Open questions on liquid-liquid phase separation

Stabilization of Condensate Interfaces Using Dynamic Protein Insertion

Coacervates have been widely used to mimic membraneless organelles (MLOs). However, coacervates without a membrane or stabilizing surface do not feature the same level of stability as MLOs. This study shows that specifically engineered surface-active proteins can interact with the interface of polypeptide coacervates, conferring resistance to coacervate dissolution and fusion. Modulating the molecular characteristics of these coacervate stabilizing proteins highlighted that their dimerization aids in achieving effective interface stabilizers. Cryo-TEM imaging showed a densely packed protein monolayer at the coacervate-liquid interface, while single-molecule super-resolution microscopy captured the dynamic nature of this protein layer, with the proteins rapidly (un)docking and moving across the coacervate interface within milliseconds. These findings suggest a dynamic form of coacervate stabilization driven by transient protein interactions at the condensate interface. This unique form of coacervate stabilization not only provides a new approach to developing stable and dynamically exchanging synthetic condensate systems but, as model systems, can also significantly contribute to our understanding of the mechanisms underlying the temporal stability of MLOs in nature.

Uncovering the Molecular Interactions Underlying MBD2 and MBD3 Phase Separation

Chromatin organization controls DNA's accessibility to regulatory factors to influence gene expression. Heterochromatin, or transcriptionally silent chromatin enriched in methylated DNA and methylated histone tails, self-assembles through multivalent interactions with its associated proteins into a condensed, but dynamic state. Liquid-liquid phase separation (LLPS) of key heterochromatin regulators, such as heterochromatin protein 1 (HP1), plays an essential role in heterochromatin assembly and function. Methyl-CpG-binding protein 2 (MeCP2), the most studied member of the methyl-CpG-binding domain (MBD) family of proteins, has been recently shown to undergo LLPS in the absence and presence of methylated DNA. These studies provide a new mechanistic framework for understanding the role of methylated DNA and its readers in heterochromatin formation. However, the details of the molecular interactions by which other MBD family members undergo LLPS to mediate genome organization and transcriptional regulation are not fully understood. Here, we focus on two MBD proteins, MBD2 and MBD3, that have distinct but interdependent roles in gene regulation. Using an integrated computational and experimental approach, we uncover the homotypic and heterotypic interactions governing MBD2 and MBD3 phase separation and DNA's influence on this process. We show that despite sharing the highest sequence identity and structural homology among all the MBD protein family members, MBD2 and MBD3 exhibit differing residue patterns resulting in distinct phase separation mechanisms. Understanding the molecular underpinnings of MBD protein condensation offers insights into the higher-order, LLPS-mediated organization of heterochromatin.

Phase separation in DNA repair: orchestrating the cellular response to genomic stability

DNA repair is a hierarchically organized, spatially and temporally regulated process involving numerous repair factors that respond to various types of damage. Despite decades of research, the mechanisms by which these factors are recruited to and depart from repair sites have been a subject of intrigue. Recent advancements in the field have increasingly highlighted the role of phase separation as a critical facilitator of the efficiency of DNA repair. This review emphasizes how phase separation enhances the concentration and coordination of repair factors at damage sites, optimizing repair efficiency. Understanding how dysregulation of phase separation can impair DNA repair and alter nuclear organization, potentially leading to diseases such as cancer and neurodegenerative disorders, is crucial. This manuscript provides a comprehensive understanding of the pivotal role of phase separation in DNA repair, sheds light on the current research, and suggests potential future directions for research and therapeutic interventions.

Alternating Binary Droplets-Based Protocell Networks Driven by Heterogeneous Liquid-Liquid Phase Separation

As the emergence of prototissues promotes the evolutionary transformations of protolife, tissue-like networks derived from cytomimetic systems have been studied by using artificial cells as building blocks to mimic prototissues at a higher organizational level. However, liquid-like networks originating from liquid-liquid phase separation (LLPS), especially heterogeneous LLPS, are less reported. Herein, we report a binary liquid droplet-based protocell network composed of coacervates and aqueous two-phase systems (ATPS) droplets arranged in an alternating sequence, integrating both associative and segregative LLPS. This network with worm-like chains can be specifically achieved only when the attached droplets are partially engulfed, mediated by the interfacial tension between coacervate and ATPS droplets. Notably, the interconnected droplets within the network are capable of spatially self-sorting of biomacromolecules into separate domains, thereby facilitating biomacromolecular extraction and biological reactions within designated droplets. Upon changes in the external environment, the network can be reconfigured to enable morphological regulation of trienzymatic cascade reactions. Overall, this work highlights that an all-aqueous network, coupling both associative and segregative LLPS, can be engineered as a possible route toward a hybrid prototissue-like system, offering new insights into the design of higher-ordered biomimetic systems utilizing liquid soft matter.

