Selectivity of Complex Coacervation in Multi-Protein Mixtures.

Liquid-liquid phase separation of biomolecules is increasingly recognized as relevant to various cellular functions, and complex coacervation of biomacromolecules, particularly proteins, is emerging as a key mechanism for this phenomenon. Complex coacervation is also being explored as a potential protein purification method due to its potential scalability, aqueous operation, and ability to produce a highly concentrated product. However, to date most studies of complex coacervation have evaluated the phase behavior of a binary mixture of two oppositely charged macromolecules. Therefore, a comprehensive understanding of the phase behavior of complex biological mixtures has yet to be established. To address this, a panel of engineered proteins was designed to allow for quantitative analysis of the complex coacervation of individual proteins within a multi-component mixture. The behavior of individual proteins was evaluated using a defined mixture of proteins that mimics the charge profile of the E. coli proteome. To allow for direct quantification of proteins in each phase, spectrally separated fluorescent proteins were used to construct the protein mixture. From this quantitative analysis, we observed that the coacervation behavior of individual proteins in the mixture was consistent with each other, which was distinctive from the behavior when each protein was evaluated in a single-protein system. Subtle differences in biophysical properties between the proteins became noticeable in the mixture, which allowed us to elucidate parameters for protein complex coacervation. With this understanding, we successfully designed methods to enrich a range of proteins of interest from a mixture of proteins.

Charge-Patterned Disordered Peptides Tune Intracellular Phase Separation in Bacteria.

Subcellular phase-separated compartments, known as biomolecular condensates, play an important role in the spatiotemporal organization of cells. To understand the sequence-determinants of phase separation in bacteria, we engineered protein-based condensates in Escherichia coli using electrostatic interactions as the main driving force. Minimal cationic disordered peptides were used to supercharge negative, neutral, and positive globular model proteins, enabling their phase separation with anionic biomacromolecules in the cell. The phase behavior was governed by the interaction strength between the cationic proteins and anionic biopolymers, in addition to the protein concentration. The interaction strength primarily depended on the overall net charge of the protein, but the distribution of charge between the globular and disordered domains also had an impact. Notably, the protein charge distribution between domains could tune mesoscale attributes such as the size, number, and subcellular localization of condensates within E. coli cells. The length and charge density of the disordered peptides had significant effects on protein expression levels, ultimately influencing the formation of condensates. Taken together, charge-patterned disordered peptides provide a platform for understanding the molecular grammar underlying phase separation in bacteria.

Designing negative feedback loops in enzymatic coacervate droplets.

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

Aberrant phase separation is a common killing strategy of positively charged peptides in biology and human disease.

Positively charged repeat peptides are emerging as key players in neurodegenerative diseases. These peptides can perturb diverse cellular pathways but a unifying framework for how such promiscuous toxicity arises has remained elusive. We used mass-spectrometry-based proteomics to define the protein targets of these neurotoxic peptides and found that they all share similar sequence features that drive their aberrant condensation with these positively charged peptides. We trained a machine learning algorithm to detect such sequence features and unexpectedly discovered that this mode of toxicity is not limited to human repeat expansion disorders but has evolved countless times across the tree of life in the form of cationic antimicrobial and venom peptides. We demonstrate that an excess in positive charge is necessary and sufficient for this killer activity, which we name 'polycation poisoning'. These findings reveal an ancient and conserved mechanism and inform ways to leverage its design rules for new generations of bioactive peptides.

Investigating Fundamental Principles of Nonequilibrium Assembly Using Temperature-Sensitive Copolymers.

Both natural biomaterials and synthetic materials benefit from complex energy landscapes that provide the foundation for structure-function relationships and environmental sensitivity. Understanding these nonequilibrium dynamics is important for the development of design principles to harness this behavior. Using a model system of poly(ethylene glycol) methacrylate-based thermoresponsive lower critical solution temperature (LCST) copolymers, we explored the impact of composition and stimulus path on nonequilibrium thermal hysteretic behavior. Through turbidimetry analysis of nonsuperimposable heat-cool cycles, we observe that LCST copolymers show clear hysteresis that varies as a function of pendent side chain length and hydrophobicity. Hysteresis is further impacted by the temperature ramp rate, as insoluble states can be kinetically trapped under optimized temperature protocols. This systematic study brings to light fundamental principles that can enable the harnessing of out-of-equilibrium effects in synthetic soft materials.

