The synergic effect of water and biomolecules in intracellular phase separation

Abstract

Phase separation has long been observed within aqueous mixtures of two or more different compounds such as proteins, salts, polysaccharides and synthetic polymers. A growing body of experimental evidence indicates that phase separation also takes place inside living cells, where intrinsically disordered proteins and other molecules such as RNA are thought to assemble into membraneless organelles. These structures represent a new paradigm of intracellular organisation and compartmentalisation in which biochemical processes can be coordinated in space and time. Two thermodynamic driving forces have been proposed for phase separation: the strengths of macromolecule-macromolecule and macromolecule-H2O interactions, and the perturbation of H2O structure about different macromolecules. In this Perspective, we propose that both driving forces act in a concerted manner to promote phase separation, which we describe in the context of the well-known structural dynamics of intrinsically disordered proteins in the cellular milieu. We further suggest that this effect can be extended to explain how the partial unfolding of globular proteins can lead to intracellular phase separation.

Interface Engineering in Multiphase Systems toward Synthetic Cells and Organelles: From Soft Matter Fundamentals to Biomedical Applications

“…Intracellular environments are crowded by concentrated macromolecules, such as oligopeptides, oligonucleotides, oligosaccharides, proteins and nuclei acids. [26,29,30,63,207] Unfolded proteins, also named intrinsically disordered proteins (IDP), and nuclei acids can drive phase separation and spontaneously assemble into membraneless organelles, enabling the spatial and timely coordination of biochemical reactions. [26,63,64,[207][208][209] The phase separation of these molecules occurs when the interaction of certain molecules to each other is stronger than that to other components in the environments.…”

“…[26,29,30,63,207] Unfolded proteins, also named intrinsically disordered proteins (IDP), and nuclei acids can drive phase separation and spontaneously assemble into membraneless organelles, enabling the spatial and timely coordination of biochemical reactions. [26,63,64,[207][208][209] The phase separation of these molecules occurs when the interaction of certain molecules to each other is stronger than that to other components in the environments. [210,211] For instance, polyelectrolytes, such as polypeptides, nucleotides and polysaccharides, can phase separate driven by electrostatic interactions; [212] nonpolar macromolecular polymers and salts also can phase separate.…”

“…[62] In addition, the recent discovery of macromolecule crowding in living cells may contribute to the high efficiency of intracellular/ subcellular enzymatic reactions, thus stimulating enormous interests of coacervate droplets. [31][32][33][34][35][36][37][63][64][65][66][67][68][69] Moreover, the development in cell-inspired novel carriers for therapeutic nuclei acids and proteins has been progressed excitingly with translational successes. For a prosperous and interdisciplinary field like synthetic cells, there are reviews summarizing from specific aspects, for instance, tailoring appearance of synthetic cells, [2,[70][71][72] elucidating specific functions of synthetic cell modules, [2,71,73] which include adhesion, [58] growth, [57] energy regeneration/conversion, [4,[59][60][61] gene circuits, [56,74] and cellular interactions, [75][76][77] exclusively focusing on applications of synthetic compartments such as delivery carriers [10,18,[78][79][80][81][82][83][84][85]…”

Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions

“…LLPS is a thermodynamic process in which interacting multivalent proteins, and in many cases oligonucleotides, find a minimal free energy state through demixing into a protein-depleted diluted phase and a protein-enriched condensed phase (10)(11)(12). LLPS becomes thermodynamically favorable at biomolecular concentrations and in solution conditions where the enthalpy gain from the dynamic formation of weak attractive intermolecular interactions (13), and the increase in entropy associated with the release of water molecules from the biomolecules' surfaces to the bulk (14), become sufficient to overcome the entropy loss due to the reduced number of available microstates upon demixing (10)(11)(12). This observation raises key questions about the nature of the molecular interactions that govern protein LLPS and of the factors that modulate them.…”

Protein phase separation and determinants of in cell crystallization

“…LLPS is a phenomenon denoting the demixing of structurally different molecules in aqueous solution above a certain concentration, considering a distinct physicochemical environment . LLPS is known to be the primary process underlying, for example, the formation of stress granules, the nucleolus, or P bodies .…”