Controlling biomolecular condensates via chemical reactions

Affinity-Controlled Partitioning of Biomolecules at Aqueous Interfaces and Their Bioanalytic Applications

All-aqueous phase separation systems play essential roles in bioanalytical and biochemical applications. Compared to conventional oil and organic solvent-based systems, these systems are characterized by their rich bulk and interfacial properties, offering superior biocompatibility. In particular, phase separation in all-aqueous systems facilitates the creation of compartments with specific physicochemical properties, and therefore largely enhances the accessibility of the systems. In addition, the all-aqueous compartments have diverse affinities, with an important property known as partitioning, which can concentrate (bio)molecules toward distinct immiscible phases. This partitioning affinity imparts all-aqueous interfaces with selective permeability, enabling the controlled enrichment of target (bio)molecules. This review introduces the basic principles and applications of partitioning-induced interfacial phenomena in a typical all-aqueous system, namely aqueous two-phase systems (ATPSs); these applications include interfacial chemical reactions, bioprinting, and assembly, as well as bio-sensing and detection. The primary challenges associated with designing all-aqueous phase separation systems and several future directions are also discussed, such as the stabilization of aqueous interfaces, the handling of low-volume samples, and exploration of suitable ATPSs compositions with the efficient protocol.

Nonequilibrium phases of a biomolecular condensate facilitated by enzyme activity

Biomolecular condensates represent a frontier in cellular organization, existing as dynamic materials driven out of equilibrium by active cellular processes. Here we explore active mechanisms of condensate regulation by examining the interplay between DEAD-box helicase activity and RNA base-pairing interactions within ribonucleoprotein condensates. We demonstrate how the ATP-dependent activity of DEAD-box helicases-a key class of enzymes in condensate regulation-acts as a nonequilibrium driver of condensate properties through the continuous remodeling of RNA interactions. By combining the LAF-1 DEAD-box helicase with a designer RNA hairpin concatemer, we unveil a complex landscape of dynamic behaviors, including time-dependent alterations in RNA partitioning, evolving condensate morphologies, and shifting condensate dynamics. Importantly, we reveal an antagonistic relationship between RNA secondary structure and helicase activity which promotes condensate homogeneity via a nonequilibrium steady state. By elucidating these nonequilibrium mechanisms, we gain a deeper understanding of cellular organization and expand the potential for active synthetic condensate systems.

Chemically reactive and aging macromolecular mixtures I: Phase diagrams, spinodals, and gelation

Multicomponent macromolecular mixtures often form higher-order structures, which may display non-ideal mixing and aging behaviors. In this work, we first propose a minimal model of a quaternary system that takes into account the formation of a complex via a chemical reaction involving two macromolecular species; the complex may then phase separate from the buffer and undergo a further transition into a gel-like state. We subsequently investigate how physical parameters such as molecular size, stoichiometric coefficients, equilibrium constants, and interaction parameters affect the phase behavior of the mixture and its propensity to undergo aging via gelation. In addition, we analyze the thermodynamic stability of the system and identify the spinodal regions and their overlap with gelation boundaries. The approach developed in this work can be readily generalized to study systems with an arbitrary number of components. More broadly, it provides a physically based starting point for the investigation of the kinetics of the coupled complex formation, phase separation, and gelation processes in spatially extended systems.

Heterogeneous nucleation and growth of sessile chemically active droplets

Droplets are essential for spatially controlling biomolecules in cells. To work properly, cells need to control the emergence and morphology of droplets. On the one hand, driven chemical reactions can affect droplets profoundly. For instance, reactions can control how droplets nucleate and how large they grow. On the other hand, droplets coexist with various organelles and other structures inside cells, which could affect their nucleation and morphology. To understand the interplay of these two aspects, we study a continuous field theory of active phase separation. Our numerical simulations reveal that reactions suppress nucleation while attractive walls enhance it. Intriguingly, these two effects are coupled, leading to shapes that deviate substantially from the spherical caps predicted for passive systems. These distortions result from anisotropic fluxes responding to the boundary conditions dictated by the Young-Dupré equation. Interestingly, an electrostatic analogy of chemical reactions confirms these effects. We thus demonstrate how driven chemical reactions affect the emergence and morphology of droplets, which could be crucial for understanding biological cells and improving technical applications, e.g., in chemical engineering.

