ArticleThe Journal of chemical physics2009
Simulations of nucleation and elongation of amyloid fibrils.
Article in The Journal of chemical physics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Production of Distinct Fibrillar, Oligomeric, and Other Aggregation States from Network Models of Multibody Interaction.Journal of chemical theory and computation · 2024Article
- Advanced computational approaches to understand protein aggregation.Biophysics reviews · 2024Review
- Evaluation of fendiline treatment in VP40 system with nucleation-elongation process: a computational model of Ebola virus matrix protein assembly.Microbiology spectrum · 2024Article
- Molecular mechanisms and emerging therapies in wild-type transthyretin amyloid cardiomyopathy.Heart failure reviews · 2024Review
- 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
- Transthyretin Stabilizers and Seeding Inhibitors as Therapies for Amyloid Transthyretin Cardiomyopathy.Pharmaceutics · 2023Review
- Amyloid seeding as a disease mechanism and treatment target in transthyretin cardiac amyloidosis.Heart failure reviews · 2022Review
- Side Chain Geometry Determines the Fibrillation Propensity of a Minimal Two-Beads-per-Residue Peptide Model.The journal of physical chemistry. B · 2022Article
- Conformational entropy limits the transition from nucleation to elongation in amyloid aggregation.Biophysical journal · 2022Article
- Mechanisms of phosphatidylserine influence on viral production: A computational model of Ebola virus matrix protein assembly.The Journal of biological chemistry · 2022Article
- Role of non-specific interactions in the phase-separation and maturation of macromolecules.PLoS computational biology · 2022Article
- Multiscale Models for Fibril Formation: Rare Events Methods, Microkinetic Models, and Population Balances.Life (Basel, Switzerland) · 2021Article
- Mechanics of a molecular mousetrap-nucleation-limited innate immune signaling.Biophysical journal · 2021Review
- Physical mechanisms of amyloid nucleation on fluid membranes.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Early stage prion assembly involves two subpopulations with different quaternary structures and a secondary templating pathway.Communications biology · 2019Article
- Assembly Mechanism for Aggregation of Amyloid Fibrils.International journal of molecular sciences · 2018Article
- Ultrafast Time-Resolved Studies on Fluorescein for Recognition Strands Architecture in Amyloid Fibrils.The journal of physical chemistry. B · 2018Article
- Monomeric Huntingtin Exon 1 Has Similar Overall Structural Features for Wild-Type and Pathological Polyglutamine Lengths.Journal of the American Chemical Society · 2017Article
- Theory of amyloid fibril nucleation from folded proteins.Israel journal of chemistry · 2017Article
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2 authors.
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Abstract
We present a coarse-grained model for the growth kinetics of amyloid fibrils from solutions of peptides and address the fundamental mechanism of nucleation and elongation by using a lattice Monte Carlo procedure. We reproduce the three main characteristics of nucleation of amyloid fibrils: (1) existence of lag time, (2) occurrence of a critical concentration, and (3) seeding. We find the nucleation of amyloid fibrils to require a quasi-two-dimensional configuration, where a second layer of beta sheet must be formed adjunct to a first layer, which in turn leads to a highly cooperative nucleation barrier. The elongation stage is found to involve the Ostwald ripening (evaporation-condensation) mechanism, whereby bigger fibrils grow at the expense of smaller ones. This new mechanism reconciles the debate as to whether protofibrils are precursors or monomer reservoirs. We have systematically investigated the roles of time, peptide concentration, temperature, and seed size. In general, we find that there are two kinds of lag time arising from two different mechanisms. For higher temperatures or low enough concentrations close to the disassembly boundary, the fibrillization follows the nucleation mechanism. However, for low temperatures, where the nucleation time is sufficiently short, there still exists an apparent lag time due to slow Ostwald ripening mechanism. Consequently, the lag time is nonmonotonic with temperature, with the shortest lag time occurring at intermediate temperatures, which in turn depend on the peptide concentration. While the nucleation dominated regime can be controlled by seeding, the Ostwald ripening regime is insensitive to seeding. Simulation results from our coarse-grained model on the fibril size, lag time, elongation rate, and solubility are consistent with available experimental observations on many specific amyloid systems.
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