Localized assembly in biological activity: Origin of life and future of nanoarchitectonics

The concept of nanoarchitectonics has emerged as a post-nanotechnology paradigm in the field of functional materials development. This concept entails the construction of functional material systems at the nanoscale, based on the knowledge acquired from nanotechnology. In biological systems, advanced nanoarchitectonics is achieved through precise structural organization governed by spatial localization, a process facilitated by localized assembly mechanisms. A thorough understanding of the principles of localized assembly is crucial for the creation of complex, asymmetric, hierarchical organizations that are similar in structure and function to living organisms. This review explores the concept of localized assembly, highlighting its biological inspiration, providing representative examples, and discussing its contributions to nanoarchitectonics. Key examples include assemblies using biological materials, those mimicking cellular functions, and those occurring within cells. Additionally, the role of interfacial interactions and liquid-liquid phase separation in localized assembly is emphasized. Particularly, the utilization of liquid-liquid phase separation demonstrates a remarkable capacity for forming intricate compartmentalized structures without discernible membranes, paving the way for multifunctional, localized systems. These localized assemblies are fundamental to essential biological functions and provide valuable insights into the molecular mechanisms underlying the origin of cells and life. Such understanding holds significant promise for advancing materials nanoarchitectonics, particularly in biomedical applications.

Dynamic Duos: Coacervate-Lipid Membrane Interactions in Regulating Membrane Transformation and Condensate Size

Biomolecular condensates interfacing with lipid membranes is crucial for several key cellular functions. However, the role of lipid membranes in regulating condensates in cells remains obscure. Here, in-depth interactions between condensates and lipid membranes are probed and unraveled by employing cell-mimetic systems like Giant unilamellar vesicles (GUVs). An unprecedented influence of the coacervate size and their electrostatic interaction with lipid membranes is revealed on the membrane properties and deformation. Importantly, these findings demonstrate that the large relative size of coacervates and minimal electrostatic interaction strength with membranes allow for budding transitions at the interface. Membranes act as nucleation site for coacervates when the charge-charge interaction is high, giving a wrinkled vesicle surface appearance. Molecular diffusion property of lipids, quantified using Fluorescence recovery after photobleaching (FRAP), is modulated at the coacervate-membrane interaction site restricting the coarsening of coacervates. Notably, these results reveal coacervate droplets are intertwined in between membrane folds and invaginations discerned using Transmission electron microscopy (TEM) and high-resolution imaging, which further controls the dimension of droplets resembling size distributions observed in cells. Finally, these findings provide mechanistic insights of lipid bilayers controlling condensate sizes that play a prominent role in comprehending nucleation and localization of cellular condensates.

Multiphasic protein condensation governed by shape and valency

Liquid-liquid phase separation (LLPS) of biological macromolecules leads to the formation of various membraneless organelles. The multilayered and multiphasic form of LLPS can mediate complex cellular functions; however, the determinants of its topological features are not fully understood. Herein, we focus on synaptic proteins consisting of Ca2+/calmodulin-dependent protein kinase II (CaMKII) and its interacting partners and present a computational model that reproduces forms of LLPS, including a form of two-phase condensates, phase-in-phase (PIP) organization. The model analyses reveal that the PIP formation requires competitive binding between the proteins. The PIP forms only when CaMKII has high valency and a short linker length. Such CaMKII exhibits low surface tension, a modular structure, and slow diffusion, enabling it to stay in small biochemical domains for a long time, which is necessary for synaptic plasticity. Thus, the computational modeling reveals new structure-function relationships for CaMKII as a synaptic memory unit.

Universal membranization of synthetic coacervates and biomolecular condensates towards ultrastability and spontaneous emulsification

Membranization of membraneless coacervates and condensates is emerging as a promising strategy to resolve their inherent susceptibility to fusion, ripening and environmental variations. Yet current membranization agents by design are largely limited to a subclass or a specific kind of coacervate or condensate systems. Here we develop a library of condensate-amphiphilic block polymers that can efficiently form a polymeric layer on the droplet interface for a wide spectrum of synthetic coacervates and biomolecular condensates. Condensate-amphiphilic block polymers are designed with a condenophilic block firmly anchored to the condensed phase, a condenophobic block extended to the dilute phase and a self-association block to promote membrane formation. Critical to our design is the condenophilic block of phenylboronic acid and amidoamine that target the disparate chemistry of condensed droplets via multivalent affinities. The condensate-amphiphilic block polymer membranes render the droplets mechanically robust against fusion, regulate interfacial properties such as permeability and stiffness, and substantially improve droplet tolerance to challenging conditions of temperature, salinity, pH and organic solvents.

Acetylation of Short Glycopeptides Enables Phase Separation

Liquid-liquid phase separation (LLPS) of biomacromolecules is crucial for regulating cellular functions. To explore their molecular mechanisms, peptide-based coacervates mimicking natural proteins have been developed, but the role of side chain modifications such as glycosylation remains underexplored. Here, we demonstrate that acetylation of short glycopeptides can induce pH- and concentration-dependent phase separation, while removing acetyl groups abolishes this behavior. Circular dichroism spectroscopy revealed a strong link between peptide structural ordering and the phase separation propensity. Peptides capable of forming liquid droplets displayed a significant ellipticity change at 205 nm upon changing solution pH. Moreover, these peptide coacervates can interact with cells and enhance the antiproliferative property of doxorubicin. Therefore, this work highlights the critical role of O-acetylation in LLPS and provides a valuable tool for studying the parameters regulating LLPS and its implications in cellular processes.