Nucleic acid liquids

The confluence of recent discoveries of the roles of biomolecular liquids in living systems and modern abilities to precisely synthesize and modify nucleic acids (NAs) has led to a surge of interest in liquid phases of NAs. These phases can be formed primarily from NAs, as driven by base-pairing interactions, or from the electrostatic combination (coacervation) of negatively charged NAs and positively charged molecules. Generally, the use of sequence-engineered NAs provides the means to tune microsopic particle properties, and thus imbue specific, customizable behaviors into the resulting liquids. In this way, researchers have used NA liquids to tackle fundamental problems in the physics of finite valence soft materials, and to create liquids with novel structured and/or multi-functional properties. Here, we review this growing field, discussing the theoretical background of NA liquid phase separation, quantitative understanding of liquid material properties, and the broad and growing array of functional demonstrations in these materials. We close with a few comments discussing remaining open questions and challenges in the field.

Emerging experimental methods to study the thermodynamics of biomolecular condensate formation

The formation of biomolecular condensates in vivo is increasingly recognized to underlie a multitude of crucial cellular functions. Furthermore, the evolution of highly dynamic protein condensates into progressively less reversible assemblies is thought to be involved in a variety of disorders, from cancer over neurodegeneration to rare genetic disorders. There is an increasing need for efficient experimental methods to characterize the thermodynamics of condensate formation and that can be used in screening campaigns to identify and rationally design condensate modifying compounds. Theoretical advances in the field are also identifying the key parameters that need to be measured in order to obtain a comprehensive understanding of the underlying interactions and driving forces. Here, we review recent progress in the development of efficient and quantitative experimental methods to study the driving forces behind and the temporal evolution of biomolecular condensates.

Chemical reaction motifs driving non-equilibrium behaviours in phase separating materials

Chemical reactions that couple to systems that phase separate have been implicated in diverse contexts from biology to materials science. However, how a particular set of chemical reactions (chemical reaction network, CRN) would affect the behaviours of a phase separating system is difficult to fully predict theoretically. In this paper, we analyse a mean field theory coupling CRNs to a combined system of phase separating and non-phase separating materials and analyse how the properties of the CRNs affect different classes of non-equilibrium behaviour: microphase separation or temporally oscillating patterns. We examine the problem of achieving microphase separated condensates by statistical analysis of the Jacobians, of which the most important motifs are negative feedback of the phase separating component and combined inhibition/activation by the non-phase separating components. We then identify CRN motifs that are likely to yield microphase by examining randomly generated networks and parameters. Molecular sequestration of the phase separating motif is shown to be the most robust towards yielding microphase separation. Subsequently, we find that dynamics of the phase separating species is promoted most easily by inducing oscillations in the diffusive components coupled to the phase separating species. Our results provide guidance towards the design of CRNs that manage the formation, dissolution and organization of compartments.

Nonequilibrium interfacial properties of chemically driven fluids

Chemically driven fluids can demix to form condensed droplets that exhibit phase behaviors not observed at equilibrium. In particular, nonequilibrium interfacial properties can emerge when the chemical reactions are driven differentially between the interior and exterior of the phase-separated droplets. Here, we use a minimal model to study changes in the interfacial tension between coexisting phases away from equilibrium. Simulations of both droplet nucleation and interface roughness indicate that the nonequilibrium interfacial tension can either be increased or decreased relative to its equilibrium value, depending on whether the driven chemical reactions are accelerated or decelerated within the droplets. Finally, we show that these observations can be understood using a predictive theory based on an effective thermodynamic equilibrium.

Nonequilibrium design strategies for functional colloidal assemblies

We use a nonequilibrium variational principle to optimize the steady-state, shear-induced interconversion of self-assembled nanoclusters of DNA-coated colloids. Employing this principle within a stochastic optimization algorithm allows us to identify design strategies for functional materials. We find that far-from-equilibrium shear flow can significantly enhance the flux between specific colloidal states by decoupling trade-offs between stability and reactivity required by systems in equilibrium. For isolated nanoclusters, we find nonequilibrium strategies for amplifying transition rates by coupling a given reaction coordinate to the background shear flow. We also find that shear flow can be made to selectively break detailed balance and maximize probability currents by coupling orientational degrees of freedom to conformational transitions. For a microphase consisting of many nanoclusters, we study the flux of colloids hopping between clusters. We find that a shear flow can amplify the flux without a proportional compromise on the microphase structure. This approach provides a general means of uncovering design principles for nanoscale, autonomous, functional materials driven far from equilibrium.

