Biomolecular Chemistry in Liquid Phase Separated Compartments

Liquid-Liquid Phase Separation in Crowded Environments

Biomolecular condensates play a key role in organizing cellular fluids such as the cytoplasm and nucleoplasm. Most of these non-membranous organelles show liquid-like properties both in cells and when studied in vitro through liquid–liquid phase separation (LLPS) of purified proteins. In general, LLPS of proteins is known to be sensitive to variations in pH, temperature and ionic strength, but the role of crowding remains underappreciated. Several decades of research have shown that macromolecular crowding can have profound effects on protein interactions, folding and aggregation, and it must, by extension, also impact LLPS. However, the precise role of crowding in LLPS is far from trivial, as most condensate components have a disordered nature and exhibit multiple weak attractive interactions. Here, we discuss which factors determine the scope of LLPS in crowded environments, and we review the evidence for the impact of macromolecular crowding on phase boundaries, partitioning behavior and condensate properties. Based on a comparison of both in vivo and in vitro LLPS studies, we propose that phase separation in cells does not solely rely on attractive interactions, but shows important similarities to segregative phase separation.

Analysis of biomolecular condensates and protein phase separation with microfluidic technology

An increasing body of evidence shows that membraneless organelles are key components in cellular organization. These observations open a variety of outstanding questions about the physico-chemical rules underlying their assembly, disassembly and functions. Some molecular determinants of biomolecular condensates are challenging to probe and understand in complex in vivo systems. Minimalistic in vitro reconstitution approaches can fill this gap, mimicking key biological features, while maintaining sufficient simplicity to enable the analysis of fundamental aspects of biomolecular condensates. In this context, microfluidic technologies are highly attractive tools for the analysis of biomolecular phase transitions. In addition to enabling high-throughput measurements on small sample volumes, microfluidic tools provide for exquisite control of self-assembly in both time and space, leading to accurate quantitative analysis of biomolecular phase transitions. Here, with a specific focus on droplet-based microfluidics, we describe the advantages of microfluidic technology for the analysis of several aspects of phase separation. These include phase diagrams, dynamics of assembly and disassembly, rheological and surface properties, exchange of materials with the surrounding environment and the coupling between compartmentalization and biochemical reactions. We illustrate these concepts with selected examples, ranging from simple solutions of individual proteins to more complex mixtures of proteins and RNA, which represent synthetic models of biological membraneless organelles. Finally, we discuss how this technology may impact the bottom-up fabrication of synthetic artificial cells and for the development of synthetic protein materials in biotechnology.

Lipid sponge droplets as programmable synthetic organelles

Living cells segregate molecules and reactions in various subcellular compartments known as organelles. Spatial organization is likely essential for expanding the biochemical functions of synthetic reaction systems, including artificial cells. Many studies have attempted to mimic organelle functions using lamellar membrane-bound vesicles. However, vesicles typically suffer from highly limited transport across the membranes and an inability to mimic the dense membrane networks typically found in organelles such as the endoplasmic reticulum. Here, we describe programmable synthetic organelles based on highly stable nonlamellar sponge phase droplets that spontaneously assemble from a single-chain galactolipid and nonionic detergents. Due to their nanoporous structure, lipid sponge droplets readily exchange materials with the surrounding environment. In addition, the sponge phase contains a dense network of lipid bilayers and nanometric aqueous channels, which allows different classes of molecules to partition based on their size, polarity, and specific binding motifs. The sequestration of biologically relevant macromolecules can be programmed by the addition of suitably functionalized amphiphiles to the droplets. We demonstrate that droplets can harbor functional soluble and transmembrane proteins, allowing for the colocalization and concentration of enzymes and substrates to enhance reaction rates. Droplets protect bound proteins from proteases, and these interactions can be engineered to be reversible and optically controlled. Our results show that lipid sponge droplets permit the facile integration of membrane-rich environments and self-assembling spatial organization with biochemical reaction systems.

Enzymatic control over coacervation

The discovery of membraneless organelles (MLOs) formed by liquid-liquid phase separation raised many questions about the spatial organization of biomolecular processes in cells, but also offered a new tool to mimic cellular media. Since disordered and charged protein domains are often necessary for phase separation, coacervates can be used as models both to understand MLO regulation and to develop dynamic cellular-like compartments. A versatile way to turn passive coacervate droplets into active and dynamic compartments is by introducing enzymatic reactions that affect parameters relevant for complex coacervation, such as the charge and length of the components. However, these reactions strictly take place in a heterogeneous medium, and the complexity thereof is hardly addressed, making it difficult to achieve true control. In this chapter we help close this gap by describing two coacervate systems in which enzymatic reactions endow coacervate droplets with a dynamic character. We further highlight the technical challenges posed by the two-phase systems and strategies to overcome them.

