ArticleProceedings of the National Academy of Sciences of the United States of America2013
From mechanical folding trajectories to intrinsic energy landscapes of biopolymers.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed, 88 citations in OpenAlex.
- Force-Induced Ankle Opening Reveals Mechanical Stabilization of the Ankle of Human β-Cardiac Myosin.ACS nano · 2026Article
- Single Molecule Force Spectroscopy to Probe Intermediates and Energetics of Membrane Protein Folding.Chemical reviews · 2026Review
- Accurate Memory Kernel Extraction from Discretized Time-Series Data.Journal of chemical theory and computation · 2024Article
- Fast protein folding is governed by memory-dependent friction.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Inferring equilibrium transition rates from nonequilibrium protocols.Biophysical journal · 2023Article
- Single-molecule mechanical studies of chaperones and their clients.Biophysics reviews · 2022Review
- Evolutionary balance between foldability and functionality of a glucose transporter.Nature chemical biology · 2022Article
- Quantitative Elasticity of Flexible Polymer Chains Using Interferometer-Based AFM.Nanomaterials (Basel, Switzerland) · 2022Article
- Single-molecule optical tweezers reveals folding steps of the domain swapping mechanism of a protein.Biophysical journal · 2021Article
- Out-of-Equilibrium Biophysical Chemistry: The Case for Multidimensional, Integrated Single-Molecule Approaches.The journal of physical chemistry. B · 2021Article
- Non-Markovian modeling of protein folding.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Energy landscapes of fast-folding proteins pushing the limits of atomic force microscope (AFM) pulling.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Molecular Fluctuations as a Ruler of Force-Induced Protein Conformations.Nano letters · 2021Article
- Modulation of a protein-folding landscape revealed by AFM-based force spectroscopy notwithstanding instrumental limitations.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Single-Molecule Studies of Protein Folding with Optical Tweezers.Annual review of biochemistry · 2020Review
- Interplay between Viscoelasticity and Force Rate Affects Sequential Unfolding in Polyproteins Pulled at Constant Velocity.Macromolecules · 2020Article
- Slow Transition Path Times Reveal a Complex Folding Barrier in a Designed Protein.Frontiers in chemistry · 2020Article
- Instrumental Effects in the Dynamics of an Ultrafast Folding Protein under Mechanical Force.The journal of physical chemistry. B · 2018Article
- Probing Position-Dependent Diffusion in Folding Reactions Using Single-Molecule Force Spectroscopy.Biophysical journal · 2018Article
- Protein unfolding mechanisms and their effects on folding experiments.F1000Research · 2017Review
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
In single-molecule laser optical tweezer (LOT) pulling experiments, a protein or RNA is juxtaposed between DNA handles that are attached to beads in optical traps. The LOT generates folding trajectories under force in terms of time-dependent changes in the distance between the beads. How to construct the full intrinsic folding landscape (without the handles and beads) from the measured time series is a major unsolved problem. By using rigorous theoretical methods--which account for fluctuations of the DNA handles, rotation of the optical beads, variations in applied tension due to finite trap stiffness, as well as environmental noise and limited bandwidth of the apparatus--we provide a tractable method to derive intrinsic free-energy profiles. We validate the method by showing that the exactly calculable intrinsic free-energy profile for a generalized Rouse model, which mimics the two-state behavior in nucleic acid hairpins, can be accurately extracted from simulated time series in a LOT setup regardless of the stiffness of the handles. We next apply the approach to trajectories from coarse-grained LOT molecular simulations of a coiled-coil protein based on the GCN4 leucine zipper and obtain a free-energy landscape that is in quantitative agreement with simulations performed without the beads and handles. Finally, we extract the intrinsic free-energy landscape from experimental LOT measurements for the leucine zipper.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.