ArticleProceedings of the National Academy of Sciences of the United States of America2015
Reconstructing folding energy landscapes from splitting probability analysis of single-molecule trajectories.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed.
- Static and dynamic rough energy landscapes can lead to identical diffusivity.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Temperature-dependent funnel-like DNA folding landscapes.Nucleic acids research · 2025Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Reaction Coordinates Are Optimal Channels of Energy Flow.Annual review of physical chemistry · 2025Review
- Transient states during the annealing of mismatched and bulged oligonucleotides.Nucleic acids research · 2024Article
- Inferring equilibrium transition rates from nonequilibrium protocols.Biophysical journal · 2023Article
- Analysis of the Passage Times for Unfolding/Folding of the Adenine Riboswitch Aptamer.ACS physical chemistry Au · 2022Article
- Mechanism for the rare fluctuation that powers protein conformational change.The Journal of chemical physics · 2022Article
- Next Generation Methods for Single-Molecule Force Spectroscopy on Polyproteins and Receptor-Ligand Complexes.Frontiers in molecular biosciences · 2020Review
- Molecular free energy profiles from force spectroscopy experiments by inversion of observed committors.The Journal of chemical physics · 2019Article
- Exact Solutions for Distributions of First-Passage, Direct-Transit, and Looping Times in Symmetric Cusp Potential Barriers and Wells.The journal of physical chemistry. B · 2019Article
- Communication: Transition-path velocity as an experimental measure of barrier crossing dynamics.The Journal of chemical physics · 2018Article
- Probing Position-Dependent Diffusion in Folding Reactions Using Single-Molecule Force Spectroscopy.Biophysical journal · 2018Article
- Transition Path Times Measured by Single-Molecule Spectroscopy.Journal of molecular biology · 2018Review
- Communication: Coordinate-dependent diffusivity from single molecule trajectories.The Journal of chemical physics · 2017Article
- Hidden dynamics in the unfolding of individual bacteriorhodopsin proteins.Science (New York, N.Y.) · 2017Article
- Direct measurement of sequence-dependent transition path times and conformational diffusion in DNA duplex formation.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Enhanced stochastic fluctuations to measure steep adhesive energy landscapes.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Article
- Reduction of All-Atom Protein Folding Dynamics to One-Dimensional Diffusion.The journal of physical chemistry. B · 2015Article
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3 authors.
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Abstract
Structural self-assembly in biopolymers, such as proteins and nucleic acids, involves a diffusive search for the minimum-energy state in a conformational free-energy landscape. The likelihood of folding proceeding to completion, as a function of the reaction coordinate used to monitor the transition, can be described by the splitting probability, p(fold)(x). P(fold) encodes information about the underlying energy landscape, and it is often used to judge the quality of the reaction coordinate. Here, we show how p(fold) can be used to reconstruct energy landscapes from single-molecule folding trajectories, using force spectroscopy measurements of single DNA hairpins. Calculating p(fold)(x) directly from trajectories of the molecular extension measured for hairpins fluctuating in equilibrium between folded and unfolded states, we inverted the result expected from diffusion over a 1D energy landscape to obtain the implied landscape profile. The results agreed well with the landscapes reconstructed by established methods, but, remarkably, without the need to deconvolve instrumental effects on the landscape, such as tether compliance. The same approach was also applied to hairpins with multistate folding pathways. The relative insensitivity of the method to the instrumental compliance was confirmed by simulations of folding measured with different tether stiffnesses. This work confirms that the molecular extension is a good reaction coordinate for these measurements, and validates a powerful yet simple method for reconstructing landscapes from single-molecule trajectories.
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