Unfolding Dynamics of Ubiquitin from Constant Force MD Simulation: Entropy–Enthalpy Interplay Shapes the Free-Energy Landscape

Abstract

Force probe methods are routinely used to study conformational transitions of biomolecules at single-molecule level. In contrast to simple kinetics, some proteins show complex response to mechanical perturbations that is manifested in terms of unusual force-dependent kinetics. Here, we study, via fully atomistic molecular dynamics simulations, constant force-induced unfolding of ubiquitin protein. Our simulations reveal a crossover at an intermediate force (about 400 pN) in the unfolding rate versus force curve. We find by calculation of multidimensional free-energy landscape (FEL) of the protein that the complex unfolding kinetics is intimately related to the force-dependent modifications in the FEL. Pearson correlation coefficient analysis allowed us to identify two appropriate order parameters describing the unfolding transition. The crossover in the rate can be explained in terms of an interplay between entropy and enthalpy with relative importance changing from low force to high force. We rationalize the results by using multidimensional transition-state theory.