Hydrogen bond guidance and aromatic stacking drive liquid-liquid phase separation of intrinsically disordered histidine-rich peptides

Phase transition of WTAP regulates m6A modification of interferon-stimulated genes

N6-methyladenosine (m6A) is the most prevalent modification of mRNA which controls diverse physiological processes. Although m6A modification has been reported to regulate type I interferon (IFN) responses by targeting the mRNA of IFN-β and the interferon-stimulated genes (ISGs), the detailed mechanism of how m6A methyltransferase complex (MTC) rapidly responds to conduct the modification on nascent mRNA during IFN-β stimulation remains largely unclear. Here, we demonstrate that WTAP, the adaptor protein of m6A MTC, undergoes dephosphorylation-regulated phase transition from aggregates to liquid-like condensates under IFN-β stimulation, thereby mediating m6A modification of a subset of ISGs to restrict their expression. The phase transition of WTAP promotes the interaction with nucleus-translocated transcription factor STAT1, recruits MTC to the promoter regions of ISGs and directs the co-transcriptional m6A modification on ISG mRNAs. Collectively, our findings reveal a novel regulatory role of WTAP phase transition in manipulating signaling pathways and fine-tuning immune response by orchestrating dynamic m6A modification through the cooperation of transcription factors and MTC. Our findings unveil a novel mechanism by which WTAP phase transition controls immune homeostasis via transcription factor-MTC-driven dynamic m6A modification, thereby proposing a potential therapeutic target for alleviating immune dysregulation.

Electrostatic Regulation of Bola-Amphiphilic Peptide Self-Assembly and Nanotube Formation Induced by Salt Ions

Peptide self-assembly into nanostructures offers substantial potential for applications in catalysis, drug delivery, and nanodevice fabrication. However, controlling the morphology of these assemblies remains a challenge. In this study, we investigate the role of salt ions in regulating the self-assembly of the bola-amphiphilic peptide KFFFFK, facilitating a transition from twisted fibrils to nanotubes. Using transmission electron microscopy, we show that the addition of NaCl induces the formation of nanotubes, and we detail the time-dependent assembly process. Increased salt concentrations reduce electrostatic repulsion, promoting the lateral merging of fibrils and supporting the formation of closed nanotubes. This phenomenon is also observed with several other salts. These findings underscore the critical role of electrostatic interactions in peptide self-assembly and highlight the importance of salt concentration in directing assembly pathways. Our results provide valuable insights into the mechanisms of peptide self-assembly and offer a versatile approach for designing advanced biomaterials and nanodevices based on well-defined peptide nanostructures.

Peptide Coacervates: Formation, Mechanism, and Biological Applications

Biomolecular coacervates, dynamic compartments formed via liquid-liquid phase separation (LLPS), are essential for orchestrating intracellular processes and have emerged as versatile tools in bioengineering. Peptides, with their modular amino acid sequences, exhibit unique potential in coacervate design due to their ability to undergo LLPS while offering precise control over molecular architecture and environmental responsiveness. Their simplicity, synthetic accessibility, and tunability make peptide-based coacervates particularly attractive for biomedical and materials applications. However, the formation and stability of these systems depend on a delicate balance of intrinsic factors (e.g., sequence charge, hydrophobicity, and chain length) and extrinsic conditions (e.g., pH, ionic strength, and temperature), necessitating a deeper understanding of their interplay. This review synthesizes recent advances in the molecular mechanisms driving peptide coacervation, emphasizing how sequence design and environmental cues govern phase behavior. We further highlight groundbreaking applications, from drug delivery platforms to protocell mimics, and discuss strategies to translate mechanistic insights into functional materials. By bridging fundamental principles with innovative applications, this work aims to accelerate the development of peptide coacervates as programmable, multifunctional systems, offering a roadmap for next-generation biochemical technologies.

Peptide nanoarchitectonics beyond long-range ordering

Long-range disordered structures are ubiquitous in biological organisms and hold crucial significance for their unique structure and function. Inspired by these natural architectures, much attention has been devoted to constructing long-range disordered materials based on biomolecules in vitro. Peptides, especially short peptides consisting of several to dozens of amino acids, have emerged as ideal building blocks due to their versatile structural and functional diversity, along with their notable biocompatibility and biodegradability. As a result, significant efforts have been made to develop short peptide nanoarchitectonics with long-range disorder (SPNLRD). Understanding the fundamental mechanisms underlying the formation of SPNLRD is crucial for the precise design and construction of these architectures with specific functionalities. This review summarizes the latest advancements in the construction and application of SPNLRD. We place particular emphasis on the design principles for SPNLRD construction and stabilization, based on a comprehensive discussion from the perspectives of thermodynamics, kinetics and intermolecular interactions. Finally, we assess the critical challenges currently facing SPNLRD and highlight the future directions in the field, proposing research strategies aimed at enhancing the stability and improving the precision of control over these materials.

Nuclear SREBP2 condensates regulate the transcriptional activation of lipogenic genes and cholesterol homeostasis

The precursor of sterol regulatory element-binding protein-2 (SREBP2) is a membrane-bound transcription factor regulating cholesterol biosynthesis. Under cholesterol-deficient conditions, mature SREBP2 is released from membrane-bound precursors through proteolytic cleavage and enters the nucleus. However, regulation of the transcriptional activity of nuclear SREBP2 (nSREBP2) is poorly understood. In the present study, we reported that nSREBP2 forms nuclear condensates through its amino-terminal, intrinsically disordered region (IDR) and works together with transcription coactivators, partly on superenhancers, for the transcriptional activation of SREBP2 target genes. Substitution of a conserved phenylalanine by alanine within the IDR abolishes the formation of nSREBP2 condensates and reduces its transcriptional activity. This can be effectively rescued by fusion with a phase separation driving FUS-IDR. Knock-in of the phenylalanine-to-alanine substitution in male mice compromises feeding-induced nSREBP2 activity and lowers hepatic and circulating cholesterol levels, underscoring the functional significance of nSREBP2 condensates. Together, the present study reveals that nuclear condensates driven by nSREBP2 N-terminal IDR facilitate the efficient activation of lipogenic genes and play an important role in cholesterol homeostasis.

