ArticlePLoS computational biology2010
Is protein folding sub-diffusive?
Article in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Glassy adhesion dynamics govern transitions between sub-diffusive and super-diffusive cancer cell migration on viscoelastic substrates.Nature communications · 2026Article
- Nonparametric Determination of the Committor in Multimolecular Systems.Journal of chemical theory and computation · 2025Article
- Convergence and equilibrium in molecular dynamics simulations.Communications chemistry · 2024Article
- Broad distributions of transition-path times are fingerprints of multidimensionality of the underlying free energy landscapes.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- 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
- Impact of hydrodynamic interactions on protein folding rates depends on temperature.Physical review. E · 2018Article
- Optimal reaction coordinate as a biomarker for the dynamics of recovery from kidney transplant.PLoS computational biology · 2014Article
- High-Resolution Free-Energy Landscape Analysis of α-Helical Protein Folding: HP35 and Its Double Mutant.Journal of chemical theory and computation · 2013Article
- Modulation of a protein free-energy landscape by circular permutation.The journal of physical chemistry. B · 2013Article
- Diffusion models of protein folding.Physical chemistry chemical physics : PCCP · 2011Article
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1 author.
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Abstract
Protein folding dynamics is often described as diffusion on a free energy surface considered as a function of one or few reaction coordinates. However, a growing number of experiments and models show that, when projected onto a reaction coordinate, protein dynamics is sub-diffusive. This raises the question as to whether the conventionally used diffusive description of the dynamics is adequate. Here, we numerically construct the optimum reaction coordinate for a long equilibrium folding trajectory of a Go model of a -repressor protein. The trajectory projected onto this coordinate exhibits diffusive dynamics, while the dynamics of the same trajectory projected onto a sub-optimal reaction coordinate is sub-diffusive. We show that the higher the (cut-based) free energy profile for the putative reaction coordinate, the more diffusive the dynamics become when projected on this coordinate. The results suggest that whether the projected dynamics is diffusive or sub-diffusive depends on the chosen reaction coordinate. Protein folding can be described as diffusion on the free energy surface as function of the optimum reaction coordinate. And conversely, the conventional reaction coordinates, even though they might be based on physical intuition, are often sub-optimal and, hence, show sub-diffusive dynamics.
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