Molecular determinants of protein-based coacervates

Supramolecular fibrillation in coacervates and other confined systems towards biomimetic function

As in natural cytoskeletons, the cooperative assembly of fibrillar networks can be hosted inside compartments to engineer biomimetic functions, such as mechanical actuation, transport, and reaction templating. Coacervates impose an optimal liquid-liquid phase separation within the aqueous continuum, functioning as membrane-less compartments that can organise such self-assembling processes as well as the exchange of information with their environment. Furthermore, biological fibrillation can often be controlled or assisted by intracellular compartments. Thus, the reconstitution of analogues of natural filaments in simplified artificial compartments, such as coacervates, offer a suitable model to unravel, mimic, and potentially exploit cellular functions. This perspective summarises the latest developments towards assembling fibrillar networks under confinement inside coacervates and related compartments, including a selection of examples ranging from biological to fully synthetic monomers. Comparative analysis between coacervates, lipid vesicles, and droplet emulsions showcases the interplay between supramolecular fibres and the boundaries of the corresponding compartment. Combining inspiration from natural systems and the custom properties of tailored synthetic fibrillators, rational monomer and compartment design will contribute towards engineering increasingly complex and more realistic artificial protocells.

Peptide-Based Biomimetic Condensates via Liquid-Liquid Phase Separation as Biomedical Delivery Vehicles

Biomolecular condensates are dynamic liquid droplets through intracellular liquid-liquid phase separation that function as membraneless organelles, which are highly involved in various complex cellular processes and functions. Artificial analogs formed via similar pathways that can be integrated with biological complexity and advanced functions have received tremendous research interest in the field of synthetic biology. The coacervate droplet-based compartments can partition and concentrate a wide range of solutes, which are regarded as attractive candidates for mimicking phase-separation behaviors and biophysical features of biomolecular condensates. The use of peptide-based materials as phase-separating components has advantages such as the diversity of amino acid residues and customized sequence design, which allows for programming their phase-separation behaviors and the physicochemical properties of the resulting compartments. In this Perspective, we highlight the recent advancements in the design and construction of biomimicry condensates from synthetic peptides relevant to intracellular phase-separating protein, with specific reference to their molecular design, self-assembly via phase separation, and biorelated applications, to envisage the use of peptide-based droplets as emerging biomedical delivery vehicles.

Single-molecule diffusivity quantification in Xenopus egg extracts elucidates physicochemical properties of the cytoplasm

The living cell creates a unique internal molecular environment that is challenging to characterize. By combining single-molecule displacement/diffusivity mapping (SM d M) with physiologically active extracts prepared from Xenopus laevis eggs, we sought to elucidate molecular properties of the cytoplasm. Quantification of the diffusion coefficients of 15 diverse proteins in extract showed that, compared to in water, negatively charged proteins diffused ∼50% slower, while diffusion of positively charged proteins was reduced by ∼80-90%. Adding increasing concentrations of salt progressively alleviated the suppressed diffusion observed for positively charged proteins, signifying electrostatic interactions within a predominately negatively charged macromolecular environment. To investigate the contribution of RNA, an abundant, negatively charged component of cytoplasm, extracts were treated with ribonuclease, which resulted in low diffusivity domains indicative of aggregation, likely due to the liberation of positively charged RNA-binding proteins such as ribosomal proteins, since this effect could be mimicked by adding positively charged polypeptides. Interestingly, negatively charged proteins of different sizes showed similar diffusivity suppression in extract, which are typically prepared under conditions that inhibit actin polymerization. Restoring or enhancing actin polymerization progressively suppressed the diffusion of larger proteins, recapitulating behaviors observed in cells. Together, these results indicate that molecular interactions in the crowded cell are defined by an overwhelmingly negatively charged macromolecular environment containing cytoskeletal networks.

Significance Statement

The complex intracellular molecular environment is notably challenging to elucidate and recapitulate. Xenopus egg extracts provide a native yet manipulatable cytoplasm model. Through single-molecule microscopy, here we decipher the cytoplasmic environment and molecular interactions by examining the diffusion patterns of diverse proteins in Xenopus egg extracts with strategic manipulations. These experiments reveal an overwhelmingly negatively charged macromolecular environment with crosslinked meshworks, offering new insight into the inner workings of the cell.

