ArticlePhysical chemistry chemical physics : PCCP2011
Diffusion models of protein folding.
Article in Physical chemistry chemical physics : PCCP, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 80 citations in OpenAlex.
- Accuracy of distance distributions and dynamics from single-molecule FRET.Biophysical journal · 2025Article
- Molecular Free Energies, Rates, and Mechanisms from Data-Efficient Path Sampling Simulations.Journal of chemical theory and computation · 2023Article
- Tuning Formation of Protein-DNA Coacervates by Sequence and Environment.The journal of physical chemistry. B · 2022Article
- Estimating transition path times and shapes from single-molecule photon trajectories: A simulation analysis.The Journal of chemical physics · 2021Article
- Atomistic mechanism of transmembrane helix association.PLoS computational biology · 2020Article
- Diverse Folding Pathways of HIV-1 Protease Monomer on a Rugged Energy Landscape.Biophysical journal · 2019Article
- Ultrafast folding kinetics of WW domains reveal how the amino acid sequence determines the speed limit to protein folding.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Position-, disorder-, and salt-dependent diffusion in binding-coupled-folding of intrinsically disordered proteins.Physical chemistry chemical physics : PCCP · 2019Article
- Accurate Protein-Folding Transition-Path Statistics from a Simple Free-Energy Landscape.The journal of physical chemistry. B · 2018Article
- Single-Molecule Test for Markovianity of the Dynamics along a Reaction Coordinate.The journal of physical chemistry letters · 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
- Dynamics of the Orientational Factor in Fluorescence Resonance Energy Transfer.The journal of physical chemistry. B · 2017Article
- When fast is better: protein folding fundamentals and mechanisms from ultrafast approaches.The Biochemical journal · 2016Review
- Diffusive Dynamics of Contact Formation in Disordered Polypeptides.Physical review letters · 2016Article
- Reduction of All-Atom Protein Folding Dynamics to One-Dimensional Diffusion.The journal of physical chemistry. B · 2015Article
- The adaptive biasing force method: everything you always wanted to know but were afraid to ask.The journal of physical chemistry. B · 2015Article
- Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application.Nano reviews · 2015Article
- Fast single-molecule FRET spectroscopy: theory and experiment.Physical chemistry chemical physics : PCCP · 2014Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
Abstract
In theory and in the analysis of experiments, protein folding is often described as diffusion along a single coordinate. We explore here the application of a one-dimensional diffusion model to interpret simulations of protein folding, where the parameters of a model that "best" describes the simulation trajectories are determined using a Bayesian analysis. We discuss the requirements for such a model to be a good approximation to the global dynamics, and several methods for testing its accuracy. For example, one test considers the effect of an added bias potential on the fitted free energies and diffusion coefficients. Such a bias may also be used to extend our approach to determining parameters for the model to systems that would not normally explore the full coordinate range on accessible time scales. Alternatively, the propagators predicted from the model at different "lag" times may be compared with observations from simulation. We then present some applications of the model to protein folding, including Kramers-like turnover in folding rates of coarse-grained models, the effect of non-native interactions on folding, and the effect of the chosen coordinate on the observed position-dependence of the diffusion coefficients. Lastly, we consider how our results are useful for the interpretation of experiments, and how this type of Bayesian analysis may eventually be applied directly to analyse experimental data.
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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.