Simulating the entropic collapse of coarse-grained chromosomes

Area of Science:

• Biophysics
• Computational Biology
• Molecular Modeling

Background:

• Depletion forces are known to influence chromosomal material compaction in cells.
• The sufficiency of depletion forces for causing chromosomal collapse remains a subject of debate.

Purpose of the Study:

• To investigate whether depletion forces alone are sufficient to induce chromosomal collapse.
• To model the behavior of supercoiled DNA in the presence of depletants using computational methods.

Main Methods:

• Coarse-grained molecular dynamics simulations were employed.
• An explicit computational model treated DNA monomers and protein crowding agents as truncated Lennard-Jones spheres.
• A theoretical model quantified depletant effects as effective solvent quality.

Main Results:

• Depletion-induced attraction was found to be sufficient for collapsing a flexible chain of large monomers in a depletant bath.
• Simulations demonstrated a rapid, continuous phase transition corresponding to chromosome collapse at a specific depletant volume fraction.
• The collapse was identified as a continuous phase transition.

Conclusions:

• Depletion forces are adequate to drive bacterial chromosome collapse in simplified models.
• Achieving a first-order phase transition for collapse would necessitate incorporating additional factors like enthalpic interactions or chain rigidity.