Nonideal Reaction-Diffusion Systems: Multiple Routes to Instability

We develop a general classification of the nature of the instabilities yielding spatial organization in open nonideal reaction-diffusion systems, based on linear stability analysis. This encompasses dynamics where chemical species diffuse, interact with each other, and undergo chemical reactions driven out of equilibrium by external chemostats. We find analytically that these instabilities can be of two types: instabilities caused by intermolecular energetic interactions (E type), and instabilities caused by multimolecular out-of-equilibrium chemical reactions (R type). Furthermore, we identify a class of chemical reaction networks, containing unimolecular networks but also extending beyond them, that can only undergo E-type instabilities. We illustrate our analytical findings with numerical simulations on two reaction-diffusion models, each displaying one of the two types of instability and generating stable patterns.

Phase Transitions of Associative Biomacromolecules

Multivalent proteins and nucleic acids, collectively referred to as multivalent associative biomacromolecules, provide the driving forces for the formation and compositional regulation of biomolecular condensates. Here, we review the key concepts of phase transitions of aqueous solutions of associative biomacromolecules, specifically proteins that include folded domains and intrinsically disordered regions. The phase transitions of these systems come under the rubric of coupled associative and segregative transitions. The concepts underlying these processes are presented, and their relevance to biomolecular condensates is discussed.

Physical interactions in non-ideal fluids promote Turing patterns

Turing's mechanism is often invoked to explain periodic patterns in nature, although direct experimental support is scarce. Turing patterns form in reaction-diffusion systems when the activating species diffuse much slower than the inhibiting species, and the involved reactions are highly nonlinear. Such reactions can originate from cooperativity, whose physical interactions should also affect diffusion. We here take direct interactions into account and show that they strongly affect Turing patterns. We find that weak repulsion between the activator and inhibitor can substantially lower the required differential diffusivity and reaction nonlinearity. By contrast, strong interactions can induce phase separation, but the resulting length scale is still typically governed by the fundamental reaction-diffusion length scale. Taken together, our theory connects traditional Turing patterns with chemically active phase separation, thus describing a wider range of systems. Moreover, we demonstrate that even weak interactions affect patterns substantially, so they should be incorporated when modelling realistic systems.

Nucleation of Chemically Active Droplets

Driven chemical reactions can control the macroscopic properties of droplets, like their size. Such active droplets are critical in structuring the interior of biological cells. Cells also need to control where and when droplets appear, so they need to control droplet nucleation. Our numerical simulations demonstrate that reactions generally suppress nucleation if they stabilize the homogeneous state. An equilibrium surrogate model reveals that reactions increase the effective energy barrier of nucleation, enabling quantitative predictions of the increased nucleation times. Moreover, the surrogate model allows us to construct a phase diagram, which summarizes how reactions affect the stability of the homogeneous phase and the droplet state. This simple picture provides accurate predictions of how driven reactions delay nucleation, which is relevant for understanding droplets in biological cells and chemical engineering.

Theory and Simulation of Multiphase Coexistence in Biomolecular Mixtures

Biomolecular condensates constitute a newly recognized form of spatial organization in living cells. Although many condensates are believed to form as a result of phase separation, the physicochemical properties that determine the phase behavior of heterogeneous biomolecular mixtures are only beginning to be explored. Theory and simulation provide invaluable tools for probing the relationship between molecular determinants, such as protein and RNA sequences, and the emergence of phase-separated condensates in such complex environments. This review covers recent advances in the prediction and computational design of biomolecular mixtures that phase-separate into many coexisting phases. First, we review efforts to understand the phase behavior of mixtures with hundreds or thousands of species using theoretical models and statistical approaches. We then describe progress in developing analytical theories and coarse-grained simulation models to predict multiphase condensates with the molecular detail required to make contact with biophysical experiments. We conclude by summarizing the challenges ahead for modeling the inhomogeneous spatial organization of biomolecular mixtures in living cells.

