Coordinate-dependent diffusion in protein folding

Diffusion on a low-dimensional free-energy surface is a remarkably successful model for the folding dynamics of small single-domain proteins. Complicating the interpretation of both simulations and experiments is the expectation that the effective diffusion coefficient D will in general depend on the position along the folding coordinate, and this dependence may vary for different coordinates. Here we explore the position dependence of D, its connection to protein internal friction, and the consequences for the interpretation of single-molecule experiments. We find a large decrease in D from unfolded to folded, for reaction coordinates that directly measure fluctuations in Cartesian configuration space, including those probed in single-molecule experiments. In contrast, D is almost independent of Q, the fraction of native amino acid contacts: Near the folded state, small fluctuations in position cause large fluctuations in Q, and vice versa for the unfolded state. In general, position-dependent free energies and diffusion coefficients for any two good reaction coordinates that separate reactant, product, and transition states, are related by a simple transformation, as we demonstrate. With this transformation, we obtain reaction coordinates with position-invariant D. The corresponding free-energy surfaces allow us to justify the assumptions used in estimating the speed limit for protein folding from experimental measurements of the reconfiguration time in the unfolded state, and also reveal intermediates hidden in the original free-energy projection. Lastly, we comment on the design of future single-molecule experiments that probe the position dependence of D directly.