ArticleScientific reports2016
An Atomistic View of Amyloidogenic Self-assembly: Structure and Dynamics of Heterogeneous Conformational States in the Pre-nucleation Phase.
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 12 papers.
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Who cites it
12 citing papers in PubMed.
- In vitro, cellular and in vivo studies of amyloid oligomers structure and toxicity: Challenges and advances.Protein science : a publication of the Protein Society · 2026Review
- Unraveling the Structure and Dynamics of Ac-PHF6-NHACS chemical neuroscience · 2024Article
- Exploring the Aggregation Propensity of PHF6 Peptide Segments of the Tau Protein Using Ion Mobility Mass Spectrometry Techniques.Analytical chemistry · 2024Article
- Rational Design of TDP-43 Derived α-Helical Peptide Inhibitors: AnACS chemical neuroscience · 2024Article
- How the Choice of Force-Field Affects the Stability and Self-Assembly Process of Supramolecular CTA Fibers.Journal of chemical theory and computation · 2022Article
- Dynamics of Amyloid Formation from Simplified Representation to Atomistic Simulations.Methods in molecular biology (Clifton, N.J.) · 2022Article
- MELD-accelerated molecular dynamics help determine amyloid fibril structures.Communications biology · 2021Article
- Aggregation of Aβ40/42 chains in the presence of cyclic neuropeptides investigated by molecular dynamics simulations.PLoS computational biology · 2021Article
- Acetylation of Aβ42 at Lysine 16 Disrupts Amyloid Formation.ACS chemical neuroscience · 2020Article
- Structural Analysis of a Trimer of βBiophysical journal · 2019Article
- ZnScientific reports · 2018Article
- Force field development and simulations of intrinsically disordered proteins.Current opinion in structural biology · 2018Review
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The formation of well-defined filamentous amyloid structures involves a polydisperse collection of oligomeric states for which relatively little is known in terms of structural organization. Here we use extensive, unbiased explicit solvent molecular dynamics (MD) simulations to investigate the structural and dynamical features of oligomeric aggregates formed by a number of highly amyloidogenic peptides at atomistic resolution on the μs time scale. A consensus approach has been adopted to analyse the simulations in multiple force fields, yielding an in-depth characterization of pre-fibrillar oligomers and their global and local structure properties. A collision cross section analysis revealed structurally heterogeneous aggregate ensembles for the individual oligomeric states that lack a single defined quaternary structure during the pre-nucleation phase. To gain insight into the conformational space sampled in early aggregates, we probed their substructure and found emerging β-sheet subunit layers and a multitude of ordered intermolecular β-structure motifs with growing aggregate size. Among those, anti-parallel out-of-register β-strands compatible with toxic β-barrel oligomers were particularly prevalent already in smaller aggregates and formed prior to ordered fibrillar structure elements. Notably, also distinct fibril-like conformations emerged in the oligomeric state and underscore the notion that pre-nucleated oligomers serve as a critical intermediate step on-pathway to fibrils.
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