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SMC Complexes pp 319-334 | Cite as

Molecular Dynamics Simulations of Condensin-Mediated Mitotic Chromosome Assembly

  • Yuji SakaiEmail author
  • Tatsuya Hirano
  • Masashi Tachikawa
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2004)

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.

Key words

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

Notes

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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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Yuji Sakai
    • 1
    • 2
    • 3
    Email author
  • Tatsuya Hirano
    • 4
  • Masashi Tachikawa
    • 2
    • 3
  1. 1.Department of Biochemistry and Molecular Biology, Graduate School and Faculty of MedicineThe University of TokyoTokyoJapan
  2. 2.Theoretical Biology LaboratoryRIKENWakoJapan
  3. 3.Interdisciplinary Theoretical and Mathematical Sciences Program (iTHEMS)RIKENWakoJapan
  4. 4.Chromosome Dynamics LaboratoryRIKENWakoJapan

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