Measuring the energy landscape roughness and the transition state location of biomolecules using single molecule mechanical unfolding experiments

Abstract

Single molecule mechanical unfolding experiments are beginning to provide profiles of the complex energy landscape of biomolecules. In order to obtain reliable estimates of the energy landscape characteristics it is necessary to combine the experimental measurements with sound theoretical models and simulations. Here, we show how by using temperature as a variable in mechanical unfolding of biomolecules in laser optical tweezer or AFM experiments the roughness of the energy landscape can be measured without making any assumptions about the underlying reaction oordinate. The efficacy of the formalism is illustrated by reviewing experimental results that have directly measured roughness in a protein-protein complex. The roughness model can also be used to interpret experiments on forced-unfolding of proteins in which temperature is varied. 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 it is in general difficult to invert the experimental data unless the curvature at the top of the one dimensional free energy profile is large, i.e the barrier is sharp. 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. We also comment on the usefulness of extension of the molecule as a surrogate reaction coordinate especially in the context of force-quench refolding of proteins and RNA.

arXiv comment44 pages, 7 figures

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Cited by in corpus (17)

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• Molten globule-like transition state of protein barnase measured with calorimetric force spectroscopy
• Compaction and tensile forces determine the accuracy of folding landscape parameters from single molecule pulling experiments
• Measurement of work in single-molecule experiments
• Evidence of disorder in biological molecules from single molecule pulling experiments
• Multiple barriers in forced rupture of protein complexes
• Weak temporal signals can synchronize and accelerate the transition dynamics of biopolymers under tension
• Force-Dependent Folding Kinetics of Single Molecules with Multiple Intermediates and Pathways
• Force-clamp spectroscopy of reversible bond breakage
• Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding
• Forced-rupture of Cell-Adhesion Complexes Reveals abrupt switch between two Brittle States
• Unfolding force definition and the unified model for the mean unfolding force dependence on the loading rate
• Extraction of kinetics from equilibrium distributions of states using the Metropolis Monte Carlo method
• Universal Aspects of Barrier Crossing Under Bias