Compaction and clustering of a heterogeneous polymer by biomolecular crowding

Abstract

Inspired by bacterial chromosome organization, we study the compaction and clustering of a heterogeneous ring polymer in a crowded medium using molecular dynamics simulations. The polymer consists of several large monomers interspersed along the backbone and small intervening monomers. In a crowded medium, the entropy of crowding particles or crowders favors the collapse of chain molecules, such as chromosomes. Our study shows that the compaction transition of heterogeneous polymers by crowders is well-correlated with the clustering of large monomers: when the large monomers are sufficiently large, both occur concomitantly in the same narrow (biologically relevant) range of the volume fraction of crowders. It also indicates that cylindrical confinement makes crowding effects more effective. The results presented here suggest that phase separation and clustering are essential features of bacterial chromosome organization.