ArticlePLoS computational biology2012
Kinetics of amyloid aggregation: a study of the GNNQQNY prion sequence.
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- The Intrinsic UV-Visible Fluorescence of Peptides Widely Used for Studying Amyloid Aggregation Devoid of Aromatic Residues.International journal of molecular sciences · 2026Article
- Structural Insights Into Amyloid Polymorphism: The Impact of Glutamine to Norleucine Substitutions in GNNQQNY Aggregation.Chemistry (Weinheim an der Bergstrasse, Germany) · 2025Article
- 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
- Clustering and Fibril Formation during GNNQQNY Aggregation: A Molecular Dynamics Study.Biomolecules · 2020Article
- Biomolecular Assemblies: Moving from Observation to Predictive Design.Chemical reviews · 2018Review
- Critical Nucleus Structure and Aggregation Mechanism of the C-terminal Fragment of Copper-Zinc Superoxide Dismutase Protein.ACS chemical neuroscience · 2016Article
- Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies.Chemical reviews · 2015Review
- Exploring the role of hydration and confinement in the aggregation of amyloidogenic peptides Aβ(16-22) and Sup35(7-13) in AOT reverse micelles.The Journal of chemical physics · 2014Article
- The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems.Chemical Society reviews · 2014Review
- A kinetic approach to the sequence-aggregation relationship in disease-related protein assembly.The journal of physical chemistry. B · 2014Article
- C-terminal domain swapping of SSB changes the size of the ssDNA binding site.BioMed research international · 2014Article
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2 authors.
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Abstract
The small amyloid-forming GNNQQNY fragment of the prion sequence has been the subject of extensive experimental and numerical studies over the last few years. Using unbiased molecular dynamics with the OPEP coarse-grained potential, we focus here on the onset of aggregation in a 20-mer system. With a total of 16.9 μs of simulations at 280 K and 300 K, we show that the GNNQQNY aggregation follows the classical nucleation theory (CNT) in that the number of monomers in the aggregate is a very reliable descriptor of aggregation. We find that the critical nucleus size in this finite-size system is between 4 and 5 monomers at 280 K and 5 and 6 at 300 K, in overall agreement with experiment. The kinetics of growth cannot be fully accounted for by the CNT, however. For example, we observe considerable rearrangements after the nucleus is formed, as the system attempts to optimize its organization. We also clearly identify two large families of structures that are selected at the onset of aggregation demonstrating the presence of well-defined polymorphism, a signature of amyloid growth, already in the 20-mer aggregate.
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