ArticleProceedings of the National Academy of Sciences of the United States of America2010
Coordinate-dependent diffusion in protein folding.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers.
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100 citing papers in PubMed.
- A Simulation-Free Topological Basis for Building Compact Koopman Models of Protein Folding.Journal of chemical information and modeling · 2026Article
- Cooperative Native Contact Formation Facilitates Free Energy Barrier Crossing in Protein Folding.Physical review letters · 2026Article
- Single Molecule Force Spectroscopy to Probe Intermediates and Energetics of Membrane Protein Folding.Chemical reviews · 2026Review
- Hierarchical friction memory leads to subdiffusive configurational dynamics of fast-folding proteins.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Contact Cluster Modeling of Allosteric Communication in PDZ Domains.The journal of physical chemistry. B · 2026Review
- Nonparametric Determination of the Committor in Multimolecular Systems.Journal of chemical theory and computation · 2025Article
- Theory on the Design Principles of Protein Molecular Oscillatory Machines.The journal of physical chemistry. B · 2025Article
- Article
- Spectral Map for Slow Collective Variables, Markovian Dynamics, and Transition State Ensembles.Journal of chemical theory and computation · 2024Article
- The role of memory-dependent friction and solvent viscosity in isomerization kinetics in viscogenic media.Nature communications · 2024Article
- 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
- Anisotropic Friction in a Ligand-Protein Complex.Nano letters · 2023Article
- Graph identification of proteins in tomograms (GRIP-Tomo).Protein science : a publication of the Protein Society · 2023Article
- Coarse-Grained Simulations of Protein Folding: Bridging Theory and Experiments.Methods in molecular biology (Clifton, N.J.) · 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
- 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
- Estimating transition path times and shapes from single-molecule photon trajectories: A simulation analysis.The Journal of chemical physics · 2021Article
- Effects of Topology and Sequence in Protein Folding Linked via Conformational Fluctuations.Biophysical journal · 2020Article
40 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
Diffusion on a low-dimensional free-energy surface is a remarkably successful model for the folding dynamics of small single-domain proteins. Complicating the interpretation of both simulations and experiments is the expectation that the effective diffusion coefficient D will in general depend on the position along the folding coordinate, and this dependence may vary for different coordinates. Here we explore the position dependence of D, its connection to protein internal friction, and the consequences for the interpretation of single-molecule experiments. We find a large decrease in D from unfolded to folded, for reaction coordinates that directly measure fluctuations in Cartesian configuration space, including those probed in single-molecule experiments. In contrast, D is almost independent of Q, the fraction of native amino acid contacts: Near the folded state, small fluctuations in position cause large fluctuations in Q, and vice versa for the unfolded state. In general, position-dependent free energies and diffusion coefficients for any two good reaction coordinates that separate reactant, product, and transition states, are related by a simple transformation, as we demonstrate. With this transformation, we obtain reaction coordinates with position-invariant D. The corresponding free-energy surfaces allow us to justify the assumptions used in estimating the speed limit for protein folding from experimental measurements of the reconfiguration time in the unfolded state, and also reveal intermediates hidden in the original free-energy projection. Lastly, we comment on the design of future single-molecule experiments that probe the position dependence of D directly.
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