ArticleBiophysical journal2009
Common structural transitions in explicit-solvent simulations of villin headpiece folding.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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Who cites it
69 citing papers in PubMed, 143 citations in OpenAlex.
- Building multiscale Markov state models by systematic mapping of temporal communities.Bioinformatics (Oxford, England) · 2026Article
- Experimental Evidence for Millisecond-Timescale Structural Evolution Following the Microsecond-Timescale Folding of a Small Protein.Physical review letters · 2024Article
- Roles of Accelerated Molecular Dynamics Simulations in Predictions of Binding Kinetic Parameters.Mini reviews in medicinal chemistry · 2024Review
- A Study of a Protein-Folding Machine: Transient Rotation of the Polypeptide Backbone Facilitates Rapid Folding of Protein Domains in All-Atom Molecular Dynamics Simulations.International journal of molecular sciences · 2023Article
- Granger Causality Analysis of Chignolin Folding.Journal of chemical theory and computation · 2022Article
- Molecular dynamics simulations reveal the selectivity mechanism of structurally similar agonists to TLR7 and TLR8.PloS one · 2022Article
- Quantitative Analysis of Protein Unfolded State Energetics: Experimental and Computational Studies Demonstrate That Non-Native Side-Chain Interactions Stabilize Local Native Backbone Structure.The journal of physical chemistry. B · 2021Article
- Data-Driven Molecular Dynamics: A Multifaceted Challenge.Pharmaceuticals (Basel, Switzerland) · 2020Review
- Including residual contact information into replica-exchange MD simulations significantly enriches native-like conformations.PloS one · 2020Article
- Exploring Dynamics and Structure of Biomolecules, Cryoprotectants, and Water Using Molecular Dynamics Simulations: Implications for Biostabilization and Biopreservation.Annual review of biomedical engineering · 2019Review
- An Overview of Molecular Modeling for Drug Discovery with Specific Illustrative Examples of Applications.Molecules (Basel, Switzerland) · 2019Review
- Applications of Molecular Dynamics Simulation in Structure Prediction of Peptides and Proteins.Computational and structural biotechnology journal · 2019Review
- Peptide and Protein Structure Prediction with a Simplified Continuum Solvent Model.The journal of physical chemistry. B · 2018Article
- Modeling protein folding in vivo.Biology direct · 2018Article
- Studying the role of cooperative hydration in stabilizing folded protein states.Journal of structural biology · 2016Article
- High Performance Molecular Visualization: In-Situ and Parallel Rendering with EGL.IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum : [proceedings]. IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum · 2016Article
- Microscopic interpretation of folding ϕ-values using the transition path ensemble.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Characterizing a partially ordered miniprotein through folding molecular dynamics simulations: Comparison with the experimental data.Protein science : a publication of the Protein Society · 2016Article
- Computational evidence that fast translation speed can increase the probability of cotranslational protein folding.Scientific reports · 2015Article
- Accelerated molecular dynamics simulations of protein folding.Journal of computational chemistry · 2015Article
9 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 1 institution in 1 country.
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Abstract
Molecular dynamics simulations of protein folding can provide very high-resolution data on the folding process; however, due to computational challenges most studies of protein folding have been limited to small peptides, or made use of approximations such as Gō potentials or implicit solvent models. We have performed a set of molecular dynamics simulations totaling >50 micros on the villin headpiece subdomain, one of the most stable and fastest-folding naturally occurring proteins, in explicit solvent. We find that the wild-type villin headpiece reliably folds to a native conformation on timescales similar to experimentally observed folding, but that a fast folding double-norleucine mutant shows significantly more heterogeneous behavior. Along with other recent simulation studies, we note the occurrence of nonnative structures intermediates, which may yield a nativelike signal in the fluorescence measurements typically used to study villin folding. Based on the wild-type simulations, we propose alternative approaches to measure the formation of the native state.
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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.