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