Connected Peptide Modules Enable Controlled Co-Existence of Self-Assembled Fibers Inside Liquid Condensates

Programmable Coacervate Droplets via Reaction-Coupled Liquid-Liquid Phase Separation (LLPS) and Competitive Inhibition

Membraneless biomolecular condensates formed by liquid-liquid phase separation (LLPS) are crucial for many spatiotemporal biological functions. Designing synthetic mimics to emulate and understand LLPS is an active area of research, which has led to the development of coacervate droplets through elegant bioinspired designs. However, recent interest in this field has shifted toward designing programmable coacervates to impart spatiotemporal control over these liquid phases. Herein, we demonstrate the programming of LLPS in synthetic systems by employing concepts of competitive binding and reaction-coupled assembly involving dynamic covalent bonds. Our results utilize small building blocks that follow a simple coacervation mechanism, distinguishing this approach from previously reported programmable complex coacervates, which often rely on reaction-controlled generation of one of the components. We introduce these concepts using dynamic covalent bonds (boronate esters) and small chromophoric building blocks appended with terminal boronic acid groups. Upon reaction with substrates (monosaccharides), these building blocks form molecular structures resembling "sticker-and-spacer" designs for coacervation, leading to a reaction-driven, temporally controlled LLPS process. The differential reactivity of various monosaccharides, combined with the reversibility of dynamic bonds, enables competitive binding-driven control over the growth, inhibition, and dissolution of the coacervation process, offering new strategies for programmable LLPS that are reminiscent of protein-induced inhibition in biomolecular condensates. Detailed spectroscopic probing and kinetic analyses provide mechanistic insights into the reaction-coupled and autocatalytic growth processes, revealing the glucose-selective nature of this coacervation system. Finally, coupling dynamic covalent reactions with temporal pH modulation results in transient coacervation, which can be visualized by using confocal microscopy. We anticipate that this approach will pave the way for designing coacervate droplets with novel biorelevant emergent properties.

Catalytically Active Coacervates Sustained Out-of-Equilibrium

Metabolically active membraneless organelles of extant biology have the capability to maintain their structure under nonequilibrium conditions by leveraging chemical reactions. Herein, we report active coacervates accessed via a mixture of minimal building blocks that featured π-electron rich short peptide, positively charged aldehyde, and a cyclic ketone under nonequilibrium conditions. Peptide bound with the aldehyde by a dynamic covalent bond and demixed to form coacervates through hydrophobic interactions. Importantly, the short-peptide could utilize its free amine (β-alanine) to catalyze C─C bond formation which eventually led to the depletion of one of the building blocks (aldehyde) via aldol reaction; an intrinsic catalytic role that helped the coacervate to suppress coalescence. Notably, under continuous additions (open system) of the depleting precursors, the active coacervates were able to demonstrate spatial stability for longer duration. This out-of-equilibrium behavior of phase separated droplets in presence of flux of building blocks is reminiscent of the active membraneless organelles seen in contemporary biochemistry.

Redox-Controlled, Sequential Self-Sorting of Supramolecular Assemblies in Model Protocells

Self-sorting of cellular components is essential for maintaining order and function in living systems, enabling complex processes to operate seamlessly. Emulating such self-sorting in synthetic self-assembly, however, has conventionally relied on structural or chirality mismatches of monomers yielding self-sorted systems under thermodynamic conditions. In contrast, reaction-coupled, kinetically controlled self-assembly, ubiquitous in biological systems, is critical for achieving spatiotemporal characteristics. Extending this principle to temporally self-sorted synthetic assemblies is key to developing multi-component biomimetic systems. Herein, we present a strategy towards this direction, to achieve sequential self-sorting of supramolecular assemblies through differences in the chemical-reactivity of monomers, coupled to redox-reactions. This approach exploits the distinct redox potentials of monomers to achieve precise temporal-control over self-sorting, while inherent structural mismatches among monomers ensure the kinetic stability of self-sorted state. Reduction reactions transiently disrupt their assemblies into dormant inactive monomeric states, while subsequent kinetically controlled reassembly occurs via reversible oxidation reactions. Finally, utilizing this sequential self-sorting, we aim to mimic multicomponent cellular self-organization by demonstrating the kinetically controlled growth of self-sorted structures in the presence of model protocells, using lipid vesicles as compartments. Although spatial-distribution remains non-selective, the dormant monomeric states facilitate monomer encapsulation and the unprecedented stepwise-formation of self-sorted assemblies within model protocells.