Charge block-driven liquid-liquid phase separation - mechanism and biological roles

Liquid-liquid phase separation (LLPS) has increasingly been found to play pivotal roles in a number of intracellular events and reactions, and has introduced a new paradigm in cell biology to explain protein-protein and enzyme-ligand interactions beyond conventional molecular and biochemical theories. LLPS is driven by the cumulative effects of weak and promiscuous interactions, including electrostatic, hydrophobic and cation-π interactions, among polypeptides containing intrinsically disordered regions (IDRs) and describes the macroscopic behaviours of IDR-containing proteins in an intracellular milieu. Recent studies have revealed that interactions between 'charge blocks' - clusters of like charges along the polypeptide chain - strongly induce LLPS and play fundamental roles in its spatiotemporal regulation. Introducing a new parameter, termed 'charge blockiness', into physicochemical models of disordered polypeptides has yielded a better understanding of how the intrinsic amino acid sequence of a polypeptide determines the spatiotemporal occurrence of LLPS within a cell. Charge blockiness might also explain why some post-translational modifications segregate within IDRs and how they regulate LLPS. In this Review, we summarise recent progress towards understanding the mechanism and biological roles of charge block-driven LLPS and discuss how this new characteristic parameter of polypeptides offers new possibilities in the fields of structural biology and cell biology.

Lipidation alters the phase-separation of resilin-like polypeptides

Biology exploits biomacromolecular phase separation to form condensates, known as membraneless organelles. Despite significant advancements in deciphering sequence determinants for phase separation, modulating these features in vivo remains challenging. A promising approach inspired by biology is to use post-translational modifications (PTMs)-to modulate the amino acid physicochemistry instead of altering protein sequences-to control the formation and characteristics of condensates. However, despite the identification of more than 300 types of PTMs, the detailed understanding of how they influence the formation and material properties of protein condensates remains incomplete. In this study, we investigated how modification with myristoyl lipid alters the formation and characteristics of the resilin-like polypeptide (RLP) condensates, a prototypical disordered protein with upper critical solution temperature (UCST) phase behaviour. Using turbidimetry, dynamic light scattering, confocal and electron microscopy, we demonstrated that lipidation-in synergy with the sequence of the lipidation site-significantly influences RLPs' thermodynamic propensity for phase separation and their condensate properties. Molecular simulations suggested these effects result from an expanded hydrophobic region created by the interaction between the lipid and lipidation site rather than changes in peptide rigidity. These findings emphasize the role of "sequence context" in modifying the properties of PTMs, suggesting that variations in lipidation sequences could be strategically used to fine-tune the effect of these motifs. Our study advances understanding of lipidation's impact on UCST phase behaviour, relevant to proteins critical in biological processes and diseases, and opens avenues for designing lipidated resilins for biomedical applications like heat-mediated drug elution.

Single-Molecule Diffusivity Quantification Unveils Ubiquitous Net Charge-Driven Protein-Protein Interaction

Recent microscopy and nuclear magnetic resonance (NMR) studies have noticed substantial suppression of intracellular diffusion for positively charged proteins, suggesting an overlooked role of electrostatic attraction in nonspecific protein interactions in a predominantly negatively charged intracellular environment. Utilizing single-molecule detection and statistics, here, we quantify in aqueous solutions how protein diffusion, in the limit of low diffuser concentration to avoid aggregate/coacervate formation, is modulated by differently charged interactor proteins over wide concentration ranges. We thus report substantially suppressed diffusion when oppositely charged interactors are added at parts per million levels, yet unvaried diffusivities when same-charge interactors are added beyond 1%. The electrostatic attraction-driven suppression of diffusion is sensitive to the protein net charge states, as probed by varying the solution pH and ionic strength or chemically modifying the proteins and is robust across different diffuser-interactor pairs. By converting the measured diffusivities to diffuser diameters, we further show that in the limit of excess interactors, a positively charged diffuser molecule effectively drags along just one monolayer of negatively charged interactors, where further interactions stop. We thus unveil ubiquitous, net charge-driven protein-protein interactions and shed new light on the mechanism of charge-based diffusion suppression in living cells.

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.