A kinetic description of how interfaces accelerate reactions in micro-compartments

A kinetic expression is derived to explain how interfaces alter bulk chemical equilibria and accelerate reactions in micro-compartments. This description, aided by the development of a stochastic model, quantitatively predicts previous experimental observations of accelerated imine synthesis in micron-sized emulsions. The expression accounts for how reactant concentration and compartment size together lead to accelerated reaction rates under micro-confinement. These rates do not depend solely on concentration, but rather the fraction of total molecules in the compartment that are at the interface. Although there are ∼10⁷ to 10¹³ solute molecules in a typical micro-compartment, a kind of "stochasticity" appears when compartment size and reagent concentration yield nearly equal numbers of bulk and interfacial molecules. Although this is distinct from the stochasticity produced by nano-confinement, these results show how interfaces can govern chemical transformations in larger atmospheric, geologic and biological compartments.

Fission and Internal Fusion of Protocell with Membraneless "Organelles" Formed by Liquid-Liquid Phase Separation

Construction of protocells with hierarchical structures and living functions is still a great challenge. Growing evidence demonstrates that the membraneless organelles, which facilitate many essential cellular processes, are formed by RNA, protein, and other biopolymers via liquid-liquid phase separation (LLPS). The formation of the protocell in the early days of Earth could follow the same principle. In this work, we develop a novel coacervate-based protocell containing membraneless subcompartments via spontaneous liquid-liquid phase separation by simply mixing single-stranded oligonucleotides (ss-oligo), quaternized dextran (Q-dextran), and poly(l-lysine) (PLL) together. The resulting biphasic droplet, with PLL/ss-oligo phase being the internal subcompartments and Q-dextran/ss-oligo phase as the surrounding medium, is capable of sequestering and partitioning biomolecules into distinct regions. When the droplet is exposed to salt or Dextranase, the surrounding Q-dextran/ss-oligo phase will be gradually dissociated, resulting in the chaotic movement and fusion of internal subcompartments. Besides, the external electric field at a lower strength can drive the biphasic droplet to undergo a deviated circulation concomitant with the fusion of localized subcompartments, while a high-strength electric field can polarize the whole droplet, resulting in the release of daughter droplets in a controllable manner. Our study highlights that liquid-liquid phase separation of biopolymers is a powerful strategy to construct hierarchically structured protocells resembling the morphology and functions of living cells and provides a step toward a better understanding of the transition mechanism from nonliving to living matter under prebiotic conditions.

Reversible photocontrol of DNA coacervation

Coacervate micro-droplets produced by liquid-liquid phase separation are increasingly used to emulate the dynamical organization of membraneless organelles found in living cells. Designing synthetic coacervates able to be formed and disassembled with improved spatiotemporal control is still challenging. In this chapter, we describe the design of photoswitchable coacervate droplets produced by phase separation of short double stranded DNA in the presence of an azobenzene cation. The droplets can be reversibly dissolved with light, which provides a new approach for the spatiotemporal regulation of coacervation. Significantly, the dynamics of light-actuated droplet formation and dissolution correlates with the capture and release of guest solutes. The reported system can find applications for the dynamic photocontrol of biomolecule compartmentalization, paving the way to the light-activated regulation of signaling pathways in artificial membraneless organelles.

Enzymatic degradation of liquid droplets of DNA is modulated near the phase boundary

Biomolecules can undergo liquid-liquid phase separation (LLPS), forming dense droplets that are increasingly understood to be important for cellular function. Analogous systems are studied as early-life compartmentalization mechanisms, for applications as protocells, or as drug-delivery vehicles. In many of these situations, interactions between the droplet and enzymatic solutes are important to achieve certain functions. To explore this, we carried out experiments in which a model LLPS system, formed from DNA "nanostar" particles, interacted with a DNA-cleaving restriction enzyme, SmaI, whose activity degraded the droplets, causing them to shrink with time. By controlling adhesion of the DNA droplet to a glass surface, we were able to carry out time-resolved imaging of this "active dissolution" process. We found that the scaling properties of droplet shrinking were sensitive to the proximity to the dissolution ("boiling") temperature of the dense liquid: For systems far from the boiling point, enzymes acted only on the droplet surface, while systems poised near the boiling point permitted enzyme penetration. This was corroborated by the observation of enzyme-induced vacuole-formation ("bubbling") events, which can only occur through enzyme internalization, and which occurred only in systems poised near the boiling point. Overall, our results demonstrate a mechanism through which the phase stability of a liquid affects its enzymatic degradation through modulation of enzyme transport properties.