Fragment-Based Approach for Hierarchical Nanotube Assembly of Small Molecules in Aqueous Phase

A fragment-based approach has proven successful in drug design and protein assemblies, yet its potential for constructing biomaterials from simple organic building blocks remains underexplored, particularly for self-assembly in aqueous phases, where water disrupts intermolecular hydrogen bonding. To the best of our knowledge, this study introduces the first case of integrating fragments from self-assembling molecules to design a small organic molecule that forms novel hierarchical nanotubes with polymorphism. The molecule's compact design incorporates three structural motifs derived from known nanotube assemblies, enabling a hierarchical assembly process: individual molecules with two conformations form dimers, which organize into hexameric units. These hexamers further assemble into nanotubes comprising 2-, 5-, and 6-protofilament fibers. The nanofibers share a nearly identical asymmetric unit - a hexameric triangular plate - with similar axial and lateral interfaces. The lateral interface, involving interactions between phosphate groups and aromatic rings, exhibits plasticity, allowing slight rotational variations between adjacent units. This adaptability facilitates the formation of diverse nanofiber architectures, showcasing the flexibility of these systems in aqueous environments. By leveraging fragments of self-assembling molecules, this work demonstrates a straightforward strategy that combines conformational flexibility and self-assembling fragments to construct advanced supramolecular biomaterials from small organic building blocks in aqueous settings.

Multiphasic condensates formed with mono-component of tetrapeptides via phase separation

Biomolecular condensates, formed by liquid-liquid phase separation of biomacromolecules, play crucial roles in regulating physiological events in biological systems. While multiphasic condensates have been extensively studied, those derived from a single component of short peptides have not yet been reported. Here, we report the symmetrical core-shell structural biomolecular condensates formed with a programmable tetrapeptide library via phase separation. Our findings reveal that tryptophan is essential for core-shell structure formation due to its strongest homotypical π-π interaction, enabling us to modulate the structure of condensates from core-shell to homogeneous by altering the amino acid composition. Molecular dynamics simulation combined with cryogenic focused ion beam scanning electron microscopy and cryogenic electron microscopy show that the inner core of multiphasic tetrapeptide condensates is solid-like, consisting of ordered structures. The core is enveloped by a liquid-like shell, stabilizing the core structure. Furthermore, we demonstrate control over multiphasic condensate formation through intrinsic redox reactions or post-translational modifications, facilitating the rational design of synthetic multiphasic condensates for various applications on demand.

The Impact of Single Amino Acid Insertion on the Supramolecular Assembly Pathway of Aromatic Peptide Amphiphiles

Understanding the mechanism of self-assembly driven by non-covalent interactions is crucial for designing supramolecular materials with desired properties. Here we investigate the self-assembly of aromatic peptide amphiphiles, Fmoc-L2QG and Fmoc-L3QG using a combination of spectroscopic, transmission electron and superresolution optical microscopy techniques. Our results show that Fmoc-L2QG leads to concentration-dependent assembly, forming fibrous assemblies at low concentrations and supramolecular droplets via liquid-liquid phase separation (LLPS) at higher concentrations. Mechanical activation using for example ultrasonication triggered the transition from metastable droplets to fibre morphologies of Fmoc-L2QG. In contrast, Fmoc-L3QG followed both on-pathway and off-pathway routes, resulting in the formation of fibrous morphologies regardless of concentration. Seeding experiments revealed that homo-seeds of the same peptide sequence accelerated the on-pathway process, while hetero-seeds of a mismatched peptide sequences accelerated the off-pathway process, highlighting the competing nature of the complex assembly profile. These findings demonstrate the significant impact of single amino acid insertion on the supramolecular assembly process of oligopeptide monomers, and highlight the potential for controlling the structure and dynamics of peptide materials. Pathway engineering of oligopeptide building blocks and multidomain supramolecular monomers will open new avenues in tailor-made and customizable supramolecular biomaterials.

Synthetic Biomolecular Condensates: Phase-Separation Control, Cytomimetic Modelling and Emerging Biomedical Potential

Liquid-liquid phase separation towards the formation of synthetic coacervate droplets represents a rapidly advancing frontier in the fields of synthetic biology, material science, and biomedicine. These artificial constructures mimic the biophysical principles and dynamic features of natural biomolecular condensates that are pivotal for cellular regulation and organization. Via adapting biological concepts, synthetic condensates with dynamic phase-separation control provide crucial insights into the fundamental cell processes and regulation of complex biological pathways. They are increasingly designed with the ability to display more complex and ambitious cell-like features and behaviors, which offer innovative solutions for cytomimetic modeling and engineering active materials with sophisticated functions. In this minireview, we highlight recent advancements in the design and construction of synthetic coacervate droplets; including their biomimicry structure and organization to replicate life-like properties and behaviors, and the dynamic control towards engineering active coacervates. Moreover, we highlight the unique applications of synthetic coacervates as catalytic centers and promising delivery vehicles, so that these biomimicry assemblies can be translated into practical applications.

