Nonequilibrium dynamics of an exactly solvable Ising-like model and protein translocation

Using an Ising-like model of protein mechanical unfolding, we introduce a diffusive dynamics on its exactly known free-energy profile, reducing the nonequilibrium dynamics of the model to a biased random walk. As an illustration, the model is then applied to the protein translocation phenomenon, taking inspiration from a recent experiment on the green fluorescent protein pulled by a molecular motor. Tie average translocation time is evaluated exactly, and the analysis of single trajectories shows that translocation proceeds through an intermediate state, similar to that observed in the experiment. Copyright (C) EPLA, 2013