Abstract
Free-energy-landscape formalisms provide the fundamental conceptual framework for physical descriptions of how proteins and nucleic acids fold into specific three-dimensional structures1,2. Although folding landscapes are difficult to measure experimentally, recent theoretical work by Hummer and Szabo3 has shown that landscape profiles can be reconstructed from non-equilibrium single-molecule force spectroscopy measurements using an extension of the Jarzynski equality4. This method has been applied to simulations5,6 and experiments7,8 but never validated experimentally. We tested it using force–extension measurements on DNA hairpins with distinct, sequence-dependent folding landscapes. Quantitative agreement was found between the landscape profiles obtained from the non-equilibrium reconstruction and those from equilibrium probability distributions9. We also tested the method on a riboswitch aptamer with three partially folded intermediate states, successfully reconstructing the landscape but finding some states difficult to resolve owing to low occupancy or overlap of the potential wells. These measurements validate the landscape-reconstruction method and provide a new test of non-equilibrium work relations.
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Acknowledgements
We thank A. Szabo, G. Hummer and D. Minh for discussion and comments. This work was supported by the National Institute for Nanotechnology, Canadian Institutes of Health Research grant reference number NHG 91374, PrioNet Canada and the nanoWorks program of Alberta Innovates Technology Solutions.
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M.T.W. designed the experiment. F.W. contributed materials. K.N., H.Y. and M.T.W. made the measurements. A.N.G., A.V. and K.N. analysed the data. A.N.G., A.V. and M.T.W. wrote the paper.
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Gupta, A., Vincent, A., Neupane, K. et al. Experimental validation of free-energy-landscape reconstruction from non-equilibrium single-molecule force spectroscopy measurements. Nature Phys 7, 631–634 (2011). https://doi.org/10.1038/nphys2022
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DOI: https://doi.org/10.1038/nphys2022
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