Spider silk self-assembly via modular liquid-liquid phase separation and nanofibrillation

Micropipette aspiration reveals differential RNA-dependent viscoelasticity of nucleolar subcompartments

The nucleolus is a multiphasic biomolecular condensate that facilitates ribosome biogenesis, a complex process involving hundreds of proteins and RNAs. The proper execution of ribosome biogenesis likely depends on the material properties of the nucleolus. However, these material properties remain poorly understood due to the challenges of in vivo measurements. Here, we use micropipette aspiration (MPA) to directly characterize the viscoelasticity and interfacial tensions of nucleoli within transcriptionally active Xenopus laevis oocytes. We examine the major nucleolar subphases, the outer granular component (GC) and the inner dense fibrillar component (DFC), which itself contains a third small phase known as the fibrillar center (FC). We show that the behavior of the GC is more liquid-like, while the behavior of the DFC/FC is consistent with that of a partially viscoelastic solid. To determine the role of ribosomal RNA in nucleolar material properties, we degrade RNA using RNase A, which causes the DFC/FC to become more fluid-like and alters interfacial tension. Together, our findings suggest that RNA underlies the partially solid-like properties of the DFC/FC and provide insights into how material properties of nucleoli in a near-native environment are related to their RNA-dependent function.

Developing an E. coli-Based Cell-Free Protein Synthesis System for Artificial Spidroin Production and Characterization

Spider silk spidroins, nature's advanced polymers, have long hampered efficient in vitro production due to their considerable size, repetitive sequences, and aggregation-prone nature. This study harnesses the power of a cell-free protein synthesis (CFPS) system, presenting the first successful in vitro production and detailed characterization of recombinant spider silk major ampullate spidroins (MaSps) utilizing a reformulated and optimizedEscherichia coli based CFPS system. Through systematic optimization, including cell strain engineering via knockout generation, energy sources, crowding agents, and amino acid supplementation, we effectively addressed the specific challenges associated with recombinant spidroin biosynthesis, resulting in high yields of 0.61 mg/mL for MaSp1 (69 kDa) and 0.52 mg/mL for MaSp2 (73 kDa). The synthesized spidroins self-assembled into micelles, facilitating efficient purification compared to in vivo methods, and were further processed into prototype silk fiber products. The functional characterization demonstrated that the purified spidroins maintain essential natural properties, such as phase separation and fiber formation triggered by pH and ions. This tailored CFPS platform also facilitates versatile cosynthesis and serves as an accessible platform for studying the supramolecular coassembly and dynamic interactions among spidroins. This CFPS platform offers a viable alternative to conventional in vivo methods, facilitating innovative approaches for silk protein engineering and biomaterial development in a high-throughput, efficient manner.

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.

Negative stain TEM imaging of native spider silk protein superstructures

Native Latrodectus hesperus (black widow) major ampullate spider silk proteins were imaged using negative stain transmission electron microscopy (NS-TEM) by isolating the silk protein hydrogel directly from the organism and solubilizing in urea. Heterogeneous micelle-like structures averaging 300 nm, similar to those imaged previously with CryoEM, were observed when stained with ammonium molybdate. A second smaller population averaging 50 nm was observed as well as large fibrils, highlighting the heterogeneous nature of the silk gland. The population of smaller silk protein micelles was enhanced at higher urea concentrations (5-8 M). This was further supported by dynamic light scattering (DLS), where two populations were observed at low urea concentrations while one small population dominated at high urea concentrations. The approach presented here provides a cost-effective route to imaging silk protein superstructures with conventional NS-TEM methods and may be applicable to other soft nanoparticle systems.

Coalescence-Driven Local Crowding Promotes Liquid-to-Solid-Like Phase Transition in a Homogeneous and Heterogeneous Droplet Assembly: Regulatory Role of Ligands

Liquid-to-solid-like phase transition (LSPT) of disordered proteins via metastable liquid-like droplets is a well-documented phenomenon in biology and is linked to many pathological conditions including neurodegenerative diseases. However, very less is known about the early microscopic events and transient intermediates involved in the irreversible protein aggregation of functional globular proteins. Herein, using a range of microscopic and spectroscopic techniques, we show that the LSPT of a functional globular protein, human serum albumin (HSA), is exclusively driven by spontaneous coalescence of liquid-like droplets involving various transient intermediates in a temporal manner. We show that interdroplet communication via coalescence is essential for both initial aggregation and growth of amorphous aggregates within individual droplets, which subsequently transform to amyloid-like fibrils. Immobilized droplets neither show any nucleation nor any growth upon aging. Moreover, we found that the exchange of materials with the dilute dispersed phase has negligible influence on the LSPT of HSA. Our findings reveal that interfacial properties effectively modulate the feasibility and kinetics of LSPT of HSA via ligand binding, suggesting a possible regulatory mechanism that cells utilize to control the dynamics of LSPT. Furthermore, using a dynamic heterogeneous droplet assembly of two functional proteins, HSA and human serum transferrin (Tf), we show an intriguing phenomenon within the fused droplets where both liquid-like and solid-like phases coexist within the same droplet, which eventually transform to a mixed fibrillar assembly. These microscopic insights not only highlight the importance of interdroplet interactions behind the LSPT of biomolecules but also showcase its adverse effect on the structure and function of other functional proteins in a crowded and heterogeneous protein assembly.

