ArticlePLoS computational biology2012
Connecting macroscopic observables and microscopic assembly events in amyloid formation using coarse grained simulations.
Article in PLoS computational biology, 2012. 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, 69 citations in OpenAlex.
- A Hybrid UA-CG Force Field for Aggregation Simulation of Amyloidogenic Peptide via Liquid-like Intermediates.Molecules (Basel, Switzerland) · 2025Article
- 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
- Phosphorylation sites are evolutionary checkpoints against liquid-solid transition in protein condensates.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Role of non-specific interactions in the phase-separation and maturation of macromolecules.PLoS computational biology · 2022Article
- Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Computational Models for the Study of Protein Aggregation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Diverse Aggregation Kinetics Predicted by a Coarse-Grained Peptide Model.The journal of physical chemistry. B · 2021Article
- Biomolecular Assemblies: Moving from Observation to Predictive Design.Chemical reviews · 2018Review
- Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments.Chemical Society reviews · 2018Review
- Quantitative computational models of molecular self-assembly in systems biology.Physical biology · 2017Review
- Physical determinants of the self-replication of protein fibrils.Nature physics · 2016Article
- A minimal conformational switching-dependent model for amyloid self-assembly.Scientific reports · 2016Article
- Monte Carlo simulation of kinetically slowed down phase separation.The European physical journal. E, Soft matter · 2015Article
- Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies.Chemical reviews · 2015Review
- Crucial role of nonspecific interactions in amyloid nucleation.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Web-based computational chemistry education with CHARMMing II: Coarse-grained protein folding.PLoS computational biology · 2014Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 3 countries.
Funding
Abstract
The pre-fibrillar stages of amyloid formation have been implicated in cellular toxicity, but have proved to be challenging to study directly in experiments and simulations. Rational strategies to suppress the formation of toxic amyloid oligomers require a better understanding of the mechanisms by which they are generated. We report Dynamical Monte Carlo simulations that allow us to study the early stages of amyloid formation. We use a generic, coarse-grained model of an amyloidogenic peptide that has two internal states: the first one representing the soluble random coil structure and the second one the [Formula: see text]-sheet conformation. We find that this system exhibits a propensity towards fibrillar self-assembly following the formation of a critical nucleus. Our calculations establish connections between the early nucleation events and the kinetic information available in the later stages of the aggregation process that are commonly probed in experiments. We analyze the kinetic behaviour in our simulations within the framework of the theory of classical nucleated polymerisation, and are able to connect the structural events at the early stages in amyloid growth with the resulting macroscopic observables such as the effective nucleus size. Furthermore, the free-energy landscapes that emerge from these simulations allow us to identify pertinent properties of the monomeric state that could be targeted to suppress oligomer formation.
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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.