Protein charge parameters that influence stability and cellular internalization of polyelectrolyte complex micelles.

Proteins are an important class of biologics, but there are several recurring challenges to address when designing protein-based therapeutics. These challenges include: the propensity of proteins to aggregate during formulation, relatively low loading in traditional hydrophobic delivery vehicles, and inefficient cellular uptake. This last criterion is particularly challenging for anionic proteins as they cannot cross the anionic plasma membrane. Here we investigated the complex coacervation of anionic proteins with a block copolymer of opposite charge to form polyelectrolyte complex (PEC) micelles for use as a protein delivery vehicle. Using genetically modified variants of the model protein green fluorescent protein (GFP), we evaluated the role of protein charge and charge localization in the formation and stability of PEC micelles. A neutral-cationic block copolymer, poly(oligoethylene glycol methacrylate-block-quaternized 4-vinylpyridine), POEGMA79-b-qP4VP175, was prepared via RAFT polymerization for complexation and microphase separation with the panel of engineered anionic GFPs. We found that isotropically supercharged proteins formed micelles at higher ionic strength relative to protein variants with charge localized to a polypeptide tag. We then studied GFP delivery by PEC micelles and found that they effectively delivered the protein cargo to mammalian cells. However, cellular delivery varied as a function of protein charge and charge distribution and we found an inverse relationship between the PEC micelle critical salt concentration and delivery efficiency. This model system has highlighted the potential of polyelectrolyte complexes to deliver anionic proteins intracellularly. Using this model system, we have identified requirements for the formation of PEC micelles that are stable at physiological ionic strength and that smaller protein-polyelectrolyte complexes effectively deliver proteins to Jurkat cells.

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.

Self-assembly of globular proteins with intrinsically disordered protein polyelectrolytes and block copolymers.

Intrinsically disordered polypeptides are a versatile class of materials, combining the biocompatibility of peptides with the disordered structure and diverse phase behaviors of synthetic polymers. Synthetic polyelectrolytes are capable of complex phase behavior when mixed with oppositely charged polyelectrolytes, facilitating nanoparticle formation and bulk phase separation. However, there has been limited exploration of intrinsically disordered protein polyelectrolytes as potential bio-based replacements for synthetic polyelectrolytes. Here, we produce negatively charged, intrinsically disordered polypeptides, capable of high-yield expression in E. coli and use this intrinsically disordered peptide to produce entirely protein-based polyelectrolyte complexes. The complexes display rich phase behavior, showing sensitivity to charge density, salt concentration, temperature, and charge fraction. We characterize this behavior through a combination of turbidity assays, dynamic light scattering, and transmission electron microscopy. The robust expression profile and stimuli-responsive phase behavior of the intrinsically disordered peptides demonstrates their potential as easily producible, biocompatible substitutes for synthetic polyelectrolytes.

Genetic and Covalent Protein Modification Strategies to Facilitate Intracellular Delivery.

Protein-based therapeutics represent a rapidly growing segment of approved disease treatments. Successful intracellular delivery of proteins is an important precondition for expanded in vivo and in vitro applications of protein therapeutics. Direct modification of proteins and peptides for improved cytosolic translocation are a promising method of increasing delivery efficiency and expanding the viability of intracellular protein therapeutics. In this Review, we present recent advances in both synthetic and genetic protein modifications for intracellular delivery. Active endocytosis-based and passive internalization pathways are discussed, followed by a review of modification methods for improved cytosolic delivery. After establishing how proteins can be modified, general strategies for facilitating intracellular delivery, such as chemical supercharging or inclusion of cell-penetrating motifs, are covered. We then outline protein modifications that promote endosomal escape. We finally examine the delivery of two potential classes of therapeutic proteins, antibodies and associated antibody fragments, and gene editing proteins, such as cas9.

