Effects of molecular crowding and confinement on the spatial organization of a biopolymer.
basic_science · Level V
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Abstract
A chain molecule can be entropically collapsed in a crowded medium in a free or confined space. Here, we present a unified view of how molecular crowding collapses a flexible polymer in three distinct spaces: free, cylindrical, and (two-dimensional) slit-like. Despite their seeming disparities, a few general features characterize all these cases, even though the ϕ<sub>c</sub>-dependence of chain compaction differs between the two cases: a > a<sub>c</sub> and a < a<sub>c</sub>, where ϕ<sub>c</sub> is the volume fraction of crowders, a is the monomer size, and a<sub>c</sub> is the crowder size. For a > a<sub>c</sub> (applicable to a coarse-grained model of bacterial chromosomes), chain size depends on the ratio aϕ<sub>c</sub>/a<sub>c</sub>, and "full" compaction occurs universally at aϕ<sub>c</sub>/a<sub>c</sub> ≈ 1; for a<sub>c</sub> > a (relevant for protein folding), it is controlled by ϕ<sub>c</sub> alone and crowding has a modest effect on chain size in a cellular environment (ϕ<sub>c</sub> ≈ 0.3). Also for a typical parameter range of biological relevance, molecular crowding can be viewed as effectively reducing the solvent quality, independent of confinement.