Modulating Phase Behavior in Fatty Acid-Modified Elastin-like Polypeptides (FAMEs): Insights into the Impact of Lipid Length on Thermodynamics and Kinetics of Phase Separation

Although post-translational lipidation is prevalent in eukaryotes, its impact on the liquid-liquid phase separation of disordered proteins is still poorly understood. Here, we examined the thermodynamic phase boundaries and kinetics of aqueous two-phase system (ATPS) formation for a library of elastin-like polypeptides modified with saturated fatty acids of different chain lengths. By systematically altering the physicochemical properties of the attached lipids, we were able to correlate the molecular properties of lipids to changes in the thermodynamic phase boundaries and the kinetic stability of droplets formed by these proteins. We discovered that increasing the chain length lowers the phase separation temperature in a sigmoidal manner due to alterations in the unfavorable interactions between protein and water and changes in the entropy of phase separation. Our kinetic studies unveiled remarkable sensitivity to lipid length, which we propose is due to the temperature-dependent interactions between lipids and the protein. Strikingly, we found that the addition of just a single methylene group is sufficient to allow tuning of these interactions as a function of temperature, with proteins modified with C7-C9 lipids exhibiting non-Arrhenius dependence in their phase separation, a behavior that is absent for both shorter and longer fatty acids. This work advances our theoretical understanding of protein-lipid interactions and opens avenues for the rational design of lipidated proteins in biomedical paradigms, where precise control over the phase separation is pivotal.

Design Rules for the Sequestration of Viruses into Polypeptide Complex Coacervates

Encapsulation is a strategy that has been used to facilitate the delivery and increase the stability of proteins and viruses. Here, we investigate the encapsulation of viruses via complex coacervation, which is a liquid-liquid phase separation resulting from the complexation of oppositely charged polymers. In particular, we utilized polypeptide-based coacervates and explored the effects of peptide chemistry, chain length, charge patterning, and hydrophobicity to better understand the effects of the coacervating polypeptides on virus incorporation. Our study utilized two nonenveloped viruses, porcine parvovirus (PPV) and human rhinovirus (HRV). PPV has a higher charge density than HRV, and they both appear to be relatively hydrophobic. These viruses were compared to characterize how the charge, hydrophobicity, and patterning of chemistry on the surface of the virus capsid affects encapsulation. Consistent with the electrostatic nature of complex coacervation, our results suggest that electrostatic effects associated with the net charge of both the virus and polypeptide dominated the potential for incorporating the virus into a coacervate, with clustering of charges also playing a significant role. Additionally, the hydrophobicity of a virus appears to determine the degree to which increasing the hydrophobicity of the coacervating peptides can enhance virus uptake. Nonintuitive trends in uptake were observed with regard to both charge patterning and polypeptide chain length, with these parameters having a significant effect on the range of coacervate compositions over which virus incorporation was observed. These results provide insights into biophysical mechanisms, where sequence effects can control the uptake of proteins or viruses into biological condensates and provide insights for use in formulation strategies.

Polyelectrolyte Brushes with Protein-Like Nanocolloids

Electrostatic interaction of ampholytic nanocolloidal particles (NPs), which mimic globular proteins, with polyelectrolyte brushes is analyzed within mean-field Poisson-Boltzmann approximation. In accordance with experimental findings, the theory predicts that an electrostatic driving force for the particle uptake by the brush may emerge when the net charge of the particle in the buffer and the charge of the brush are of the same sign. The origin of this driving force is change in the ionization state of weak cationic and anionic groups on the NP surface provoked by interaction with the brush. In experimental systems, the ionic interactions are complemented by excluded-volume, hydrophobic, and other types of interactions that all together control NP uptake by or expulsion from the brush. Here, we focus on the NP-brush ionic interactions. It is demonstrated that deviation between the buffer pH and the NP isoelectric point, considered usually as the key control parameter, does not uniquely determine the insertion free energy patterns. The latter depends also on the proportion of cationic and anionic groups in the NPs and their specific ionization constants as well as on salt concentration in the buffer. The analysis of the free energy landscape proves that a local minimum in the free energy inside the brush appears, provided the NP charge reversal occurs upon insertion into the brush. This minimum corresponds either to a thermodynamically stable or to a metastable state, depending on the pH offset from the IEP and salt concentration, and is separated from the bulk of the solution by a free energy barrier. The latter, being fairly independent of salt concentration in height, may strongly impede the NP absorption kinetically even when it is thermodynamically favorable. Hence, change reversal is a necessary but insufficient condition for the uptake of the NPs by similarly charged polyelectrolyte brushes.

