The free energy landscape analysis of protein (FIP35) folding dynamics

A fundamental problem in the analysis of protein folding and other complex reactions is the determination of the reaction free energy landscape. The current experimental techniques lack the necessary spatial and temporal resolution to construct such landscapes. The properties of the landscapes can be probed only indirectly. Simulation, assuming that it reproduces the experimental dynamics, can provide the necessary spatial and temporal resolution. It is, arguably, the only way for direct rigorous construction of the quantitatively accurate free energy landscapes. Here, such landscape is constructed from the equilibrium folding simulation of FIP35 protein reported by Shaw et al. Science 2010, 330, 341-346. For the dynamics to be accurately described as diffusion on the free energy landscape, the choice of reaction coordinates is crucial. The reaction coordinate used here is such that the dynamics projected on it is diffusive, so the description is consistent and accurate. The obtained landscape suggests an alternative interpretation of the simulation, markedly different from that of Shaw et al. In particular, FIP35 is not an incipient downhill folder, it folds via a populated on-pathway intermediate separated by high free energy barriers; the high free energy barriers rather than landscape roughness are a major determinant of the rates for conformational transitions; the preexponential factor of folding kinetics 1/k(0) ∼ 10 ns rather than 1 μs.