Growth, replication and division enable evolution of coacervate protocells

Effect of Phosphate on the Molecular Properties, Interactions, and Assembly of Engineered Spider Silk Proteins

Phosphate plays a vital role in spider silk spinning and has been utilized in numerous artificial silk spinning attempts to replicate the remarkable mechanical properties of natural silk fiber. Its application in artificial processes has, however, yielded varying outcomes. It is thus necessary to investigate the origins and mechanisms behind these differences. By using recombinant silk protein SC-ADF3 derived from the garden spider Araneus diadematus, here, we describe its conformational changes under various conditions, elucidating the effect of phosphate on SC-ADF3 silk protein properties and interactions. Our results demonstrate that elevated phosphate levels induce the irreversible conformational conversion of SC-ADF3 from random coils to β-sheet structures, leading to decreased protein solubility over time. Furthermore, exposure of SC-ADF3 to phosphate stiffens already formed structures and reduces the ability to form new interactions. Our findings offer insights into the underlying mechanism through which phosphate-induced β-sheet structures in ADF3-related silk proteins impede fiber formation in the subsequent phases. From a broader perspective, our studies emphasize the significance of silk protein conformation for functional material formation, highlighting that the formation of β-sheet structures at the initial stages of protein assembly will affect the outcome of material forming processes.

Macromolecular Crowding Effect on Chitosan-Hyaluronic Acid Complexation and the Activity of Encapsulated Catalase

The associative phase separation of charged biomacromolecules plays a key role in many biophysical events that take place in crowded intracellular environments. Such natural polyelectrolyte complexation and phase separation often occur at nonstoichiometric charge ratios with the incorporation of bioactive proteins, which is not studied as extensively as those complexations at stoichiometric ratios. In this work, we investigated how the addition of a crowding agent (polyethylene glycol, PEG) affected the complexation between chitosan (CS) and hyaluronic acid (HA), especially at nonstoichiometric ratios, and the encapsulation of enzyme (catalase, CAT) by the colloidal complexes. The crowded environment promoted colloidal phase separation at low charge ratios, forming complexes with increased colloidal and dissolution stability, which resulted in a smaller size and polydispersity (PDI). The binding isotherms revealed that the addition of PEG greatly enhanced the ion-pairing strength (with increased ion-pairing equilibrium constant Ka from 4.92 × 104 without PEG to 1.08 × 106 with 200 g/L PEG) and switched the coacervation from endothermic to exothermic, which explained the promoted complexation and phase separation. At the stoichiometric charge ratio, the enhanced CS-HA interaction in crowded media generated a more solid-like coacervate phase with a denser network, slower chain relaxation, and higher modulus. Moreover, both crowding and complex encapsulation enhanced the activity and catalytic efficiency of CAT, represented by a 2-fold increase in catalytic efficiency (Kcat/Km) under 100 g/L PEG crowding and CS-HA complex encapsulation. This is likely due to the lower polarity in the microenvironment surrounding the enzyme molecules. By a systematic investigation of both nonstoichiometric and stoichiometric charge ratios under macromolecular crowding, this work provided new insights into the complexation between natural polyelectrolytes in a scenario closer to an intracellular environment.

Constrained dynamics of DNA oligonucleotides in phase-separated droplets

Understanding the dynamics of biomolecules in complex environments is crucial for elucidating the effect of condensed and heterogeneous environments on their functional properties. A relevant environment-and one that can also be mimicked easily in vitro-is that of phase-separated droplets. While phase-separated droplet systems have been shown to compartmentalize a wide range of functional biomolecules, the effects of internal structuration of droplets on the dynamics and mobility of internalized molecules remain poorly understood. Here, we use fluorescence correlation spectroscopy to measure the dynamics of short oligonucleotides encapsulated within two representative kinds of uncharged and charged phase-separated droplets. We find that the internal structuration controls the oligonucleotide dynamics in these droplets, revealed by measuring physical parameters at high spatiotemporal resolution. By varying oligonucleotide length and salt concentrations (and thereby charge screening), we found that the dynamics are significantly affected in the noncharged droplets compared to the charged system. Our work lays the foundation for unraveling and quantifying the physical parameters governing biomolecular transport in the condensed environment.

