Physiochemical Mechanisms of Biomolecular Liquid-Liquid Phase Separation

The discoveries about the functions of biomolecular liquid-liquid phase separation in cell have been increased rapidly in the past decade. Condensates produced by phase separation play key roles in many cellular curial events. These biological functions are based on the physicochemical properties of phase separation. This review discusses the recent progress in understanding the physical and chemical mechanisms of biological liquid-liquid phase separation. (1) We summarized the basic properties and experimental characterization methods of phase separation droplets, including the morphology, fusion, and wetting, along with the dynamic properties of molecules in droplets, which are usually described by diffusion coefficients or viscosity and permeability. (2) We discussed the conditions affecting the liquid-liquid phase separation of biological molecules, including concentration, temperature, ionic strength, pH, and crowding effects. A database for liquid-liquid phase separation, LLPSDB, was introduced, and three types of nucleic acid concentration effects on the phase separation of protein molecules are discussed. These effects depend on the relative interaction strengths of protein-nucleic acid and protein-protein interactions. The major driving force of phase separation is multivalent interactions, and molecular flexibility is necessary for the dynamic properties. We summarized the diverse sources of multivalence, including multiple tandem repetitive domains, regular oligomerization, low-complexity domains (usually intrinsically disordered with repeat motifs for binding), and nucleic acid molecules via the main chain phosphates or repeat sequences. (3) We reviewed the statistical thermodynamics theories for describing the macromolecular liquid-liquid separation, including the Flory-Huggins theory, Overbeek-Voorn correction, random phase approximation method, and field theory simulation method. We discussed the experimental and simulation methods for studying the physiochemical mechanism of liquid-liquid phase separation. Model systems with simplified sequences for experimental studies were listed, including systems for studying the effects of charge properties, residue types, sequence length, and other properties. Molecular simulation methods can provide detailed information regarding the liquid-liquid phase separation process. We introduced two coarse-grain methods, the slab molecular dynamic simulation and Monte Carlo simulation using the lattice model. (4) The physiochemical properties of liquid-liquid phase separation govern the diverse functions of reversible phase transitions in a cell. We collected and analyzed important cases of biomolecular phase separation in cell activities. These biological functions were classified into five categories, including enrichment, sequestration, biological switching cooperation, localization, and mechanical force generation. We linked these functions with the physiochemical properties of liquid-liquid phase separation. To understand the specific phase-separation processes in biological activities, three types of related molecules must be studied: scaffold molecules mainly contributing to aggregate formation, recruited functional client molecules, and molecules that regulate the formation and disassembly of aggregates. We reviewed four regulation methods for the phase separation process, including changing the charge distribution by post-translational modification, changing the molecular concentration by gene expression or degradation regulation, changing the oligomerization state, and changing the cell solution environment (such as pH). Designing compounds for phase separation regulation has attracted significant attention for treating related diseases. Methods for discovering molecules that can regulate post-translational modifications or inhibit interactions in the droplets are emerging. The recently discovered phase separation phenomena and molecules in living organisms represent only the tip of the iceberg. In the future, it will be necessary to systematically examine liquid-liquid phase separation events and related molecules in all phases of biological processes.