Designing negative feedback loops in enzymatic coacervate droplets

Membraneless organelles within the living cell use phase separation of biomolecules coupled with enzymatic reactions to regulate cellular processes. The diverse functions of these biomolecular condensates motivate the pursuit of simpler in vitro models that exhibit primitive forms of self-regulation based on internal feedback mechanisms. Here, we investigate one such model based on complex coacervation of the enzyme catalase with an oppositely charge polyelectrolyte DEAE-dextran to form pH-responsive catalytic droplets. Upon addition of hydrogen peroxide "fuel", enzyme activity localized within the droplets causes a rapid increase in the pH. Under appropriate conditions, this reaction-induced pH change triggers coacervate dissolution owing to its pH-responsive phase behavior. Notably, this destabilizing effect of the enzymatic reaction on phase separation depends on droplet size owing to the diffusive delivery and removal of reaction components. Reaction-diffusion models informed by the experimental data show that larger drops support larger changes in the local pH thereby enhancing their dissolution relative to smaller droplets. Together, these results provide a basis for achieving droplet size control based on negative feedback between pH-dependent phase separation and pH-changing enzymatic reactions.

Developments in describing equilibrium phase transitions of multivalent associative macromolecules

Biomolecular condensates are distinct cellular bodies that form and dissolve reversibly to organize cellular matter and biochemical reactions in space and time. Condensates are thought to form and dissolve under the influence of spontaneous and driven phase transitions of multivalent associative macromolecules. These include phase separation, which is defined by segregation of macromolecules from the solvent or from one another, and percolation or gelation, which is an inclusive networking transition driven by reversible associations among multivalent macromolecules. Considerable progress has been made to model sequence-specific phase transitions, especially for intrinsically disordered proteins. Here, we summarize the state-of-the-art of theories and computations aimed at understanding and modeling sequence-specific, thermodynamically controlled, coupled associative and segregative phase transitions of archetypal multivalent macromolecules.

Enzyme-Enriched Condensates Show Self-Propulsion, Positioning, and Coexistence

Enzyme-enriched condensates can organize the spatial distribution of their substrates by catalyzing nonequilibrium reactions. Conversely, an inhomogeneous substrate distribution induces enzyme fluxes through substrate-enzyme interactions. We find that condensates move toward the center of a confining domain when this feedback is weak. Above a feedback threshold, they exhibit self-propulsion, leading to oscillatory dynamics. Moreover, catalysis-driven enzyme fluxes can lead to interrupted coarsening, resulting in equidistant condensate positioning, and to condensate division.

Tuning Nucleation Kinetics via Nonequilibrium Chemical Reactions

Unlike fluids at thermal equilibrium, biomolecular mixtures in living systems can sustain nonequilibrium steady states, in which active processes modify the conformational states of the constituent molecules. Despite qualitative similarities between liquid-liquid phase separation in these systems, the extent to which the phase-separation kinetics differ remains unclear. Here we show that inhomogeneous chemical reactions can alter the nucleation kinetics of liquid-liquid phase separation in a manner that is consistent with classical nucleation theory, but can only be rationalized by introducing a nonequilibrium interfacial tension. We identify conditions under which nucleation can be accelerated without changing the energetics or supersaturation, thus breaking the correlation between fast nucleation and strong driving forces that is typical of phase separation and self-assembly at thermal equilibrium.

Effective simulations of interacting active droplets

Droplets form a cornerstone of the spatiotemporal organization of biomolecules in cells. These droplets are controlled using physical processes like chemical reactions and imposed gradients, which are costly to simulate using traditional approaches, like solving the Cahn-Hilliard equation. To overcome this challenge, we here present an alternative, efficient method. The main idea is to focus on the relevant degrees of freedom, like droplet positions and sizes. We derive dynamical equations for these quantities using approximate analytical solutions obtained from a sharp interface limit and linearized equations in the bulk phases. We verify our method against fully-resolved simulations and show that it can describe interacting droplets under the influence of chemical reactions and external gradients using only a fraction of the computational costs of traditional methods. Our method can be extended to include other processes in the future and will thus serve as a relevant platform for understanding the dynamics of droplets in cells.

