ArticleJournal of the American Chemical Society2011
Atomistic folding simulations of the five-helix bundle protein λ(6−85).
Article in Journal of the American Chemical Society, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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Who cites it
61 citing papers in PubMed, 140 citations in OpenAlex.
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- A Kinetic Transition Network Model Reveals the Diversity of Protein Dimer Formation Mechanisms.Biomolecules · 2023Article
- Folding@home: Achievements from over 20 years of citizen science herald the exascale era.Biophysical journal · 2023Review
- Chemical interactions modulate λProtein science : a publication of the Protein Society · 2023Article
- Folding@home: achievements from over twenty years of citizen science herald the exascale era.ArXiv · 2023Article
- Computational investigations on target-site searching and recognition mechanisms by thymine DNA glycosylase during DNA repair process.Acta biochimica et biophysica Sinica · 2022Review
- Unsupervised Learning Methods for Molecular Simulation Data.Chemical reviews · 2021Article
- Temperature-dependent kinetic pathways of heterogeneous ice nucleation competing between classical and non-classical nucleation.Nature communications · 2021Article
- Atomic resolution of short-range sliding dynamics of thymine DNA glycosylase along DNA minor-groove for lesion recognition.Nucleic acids research · 2021Article
- Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix.Acta crystallographica. Section D, Structural biology · 2020Article
- Dynamic graphical models of molecular kinetics.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Applications of Molecular Dynamics Simulation in Structure Prediction of Peptides and Proteins.Computational and structural biotechnology journal · 2019Review
- Choice of Adaptive Sampling Strategy Impacts State Discovery, Transition Probabilities, and the Apparent Mechanism of Conformational Changes.Journal of chemical theory and computation · 2018Article
- Dynamics of the excised base release in thymine DNA glycosylase during DNA repair process.Nucleic acids research · 2018Article
- Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations.Nature communications · 2017Article
- Dielectric screening effect of electronic polarization and intramolecular hydrogen bonding.Protein science : a publication of the Protein Society · 2017Article
- Optimized parameter selection reveals trends in Markov state models for protein folding.The Journal of chemical physics · 2016Article
- The allosteric switching mechanism in bacteriophage MS2.The Journal of chemical physics · 2016Article
- Multiensemble Markov models of molecular thermodynamics and kinetics.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Role of Conformational Motions in Enzyme Function: Selected Methodologies and Case Studies.Catalysts (Basel, Switzerland) · 2016Article
1 more citing papers are in PubMed but not listed here.
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3 authors at 1 institution in 1 country.
Funding
Abstract
Protein folding is a classic grand challenge that is relevant to numerous human diseases, such as protein misfolding diseases like Alzheimer’s disease. Solving the folding problem will ultimately require a combination of theory, simulation, and experiment, with theory and simulation providing an atomically detailed picture of both the thermodynamics and kinetics of folding and experimental tests grounding these models in reality. However, theory and simulation generally fall orders of magnitude short of biologically relevant time scales. Here we report significant progress toward closing this gap: an atomistic model of the folding of an 80-residue fragment of the λ repressor protein with explicit solvent that captures dynamics on a 10 milliseconds time scale. In addition, we provide a number of predictions that warrant further experimental investigation. For example, our model’s native state is a kinetic hub, and biexponential kinetics arises from the presence of many free-energy basins separated by barriers of different heights rather than a single low barrier along one reaction coordinate (the previously proposed incipient downhill folding scenario).
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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.