Intrinsically disordered proteins and liquid-liquid phase separation: Molecular grammar, condensate physiology, and...

Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) of proteins constitute a substantial and functionally critical fraction of the eukaryotic proteome. Through multivalent, low-affinity interactions encoded in their low-complexity domains (LCDs), IDPs drive liquid-liquid phase separation (LLPS)-a physicochemical process that produces membraneless biomolecular condensates serving as dynamic reaction hubs within cells. Recent advances have substantially refined the conceptual framework governing condensate biophysics: the phase separation coupled to percolation (PSCP) model now recognizes that condensates are viscoelastic network fluids arising from the synergy between density transitions and connectivity (percolation) transitions, rather than simple LLPS alone. This updated mechanistic understanding, combined with proteome-wide computational tools and AI-driven prediction models, is rapidly transforming the field. Physiologically, condensates regulate transcription at super-enhancers, modulate RNA metabolism in stress granules, and orchestrate ribosome biogenesis in the nucleolus. Pathologically, aberrant liquid-to-solid transitions of disease-associated IDPs-including TDP-43 and FUS in amyotrophic lateral sclerosis and frontotemporal dementia, tau in Alzheimer's disease, and α-synuclein in Parkinson's disease-represent a convergent pathomechanism across neurodegenerative proteinopathies. Post-translational modifications, particularly phosphorylation, arginine methylation, and ubiquitination, function as a dynamic regulatory code controlling condensate assembly and dissolution. The emerging paradigm of condensate-modifying therapeutics (c-mods) identifies biomolecular condensates as druggable entities and proposes four mechanistic strategies-dissolvers, inducers, localizers, and morphers-to restore normal phase behavior in disease. This review integrates the most current molecular, cellular, and biomedical insights into IDP-driven phase separation, highlighting open questions and translational opportunities.