Formation of dissipative structures in microscopic models of mixtures with species interconversion

The separation of substances into different phases is ubiquitous in nature and important scientifically and technologically. This phenomenon may become drastically different if the species involved, whether molecules or supramolecular assemblies, interconvert. In the presence of an external force large enough to overcome energetic differences between the interconvertible species (forced interconversion), the two alternative species will be present in equal amounts, and the striking phenomenon of steady-state, restricted phase separation into mesoscales is observed. Such microphase separation is one of the simplest examples of dissipative structures in condensed matter. In this work, we investigate the formation of such mesoscale steady-state structures through Monte Carlo and molecular dynamics simulations of three physically distinct microscopic models of binary mixtures that exhibit both equilibrium (natural) interconversion and a nonequilibrium source of forced interconversion. We show that this source can be introduced through an internal imbalance of intermolecular forces or an external flux of energy that promotes molecular interconversion, possible manifestations of which could include the internal nonequilibrium environment of living cells or a flux of photons. The main trends and observations from the simulations are well captured by a nonequilibrium thermodynamic theory of phase transitions affected by interconversion. We show how a nonequilibrium bicontinuous microemulsion or a spatially modulated state may be generated depending on the interplay between diffusion, natural interconversion, and forced interconversion.

Size distributions of intracellular condensates reflect competition between coalescence and nucleation

Phase separation of biomolecules into condensates has emerged as a mechanism for intracellular organization and affects many intracellular processes, including reaction pathways through the clustering of enzymes and pathway intermediates. Precise and rapid spatiotemporal control of reactions by condensates requires tuning of their sizes. However, the physical processes that govern the distribution of condensate sizes remain unclear. Here we show that both native and synthetic condensates display an exponential size distribution, which is captured by Monte Carlo simulations of fast nucleation followed by coalescence. In contrast, pathological aggregates exhibit a power-law size distribution. These distinct behaviours reflect the relative importance of nucleation and coalescence kinetics. We demonstrate this by utilizing a combination of synthetic and native condensates to probe the underlying physical mechanisms determining condensate size. The appearance of exponential distributions for abrupt nucleation versus power-law distributions under continuous nucleation may reflect a general principle that determines condensate size distributions.

Enhanced DNA repair through droplet formation and p53 oscillations

Living organisms are constantly exposed to DNA damage, and optimal repair is therefore crucial. A characteristic hallmark of the response is the formation of sub-compartments around the site of damage, known as foci. Following multiple DNA breaks, the transcription factor p53 exhibits oscillations in its nuclear concentration, but how this dynamics can affect the repair remains unknown. Here, we formulate a theory for foci formation through droplet condensation and discover how oscillations in p53, with its specific periodicity and amplitude, optimize the repair process by preventing Ostwald ripening and distributing protein material in space and time. Based on the theory predictions, we reveal experimentally that the oscillatory dynamics of p53 does enhance the repair efficiency. These results connect the dynamical signaling of p53 with the microscopic repair process and create a new paradigm for the interplay of complex dynamics and phase transitions in biology.

Mesoscale structure-function relationships in mitochondrial transcriptional condensates

In live cells, phase separation is thought to organize macromolecules into membraneless structures known as biomolecular condensates. Here, we reconstituted transcription in condensates from purified mitochondrial components using optimized in vitro reaction conditions to probe the structure-function relationships of biomolecular condensates. We find that the core components of the mt-transcription machinery form multiphasic, viscoelastic condensates in vitro. Strikingly, the rates of condensate-mediated transcription are substantially lower than in solution. The condensate-mediated decrease in transcriptional rates is associated with the formation of vesicle-like structures that are driven by the production and accumulation of RNA during transcription. The generation of RNA alters the global phase behavior and organization of transcription components within condensates. Coarse-grained simulations of mesoscale structures at equilibrium show that the components stably assemble into multiphasic condensates and that the vesicles formed in vitro are the result of dynamical arrest. Overall, our findings illustrate the complex phase behavior of transcribing, multicomponent condensates, and they highlight the intimate, bidirectional interplay of structure and function in transcriptional condensates.