Histidine-rich enantiomeric peptide coacervates enhance antigen sequestration and presentation to T cells

Peptides and peptidomimetics that self-assemble through LLPS have recently emerged as vital building blocks for creating functional biomaterials, thanks to their unique physicochemical properties and dynamic nature. One of life's most distinctive features is its selectivity for chiral molecules. To date, coacervates comprised of d-amino acids have not been reported. Here, we demonstrate that histidine-rich repeats of (GHGXY)4 (X = L/V/P) and their enantiomers undergo LLPS, paving the way for improved coacervate stability. Through a series of biophysical studies, we found that the droplet size can be tuned based on L, V, or P substitution, and molecular cargo between 600 and 150 000 Da is efficiently recruited in a bioactivity-preserving aqueous environment during phase separation. Mechanistic studies reveal that the droplets enter cells via energy-dependent endocytic pathways, exhibit composition-selective fusion properties, and effectively deliver molecular therapeutics across various cell types. Finally, we demonstrate that the coacervates enhance antigen presentation to CD4+ and CD8+ T cells, resulting in robust proliferation and the production of functional cytokines. Our study outlines the development and characterization of enantiomeric peptide coacervates as promising vaccine delivery vehicles with tunable physicochemical properties.

Engineered Peptide Coacervates Enable Efficient Intracellular Delivery of the MYC Inhibitor omoMYC

Intracellular delivery is a bottleneck in the development of therapeutic peptides and proteins. Here, we demonstrate the efficient delivery of omoMYC, the first MYC inhibitor in clinical trials, using HBpep-SP, an engineered peptide forming liquid-liquid phase-separated coacervates. HBpep-SP coacervates facilitate efficient cellular uptake and intracellular delivery of the omoMYC peptide at concentrations lower than those required for spontaneous uptake. Strikingly, omoMYC coacervates result in reduced proliferation and apoptosis induction in the low c-MYC expressing cell lines HEK293 and SH-SY5Y cells, but not in HeLa and SK-N-BE(2) cells with high c-MYC/MYCN expression, respectively, suggesting that endogenous MYC/N levels may impact the effects of omoMYC. Importantly, our approach bypasses the need for cell penetration-enhancing chemical modifications, offering a novel strategy for the investigation of peptide drug mechanisms in therapeutic development.

Cephalopod proteins for bioinspired and sustainable biomaterials design

Nature offers a boundless source of inspiration for designing bio-inspired technologies and advanced materials. Cephalopods, including octopuses, squids, and cuttlefish, exhibit remarkable biological adaptations, such as dynamic camouflage for predator evasion and communication, as well as robust prey-capturing tools, including beaks and sucker-ring teeth that operate under extreme mechanical stresses in aqueous environments. Central to these remarkable traits are structural proteins that serve as versatile polymeric materials. From a materials science perspective, proteins present unique opportunities due to their genetically encoded sequences, enabling access to a diversity of sequences and precise control over polymer composition and properties. This intrinsic programmability allows scalable, environmentally sustainable production through recombinant biotechnology, in contrast to petroleum-derived polymers. This review highlights recent advances in understanding cephalopod-specific proteins, emphasizing their potential for creating next-generation bioengineered materials and driving sustainable innovation in biomaterials science.

Supramolecular Switching of Liquid-Liquid Phase Separation for Orchestrating Enzyme Kinetics

Dynamic liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs) and associated assembly and disassembly of biomolecular condensates play crucial roles in cellular organization and metabolic networks. These processes are often regulated by supramolecular interactions. However, the complex and disordered structures of IDPs, coupled with their rapid conformational fluctuations, pose significant challenges for reconstructing supramolecularly-regulated dynamic LLPS systems and quantitatively illustrating variations in molecular interactions. Inspired by the structural feature of IDPs that facilitates LLPS, we designed a simplified phase-separating molecule, Nap-o-Nap, consisting of two naphthalene moieties linked by an ethylene glycol derivative. This compound exhibits LLPS under physiological conditions, forming coacervate microdroplets that undergo multiple cycles of disassembly and reassembly upon stoichiometric addition of Cucurbit[7]uril and Adamantane, respectively, based upon competitive host-guest interactions. Importantly, such reversible control offers a unique route to quantify entropically dominant nature (ΔS=14.0 cal ⋅ mol-1 ⋅ K-1) within the LLPS process, in which the binding affinity of host-guest interactions (ΔG=-14.9 kcal ⋅ mol-1) surpass that of the LLPS of Nap-o-Nap (ΔG=-2.1 kcal ⋅ mol-1), enabling the supramolecular regulation process. The supramolecularly switched LLPS, along with selective client recruitment and exclusion by resultant coacervates, provides a promising platform for either boosting or retarding enzymatic reactions, thereby orchestrating biological enzyme kinetics.

Martini3-IDP: improved Martini 3 force field for disordered proteins

Coarse-grained (CG) molecular dynamics (MD) is widely used for the efficient simulation of intrinsically disordered proteins (IDPs). The Martini model, one of the most popular CG force fields in biomolecular simulation, was reported to yield too compact IDP conformations, limiting its applications. Addressing this, we optimized the bonded parameters based on fitting to reference simulations of a diverse set of IDPs at atomistic resolution, resulting in a Martini3-based disordered protein model coined Martini3-IDP. This model leads to expanded IDP conformations, greatly improving the reproduction of the experimentally measured radii of gyration. Moreover, contrary to ad-hoc fixes based on scaling of protein-protein or protein-water interactions, Martini3-IDP keeps the overall interaction balance underlying Martini 3. To validate that, we perform a comprehensive testing including full-length multidomain proteins, IDP-lipid membrane binding and IDP-small molecule binding, confirming its ability to successfully capture the complex interplay between disordered proteins and diverse biomolecular components. Finally, the recently emerging concept of biomolecular condensate, through liquid-liquid phase separation, was also reproduced by Martini3-IDP for a number of both homotypic and heterotypic systems. With the improved Martini3-IDP model, we expand the ability to simulate processes involving IDPs in complex environments, at spatio-temporal scales inaccessible with all-atom models.

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.

Peptide-mediated liquid-liquid phase separation and biomolecular condensates

Liquid-liquid phase separation (LLPS) is a cornerstone of cellular organization, driving the formation of biomolecular condensates that regulate diverse biological processes and inspire innovative applications. This review explores the molecular mechanisms underlying peptide-mediated LLPS, emphasizing the roles of intermolecular interactions such as hydrophobic effects, electrostatic interactions, and π-π stacking in phase separation. The influence of environmental factors, such as pH, temperature, ionic strength, and molecular crowding on the stability and dynamics of peptide coacervates is examined, highlighting their tunable properties. Additionally, the unique physicochemical properties of peptide coacervates, including their viscoelastic behavior, interfacial dynamics, and stimuli-responsiveness, are discussed in the context of their biological relevance and engineering potential. Peptide coacervates are emerging as versatile platforms in biotechnology and medicine, particularly in drug delivery, tissue engineering, and synthetic biology. By integrating fundamental insights with practical applications, this review underscores the potential of peptide-mediated LLPS as a transformative tool for advancing science and healthcare.

