an estimate of the height of the free-energy barrier separating the folded and unfolded states, while the theoretical model provides a detailed picture of the free-energy surface and a residue-by-residue description of the evolution of the folded structure, yet contains many fewer adjustable parameters than either the chemical- or physical-kinetics models. ? ? We are also refining our Tertiary Two State model for allosteric inetractions, and are carrying out collaborative research with the group in Parma, Italy to test its theoretical predictions.
| Godoy-Ruiz, Raquel; Henry, Eric R; Kubelka, Jan et al. (2008) Estimating free-energy barrier heights for an ultrafast folding protein from calorimetric and kinetic data. J Phys Chem B 112:5938-49 |
| Eaton, William A; Henry, Eric R; Hofrichter, James et al. (2007) Evolution of allosteric models for hemoglobin. IUBMB Life 59:586-99 |
| Cellmer, Troy; Henry, Eric R; Kubelka, Jan et al. (2007) Relaxation rate for an ultrafast folding protein is independent of chemical denaturant concentration. J Am Chem Soc 129:14564-5 |
