ArticleProtein science : a publication of the Protein Society2016
Extracting intrinsic dynamic parameters of biomolecular folding from single-molecule force spectroscopy experiments.
Article in Protein science : a publication of the Protein Society, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed.
- Single Molecule Force Spectroscopy to Probe Intermediates and Energetics of Membrane Protein Folding.Chemical reviews · 2026Review
- How specific ion effects influence the mechanical behaviors of amide macromolecules? A cross-scale study.RSC advances · 2024Article
- Nonlinear effects in optical trapping of titanium dioxide and diamond nanoparticles.Biophysical journal · 2023Article
- The Effect of Time Resolution on Apparent Transition Path Times Observed in Single-Molecule Studies of Biomolecules.The journal of physical chemistry. B · 2022Article
- Observing the base-by-base search for native structure along transition paths during the folding of single nucleic acid hairpins.Proceedings of the National Academy of Sciences of the United States of America · 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
- Mechanical unfolding of spectrin reveals a super-exponential dependence of unfolding rate on force.Scientific reports · 2019Article
- Measuring the average shape of transition paths during the folding of a single biological molecule.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Instrumental Effects in the Dynamics of an Ultrafast Folding Protein under Mechanical Force.The journal of physical chemistry. B · 2018Article
- 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 paths in single-molecule force spectroscopy.The Journal of chemical physics · 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
- Quantifying Instrumental Artifacts in Folding Kinetics Measured by Single-Molecule Force Spectroscopy.Biophysical journal · 2016Article
- Pharmacological chaperone reshapes the energy landscape for folding and aggregation of the prion protein.Nature communications · 2016Article
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Abstract
Single-molecule studies in which a mechanical force is transmitted to the molecule of interest and the molecular extension or position is monitored as a function of time are versatile tools for probing the dynamics of protein folding, stepping of molecular motors, and other biomolecular processes involving activated barrier crossing. One complication in interpreting such studies, however, is the fact that the typical size of a force probe (e.g., a dielectric bead in optical tweezers or the atomic force microscope tip/cantilever assembly) is much larger than the molecule itself, and so the observed molecular motion is affected by the hydrodynamic drag on the probe. This presents the experimenter with a nontrivial task of deconvolving the intrinsic molecular parameters, such as the intrinsic free energy barrier and the effective diffusion coefficient exhibited while crossing the barrier from the experimental signal. Here we focus on the dynamical aspect of this task and show how the intrinsic diffusion coefficient along the molecular reaction coordinate can be inferred from single-molecule measurements of the rates of biomolecular folding and unfolding. We show that the feasibility of accomplishing this task is strongly dependent on the relationship between the intrinsic molecular elasticity and that of the linker connecting the molecule to the force probe and identify the optimal range of instrumental parameters allowing determination of instrument-free molecular dynamics.
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