Effects of molecular crowding and confinement on the spatial organization of a biopolymer

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_c-dependence of chain compaction differs between the two cases: a > a_c and a < a_c, where ϕ_c is the volume fraction of crowders, a is the monomer size, and a_c is the crowder size. For a > a_c (applicable to a coarse-grained model of bacterial chromosomes), chain size depends on the ratio aϕ_c/a_c, and "full" compaction occurs universally at aϕ_c/a_c ≈ 1; for a_c > a (relevant for protein folding), it is controlled by ϕ_c alone and crowding has a modest effect on chain size in a cellular environment (ϕ_c ≈ 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.