Nanoscale Hydrophobicity of Transport Barriers in the Nuclear Pore Complex as Compared with the Liquid/Liquid Interface by Scanning Electrochemical Microscopy

The nuclear pore complex (NPC) is the proteinous nanopore that solely regulates molecular transport between the nucleus and cytoplasm of a eukaryotic cell. Hypothetically, the NPC utilizes the hydrophobic barriers based on the repeats of phenylalanine-glycine (FG) units to selectively and efficiently transport macromolecules. Herein, we quantitatively assess the hydrophobicity of transport barriers confined in the nanopore by applying scanning electrochemical microscopy (SECM). The hypothesis deduced from studies of isolated FG-rich nucleoporins is supported quantitatively by investigating the authentic NPC for the first time. Specifically, we employ the n repeats of neurotoxic glycine-arginine dipeptide, GRn, as the molecular probes that engage in hydrophobic interactions with transport barriers in the NPC. We apply ion-transfer voltammetry at a micropipet-supported interface between aqueous and organic electrolyte solutions to confirm that larger GRn among n = 5-25 is more hydrophobic, as expected theoretically. The micropipet also serves as the tip of transient SECM to demonstrate that the NPC interacts more strongly with larger GRn, which supports the hydrophobicity of transport barriers. Kinetically, larger GRn stays in the NPC for longer to clog the nanopore, thereby expressing neurotoxicity. Significantly, this work implies that the efficient and safe nuclear import of genetic therapeutics requires an optimum balance between strong association with and fast dissociation from the NPC. Interestingly, this work represents the unexplored utility of liquid/liquid interfaces as models of hydrophobic protein condensates based on liquid-liquid phase separation as exemplified by nanoscale transport barriers in the NPC.

Microscopic and stochastic simulations of chemically active droplets

Biomolecular condensates play a central role in the spatial organization of living matter. Their formation is now well understood as a form of liquid-liquid phase separation that occurs very far from equilibrium. For instance, they can be modeled as active droplets, where the combination of molecular interactions and chemical reactions result in microphase separation. However, so far, models of chemically active droplets are spatially continuous and deterministic. Therefore, the relationship between the microscopic parameters of the models and some crucial properties of active droplets (such as their polydispersity, their shape anisotropy, or their typical lifetime) is yet to be established. In this work, we address this question computationally, using Brownian dynamics simulations of chemically active droplets: the building blocks are represented explicitly as particles that interact with attractive or repulsive interactions, depending on whether they are in a droplet-forming state or not. Thanks to this microscopic and stochastic view of the problem, we reveal how driving the system away from equilibrium in a controlled way determines the fluctuations and dynamics of active emulsions.

Peptides for Liquid-Liquid Phase Separation: An Emerging Biomaterial

Liquid-liquid phase separation (LLPS) refers to a spontaneous separation behavior of biomacromolecules under specific physiological conditions, playing a crucial role in regulating various biological processes. Recent advances in synthetic peptides have greatly improved our understanding of peptide-based coacervate droplets and expanded their applications in biomedicine. Numerous peptide sequences have been reported that undergo phase separation, enabling the concentration and sequestration of different guest molecules for purposes such as drug delivery, catalytic performance, and bioanalytical techniques. Particularly, some of these peptides offer significant advantages in controlled drug release, efficient cell transfection, accelerated reaction kinetics, and selective biomarker detection. This review provides an overview of recent developments in peptide-based LLPS, exploring various strategies for designing peptide sequences and their biomedical applications. It also addresses the challenges and future directions for LLPS peptide vehicles as promising biomaterials.

Membraneless Compartmentalization of Cell-Free Transcription-Translation by Polymer-Assisted Liquid-Liquid Phase Separation

Living cells use liquid-liquid phase separation (LLPS) to compartmentalize metabolic functions into mesoscopic-sized droplets. Deciphering the mechanisms at play in LLPS is therefore critical to understanding the structuration and functions of cells at the subcellular level. Although observed and achieved to a significant degree of control in vivo, the reconstitution of LLPS integrating advanced biological functions, such as gene expression, has been so far limited in vitro. LLPS of cell-free transcription-translation (TXTL) reactions require multi-step experimental approaches that lack biomimetic and have relatively poor efficacy, thus limiting their usage in cell-free engineered systems such as synthetic cells. Here the polymer-assisted LLPS of TXTL reactions are reported as the single-pot one-step compartmentalization of a model complex metabolic system obtain without using solvents or surfactants. LLPS occurs by adding the biocompatible polymers poly(ethylene glycol), poly(vinyl alcohol), and dextran to a TXTL reaction, that remains highly active. These polymers serve as partitioning agents that localize TXTL in mesoscopic-sized droplets rich in dextran. Cytoplasmic and membrane-interacting proteins are synthesized preferentially inside these droplets, and localize either uniformly or preferentially at the interface, depending on their nature. The LLPS-TXTL system presented in this work is a step toward the design of synthetic membraneless active organelles.

