Valency and Binding Affinity Variations Can Regulate the Multilayered Organization of Protein Condensates with Many Components

Biomolecular condensates, which assemble via the process of liquid–liquid phase separation (LLPS), are multicomponent compartments found ubiquitously inside cells. Experiments and simulations have shown that biomolecular condensates with many components can exhibit multilayered organizations. Using a minimal coarse-grained model for interacting multivalent proteins, we investigate thermodynamic parameters governing formation through changes in protein valency binding affinity. We focus on formed by scaffold proteins (high-valency separate their own homotypic interactions) clients (proteins recruited to heterotypic scaffold–client interactions). demonstrate higher species sequestered center while lower cluster towards condensate interface. Such architecture maximizes density LLPS-stabilizing molecular interactions, simultaneously reducing surface tension condensates. In addition, rapid exchanges low out, keeping proteins—the key biomolecules involved nucleation—mostly within. also how modulating affinities among different significantly transform its structure, even trigger fission into multiple droplets compositions.