Speaker
Description
The interior of cells is a highly dense space in which macromolecules occupy a substantial fraction of the volume. Crowding effects have been shown to impact the conformations and diffusion of proteins, including polymer-like intrinsically disordered proteins. Here we study macromolecular crowding effects in a polymer system consisting of polyethylene glycol (PEG) and Ficoll, which acts as a crowder molecule. The goal of this research is to understand the chain compaction and reduced diffusion of PEG chains in the presence of a high volume fraction of crowders.
PEG is modeled as a bead-spring chain with additional angular and torsional interactions, as well as non-bonded Lennard-Jones interactions. Conformational sampling of the system is carried out using Langevin dynamics. The model is first parametrized with experimental data by tuning the nonbonded interaction strength to reproduce experimentally measured scaling of the radius of gyration, $R_g$, with the number of monomer units, $N$. Crowders are modeled as spheres of radius $R_c$, and their effect on $R_g$ is in terms of the ratio, $\lambda=R_g/R_c$, and further compared with their concentration, denoted by packing fraction $\phi_c$.
Simulation results reproduce key experimental trends: polymer dimensions are weakly affected when polymers and crowders are comparable in size ($\lambda\sim1$), while significant compression occurs for $\lambda>1$. By isolating individual parameters that are inaccessible in experiment, these simulations provide insight into how excluded-volume effects and crowding geometry contribute to polymer behavior in experiments. This work demonstrates the utility of CGMD simulations for bridging experiment and theory in crowded polymer systems and for improving coarse-grained models of macromolecular behavior in complex environments.
| Keyword-1 | PEG |
|---|---|
| Keyword-2 | crowders |
| Keyword-3 | molecular dynamics |