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 fc-dependence of chain compaction differs between the two cases. Chain size depends on the ratio a phi/ac, and ‘‘full’’ compaction occurs universally at a phi/ac; it is controlled by fc alone and crowding has a modest effect on chain size in a cellular environment. Also for a typical parameter range of biological relevance, molecular crowding can be viewed as effectively reducing the solvent quality, independent of confinement.