Microscopic theory of protein folding rates. II. Local reaction coordinates and chain dynamics

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Abstract
The motions involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the preceding paper. Local reaction coordinates are identified as collective growth modes 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 from the elementary isomerization of the backbone dihedral angles. We find that the folding rate 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 barrier from the variational theory, gives a folding rate that agrees well with the experimentally determined rate under highly stabilizing conditions, but the theory predicts too large a folding rate at the transition midpoint. This discrepancy obtained using a fairly complete quantitative theory inspires a new set of questions about chain dynamics, specifically detailed motions in individual contact formation.
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