ArticleThe journal of physical chemistry. B2013
Characterization of folding mechanisms of Trp-cage and WW-domain by network analysis of simulations with a hybrid-resolution model.
Article in The journal of physical chemistry. B, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 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
18 citing papers in PubMed, 39 citations in OpenAlex.
- Simulations of Functional Motions of Super Large Biomolecules with a Mixed-Resolution Model.Journal of chemical theory and computation · 2024Article
- Effect of Main and Side Chains on the Folding Mechanism of the Trp-Cage Miniprotein.ACS omega · 2023Article
- An Efficient Path Classification Algorithm Based on Variational Autoencoder to Identify Metastable Path Channels for Complex Conformational Changes.Journal of chemical theory and computation · 2023Article
- The "Beacon" Structural Model of Protein Folding: Application for Trp-Cage in Water.Molecules (Basel, Switzerland) · 2023Article
- Analysis of Protein Folding Simulation with Moving Root Mean Square Deviation.Journal of chemical information and modeling · 2023Article
- Resolution exchange with tunneling for enhanced sampling of protein landscapes.Physical review. E · 2022Article
- Anatomy and formation mechanisms of early amyloid-β oligomers with lateral branching: graph network analysis on large-scale simulations.Chemical science · 2022Article
- Exploration of the Misfolding Mechanism of Transthyretin Monomer: Insights from Hybrid-Resolution Simulations and Markov State Model Analysis.Biomolecules · 2019Article
- α-Helical Motif as Inhibitors of Toxic Amyloid-β Oligomer Generation via Highly Specific Recognition of Amyloid Surface.iScience · 2019Article
- Temperature evolution of Trp-cage folding pathways: An analysis by dividing the probability flux field into stream tubes.Journal of biological physics · 2017Article
- Evaluation of the hybrid resolution PACE model for the study of folding, insertion, and pore formation of membrane associated peptides.Journal of computational chemistry · 2017Article
- Turbulence in protein folding: Vorticity, scaling and diffusion of probability flows.PloS one · 2017Article
- A time course of orchestrated endophilin action in sensing, bending, and stabilizing curved membranes.Molecular biology of the cell · 2016Article
- A hydrodynamic view of the first-passage folding of Trp-cage miniprotein.European biophysics journal : EBJ · 2016Article
- A β-solenoid model of the Pmel17 repeat domain: insights to the formation of functional amyloid fibrils.Journal of computer-aided molecular design · 2016Article
- Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation.The Journal of chemical physics · 2015Article
- Fibril elongation by Aβ(17-42): kinetic network analysis of hybrid-resolution molecular dynamics simulations.Journal of the American Chemical Society · 2014Article
- Role of tryptophan side chain dynamics on the Trp-cage mini-protein folding studied by molecular dynamics simulations.PloS one · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
In this study, we apply a hybrid-resolution model, namely, PACE, to characterize the free energy surfaces (FESs) of Trp-cage and a WW-domain variant along with the respective folding mechanisms. Unbiased, independent simulations with PACE are found to achieve together multiple folding and unfolding events for both proteins, allowing us to perform network analysis of the FESs to identify folding pathways. PACE reproduces for both proteins expected complexity hidden in the folding FESs, in particular metastable non-native intermediates. Pathway analysis shows that some of these intermediates are, actually, on-pathway folding intermediates and that intermediates kinetically closest to the native states can be either critical on-pathway or off-pathway intermediates, depending on the protein. Apart from general insights into folding, specific folding mechanisms of the proteins are resolved. We find that Trp-cage folds via a dominant pathway in which hydrophobic collapse occurs before the N-terminal helix forms; full incorporation of Trp6 into the hydrophobic core takes place as the last step of folding, which, however, may not be the rate-limiting step. For the WW-domain variant studied, we observe two main folding pathways with opposite orders of formation of the two hairpins involved in the structure; for either pathway, formation of hairpin 1 is more likely to be the rate-limiting step. Altogether, our results suggest that PACE combined with network analysis is a computationally efficient and valuable tool for the study of protein folding.
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.