ArticleThe journal of physical chemistry. B2014
A kinetic approach to the sequence-aggregation relationship in disease-related protein assembly.
Article in The journal of physical chemistry. B, 2014. 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, 72 citations in OpenAlex.
- Effects of ion type and concentration on the structure and aggregation of the amyloid peptide AProteins · 2025Article
- Transition Networks Unveil Disorder-to-Order Transformations in AInternational journal of molecular sciences · 2023Article
- Ingenuity in performing replica permutation: How to order the state labels for improving sampling efficiency.Journal of computational chemistry · 2023Article
- Computational and Experimental Evaluation of the Stability of a GLP-1-like Peptide in Ethanol-Water Mixtures.Pharmaceutics · 2022Article
- Molecular Dynamics Simulation Studies on the Aggregation of Amyloid-β Peptides and Their Disaggregation by Ultrasonic Wave and Infrared Laser Irradiation.Molecules (Basel, Switzerland) · 2022Review
- Aggregation Behavior of Structurally Similar Therapeutic Peptides Investigated byMolecular pharmaceutics · 2022Article
- Molecular dynamics simulations of amyloid-β peptides in heterogeneous environments.Biophysics and physicobiology · 2022Article
- Amyloid-β peptide dimers undergo a random coil to β-sheet transition in the aqueous phase but not at the neuronal membrane.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Promotion and Inhibition of Amyloid-β Peptide Aggregation: Molecular Dynamics Studies.International journal of molecular sciences · 2021Review
- Clustering and Fibril Formation during GNNQQNY Aggregation: A Molecular Dynamics Study.Biomolecules · 2020Article
- Amyloid assembly is dominated by misregistered kinetic traps on an unbiased energy landscape.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Effects of All-Atom Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of AβJournal of chemical theory and computation · 2019Article
- Biomolecular Assemblies: Moving from Observation to Predictive Design.Chemical reviews · 2018Review
- The Levinthal Problem in Amyloid Aggregation: Sampling of a Flat Reaction Space.The journal of physical chemistry. B · 2017Article
- 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
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
It is generally accepted that oligomers of aggregating proteins play an important role in the onset of neurodegenerative diseases. While in silico aggregation studies of full length amyloidogenic proteins are computationally expensive, the assembly of short protein fragments derived from these proteins with similar aggregating properties has been extensively studied. In the present work, molecular dynamics simulations are performed to follow peptide aggregation on the microsecond time scale. By defining aggregation states, we identify transition networks, disconnectivity graphs, and first passage time distributions to describe the kinetics of the assembly process. This approach unravels differences in the aggregation into hexamers of two peptides with different primary structures. The first is GNNQQNY, a hydrophilic fragment from the prion protein Sup35, and the second is KLVFFAE, a fragment from amyloid-β protein, with a hydrophobic core delimited by two charged amino acids. The assembly of GNNQQNY suggests a mechanism of monomer addition, with a bias toward parallel peptide pairs and a gradual increase in the amount of β-strand content. For KLVFFAE, a mechanism involving dimers rather than monomers is revealed, involving a generally higher β-strand content and a transition toward a larger number of antiparallel peptide pairs during the rearrangement of the hexamer. The differences observed for the aggregation of the two peptides suggests the existence of a sequence-aggregation relationship.
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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.