Multiscale Molecular Dynamics Simulations of Ice-Binding Proteins.
Ice-binding proteins
Interfacial water
Molecular dynamics simulation
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:
2024
2024
Historique:
medline:
10
11
2023
pubmed:
9
11
2023
entrez:
9
11
2023
Statut:
ppublish
Résumé
Ice-binding proteins (IBPs) are a diverse class of proteins that are essential for the survival of organisms in cold conditions. IBPs are diverse in their function and can prevent or promote ice growth and selectively bind to specific crystallographic planes of the growing ice lattice. Moreover, IBPs are widely utilized to modulate ice crystal growth and recrystallization in the food industry and as cryoprotectants to preserve biological matter. A key unresolved aspect of the mode of action is how the ice-binding sites of these proteins distinguish between ice and water and interact with multiple crystal facets of the ice. The use of molecular dynamics (MD) simulation allows us to thoroughly investigate the binding mechanism and energetics of ice-binding proteins, to complement and expand on the mechanistic understandings gained from experiments. In this chapter, we describe a series of molecular dynamics simulation methodologies to investigate the mechanism of action of ice-binding proteins. Specifically, we provide detailed instructions to set up MD simulations to study the binding and interaction of ice-binding proteins using atomistic and coarse-grained simulations.
Identifiants
pubmed: 37943459
doi: 10.1007/978-1-0716-3503-2_13
doi:
Substances chimiques
Carrier Proteins
0
Ice
0
Caspase 1
EC 3.4.22.36
Water
059QF0KO0R
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
185-202Informations de copyright
© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
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