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The motion involved in barrier crossing for protein folding are investigatedin terms of the chain dynamics of the polymer backbone, completing themicroscopic description of protein folding presented in the previous paper.Local reaction coordinates are identified as collective growth modes of theunstable fluctuations about the saddle-points in the free energy surface. Thedescription of the chain dynamics incorporates internal friction (independentof the solvent viscosity) arising from the elementary isomerizations of thebackbone dihedral angles. We find that the folding rate depends linearly on thesolvent friction for high viscosity, but saturates at low viscosity because ofinternal friction. For $\lambda$-repressor, the calculated folding rateprefactor, along with the free energy barrier from the variational theory,gives a folding rate that agrees well with the experimentally determined rateunder highly stabilizing conditions, but the theory predicts too large afolding rate at the transition midpoint. This discrepancy obtained using afairly complete quantitative theory inspires a new set of questions about chaindynamics, specifically detailed motions in individual contact formation.Comment: 18 pages, 8 figure

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