ArticleProceedings of the National Academy of Sciences of the United States of America2007
Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
44 citing papers in PubMed.
- Nonparametric Determination of the Committor in Multimolecular Systems.Journal of chemical theory and computation · 2025Article
- Spectral Map for Slow Collective Variables, Markovian Dynamics, and Transition State Ensembles.Journal of chemical theory and computation · 2024Article
- Coarse-Grained Simulations of Protein Folding: Bridging Theory and Experiments.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Non-Markovian modeling of protein folding.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase.eLife · 2020Article
- The Role of Electrostatics and Folding Kinetics on the Thermostability of Homologous Cold Shock Proteins.Journal of chemical information and modeling · 2020Article
- Position-, disorder-, and salt-dependent diffusion in binding-coupled-folding of intrinsically disordered proteins.Physical chemistry chemical physics : PCCP · 2019Article
- Probing Position-Dependent Diffusion in Folding Reactions Using Single-Molecule Force Spectroscopy.Biophysical journal · 2018Article
- 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 Nonnative Interactions in the Protein-Folding Free-Energy Landscape.Biophysical journal · 2016Article
- Infrared and Fluorescence Assessment of Protein Dynamics: From Folding to Function.The journal of physical chemistry. B · 2016Article
- Protein misfolding occurs by slow diffusion across multiple barriers in a rough energy landscape.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Native contact density and nonnative hydrophobic effects in the folding of bacterial immunity proteins.PLoS computational biology · 2015Article
- Resolution of Two Sub-Populations of Conformers and Their Individual Dynamics by Time Resolved Ensemble Level FRET Measurements.PloS one · 2015Article
- Folding pathway of a multidomain protein depends on its topology of domain connectivity.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Fast protein folding kinetics.Quarterly reviews of biophysics · 2014Review
- Observation of complete pressure-jump protein refolding in molecular dynamics simulation and experiment.Journal of the American Chemical Society · 2014Article
- Assessment of local friction in protein folding dynamics using a helix cross-linker.The journal of physical chemistry. B · 2013Article
- Confinement-dependent friction in peptide bundles.Biophysical journal · 2013Article
- Connecting the kinetics and energy landscape of tRNA translocation on the ribosome.PLoS computational biology · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We show that diffusion can play an important role in protein-folding kinetics. We explicitly calculate the diffusion coefficient of protein folding in a lattice model. We found that diffusion typically is configuration- or reaction coordinate-dependent. The diffusion coefficient is found to be decreasing with respect to the progression of folding toward the native state, which is caused by the collapse to a compact state constraining the configurational space for exploration. The configuration- or position-dependent diffusion coefficient has a significant contribution to the kinetics in addition to the thermodynamic free-energy barrier. It effectively changes (increases in this case) the kinetic barrier height as well as the position of the corresponding transition state and therefore modifies the folding kinetic rates as well as the kinetic routes. The resulting folding time, by considering both kinetic diffusion and the thermodynamic folding free-energy profile, thus is slower than the estimation from the thermodynamic free-energy barrier with constant diffusion but is consistent with the results from kinetic simulations. The configuration- or coordinate-dependent diffusion is especially important with respect to fast folding, when there is a small or no free-energy barrier and kinetics is controlled by diffusion. Including the configurational dependence will challenge the transition state theory of protein folding. The classical transition state theory will have to be modified to be consistent. The more detailed folding mechanistic studies involving phi value analysis based on the classical transition state theory also will have to be modified quantitatively.
Indexed as
Identifiers
What OpenQuestion holds
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.