Programmable Enzymatic Reaction Network in Artificial Cell-Like Polymersomes

The ability to precisely control in vitro enzymatic reactions in synthetic cells plays a crucial role in the bottom-up design of artificial cell models that can recapitulate the key cellular features and functions such as metabolism. However, integration of enzymatic reactions has been limited to bulk or microfluidic emulsions without a membrane, lacking the ability to design more sophisticated higher-order artificial cell communities for reconstituting spatiotemporal biological information at multiple length scales. Herein, droplet microfluidics is utilized to synthesize artificial cell-like polymersomes with distinct molecular permeability for spatiotemporal control of enzymatic reactions driven by external signals and fuels. The presence of a competing reverse enzymatic reaction that depletes the active substrates is shown to enable demonstration of fuel-driven formation of sub-microcompartments within polymersomes as well as realization of out-of-equilibrium systems. In addition, the different permeability characteristics of polymersome membranes are exploited to successfully construct a programmable enzymatic reaction network that mimics cellular communication within a heterogeneous cell community through selective molecular transport.

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.

Probing the surface charge of condensates using microelectrophoresis

Biomolecular condensates play an important role in cellular organization. Coacervates are commonly used models that mimic the physicochemical properties of biomolecular condensates. The surface of condensates plays a key role in governing molecular exchange between condensates, accumulation of species at the interface, and the stability of condensates against coalescence. However, most important surface properties, including the surface charge and zeta potential, remain poorly characterized and understood. The zeta potential of coacervates is often measured using laser doppler electrophoresis, which assumes a size-independent electrophoretic mobility. Here, we show that this assumption is incorrect for liquid-like condensates and present an alternative method to study the electrophoretic mobility of coacervates and in vitro condensate models by microelectrophoresis and single-particle tracking. Coacervates have a size-dependent electrophoretic mobility, originating from their fluid nature, from which a well-defined zeta potential is calculated. Interestingly, microelectrophoresis measurements reveal that polylysine chains are enriched at the surface of polylysine/polyaspartic acid complex coacervates, which causes the negatively charged protein ɑ-synuclein to adsorb and accumulate at the interface. Addition of ATP inverts the surface charge, displaces ɑ-synuclein from the surface and may help to suppress its interface-catalyzed aggregation. Together, these findings show how condensate surface charge can be measured and altered, making this microelectrophoresis platform combined with automated single-particle tracking a promising characterization technique for both biomolecular condensates and coacervate protocells.

Self-assembly of stabilized droplets from liquid-liquid phase separation for higher-order structures and functions

Dynamic microscale droplets produced by liquid-liquid phase separation (LLPS) have emerged as appealing biomaterials due to their remarkable features. However, the instability of droplets limits the construction of population-level structures with collective behaviors. Here we first provide a brief background of droplets in the context of materials properties. Subsequently, we discuss current strategies for stabilizing droplets including physical separation and chemical modulation. We also discuss the recent development of LLPS droplets for various applications such as synthetic cells and biomedical materials. Finally, we give insights on how stabilized droplets can self-assemble into higher-order structures displaying coordinated functions to fully exploit their potentials in bottom-up synthetic biology and biomedical applications.

Cell-Like Synthetic Supramolecular Soft Materials Realized in Multicomponent, Non-/Out-of-Equilibrium Dynamic Systems

Living cells are complex, nonequilibrium supramolecular systems capable of independently and/or cooperatively integrating multiple bio-supramolecules to execute intricate physiological functions that cannot be accomplished by individual biomolecules. These biological design strategies offer valuable insights for the development of synthetic supramolecular systems with spatially controlled hierarchical structures, which, importantly, exhibit cell-like responses and functions. The next grand challenge in supramolecular chemistry is to control the organization of multiple types of supramolecules in a single system, thus integrating the functions of these supramolecules in an orthogonal and/or cooperative manner. In this perspective, the recent progress in constructing multicomponent supramolecular soft materials through the hybridization of supramolecules, such as self-assembled nanofibers/gels and coacervates, with other functional molecules, including polymer gels and enzymes is highlighted. Moreover, results show that these materials exhibit bioinspired responses to stimuli, such as bidirectional rheological responses of supramolecular double-network hydrogels, temporal stimulus pattern-dependent responses of synthetic coacervates, and 3D hydrogel patterning in response to reaction-diffusion processes are presented. Autonomous active soft materials with cell-like responses and spatially controlled structures hold promise for diverse applications, including soft robotics with directional motion, point-of-care disease diagnosis, and tissue regeneration.

