Book of Abstracts: Albany 2011
June 14-18 2011
©Adenine Press (2010)
Folding Globular Proteins: Collapse Kinetics and Chevron Plots
Quantitative description of how proteins fold under experimental conditions remains a challenging problem. Experiments often use urea and Guanidinium Chloride (GdmCl) to study folding whereas the natural variable in simulations is temperature. To bridge the gap, we use the Molecular Transfer Model that combines measured denaturant-dependent transfer free energies for the peptide group and amino acid residues, and a coarse-grained model for polypeptide chains to simulate the folding mechanism of src SH3. Stability of the native state decreases linearly as [C] (the concentration of GdmCl) increases with the slope that is in excellent agreement with experiments. We show that lnkobs (kobs is the sum of folding and unfolding rates) as a function of [C] has the characteristic V (Chevron) shape. In the dominant transition state, which does not vary significantly at low [C], the core of the protein and certain loops are structured. Besides solving the long-standing problem of computing the Chevron plot, our work lays the foundation for incorporating denaturant effects in a physically transparent manner either in all atom or coarse-grained simulations.
Institute for Physical Science and Technology