Sequence-Tunable Phase Behavior and Intrinsic Fluorescence in Dynamically Interacting Peptides

A conceptual framework towards understanding biological condensed phases is emerging, derived from biological, biomimetic, and synthetic sequences. However, de novo peptide condensate design remains a challenge due to an incomplete understanding of the structural and interactive complexity. We designed peptide modules based on a simple repeat motif composed of tripeptide spacers (GSG, SGS, GLG) interspersed with adhesive amino acids (R/H and Y). We show, using sequence editing and a combination of computation and experiment, that n→π* interactions in GLG backbones are a dominant factor in providing sufficient backbone structure, which in turn regulates the water interface, collectively promoting liquid droplet formation. Moreover, these R(GLG)Y and H(GLG)Y condensates unexpectedly display sequence-dependent emission that is a consequence of their non-covalent network interactions, and readily observable by confocal microscopy.

Interaction of Polyanionic and Polycationic Brushes with Globular Proteins and Protein-like Nanocolloids

A large number of experimental studies have demonstrated that globular proteins can be absorbed from the solution by both polycationic and polyanionic brushes when the net charge of protein globules is of the same or of the opposite sign with respect to that of brush-forming polyelectrolyte chains. Here, we overview the results of experimental studies on interactions between globular proteins and polycationic or polyanionic brushes, and present a self-consistent field theoretical model that allows us to account for the asymmetry of interactions of protein-like nanocolloid particles comprising weak (pH-sensitive) cationic and anionic groups with a positively or negatively charged polyelectrolyte brush. The position-dependent insertion free energy and the net charge of the particle are calculated. The theoretical model predicts that if the numbers of cationic and anionic ionizable groups of the protein are approximately equal, then the interaction patterns for both cationic and anionic brushes at equal offset on the "wrong side" from the isoelectric point (IEP), i.e., when the particle and the brush charge are of the same sign, are similar. An essential asymmetry in interactions of particles with polycationic and polyanionic brushes is predicted when fractions of cationic and anionic groups differ significantly. That is, at a pH above IEP, the anionic brush better absorbs negatively charged particles with a larger fraction of ionizable cationic groups and vice versa.

Protein separation by sequential selective complex coacervation

In food manufacturing and particular biomedical products selected proteins are often required. Obtaining the desired proteins in a pure form from natural resources is therefore important, but often very challenging. Herein, we design a sequential coacervation process that allows to efficiently isolate and purify proteins with different isoelectric points (pIs) from a mixed solution, namely Bovine Serum Albumin (BSA, pI = 4.9) and Peroxidase from Horseradish (HRP, pI = 7.2). The key to separation is introducing a suitable polyelectrolyte that causes selective complex coacervation at appropriate pH and ionic strength. Specifically, polyethyleneimine (PEI), when added into the mixture at pH 6.0, produces a coacervation which exclusively contains BSA, leading to a supernatant solution containing 100 % HRP with a purity of 91 %. After separating the dilute and dense phases, BSA is recovered by adding poly(acrylic acid) (PAA) to the concentrated phase, which displaces BSA from the complex because it interacts more strongly with PEI. The supernatant phase after this step contains approximately 75 % of the initial amount of BSA with a purity of 99 %. Our results confirm that coacervation under well-defined conditions can be selective, enabling separation of proteins with adequate purity. Therefore, the established approach demonstrates a facile and sustainable strategy with potential for protein separation at industrial scale.

The Role of Chemically Innocent Polyanions in Active, Chemically Fueled Complex Coacervate Droplets

Complex coacervation describes the liquid-liquid phase separation of oppositely charged polymers. Active coacervates are droplets in which one of the electrolyte's affinity is regulated by chemical reactions. These droplets are particularly interesting because they are tightly regulated by reaction kinetics. For example, they serve as a model for membraneless organelles that are also often regulated by biochemical transformations such as post-translational modifications. They are also a great protocell model or could be used to synthesize life-they spontaneously emerge in response to reagents, compete, and decay when all nutrients have been consumed. However, the role of the unreactive building blocks, e.g., the polymeric compounds, is poorly understood. Here, we show the important role of the chemically innocent, unreactive polyanion of our chemically fueled coacervation droplets. We show that the polyanion drastically influences the resulting droplets' life cycle without influencing the chemical reaction cycle-either they are very dynamic or have a delayed dissolution. Additionally, we derive a mechanistic understanding of our observations and show how additives and rational polymer design help to create the desired coacervate emulsion life cycles.