Catalysis-Induced Phase Separation and Autoregulation of Enzymatic Activity

We present a thermodynamically consistent model describing the dynamics of a multicomponent mixture where one enzyme component catalyzes a reaction between other components. We find that the catalytic activity alone can induce phase separation for sufficiently active systems and large enzymes, without any equilibrium interactions between components. In the limit of fast reaction rates, binodal lines can be calculated using a mapping to an effective free energy. We also explain how this catalysis-induced phase separation can act to autoregulate the enzymatic activity, which points at the biological relevance of this phenomenon.

Growth, replication and division enable evolution of coacervate protocells

Living and proliferating cells undergo repeated cycles of growth, replication and division, all orchestrated by complex molecular networks. How a minimal cell cycle emerged and helped primitive cells to evolve remains one of the biggest mysteries in modern science, and is an active area of research in chemistry. Protocells are cell-like compartments that recapitulate features of living cells and may be seen as the chemical ancestors of modern life. While compartmentalization is not strictly required for primitive, open-ended evolution of self-replicating systems, it gives such systems a clear identity by setting the boundaries and it can help them overcome three major obstacles of dilution, parasitism and compatibility. Compartmentalization is therefore widely considered to be a central hallmark of primitive life, and various types of protocells are actively investigated, with the ultimate goal of developing a protocell capable of autonomous proliferation by mimicking the well-known cell cycle of growth, replication and division. We and others have found that coacervates are promising protocell candidates in which chemical building blocks required for life are naturally concentrated, and chemical reactions can be selectively enhanced or suppressed. This feature article provides an overview of how growth, replication and division can be realized with coacervates as protocells and what the bottlenecks are. Considerations are given for designing chemical networks in coacervates that can lead to sustained growth, selective replication and controlled division, in a way that they are linked together like in the cell cycle. Ultimately, such a system may undergo evolution by natural selection of certain phenotypes, leading to adaptation and the gain of new functions, and we end with a brief discussion of the opportunities for coacervates to facilitate this.

Evolved interactions stabilize many coexisting phases in multicomponent liquids

Phase separation has emerged as an essential concept for the spatial organization inside biological cells. However, despite the clear relevance to virtually all physiological functions, we understand surprisingly little about what phases form in a system of many interacting components, like in cells. Here we introduce a numerical method based on physical relaxation dynamics to study the coexisting phases in such systems. We use our approach to optimize interactions between components, similar to how evolution might have optimized the interactions of proteins. These evolved interactions robustly lead to a defined number of phases, despite substantial uncertainties in the initial composition, while random or designed interactions perform much worse. Moreover, the optimized interactions are robust to perturbations, and they allow fast adaption to new target phase counts. We thus show that genetically encoded interactions of proteins provide versatile control of phase behavior. The phases forming in our system are also a concrete example of a robust emergent property that does not rely on fine-tuning the parameters of individual constituents.

Field theory description of ion association in re-entrant phase separation of polyampholytes

Phase separation of several different overall neutral polyampholyte species (with zero net charge) is studied in solution with two oppositely charged ion species that can form ion-pairs through an association reaction. A field theory description of the system, that treats polyampholyte charge sequence dependent electrostatic interactions as well as excluded volume effects, is hereby given. Interestingly, analysis of the model using random phase approximation and field theoretic simulation consistently show evidence of a re-entrant polyampholyte phase separation at high ion concentrations when there is an overall decrease of volume upon ion-association. As an illustration of the ramifications of our theoretical framework, several polyampholyte concentration vs ion concentration phase diagrams under constant temperature conditions are presented to elucidate the dependence of phase separation behavior on polyampholyte sequence charge pattern as well as ion-pair dissociation constant, volumetric effects on ion association, solvent quality, and temperature.

RNA at the surface of phase-separated condensates impacts their size and number

While it is now recognized that specific RNAs and protein families are critical for the biogenesis of ribonucleoprotein (RNP) condensates, how these molecular constituents determine condensate size and morphology is unknown. To circumvent the biochemical complexity of endogenous RNP condensates, the use of programmable tools to reconstitute condensate formation with minimal constituents can be instrumental. Here we report a methodology to form RNA-containing condensates in living cells programmed to specifically recruit a single RNA species. Our bioengineered condensates are made of ArtiGranule scaffolds composed of an orthogonal protein that can bind to a specific heterologously expressed RNA. These scaffolds undergo liquid-liquid phase separation in cells and can be chemically controlled to prevent condensation or to trigger condensate dissolution. We found that the targeted RNAs localize at the condensate surface, either as isolated RNA molecules or as a homogenous corona of RNA molecules around the condensate. The recruitment of RNA changes the material properties of condensates by hardening the condensate body. Moreover, the condensate size scales with RNA surface density; the higher the RNA density, the smaller and more frequent the condensates. These results suggest a mechanism based on physical constraints, provided by RNAs at the condensate surface, that limit condensate growth and coalescence.

