Molecular Dynamics Simulation of Supercoiled, Knotted, and Catenated DNA Molecules, Including Modeling of Action of DNA Gyrase.

Détails

ID Serval
serval:BIB_E48F1B04C7E2
Type
Article: article d'un périodique ou d'un magazine.
Sous-type
Synthèse (review): revue aussi complète que possible des connaissances sur un sujet, rédigée à partir de l'analyse exhaustive des travaux publiés.
Collection
Publications
Titre
Molecular Dynamics Simulation of Supercoiled, Knotted, and Catenated DNA Molecules, Including Modeling of Action of DNA Gyrase.
Périodique
Methods in Molecular Biology
Auteur(s)
Racko D., Benedetti F., Dorier J., Burnier Y., Stasiak A.
ISSN
1940-6029 (Electronic)
ISSN-L
1064-3745
Statut éditorial
Publié
Date de publication
2017
Peer-reviewed
Oui
Volume
1624
Pages
339-372
Langue
anglais
Résumé
A detailed protocol of molecular dynamics simulations of supercoiled DNA molecules that can be in addition knotted or catenated is described. We also describe how to model ongoing action of DNA gyrase that introduces negative supercoing into DNA molecules. The protocols provide detailed instructions about model parameters, equations of used potentials, simulation, and visualization. Implementation of the model into a frequently used molecular dynamics simulation environment, ESPResSo, is shown step by step.

Mots-clé
Algorithms, Computational Biology/methods, DNA/chemistry, DNA Gyrase/metabolism, DNA, Catenated/chemistry, DNA, Superhelical/chemistry, Molecular Dynamics Simulation, Nucleic Acid Conformation, DNA gyrase, DNA knots and catenanes, DNA topoisomerases, Molecular dynamics, Supercoiled DNA
Pubmed
Web of science
Création de la notice
12/09/2017 13:28
Dernière modification de la notice
20/08/2019 16:08
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