ArticleBiophysical journal2011
Spontaneous formation of twisted Aβ(16-22) fibrils in large-scale molecular-dynamics simulations.
Article in Biophysical journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- K16F/E22F Mutation Promotes Oligomerization and Alters β-Sheet Topology of Aβ16-22 Peptides: Insights from Molecular Dynamics Simulations.ACS chemical neuroscience · 2026Article
- In silico peptide self-assembly reveals the importance of N-terminal motifs and the inhibition mechanism of the mutation L38M in α-synuclein fibrillation.Protein science : a publication of the Protein Society · 2026Article
- Computational Study of the Dimerization of the Parathyroid Hormone.The journal of physical chemistry. B · 2025Article
- Origins of the Superiority of Oscillating Electric Fields for Disrupting Senile Plaques: Insights from the 7-Residue Fragment and the Full-length Aβ-42 Peptide.Journal of the American Chemical Society · 2025Article
- Advanced computational approaches to understand protein aggregation.Biophysics reviews · 2024Review
- Visualization of Self-Assembly and Hydration of a β-Hairpin through Integrated Small and Wide-Angle Neutron Scattering.Biomacromolecules · 2023Article
- De novo design of peptides that coassemble into β sheet-based nanofibrils.Science advances · 2021Article
- Structural insights into peptide self-assembly using photo-induced crosslinking experiments and discontinuous molecular dynamics.AIChE journal. American Institute of Chemical Engineers · 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
- From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules.Frontiers in molecular biosciences · 2021Review
- Charge guides pathway selection in β-sheet fibrillizing peptide co-assembly.Communications chemistry · 2020Article
- Amyloid assembly is dominated by misregistered kinetic traps on an unbiased energy landscape.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Anatomy of a selectively coassembled β-sheet peptide nanofiber.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications.International journal of molecular sciences · 2019Review
- Molecular insights into the surface-catalyzed secondary nucleation of amyloid-βScience advances · 2019Article
- Thermodynamic phase diagram of amyloid-β (16-22) peptide.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Seeding and cross-seeding fibrillation of N-terminal prion protein peptides PrP(120-144).Protein science : a publication of the Protein Society · 2018Article
- Simulations and Experiments Delineate Amyloid Fibrilization by Peptides Derived from Glaucoma-Associated Myocilin.The journal of physical chemistry. B · 2018Article
- Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments.Chemical Society reviews · 2018Review
- Amyloid scaffolds as alternative chlorosomes.Organic & biomolecular chemistry · 2017Review
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Authors and funding
3 authors.
Funding
Abstract
Protein aggregation is associated with fatal neurodegenerative diseases, including Alzheimer's and Parkinson's. Mapping out kinetics along the aggregation pathway could provide valuable insights into the mechanisms that drive oligomerization and fibrillization, but that is beyond the current scope of computational research. Here we trace out the full kinetics of the spontaneous formation of fibrils by 48 Aβ(16-22) peptides, following the trajectories in molecular detail from an initial random configuration to a final configuration of twisted protofilaments with cross-β-structure. We accomplish this by performing large-scale molecular-dynamics simulations based on an implicit-solvent, intermediate-resolution protein model, PRIME20. Structural details such as the intersheet distance, perfectly antiparallel β-strands, and interdigitating side chains analogous to a steric zipper interface are explained by and in agreement with experiment. Two characteristic fibrillization mechanisms - nucleation/templated growth and oligomeric merging/structural rearrangement - emerge depending on the temperature.
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Registered trials
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