Site-Specific Detection of Arginine Methylation in Highly Repetitive Protein Motifs of Low Sequence Complexity by NMR

Post-translational modifications of proteins are widespread in eukaryotes. To elucidate the functional role of these modifications, detection methods need to be developed that provide information at atomic resolution. Here, we report on the development of a novel Arg-specific NMR experiment that detects the methylation status and symmetry of each arginine side chain even in highly repetitive RGG amino acid sequence motifs found in numerous proteins within intrinsically disordered regions. The experiment relies on the excellent resolution of the backbone H,N correlation spectra even in these low complexity sequences. It requires ¹³C, ¹⁵N labeled samples.

Simple Calculation of Phase Diagrams for Liquid-Liquid Phase Separation in Solutions of Two Macromolecular Solute Species

A simple method is described for the calculation of two- and three-dimensional phase diagrams describing stability and coexistence curves or surfaces separating one- and two-phase regions in composition/temperature space of a solution containing solute species 1 and 2. The calculation requires a quantitative description of the intermolecular potentials of mean force acting between like (1–1 and 2–2) and unlike (1–2) species. Example calculations are carried out for solutions of species interacting via spherically symmetric square-well potentials as first-order models for protein–protein interaction. When the interaction between species 1 and 2 is more repulsive than those acting between like species, the two-phase region is characterized by an equilibrium between a phase enriched in 1 and depleted in 2 and a phase enriched in 2 and depleted in 1. When the interaction between species 1 and 2 is more attractive than those acting between like species, the two-phase region is characterized by an equilibrium between a phase enriched in both species and a phase depleted in both species. The latter example provides a first-order description of coacervate formation without postulating specific interactions between the two solute species.

A guide to regulation of the formation of biomolecular condensates

Cellular organelles that lack a surrounding lipid bilayer, such as the nucleolus and stress granule, represent a newly recognized, general paradigm of cellular organization. The formation of such biomolecular condensates that include 'membraneless organelles' (MLOs) by liquid-liquid phase separation (LLPS) has been in the focus of a surge of recent studies. Through a combination of in vitro and in vivo approaches, thousands of potential phase-separating proteins have been identified, and it was found that different cellular MLOs share many common components. These perplexing observations raise the question of how cells regulate the timing and specificity of LLPS, and ensure that different MLOs form and disperse at the right moment and cellular location and can preserve their identity and physical separation. This guide gives an overview of basic regulatory mechanisms, which manifest through the action of intrinsic regulatory elements, alternative splicing, post-translational modifications, and a broad range of phase-separating partners. We also elaborate on the cellular integration of these different mechanisms and highlight how complex regulation can orchestrate the parallel functioning of a dozen or so different MLOs in the cell.

Solution NMR insights into dynamic supramolecular assemblies of disordered amyloidogenic proteins

The extraordinary flexibility and structural heterogeneity of intrinsically disordered proteins (IDP) make them functionally versatile molecules. We have now begun to better understand their fundamental role in biology, however many aspects of their behaviour remain difficult to grasp experimentally. This is especially true for the intermolecular interactions which lead to the formation of transient or highly dynamic supramolecular self-assemblies, such as oligomers, aggregation intermediates and biomolecular condensates. Both the emerging functions and pathogenicity of these structures have stimulated great efforts to develop methodologies capable of providing useful insights. Significant progress in solution NMR spectroscopy has made this technique one of the most powerful to describe structural and dynamic features of IDPs within such assemblies at atomic resolution. Here, we review the most recent works that have illuminated key aspects of IDP assemblies and contributed significant advancements towards our understanding of the complex conformational landscape of prototypical disease-associated proteins. We also include a primer on some of the fundamental and innovative NMR methods being used in the discussed studies.

Multiphase Complex Coacervate Droplets

Liquid-liquid phase separation plays an important role in cellular organization. Many subcellular condensed bodies are hierarchically organized into multiple coexisting domains or layers. However, our molecular understanding of the assembly and internal organization of these multicomponent droplets is still incomplete, and rules for the coexistence of condensed phases are lacking. Here, we show that the formation of hierarchically organized multiphase droplets with up to three coexisting layers is a generic phenomenon in mixtures of complex coacervates, which serve as models of charge-driven liquid-liquid phase separated systems. We present simple theoretical guidelines to explain both the hierarchical arrangement and the demixing transition in multiphase droplets using the interfacial tensions and critical salt concentration as inputs. Multiple coacervates can coexist if they differ sufficiently in macromolecular density, and we show that the associated differences in critical salt concentration can be used to predict multiphase droplet formation. We also show that the coexisting coacervates present distinct chemical environments that can concentrate guest molecules to different extents. Our findings suggest that condensate immiscibility may be a very general feature in biological systems, which could be exploited to design self-organized synthetic compartments to control biomolecular processes.

