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Methods Mol Biol. 2019;2004:319-334. doi: 10.1007/978-1-4939-9520-2_22.

Molecular Dynamics Simulations of Condensin-Mediated Mitotic Chromosome Assembly.

Author information

1
Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan. yuji-sakai@m.u-tokyo.ac.jp.
2
Theoretical Biology Laboratory, RIKEN, Wako, Japan. yuji-sakai@m.u-tokyo.ac.jp.
3
Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS), RIKEN, Wako, Japan. yuji-sakai@m.u-tokyo.ac.jp.
4
Chromosome Dynamics Laboratory, RIKEN, Wako, Japan.
5
Theoretical Biology Laboratory, RIKEN, Wako, Japan.
6
Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS), RIKEN, Wako, Japan.

Abstract

Molecular dynamics simulation is a powerful tool used in modern molecular modeling, which enables a deeper comprehension of the physical behavior of atoms and molecules at a micro level. In this study, we simulated mitotic chromosome assembly mediated by condensins, a class of large protein complexes containing a pair of structural maintenance of chromosomes (SMC) subunits that are central to this process. In this chapter, we present the construction of a coarse-grained physical model of chromosomal DNA fibers and condensin molecules, and monitoring of the function of condensins in mitotic chromosome assembly, using computer-based molecular dynamics simulation. We explain how our model of chromosomes and condensins may be simulated using a package of molecular dynamics simulation. Procedures involved in calculating the observables of dynamics are described, together with an example of the simulation results.

KEYWORDS:

Coarse-grained polymer model; Condensin; Mitotic chromosome assembly; Molecular dynamics; Simulation

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