A Novel Gene Synthesis Platform for Designing Functional Protein Polymers

Recombinant protein polymers with repeat sequences of specific amino acids can be regarded as sustainable functional materials that can be designed using genetic engineering. However, synthesizing genes encoding these proteins is significantly time-consuming and labor-intensive owing to the difficulty of using common gene synthesis tools, such as restriction enzymes and PCR primers. To overcome these obstacles, a novel method is proposed herein: seamless cloning of rolling-circle amplicons (SCRCA). This method involves one-pot preparation of repetitive-sequence genes with overlapping ends for cloning, facilitating the easy construction of the desired recombinants. SCRCA is used to synthesize 10 genes encoding hydrophilic resilin-like and hydrophobic elastin-like repeat units that induce liquid-liquid phase separation. SCRCA shows higher transformation efficiency and better workability than conventional methods, and the time and budget required for SCRCA are comparable to those required for non-repetitive-sequence gene synthesis. Additionally, SCRCA facilitates the construction of a repeat unit library at a low cost. The library shows considerably higher diversity than that of the current state-of-the-art method. By combining this library construction with the directed evolution concept, an elastin-like protein polymer with the desired functions can be rapidly developed. SCRCA can greatly accelerate research on protein polymers.

Recreating Silk's Fibrillar Nanostructure by Spinning Solubilized, Undegummed Silk

The remarkable toughness (>70 MJ m-3) of silkworm silk is largely attributed to its hierarchically arranged nanofibrillar nanostructure. Recreating such tough fibers through artificial spinning is often challenging, in part because degummed, dissolved silk is drastically different to the unspun native feedstock found in the spinning gland. The present work demonstrates a method to dissolve silk without degumming to produce a solution containing undegraded fibroin and sericin. This solution exhibits liquid-liquid phase separation above 10% (wt/wt), a behavior observed in the silk gland but not in degummed silk solutions to date. This partitioning enhances the stability of the undegummed solution, delaying gelation two-fold compared with degummed silk at the same concentration. When spun under identical conditions, undegummed solutions produces fibers 8× stronger and 218× tougher than degummed silk feedstocks. Through ultrasonication, undegummed wet spun fibers are seen to possess hierarchical structure of densely packed ≈20 nm nanofibrils, similar to native silks, although completely absent from fibers wet-spun from degummed silk solutions. This work demonstrates that the preservation of molecular weight, presence of sericin and stimulation of liquid-liquid phase separation underpin a new pathway to recreate a hierarchical fiber with structures akin to native silk.

Probing the Interplay of Protein Self-Assembly and Covalent Bond Formation in Photo-Crosslinked Silk Fibroin Hydrogels

Covalent crosslinking of silk fibroin via native tyrosine residues has been extensively explored; however, while these materials are very promising for biomedical, optical, soft robotics, and sensor applications, their structure and mechanical properties are unstable over time. This instability results in spontaneous silk self-assembly and stiffening over time, a process that is poorly understood. This study investigates the interplay between self-assembly and di-tyrosine bond formation in silk hydrogels photo-crosslinked using ruthenium (Ru) and sodium persulfate (SPS) with visible light. The effects of silk concentration, molecular weight, Ru/SPS concentration, and solvent conditions are examined. The Ru/SPS system enables rapid crosslinking, achieving gelation within seconds and incorporating over 90% of silk into the network, even at very low protein concentrations (≥0.75% wt/v). A model emerges where silk self-assembly both before and after crosslinking affects protein phase separation, mesoscale structure, and dynamic changes in the hydrogel network over time. Silk concentration has the greatest impact on hydrogel properties, with higher silk concentration hydrogels experiencing two orders of magnitude increase in stiffness within 1 week. This new understanding and ability to tune hydrogel properties and dynamic stiffening aids in developing advanced materials for 4D biofabrication, sensing, 3D cancer models, drug delivery, and soft robotics.

