Molecular Dynamics Simulation of a Feather-Boa Model of a Bacterial Chromosome
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.
|The Netherlands Organisation for Scientific Research (NWO)|
|Methods Mol. Biol.|
|Organisation||Theory of Biomolecular Matter|
Chaudhuri, D, & Mulder, B.M. (2018). Molecular Dynamics Simulation of a Feather-Boa Model of a Bacterial Chromosome. In R.T Dame (Ed.), Bacterial Chromatin: Methods and protocols (pp. 403–415). Springer Nature. doi:10.1007/978-1-4939-8675-0_20