Structure and Dynamics of Hybrid Colloid-Polyelectrolyte Coacervates: Insights from Molecular Simulations

Electrostatic interactions in polymeric systems are responsible for a wide range of liquid-liquid phase transitions that are of importance for biology and materials science. Such transitions are referred to as complex coacervation, and recent studies have sought to understand the underlying physics and chemistry. Most theoretical and simulation efforts to date have focused on oppositely charged linear polyelectrolytes, which adopt nearly ideal-coil conformations in the condensed phase. However, when one of the coacervate components is a globular protein, a better model of complexation should replace one of the species with a spherical charged particle or colloid. In this work, we perform coarse-grained simulations of colloid-polyelectrolyte coacervation using a spherical model for the colloid. Simulation results indicate that the electroneutral cell of the resulting (hybrid) coacervates consists of a polyelectrolyte layer adsorbed on the colloid. Power laws for the structure and the density of the condensed phase, which are extracted from simulations, are found to be consistent with the adsorption-based scaling theory of hybrid coacervation. The coacervates remain amorphous (disordered) at a moderate colloid charge, Q, while an intra-coacervate colloidal crystal is formed above a certain threshold, at Q > Q*. In the disordered coacervate, if Q is sufficiently low, colloids diffuse as neutral nonsticky nanoparticles in the semidilute polymer solution. For higher Q, adsorption is strong and colloids become effectively sticky. Our findings are relevant for the coacervation of polyelectrolytes with proteins, spherical micelles of ionic surfactants, and solid organic or inorganic nanoparticles.

Complex Coacervates as a Promising Vehicle for mRNA Delivery: A Comprehensive Review of Recent Advances and Challenges

Messenger RNA (mRNA)-based therapies have gained significant attention, following the successful deployment of mRNA-based COVID-19 vaccines. Compared with traditional methods of genetic modification, mRNA-based therapies offer several advantages, including a lower risk of genetic mutations, temporary and controlled therapeutic gene expression, and a shorter production time, which facilitates rapid responses to emerging health challenges. Moreover, mRNA-based therapies have shown immense potential in treating a wide range of diseases including cancers, immune diseases, and neurological disorders. However, the current limitations of non-viral vectors for efficient and safe delivery of mRNA therapies, such as low encapsulation efficiency, potential toxicity, and limited stability, necessitate the exploration of novel strategies to overcome these challenges and fully realize the potential of mRNA-based therapeutics. Coacervate-based delivery systems have recently emerged as promising strategies for enhancing mRNA delivery. Coacervates, which are formed by the aggregation of two or more macromolecules, have shown great potential in delivering a wide range of therapeutics due to their ability to form a separated macromolecular-rich fluid phase in an aqueous environment. This phase separation enables the entrapment and protection of therapeutic agents from degradation as well as efficient cellular uptake and controlled release. Additionally, the natural affinity of coacervates for mRNA molecules presents an excellent opportunity for enhancing mRNA delivery to targeted cells and tissues, making coacervate-based delivery systems an attractive option for mRNA-based therapies. This review highlights the limitations of current strategies for mRNA delivery and the advantages of coacervate-based delivery systems to enable mRNA therapeutics. Coacervates protect mRNA from enzymatic degradation and enhance cellular uptake, leading to sustained and controlled gene expression. Despite their promising properties, the specific use of coacervates as mRNA delivery vehicles remains underexplored. This review aims to provide a comprehensive overview of coacervate-mediated delivery of mRNA, exploring the properties and applications of different coacervating agents as well as the challenges and optimization strategies involved in mRNA encapsulation, release, stability, and translation via coacervate-mediated delivery. Through a comprehensive analysis of recent advancements and recommended future directions, our review sheds light on the promising role of coacervate-mediated delivery for RNA therapeutics, highlighting its potential to enable groundbreaking applications in drug delivery and gene therapy.

