Microscopic Theory of Protein Folding Rates.II Local Reaction Coordinates and Chain Dynamic.pdfVIP

Microscopic Theory of Protein Folding Rates.II: Local Reaction Coordinates and Chain Dynamics John J. Portman ∗ , Shoji Takada † , and Peter G. Wolynes ∗‡ ∗ Departments of Physics and Chemistry, University of Illinois, Urbana, Illinois, 61801 † Department of Chemistry, Kobe University, Rokkodai, Kobe, 657 Japan ‡ Current address: Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 0 92093 0 (August 23, 2000) 0 2 The motion involved in barrier crossing for protein folding are investigated in terms of the chain g dynamics of the polymer backbone, completing the microscopic description of protein folding pre- u sented in the previous paper. Local reaction coordinates are identified as collective growth modes A of the unstable fluctuations about the saddle-points in the free energy surface. The description of the chain dynamics incorporates internal friction (independent of the solvent viscosity) arising 0 from the elementary isomerizations of the backbone dihedral angles. We find that the folding rate 3 depends linearly on the solvent friction for high viscosity, but saturates at low viscosity because of internal friction. For λ-repressor, the calculated folding rate prefactor, along with the free energy ] t barrier from the variational theory, gives a folding rate that