Coacervate Droplets as Biomimetic Models for Designing Cell-Like Microreactors

Coacervates are versatile compartments formed by liquid-liquid phase separation. Their dynamic behavior and molecularly crowded microenvironment make them ideal materials for creating cell-like systems such as synthetic cells and microreactors. Recently, combinations of synthetic and natural molecules have been exploited via simple or complex coacervation to create compartments that can be used to build hierarchical chemical systems with life-like properties. This review highlights recent advances in the design of coacervate compartments and their application as biomimetic compartments for the design of cell-like chemical reactors and cell mimicking systems. It first explores the variety of materials used for coacervation and the influence of their chemical structure on their controlled dynamic behavior. Then, the applications of coacervates as cell-like systems are reviewed, focusing on how they can be used as cell-like microreactors through their ability to sequester molecules and provide a distinct and regulatory microenvironment for chemical reactions in aqueous media.

Spatial Control over Reactions via Localized Transcription within Membraneless DNA Nanostar Droplets

Biomolecular condensates control where and how fast many chemical reactions occur in cells by partitioning reactants and catalysts, enabling simultaneous reactions in different spatial locations of a cell. Even without a membrane or physical barrier, the partitioning of the reactants can affect the rates of downstream reaction cascades in ways that depend on reaction location. Such effects can enable systems of biomolecular condensates to spatiotemporally orchestrate chemical reaction networks in cells to facilitate complex behaviors such as ribosome assembly. Here, we develop a system for developing such control in synthetic systems. We localize different transcription templates within different phase-separated, membraneless DNA nanostar (NS) droplets─programmable, in vitro liquid-liquid phase separation systems for partitioning of substrates and localization of reactions to membraneless droplets. When RNA produced within such droplets is also degraded in the bulk, droplet-localized transcription creates RNA concentration gradients. Consistent with the formation of these gradients, toehold-mediated strand displacement reactions involving transcripts are 2-fold slower far from the site of transcription than when nearby. We then demonstrate how multiple such gradients can form and be maintained independently by simultaneous transcription reactions occurring in tandem, each localized to different NS droplet types. Our results provide a means for constructing reaction systems in which different reactions are spatially localized and controlled without the need for physical membranes. This system also provides a means for generally studying how localized reactions and the exchange of reaction products might occur between protocells.

How Salt and Temperature Drive Reentrant Condensation of Aβ40

Within the framework of liquid-liquid phase separation (LLPS), biomolecular condensation orchestrates vital cellular processes, and its dysregulation is implicated in severe pathological conditions. Recent studies highlight the role of intrinsically disordered proteins (IDPs) in LLPS, yet the influence of microenvironmental factors has remained a puzzling factor. Here, via computational simulation of the impact of solution conditions on LLPS behavior of neurologically pathogenic IDP Aβ40, we chanced upon a salt-driven reentrant condensation phenomenon, wherein Aβ40 aggregation increases with low salt concentrations (25-50 mM), followed by a decline with further salt increments. An exploration of the thermodynamic and kinetic signatures of reentrant condensation unveils a nuanced interplay between protein electrostatics and ionic strength as potential drivers. Notably, the charged residues of the N-terminus exhibit a nonmonotonic response to salt screening, intricately linked to the recurrence of reentrant behavior in hydrophobic core-induced condensation. Intriguingly, our findings also unveil the reappearance of similar reentrant condensation phenomena under varying temperature conditions. Collectively, our study illuminates the profoundly context-dependent nature of Aβ40s liquid-liquid phase separation behavior, extending beyond its intrinsic molecular framework, where microenvironmental cues wield significant influence over its aberrant functionality.

The interplay between peptides and RNA is critical for protoribosome compartmentalization and stability

The ribosome, owing to its exceptional conservation, harbours a remarkable molecular fossil known as the protoribosome. It surrounds the peptidyl transferase center (PTC), responsible for peptide bond formation. While previous studies have demonstrated the PTC activity in RNA alone, our investigation reveals the intricate roles of the ribosomal protein fragments (rPeptides) within the ribosomal core. This research highlights the significance of rPeptides in stability and coacervation of two distinct protoribosomal evolutionary stages. The 617nt 'big' protoribosome model, which associates with rPeptides specifically, exhibits a structurally defined and rigid nature, further stabilized by the peptides. In contrast, the 136nt 'small' model, previously linked to peptidyltransferase activity, displays greater structural flexibility. While this construct interacts with rPeptides with lower specificity, they induce coacervation of the 'small' protoribosome across a wide concentration range, which is concomitantly dependent on the RNA sequence and structure. Moreover, these conditions protect RNA from degradation. This phenomenon suggests a significant evolutionary advantage in the RNA-protein interaction at the early stages of ribosome evolution. The distinct properties of the two protoribosomal stages suggest that rPeptides initially provided compartmentalization and prevented RNA degradation, preceding the emergence of specific RNA-protein interactions crucial for the ribosomal structural integrity.

