ArticleBiophysical journal2013
Computational assembly of polymorphic amyloid fibrils reveals stable aggregates.
Article in Biophysical journal, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 40 citations in OpenAlex.
- Exploring Abeta42 monomer diffusion dynamics on fibril surfaces through molecular simulations.Protein science : a publication of the Protein Society · 2025Article
- Aggregating amyloid resources: A comprehensive review of databases on amyloid-like aggregation.Computational and structural biotechnology journal · 2024Review
- Challenges in studying the liquid-to-solid phase transitions of proteins using computer simulations.Current opinion in chemical biology · 2023Review
- Toward the Noninvasive Diagnosis of Alzheimer's Disease: Molecular Basis for the Specificity of Curcumin for Fibrillar Amyloid-β.ACS omega · 2022Article
- Bioinformatics Methods in Predicting Amyloid Propensity of Peptides and Proteins.Methods in molecular biology (Clifton, N.J.) · 2022Article
- A protein self-assembly model guided by electrostatic and hydrophobic dipole moments.PloS one · 2019Article
- Diabetes Drug Discovery: hIAPPMolecules (Basel, Switzerland) · 2018Article
- Amyloid fibril polymorphism: a challenge for molecular imaging and therapy.Journal of internal medicine · 2018Review
- On the ability of molecular dynamics simulation and continuum electrostatics to treat interfacial water molecules in protein-protein complexes.Scientific reports · 2016Article
- Molecular docking as a popular tool in drug design, an in silico travel.Advances and applications in bioinformatics and chemistry : AABC · 2016Review
- Probing the binding affinity of amyloids to reduce toxicity of oligomers in diabetes.Bioinformatics (Oxford, England) · 2015Article
- On the lack of polymorphism in Aβ-peptide aggregates derived from patient brains.Protein science : a publication of the Protein Society · 2015Article
- Preclinical Validation of the Heparin-Reactive Peptide p5+14 as a Molecular Imaging Agent for Visceral Amyloidosis.Molecules (Basel, Switzerland) · 2015Article
- Computational re-engineering of Amylin sequence with reduced amyloidogenic potential.BMC structural biology · 2015Article
- Stability of Iowa mutant and wild type Aβ-peptide aggregates.The Journal of chemical physics · 2014Article
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Corrections and comments
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Authors and funding
6 authors at 5 institutions in 3 countries.
Funding
Abstract
Amyloid proteins aggregate into polymorphic fibrils that damage tissues of the brain, nerves, and heart. Experimental and computational studies have examined the structural basis and the nucleation of short fibrils, but the ability to predict and precisely quantify the stability of larger aggregates has remained elusive. We established a complete classification of fibril shapes and developed a tool called CreateFibril to build such complex, polymorphic, modular structures automatically. We applied stability landscapes, a technique we developed to reveal reliable fibril structural parameters, to assess fibril stability. CreateFibril constructed HET-s, Aβ, and amylin fibrils up to 17 nm in length, and utilized a novel dipolar solvent model that captured the effect of dipole-dipole interactions between water and very large molecular systems to assess their aqueous stability. Our results validate experimental data for HET-s and Aβ, and suggest novel (to our knowledge) findings for amylin. In particular, we predicted the correct structural parameters (rotation angles, packing distances, hydrogen bond lengths, and helical pitches) for the one and three predominant HET-s protofilaments. We reveal and structurally characterize all known Aβ polymorphic fibrils, including structures recently classified as wrapped fibrils. Finally, we elucidate the predominant amylin fibrils and assert that native amylin is more stable than its amyloid form. CreateFibril and a database of all stable polymorphic fibril models we tested, along with their structural energy landscapes, are available at http://amyloid.cs.mcgill.ca.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.