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Single molecule mechanical unfolding experiments are beginning to provideprofiles of the complex energy landscape of biomolecules. In order to obtainreliable estimates of the energy landscape characteristics it is necessary tocombine the experimental measurements with sound theoretical models andsimulations. Here, we show how by using temperature as a variable in mechanicalunfolding of biomolecules in laser optical tweezer or AFM experiments theroughness of the energy landscape can be measured without making anyassumptions about the underlying reaction oordinate. The efficacy of theformalism is illustrated by reviewing experimental results that have directlymeasured roughness in a protein-protein complex. The roughness model can alsobe used to interpret experiments on forced-unfolding of proteins in whichtemperature is varied. Estimates of other aspects of the energy landscape suchas free energy barriers or the transition state (TS) locations could depend onthe precise model used to analyze the experimental data. We illustrate theinherent difficulties in obtaining the transition state location from loadingrate or force-dependent unfolding rates. Because the transition state moves asthe force or the loading rate is varied it is in general difficult to invertthe experimental data unless the curvature at the top of the one dimensionalfree energy profile is large, i.e the barrier is sharp. The independence of theTS location on force holds good only for brittle or hard biomolecules whereasthe TS location changes considerably if the molecule is soft or plastic. Wealso comment on the usefulness of extension of the molecule as a surrogatereaction coordinate especially in the context of force-quench refolding ofproteins and RNA.Comment: 44 pages, 7 figure

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