ArticleScientific reports2016
Structural and fluctuational difference between two ends of Aβ amyloid fibril: MD simulations predict only one end has open conformations.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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26 citing papers in PubMed, 72 citations in OpenAlex.
- Epigallocatechin Gallate as a State-Dependent Modulator of Amyloid-Biomolecules · 2026Review
- High-speed atomic force microscopy reveals a surface-catalyzed elongation mechanism of the fungal functional amyloid hydrophobin RolA.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- A lattice Monte Carlo model for amyloid fibril formation.Biophysics and physicobiology · 2026Article
- Computational study of conformational interconversion of an amyloid β double layer system.RSC advances · 2025Article
- Exploring Abeta42 monomer diffusion dynamics on fibril surfaces through molecular simulations.Protein science : a publication of the Protein Society · 2025Article
- Single-Molecule Kinetic Observation of Antibody Interactions with Growing Amyloid β Fibrils.Journal of the American Chemical Society · 2024Article
- Direct Observation of Seeded Conformational Conversion of hIAPPJournal of chemical information and modeling · 2023Article
- The Double-Layered Structure of Amyloid-β Assemblage on GM1-Containing Membranes Catalytically Promotes Fibrillization.ACS chemical neuroscience · 2023Article
- SEVI Inhibits Aβ Amyloid Aggregation by Capping the β-Sheet Elongation Edges.Journal of chemical information and modeling · 2023Article
- Ingenuity in performing replica permutation: How to order the state labels for improving sampling efficiency.Journal of computational chemistry · 2023Article
- Article
- Inhibition of amyloid-β(16-22) aggregation by polyphenols using replica permutation with solute tempering molecular dynamics simulation.Biophysics and physicobiology · 2023Article
- Key Residue for Aggregation of Amyloid-β Peptides.ACS chemical neuroscience · 2022Article
- State-of-the-Art Molecular Dynamics Simulation Studies of RNA-Dependent RNA Polymerase of SARS-CoV-2.International journal of molecular sciences · 2022Review
- Conformational Variability of Amyloid-β and the Morphological Diversity of Its Aggregates.Molecules (Basel, Switzerland) · 2022Review
- Molecular Dynamics Simulation Studies on the Aggregation of Amyloid-β Peptides and Their Disaggregation by Ultrasonic Wave and Infrared Laser Irradiation.Molecules (Basel, Switzerland) · 2022Review
- Molecular dynamics simulations of amyloid-β peptides in heterogeneous environments.Biophysics and physicobiology · 2022Article
- "Bucket brigade" using lysine residues in RNA-dependent RNA polymerase of SARS-CoV-2.Biophysical journal · 2021Article
- Dynamic properties of SARS-CoV and SARS-CoV-2 RNA-dependent RNA polymerases studied by molecular dynamics simulations.Chemical physics letters · 2021Article
- Promotion and Inhibition of Amyloid-β Peptide Aggregation: Molecular Dynamics Studies.International journal of molecular sciences · 2021Review
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Aβ amyloid fibrils, which are related to Alzheimer's disease, have a cross-β structure consisting of two β-sheets: β1 and β2. The Aβ peptides are thought to be serially arranged in the same molecular conformation along the fibril axis. However, to understand the amyloid extension mechanism, we must understand the amyloid fibril structure and fluctuation at the fibril end, which has not been revealed to date. Here, we reveal these features by all-atom molecular dynamics (MD) simulations of Aβ42 and Aβ40 fibrils in explicit water. The structure and fluctuation were observed to differ between the two ends. At the even end, the Aβ peptide always took a closed form wherein β1 and β2 were closely spaced. The Aβ peptide fluctuated more at the odd end and took an open form wherein the two β-sheets were well separated. The differences are attributed to the stronger β-sheet formation by the β1 exposed at the even end than the β2 exposed at the odd end. Along with the small fluctuations at the even end, these results explain why the fibril extends from one end only, as observed in experiments. Our MD results agree well with recent observations by high-speed atomic force microscopy.
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