ArticleBiophysical journal2004
Sampling the self-assembly pathways of KFFE hexamers.
Article in Biophysical journal, 2004. 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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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
22 citing papers in PubMed, 76 citations in OpenAlex.
- Peptide Self-Assembly into Amyloid Fibrils: Unbiased All-Atom Simulations.The journal of physical chemistry. B · 2024Review
- Nucleation and Growth of Amyloid Fibrils.The journal of physical chemistry. B · 2023Article
- Distribution and Structure Analysis of Fibril-Forming Peptides Focusing on Concentration Dependency.ACS omega · 2022Article
- Dynamics of Amyloid Formation from Simplified Representation to Atomistic Simulations.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Direct Observation of β-Barrel Intermediates in the Self-Assembly of Toxic SOD1Journal of chemical information and modeling · 2021Article
- β-barrel Oligomers as Common Intermediates of Peptides Self-Assembling into Cross-β Aggregates.Scientific reports · 2018Article
- Multiscale simulation of molecular processes in cellular environments.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2016Review
- Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies.Chemical reviews · 2015Review
- The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems.Chemical Society reviews · 2014Review
- Article
- Reduced atomic pair-interaction design (RAPID) model for simulations of proteins.The Journal of chemical physics · 2013Article
- Kinetics of amyloid aggregation: a study of the GNNQQNY prion sequence.PLoS computational biology · 2012Article
- Carbon nanotube inhibits the formation of β-sheet-rich oligomers of the Alzheimer's amyloid-β(16-22) peptide.Biophysical journal · 2011Article
- Atomic-scale simulations confirm that soluble beta-sheet-rich peptide self-assemblies provide amyloid mimics presenting similar conformational properties.Biophysical journal · 2010Article
- Computational validation of protein nanotubes.Nano letters · 2009Article
- What determines the structure and stability of KFFE monomers, dimers, and protofibrils?Biophysical journal · 2009Article
- Formation and growth of oligomers: a Monte Carlo study of an amyloid tau fragment.PLoS computational biology · 2008Article
- Probing the mechanisms of fibril formation using lattice models.The Journal of chemical physics · 2008Article
- Structure and aggregation mechanism of beta(2)-microglobulin (83-99) peptides studied by molecular dynamics simulations.Biophysical journal · 2007Article
- Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities.Biophysical journal · 2007Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The formation of amyloid fibrils is often encountered in Alzheimer's disease, type II diabetes, and transmissible spongiform encephalopathies. In the last few years, however, mounting evidence has suggested that the soluble oligomers of amyloid-forming peptides are also cytotoxic agents. Understanding the early pathway steps of amyloid self-assembly at atomic detail might therefore be crucial for the development of specific inhibitors to prevent amyloidosis in humans. Using the activation-relaxation technique and a generic energy model, we study in detail the aggregation of a hexamer of KFFE peptide. Our simulations show that a monomer remains disordered, but that six monomers placed randomly in an open box self-associate to adopt, with various orientations, three possible distant low-energy structures. Two of these structures show a double-layer beta-sheet organization, in agreement with the structure of amyloid fibrils as observed by x-ray diffraction, whereas the third one consists of a barrel-like curved single-layer hexamer. Based on these results, we propose a bidirectional growth mode of amyloid fibril, involving alternate lateral and longitudinal growths.
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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.