Formation of Multiphase Complex Coacervates and Partitioning of Biomolecules within them

Biological systems employ liquid-liquid phase separation to localize macromolecules and processes. The properties of intracellular condensates that allow for multiple, distinct liquid compartments and the impact of their coexistence on phase composition and solute partitioning are not well understood. Here, we generate two and three coexisting macromolecule-rich liquid compartments by complex coacervation based on ion pairing in mixtures that contain two or three polyanions together with one, two, or three polycations. While in some systems polyelectrolyte order-of-addition was important to achieve coexisting liquid phases, for others it was not, suggesting that the observed multiphase droplet morphologies are energetically favorable. Polyelectrolytes were distributed across all coacervate phases, depending on the relative interactions between them, which in turn impacted partitioning of oligonucleotide and oligopeptide solutes. These results show the ease of generating multiphase coacervates and the ability to tune their partitioning properties via the polyelectrolyte sharing inherent to multiphase complex coacervate systems.

Multi-Step Concanavalin A Phase Separation and Early-Stage Nucleation Monitored Via Dynamic and Depolarized Light Scattering

Protein phase separation and protein liquid cluster formation have been observed and analysed in protein crystallization experiments and, in recent years, have been reported more frequently, especially in studies related to membraneless organelles and protein cluster formation in cells. A detailed understanding about the phase separation process preceding liquid dense cluster formation will elucidate what has, so far, been poorly understood—despite intracellular crowding and phase separation being very common processes—and will also provide more insights into the early events of in vitro protein crystallization. In this context, the phase separation and crystallization kinetics of concanavalin A were analysed in detail, which applies simultaneous dynamic light scattering and depolarized dynamic light scattering to obtain insights into metastable intermediate states between the soluble phase and the crystalline form. A multi-step mechanism was identified for ConA phase separation, according to the resultant ACF decay, acquired after an increase in the concentration of the crowding agent until a metastable ConA gel intermediate between the soluble and final crystalline phases was observed. The obtained results also revealed that ConA is trapped in a macromolecular network due to short-range intermolecular protein interactions and is unable to transform back into a non-ergodic solution.

The model of local axon homeostasis - explaining the role and regulation of microtubule bundles in axon maintenance and pathology

Axons are the slender, cable-like, up to meter-long projections of neurons that electrically wire our brains and bodies. In spite of their challenging morphology, they usually need to be maintained for an organism's lifetime. This makes them key lesion sites in pathological processes of ageing, injury and neurodegeneration. The morphology and physiology of axons crucially depends on the parallel bundles of microtubules (MTs), running all along to serve as their structural backbones and highways for life-sustaining cargo transport and organelle dynamics. Understanding how these bundles are formed and then maintained will provide important explanations for axon biology and pathology. Currently, much is known about MTs and the proteins that bind and regulate them, but very little about how these factors functionally integrate to regulate axon biology. As an attempt to bridge between molecular mechanisms and their cellular relevance, we explain here the model of local axon homeostasis, based on our own experiments in Drosophila and published data primarily from vertebrates/mammals as well as C. elegans. The model proposes that (1) the physical forces imposed by motor protein-driven transport and dynamics in the confined axonal space, are a life-sustaining necessity, but pose a strong bias for MT bundles to become disorganised. (2) To counterbalance this risk, MT-binding and -regulating proteins of different classes work together to maintain and protect MT bundles as necessary transport highways. Loss of balance between these two fundamental processes can explain the development of axonopathies, in particular those linking to MT-regulating proteins, motors and transport defects. With this perspective in mind, we hope that more researchers incorporate MTs into their work, thus enhancing our chances of deciphering the complex regulatory networks that underpin axon biology and pathology.

Driving Forces of Liquid-Liquid Phase Separation in Biological Systems

Analysis of liquid–liquid phase separation in biological systems shows that this process is similar to the phase separation observed in aqueous two-phase systems formed by nonionic polymers, proteins, and polysaccharides. The emergence of interfacial tension is a necessary condition of phase separation. The situation in this regard is similar to that of phase separation in mixtures of partially miscible solvents. It is suggested that the evaluation of the effects of biological macromolecules on the solvent properties of aqueous media and the measurement of the interfacial tension as a function of these solvent properties may be more productive for gaining insights into the mechanism of liquid–liquid phase separation than the study of structural details of proteins and RNAs engaged in the process.

Dynamic Synthetic Cells Based on Liquid-Liquid Phase Separation

Living cells have long been a source of inspiration for chemists. Their capacity of performing complex tasks relies on the spatiotemporal coordination of matter and energy fluxes. Recent years have witnessed growing interest in the bottom-up construction of cell-like models capable of reproducing aspects of such dynamic organisation. Liquid-liquid phase-separation (LLPS) processes in water are increasingly recognised as representing a viable compartmentalisation strategy through which to produce dynamic synthetic cells. Herein, we highlight examples of the dynamic properties of LLPS used to assemble synthetic cells, including their biocatalytic activity, reversible condensation and dissolution, growth and division, and recent directions towards the design of higher-order structures and behaviour.