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

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