ArticleBiophysical journal2009
Replica exchange simulations of the thermodynamics of Abeta fibril growth.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
- Survey of the Aβ-peptide structural diversity: molecular dynamics approaches.Biophysical reviews · 2024Review
- Direct Observation of Seeded Conformational Conversion of hIAPPJournal of chemical information and modeling · 2023Article
- 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
- Mechanistic Kinetic Model Reveals How Amyloidogenic Hydrophobic Patches Facilitate the Amyloid-β Fibril Elongation.ACS chemical neuroscience · 2022Article
- Molecular dynamics simulations of amyloid-β peptides in heterogeneous environments.Biophysics and physicobiology · 2022Article
- Probing Protein Aggregation Using the Coarse-Grained UNRES Force Field.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Multiscale Models for Fibril Formation: Rare Events Methods, Microkinetic Models, and Population Balances.Life (Basel, Switzerland) · 2021Article
- Promotion and Inhibition of Amyloid-β Peptide Aggregation: Molecular Dynamics Studies.International journal of molecular sciences · 2021Review
- Insight Into Seeded Tau Fibril Growth From Molecular Dynamics Simulation of the Alzheimer's Disease Protofibril Core.Frontiers in molecular biosciences · 2021Article
- Thermodynamics of Amyloid-β Fibril Elongation: Atomistic Details of the Transition State.ACS chemical neuroscience · 2018Article
- Out-of-Register AβJournal of chemical theory and computation · 2018Article
- Conversion between parallel and antiparallel β-sheets in wild-type and Iowa mutant AβThe Journal of chemical physics · 2018Article
- Elongation affinity, activation barrier, and stability of Aβ42 oligomers/fibrils in physiological saline.Biochemical and biophysical research communications · 2017Article
- Elucidating Important Sites and the Mechanism for Amyloid Fibril Formation by Coarse-Grained Molecular Dynamics.ACS chemical neuroscience · 2017Article
- Structure of ring-shaped Aβ₄₂ oligomers determined by conformational selection.Scientific reports · 2016Article
- Fibril elongation by Aβ(17-42): kinetic network analysis of hybrid-resolution molecular dynamics simulations.Journal of the American Chemical Society · 2014Article
- A simple lattice model that captures protein folding, aggregation and amyloid formation.PloS one · 2014Article
- Binding to the lipid monolayer induces conformational transition in Aβ monomer.Journal of molecular modeling · 2013Article
- Conformational stability of fibrillar amyloid-beta oligomers via protofilament pair formation - a systematic computational study.PloS one · 2013Article
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2 authors.
Funding
Abstract
Replica exchange molecular dynamics and an all-atom implicit solvent model are used to probe the thermodynamics of deposition of Alzheimer's Abeta monomers on preformed amyloid fibrils. Consistent with the experiments, two deposition stages have been identified. The docking stage occurs over a wide temperature range, starting with the formation of the first peptide-fibril interactions at 500 K. Docking is completed when a peptide fully adsorbs on the fibril edge at the temperature of 380 K. The docking transition appears to be continuous, and occurs without free energy barriers or intermediates. During docking, incoming Abeta monomer adopts a disordered structure on the fibril edge. The locking stage occurs at the temperature of approximately 360 K and is characterized by the rugged free energy landscape. Locking takes place when incoming Abeta peptide forms a parallel beta-sheet structure on the fibril edge. Because the beta-sheets formed by locked Abeta peptides are typically off-registry, the structure of the locked phase differs from the structure of the fibril interior. The study also reports that binding affinities of two distinct fibril edges with respect to incoming Abeta peptides are different. The peptides bound to the concave edge have significantly lower free energy compared to those bound on the convex edge. Comparison with the available experimental data is discussed.
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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.