The effects of protein charge patterning on complex coacervation.

The complex coacervation of proteins with other macromolecules has applications in protein encapsulation and delivery and for determining the function of cellular coacervates. Theoretical or empirical predictions for protein coacervates would enable the design of these coacervates with tunable and predictable structure-function relationships; unfortunately, no such theories exist. To help establish predictive models, the impact of protein-specific parameters on complex coacervation were probed in this study. The complex coacervation of sequence-specific, polypeptide-tagged, GFP variants and a strong synthetic polyelectrolyte was used to evaluate the effects of protein charge patterning on phase behavior. Phase portraits for the protein coacervates demonstrated that charge patterning dictates the protein's binodal phase boundary. Protein concentrations over 100 mg mL-1 were achieved in the coacervate phase, with concentrations dependent on the tag polypeptide sequence covalently attached to the globular protein domain. In addition to shifting the binodal phase boundary, polypeptide charge patterning provided entropic advantages over isotropically patterned proteins. Together, these results show that modest changes of only a few amino acids in the tag polypeptide sequence alter the coacervation thermodynamics and can be used to tune the phase behavior of polypeptides or proteins of interest.

Formation of Biomolecular Condensates in Bacteria by Tuning Protein Electrostatics.

While eukaryotic cells have a myriad of membrane-bound organelles enabling the isolation of different chemical environments, prokaryotic cells lack these defined reaction vessels. Biomolecular condensates-organelles that lack a membrane-provide a strategy for cellular organization without a physical barrier while allowing for the dynamic, responsive organization of the cell. It is well established that intrinsically disordered protein domains drive condensate formation via liquid-liquid phase separation; however, the role of globular protein domains on intracellular phase separation remains poorly understood. We hypothesized that the overall charge of globular proteins would dictate the formation and concentration of condensates and systematically probed this hypothesis with supercharged proteins and nucleic acids in E. coli. Within this study, we demonstrated that condensates form via electrostatic interactions between engineered proteins and RNA and that these condensates are dynamic and only enrich specific nucleic acid and protein components. Herein, we propose a simple model for the phase separation based on protein charge that can be used to predict intracellular condensate formation. With these guidelines, we have paved the way to designer functional synthetic membraneless organelles with tunable control over globular protein function.

Predicting Protein-Polymer Block Copolymer Self-Assembly from Protein Properties.

Protein-polymer bioconjugate self-assembly has attracted a great deal of attention as a method to fabricate protein nanomaterials in solution and the solid state. To identify protein properties that affect phase behavior in protein-polymer block copolymers, a library of 15 unique protein-b-poly(N-isopropylacrylamide) (PNIPAM) copolymers comprising 11 different proteins was compiled and analyzed. Many attributes of phase behavior are found to be similar among all studied bioconjugates regardless of protein properties, such as formation of micellar phases at high temperature and low concentration, lamellar ordering with increasing temperature, and disordering at high concentration, but several key protein-dependent trends are also observed. In particular, hexagonal phases are only observed for proteins within the molar mass range 20-36 kDa, where ordering quality is also significantly enhanced. While ordering is generally found to improve with increasing molecular weight outside of this range, most large bioconjugates exhibited weaker than predicted assembly, which is attributed to chain entanglement with increasing polymer molecular weight. Additionally, order-disorder transition boundaries are found to be largely uncorrelated to protein size and quality of ordering. However, the primary finding is that bioconjugate ordering can be accurately predicted using only protein molecular weight and percentage of residues contained within ß sheets. This model provides a basis for designing protein-PNIPAM bioconjugates that exhibit well-defined self-assembly and a modeling framework that can generalize to other bioconjugate chemistries.

Catalytic Biosensors from Complex Coacervate Core Micelle (C3M) Thin Films.

