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 that arise due to liquid-liquid phase separation, or a via a “bridging-induced attraction” mechanism. For proteins that 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. A specific example that inspired our model is heterochromatin protein 1, or HP1. Recent in vivo experiments have shown that HP1 exhibits similar droplet size buffering behavior as our simulations. Overall, our results provide biologically relevant insights into the general nature of protein-chromatin condensates in living cells.

我们对包含简单模型蛋白质和代表染色质的聚合物的系统进行模拟。我们研究蛋白质-蛋白质和蛋白质-染色质相互作用之间的相互作用，以及由于液-液相分离或通过“桥联诱导吸引”机制而产生的冷凝物。对于多价相互作用的蛋白质，我们获得了一个相图，其中包括液体状液滴、吸收聚合物的液滴和涂覆的聚合物状态。特别令人感兴趣的是蛋白质液滴仅由于与聚合物相互作用而形成的状态；在这里，与标准相分离系统不同，液滴密度而不是尺寸随总体蛋白质浓度变化。我们还观察到，随着染色质被吸收，液滴内的蛋白质动力学减慢。如果蛋白质-蛋白质相互作用具有严格限制的价态，则会观察到分形或凝胶状凝聚物。启发我们模型的一个具体例子是异染色质蛋白 1，即 HP1。最近的体内实验表明，HP1 表现出与我们的模拟相似的液滴尺寸缓冲行为。总的来说，我们的结果为活细胞中蛋白质-染色质凝聚物的一般性质提供了生物学相关的见解。