超螺旋、打结和连环DNA分子的分子动力学模拟，包括DNA促旋酶作用的建模。

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

作者信息

Racko Dusan, Benedetti Fabrizio, Dorier Julien, Burnier Yannis, Stasiak Andrzej

机构信息

Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland.

SIB Swiss Institute for Bioinformatics, 1015, Lausanne, Switzerland.

出版信息

Methods Mol Biol. 2017;1624:339-372. doi: 10.1007/978-1-4939-7098-8_24.

DOI:10.1007/978-1-4939-7098-8_24

PMID:28842894

Abstract

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.

摘要

本文描述了超螺旋DNA分子的分子动力学模拟详细方案，这些分子还可能打结或连环。我们还描述了如何对DNA促旋酶的持续作用进行建模，该酶将负超螺旋引入DNA分子。这些方案提供了关于模型参数、所用势函数方程、模拟和可视化的详细说明。逐步展示了如何将该模型在常用的分子动力学模拟环境ESPResSo中实现。