Simulating the Entropic Collapse of Coarse-Grained Chromosomes

Tyler N. Shendruk, Martin Bertrand, Hendrick W. de Haan, James L. Harden, Gary W. Slater

Research output: Contribution to journalArticlepeer-review

Abstract

Depletion forces play a role in the compaction and decompaction of chromosomal material in simple cells, but it has remained 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 continuous 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.
Original languageEnglish
Pages (from-to)810-820
Number of pages11
JournalBiophysical Journal
Volume108
Issue number4
DOIs
Publication statusPublished - 17 Feb 2015

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