Chirality-Selected Coacervate by Chiral Gemini Surfactant

Chiral surfactants present opportunities to self-assemble into supramolecules with a chiral trait; however, the effects of stereochemistry on the formation of simple coacervates remain unclear. Here, we investigate the chirality-selected phase behavior in mixtures of chiral gemini surfactant 1,4-bis(dodecyl-N,N-dimethylammonium bromide)-2,3-butanediol (12-4(OH)2-12) with an oppositely charged chiral mandelic acid (MA). It demonstrates that altering the chirality of surfactants yields a heightened ability to regulate the phase behavior, leading to the formation of three different network-like structures, i.e., wormlike micelle, coacervate, and hydrogel, in the racemate, enantiomer, and mesomer, respectively. The different aggregate structures arise from the intermolecular and intramolecular hydrogen-bond interactions of the two hydroxyl groups located at stereogenic centers. Intriguingly, although they contain similar microstructures, the solid-like hydrogel and liquid-like wormlike micelle show similar low hydration ability and have no encapsulation capability, whereas only coacervate formed by the enantiomers of 12-4(OH)2-12 displays liquid-like characteristics, strong capacity to sequester diverse solutes, and high affinity for tightly bound water simultaneously. These findings further highlight the unique and advantageous properties of coacervates as a promising model for exploring the biological process and understanding how chirality plays a crucial role in early life scenarios and cell evolution at the molecular level.

Toward Artificial Cell-Mediated Tissue Engineering: A New Perspective

The fast-growing pace of regenerative medicine research has allowed the development of a range of novel approaches to tissue engineering applications. Until recently, the main points of interest in the majority of studies have been to combine different materials to control cellular behavior and use different techniques to optimize tissue formation, from 3-D bioprinting to in situ regeneration. However, with the increase of the understanding of the fundamentals of cellular organization, tissue development, and regeneration, has also come the realization that for the next step in tissue engineering, a higher level of spatiotemporal control on cell-matrix interactions is required. It is proposed that the combination of artificial cell research with tissue engineering could provide a route toward control over complex tissue development. By equipping artificial cells with the underlying mechanisms of cellular functions, such as communication mechanisms, migration behavior, or the coherent behavior of cells depending on the surrounding matrix properties, they can be applied in instructing native cells into desired differentiation behavior at a resolution not to be attained with traditional matrix materials.

Optimization and Enhancement of the Peroxidase-like Activity of Hemin in Aqueous Solutions of Sodium Dodecylsulfate

Iron porphyrins play several important roles in present-day living systems and probably already existed in very early life forms. Hemin (= ferric protoporphyrin IX = ferric heme b), for example, is the prosthetic group at the active site of heme peroxidases, catalyzing the oxidation of a number of different types of reducing substrates after hemin is first oxidized by hydrogen peroxide as the oxidizing substrate of the enzyme. The active site of heme peroxidases consists of a hydrophobic pocket in which hemin is embedded noncovalently and kept in place through coordination of the iron atom to a proximal histidine side chain of the protein. It is this partially hydrophobic local environment of the enzyme which determines the efficiency with which the sequential reactions of the oxidizing and reducing substrates proceed at the active site. Free hemin, which has been separated from the protein moiety of heme peroxidases, is known to aggregate in an aqueous solution and exhibits low catalytic activity. Based on previous reports on the use of surfactant micelles to solubilize free hemin in a nonaggregated state, the peroxidase-like activity of hemin in the presence of sodium dodecyl sulfate (SDS) at concentrations below and above the critical concentration for SDS micelle formation (critical micellization concentration (cmc)) was systematically investigated. In most experiments, 3,3',5,5'-tetramethylbenzidine (TMB) was applied as a reducing substrate at pH = 7.2. The presence of SDS clearly had a positive effect on the reaction in terms of initial reaction rate and reaction yield, even at concentrations below the cmc. The highest activity correlated with the cmc value, as demonstrated for reactions at three different HEPES concentrations. The 4-(2-hydroxyethyl)-1-piperazineethanesulfonate salt (HEPES) served as a pH buffer substance and also had an accelerating effect on the reaction. At the cmc, the addition of l-histidine (l-His) resulted in a further concentration-dependent increase in the peroxidase-like activity of hemin until a maximal effect was reached at an optimal l-His concentration, probably corresponding to an ideal mono-l-His ligation to hemin. Some of the results obtained can be understood on the basis of molecular dynamics simulations, which indicated the existence of intermolecular interactions between hemin and HEPES and between hemin and SDS. Preliminary experiments with SDS/dodecanol vesicles at pH = 7.2 showed that in the presence of the vesicles, hemin exhibited similar peroxidase-like activity as in the case of SDS micelles. This supports the hypothesis that micelle- or vesicle-associated ferric or ferrous iron porphyrins may have played a role as primitive catalysts in membranous prebiotic compartment systems before cellular life emerged.