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.

Quantifying surface tension and viscosity in biomolecular condensates by FRAP-ID

Many proteins with intrinsically disordered regions undergo liquid-liquid phase separation under specific conditions in vitro and in vivo. These complex biopolymers form a metastable phase with distinct mechanical properties defining the timescale of their biological functions. However, determining these properties is nontrivial, even in vitro, and often requires multiple techniques. Here we report the measurement of both viscosity and surface tension of biomolecular condensates via correlative fluorescence microscopy and atomic force microscopy (AFM) in a single experiment (fluorescence recovery after probe-induced dewetting, FRAP-ID). Upon surface tension evaluation via regular AFM-force spectroscopy, controlled AFM indentations induce dry spots in fluorescent condensates on a glass coverslip. The subsequent rewetting exhibits a contact line velocity that is used to quantify the condensed-phase viscosity. Therefore, in contrast with fluorescence recovery after photobleaching (FRAP), where molecular diffusion is observed, in FRAP-ID fluorescence recovery is obtained through fluid rewetting and the subsequent morphological relaxation. We show that the latter can be used to cross-validate viscosity values determined during the rewetting regime. Making use of fluid mechanics, FRAP-ID is a valuable tool to evaluate the mechanical properties that govern the dynamics of biomolecular condensates and determine how these properties impact the temporal aspects of condensate functionality.

Optical Control over Liquid–Liquid Phase Separation

Liquid-liquid phase separation (LLPS) is responsible for the emergence of intracellular membrane-less organelles and the development of coacervate protocells. Benefitting from the advantages of simplicity, precision, programmability, and noninvasiveness, light has become an effective tool to regulate the assembly dynamics of LLPS, and mediate various biochemical processes associated with LLPS. In this review, recent advances in optically controlling membrane-less organelles within living organisms are summarized, thereby modulating a series of biological processes including irreversible protein aggregation pathologies, transcription activation, metabolic flux, genomic rearrangements, and enzymatic reactions. Among these, the intracellular systems (i.e., optoDroplet, Corelet, PixELL, CasDrop, and other optogenetic systems) that enable the photo-mediated control over biomolecular condensation are highlighted. The design of photoactive complex coacervate protocells in laboratory settings by utilizing photochromic molecules such as azobenzene and diarylethene is further discussed. This review is expected to provide in-depth insights into phase separation-associated biochemical processes, bio-metabolism, and diseases.

Reaction-Driven Diffusiophoresis of Liquid Condensates: Potential Mechanisms for Intracellular Organization

The cellular environment, characterized by its intricate composition and spatial organization, hosts a variety of organelles, ranging from membrane-bound ones to membraneless structures that are formed through liquid-liquid phase separation. Cells show precise control over the position of such condensates. We demonstrate that organelle movement in external concentration gradients, diffusiophoresis, is distinct from the one of colloids because fluxes can remain finite inside the liquid-phase droplets and movement of the latter arises from incompressibility. Within cellular domains diffusiophoresis naturally arises from biochemical reactions that are driven by a chemical fuel and produce waste. Simulations and analytical arguments within a minimal model of reaction-driven phase separation reveal that the directed movement stems from two contributions: Fuel and waste are refilled or extracted at the boundary, resulting in concentration gradients, which (i) induce product fluxes via incompressibility and (ii) result in an asymmetric forward reaction in the droplet's surroundings (as well as asymmetric backward reaction inside the droplet), thereby shifting the droplet's position. We show that the former contribution dominates and sets the direction of the movement, toward or away from fuel source and waste sink, depending on the product molecules' affinity toward fuel and waste, respectively. The mechanism thus provides a simple means to organize condensates with different composition. Particle-based simulations and systems with more complex reaction cycles corroborate the robustness and universality of this mechanism.

Chemotactic Interactions Drive Migration of Membraneless Active Droplets

In nature, chemotactic interactions are ubiquitous and play a critical role in driving the collective behavior of living organisms. Reproducing these interactions in vitro is still a paramount challenge due to the complexity of mimicking and controlling cellular features, such as tangled metabolic networks, cytosolic macromolecular crowding, and cellular migration, on a microorganism size scale. Here, we generate enzymatically active cell-sized droplets able to move freely, and by following a chemical gradient, able to interact with the surrounding droplets in a collective manner. The enzyme within the droplets generates a pH gradient that extends outside the edge of the droplets. We discovered that the external pH gradient triggers droplet migration and controls its directionality, which is selectively toward the neighboring droplets. Hence, by changing the enzyme activity inside the droplet, we tuned the droplet migration speed. Furthermore, we showed that these cellular-like features can facilitate the reconstitution of a simple and linear protometabolic pathway and increase the final reaction product generation. Our work suggests that simple and stable membraneless droplets can reproduce complex biological phenomena, opening new perspectives as bioinspired materials and synthetic biology tools.

