ArticlePLoS computational biology2011
A multiscale approach to characterize the early aggregation steps of the amyloid-forming peptide GNNQQNY from the yeast prion sup-35.
Article in PLoS computational biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed.
- Mapping the configurational landscape and aggregation phase behavior of the tau protein fragment PHF6.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Disassembly of Amyloid Fibril with Infrared Free Electron Laser.International journal of molecular sciences · 2023Review
- Dynamics of Amyloid Formation from Simplified Representation to Atomistic Simulations.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Sampling of the conformational landscape of small proteins with Monte Carlo methods.Scientific reports · 2020Article
- Clustering and Fibril Formation during GNNQQNY Aggregation: A Molecular Dynamics Study.Biomolecules · 2020Article
- An Atomistic View of Amyloidogenic Self-assembly: Structure and Dynamics of Heterogeneous Conformational States in the Pre-nucleation Phase.Scientific reports · 2016Article
- Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies.Chemical reviews · 2015Review
- Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics.Journal of chemical theory and computation · 2015Article
- The architecture of amyloid-like peptide fibrils revealed by X-ray scattering, diffraction and electron microscopy.Acta crystallographica. Section D, Biological crystallography · 2015Article
- Role of monomer arrangement in the amyloid self-assembly.Biochimica et biophysica acta · 2015Article
- 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
- Conformational distribution and α-helix to β-sheet transition of human amylin fragment dimer.Biomacromolecules · 2014Article
- C-terminal domain swapping of SSB changes the size of the ssDNA binding site.BioMed research international · 2014Article
- Importance of the ion-pair interactions in the OPEP coarse-grained force field: parametrization and validation.Journal of chemical theory and computation · 2013Article
- SAHBNET, an accessible surface-based elastic network: an application to membrane protein.International journal of molecular sciences · 2013Article
- Computational modeling of the relationship between amyloid and disease.Biophysical reviews · 2012Article
- Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides.Journal of chemical theory and computation · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The self-organization of peptides into amyloidogenic oligomers is one of the key events for a wide range of molecular and degenerative diseases. Atomic-resolution characterization of the mechanisms responsible for the aggregation process and the resulting structures is thus a necessary step to improve our understanding of the determinants of these pathologies. To address this issue, we combine the accelerated sampling properties of replica exchange molecular dynamics simulations based on the OPEP coarse-grained potential with the atomic resolution description of interactions provided by all-atom MD simulations, and investigate the oligomerization process of the GNNQQNY for three system sizes: 3-mers, 12-mers and 20-mers. Results for our integrated simulations show a rich variety of structural arrangements for aggregates of all sizes. Elongated fibril-like structures can form transiently in the 20-mer case, but they are not stable and easily interconvert in more globular and disordered forms. Our extensive characterization of the intermediate structures and their physico-chemical determinants points to a high degree of polymorphism for the GNNQQNY sequence that can be reflected at the macroscopic scale. Detailed mechanisms and structures that underlie amyloid aggregation are also provided.
Indexed as
Identifiers
What OpenQuestion holds
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.