title: Reconstructing folding energy landscapes by single-molecule force spectroscopy.
abstract: Folding may be described conceptually in terms of trajectories over a landscape of free energies corresponding to different molecular configurations. In practice, energy landscapes can be difficult to measure. Single-molecule force spectroscopy (SMFS), whereby structural changes are monitored in molecules subjected to controlled forces, has emerged as a powerful tool for probing energy landscapes. We summarize methods for reconstructing landscapes from force spectroscopy measurements under both equilibrium and nonequilibrium conditions. Other complementary, but technically less demanding, methods provide a model-dependent characterization of key features of the landscape. Once reconstructed, energy landscapes can be used to study critical folding parameters, such as the characteristic transition times required for structural changes and the effective diffusion coefficient setting the timescale for motions over the landscape. We also discuss issues that complicate measurement and interpretation, including the possibility of multiple states or pathways and the effects of projecting multiple dimensions onto a single coordinate.
authors.affiliation: Department of Physics, University of Alberta, Edmonton, Alberta T6G2E1, Canada; email: michael.woodside@ualberta.ca.
authors.forename: Michael T
authors.initials: MT
authors.lastname: Woodside
authors.forename: Steven M
authors.initials: SM
authors.lastname: Block
mesh_terms: D004247:DNA / Q000737:chemistry; D004734:Energy Metabolism; D011506:Proteins / Q000737:chemistry; D013057:Spectrum Analysis / Q000379:methods*; D013816:Thermodynamics
chemical_list: D011506:Proteins; D004247:DNA
keywords: AFM; nucleic acid folding; optical trapping; protein folding; reaction coordinate; statistical mechanics