ArticleJournal of the American Chemical Society2015
Dependence of internal friction on folding mechanism.
Article in Journal of the American Chemical Society, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 51 citations in OpenAlex.
- Hydrogen bonding heterogeneity correlates with protein folding transition state passage time as revealed by data sonification.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The role of memory-dependent friction and solvent viscosity in isomerization kinetics in viscogenic media.Nature communications · 2024Article
- Effects of Proline on Internal Friction in Simulated Folding Dynamics of Several Alanine-Based α-Helical Peptides.The journal of physical chemistry. B · 2024Article
- Activation and friction in enzymatic loop opening and closing dynamics.Nature communications · 2024Article
- Analytical Approaches for Deriving Friction Coefficients for Selected α-Helical Peptides Based Entirely on Molecular Dynamics Simulations.The journal of physical chemistry. B · 2022Article
- Modern Kinetics and Mechanism of Protein Folding: A Retrospective.The journal of physical chemistry. B · 2021Article
- Friction-Limited Folding of Disulfide-Reduced Monomeric SOD1.Biophysical journal · 2020Article
- Origin of Internal Friction in Disordered Proteins Depends on Solvent Quality.The journal of physical chemistry. B · 2018Article
- Butane dihedral angle dynamics in water is dominated by internal friction.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Transition Path Times Measured by Single-Molecule Spectroscopy.Journal of molecular biology · 2018Review
- Protein folding transition path times from single molecule FRET.Current opinion in structural biology · 2018Review
- Integrated view of internal friction in unfolded proteins from single-molecule FRET, contact quenching, theory, and simulations.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Modulation of Folding Internal Friction by Local and Global Barrier Heights.The journal of physical chemistry letters · 2016Article
- Using Local States To Drive the Sampling of Global Conformations in Proteins.Journal of chemical theory and computation · 2016Article
- Structural origin of slow diffusion in protein folding.Science (New York, N.Y.) · 2015Article
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Authors and funding
4 authors at 2 institutions in 3 countries.
Funding
Abstract
An outstanding challenge in protein folding is understanding the origin of "internal friction" in folding dynamics, experimentally identified from the dependence of folding rates on solvent viscosity. A possible origin suggested by simulation is the crossing of local torsion barriers. However, it was unclear why internal friction varied from protein to protein or for different folding barriers of the same protein. Using all-atom simulations with variable solvent viscosity, in conjunction with transition-path sampling to obtain reaction rates and analysis via Markov state models, we are able to determine the internal friction in the folding of several peptides and miniproteins. In agreement with experiment, we find that the folding events with greatest internal friction are those that mainly involve helix formation, while hairpin formation exhibits little or no evidence of friction. Via a careful analysis of folding transition paths, we show that internal friction arises when torsion angle changes are an important part of the folding mechanism near the folding free energy barrier. These results suggest an explanation for the variation of internal friction effects from protein to protein and across the energy landscape of the same protein.
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