Selective peptide bond formation via side chain reactivity and self-assembly of abiotic phosphates

In the realm of biology, peptide bonds are formed via reactive phosphate-containing intermediates, facilitated by compartmentalized environments that ensure precise coupling and folding. Herein, we use aminoacyl phosphate esters, synthetic counterparts of biological aminoacyl adenylates, that drive selective peptide bond formation through side chain-controlled reactivity and self-assembly. This strategy results in the preferential incorporation of positively charged amino acids from mixtures containing natural and non-natural amino acids during the spontaneous formation of amide bonds in water. Conversely, aminoacyl phosphate esters that lack assembly and exhibit fast reactivity result in random peptide coupling. By introducing structural modifications to the phosphate esters (ethyl vs. phenyl) while retaining aggregation, we are able to tune the selectivity by incorporating aromatic amino acid residues. This approach enables the synthesis of sequences tailored to the specific phosphate esters, overcoming limitations posed by certain amino acid combinations. Furthermore, we demonstrate that a balance between electrostatic and aromatic stacking interactions facilitates covalent self-sorting or co-assembly during oligomerization reactions using unprotected N-terminus aminoacyl phosphate esters. These findings suggest that self-assembly of abiotic aminoacyl phosphate esters can activate a selection mechanism enabling the departure from randomness during the autonomous formation of amide bonds in water.

Dynamic Peptide Nanoframework-Guided Protein Coassembly: Advancing Adhesion Performance with Hierarchical Structures

Hierarchical structures are essential in natural adhesion systems. Replicating these in synthetic adhesives is challenging due to intricate molecular mechanisms and multiscale processes. Here, we report three phosphorylated peptides featuring a hydrophobic self-assembly motif linked to a hydrophilic phosphorylated sequence (pSGSS), forming peptide fibril nanoframeworks. These nanoframeworks effectively coassemble with elastin-derived positively charged proteins (PCP), resulting in complex coacervate-based adhesives with hierarchical structures. Our method enables the controlled regulation of both cohesion and adhesion properties in the adhesives. Notably, the complex adhesives formed by the dityrosine-containing peptide and PCP demonstrate an exceptional interfacial adhesion strength of up to 30 MPa, outperforming most known supramolecular adhesives and rivaling cross-linked chemical adhesives. Additionally, these adhesives show promising biocompatibility and bioactivity, making them suitable for applications such as visceral hemostasis and tissue repair. Our findings highlight the utility of bioinspired hierarchical assembly combined with bioengineering techniques in advancing biomedical adhesives.

Bioinspired programmable coacervate droplets and self-assembled fibers through pH regulation of monomers

Phase separation and phase transitions pervade the biological domain, where proteins and RNA engage in liquid-liquid phase separation (LLPS), forming liquid-like membraneless organelles. The misregulation or dysfunction of these proteins culminates in the formation of solid aggregates via a liquid-to-solid transition, leading to pathogenic conditions. To decipher the underlying mechanisms, synthetic LLPS has been examined through complex coacervate formation from charged polymers. Nonetheless, temporal control over phase transitions from prebiotically relevant small organic synthons remains largely unexplored. Herein, we propose utilizing pH modulation to regulate the charge of small molecular building blocks, thereby controlling the LLPS process. Through a bio-inspired, enzyme-mediated pH-regulated reaction, we introduce temporal control over both LLPS and the transition from coacervates to supramolecular polymers. Additionally, by incorporating antagonistic pH modulators, we achieve transient LLPS and further temporal regulation of supramolecular polymer disassembly. Our investigation into pH-regulated LLPS provides a new avenue for exploring the stimuli-responsive, dynamic, and transient nature of LLPS.

Construction of Somatostatin-Based Multiphase "Core-Shell" Coacervates as Photodynamic Biomimetic Organelles

Biomimetic coacervates have recently attracted great interest in biomedical fields, especially for drug delivery and as protocells. However, these membraneless structures are easily coalesced and poorly targetable, limiting their real biomedical applications. Here multiphase "core-shell" coacervate (CSC) constructed by dsDNA and somatostatin (SST), a 14-mer cyclopeptide is designed. The CSC shows enhanced tumor targetability through SST binding to SST receptors on the tumor cells' surface. G4 quadruplex-hemin complex can be embedded in the CSC by interaction with SST, as demonstrated by molecular simulation and isothermal titration calorimetry. The G4-hemin embedded CSC can further recruit photosensitizers such as tetracarboxyphenyl porphyrin to form the CSC-GHT composite for photodynamic therapy (PDT). As photodynamic biomimetic organelles, CSC-GHT can convert oxygen to singlet oxygen (catalyzed by the catalase-mimetic activity of G4-hemin), resulting in enhanced PDT effect, which allows the inhibition of cellular migration in vitro and tumor growth in vivo. Owing to high stability, targetability, and biosafety, the proposed CSC can recruit various cargos from small dyes to large biomacromolecules (up to 430 kDa), providing promising theranostic applications.

