Mechanical unfolding and refolding pathways of ubiquitin

TL;DR

This study uses Monte Carlo simulations of a Go model to analyze the mechanical unfolding and refolding pathways of ubiquitin, confirming experimental observations and revealing intermediate states and pathway details.

Contribution

It introduces a simplified binary-variable Go model to simulate ubiquitin's mechanical folding, aligning well with experimental data and previous detailed models.

Findings

Exponential dependence of time constants on force verified

Intermediate kinetic states observed in simulations

Unfolding and refolding pathways consistent with experiments

Abstract

Mechanical unfolding and refolding of ubiquitin are studied by Monte Carlo simulations of a Go 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.