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In recent years single molecule force spectroscopy has opened a new avenue toprovide profiles of the complex energy landscape of biomolecules. In thisfield, quantitative analyses of the data employing sound theoretical models,have played a major role in interpreting data and anticipating outcomes ofexperiments. Here, we explain how by using temperature as a variable inmechanical unfolding of biomolecules in force spectroscopy, the roughness ofthe energy landscape can be measured without making any assumptions about theunderlying reaction coordinate. Estimates of other aspects of the energylandscape such as free energy barriers or the transition state (TS) locationscould depend on the precise model used to analyze the experimental data. Weillustrate the inherent difficulties in obtaining the transition state locationfrom loading rate or force-dependent unfolding rates. Because the transitionstate moves as the force or the loading rate is varied, which is reminiscent ofthe 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 orhard biomolecules whereas the TS location changes considerably if the moleculeis 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 asituation like force-induced ligand-unbinding from a gated molecular receptoras well as force-quench refolding of an RNA hairpin.

Extracting folding landscape characteristics of biomolecules using mechanical forces