Entropic Collapse of Coarse-Grained Chromosomes

Figure 1
Illustration by David Goodsell from Chromosome, Cell Cycle, and Entropy.

Entropy can be tricky to understand, but one rule often quoted in pop-culture is that entropy increases as time goes on, which leads to more and more disorder. Depletion forces can therefore be surprising since they seem to break this rule-of-thumb; the depletion force is an entropically induced attraction between large colloids due many smaller surrounding “depletant” particles. By bringing the large colloids together, the attraction orders the larger colloids but this is at the benefit of the many small depletants, which gain increased entropy and are more disordered.

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Such entropic forces exist in biological systems. For example, depletion forces lead to fibre bundling, aggregation of red blood cells, and change the reaction kinetics of polymerase chain reactions. They are also ubiquitous in the complex and crowded interior of cells.

Prior to our work, it was hypothesized that depletion forces acting on chromosomes in simple bacteria by surrounding cytoplasmic proteins could explain the collapse from a swollen conformation to a compact state. We performed simulations to explicitly test whether depletion-induced attraction is actually enough to collapse model chromosomes. The resulting simulations gave us strong evidence that depletion effects are enough to collapse chromosomes; however, this collapse is a continuous phase transition rather than a discontinuous one (as is seen in experiments). This suggests that some proteins must act in specific biological ways (rather than as generic depletants) to fully account for the compaction of nucleoids.

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To read more, see our paper on the entropic collapse of coarse-grained chromosomes, or a News and Views by Suckjoon Jun discussing our work.

 

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