A Molecular Grammar for Programmable Multiphase Protein–RNA Vesicles

Protein-RNA phase separation gives rise to biomolecular condensates with rich internal organization, yet the molecular rules that connect sequence-encoded interactions to the emergent condensate spatial organization remain poorly understood. Here, using large-scale residue-level coarse-grained simulations, we identify a molecular grammar that governs the formation of multiphase protein-RNA condensates. We show that asymmetries in protein-protein and protein-RNA interactions, together with protein stoichiometry, chain length, and condensate density, collectively determine whether condensates adopt homogeneous, layered, biphasic, or vesicle-like morphologies. Vesicular condensates form spontaneously from well-mixed initial conditions without requiring flux-driven oversaturation or extreme charge imbalance, distinguishing this mechanism from previously proposed routes to condensate hollowing. We rationalize the full morphological progression as sequence-encoded amphiphile self-assembly: the protein-RNA complex behaves as a single-chain amphiphile whose effective packing parameter is set by Domain H/L stoichiometry, spanning micelles, cylinders, hollow vesicles, and inverse phases.