Molecular Dynamics Simulation of a Feather-Boa Model of a Bacterial Chromosome

Back to all publications

Publication date
DOI http://dx.doi.org/10.1007/978-1-4939-8675-0_20
Reference D. Chaudhuri and B.M. Mulder: Molecular Dynamics Simulation of a Feather-Boa Model of a Bacterial Chromosome In: Bacterial Chromatin: Methods and protocols /ed. R.T. Dame, Springer Nature, 2018. - pp. 403-415 (Methods Mol. Biol.;)
Group Theory of Biomolecular Matter

The chromosome of a bacterium consists of a mega-base pair long circular DNA, which self-organizes within the micron-sized bacterial cell volume, compacting itself by three orders of magnitude. Unlike in eukaryotes, it lacks a nuclear membrane, and freely floats in the cytosol confined by the cell membrane. It is believed that strong confinement, cross-linking by associated proteins, and molecular crowding all contribute to determine chromosome size and morphology. Modeling the chromosome simply as a circular polymer decorated with closed side-loops in a cylindrical confining volume, has been shown to already recapture some of the salient properties observed experimentally. Here, we describe how a computer simulation can be set up to study structure and dynamics of bacterial chromosomes using this model.