Enzymes have been applied to a variety of industrially and medically relevant chemistries as both catalysts and sensors. Incorporation of proteins and enzymes into complex coacervates has been demonstrated to improve the thermal, chemical, and temporal stability of enzymes in solution. In this work, a neutral-cationic block copolymer and an enzyme, alkaline phosphatase, are incorporated into complex coacervate core micelles (C3Ms) and coated onto a solid substrate to create a biocatalytic film from aqueous solution. The incorporation of photo-cross-linkable groups into the neutral block of the polymer allows the film to be cross-linked under ultraviolet light, rendering it insoluble. The morphology of the film is shown to depend most strongly on the protein loading within the film, while solvent annealing is shown to have a minimal effect. These films are then demonstrated as specific sensors for Zn2+ in solution in the presence of other metals, a model reaction for ion-selective heavy metal biosensing useful in environmental monitoring. They are shown to have low leaching and maintain sufficient activity and response for sensing for 1 month after aging under ambient conditions and at 40 °C and 50% relative humidity. The C3M immobilization method demonstrated can be applied to a wide variety of proteins with minimal chemical or genetic modification and could be used for immobilization of charged macromolecules in general to produce a wide variety of thin-film devices.

Macro- and Microphase Separated Protein-Polyelectrolyte Complexes: Design Parameters and Current Progress.

Protein-containing polyelectrolyte complexes (PECs) are a diverse class of materials, composed of two or more oppositely charged polyelectrolytes that condense and phase separate near overall charge neutrality. Such phase-separation can take on a variety of morphologies from macrophase separated liquid condensates, to solid precipitates, to monodispersed spherical micelles. In this review, we present an overview of recent advances in protein-containing PECs, with an overall goal of defining relevant design parameters for macro- and microphase separated PECs. For both classes of PECs, the influence of protein characteristics, such as surface charge and patchiness, co-polyelectrolyte characteristics, such as charge density and structure, and overall solution characteristics, such as salt concentration and pH, are considered. After overall design features are established, potential applications in food processing, biosensing, drug delivery, and protein purification are discussed and recent characterization techniques for protein-containing PECs are highlighted.

Ionic polypeptide tags for protein phase separation.

Polyelectrolytes of opposite charge in aqueous solution can undergo a liquid-liquid phase separation known as complex coacervation. Complex coacervation of ampholytic proteins with oppositely charged polyelectrolytes is of increasing interest as it results in a protein rich phase that has potential applications in protein therapeutics, protein purification, and biocatalysis. However, many globular proteins do not phase separate when mixed with an oppositely charged polyelectrolyte, and those that do phase separate do so over narrow concentration, pH, and ionic strength ranges. The protein design factors that govern complex coacervation under varying conditions are still relatively unexplored. Recent work indicates that proteins with an intrinsically disordered region, a higher net charge, or a patch of charged residues are more likely to undergo a phase transition. Based on these design parameters, polyionic coacervation tags were designed and assessed for their ability to promote protein complex coacervation with oppositely charged polyelectrolytes. The phase behavior of a panel of engineered proteins was evaluated with the strong polycation poly(4-vinyl N-methyl pyridinium iodide). Proteins containing the ionic tags formed liquid coacervate droplets, while isotropically charged protein variants formed solid precipitates. The ionic tags also promoted phase separation at higher salt concentrations than an isotropic distribution of charge on the protein surface. The salt dependence of the protein complex coacervation could be predicted independently for tagged or isotropic variants by the ratio of negative-to-positive residues on the proteins and universally by calculating the distance between like charges. The addition of just a six residue polyionic tag generated a globular protein capable of liquid-liquid phase separation at physiological pH and ionic strength. This model system has provided the initial demonstration that short, ionic polypeptide sequences (6-18 amino acids) can drive the liquid-liquid phase separation of globular proteins.

Phase Separation Behavior of Supercharged Proteins and Polyelectrolytes.