Peptide-Based Complex Coacervates Stabilized by Cation-π Interactions for Cell Engineering

Complex coacervation is a form of liquid-liquid phase separation, whereby two types of macromolecules, usually bearing opposite net charges, self-assemble into dense microdroplets driven by weak molecular interactions. Peptide-based coacervates have recently emerged as promising carriers to deliver large macromolecules (nucleic acids, proteins and complex thereof) inside cells. Thus, it is essential to understand their assembly/disassembly mechanisms at the molecular level in order to tune the thermodynamics of coacervates formation and the kinetics of cargo release upon entering the cell. In this study, we designed histidine-rich peptides consisting of modular sequences in which we systematically incorporate cationic, anionic, or aromatic residues at specific positions along the sequence in order to modulate intermolecular interactions and the resulting coacervation stability. We show that cation-π interactions between arginine and aromatic side chains are particularly efficient in stabilizing complex coacervates, and these interactions can be disrupted in the protein-rich intracellular environment, triggering the disassembly of complex coacervates followed by cargo release. With the additional grafting of a disulfide-based self-immolative side chain, these complex coacervates exhibited enhanced stability and could deliver proteins, mRNA, and CRISPR/Cas9 genome editing tools with tunable release kinetics into cells. This capability extends to challenging cell types, such as macrophages. Our study highlights the critical role of cation-π interactions in the design of peptide-based coacervates, expanding the biomedical and biotechnology potential of this emerging intracellular delivery platform.

A Universal Strategy to Mitigate Microphase Separation via Cellulose Nanocrystal Hydration in Fabricating Strong, Tough, and Fatigue-Resistant Hydrogels

As a common natural phenomenon, phase separation is exploited for the development of high-performance hydrogels. Using supersaturated salt to create microphase-separated hydrogels with strengthened mechanical properties has gained widespread attention. However, such strengthened hydrogel loses its intrinsic flexibility, making the phase separation strategy unsuitable for the fabrication of stretchable and tough hydrogels. Here, a phase-engineering design strategy is introduced to produce stretchable yet tough hydrogels using supersaturated NaAc salt, by leveraging the hydration effect of cellulose nanocrystal (CNC) to mitigate microphase separation. The CNC-mitigated microphase-separated hydrogel presents unprecedented mechanical properties, for example, tensile strength of 1.8 MPa with a fracture strain of 4730%, toughness of 43.1 MJ m-3, fracture energy of 75.4 kJ m-2, and fatigue threshold up to 3884.7 J m-2. Furthermore, this approach is universal in synthesizing various microphase separation-enhanced polymer gels, including polyacrylic acid, poly(acrylic acid-co-acrylamide), gelatin, and alginate. These advancements provide insights into the incorporation of CNC-mediated microphase separation structures in hydrogels, which will foster the future development of high-performance soft materials.

Hydrogen Bonding-Driven Adaptive Coacervates as Protocells

Coacervation based on liquid-liquid phase separation (LLPS) has been widely used for the preparation of artificial protocells and to mimic the dynamic organization of membrane-free organelles. Most complex synthetic coacervates are formed through electrostatic interactions but cannot withstand high ionic strength conditions (>0.1 M). Alternative components and driving forces are highly desired for the formation of natural organelles to overcome the drawbacks of traditional coacervates. Herein, hydrogen bonding-driven adaptive coacervates are reported via the complexation of poly(ethylene glycol) (PEG) and tannic acid (TA). The LLPS behavior of these adaptive coacervates is dependent on the concentration and mass ratio of PEG and TA, which can be used to tune the size of coacervates ranging from 70 nm to 10 μm as well as the morphology of isotropic particles and hollow capsules. Coacervates are stable at high ionic concentrations up to 1 M and can serve as protocells to mimic cellular behaviors including metabolism (e.g., nutrient uptake), phagocytosis, and membrane fusion. The reported approach provides a platform for the rational design of hydrogen bonding-driven coacervates with controllable size and morphology, offering potential applications in protocell construction and therapeutic delivery.

Biphasic Coacervation Controlled by Kinetics as Studied by De Novo-Designed Peptides

Coacervation is generally treated as a liquid-liquid phase separation process and is controlled mainly by thermodynamics. However, kinetics could make a dominant contribution, especially in systems containing multiple interactions. In this work, using peptides of (XXLY)6SSSGSS to tune the charge density and the degree of hydrophobicity, as well as to introduce secondary structures, we evaluated the effect of kinetics on biphasic coacervates formed by peptides with single-stranded oligonucleotides and quaternized dextran at varying pH values. Only in the case where the charge density is constant and the electrostatic interaction is the major driving force for Coacervation is the effect of kinetics negligible. When pH-dependent electrostatic interaction and hydrophobic interaction are involved or the peptides form secondary structures, the Coacervation process is then path-dependent, indicating that the kinetics controls the phase separation process. The Coacervation by combining two different peptides suggests that the peptide with a higher charge density plays a leading role in the early stage, while the cooperation of both peptides takes over afterward. Our work demonstrates that it is normal to observe coacervates with different morphologies and functions due to kinetic control, especially in living cells. Peptides with minimized sequences are a practical approach to reveal the mechanism of Coacervation processes controlled by kinetics.

Trifluoroacetic Acid as a Molecular Probe for the Dense Phase in Liquid-Liquid Phase-Separating Peptide Systems

Although trifluoroacetic acid (TFA) is not typically considered a Hofmeister reagent, it has been demonstrated to modulate biocoacervation. We show that TFA can be employed to probe specific interactions in coacervating bioinspired peptide phenylalanine (Phe) 19F-labeled at a single site, altering its liquid-liquid phase separation (LLPS) behavior. Solid-state nuclear magnetic resonance (NMR) spectroscopy revealed two dynamically distinct binding modes of TFA with Phe, resulting in a structured, dipolar-ordered complex and a more dynamic complex, highlighting the proximity between TFA and Phe. Quantum chemistry modeling of 19F chemical shift differences indicates that the structured complex is formed by the intercalation of one TFA molecule between two stacked Phe aromatic rings, possibly contributing to the stabilization of the condensed dense phase. Thus, we propose that TFA can be used as a convenient molecular probe in 19F NMR-based studies of the structure and dynamics of the dense phase in LLPS peptide systems.