What are the distinguishing features and size requirements of biomolecular condensates and their implications for RNA-containing condensates?

Exciting recent work has highlighted that numerous cellular compartments lack encapsulating lipid bilayers (often called "membraneless organelles"), and that their structure and function are central to the regulation of key biological processes, including transcription, RNA splicing, translation, and more. These structures have been described as "biomolecular condensates" to underscore that biomolecules can be significantly concentrated in them. Many condensates, including RNA granules and processing bodies, are enriched in proteins and nucleic acids. Biomolecular condensates exhibit a range of material states from liquid- to gel-like, with the physical process of liquid-liquid phase separation implicated in driving or contributing to their formation. To date, in vitro studies of phase separation have provided mechanistic insights into the formation and function of condensates. However, the link between the often micron-sized in vitro condensates with nanometer-sized cellular correlates has not been well established. Consequently, questions have arisen as to whether cellular structures below the optical resolution limit can be considered biomolecular condensates. Similarly, the distinction between condensates and discrete dynamic hub complexes is debated. Here we discuss the key features that define biomolecular condensates to help understand behaviors of structures containing and generating RNA.

Phase separation in fluids with many interacting components

Fluids in natural systems, like the cytoplasm of a cell, often contain thousands of molecular species that are organized into multiple coexisting phases that enable diverse and specific functions. How interactions between numerous molecular species encode for various emergent phases is not well understood. Here, we leverage approaches from random-matrix theory and statistical physics to describe the emergent phase behavior of fluid mixtures with many species whose interactions are drawn randomly from an underlying distribution. Through numerical simulation and stability analyses, we show that these mixtures exhibit staged phase-separation kinetics and are characterized by multiple coexisting phases at steady state with distinct compositions. Random-matrix theory predicts the number of coexisting phases, validated by simulations with diverse component numbers and interaction parameters. Surprisingly, this model predicts an upper bound on the number of phases, derived from dynamical considerations, that is much lower than the limit from the Gibbs phase rule, which is obtained from equilibrium thermodynamic constraints. We design ensembles that encode either linear or nonmonotonic scaling relationships between the number of components and coexisting phases, which we validate through simulation and theory. Finally, inspired by parallels in biological systems, we show that including nonequilibrium turnover of components through chemical reactions can tunably modulate the number of coexisting phases at steady state without changing overall fluid composition. Together, our study provides a model framework that describes the emergent dynamical and steady-state phase behavior of liquid-like mixtures with many interacting constituents.

Size conservation emerges spontaneously in biomolecular condensates formed by scaffolds and surfactant clients

Biomolecular condensates are liquid-like membraneless compartments that contribute to the spatiotemporal organization of proteins, RNA, and other biomolecules inside cells. Some membraneless compartments, such as nucleoli, are dispersed as different condensates that do not grow beyond a certain size, or do not present coalescence over time. In this work, using a minimal protein model, we show that phase separation of binary mixtures of scaffolds and low-valency clients that can act as surfactants-i.e., that significantly reduce the droplet surface tension-can yield either a single drop or multiple droplets that conserve their sizes on long timescales (herein 'multidroplet size-conserved' scenario'), depending on the scaffold to client ratio. Our simulations demonstrate that protein connectivity and condensate surface tension regulate the balance between these two scenarios. The multidroplet size-conserved scenario spontaneously arises at increasing surfactant-to-scaffold concentrations, when the interfacial penalty for creating small liquid droplets is sufficiently reduced by the surfactant proteins that are preferentially located at the interface. In contrast, low surfactant-to-scaffold concentrations enable continuous growth and fusion of droplets without restrictions. Overall, our work proposes one thermodynamic mechanism to help rationalize how size-conserved coexisting condensates can persist inside cells-shedding light on the roles of protein connectivity, binding affinity, and droplet composition in this process.