Simulating the Entropic Collapse of Coarse-Grained Chromosomes
arXiv:1407.2850 · doi:10.1016/j.bpj.2014.11.3487
Abstract
Depletion forces play a role in the compaction and de-compation of chromosomal material in simple cells but it remains debatable whether they are sufficient to account for chromosomal collapse. We present coarse-grained molecular dynamics simulations, which reveal that depletion-induced attraction is sufficient to cause the collapse of a flexible chain of large structural monomers immersed in a bath of smaller depletants. These simulations use an explicit coarse-grained computational model that treats both the supercoiled DNA structural monomers and the smaller protein crowding agents as combinatorial, truncated Lennard-Jones spheres. By presenting a simple theoretical model, we quantitatively cast the action of depletants on supercoiled bacterial DNA as an effective solvent quality. The rapid collapse of the simulated flexible chromosome at the predicted volume fraction of depletants is a continous phase transition. Additional physical effects to such simple chromosome models, such as enthalpic interactions between structural monomers or chain rigidity, are required if the collapse is to be a first-order phase transition.
arXiv comment12 pages, 5 figures
References in corpus (15)
- Depletion potential in hard-sphere mixtures: theory and applications
- Phase diagram of the adhesive hard sphere fluid
- Collapse of a semiflexible polymer in poor solvent
- Depletion forces near curved surfaces
- Metastable Intermediates in the Condensation of Semiflexible Polymers
- Time scale of entropic segregation of flexible polymers in confinement: Implications for chromosome segregation in filamentous bacteria
- Physical descriptions of the bacterial nucleoid at large scales, and their biological implications
- Depletion potentials in highly size-asymmetric binary hard-sphere mixtures: Comparison of accurate simulation results with theory
- Hard sphere fluids in annular wedges: density distributions and depletion potentials
- Elongation/Compaction of Giant DNA Caused by Depletion Interaction with a Flexible Polymer
- Depletion force between two large spheres suspended in a bath of small spheres: Onset of the Derjaguin limit
- Coarse-Grained Molecular Dynamics Simulations of Depletion-Induced Interactions for Soft Matter Systems
- Depletion forces between non-spherical objects
- Theory of molecular crowding in Brownian hard-sphere liquids with application to the polymer coil-globule transition
- Quantifying the effects of neglecting many-body interactions in coarse-grained models of complex fluids