Peptides for Liquid-Liquid Phase Separation: An Emerging Biomaterial

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

Microscopic Origins of Flow Activation Energy in Biomolecular Condensates

The material properties of biomolecular condensates govern their dynamics and functions by influencing the molecular diffusion rates and biochemical interactions. A recent report has identified a characteristic timescale of temperature-dependent viscosity in biomolecular condensates arising from an activated dissociation events collectively referred to as flow activation energy. The microscopic origin of this activation energy is a complex function of sequence, stoichiometry, and external conditions. In this study, we elucidate the microscopic origins of flow activation energy in single and multicomponent condensates formed from model peptide sequences with varying "sticker" and "spacer" motifs, incorporating RNA as a secondary component. We examined how condensate density, RNA stoichiometry, and peptide sequence patterning impact these properties through detailed sequence-resolved coarse-grained simulations. Our findings reveal that flow activation energy is closely tied to the lifetime of sticker-sticker interactions under specific conditions. However, the presence of multiple competing stickers may complicate this relationship leading to frustrated interactions in condensates and lowering of activation energy. The findings of this study should help to create predictive models of material properties of condensates, which in turn can facilitate a more profound understanding of functions and programmable design principles of biomolecular condensates.

Phase-separating peptide coacervates with programmable material properties for universal intracellular delivery of macromolecules

Phase-separating peptides (PSPs) self-assembling into coacervate microdroplets (CMs) are a promising class of intracellular delivery vehicles that can release macromolecular modalities deployed in a wide range of therapeutic treatments. However, the molecular grammar governing intracellular uptake and release kinetics of CMs remains elusive. Here, we systematically manipulate the sequence of PSPs to unravel the relationships between their molecular structure, the physical properties of the resulting CMs, and their delivery efficacy. We show that a few amino acid alterations are sufficient to modulate the viscoelastic properties of CMs towards either a gel-like or a liquid-like state as well as their binding interaction with cellular membranes, collectively enabling to tune the kinetics of intracellular cargo release. We also demonstrate that the optimized PSPs CMs display excellent transfection efficiency in hard-to-transfect cells such as primary fibroblasts and immune cells. Our findings provide molecular guidelines to precisely program the material properties of PSP CMs and achieve tunable cellular uptake and release kinetics depending on the cargo modality, with broad implications for therapeutic applications such as protein, gene, and immune cell therapies.

How Salt and Temperature Drive Reentrant Condensation of Aβ40

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

Thermostable Nucleoid Protein Cren7 Slides Along DNA and Rapidly Dissociates From DNA While Not Inhibiting the Sliding of Other DNA-binding Protein

A nucleoid protein Cren7 compacts DNA, contributing to the living of Crenarchaeum in high temperature environment. In this study, we investigated the dynamic behavior of Cren7 on DNA and its functional relation using single-molecule fluorescence microscopy. We found two mobility modes of Cren7, sliding along DNA and pausing on it, and the rapid dissociation kinetics from DNA. The salt dependence analysis suggests a sliding with continuous contact to DNA, rather than hopping/jumping. The mutational analysis demonstrates that Cren7 slides along DNA while Trp (W26) residue interacts with the DNA. Furthermore, Cren7 does not impede the target search by a model transcription factor p53, implying no significant interference to other DNA-binding proteins on DNA. At high concentration of Cren7, the molecules form large clusters on DNA via bridging, which compacts DNA. We discuss how the dynamic behavior of Cren7 on DNA enables DNA-compaction and protein-bypass functions.

π-π Interactions Drive the Homotypic Phase Separation of the Prion-like Diatom Pyrenoid Scaffold PYCO1

CO2 fixation in most unicellular algae relies on the pyrenoid, a biomolecular condensate, which sequesters the cell's carboxylase Rubisco. In the marine diatom Phaeodactylum tricornutum, the pyrenoid tandem repeat protein Pyrenoid Component 1 (PYCO1) multivalently binds Rubisco to form a heterotypic Rubisco condensate. PYCO1 contains prion-like domains and can phase-separate homotypically in a salt-dependent manner. Here we dissect PYCO1 homotypic liquid-liquid phase separation (LLPS) by evaluating protein fragments and the effect of site-directed mutagenesis. Two of PYCO1's six repeats are required for homotypic LLPS. Mutagenesis of a minimal phase-separating fragment reveals tremendous sensitivity to the substitution of aromatic residues. Removing positively charged lysines and arginines instead enhances the propensity of the fragment to condense. We conclude that PYCO1 homotypic LLPS is mostly driven by π-π interactions mediated by tyrosine and tryptophan stickers. In contrast π-cation interactions involving arginine or lysine are not significant drivers of LLPS in this system.

Cell Surface Engineering by Phase-Separated Coacervates for Antibody Display and Targeted Cancer Cell Therapy

Cell therapies such as CAR-T have demonstrated significant clinical successes, driving the investigation of immune cell surface engineering using natural and synthetic materials to enhance their therapeutic performance. However, many of these materials do not fully replicate the dynamic nature of the extracellular matrix (ECM). This study presents a cell surface engineering strategy that utilizes phase-separated peptide coacervates to decorate the surface of immune cells. We meticulously designed a tripeptide, Fmoc-Lys-Gly-Dopa-OH (KGdelta; Fmoc=fluorenylmethyloxycarbonyl; delta=Dopa, dihydroxyphenylalanine), that forms coacervates in aqueous solution via phase separation. These coacervates, mirroring the phase separation properties of ECM proteins, coat the natural killer (NK) cell surface with the assistance of Fe3+ ions and create an outer layer capable of encapsulating monoclonal antibodies (mAb), such as Trastuzumab. The antibody-embedded coacervate layer equips the NK cells with the ability to recognize cancer cells and eliminate them through enhanced antibody-dependent cellular cytotoxicity (ADCC). This work thus presents a unique strategy of cell surface functionalization and demonstrates its use in displaying cancer-targeting mAb for cancer therapies, highlighting its potential application in the field of cancer therapy.

Microscopic Origins of Flow Activation Energy in Biomolecular Condensates

Material properties of biomolecular condensates dictate their form and function, influencing the diffusion of regulatory molecules and the dynamics of biochemical reactions. The increasing quality and quantity of microrheology experiments on biomolecular condensates necessitate a deeper understanding of the molecular grammar that encodes their material properties. Recent reports have identified a characteristic timescale related to network relaxation dynamics in condensates, which governs their temperature-dependent viscoelastic properties. This timescale is intimately connected to an activated process involving the dissociation of sticker regions, with the energetic barrier referred to as flow activation energy. The microscopic origin of activation energy is a complex function of sequence patterns, component stoichiometry, and external conditions. This study elucidates the microscopic origins of flow activation energy in single and multicomponent condensates composed of model peptide sequences with varying sticker and spacer motifs, with RNA as a secondary component. We dissected the effects of condensate density, RNA stoichiometry, and peptide sequence patterning using extensive sequence-resolved coarse-grained simulations. We found that flow activation energy is closely linked to the lifetime of sticker-sticker pairs under certain conditions, though the presence of multiple competing stickers further complicates this relationship. The insights gained in this study should help establish predictive multiscale models for the material properties and serve as a valuable guide for the programmable design of condensates.