Interaction of Hyaluronan Acid with Some Proteins in Aqueous Solution as Studied by NMR

According to actual literature data, hyaluronic acid (HA) that is presented in the extracellular matrix can interact with proteins and thereby affect several important functions of the cell membrane. The purpose of this work was to reveal the features of the interaction of HA with proteins using the PFG NMR method by sampling two systems: aqueous solutions of HA with bovine serum albumin (BSA) and aqueous solutions of HA with hen egg-white lysozyme (HEWL). It was found that the presence of BSA in the HA aqueous solution initiates a certain additional mechanism; as a result, the population of HA molecules in the gel structure increases to almost 100%. At the same time, for an aqueous solution of HA/HEWL, even in the range of low (0.01-0.2%) HEWL contents, strong signs of degradation (depolymerization) of some HA macromolecules were observed such that they lost the ability to form a gel. Moreover, lysozyme molecules form a strong complex with degraded HA molecules and lose their enzymatic function. Thus, the presence of HA molecules in the intercellular matrix, as well as in the state associated with the surface of the cell membrane, can, in addition to the known ones, perform one more important function: the function of protecting the cell membrane from the destructive action of lysozymes. The obtained results are important for understanding the mechanism and features of the interaction of extracellular matrix glycosaminoglycan with cell membrane proteins.

Structure and Dynamics of Hybrid Colloid-Polyelectrolyte Coacervates

We develop a scaling theory for the structure and dynamics of "hybrid" complex coacervates formed from linear polyelectrolytes (PEs) and oppositely charged spherical colloids, such as globular proteins, solid nanoparticles, or spherical micelles of ionic surfactants. At low concentrations, in stoichiometric solutions, PEs adsorb at the colloids to form electrically neutral finite-size complexes. These clusters attract each other through bridging between the adsorbed PE layers. Above a threshold concentration, macroscopic phase separation sets in. The coacervate internal structure is defined by (i) the adsorption strength and (ii) the ratio of the resulting shell thickness to the colloid radius, H/R. A scaling diagram of different coacervate regimes is constructed in terms of the colloid charge and its radius for Θ and athermal solvents. For high charges of the colloids, the shell is thick, H ≫ R, and most of the volume of the coacervate is occupied by PEs, which determine its osmotic and rheological properties. The average density of hybrid coacervates exceeds that of their PE-PE counterparts and increases with nanoparticle charge, Q. At the same time, their osmotic moduli remain equal, and the surface tension of hybrid coacervates is lower, which is a consequence of the shell's inhomogeneous density decreasing with the distance from the colloid surface. When charge correlations are weak, hybrid coacervates remain liquid and follow Rouse/reptation dynamics with a Q-dependent viscosity, η Rouse ∼ Q 4/5 and η rep ∼ Q 28/15 for a Θ solvent. For an athermal solvent, these exponents are equal to 0.89 and 2.68, respectively. The diffusion coefficients of colloids are predicted to be strongly decreasing functions of their radius and charge. Our results on how Q affects the threshold coacervation concentration and colloidal dynamics in condensed phases are consistent with experimental observations for in vitro and in vivo studies of coacervation between supercationic green fluorescent proteins (GFPs) and RNA.

Bovine Serum Albumin Interaction with Polyanionic and Polycationic Brushes: The Case Theoretical Study

We apply a coarse-grained self-consistent field Poisson-Boltzmann framework to study interaction between Bovine Serum Albumin (BSA) and a planar polyelectropyte brush. Both cases of negatively (polyanionic) and positively (polycationic) charged brushes are considered. Our theoretical model accounts for (1) re-ionization free energy of the amino acid residues upon protein insertion into the brush; (2) osmotic force repelling the protein globule from the brush; (3) hydrophobic interactions between non-polar areas on the globule surface and the brush-forming chains. We demonstrate that calculated position-dependent insertion free energy exhibits different patterns, corresponding to either thermodynamically favourable BSA absorption in the brush or thermodynamically or kinetically hindered absorption (expulsion) depending on the pH and ionic strength of the solution. The theory predicts that due to the re-ionization of BSA within the brush, a polyanionic brush can efficiently absorb BSA over a wider pH range on the "wrong side" of the isoelectric point (IEP) compared to a polycationic brush. The results of our theoretical analysis correlate with available experimental data and thus validate the developed model for prediction of the interaction patterns for various globular proteins with polyelectrolyte brushes.