A facile DNA coacervate platform for engineering wetting, engulfment, fusion and transient behavior

Biomolecular coacervates are emerging models to understand biological systems and important building blocks for designer applications. DNA can be used to build up programmable coacervates, but often the processes and building blocks to make those are only available to specialists. Here, we report a simple approach for the formation of dynamic, multivalency-driven coacervates using long single-stranded DNA homopolymer in combination with a series of palindromic binders to serve as a synthetic coacervate droplet. We reveal details on how the length and sequence of the multivalent binders influence coacervate formation, how to introduce switching and autonomous behavior in reaction circuits, as well as how to engineer wetting, engulfment and fusion in multi-coacervate system. Our simple-to-use model DNA coacervates enhance the understanding of coacervate dynamics, fusion, phase transition mechanisms, and wetting behavior between coacervates, forming a solid foundation for the development of innovative synthetic and programmable coacervates for fundamental studies and applications.

Uncovering the molecular interactions underlying MBD2 and MBD3 phase separation

Chromatin organization controls DNA's accessibility to regulatory factors to influence gene expression. Heterochromatin, or transcriptionally silent chromatin enriched in methylated DNA and methylated histone tails, self-assembles through multivalent interactions with its associated proteins into a condensed, but dynamic state. Liquid-liquid phase separation (LLPS) of key heterochromatin regulators, such as heterochromatin protein 1 (HP1), plays an essential role in heterochromatin assembly and function. Methyl-CpG-binding protein 2 (MeCP2), the most studied member of the methyl-CpG-binding domain (MBD) family of proteins, has been recently shown to undergo LLPS in the absence and presence of methylated DNA. These studies provide a new mechanistic framework for understanding the role of methylated DNA and its readers in heterochromatin formation. However, the details of the molecular interactions by which other MBD family members undergo LLPS to mediate genome organization and transcriptional regulation are not fully understood. Here, we focus on two MBD proteins, MBD2 and MBD3, that have distinct but interdependent roles in gene regulation. Using an integrated computational and experimental approach, we uncover the homotypic and heterotypic interactions governing MBD2 and MBD3 phase separation and DNA's influence on this process. We show that despite sharing the highest sequence identity and structural homology among all the MBD protein family members, MBD2 and MBD3 exhibit differing residue patterns resulting in distinct phase separation mechanisms. Understanding the molecular underpinnings of MBD protein condensation offers insights into the higher-order, LLPS-mediated organization of heterochromatin.

Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions

Macromolecular crowding affects the activity of proteins and functional macromolecular complexes in all cells, including bacteria. Crowding, together with physicochemical parameters such as pH, ionic strength, and the energy status, influences the structure of the cytoplasm and thereby indirectly macromolecular function. Notably, crowding also promotes the formation of biomolecular condensates by phase separation, initially identified in eukaryotic cells but more recently discovered to play key functions in bacteria. Bacterial cells require a variety of mechanisms to maintain physicochemical homeostasis, in particular in environments with fluctuating conditions, and the formation of biomolecular condensates is emerging as one such mechanism. In this work, we connect physicochemical homeostasis and macromolecular crowding with the formation and function of biomolecular condensates in the bacterial cell and compare the supramolecular structures found in bacteria with those of eukaryotic cells. We focus on the effects of crowding and phase separation on the control of bacterial chromosome replication, segregation, and cell division, and we discuss the contribution of biomolecular condensates to bacterial cell fitness and adaptation to environmental stress.

Phase separation of multicomponent peptide mixtures into dehydrated clusters with hydrophilic cores

Phase separation of biomolecules underlies the formation and regulation of various membraneless condensates in cells. How condensates function reliably while surrounded by heterogeneous and dynamic mixtures of biomolecular components with specific and nonspecific interactions is yet to be understood. Studying multicomponent biomolecular mixtures with designer peptides has recently become an attractive avenue for learning about physicochemical principles governing cellular condensates. In this work, we employed long-timescale atomistic simulations of multicomponent tripeptide mixtures with all residue substitutions to illuminate the nature of direct and water-mediated interactions in a prototypical cellular condensate environment. We find that peptide mixtures form clusters with inverse hydrophobic order. Most multivalent and charged residues are localized in the cluster's core, with a large fraction of nonaromatic hydrophobic residues remaining on the surface. This inverse hydrophobic order in peptide clusters is partly driven by the expulsion of nonspecifically bound water molecules following peptide cluster growth. The growth of clusters is also accompanied by the formation of increasing numbers of specific water-mediated interactions between polar and charged residues. While the present study focused on the condensation of short peptide motifs, the general findings and analysis techniques should be helpful for future studies on larger peptides and protein condensation.

