ArticleThe Journal of chemical physics2019
The combined force field-sampling problem in simulations of disordered amyloid-β peptides.
Article in The Journal of chemical physics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Epigallocatechin Gallate as a State-Dependent Modulator of Amyloid-Biomolecules · 2026Review
- How Well Do Molecular Dynamics Force Fields Model Peptides: A Systematic Benchmark across Diverse Folding Behaviors.The journal of physical chemistry. B · 2026Article
- Sizes, conformational fluctuations, and SAXS profiles for intrinsically disordered proteins.Protein science : a publication of the Protein Society · 2025Article
- Pyroglutamylation modulates electronic properties and the conformational ensemble of the amyloid β-peptide.Proteins · 2024Article
- Critical Assessment of Self-Consistency Checks in the All-Atom Molecular Dynamics Simulation of Intrinsically Disordered Proteins.Journal of chemical theory and computation · 2023Article
- Interpreting Transient Interactions of Intrinsically Disordered Proteins.The journal of physical chemistry. B · 2023Article
- Review
- Incorporation of DThe journal of physical chemistry. B · 2022Article
- Fast Polarizable Water Model for Atomistic Simulations.Journal of chemical theory and computation · 2022Article
- Effects of Familial Alzheimer's Disease Mutations on the Folding Free Energy and Dipole-Dipole Interactions of the Amyloid β-Peptide.The journal of physical chemistry. B · 2022Article
- Protein Dynamics to Define and Refine Disordered Protein Ensembles.The journal of physical chemistry. B · 2022Article
- Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins.Methods (San Diego, Calif.) · 2021Article
- Thermodynamics and kinetics of the amyloid-β peptide revealed by Markov state models based on MD data in agreement with experiment.Chemical science · 2021Article
- Configurational Entropy of Folded Proteins and Its Importance for Intrinsically Disordered Proteins.International journal of molecular sciences · 2021Article
- Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis.Chemical reviews · 2021Review
- Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations.Communications biology · 2021Article
- High resolution ensemble description of metamorphic and intrinsically disordered proteins using an efficient hybrid parallel tempering scheme.Nature communications · 2021Article
- Emergence of Barrel Motif in Amyloid-β Trimer: A Computational Study.The journal of physical chemistry. B · 2020Article
- Differences in the free energies between the excited states of AProceedings of the National Academy of Sciences of the United States of America · 2020Article
- Fluorescence-Labeled Amyloid Beta Monomer: A Molecular Dynamical Study.Molecules (Basel, Switzerland) · 2020Article
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3 authors.
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Abstract
Molecular dynamics simulations of intrinsically disordered proteins (IDPs) can provide high resolution structural ensembles if the force field is accurate enough and if the simulation sufficiently samples the conformational space of the IDP with the correct weighting of sub-populations. Here, we investigate the combined force field-sampling problem by testing a standard force field as well as newer fixed charge force fields, the latter specifically motivated for better description of unfolded states and IDPs, and comparing them with a standard temperature replica exchange (TREx) protocol and a non-equilibrium Temperature Cool Walking (TCW) sampling algorithm. The force field and sampling combinations are used to characterize the structural ensembles of the amyloid-beta peptides Aβ42 and Aβ43, which both should be random coils as shown recently by experimental nuclear magnetic resonance (NMR) and 2D Förster resonance energy transfer (FRET) experiments. The results illustrate the key importance of the sampling algorithm: while the standard force field using TREx is in poor agreement with the NMR J-coupling and nuclear Overhauser effect and 2D FRET data, when using the TCW method, the standard and optimized protein-water force field combinations are in very good agreement with the same experimental data since the TCW sampling method produces qualitatively different ensembles than TREx. We also discuss the relative merit of the 2D FRET data when validating structural ensembles using the different force fields and sampling protocols investigated in this work for small IDPs such as the Aβ42 and Aβ43 peptides.
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