Extracting folding landscape characteristics of biomolecules using mechanical forces

TL;DR

This paper discusses how temperature variation in force spectroscopy can measure the energy landscape roughness of biomolecules without assuming a specific reaction coordinate, highlighting challenges in locating transition states and evaluating reaction coordinates.

Contribution

It introduces a method to measure energy landscape roughness using temperature in force spectroscopy without assuming a reaction coordinate, and analyzes the limitations in locating transition states.

Findings

Energy landscape roughness can be measured without reaction coordinate assumptions.

Transition state location varies with force and loading rate, complicating analysis.

End-to-end distance may not always be an ideal reaction coordinate.

Abstract

In recent years single molecule force spectroscopy has opened a new avenue to provide profiles of the complex energy landscape of biomolecules. In this field, quantitative analyses of the data employing sound theoretical models, have played a major role in interpreting data and anticipating outcomes of experiments. Here, we explain how by using temperature as a variable in mechanical unfolding of biomolecules in force spectroscopy, the roughness of the energy landscape can be measured without making any assumptions about the underlying reaction coordinate. Estimates of other aspects of the energy landscape such as free energy barriers or the transition state (TS) locations could depend on the precise model used to analyze the experimental data. We illustrate the inherent difficulties in obtaining the transition state location from loading rate or force-dependent unfolding rates. Because the transition state moves as the force or the loading rate is varied, which is reminiscent of the Hammond effect, it is in general difficult to invert the experimental data. The independence of the TS location on force holds good only for brittle or hard biomolecules whereas the TS location changes considerably if the molecule is soft or plastic. Finally, we discuss the goodness of the end-to-end distance (or pulling) coordinate of the molecule as a surrogate reaction coordinate in a situation like force-induced ligand-unbinding from a gated molecular receptor as well as force-quench refolding of an RNA hairpin.