Simulating the chromatin mediated phase separation of model proteins with multiple domains
Data CreatorBrackley, Chris
PublisherUniversity of Edinburgh. School of Physics and Astronomy
Relation (Is Referenced By)https://arxiv.org/abs/2107.14518
MetadataShow full item record
CitationBrackley, Chris; Ancona, Marco. (2022). Simulating the chromatin mediated phase separation of model proteins with multiple domains, [dataset]. University of Edinburgh. School of Physics and Astronomy. https://doi.org/10.7488/ds/3474.
DescriptionSimulation data related to the paper "Simulating the chromatin mediated phase separation of model proteins with multiple domains". We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates which arise due to liquid-liquid phase separation, or a via a 'bridging-induced attraction' mechanism. We uncover a regime where protein droplets only form due to interaction with the polymer; here, unlike a standard phase separating system, droplet density rather than size varies with the overall protein concentration. We also observe that protein dynamics within droplets slow down as chromatin is absorbed. If the protein-protein interactions have a strictly limited valence, fractal or gel-like condensates are instead observed. Overall, our results provide biologically relevant insights into the general nature of protein-chromatin condensates in living cells.
Data from LAMMPS simulations of a simple multivalent protein model interacting with a polymer (1.015Gb)
Data from LAMMPS simulations of a simple limited valence protein model interacting with a polymer (4.313Gb)