Enzymatic Reaction Network-Driven Polymerization-Induced Transient Coacervation

A living cell has a highly complex microenvironment whereas numerous enzyme-driven processes are active at once. These procedures are incredibly accurate and efficient, although comparable control has not yet been established in vitro. Here, we design an enzymatic reaction network (ERN) that combines antagonistic and orthogonal enzymatic networks to produce adjustable dynamics of ATP-fueled transient coacervation. Using horseradish peroxidase (HRP)-mediated Biocatalytic Atom Transfer Radical Polymerization (BioATRP), we synthesized poly(dimethylaminoethyl methacrylate), which subsequently formed coacervates with ATP. We rationally explored enzymatic control over coacervation and dissolution, using orthogonal and antagonistic enzyme pairs viz., alkaline phosphatase, Creatine phosphokinase, hexokinase, esterase, and urease. ATP-fuelled coacervates also demonstrate the enzymatic catalysis to prove its potential to be exploited as a cellular microreactor. Additionally, we developed ERN-polymerization-induced transient coacervation (ERN-PIC), with complete control over the system, polymerization, coacervation, and dissolution. Notably, the coacervation process itself determines functional properties, as seen in selective cargo uptake. The strategy offers cutting-edge biomimetic applications, and insights into cellular compartmentalization by bridging the gap between synthetic and biological systems. The development of temporally programmed coacervation is promising for the spatial arrangement of multienzyme cascades, and offers novel ideas on the architecture of artificial cells.

Liquid-Liquid Phase Separation Mediated Formation of Chiral 2D Crystalline Nanosheets of a Co-Assembled System

The role of macromolecule-macromolecule and macromolecule-H2O interactions and the resulting perturbation of the H-bonded network of H2O in the liquid-liquid phase separation (LLPS) process of biopolymers are well-known. However, the potential of the hydrated state of supramolecular structures (non-covalent analogs of macromolecules) of synthetic molecules is not widely recognized for playing a similar role in the LLPS process. Herein, LLPS occurred during the co-assembly of hydrated supramolecular vesicles (bolaamphiphile, BA1) with a net positive charge (zeta potential, ζ = +60 ± 2 mV) and a dianionic chiral molecule (disodium l-[+]-tartrate) is reported. As inferred from cryo-transmission electron microscopy (TEM), the LLPS-formed droplets serve as the nucleation precursors, dictating the structure and properties of the co-assembly. The co-assembled structure formed by LLPS effectively integrates the counter anion's asymmetry, resulting in the formation of ultrathin free-standing, chiral 2D crystalline sheets. The significance of the hydrated state of supramolecular structures in influencing LLPS is unraveled through studies extended to a less hydrated supramolecular structure of a comparable system (BA2). The role of LLPS in modulating the hydrophobic interaction in water paves the way for the creation of advanced functional materials in an aqueous environment.

Nucleotide-mediated modulation of chemoselective protein functionalization in a liquid-like condensed phase

Liquid-like protein condensates are ubiquitous in cellular system and are increasingly recognized for their roles in physiological processes. Condensed phase harbors distinctive chemical microenvironment, markedly different than dilute aqueous phase. Herein, we demonstrate chemoselective modification pattern of nucleophilic canonical amino acid sidechains (namely - cysteine, tyrosine and lysine) of the protein towards 4-chloro-7-nitrobenzofurazan in the dilute and condensed phase. We also delineate how the effect of nucleotides and their in situ enzymatic dissociation temporally modulate the protein condensate's pH and the protein's corresponding chemoselective modification. We have shown that the pH of the condensate decreases in the presence of nucleoside triphosphate, whereas it increases in the presence of nucleoside monophosphates or phosphate ion. For instance, we find lysine-specific modification gets inhibited in the presence of adenosine triphosphate (ATP), but significantly enhanced in the presence of monophosphates. This feature enables us to gain temporal control over dynamic change in protein functionalization via enzymatic ATP hydrolysis. Overall, this work substantiates the alteration in pH-responsiveness of Brønsted basicity of a protein's ε-amine in the condensed phase. Furthermore, this environment sensitivity in chemoselective protein functionalization in condensed phase will be important in adaptable protein engineering to the chemical biology of protein phase separation.

