ArticleThe journal of physical chemistry letters2012
Structural Characterization of λ-Repressor Folding from All-Atom Molecular Dynamics Simulations.
Article in The journal of physical chemistry letters, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 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
24 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
- Peptidomimetics for CVD screened via TRADD-TRAF2 complex interface assessments.In silico pharmacology · 2023Article
- The Role of Protein Arginine Methyltransferases in DNA Damage Response.International journal of molecular sciences · 2022Review
- Natural Food Colorants and Preservatives: A Review, a Demand, and a Challenge.Journal of agricultural and food chemistry · 2022Review
- Granger Causality Analysis of Chignolin Folding.Journal of chemical theory and computation · 2022Article
- Dramatic Shape Changes Occur as CytochromeThe journal of physical chemistry. B · 2020Article
- A Review on Applications of Computational Methods in Drug Screening and Design.Molecules (Basel, Switzerland) · 2020Review
- Choice of Adaptive Sampling Strategy Impacts State Discovery, Transition Probabilities, and the Apparent Mechanism of Conformational Changes.Journal of chemical theory and computation · 2018Article
- Co-translational folding of α-helical proteins: structural studies of intermediate-length variants of the λ repressor.FEBS open bio · 2018Article
- The Surface of Protein λBiochemistry · 2017Article
- Protein Folding and Structure Prediction from the Ground Up II: AAWSEM for α/β Proteins.The journal of physical chemistry. B · 2017Article
- Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Mapping fast protein folding with multiple-site fluorescent probes.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Enhanced sampling techniques in molecular dynamics simulations of biological systems.Biochimica et biophysica acta · 2015Review
- Benchmarking all-atom simulations using hydrogen exchange.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Parallel continuous simulated tempering and its applications in large-scale molecular simulations.The Journal of chemical physics · 2014Article
- The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems.Chemical Society reviews · 2014Review
- Observation of complete pressure-jump protein refolding in molecular dynamics simulation and experiment.Journal of the American Chemical Society · 2014Article
- Misplaced helix slows down ultrafast pressure-jump protein folding.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Native states of fast-folding proteins are kinetic traps.Journal of the American Chemical Society · 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
5 authors.
Funding
Abstract
The five-helix bundle λ-repressor fragment is a fast-folding protein. A length of 80 amino acid residues puts it on the large end among all known microsecond folders and its size poses a computational challenge for molecular dynamics (MD) studies. We simulated the folding of a novel λ-repressor fast-folding mutant (λ-HG) in explicit solvent using an all-atom description. By means of a recently developed tempering method, we observed reversible folding and unfolding of λ-repressor in a 10-microsecond trajectory. The folding kinetics was also investigated through a set of MD simulations run at different temperatures that together covered more than 125 microseconds. The protein was seen to fold into a native-like topology at intermediate temperature and a slow-folding pathway was identified. The simulations suggest new experimental observables for better monitoring the folding process, and a novel mutation expected to accelerate λ-repressor folding.
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.