Phase separation

In this issue we feature several articles that explore advances in the study of phase separation. They highlight some recently reported mechanistic features and progress in the methodology used to study it within cells, and they delve into the implications that phase separation has for select cellular functions.

Tanja Mittag talks to Nature Chemistry about how her path in research led to her work in phase separation and her thoughts about the future of the field.

High-throughput proteome-wide methods for identifying endogenous proteins that phase separate or partition into condensates during certain physiological events are needed but remain a challenge. Now, a high-throughput, unbiased and quantitative strategy can identify endogenous biomolecular condensates and screen proteins involved in phase separation on a proteome-wide scale.

We developed a high-throughput, unbiased strategy for the identification of endogenous biomolecular condensates by merging cell volume compression, sucrose density gradient centrifugation and quantitative mass spectrometry. We demonstrated the performance of this strategy by identifying both global condensate proteins and those responding to specific biological processes on a proteome-wide scale.

Cells spatially organize biochemical reactions within membrane-bound and membraneless compartments. The extent to which intrinsically disordered proteins themselves can form discrete compartments or condensed phases is poorly understood. Now a pair of model IDRs that display orthogonality in condensation and the chain features governing selective assembly have been identified.

The biomolecular principles underlying the formation of multiphasic condensates have been difficult to elucidate owing to a paucity of tools, especially within living cells. In this work synthetic orthogonal protein scaffolds alongside molecular simulations are used to highlight how the oligomerization of disordered proteins can asymmetrically drive miscibility–immiscibility transitions.

Liquid droplets form in cells to concentrate specific biomolecules (while excluding others) in order to perform specific functions. The molecular mechanisms that determine whether different macromolecules undergo co-partitioning or exclusion has so far remained elusive. Now, two studies uncover key principles underlying this selectivity.

Key molecular features that drive protein liquid–liquid phase separation (LLPS) for biomolecular condensate have been reported. A spectrum of additional interactions that influence protein LLPS and material properties have now been characterized. These interactions extend beyond a limited set of residue types and can be modulated by environmental factors such as temperature and salt concentration.

The underlying mechanism for how heterotypic protein–RNA interactions modulate the liquid to amyloid transition of hnRNPA1A, a protein involved in amyotrophic lateral sclerosis, has so far remained elusive. Now characterization of hnRNPA1A condensate formation and aggregation in vitro reveals that the RNA/protein stoichiometry affects the molecular pathways leading to amyloid formation.

The physicochemical driving forces of protein-free, RNA-driven phase transitions were previously unclear, but it is now shown that RNAs undergo entropically driven liquid–liquid phase separation upon heating in the presence of magnesium ions. In the condensed phase, RNAs can undergo an enthalpically favourable percolation transition that leads to arrested condensates.

Understanding of the molecular mechanisms underlying the maturation of protein condensates into amyloid fibrils associated with neurodegenerative diseases has so far remained elusive. Now it has been shown that in condensates formed by the low-complexity domain of the amyotrophic lateral sclerosis-associated protein hnRNPA1, fibril formation is promoted at the interface, which provides a potential therapeutic target for counteracting aberrant protein aggregation.

The mechanism of α-synuclein amyloid aggregation via liquid–liquid phase separation has so far remained elusive. Now, the existence of nanoscale clusters of α-synuclein in sub-saturated concentrations is observed using mass photometry. These nanoscale clusters can act as precursors to both macroscopic condensate droplets as well as amyloid fibrils.

Protein solutions can undergo liquid–liquid phase separation, by condensing into a dense phase that often resembles liquid droplets, which coexist with a dilute phase. Now it is shown that hydrophobic interactions, specifically at interfaces, can trigger a liquid–solid phase separation of a protein solution.