Functional partitioning of transcriptional regulators by patterned charge blocks

Components of transcriptional machinery are selectively partitioned into specific condensates, often mediated by protein disorder, yet we know little about how this specificity is achieved. Here, we show that condensates composed of the intrinsically disordered region (IDR) of MED1 selectively partition RNA polymerase II together with its positive allosteric regulators while excluding negative regulators. This selective compartmentalization is sufficient to activate transcription and is required for gene activation during a cell-state transition. The IDRs of partitioned proteins are necessary and sufficient for selective compartmentalization and require alternating blocks of charged amino acids. Disrupting this charge pattern prevents partitioning, whereas adding the pattern to proteins promotes partitioning with functional consequences for gene activation. IDRs with similar patterned charge blocks show similar partitioning and function. These findings demonstrate that disorder-mediated interactions can selectively compartmentalize specific functionally related proteins from a complex mixture of biomolecules, leading to regulation of a biochemical pathway.

Intracellular phase separation of globular proteins facilitated by short cationic peptides

Phase separation provides intracellular organization and underlies a variety of cellular processes. These biomolecular condensates exhibit distinct physical and material properties. Current strategies for engineering condensate formation include using intrinsically disordered domains and altering protein surface charge by chemical supercharging or site-specific mutagenesis. We propose adding to this toolbox designer peptide tags that provide several potential advantages for engineering protein phase separation in bacteria. Herein, we demonstrate the use of short cationic peptide tags for sequestration of proteins of interest into bacterial condensates and provide a foundational study for their development as tools for condensate engineering. Using a panel of GFP variants, we demonstrate how cationic tag and globular domain charge contribute to intracellular phase separation in E. coli and observe that the tag can affect condensate disassembly at a given net charge near the phase separation boundary. We showcase the broad applicability of these tags by appending them onto enzymes and demonstrating that the sequestered enzymes remain catalytically active.

Droplet Microfluidics for the Label-Free Extraction of Complete Phase Diagrams and Kinetics of Liquid-Liquid Phase Separation in Finite Volumes

Liquid-liquid phase separation of polymer and protein solutions is central in many areas of biology and material sciences. Here, an experimental and theoretical framework is provided to investigate the thermodynamics and kinetics of liquid-liquid phase separation in volumes comparable to cells. The strategy leverages droplet microfluidics to accurately measure the volume of the dense phase generated by liquid-liquid phase separation of solutions confined in micro-sized compartments. It is shown that the measurement of the volume fraction of the dense phase at different temperatures allows the evaluation of the binodal lines that determine the coexistence region of the two phases in the temperature-concentration phase diagram. By applying a thermodynamic model of phase separation in finite volumes, it is further shown that the platform can predict and validate kinetic barriers associated with the formation of a dense droplet in a parent dilute phase, therefore connecting thermodynamics and kinetics of liquid-liquid phase separation.

An Overview of Coacervates: The Special Disperse State of Amphiphilic and Polymeric Materials in Solution

Individual amphiphiles, polymers, and colloidal dispersions influenced by temperature, pH, and environmental conditions or interactions between their oppositely charged pairs in solvent medium often produce solvent-rich and solvent-poor phases in the system. The solvent-poor denser phase found either on the top or the bottom of the system is called coacervate. Coacervates have immense applications in various technological fields. This review comprises a concise introduction, focusing on the types of coacervates, and the influence of different factors in their formation, structures, and stability. In addition, their physicochemical properties, thermodynamics of formation, and uses and multifarious applications are also concisely presented and discussed.

Random copolymer adsorption onto a periodic heterogeneous surface: A partially directed walk model

The adsorption of a single AB random copolymer (RC) chain onto an inhomogeneous ab surface with a regular periodic pattern is studied theoretically. The problem is considered within the simplest model of a partially directed random walk in two dimensions by using the method of generating functions and the annealed approximation for the averaging over disorder in the RC sequence. The existence of the "optimal" RC composition and the degree of correlation in the monomer sequence, at which the inverse transition temperature has a local minimum, is shown. This is characteristic for symmetric and weakly asymmetric surfaces, whereas for surfaces with pronounced asymmetry there is no such local minimum. The best adsorbate for a strongly asymmetric surface is the homopolymer composed of monomer units that are complimentary to the majority sites on the surface. The results for the adsorption transition point obtained in the annealed approximation are compared with the numerical results for random-periodic AB-copolymers with a long period being a quenched random sequence of A and B units. The comparison shows that the annealed approximation provides a very good quantitative estimate of the adsorption transition point.

