Single molecules in an extension clamp: extracting rates and activation barriers

When a macromolecule, held at a fixed end-to-end separation, undergoes conformational rearrangements, the fluctuating mechanical force generated by the molecule can be used as a reporter of the molecular conformational dynamics. We present an analytical framework for extracting the intrinsic rates of conformational transitions and the locations and heights of the rate-limiting barriers from such extension clamp measurements. The unique nature of the bias imposed by the extension clamp on the activation barriers allows access to biomolecular transitions currently not accessible in pulling experiments. A mapping rule is established between the outputs of different types of experiments, providing information about poorly accessible regions of the molecular landscape.