Robust and Irreversible Sortase-Mediated Ligation by Empolyment of Sarkosyl

Sortase-mediated ligation (SML) is a widely used method for peptide and protein ligation due to ease of substrate preparation and fast enzymatic kinetics. But there are drawbacks that limit broader applications. Sorting motif in substrates may not be exposed to sortase efficiently due to folding or aggregation. In addition, the ligation is reversible under transpeptidation equilibrium that restricts ligation yield. Here we report a simple but robust method to overcome such limitations. By employment of sarkosyl, the detergent alters substrate conformation to raise sorting motif accessibility for sortase catalysis. Moreover, transpeptidation becomes irreversible presumably by formation of micelle to shield ligation products from sortase. In consequence, excellent yields were achieved from sortase variants with different substrate specificity. Notably, this method is compatible with peptides or proteins capable of forming liquid-liquid phase separation (LLPS), presenting a powerful approach for the conjugation of aggregation-prone substrates. Therefore, we believe the sarkosyl-enhanced SML could be widely applied in peptide and protein chemistry and the unique irreversible transpeptidation mechanism offers an insight to detergent-driven equilibrium.

Aromatic Residues in Proteins: Re-Evaluating the Geometry and Energetics of π-π, Cation-π, and CH-π Interactions

Aromatic residues can participate in various biomolecular interactions, such as π-π, cation-π, and CH-π interactions, which are essential for protein structure and function. Here, we re-evaluate the geometry and energetics of these interactions using quantum mechanical (QM) calculations, focusing on pairwise interactions involving the aromatic amino acids Phe, Tyr, and Trp and the cationic amino acids Arg and Lys. Our findings reveal that π-π interactions, while energetically favorable, are less abundant in structured proteins than commonly assumed and are often overshadowed by previously underappreciated, yet prevalent, CH-π interactions. Cation-π interactions, particularly those involving Arg, show strong binding energies and a specific geometric preference toward stacked conformations, despite the global QM minimum, suggesting that a rather perpendicular T-shape conformation should be more favorable. Our results support a more nuanced understanding of protein stabilization via interactions involving aromatic residues. On the one hand, our results challenge the traditional emphasis on π-π interactions in structured proteins by showing that CH-π and cation-π interactions contribute significantly to their structure. On the other hand, π-π interactions appear to be key stabilizers in solvated regions and thus may be particularly important to the stabilization of intrinsically disordered proteins.

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.

Exploring Stimuli-Responsive Natural Processes for the Fabrication of High-Performance Materials

Climate change and environmental pollution have underscored the urgency for more sustainable alternatives in synthetic polymer production. Nature's repertoire of biopolymers with excellent multifaceted properties alongside biodegradability could inspire next-generation innovative green polymer fabrication routes. Stimuli-induced processing, driven by changes in environmental factors, such as pH, ionic strength, and mechanical forces, plays a crucial role in natural polymeric self-assembly process. This perspective aims to close the gap in understanding biopolymer formation by highlighting the essential role of stimuli triggers in facilitating the bottom-up fabrication, allowing for the formation of intricate hierarchical structures. In particular, this perspective will delve into the stimuli-responsive processing of high-performance biopolymers produced by mussels, caddisflies, velvet worms, sharks, whelks, and squids, which are known for their robust mechanical properties, durability, and wet adhesion capabilities. Finally, we provide an overview of current advancements and challenges in understanding stimuli-induced natural formation pathways and their translation to biomimetic materials.

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.

Chromosome compartmentalization: causes, changes, consequences, and conundrums

The spatial segregation of the genome into compartments is a major feature of 3D genome organization. New data on mammalian chromosome organization across different conditions reveal important information about how and why these compartments form and change. A combination of epigenetic state, nuclear body tethering, physical forces, gene expression, and replication timing (RT) can all influence the establishment and alteration of chromosome compartments. We review the causes and implications of genomic regions undergoing a 'compartment switch' that changes their physical associations and spatial location in the nucleus. About 20-30% of genomic regions change compartment during cell differentiation or cancer progression, whereas alterations in response to a stimulus within a cell type are usually much more limited. However, even a change in 1-2% of genomic bins may have biologically relevant implications. Finally, we review the effects of compartment changes on gene regulation, DNA damage repair, replication, and the physical state of the cell.

Controlling Drug Partitioning in Individual Protein Condensates through Laser-Induced Microscale Phase Transitions

Gelation of protein condensates formed by liquid-liquid phase separation occurs in a wide range of biological contexts, from the assembly of biomaterials to the formation of fibrillar aggregates, and is therefore of interest for biomedical applications. Soluble-to-gel (sol-gel) transitions are controlled through macroscopic processes such as changes in temperature or buffer composition, resulting in bulk conversion of liquid droplets into microgels within minutes to hours. Using microscopy and mass spectrometry, we show that condensates of an engineered mini-spidroin (NT2repCTYF) undergo a spontaneous sol-gel transition resulting in the loss of exchange of proteins between the soluble and the condensed phase. This feature enables us to specifically trap a silk-domain-tagged target protein in the spidroin microgels. Surprisingly, laser pulses trigger near-instant gelation. By loading the condensates with fluorescent dyes or drugs, we can control the wavelength at which gelation is triggered. Fluorescence microscopy reveals that laser-induced gelation significantly further increases the partitioning of the fluorescent molecules into the condensates. In summary, our findings demonstrate direct control of phase transitions in individual condensates, opening new avenues for functional and structural characterization.