Vesicle condensation induced by synapsin: condensate size, geometry, and vesicle shape deformations

We study the formation of vesicle condensates induced by the protein synapsin, as a cell-free model system mimicking vesicle pool formation in the synapse. The system can be considered as an example of liquid-liquid phase separation (LLPS) in biomolecular fluids, where one phase is a complex fluid itself consisting of vesicles and a protein network. We address the pertinent question why the LLPS is self-limiting and stops at a certain size, i.e., why macroscopic phase separation is prevented. Using fluorescence light microscopy, we observe different morphologies of the condensates (aggregates) depending on the protein-to-lipid ratio. Cryogenic electron microscopy then allows us to resolve individual vesicle positions and shapes in a condensate and notably the size and geometry of adhesion zones between vesicles. We hypothesize that the membrane tension induced by already formed adhesion zones then in turn limits the capability of vesicles to bind additional vesicles, resulting in a finite condensate size. In a simple numerical toy model we show that this effect can be accounted for by redistribution of effective binding particles on the vesicle surface, accounting for the synapsin-induced adhesion zone.

Tuning of Cationic Polymer Functionality in Complex Coacervate Artificial Cells for Optimized Enzyme Activity

Complex coacervates are a versatile platform to mimic the structure of living cells. In both living systems and artificial cells, a macromolecularly crowded condensate phase has been shown to be able to modulate enzyme activity. Yet, how enzyme activity is affected by interactions (particularly with cationic charges) inside coacervates is not well studied. Here, we synthesized a series of amino-functional polymers to investigate the effect of the type of amine and charge density on coacervate formation, stability, protein partitioning, and enzyme function. The polymers were prepared by RAFT polymerization using as monomers aminoethyl methacrylate (AEAM), 2-(dimethylamino)ethyl methacrylate (DMAEMA), imidazolepropyl methacrylamide (IPMAm), and [2-(methacryloyloxy)ethyl] trimethylammonium chloride (TMAEMA). Membranized complex coacervate artificial cells were formed with these polycations and an anionic amylose derivative. Results show that polycations with reduced charge density result in higher protein mobility in the condensates and also higher enzyme activity. Insights described here could help guide the use of coacervate artificial cells in applications such as sensing, catalysis, and therapeutic formulations.

Tuning the viscoelastic properties of peptide coacervates by single amino acid mutations and salt kosmotropicity

Coacervation, or liquid-liquid phase separation (LLPS) of biomacromolecules, is increasingly recognized to play an important role both intracellularly and in the extracellular space. Central questions that remain to be addressed are the links between the material properties of coacervates (condensates) and both the primary and the secondary structures of their constitutive building blocks. Short LLPS-prone peptides, such as GY23 variants explored in this study, are ideal model systems to investigate these links because simple sequence modifications and the chemical environment strongly affect the viscoelastic properties of coacervates. Herein, a systematic investigation of the structure/property relationships of peptide coacervates was conducted using GY23 variants, combining biophysical characterization (plate rheology and surface force apparatus, SFA) with secondary structure investigations by infrared (IR) and circular dichroism (CD) spectroscopy. Mutating specific residues into either more hydrophobic or more hydrophilic residues strongly regulates the viscoelastic properties of GY23 coacervates. Furthermore, the ionic strength and kosmotropic characteristics (Hofmeister series) of the buffer in which LLPS is induced also significantly impact the properties of formed coacervates. Structural investigations by CD and IR indicate a direct correlation between variations in properties induced by endogenous (peptide sequence) or exogenous (ionic strength, kosmotropic characteristics, aging) factors and the β-sheet content within coacervates. These findings provide valuable insights to rationally design short peptide coacervates with programmable materials properties that are increasingly used in biomedical applications.

Condensation of the N-terminal domain of human topoisomerase 1 is driven by electrostatic interactions and tuned by its charge distribution

Liquid-liquid phase separation (LLPS) is pivotal in forming biomolecular condensates, which are crucial in several biological processes. Intrinsically disordered regions (IDRs) are typically responsible for driving LLPS due to their multivalency and high content of charged residues that enable the establishment of electrostatic interactions. In our study, we examined the role of charge distribution in the condensation of the disordered N-terminal domain of human topoisomerase I (hNTD). hNTD is densely charged with oppositely charged residues evenly distributed along the sequence. Its LLPS behavior was compared with that of charge permutants exhibiting varying degrees of charge segregation. At low salt concentrations, hNTD undergoes LLPS. However, LLPS is inhibited by high concentrations of salt and RNA, disrupting electrostatic interactions. Our findings show that, in hNTD, moderate charge segregation promotes the formation of liquid condensates that are sensitive to salt and RNA, whereas marked charge segregation results in the formation of aberrant condensates. Although our study is based on a limited set of protein variants, it supports the applicability of the "stickers-and-spacers" model to biomolecular condensates involving highly charged IDRs. These results may help generate reliable models of the overall LLPS behavior of supercharged polypeptides.

