ArticleBiochemistry2014
Folding dynamics and pathways of the trp-cage miniproteins.
Article in Biochemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed.
- DreamFold: A World Model to efficiently generate protein folding pathways in the latent space.Protein science : a publication of the Protein Society · 2026Article
- Probabilistic Forecasting for Coarse-Grained Molecular Dynamics.Journal of chemical theory and computation · 2026Article
- Comparative unfolding of the Trp-cage miniprotein in anionic and cationic surfactants.PloS one · 2026Article
- The Arch from the Stones: Understanding Protein Folding Energy Landscapes via Bioinspired Collective Variables.The journal of physical chemistry letters · 2025Article
- Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0].Living journal of computational molecular science · 2025Article
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- Effect of Main and Side Chains on the Folding Mechanism of the Trp-Cage Miniprotein.ACS omega · 2023Article
- The "Beacon" Structural Model of Protein Folding: Application for Trp-Cage in Water.Molecules (Basel, Switzerland) · 2023Article
- Exploring the Transferability of Replica Exchange Structure Reservoirs to Accelerate Generation of Ensembles for Alternate Hamiltonians or Protein Mutations.Journal of chemical theory and computation · 2023Article
- Analysis of Protein Folding Simulation with Moving Root Mean Square Deviation.Journal of chemical information and modeling · 2023Article
- Computational Modeling of the Thermodynamics of the Mesophilic and Thermophilic Mutants of Trp-Cage Miniprotein.ACS omega · 2022Article
- Kirkwood-Buff-Derived Force Field for Peptides and Proteins: Applications of KBFF20.Journal of chemical theory and computation · 2021Article
- The Uniqueness of Tryptophan in Biology: Properties, Metabolism, Interactions and Localization in Proteins.International journal of molecular sciences · 2020Review
- Unperturbed Detection of the Dynamic Structure in the Hydrophobic Core of Trp-Cage via Two-Dimensional Infrared Spectroscopy.The journal of physical chemistry letters · 2020Article
- Approximating dynamic proximity with a hybrid geometry energy-based kernel for diffusion maps.The Journal of chemical physics · 2019Article
- Temperature evolution of Trp-cage folding pathways: An analysis by dividing the probability flux field into stream tubes.Journal of biological physics · 2017Article
- Article
- A hydrodynamic view of the first-passage folding of Trp-cage miniprotein.European biophysics journal : EBJ · 2016Article
- Tuning the Attempt Frequency of Protein Folding Dynamics via Transition-State Rigidification: Application to Trp-Cage.The journal of physical chemistry letters · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Using alternate measures of fold stability for a wide variety of Trp-cage mutants has raised the possibility that prior dynamics T-jump measures may not be reporting on complete cage formation for some species. NMR relaxation studies using probes that only achieve large chemical shift difference from unfolded values on complete cage formation indicate slower folding in some but not all cases. Fourteen species have been examined, with cage formation time constants (1/kF) ranging from 0.9-7.5 μs at 300 K. The present study does not change the status of the Trp-cage as a fast folding, essentially two-state system, although it does alter the stage at which this description applies. A diversity of prestructuring events, depending on the specific analogue examined, may appear in the folding scenario, but in all cases, formation of the N-terminal helix is complete either at or before the cage-formation transition state. In contrast, the fold-stabilizing H-bonding interactions of the buried Ser14 side chain and the Arg/Asp salt bridge are post-transition state features on the folding pathway. The study has also found instances in which a [P12W] mutation is fold destabilizing but still serves to accelerate the folding process.
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.