Probing Protein Aggregation Using the Coarse-Grained UNRES Force Field.
Coarse graining
Molecular dynamics
Protein aggregation
UNRES force field
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2022
2022
Historique:
entrez:
15
2
2022
pubmed:
16
2
2022
medline:
19
2
2022
Statut:
ppublish
Résumé
Protein aggregation is the cause of many, often lethal, diseases, including the Alzheimer's, Parkinson's, and Huntington's diseases, and familial amyloidosis. Theoretical investigation of the mechanism of this process, including the structures of the oligomeric intermediates which are the most toxic, is difficult because of long time scale of aggregation. Coarse-grained models, which enable us to extend the simulation time scale by three or more orders of magnitude, are, therefore, of great advantage in such studies. In this chapter, we describe the application of the physics-based UNited RESidue (UNRES) force field developed in our laboratory to study protein aggregation, in both free simulations and simulations of aggregation propagation from an existing template (seed), and illustrate it with the examples of Aβ-peptide aggregation and Aβ-peptide-assisted aggregation of the peptides derived from the repeat domains of tau (TauRD).
Identifiants
pubmed: 35167071
doi: 10.1007/978-1-0716-1546-1_5
doi:
Substances chimiques
Peptides
0
Protein Aggregates
0
Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
79-104Informations de copyright
© 2022. Springer Science+Business Media, LLC, part of Springer Nature.
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