Thermodynamics and kinetics of phase separation of protein-RNA mixtures by a minimal model.

Abstract Intracellular liquid–liquid phase separation (LLPS) enables the formation of biomolecular condensates, such as ribonucleoprotein granules, which play a crucial role in the spatiotemporal organization of biomolecules (e.g., proteins and RNAs). Here, we introduce a patchy-particle–polymer model to investigate LLPS of protein–RNA mixtures. We demonstrate that, at low to moderate concentrations, RNA enhances the stability of RNA-binding protein (RBP) condensates because it increases the molecular connectivity of the condensed-liquid phase. Importantly, we find that RNA can also accelerate the nucleation stage of phase separation. Additionally, we asses how the capacity of RNA to increase the stability of condensates is modulated by the relative protein–protein/protein–RNA binding strengths. We find that phase separation and multiphase organization of multicomponent condensates is favored when the RNA binds with higher affinity to the lower valency proteins in the mixture, than to the cognate higher valency proteins. Collectively, our results shed light on the roles of RNA in ribonucleoprotein granule formation and the internal structuring of stress granules. SIGNIFICANCE The interior of cells contains several membraneless compartments that are composed of proteins and RNA. These compartments are formed and sustained by LLPS. Here, we introduce a minimal coarse-grained model to study LLPS of protein–RNA mixtures. We find that RNA can increase the stability of phase-separated compartments by enhancing the molecular connectivity of proteins. Additionally, our results show that RNA actively recruits proteins—accelerating the nucleation and fusion stages of LLPS. Interestingly, we find that spatial segregation within protein–RNA compartments is controlled by fine-tuning the interaction strengths and stoichiometries of components. Our model, therefore, provides a useful tool for building a comprehensive mechanistic and thermodynamic view of protein–RNA LLPS.