How Droplets Can Accelerate Reactions─Coacervate Protocells as Catalytic Microcompartments

Coacervates are droplets formed by liquid-liquid phase separation (LLPS) and are often used as model protocells-primitive cell-like compartments that could have aided the emergence of life. Their continued presence as membraneless organelles in modern cells gives further credit to their relevance. The local physicochemical environment inside coacervates is distinctly different from the surrounding dilute solution and offers an interesting microenvironment for prebiotic reactions. Coacervates can selectively take up reactants and enhance their effective concentration, stabilize products, destabilize reactants and lower transition states, and can therefore play a similar role as micellar catalysts in providing rate enhancement and selectivity in reaction outcome. Rate enhancement and selectivity must have been essential for the origins of life by enabling chemical reactions to occur at appreciable rates and overcoming competition from hydrolysis. In this Accounts, we dissect the mechanisms by which coacervate protocells can accelerate reactions and provide selectivity. These mechanisms can similarly be exploited by membraneless organelles to control cellular processes. First, coacervates can affect the local concentration of reactants and accelerate reactions by copartitioning of reactants or exclusion of a product or inhibitor. Second, the local environment inside the coacervate can change the energy landscape for reactions taking place inside the droplets. The coacervate is more apolar than the surrounding solution and often rich in charged moieties, which can affect the stability of reactants, transition states and products. The crowded nature of the droplets can favor complexation of large molecules such as ribozymes. Their locally different proton and water activity can facilitate reactions involving a (de)protonation step, condensation reactions and reactions that are sensitive to hydrolysis. Not only the coacervate core, but also the surface can accelerate reactions and provides an interesting site for chemical reactions with gradients in pH, water activity and charge. The coacervate is often rich in catalytic amino acids and can localize catalysts like divalent metal ions, leading to further rate enhancement inside the droplets. Lastly, these coacervate properties can favor certain reaction pathways, and thereby give selectivity over the reaction outcome. These mechanisms are further illustrated with a case study on ribozyme reactions inside coacervates, for which there is a fine balance between concentration and reactivity that can be tuned by the coacervate composition. Furthermore, coacervates can both catalyze ribozyme reactions and provide product selectivity, demonstrating that coacervates could have functioned as enzyme-like catalytic microcompartments at the origins of life.

Fundamental Aspects of Phase-Separated Biomolecular Condensates

Biomolecular condensates, formed through phase separation, are upending our understanding in much of molecular, cell, and developmental biology. There is an urgent need to elucidate the physicochemical foundations of the behaviors and properties of biomolecular condensates. Here we aim to fill this need by writing a comprehensive, critical, and accessible review on the fundamental aspects of phase-separated biomolecular condensates. We introduce the relevant theoretical background, present the theoretical basis for the computation and experimental measurement of condensate properties, and give mechanistic interpretations of condensate behaviors and properties in terms of interactions at the molecular and residue levels.

Tyrosine - a structural glue for hierarchical protein assembly

Protein self-assembly, guided by the interplay of sequence- and environment-dependent liquid-liquid phase separation (LLPS), constitutes a fundamental process in the assembly of numerous intrinsically disordered proteins. Heuristic examination of these proteins has underscored the role of tyrosine residues, evident in their conservation and pivotal involvement in initiating LLPS and subsequent liquid-solid phase transitions (LSPT). The development of tyrosine-templated constructs, designed to mimic their natural counterparts, emerges as a promising strategy for creating adaptive, self-assembling systems with diverse applications. This review explores the central role of tyrosine in orchestrating protein self-assembly, delving into key interactions and examining its potential in innovative applications, including responsive biomaterials and bioengineering.

The effects of histidine substitution of aromatic residues on the amyloidogenic properties of the fragment 264-277 of nucleophosmin 1

Histidine (His) plays a key role in mediating protein interactions and its unique side chain determines pH responsive self-assembling processes and thus in the formation of nanostructures. In this study, To identify novel self-assembling bioinspired sequences, we analyzed a series of peptide sequences obtained through the point mutation of aromatic residues of 264-277 fragment of nucleophosmin 1 (NPM1) with single and double histidines. Through several orthogonal biophysical techniques and under different pH and ionic strength conditions we evaluated the effects of these substitutions in the amyloidogenic features of derived peptides. The results clearly indicate that both the type of aromatic mutated residue and its position can have different effect on amyloid-like behaviors. They corroborate the crucial role exerted by Tyr271 in the self-assembling process of CTD of NPM1 in AML mutated form and add novel insights in the accurate investigation of how side chain orientations can determine successful design of innovative bioinspired materials.

Intrinsic disorder in the human vitreous proteome

The vitreous is a vital component of the eye, occupying a substantial portion of its volume and maintaining its structure. This study delves into the presence and significance of intrinsically disordered proteins (IDPs) within the vitreous, utilizing a dataset of 1240 vitreous proteins previously discovered in the vitreous proteome by Murthy et al.in five healthy subjects. The results indicate that 26.9 % of vitreous proteins are highly disordered, 68.8 % possess moderate disorder, and only 4.3 % are highly ordered. A complex interaction network among these proteins suggests their biological importance, and approximately 25 % may undergo liquid-liquid phase separation (LLPS). These findings offer new perspectives on the vitreous' molecular composition and behavior, potentially impacting our understanding of eye-related diseases, physiological changes such as vitreous syneresis. Further research is needed to translate these insights into clinical applications, although the intrinsic protein disorder and its association with LLPS appears to play a role in vitreous proteome function.

Life at the interface: Engineering bio-nanomaterials through interfacial molecular self-assembly

Interfacial self-assembly describes the directed organization of molecules and colloids at phase boundaries. Believed to be fundamental to the inception of primordial life, interfacial assembly is exploited by a myriad of eukaryotic and prokaryotic organisms to execute physiologic activities and maintain homeostasis. Inspired by these natural systems, chemists, engineers, and materials scientists have sought to harness the thermodynamic equilibria at phase boundaries to create multi-dimensional, highly ordered, and functional nanomaterials. Recent advances in our understanding of the biophysical principles guiding molecular assembly at gas-solid, gas-liquid, solid-liquid, and liquid-liquid interphases have enhanced the rational design of functional bio-nanomaterials, particularly in the fields of biosensing, bioimaging and biotherapy. Continued development of non-canonical building blocks, paired with deeper mechanistic insights into interphase self-assembly, holds promise to yield next generation interfacial bio-nanomaterials with unique, and perhaps yet unrealized, properties. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Therapeutic Approaches and Drug Discovery > Emerging Technologies.

Regulation of enzymatic reactions by chemical composition of peptide biomolecular condensates

Biomolecular condensates are condensed intracellular phases that are formed by liquid-liquid phase separation (LLPS) of proteins, either in the absence or presence of nucleic acids. These condensed phases regulate various biochemical reactions by recruitment of enzymes and substrates. Developments in the field of LLPS facilitated new insights on the regulation of compartmentalized enzymatic reactions. Yet, the influence of condensate chemical composition on enzymatic reactions is still poorly understood. Here, by using peptides as minimalistic condensate building blocks and β-galactosidase as a simple enzymatic model we show that the reaction is restricted in homotypic peptide condensates, while product formation is enhanced in peptide-RNA condensates. Our findings also show that condensate composition affects the recruitment of substrate, the spatial distribution, and the kinetics of the reaction. Thus, these findings can be further employed for the development of microreactors for biotechnological applications.