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.

Regulation of Peptide Liquid-Liquid Phase Separation by Aromatic Amino Acid Composition

Membraneless organelles are cellular biomolecular condensates that are formed by liquid-liquid phase separation (LLPS) of proteins and nucleic acids. LLPS is driven by multiple weak attractive forces, including intermolecular interactions mediated by aromatic amino acids. Considering the contribution of π-electron bearing side chains to protein-RNA LLPS, systematically study sought to how the composition of aromatic amino acids affects the formation of heterotypic condensates and their physical properties. For this, a library of minimalistic peptide building blocks is designed containing varying number and compositions of aromatic amino acids. It is shown that the number of aromatics in the peptide sequence affect LLPS propensity, material properties and (bio)chemical stability of peptide/RNA heterotypic condensates. The findings shed light on the contribution of aromatics' composition to the formation of heterotypic condensates. These insights can be applied for regulation of condensate material properties and improvement of their (bio)chemical stability, for various biomedical and biotechnological applications.

Emergence of a short peptide based reductase via activation of the model hydride rich cofactor

In extant biology, large and complex enzymes employ low molecular weight cofactors such as dihydronicotinamides as efficient hydride transfer agents and electron carriers for the regulation of critical metabolic processes. In absence of complex contemporary enzymes, these molecular cofactors are generally inefficient to facilitate any reactions on their own. Herein, we report short peptide-based amyloid nanotubes featuring exposed arrays of cationic and hydrophobic residues that can bind small molecular weak hydride transfer agents (NaBH4) to facilitate efficient reduction of ester substrates in water. In addition, the paracrystalline amyloid phases loaded with borohydrides demonstrate recyclability, substrate selectivity and controlled reduction and surpass the capabilities of standard reducing agent such as LiAlH4. The amyloid microphases and their collaboration with small molecular cofactors foreshadow the important roles that short peptide-based assemblies might have played in the emergence of protometabolism and biopolymer evolution in prebiotic earth.

Protein misfolding and amyloid nucleation through liquid-liquid phase separation

Liquid-liquid phase separation (LLPS) is an emerging phenomenon in cell physiology and diseases. The weak multivalent interaction prerequisite for LLPS is believed to be facilitated through intrinsically disordered regions, which are prevalent in neurodegenerative disease-associated proteins. These aggregation-prone proteins also exhibit an inherent property for phase separation, resulting in protein-rich liquid-like droplets. The very high local protein concentration in the water-deficient confined microenvironment not only drives the viscoelastic transition from the liquid to solid-like state but also most often nucleate amyloid fibril formation. Indeed, protein misfolding, oligomerization, and amyloid aggregation are observed to be initiated from the LLPS of various neurodegeneration-related proteins. Moreover, in these cases, neurodegeneration-promoting genetic and environmental factors play a direct role in amyloid aggregation preceded by the phase separation. These cumulative recent observations ignite the possibility of LLPS being a prominent nucleation mechanism associated with aberrant protein aggregation. The present review elaborates on the nucleation mechanism of the amyloid aggregation pathway and the possible early molecular events associated with amyloid-related protein phase separation. It also summarizes the recent advancement in understanding the aberrant phase transition of major proteins contributing to neurodegeneration focusing on the common disease-associated factors. Overall, this review proposes a generic LLPS-mediated multistep nucleation mechanism for amyloid aggregation and its implication in neurodegeneration.

Controlled Supramolecular Polymerization via Bioinspired, Liquid-Liquid Phase Separation of Monomers

Dynamic supramolecular assemblies, driven by noncovalent interactions, pervade the biological realm. In the synthetic domain, their counterparts, supramolecular polymers, endowed with remarkable self-repair and adaptive traits, are often realized through bioinspired designs. Recently, controlled supramolecular polymerization strategies have emerged, drawing inspiration from protein self-assembly. A burgeoning area of research involves mimicking the liquid-liquid phase separation (LLPS) observed in proteins to create coacervate droplets and recognizing their significance in cellular organization and diverse functions. Herein, we introduce a novel perspective on synthetic coacervates, extending beyond their established role in synthetic biology as dynamic, membraneless phases to enable structural control in synthetic supramolecular polymers. Drawing parallels with the cooperative growth of amyloid fibrils through LLPS, we present metastable coacervate droplets as dormant monomer phases for controlled supramolecular polymerization. This is achieved via a π-conjugated monomer design that combines structural characteristics for both coacervation through its terminal ionic groups and one-dimensional growth via a π-conjugated core. This design leads to a unique temporal LLPS, resulting in a metastable coacervate phase, which subsequently undergoes one-dimensional growth via nucleation within the droplets. In-depth spectroscopic and microscopic characterization provides insights into the temporal evolution of disordered and ordered phases. Furthermore, to modulate the kinetics of liquid-to-solid transformation and to achieve precise control over the structural characteristics of the resulting supramolecular polymers, we invoke seeding in the droplets, showcasing living growth characteristics. Our work thus opens up new avenues in the exciting field of supramolecular polymerization, offering general design principles and controlled synthesis of precision self-assembled structures in confined environments.

