ArticleProceedings of the National Academy of Sciences of the United States of America2007
Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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79 citing papers in PubMed.
- Topological Analysis Reveals Multiple Pathways in Molecular Dynamics.Journal of chemical theory and computation · 2025Article
- Unfolding of the Villin Headpiece Domain: Revealing Structural Heterogeneity with Time-Resolved X-Ray Solution Scattering and Markov State Modeling.Chemphyschem : a European journal of chemical physics and physical chemistry · 2025Article
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- Molecular Interactions Governing the Rat Aryl Hydrocarbon Receptor Activities of Polycyclic Aromatic Compounds and Predictive Model Development.Molecules (Basel, Switzerland) · 2024Article
- Molecular dynamics simulations suggest the potential toxicity of fluorinated graphene to HP35 protein via unfolding the α-helix structure.Scientific reports · 2024Article
- How do Antimicrobial Peptides Interact with the Outer Membrane of Gram-Negative Bacteria? Role of Lipopolysaccharides in Peptide Binding, Anchoring, and Penetration.ACS infectious diseases · 2024Article
- Energy, water, and protein folding: A molecular dynamics-based quantitative inventory of molecular interactions and forces that make proteins stable.Protein science : a publication of the Protein Society · 2024Article
- Villin headpiece unfolding upon binding to boridene mediated by the "anchoring-perturbation" mechanism.iScience · 2024Article
- Calculation of Protein Folding Thermodynamics Using Molecular Dynamics Simulations.Journal of chemical information and modeling · 2023Article
- Moderate binding of villin headpiece protein to CScientific reports · 2023Article
- A wrinkled nanosurface causes accelerated protein unfolding revealing its critical role in nanotoxicity.RSC advances · 2022Article
- Unusual RNA binding of FUS RRM studied by molecular dynamics simulation and enhanced sampling method.Biophysical journal · 2021Article
- Sampling of the conformational landscape of small proteins with Monte Carlo methods.Scientific reports · 2020Article
- Including residual contact information into replica-exchange MD simulations significantly enriches native-like conformations.PloS one · 2020Article
- Anti-Correlation between the Dynamics of the Active Site Loop and C-Terminal Tail in Relation to the Homodimer Asymmetry of the Mouse Erythroid 5-Aminolevulinate Synthase.International journal of molecular sciences · 2018Article
- Examination of the quality of various force fields and solvation models for the equilibrium simulations of GA88 and GB88.Journal of molecular modeling · 2016Article
- Study on the Application of the Combination of TMD Simulation and Umbrella Sampling in PMF Calculation for Molecular Conformational Transitions.International journal of molecular sciences · 2016Article
- The Folding of de Novo Designed Protein DS119 via Molecular Dynamics Simulations.International journal of molecular sciences · 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
- Characterizing the Conformational Landscape of Flavivirus Fusion Peptides via Simulation and Experiment.Scientific reports · 2016Article
19 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
High-accuracy ab initio folding has remained an elusive objective despite decades of effort. To explore the folding landscape of villin headpiece subdomain HP35, we conducted two sets of replica exchange molecular dynamics for 200 ns each and three sets of conventional microsecond-long molecular dynamics simulations, using AMBER FF03 force field and a generalized-Born solvation model. The protein folded consistently to the native state; the lowest C(alpha)-rmsd from the x-ray structure was 0.46 A, and the C(alpha)- rmsd of the center of the most populated cluster was 1.78 A at 300 K. ab initio simulations have previously not reached this level. The folding landscape of HP35 can be partitioned into the native, denatured, and two intermediate-state regions. The native state is separated from the major folding intermediate state by a small barrier, whereas a large barrier exists between the major folding intermediate and the denatured states. The melting temperature T(m) = 339 K extracted from the heat-capacity profile was in close agreement with the experimentally derived T(m) = 342 K. A comprehensive picture of the kinetics and thermodynamics of HP35 folding emerges when the results from replica exchange and conventional molecular dynamics simulations are combined.
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