Pleiotropic Nanostructures Built from l-Histidine Show Biologically Relevant Multicatalytic Activities

The essential amino acid histidine plays a central role in the manifestation of several metabolic processes, including protein synthesis, enzyme-catalysis, and key biomolecular interactions. However, excess accumulation of histidine causes histidinemia, which shows brain-related medical complications, and the molecular mechanism of such histidine-linked complications is largely unknown. Here, we show that histidine undergoes a self-assembly process, leading to the formation of amyloid-like cytotoxic and catalytically active nanofibers. The kinetics of histidine self-assembly was favored in the presence of Mg(II) and Co(II) ions. Molecular dynamics data showed that preferential noncovalent interactions dominated by H-bonds between histidine molecules facilitate the formation of histidine nanofibers. The histidine nanofibers induced amyloid cross-seeding reactions in several proteins and peptides including pathogenic Aβ1-42 and brain extract components. Further, the histidine nanofibers exhibited oxidase activity and enhanced the oxidation of neurotransmitters. Cell-based studies confirmed the cellular internalization of histidine nanofibers in SH-SY5Y cells and subsequent cytotoxic effects through necrosis and apoptosis-mediated cell death. Since several complications including behavioral abnormality, developmental delay, and neurological disabilities are directly linked to abnormal accumulation of histidine, our findings provide a foundational understanding of the mechanism of histidine-related complications. Further, the ability of histidine nanofibers to catalyze amyloid seeding and oxidation reactions is equally important for both biological and materials science research.

The RNA-binding protein Cpeb4 regulates splicing of the Id2 gene in osteoclast differentiation

Cytoplasmic polyadenylation element-binding protein 4 (Cpeb4) is an RNA-binding protein that regulates posttranscriptional regulation, such as regulation of messenger RNA stability and translation. In the previous study, we reported that Cpeb4 localizes to nuclear bodies upon induction of osteoclast differentiation by RANKL. However, the mechanisms of the localization of Cpeb4 and osteoclastogenesis by Cpeb4 remain unknown. Here, we show that Cpeb4 localizes to the nuclear bodies by its RNA-binding ability and partially regulates normal splicing during osteoclast differentiation. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis with Phos-tag® revealed that the phosphorylation levels of Cpeb4 were already high in the RAW264.7 cells and were not altered by RANKL treatment. Immunofluorescence showed that exogenous Cpeb4 in HEK293T cells without RANKL stimulation localized to the same foci as shown in RANKL-stimulated RAW264.7 cells. Furthermore, when nuclear export was inhibited by leptomycin B treatment, Cpeb4 accumulated throughout the nucleus. Importantly, RNA recognition motif (RRM) 7 of Cpeb4 was essential for the localization. In contrast, the intrinsically disordered region, RRM1, and zinc finger domain CEBP_ZZ were not necessary for the localization. The mechanistic study showed that Cpeb4 co-localized and interacted with the splicing factors serine/arginine-rich splicing factor 5 (SRSF5) and SRSF6, suggesting that Cpeb4 may be involved in the splicing reaction. RNA-sequencing analysis revealed that the expression of genes related to cell proliferation processes, such as mitotic cell cycle and regulation of cell cycle processes, was elevated in osteoclasts depleted of Cpeb4. Interestingly, the splicing pattern of the inhibitor of DNA binding 2 (Id2) gene, which suppresses osteoclast differentiation, was altered by the depletion of Cpeb4. These results provide new insight into the role of Cpeb4 as a player of normal splicing of Id2 in osteoclast differentiation.

Molecular Crowding: The History and Development of a Scientific Paradigm

It is now generally accepted that macromolecules do not act in isolation but "live" in a crowded environment, that is, an environment populated by numerous different molecules. The field of molecular crowding has its origins in the far 80s but became accepted only by the end of the 90s. In the present issue, we discuss various aspects that are influenced by crowding and need to consider its effects. This Review is meant as an introduction to the theme and an analysis of the evolution of the crowding concept through time from colloidal and polymer physics to a more biological perspective. We introduce themes that will be more thoroughly treated in other Reviews of the present issue. In our intentions, each Review may stand by itself, but the complete collection has the aspiration to provide different but complementary perspectives to propose a more holistic view of molecular crowding.

Surface Charge Can Modulate Phase Separation of Multidomain Proteins

Phase separation has emerged as an important mechanism explaining the formation of certain biomolecular condensates. Biological phase separation is often driven by the multivalent interactions of modular protein domains. Beyond valency, the physical features of folded domains that promote phase separation are poorly understood. We used a model system─the small ubiquitin modifier (SUMO) and its peptide ligand, the SUMO interaction motif (SIM)─to examine how domain surface charge influences multivalency-driven phase separation. Phase separation of polySUMO and polySIM was altered by pH via a change in the protonation state of SUMO surface histidines. These effects were recapitulated by histidine mutations, which modulated SUMO solubility and polySUMO-polySIM phase separation in parallel and were quantitatively explained by atomistic modeling of weak interactions among proteins in the system. Thus, surface charge can tune the phase separation of multivalent proteins, suggesting a means of controlling phase separation biologically, evolutionarily, and therapeutically.

Spontaneous Transition of Spherical Coacervate to Vesicle-Like Compartment

Numerous biological systems contain vesicle-like biomolecular compartments without membranes, which contribute to diverse functions including gene regulation, stress response, signaling, and skin barrier formation. Coacervation, as a form of liquid-liquid phase separation (LLPS), is recognized as a representative precursor to the formation and assembly of membrane-less vesicle-like structures, although their formation mechanism remains unclear. In this study, a coacervation-driven membrane-less vesicle-like structure is constructed using two proteins, GG1234 (an anionic intrinsically disordered protein) and bhBMP-2 (a bioengineered human bone morphogenetic protein 2). GG1234 formed both simple coacervates by itself and complex coacervates with the relatively cationic bhBMP-2 under acidic conditions. Upon addition of dissolved bhBMP-2 to the simple coacervates of GG1234, a phase transition from spherical simple coacervates to vesicular condensates occurred via the interactions between GG1234 and bhBMP-2 on the surface of the highly viscoelastic GG1234 simple coacervates. Furthermore, the shell structure in the outer region of the GG1234/bhBMP-2 vesicular condensates exhibited gel-like properties, leading to the formation of multiphasic vesicle-like compartments. A potential mechanism is proposed for the formation of the membrane-less GG1234/bhBMP-2 vesicle-like compartments. This study provides a dynamic process underlying the formation of biomolecular multiphasic condensates, thereby enhancing the understanding of these biomolecular structures.

