Role of Loading Device on Single-Molecule Mechanical Manipulation of Free Energy Landscape

TL;DR

This study investigates how the stiffness of the loading device influences the kinetics of bond rupture and protein unfolding in single-molecule mechanical experiments through theoretical and computational models.

Contribution

It provides a theoretical and simulation-based analysis of the impact of loading device stiffness on rupture and unfolding forces, highlighting its significance in experimental outcomes.

Findings

Higher loading-device stiffness increases rupture and unfolding forces.

The force constant of the loading device governs rupture kinetics.

Simulation validates the theoretical dependence on device stiffness.

Abstract

Single-molecule mechanical manipulation has enabled the quantitative understanding of the kinetics of bond ruptures as well as protein unfolding mechanism. Single-molecule experiments with theoretical models have allowed one to gain insight into free energy landscape for chemical bond and/or protein folding. For mechanically induced bond rupture, the bond-rupture kinetics may be governed by loading device. However, the role of loading device on the kinetics of mechanical rupture has been rarely received much attention until recently. In this work, we have theoretically and/or computationally studied the effect of loading-device stiffness on the kinetics of mechanical unfolding. Specifically, we have considered a one-dimensional model for a bond rupture whose kinetics is depicted by Kramers' theory. It is elucidated that the kinetics of bond rupture is determined by force constant of loading device. The Brownian dynamics simulation of a bond rupture is considered in order to validate our theory. It is illustrated that the mean rupture force is dependent on the force constant of a loading device, such that increase in the loading-device stiffness leads to the higher bond rupture force. Moreover, we have taken into account the computational simulation of mechanical unfolding of a small protein, i.e. {\beta}-hairpin. Our simulation shows that unfolding force is highly correlated with the stiffness of a loading device. Our numerical and theoretical studies highlight the significance of a loading device on the kinetics of mechanical unfolding of a chemical bond and/or a folded domain in the single-molecule mechanical experiments.