Spectroscopic and Biophysical Methods to Determine Differential Salt-Uptake by Primitive Membraneless Polyester Microdroplets

α-Hydroxy acids are prebiotic monomers that undergo dehydration synthesis to form polyester gels, which assemble into membraneless microdroplets upon aqueous rehydration. These microdroplets are proposed as protocells that can segregate and compartmentalize primitive molecules/reactions. Different primitive aqueous environments with a variety of salts could have hosted chemistries that formed polyester microdroplets. These salts could be essential cofactors of compartmentalized prebiotic reactions or even directly affect protocell structure. However, fully understanding polyester-salt interactions remains elusive, partially due to technical challenges of quantitative measurements in condensed phases. Here, spectroscopic and biophysical methods are applied to analyze salt uptake by polyester microdroplets. Inductively coupled plasma mass spectrometry is applied to measure the cation concentration within polyester microdroplets after addition of chloride salts. Combined with methods to determine the effects of salt uptake on droplet turbidity, size, surface potential and internal water distribution, it was observed that polyester microdroplets can selectively partition salt cations, leading to differential microdroplet coalescence due to ionic screening effects reducing electrostatic repulsion forces between microdroplets. Through applying existing techniques to novel analyses related to primitive compartment chemistry and biophysics, this study suggests that even minor differences in analyte uptake can lead to significant protocellular structural change.

Location of the photosynthetic carbon metabolism in microcompartments and separated phases in microalgal cells

Carbon acquisition, assimilation and storage in eukaryotic microalgae and cyanobacteria occur in multiple compartments that have been characterised by the location of the enzymes involved in these functions. These compartments can be delimited by bilayer membranes, such as the chloroplast, the lumen, the peroxisome, the mitochondria or monolayer membranes, such as lipid droplets or plastoglobules. They can also originate from liquid-liquid phase separation such as the pyrenoid. Multiple exchanges exist between the intracellular microcompartments, and these are reviewed for the CO2 concentration mechanism, the Calvin-Benson-Bassham cycle, the lipid metabolism and the cellular energetic balance. Progress in microscopy and spectroscopic methods opens new perspectives to characterise the molecular consequences of the location of the proteins involved, including intrinsically disordered proteins.

Redox-responsive peptide-based complex coacervates as delivery vehicles with controlled release of proteinous drugs

Proteinous drugs are highly promising therapeutics to treat various diseases. However, they suffer from limited circulation times and severe off-target side effects. Inspired by active membraneless organelles capable of dynamic recruitment and releasing of specific proteins, here, we present the design of coacervates as therapeutic protocells, made from small metabolites (anionic molecules) and simple arginine-rich peptides (cationic motif) through liquid-liquid phase separation. These complex coacervates demonstrate that their assembly and disassembly can be regulated by redox chemistry, which helps to control the release of the therapeutic protein. A model proteinous drugs, tissue plasminogen activator (tPA), can rapidly compartmentalize inside the complex coacervates, and the coacervates formed from peptides conjugated with arginine-glycine-aspartic acid (RGD) motif (a fibrinogen-derived peptide sequence), show selective binding to the thrombus site and thus enhance on-target efficacy of tPA. Furthermore, the burst release of tPA can be controlled by the redox-induced dissolution of the coacervates. Our proof-of-principle complex coacervate system provides insights into the sequestration and release of proteinous drugs from advanced drug delivery systems and represents a step toward the construction of synthetic therapeutic protocells for biomedical applications.

Coacervate-Enhanced Deposition of Sprayed Pesticide on Hydrophobic/Superhydrophobic Abaxial Leaf Surfaces

Deposition of high-speed droplets on inverted surfaces is important to many fundamental scientific principles and technological applications. For example, in pesticide spraying to target pests and diseases emerging on abaxial side of leaves, the downward rebound and gravity of the droplets make the deposition exceedingly difficult on hydrophobic/superhydrophobic leaf underside, causing serious pesticide waste and environmental pollution. Here, a series of bile salt/cationic surfactant coacervates are developed to attain efficient deposition on the inverted surfaces of diverse hydrophobic/superhydrophobic characteristics. The coacervates have abundant nanoscale hydrophilic/hydrophobic domains and intrinsic network-like microstructures, which endow them with efficient encapsulation of various solutes and strong adhesion to surface micro/nanostructures. Thus, the coacervates with low viscosity achieve high-efficient deposition on superhydrophobic abaxial-side of tomato leaves and inverted artificial surfaces with a water contact angle from 170° to 124°, much better than that of commercial agricultural adjuvants. Intriguingly, the compactness of network-like structures dominantly controls adhesion force and deposition efficiency, and the most crowded one leads to the most efficient deposition. The tunable coacervates can help comprehensively understand the complex dynamic deposition, and provide innovative carriers for depositing sprayed pesticides on abaxial and adaxial sides of leaves, thereby potentially reducing pesticide use and promoting sustainable agriculture.