Biomolecular condensates enable spatial and temporal control over cellular processes by concentrating biomolecules into nonstoichiometric assemblies. Many condensates form via reversible phase transitions of condensate-specific multivalent macromolecules known as scaffolds. Phase transitions of scaffolds can be regulated by changing the concentrations of ligands, which are defined as nonscaffold molecules that bind to specific sites on scaffolds. Here, we use theory and computation to uncover rules that underlie ligand-mediated control over scaffold phase behavior. We use the stickers-and-spacers model wherein reversible noncovalent cross-links among stickers drive phase transitions of scaffolds, and spacers modulate the driving forces for phase transitions. We find that the modulatory effects of ligands are governed by the valence of ligands, whether they bind directly to stickers versus spacers, and the relative affinities of ligand–scaffold versus scaffold–scaffold interactions. In general, all ligands have a diluting effect on the concentration of scaffolds within condensates. Whereas monovalent ligands destabilize condensates, multivalent ligands can stabilize condensates by binding directly to spacers or destabilize condensates by binding directly to stickers. Bipartite ligands that bind to stickers and spacers can alter the structural organization of scaffold molecules within condensates even when they have a null effect on condensate stability. Our work highlights the importance of measuring dilute phase concentrations of scaffolds as a function of ligand concentration in cells. This can reveal whether ligands modulate scaffold phase behavior by enabling or suppressing phase separation at endogenous levels, thereby regulating the formation and dissolution of condensates in vivo.

生物分子凝聚物通过将生物分子浓缩到非化学计量组装中，实现对细胞过程的空间和时间控制。许多冷凝物通过称为支架的冷凝物特异性多价大分子的可逆相变形成。支架的相变可以通过改变配体的浓度来调节，配体被定义为与支架上特定位点结合的非支架分子。在这里，我们使用理论和计算来揭示配体介导的支架相行为控制的基础规则。我们使用贴纸和垫片模型，其中贴纸之间的可逆非共价交联驱动支架的相变，而垫片调节相变的驱动力。我们发现配体的调节作用受配体的价态支配，它们是否直接与贴纸或间隔物结合，以及配体-支架与支架-支架相互作用的相对亲和力。一般而言，所有配体对缩合物内的支架浓度具有稀释作用。单价配体会使缩合物​​不稳定，而多价配体可以通过直接与间隔物结合来稳定缩合物，或者通过直接与贴纸结合来使缩合物不稳定。与贴纸和间隔物结合的二分配体可以改变冷凝物中支架分子的结构组织，即使它们对冷凝物稳定性没有影响。我们的工作强调了测量支架稀释相浓度作为细胞中配体浓度的函数的重要性。