Toward Accurate Simulation of Coupling between Protein Secondary Structure and Phase Separation

Intrinsically disordered proteins (IDPs) frequently mediate phase separation that underlies the formation of a biomolecular condensate. Together with theory and experiment, efficient coarse-grained (CG) simulations have been instrumental in understanding the sequence-specific phase separation of IDPs. However, the widely used Cα-only models are limited in capturing the peptide nature of IDPs, particularly backbone-mediated interactions and effects of secondary structures, in phase separation. Here, we describe a hybrid resolution (HyRes) protein model toward a more accurate description of the backbone and transient secondary structures in phase separation. With an atomistic backbone and coarse-grained side chains, HyRes can semiquantitatively capture the residue helical propensity and overall chain dimension of monomeric IDPs. Using GY-23 as a model system, we show that HyRes is efficient enough for the direct simulation of spontaneous phase separation and, at the same time, appears accurate enough to resolve the effects of single His to Lys mutations. HyRes simulations also successfully predict increased β-structure formation in the condensate, consistent with available experimental CD data. We further utilize HyRes to study the phase separation of TPD-43, where several disease-related mutants in the conserved region (CR) have been shown to affect residual helicities and modulate the phase separation propensity as measured by the saturation concentration. The simulations successfully recapitulate the effect of these mutants on the helicity and phase separation propensity of TDP-43 CR. Analyses reveal that the balance between backbone and side chain-mediated interactions, but not helicity itself, actually determines phase separation propensity. These results support that HyRes represents an effective protein model for molecular simulation of IDP phase separation and will help to elucidate the coupling between transient secondary structures and phase separation.

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

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

Bioinspired Squid Peptides─A Tale of Curiosity-Driven Research Leading to Unforeseen Biomedical Applications

The molecular design of many peptide-based materials originates from structural proteins identified in living organisms. Prominent examples that have garnered broad interdisciplinary research interest (chemistry, materials science, bioengineering, etc.) include elastin, silk, or mussel adhesive proteins. The critical first steps in this type of research are to identify a convenient model system of interest followed by sequencing the prevailing proteins from which these biological structures are assembled. In our laboratory, the main model systems for many years have been the hard biotools of cephalopods, particularly their parrot-like tough beak and their sucker ring teeth (SRT) embedded within the sucker cuptions that line the interior surfaces of their arms and tentacles. Unlike the majority of biological hard tissues, these structures are devoid of biominerals and consist of protein/polysaccharide biomolecular composites (the beak) or, in the case of SRT, are entirely made of proteins that are assembled by supramolecular interactions.In this Account, we chronicle our journey into the discovery of these intriguing biological materials. We initially focus on their excellent mechanical robustness followed by the identification and sequencing of the structural proteins from which they are built, using the latest "omics" techniques including next-generation sequencing and high-throughput proteomics. A common feature of these proteins is their modular architecture at the molecular level consisting of short peptide repeats. We describe the molecular design of these peptide building blocks, highlighting the consensus motifs identified to play a key role in biofabrication and in regulating the mechanical properties of the macroscopic biological material. Structure/property relationships unveiled through advanced spectroscopic and scattering techniques, including Raman, infrared, circular dichroism, and NMR spectroscopies as well as wide-angle and small-angle X-ray scattering, are also discussed.We then present recent developments in exploiting the discovered molecular designs to engineer peptides and their conjugates for promising biomedical applications. One example includes short peptide hydrogels that self-assemble entirely under aqueous conditions and simultaneously encapsulate large macromolecules during the gelation process. A second example involves peptide coacervate microdroplets produced by liquid-liquid phase separation. These microdroplets are capable of recruiting and delivering large macromolecular therapeutics (genes, mRNA, proteins, peptides, CRISPR/Cas 9 modalities, etc.) into mammalian cells, which introduces exciting prospects in cancer, gene, and immune therapies.This Account also serves as a testament to how curiosity-driven explorations, which may lack an obvious practical goal initially, can lead to discoveries with unexpected and promising translational potential.

Selective amide bond formation in redox-active coacervate protocells

Coacervate droplets are promising protocell models because they sequester a wide range of guest molecules and may catalyze their conversion. However, it remains unclear how life's building blocks, including peptides, could be synthesized from primitive precursor molecules inside such protocells. Here, we develop a redox-active protocell model formed by phase separation of prebiotically relevant ferricyanide (Fe(CN)63-) molecules and cationic peptides. Their assembly into coacervates can be regulated by redox chemistry and the coacervates act as oxidizing hubs for sequestered metabolites, like NAD(P)H and gluthathione. Interestingly, the oxidizing potential of Fe(CN)63- inside coacervates can be harnessed to drive the formation of new amide bonds between prebiotically relevant amino acids and α-amidothioacids. Aminoacylation is enhanced in Fe(CN)63-/peptide coacervates and selective for amino acids that interact less strongly with the coacervates. We finally use Fe(CN)63--containing coacervates to spatially control assembly of fibrous networks inside and at the surface of coacervate protocells. These results provide an important step towards the prebiotically relevant integration of redox chemistry in primitive cell-like compartments.

Liquid-Liquid Phase Separation of the Intrinsically Disordered Domain of the Fused in Sarcoma Protein Results in Substantial Slowing of Hydration Dynamics

Formation of liquid condensates plays a critical role in biology via localization of different components or via altered hydrodynamic transport, yet the hydrogen-bonding environment within condensates, pivotal for solvation, has remained elusive. We explore the hydrogen-bond dynamics within condensates formed by the low-complexity domain of the fused in sarcoma protein. Probing the hydrogen-bond dynamics sensed by condensate proteins using two-dimensional infrared spectroscopy of the protein amide I vibrations, we find that frequency-frequency correlations of the amide I vibration decay on a picosecond time scale. Interestingly, these dynamics are markedly slower for proteins in the condensate than in a homogeneous protein solution, indicative of different hydration dynamics. All-atom molecular dynamics simulations confirm that lifetimes of hydrogen-bonds between water and the protein are longer in the condensates than in the protein in solution. Altered hydrogen-bonding dynamics may contribute to unique solvation and reaction dynamics in such condensates.