Visualizing Formation and Dynamics of a Three-Dimensional Sponge-like Network of a Coacervate in Real Time

Coacervates, which are formed by liquid-liquid phase separation, have been extensively explored as models for synthetic cells and membraneless organelles, so their in-depth structural analysis is crucial. However, both the inner structure dynamics and formation mechanism of coacervates remain elusive. Herein, we demonstrate real-time confocal observation of a three-dimensional sponge-like network in a dipeptide-based coacervate. In situ generation of the dipeptide allowed us to capture the emergence of the sponge-like network via unprecedented membrane folding of vesicle-shaped intermediates. We also visualized dynamic fluctuation of the network, including reversible engagement/disengagement of cross-links and a stochastic network kissing event. Photoinduced transient formation of a multiphase coacervate was achieved with a thermally responsive phase transition. Our findings expand the fundamental understanding of synthetic coacervates and provide opportunities to manipulate their physicochemical properties by engineering the inner network for potential applications in development of artificial cells and life-like material fabrication.

Multispecies autocatalytic RNA reaction networks in coacervates

Robust localization of self-reproducing autocatalytic chemistries is a key step in the realization of heritable and evolvable chemical systems. While autocatalytic chemical reaction networks already possess attributes such as heritable self-reproduction and evolvability, localizing functional multispecies networks within complex primitive phases, such as coacervates, has remained unexplored. Here, we show the self-reproduction of the Azoarcus ribozyme system within charge-rich coacervates where catalytic ribozymes are produced by the autocatalytic assembly of constituent smaller RNA fragments. We systematically demonstrate the catalytic assembly of active ribozymes within phase-separated coacervates-both in micron-sized droplets as well as in a coalesced macrophase, underscoring the facility of the complex, charge-rich phase to support these reactions in multiple configurations. By constructing multispecies reaction networks, we show that these newly assembled molecules are active, participating both in self- and cross-catalysis within the coacervates. Finally, due to differential molecular transport, these phase-separated compartments endow robustness to the composition of the collectively autocatalytic networks against external perturbations. Altogether, our results establish the formation of multispecies self-reproducing reaction networks in phase-separated compartments which in turn render transient robustness to the network composition.

DNA Droplets: Intelligent, Dynamic Fluid

Breathtaking advances in DNA nanotechnology have established DNA as a promising biomaterial for the fabrication of programmable higher-order nano/microstructures. In the context of developing artificial cells and tissues, DNA droplets have emerged as a powerful platform for creating intelligent, dynamic cell-like machinery. DNA droplets are a microscale membrane-free coacervate of DNA formed through phase separation. This new type of DNA system couples dynamic fluid-like property with long-established DNA programmability. This hybrid nature offers an advantageous route to facile and robust control over the structures, functions, and behaviors of DNA droplets. This review begins by describing programmable DNA condensation, commenting on the physical properties and fabrication strategies of DNA hydrogels and droplets. By presenting an overview of the development pathways leading to DNA droplets, it is shown that DNA technology has evolved from static, rigid systems to soft, dynamic systems. Next, the basic characteristics of DNA droplets are described as intelligent, dynamic fluid by showcasing the latest examples highlighting their distinctive features related to sequence-specific interactions and programmable mechanical properties. Finally, this review discusses the potential and challenges of numerical modeling able to connect a robust link between individual sequences and macroscopic mechanical properties of DNA droplets.

Open questions on liquid-liquid phase separation

Liquid-liquid phase separation (LLPS) underlies the formation of intracellular membraneless compartments in biology and may have played a role in the formation of protocells that concentrate key chemicals during the origins of life. While LLPS of simple systems, such as oil and water, is well understood, many aspects of LLPS in complex, out-of-equilibrium molecular systems remain elusive. Here, the author discusses open questions and recent insights related to the formation, function and fate of such condensates both in cell biology and protocell research.