Simulating the chromatin mediated phase separation of model proteins with multiple domains

Marco Ancona, Chris A. Brackley*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

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. For proteins which interact multivalently, we obtain a phase diagram which includes liquid-like droplets, droplets with absorbed polymer, and coated polymer regimes. Of particular interest is 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. Together this provides biologically relevant insights into the nature of protein-chromatin condensates in living cells.
Original languageEnglish
Pages (from-to)2600-2612
Number of pages13
JournalBiophysical Journal
Volume121
Issue number13
Early online date27 May 2022
DOIs
Publication statusPublished - 5 Jul 2022

Keywords

  • cond-mat.soft
  • physics.bio-ph
  • physics.comp-ph
  • Chromatin
  • Polymers
  • Chromobox Protein Homolog 5

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