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.
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Notes
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ESPResSo is downloaded from: http://espressomd.org/wordpress/.
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Acknowledgments
This work was supported by JSPS KAKENHI Grant Number (JP18H04708). The computations were performed using the RIKEN Integrated Cluster of Clusters (RICC) facility.
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Sakai, Y., Hirano, T., Tachikawa, M. (2019). Molecular Dynamics Simulations of Condensin-Mediated Mitotic Chromosome Assembly. In: Badrinarayanan, A. (eds) SMC Complexes. Methods in Molecular Biology, vol 2004. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9520-2_22
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DOI: https://doi.org/10.1007/978-1-4939-9520-2_22
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