ArticleChemical science2021
Thermodynamics and kinetics of the amyloid-β peptide revealed by Markov state models based on MD data in agreement with experiment.
Article in Chemical science, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Membrane Complexity and Phase Behavior Dictate the Stability of Membrane-Inserted AβChemphyschem : a European journal of chemical physics and physical chemistry · 2026Article
- The Monomeric Conformational Ensembles of Aβ40 and Aβ42 Encode Their Differential Amyloid Aggregation Propensity.The journal of physical chemistry. B · 2026Article
- Transient Aggregation-Prone States in Disordered Proteins as Therapeutic Targets: The Amyloid-β Case.Journal of chemical information and modeling · 2026Article
- Epigallocatechin Gallate as a State-Dependent Modulator of Amyloid-Biomolecules · 2026Review
- Time-resolved solid-state nuclear magnetic resonance studies of amyloid-β oligomer formation.Methods in enzymology · 2026Review
- Energy Landscape and Kinetic Analysis of Molecular Dynamics Simulations for Intrinsically Disordered Proteins.The journal of physical chemistry. B · 2025Article
- Chameleonic Nature of Aβ: Implications for Alzheimer's and Other Amyloid Diseases.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Effects of ion type and concentration on the structure and aggregation of the amyloid peptide AProteins · 2025Article
- Helix-to-sheet transition of the Aβ42 peptide revealed using an enhanced sampling strategy and Markov state model.Computational and structural biotechnology journal · 2024Article
- Survey of the Aβ-peptide structural diversity: molecular dynamics approaches.Biophysical reviews · 2024Review
- Computational Methods to Investigate Intrinsically Disordered Proteins and their Complexes.ArXiv · 2024Article
- Article
- CoVAMPnet: Comparative Markov State Analysis for Studying Effects of Drug Candidates on Disordered Biomolecules.JACS Au · 2024Article
- Using NMR diffusion data to validate MD models of disordered proteins: Test case of N-terminal tail of histone H4.Biophysical journal · 2024Article
- Hyperoside Prevents Aβ42-Induced Neurotoxicity in PC12 Cells and Caenorhabditis elegans.Molecular neurobiology · 2023Article
- A Hairpin Motif in the Amyloid-β Peptide Is Important for Formation of Disease-Related Oligomers.Journal of the American Chemical Society · 2023Article
- Uncertainties in Markov State Models of Small Proteins.Journal of chemical theory and computation · 2023Article
- Transition Networks Unveil Disorder-to-Order Transformations in AInternational journal of molecular sciences · 2023Article
- Critical Assessment of Self-Consistency Checks in the All-Atom Molecular Dynamics Simulation of Intrinsically Disordered Proteins.Journal of chemical theory and computation · 2023Article
- Identification of Catechins' Binding Sites in Monomeric AInternational journal of molecular sciences · 2023Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The amlyoid-β peptide (Aβ) is closely linked to the development of Alzheimer's disease. Molecular dynamics (MD) simulations have become an indispensable tool for studying the behavior of this peptide at the atomistic level. General key aspects of MD simulations are the force field used for modeling the peptide and its environment, which is important for accurate modeling of the system of interest, and the length of the simulations, which determines whether or not equilibrium is reached. In this study we address these points by analyzing 30-μs MD simulations acquired for Aβ40 using seven different force fields. We assess the convergence of these simulations based on the convergence of various structural properties and of NMR and fluorescence spectroscopic observables. Moreover, we calculate Markov state models for the different MD simulations, which provide an unprecedented view of the thermodynamics and kinetics of the amyloid-β peptide. This further allows us to provide answers for pertinent questions, like: which force fields are suitable for modeling Aβ? (a99SB-UCB and a99SB-ILDN/TIP4P-D); what does Aβ peptide really look like? (mostly extended and disordered) and; how long does it take MD simulations of Aβ to attain equilibrium? (at least 20-30 μs). We believe the analyses presented in this study will provide a useful reference guide for important questions relating to the structure and dynamics of Aβ in particular, and by extension other similar disordered proteins.
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Registered trials
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