Response of Polymer Conformations to Crowded Environments

Quantifying the effects of macromolecular crowding on conformations of polymers is important for understanding the structure and function of macromolecules in cellular environments, e.g., biochemical reactions between biopolymers. To efficiently study conformations of crowded polymers in good solvents, we adopt a coarse-grained model of a polymer as a penetrable ellipsoid whose size and shape fluctuate according to the statistics of a self-avoiding walk [1]. We model the crowders as spherical particles that interact via Lennard-Jones or Yukawa pair potentials with hard cores that can penetrate the polymer at a cost in entropy predicted by polymer field theory. To compute the polymer shape distribution, radius of gyration, and asphericity, we perform Monte Carlo simulations, including trial displacements and trial changes in polymer conformation. By varying interactions between crowders, we find that with increasing strength of attraction, the polymer geometric properties settle towards their uncrowded limits as a result of clustering of the crowders. These results may offer insight into reaction rates and functions of folded proteins within cells.

[1] W. J. Davis and A. R. Denton, J. Chem. Phys. 149, 124901 (2018).