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.

Understanding and fine tuning the propensity of ATP-driven liquid-liquid phase separation with oligolysine

Liquid-liquid phase separation (LLPS) plays a pivotal role in the organization and functionality of living cells. It is imperative to understand the underlying driving forces behind LLPS and to control its occurrence. In this study, we employed coarse-grained (CG) simulations as a research tool to investigate systems comprising oligolysine and adenosine triphosphate (ATP) under conditions of various ionic concentrations and oligolysine lengths. Consistent with experimental observations, our CG simulations captured the formation of LLPS upon the addition of ATP and tendency of dissociating under high ionic concentration. The electrostatic interaction between oligolysine and ATP is of great importance in forming LLPS. An in-depth analysis on the structural properties of LLPS was conducted, where the oligolysine structure remained unchanged with increased ionic concentration and the addition of ATP led to a more pronounced curvature, aligning with the observed enhancement of α-helical secondary structure in experiments. In terms of the dynamic properties, the introduction of ATP led to a significant reduction in translational and vibrational degrees of freedom but not rotational degrees of freedom. Through keeping the total number of charged residues constant and varying their entropic effects, we constructed two systems of similar biochemical significance and further validated the entropy effects on the LLPS formation. These findings provide a deeper understanding of LLPS formation and shed lights on the development of novel bioreactor and primitive artificial cells for synthesizing key chemicals for certain diseases.

Sequestration within peptide coacervates improves the fluorescence intensity, kinetics, and limits of detection of dye-based DNA biosensors

Peptide-based liquid-liquid phase separated domains, or coacervates, are a biomaterial gaining new interest due to their exciting potential in fields ranging from biosensing to drug delivery. In this study, we demonstrate that coacervates provide a simple and biocompatible medium to improve nucleic acid biosensors through the sequestration of both the biosensor and target strands within the coacervate, thereby increasing their local concentration. Using the well-established polyarginine (R9) - ATP coacervate system and an energy transfer-based DNA molecular beacon we observed three key improvements: i) a greater than 20-fold reduction of the limit of detection within coacervates when compared to control buffer solutions; ii) an increase in the kinetics, equilibrium was reached more than 4-times faster in coacervates; and iii) enhancement in the dye fluorescent quantum yields within the coacervates, resulting in greater signal-to-noise. The observed benefits translate into coacervates greatly improving bioassay functionality.

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.

Exploring Peptido-Nanocomposites in the Context of Amyloid Diseases

Therapeutic peptides are a major class of pharmaceutical drugs owing to their target-binding specificity as well as their versatility in inhibiting aberrant protein-protein interactions associated with human pathologies. Within the realm of amyloid diseases, the use of peptides and peptidomimetics tailor-designed to overcome amyloidogenesis has been an active research endeavor since the late 90s. In more recent years, incorporating nanoparticles for enhancing the biocirculation and delivery of peptide drugs has emerged as a frontier in nanomedicine, and nanoparticles have further demonstrated a potency against amyloid aggregation and cellular inflammation to rival strategies employing small molecules, peptides, and antibodies. Despite these efforts, however, a fundamental understanding of the chemistry, characteristics and function of peptido-nanocomposites is lacking, and a systematic analysis of such strategy for combating a range of amyloid pathogeneses is missing. Here we review the history, principles and evolving chemistry of constructing peptido-nanocomposites from bottom up and discuss their future application against amyloid diseases that debilitate a significant portion of the global population.

