ArticleThe journal of physical chemistry. B2014
Effects of macromolecular crowding on amyloid beta (16-22) aggregation using coarse-grained simulations.
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 28 papers.
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Who cites it
28 citing papers in PubMed.
- Cosolutes Modulate Polyubiquitin Fibrillation.ACS omega · 2026Article
- In silico peptide self-assembly reveals the importance of N-terminal motifs and the inhibition mechanism of the mutation L38M in α-synuclein fibrillation.Protein science : a publication of the Protein Society · 2026Article
- Hidden faces of alpha-synuclein: Cryo-EM revelation of fibril polymorphs driven by disease, mutations, and PTMs.BBA advances · 2026Review
- Article
- Can local heating and molecular crowders disintegrate amyloid aggregates?Chemical science · 2024Article
- Fibrillization Process of Human Amyloid-Beta Protein (1-40) under a Molecular Crowding Environment Mimicking the Interior of Living Cells Using Cell Debris.Molecules (Basel, Switzerland) · 2023Article
- Energy landscapes of Aβ monomers are sculpted in accordance with Ostwald's rule of stages.Science advances · 2023Article
- Distribution and Structure Analysis of Fibril-Forming Peptides Focusing on Concentration Dependency.ACS omega · 2022Article
- An Alzheimer's Disease Mechanism Based on Early Pathology, Anatomy, Vascular-Induced Flow, and Migration of Maximum Flow Stress Energy Location with Increasing Vascular Disease.Journal of Alzheimer's disease : JAD · 2022Article
- Polymorphism of Alpha-Synuclein Amyloid Fibrils Depends on Ionic Strength and Protein Concentration.International journal of molecular sciences · 2021Article
- An Overview of Several Inhibitors for Alzheimer's Disease: Characterization and Failure.International journal of molecular sciences · 2021Review
- Crowding affects structural dynamics and contributes to membrane association of the NS3/4A complex.Biophysical journal · 2021Article
- De novo design of peptides that coassemble into β sheet-based nanofibrils.Science advances · 2021Article
- Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis.Chemical reviews · 2021Review
- Different Aggregation Pathways and Structures for Aβ40 and Aβ42 Peptides.Biomolecules · 2021Article
- On the Conformational Dynamics of β-Amyloid Forming Peptides: A Computational Perspective.Frontiers in bioengineering and biotechnology · 2020Review
- Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications.International journal of molecular sciences · 2019Review
- Thermodynamic phase diagram of amyloid-β (16-22) peptide.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Modeling Crowded Environment in Molecular Simulations.Frontiers in molecular biosciences · 2019Review
- Seeding and cross-seeding fibrillation of N-terminal prion protein peptides PrP(120-144).Protein science : a publication of the Protein Society · 2018Article
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3 authors.
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Abstract
To examine the effect of crowding on protein aggregation, discontinuous molecular dynamics (DMD) simulations combined with an intermediate resolution protein model, PRIME20, were applied to a peptide/crowder system. The systems contained 192 Aβ(16-22) peptides and crowders of diameters 5, 20, and 40 Å, represented here by simple hard spheres, at crowder volume fractions of 0.00, 0.10, and 0.20. Results show that both crowder volume fraction and crowder diameter have a large impact on fibril and oligomer formation. The addition of crowders to a system of peptides increases the rate of oligomer formation, shifting from a slow ordered formation of oligomers in the absence of crowders, similar to nucleated polymerization, to a fast collapse of peptides and subsequent rearrangement characteristic of nucleated conformational conversion with a high maximum in the number of peptides in oligomers as the total crowder surface area increases. The rate of conversion from oligomers to fibrils also increases with increasing total crowder surface area, giving rise to an increased rate of fibril growth. In all cases, larger volume fractions and smaller crowders provide the greatest aggregation enhancement effects. We also show that the size of the crowders influences the formation of specific oligomer sizes. In our simulations, the 40 Å crowders enhance the number of dimers relative to the numbers of trimers, hexamers, pentamers, and hexamers, while the 5 Å crowders enhance the number of hexamers relative to the numbers of dimers, trimers, tetramers, and pentamers. These results are in qualitative agreement with previous experimental and theoretical work.
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