Membraneless organelles, like membrane-bound organelles, are essential to cell homeostasis and provide discrete cellular subcompartments. Unlike classical organelles, membraneless organelles possess no physical barrier but rather arise by phase separation of the organelle components from the surrounding cytoplasm or nucleoplasm. Complex coacervation, the liquid-liquid phase separation of oppositely charged polyelectrolytes, is one of several phenomena that are hypothesized to drive the formation and regulation of some membraneless organelles. Studies of the molecular properties of globular proteins that drive complex coacervation are limited as many proteins do not form complexes with oppositely charged macromolecules at neutral pH and moderate ionic strengths. Protein supercharging overcomes this problem and drives complexation with oppositely charged macromolecules. In this work, several distinct cationic supercharged green fluorescent protein (GFP) variants were designed to examine the phase behavior with oppositely charged polyanionic macromolecules. Cationic GFP variants phase separated with oppositely charged macromolecules at various mixing ratios, salt concentrations, and pH values. Efficient protein incorporation in the macromolecule rich phase occurred over a range of protein and polymer mass fractions, but the protein encapsulation efficiency was highest at the midpoint of the phase separation regime. More positively charged proteins phase separated over broader pH and salt ranges than those of proteins with a lower charge density. Interestingly, each GFP variant phase separated at higher salt concentrations with anionic synthetic macromolecules compared to anionic biological macromolecules. Optical microscopy revealed that most variants, depending on solution conditions, formed liquid-liquid phase separations, except for GFP/DNA pairs that formed solid aggregates under all tested conditions.

Three-Dimensional Ordered Antibody Arrays Through Self-Assembly of Antibody-Polymer Conjugates.

Three-dimensional (3D) ordered arrays of human immunoglobulin G (IgG) were fabricated using well-defined full-length antibody-polymer conjugates (APCs). The conjugates were prepared through a two-step sequential click approach with a combination of oxime ligation and strain promoted alkyne-azide cycloaddition. They were able to self-assemble into lamellar nanostructures with alternating IgG and poly(N-isopropylacrylamide) (PNIPAM) nanodomains. As a proof-of-concept, these materials were fabricated into thin films and their specific binding ability was tested. The nanostructure not only improves the packing density and the proper orientation of the IgG, but also provides nanochannels to facilitate substrate transport.

Complex Coacervate Core Micelles for the Dispersion and Stabilization of Organophosphate Hydrolase in Organic Solvents.

Organophosphate (OP) nerve agents are a class of chemical warfare agents (CWAs) that exist as bulk stocks in current and past war zones. Thus, a technology that can perform on-site decontamination in a safe and timely fashion is desirable. Here, complex coacervate core micelles (C3Ms) were used to encapsulate organophosphate hydrolase (OPH) and chemostabilize it to maintain activity after exposure to organophosphate simulants ethanol and dimethyl methylphosphonate (DMMP). C3Ms were formed by two polymers-poly(acrylic acid) (PAA) and poly(oligo(ethylene glycol) methacrylate)-b-poly(4-vinyl N-methylpyridyl iodide), (POEGMA-b-qP4VP). Complexes of the coacervate micelles with the enzyme OPH were investigated by small angle neutron scattering (SANS), dynamic light scattering (DLS), and transmission electron microscopy (TEM), demonstrating the formation of micellar structures in solution. The activity of OPH against methyl paraoxon in these C3Ms under aqueous conditions was assayed after heat treatment for 3 days at 37 °C. The OPH in C3Ms retained 88 ± 7% of its initial activity, as compared to the 48 ± 3% activity retained by OPH alone, indicating that the C3Ms were able to stabilize the enzyme to heat treatment. C3Ms transferred into the two organic solvents formed larger structures than inverse micelles formed by the block copolymer alone. The addition of OPH to the C3Ms in organic solvents did not significantly change their structure. The activity of OPH (again, against methyl paraoxon) after 24 h of incubation at 4 °C was measured and compared to that of OPH in C3Ms. While OPH alone retained less than 5% of its activity after this incubation in both solvents, OPH in C3Ms retained 35 ± 3% of its activity in DMMP and 26 ± 1% of its activity in ethanol.

Direct detection of nitrotyrosine-containing proteins using an aniline-based oxidative coupling strategy.

A convenient two-step method is described for the detection of nitrotyrosine-containing proteins. First, nitrotyrosines are reduced to aminophenols using sodium dithionite. Following this, an oxidative coupling reaction is used to attach anilines bearing fluorescence reporters or affinity probes. Features of this approach include fast reaction times, pmol-level sensitivity, and excellent chemoselectivity.