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

Abstract

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. The 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.

References in corpus (9)

• An Ising-Like model for protein mechanical unfolding
• Mechanical unfolding and refolding pathways of ubiquitin
• Rate Determining Factors in Protein Model Structures
• Protein mechanical unfolding: a model with binary variables
• Exactness of the cluster variation method and factorization of the equilibrium probability for the Wako-Saito-Munoz-Eaton model of protein folding
• Direction dependent mechanical unfolding and Green Fluorescent Protein as a force sensor
• Equilibrium properties and force-driven unfolding pathways of RNA molecules
• Pathways of mechanical unfolding of FnIII_{10}: low force intermediates
• An exactly solvable model for a beta-hairpin with random interactions