ArticleProtein science : a publication of the Protein Society2013
How long does it take to equilibrate the unfolded state of a protein?
Article in Protein science : a publication of the Protein Society, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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
14 citing papers in PubMed.
- What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models.Journal of chemical theory and computation · 2021Article
- Piecewise All-Atom SMD Simulations Reveal Key Secondary Structures in Luciferase Unfolding Pathway.Biophysical journal · 2020Article
- Origins of the Mechanochemical Coupling of Peptide Bond Formation to Protein Synthesis.Journal of the American Chemical Society · 2018Article
- RNA folding kinetics using Monte Carlo and Gillespie algorithms.Journal of mathematical biology · 2018Article
- Theoretical and computational validation of the Kuhn barrier friction mechanism in unfolded proteins.Scientific reports · 2017Article
- Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit.The journal of physical chemistry. B · 2016Article
- Influence of Glu/Arg, Asp/Arg, and Glu/Lys Salt Bridges on α-Helical Stability and Folding Kinetics.Biophysical journal · 2016Article
- Recollection.Protein science : a publication of the Protein Society · 2016Article
- Extracting intrinsic dynamic parameters of biomolecular folding from single-molecule force spectroscopy experiments.Protein science : a publication of the Protein Society · 2016Article
- First Passage Times, Lifetimes, and Relaxation Times of Unfolded Proteins.Physical review letters · 2015Article
- Article
- First passage analysis of the folding of a β-sheet miniprotein: is it more realistic than the standard equilibrium approach?The journal of physical chemistry. B · 2014Article
- Solvent-Exposed Salt Bridges Influence the Kinetics of α-Helix Folding and Unfolding.The journal of physical chemistry letters · 2014Article
- Probing the origins of two-state folding.The Journal of chemical physics · 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
Abstract
How long does it take to equilibrate the unfolded state of a protein? The answer to this question has important implications for our understanding of why many small proteins fold with two state kinetics. When the equilibration within the unfolded state U is much faster than the folding, the folding kinetics will be two state even if there are many folding pathways with different barriers. Yet the mean first passage times (MFPTs) between different regions of the unfolded state can be much longer than the folding time. This seems to imply that the equilibration within U is much slower than the folding. In this communication we resolve this paradox. We present a formula for estimating the time to equilibrate the unfolded state of a protein. We also present a formula for the MFPT to any state within U, which is proportional to the average lifetime of that state divided by the state population. This relation is valid when the equilibration within U is very fast as compared with folding as it often is for small proteins. To illustrate the concepts, we apply the formulas to estimate the time to equilibrate the unfolded state of Trp-cage and MFPTs within the unfolded state based on a Markov State Model using an ultra-long 208 microsecond trajectory of the miniprotein to parameterize the model. The time to equilibrate the unfolded state of Trp-cage is ∼100 ns while the typical MFPTs within U are tens of microseconds or longer.
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.