Mechanical unfolding and refolding pathways of ubiquitin

Mechanical unfolding and refolding of ubiquitin are studied by Monte Carlo simulations of a G (o) over bar model with binary variables. The exponential dependence of the time constants on the force is verified, and folding and unfolding lengths are computed, with good agreement with experimental results. Furthermore, the model exhibits intermediate kinetic states, as observed in experiments. Unfolding and refolding pathways and intermediate states, obtained by tracing single secondary structure elements, are consistent with simulations of previous all-atom models and with the experimentally observed step sizes.