Abstract

Protein unfolding and refolding trajectories under a constant stretching force measure manifestations of the underlying molecular processes in the end-to-end length fluctuations. In the case of ubiquitin, I27 and NuG2 protein, the distribution of unfolding times at a given force is best fit with a stretched exponential function, which requires an alternative physical interpretation than the commonly used Kramer’s theory. On the other hand, we show that the collapse from a highly extended state to the folded length is well captured by simple diffusion along the free energy of the end-to-end length. The estimated diffusion coefficient of ?100nm2s?1 is significantly slower than expected from viscous effects alone, possibly because of the internal degrees of freedom of the protein. The reconstructed free energy profiles give validity to a physical model in which the multiple protein domains collapse all at once, independent of the number of domains in the in the chain.