Thermo-Chemical Cues-Mediated Strategy to Control Peptide Self-Assembly and Charge Transfer Complexation

Peptide amphiphiles (PAs) are known for their remarkable ability to undergo molecular self-assembly, a process that is highly responsive to the local microenvironment. Herein, we design a pyrene tethered peptide amphiphile Py-VFFAKK, 1 that exhibits pathway-driven self-assembly from metastable nanoparticles to kinetically controlled nanofibers and thermodynamically stable twisted bundles upon modulations in pH, temperature, and chemical cues. The presence of the pyrene moiety ensures donation of the electron to an electron acceptor, namely, 7,7,8,8-tetracyanoquinodimethane (TCNQ), to form a supramolecular charge transfer complex in aqueous solution that was studied in detail with microscopic and spectroscopic techniques. Excitation of the donor species in its excimer state facilitates electron donation to the acceptor moiety, paving away a long-lived charge-separated state that persists for over a nanosecond, as ascertained through transient absorption spectroscopy. Finally, the self-assembled charge transfer complex is explored toward antimicrobial properties with Escherichia coli while maintaining biocompatibility toward L929 mice fibroblast cells.

Coacervate Droplets for Synthetic Cells

The design and construction of synthetic cells - human-made microcompartments that mimic features of living cells - have experienced a real boom in the past decade. While many efforts have been geared toward assembling membrane-bounded compartments, coacervate droplets produced by liquid-liquid phase separation have emerged as an alternative membrane-free compartmentalization paradigm. Here, the dual role of coacervate droplets in synthetic cell research is discussed: encapsulated within membrane-enclosed compartments, coacervates act as surrogates of membraneless organelles ubiquitously found in living cells; alternatively, they can be viewed as crowded cytosol-like chassis for constructing integrated synthetic cells. After introducing key concepts of coacervation and illustrating the chemical diversity of coacervate systems, their physicochemical properties and resulting bioinspired functions are emphasized. Moving from suspensions of free floating coacervates, the two nascent roles of these droplets in synthetic cell research are highlighted: organelle-like modules and cytosol-like templates. Building the discussion on recent studies from the literature, the potential of coacervate droplets to assemble integrated synthetic cells capable of multiple life-inspired functions is showcased. Future challenges that are still to be tackled in the field are finally discussed.

Localized and regulated peptide pigment formation inside liquid droplets through confined enzymatic oxidation

Melanin pigments are found in most life forms, where they are responsible for coloration and ultraviolet (UV) light protection. Natural melanin is a poorly soluble and complex biosynthesis product produced through confined and templated enzymatic oxidation of tyrosine. It has been challenging to create water-soluble synthetic mimics. This study demonstrates the enzymatic synthesis of oxidized phenols confined inside liquid droplets. We use an amphiphilic, bifunctional peptide, DYFR9, that combines a tyrosine tripeptide previously shown to undergo enzymatic oxidation to form peptide pigments with broad absorbance, and polyarginine to facilitate complex coacervation in the presence of ATP. When ATP, DYFR9 are mixed and exposed to tyrosinase, pigmented liquid droplets result, while no appreciable oxidation is observed in the bulk.

Liquid-Liquid Phase Separation (LLPS)-Driven Fibrilization of Amyloid-β Protein

Amyloid-β [Aβ(1-40)] aggregation into a fibrillar network is one of the major hallmarks of Alzheimer's disease (AD). Recently, a few studies reported that polyphosphate (polyP), an anionic biopolymer that participates in various cellular physiological processes in humans, induces fibrilization in many amyloidogenic proteins [ 2020 Alzheimer's Disease Facts and Figures; John Wiley and Sons Inc., 2020; Tanzi, R. E.; Bertram, L. Cell 2005, 120, 545-555; Selkoe, D. J. Proc. Natl. Acad. Sci. U.S.A. 1995, 275, 630-631; and Rambaran, R. N.; Serpell, L. C. Prion 2008, 2, 112-117]. However, the role of polyP in Aβ(1-40) fibrilization and the underlying mechanism are unclear. In this study, we report experimental investigations on the role of polyP in the fibrilization kinetics of Aβ(1-40). It is found that polyP exhibits a dual effect depending upon the pH value. At pH = 7 (neutral), polyP inhibits amyloid fibrilization in a dose-dependent manner similar to negatively charged nanoparticles. On the contrary, at pH = 3 (acidic), polyP accelerates amyloid fibrilization kinetics via liquid-liquid phase separation (LLPS), wherein the protein-rich droplets contain mature fibrils. In the parameter space spanned by concentrations of Aβ(1-40) and polyP, a phase diagram is constructed to demark the domain where LLPS is observed at pH = 3. Characterization of the protein aggregates, secondary structure content in the aggregates, and cell viability studies in the presence of aggregates are discussed at both pH values. This study reveals that anionic biopolymers can modulate amyloid fibrilization kinetics, linked to neurodegenerative diseases, depending upon their local concentrations and pH.

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.