Chemical Communication in Artificial Cells: Basic Concepts, Design and Challenges

In the past decade, the focus of bottom-up synthetic biology has shifted from the design of complex artificial cell architectures to the design of interactions between artificial cells mediated by physical and chemical cues. Engineering communication between artificial cells is crucial for the realization of coordinated dynamic behaviours in artificial cell populations, which would have implications for biotechnology, advanced colloidal materials and regenerative medicine. In this review, we focus our discussion on molecular communication between artificial cells. We cover basic concepts such as the importance of compartmentalization, the metabolic machinery driving signaling across cell boundaries and the different modes of communication used. The various studies in artificial cell signaling have been classified based on the distance between sender and receiver cells, just like in biology into autocrine, juxtacrine, paracrine and endocrine signaling. Emerging tools available for the design of dynamic and adaptive signaling are highlighted and some recent advances of signaling-enabled collective behaviours, such as quorum sensing, travelling pulses and predator-prey behaviour, are also discussed.

Functional enzyme-polymer complexes

SignificanceThe use of biological enzyme catalysts could have huge ramifications for chemical industries. However, these enzymes are often inactive in nonbiological conditions, such as high temperatures, present in industrial settings. Here, we show that the enzyme PETase (polyethylene terephthalate [PET]), with potential application in plastic recycling, is stabilized at elevated temperature through complexation with random copolymers. We demonstrate this through simulations and experiments on different types of substrates. Our simulations also provide strategies for designing more enzymatically active complexes by altering polymer composition and enzyme charge distribution.

Active Controlled and Tunable Coacervation Using Side-Chain Functional α-Helical Homopolypeptides

We report the development of new side-chain amino acid-functionalized α-helical homopolypeptides that reversibly form coacervate phases in aqueous media. The designed multifunctional nature of the side-chains was found to provide a means to actively control coacervation via mild, biomimetic redox chemistry as well as allow response to physiologically relevant environmental changes in pH, temperature, and counterions. These homopolypeptides were found to possess properties that mimic many of those observed in natural coacervate forming intrinsically disordered proteins. Despite ordered α-helical conformations that are thought to disfavor coacervation, molecular dynamics simulations of a polypeptide model revealed a high degree of side-chain conformational disorder and hydration around the ordered backbone, which may explain the ability of these polypeptides to form coacervates. Overall, the modular design, uniform nature, and ordered chain conformations of these polypeptides were found to provide a well-defined platform for deconvolution of molecular elements that influence biopolymer coacervation and tuning of coacervate properties for downstream applications.

Deciphering the Role of π-Interactions in Polyelectrolyte Complexes Using Rationally Designed Peptides

Electrostatic interactions, and specifically π-interactions play a significant role in the liquid-liquid phase separation of proteins and formation of membraneless organelles/or biological condensates. Sequence patterning of peptides allows creating protein-like structures and controlling the chemistry and interactions of the mimetic molecules. A library of oppositely charged polypeptides was designed and synthesized to investigate the role of π-interactions on phase separation and secondary structures of polyelectrolyte complexes. Phenylalanine was chosen as the π-containing residue and was used together with lysine or glutamic acid in the design of positively or negatively charged sequences. The effect of charge density and also the substitution of fluorine on the phenylalanine ring, known to disrupt π-interactions, were investigated. Characterization analysis using MALDI-TOF mass spectroscopy, H NMR, and circular dichroism (CD) confirmed the molecular structure and chiral pattern of peptide sequences. Despite an alternating sequence of chirality previously shown to promote liquid-liquid phase separation, complexes appeared as solid precipitates, suggesting strong interactions between the sequence pairs. The secondary structures of sequence pairs showed the formation of hydrogen-bonded structures with a β-sheet signal in FTIR spectroscopy. The presence of fluorine decreased hydrogen bonding due to its inhibitory effect on π-interactions. π-interactions resulted in enhanced stability of complexes against salt, and higher critical salt concentrations for complexes with more π-containing amino acids. Furthermore, UV-vis spectroscopy showed that sequences containing π-interactions and increased charge density encapsulated a small charged molecule with π-bonds with high efficiency. These findings highlight the interplay between ionic, hydrophobic, hydrogen bonding, and π-interactions in polyelectrolyte complex formation and enhance our understanding of phase separation phenomena in protein-like structures.