Topology-Encoded Polarity in Oppositely Charged Binary IDPP Condensates: Multiphase Organization from Non-Coacervating Partners as a Minimal Model of Complex Coacervation

Abstract

Synthetic condensates provide a way to engineer compartmentalized microenvironments that mimic the properties and functions of natural ones, yet the principles that govern their phase behavior and internal organization remain incompletely defined. Introducing charged residues into intrinsically disordered protein polymers (IDPPs) with LCST phase behavior typically suppresses phase separation under physiological conditions. Here we show that pairing two such oppositely charged IDPPs restores and programs LCST-driven liquid-liquid phase separation (LLPS), enabling a minimalist two-component platform for constructing synthetic condensates whose formation, size, and internal organization are encoded directly in sequence. LLPS emerges from an asymmetric, entropy-driven interplay between hydrophobic collapse, solvent reorganization, and salt-bridge topology. The balance between inter- and intrachain ionic pairing leads to distinct dense-phase microenvironments with tunable residual charge and micropolarity, thereby controlling condensate formation, and miscibility and the emergence of single-phase or multiphase protein condensates. The condensate interior further alters the ionization thermodynamics of charged residues shifting their apparent pKa and enabling tunable pH responses. Systems dominated by interchain salt bridges form low-polarity condensates that mix uniformly with hydrophobic partners, whereas molecular architectures favoring intrachain pairing retain residual charge and, in the presence of hydrophobic partners, undergo spontaneous internal demixing into multiphase assemblies. These findings establish a mechanistic, sequence-level framework for encoding phase behavior, micropolarity, and mesoscale organization in synthetic condensates, and demonstrate how minimalistic LCST-IDPP pairs can be engineered to create programmable microenvironments, opening avenues toward engineered condensates with higher-order organization and adaptive capabilities.