Macromolecular Crowding Promotes Re-entrant Liquid-Liquid Phase Separation of Human Serum Transferrin and Prevents Surface-Induced Fibrillation

Protein aggregation and inactivation upon surface immobilization are major limiting factors for analytical applications in biotechnology-related fields. Protein immobilization on solid surfaces often requires multi-step surface passivation, which is time-consuming and inefficient. Herein, we have discovered that biomolecular condensates of biologically active human serum transferrin (Tf) can effectively prevent surface-induced fibrillation and preserve the native-like conformation of phase-separated Tf over a period of 30 days. It has been observed that macromolecular crowding promotes homotypic liquid-liquid phase separation (LLPS) of Tf through enthalpically driven multivalent hydrophobic interactions possibly via the involvement of its low-complexity domain (residues 3-20) containing hydrophobic amino acids. The present LLPS of Tf is a rare example of salt-mediated re-entrant phase separation in a broad range of salt concentrations (0-3 M) solely via the involvement of hydrophobic interactions. Notably, no liquid-to-solid-like phase transition has been observed over a period of 30 days, suggesting the intact conformational integrity of phase-separated Tf, as revealed from single droplet Raman, circular dichroism, and Fourier transform infrared spectroscopy measurements. More importantly, we discovered that the phase-separated condensates of Tf completely inhibit the surface-induced fibrillation of Tf, illustrating the protective role of these liquid-like condensates against denaturation and aggregation of biomolecules. The cell mimicking compact aqueous compartments of biomolecular condensates with a substantial amount of interfacial water preserve the structure and functionality of Tf. Our present study highlights an important functional aspect of biologically active protein condensates and may have wide-ranging implications in cell physiology and biotechnological applications.

Liquid-Droplet-Mediated ATP-Triggered Amyloidogenic Pathway of Insulin-Derived Chimeric Peptides: Unraveling the Microscopic and Molecular Processes

Disease-associated progression of protein dysfunction is typically determined by an interplay of transition pathways leading to liquid-liquid phase separation (LLPS) and amyloid fibrils. As LLPS introduces another layer of complexity into fibrillization of metastable proteins, a need for tunable model systems to study these intertwined processes has emerged. Here, we demonstrate the LLPS/fibrillization properties of a family of chimeric peptides, ACC1-13Kn, in which the highly amyloidogenic fragment of insulin (ACC1-13) is merged with oligolysine segments of various lengths (Kn, n = 8, 16, 24, 32, 40). LLPS and fibrillization of ACC1-13Kn are triggered by ATP through Coulombic interactions with Kn fragments. ACC1-13K8 and ACC1-13K16 form fibrils after a short lag phase without any evidence of LLPS. However, in the case of the three longest peptides, ATP triggers instantaneous LLPS followed by the disappearance of droplets occurring in-phase with the formation of amyloid fibrils. The kinetics of the phase transition and the stability of mature co-aggregates are highly sensitive to ionic strength, indicating that electrostatic interactions play a pivotal role in selecting the LLPS-fibrillization transition pathway. Densely packed ionic interactions that characterize ACC1-13Kn-ATP fibrils render them highly sensitive to hydrostatic pressure due to solvent electrostriction, as demonstrated by infrared spectroscopy. Using atomic force microscopy imaging of rapidly frozen samples, we demonstrate that early fibrils form within single liquid droplets, starting at the droplet/bulk interface through the formation of single bent fibers. A hypothetical molecular scenario underlying the emergence of the LLPS-to-fibrils pathway in the ACC1-13Kn-ATP system has been put forward.

Supramolecular localization in liquid-liquid phase separation and protein recruitment in confined droplets

This study investigated the localization of artificial peptide supramolecular fibers in liquid-liquid phase separation (LLPS). Hierarchical organization led to the localization of supramolecules in LLPS droplets. Moreover, proteins were recruited into confined droplets by the physical adsorption of proteins on the supramolecules, enabling an enhanced cascade reaction.

Peptide-based coacervates in therapeutic applications

Coacervates are droplets formed by liquid‒liquid phase separation. An increasing number of studies have reported that coacervates play an important role in living cells, such as in the generation of membraneless organelles, and peptides contribute to condensate droplet formation. Peptides with versatile functional groups and special secondary structures, including α-helices, β-sheets and intrinsically disordered regions, provide novel insights into coacervation, such as biomimetic protocells, neurodegenerative diseases, modulations of signal transmission, and drug delivery systems. In this review, we introduce different types of peptide-based coacervates and the principles of their interactions. Additionally, we summarize the thermodynamic and kinetic mechanisms of peptide-based coacervates and the associated factors, including salt, pH, and temperature, affecting the phase separation process. We illustrate recent studies on modulating the functions of peptide-based coacervates applied in biological diseases. Finally, we propose their promising broad applications and describe the challenges of peptide-based coacervates in the future.