Characterization of the second type of tubuliform spidroin (TuSp1 variant 2) elucidates the essential role of cysteine within the repetitive domain in liquid-liquid phase separation-mediated silk formation and the mechanical properties of silk fibers

Orb-weaver spiders utilize morphologically differentiated abdominal glands to produce up to seven types of silks throughout their life cycles. Tubuliform silk is unique as it serves to protect developing embryos and hatchlings. However, our current understanding of the relationship between structure and function of tubuliform silk protein remains limited. Here, we present the full-length gene sequence of the second type of tubuliform spidroin (TuSp1 variant 2) from the orb-weaver spider Leucauge blanda. The L. blanda TuSp1 variant 2 (TuSp1-v2) contains 18 tandemly arrayed repeats, with each repeat having a cysteine residue. We demonstrate that the cysteine in L. blanda TuSp1-v2 repeats can form intermolecular disulfide bond and promote the liquid-liquid phase separation (LLPS) for silk formation. Moreover, the presence of cysteine partially enhances the thermostability of soluble spidroins and the mechanical properties of fibers, as demonstrated by comparative analyses of miniature TuSp1-v2 and its mutants. The integration of mechanical and structural data indicates that the recombinant TuSp1-v2 fiber exhibits high UV-A stability in both its mechanical and structural properties. This study provides new insights into the functions of cysteine in repetitive region and implies promising potentials for development new spidroin-based biomaterials.

The role of phosphate in silk fibroin self-assembly: a Hofmeister study

Silk fibroin is the primary protein component of the threads of Bombyx mori silkworm cocoons. Previous work has demonstrated that silk fibroin can self-assemble at solid-liquid interfaces to form dense, nanothin coatings that grow continuously from a substrate surface when exposed to potassium phosphate, a kosmotropic salt. Herein, the role of potassium phosphate in promoting silk fibroin self-assembly in solution and on surfaces is studied and compared to other salts in the Hofmeister series. Results show that strong kosmotropes, such as ammonium sulfate and potassium phosphate, promote a bimodal distribution of assembled species in solution that is indicative of a nucleation-growth mechanism. Interestingly, silk fibroin assemblies formed by potassium phosphate contain the highest β-sheet content, suggesting that phosphate-specific interactions play a role in silk fibroin self-assembly. In the presence of kosmotropic salts, silk fibroin nanoaggregates continuously accumulate at solid-liquid interfaces with varying early- and late-stage adsorption rates. Interfacial coatings formed in the presence of potassium phosphate are smooth, dense, and completely cover the underlying substrate without evidence of large-scale aggregation, whereas other kosmotropes generate rough, heterogeneous coatings. These studies thus decouple the kosmotropic effects of phosphate (via disruption of the protein hydration shell) from ion-specific behavior in driving silk fibroin self-assembly.

The Biology of Natural Polymers Accelerates and Expands the Science of Biomacromolecules: A Focus on Structural Proteins

This Perspective explores the use of biomacromolecules in natural materials synthesized by living organisms, such as spider silk, in the development of sustainable synthetic materials. Currently employed synthetic polymers lack the hierarchical complexity and unique properties of natural materials composed of biomacromolecules. By understanding the composition of these natural materials, it may be able to reproduce their properties synthetically. Additionally, research directions involving the use of renewable resources such as nitrogen and carbon dioxide from the air and seawater to develop biomacromolecules such as spider silk and biopolyester via photosynthetic organisms are reviewed. Next-generation biomacromolecule research will aid in the creation of a sustainable global society, advancing fields such as biomanufacturing, agriculture, aquaculture, and other industries.

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.

Control Intracellular Protein Condensates with Light

Protein phase transitions are gaining traction among biologists for their wide-ranging roles in biological regulation. However, achieving precise control over these phenomena in vivo remains a formidable task. Optogenetic techniques present us with a potential means to control protein phase behavior with spatiotemporal precision. This review delves into the design of optogenetic tools, particularly those aimed at manipulating protein phase transitions in complex biological systems. We begin by discussing the pivotal roles of subcellular phase transitions in physiological and pathological processes. Subsequently, we offer a thorough examination of the evolution of optogenetic tools and their applications in regulating these protein phase behaviors. Furthermore, we highlight the tailored design of optogenetic tools for controlling protein phase transitions and the construction of synthetic condensates using these innovative techniques. In the long run, the development of optogenetic tools not only holds the potential to elucidate the roles of protein phase transitions in various physiological processes but also to antagonize pathological ones to reinstate cellular homeostasis, thus bringing about novel therapeutic strategies. The integration of optogenetic techniques into the study of protein phase transitions represents a significant step forward in our understanding and manipulation of biology at the subcellular level.

Correlating Mechanical Properties and Sequence Motifs in Artificial Spider Silk by Targeted Motif Substitution

The major ampullate silk of orb-weaving spiders is renowned for its exceptional mechanical properties, including high tensile strength and extensibility. The development of artificial spider silk presents a promising alternative to traditional fibers with significant environmental impacts. This study aims to elucidate the relationship between sequence motifs of natural spider silk and the mechanical properties of artificial spider silk. Using the Spider Silkome Database, we identified motifs correlated with specific physical properties and substituted them into MaSp2-based mini-spidroin BP1. We then measured the mechanical properties of the resulting recombinant artificial spider silk through tensile tests, observed structural properties via birefringence measurement and wide-angle X-ray scattering, and evaluated the water response through boiled water shrinkage tests. Introducing a positively correlated motif increased the tensile strength by 9.3%, while a negatively correlated motif decreased it by 5.1%, confirming the sequence-property relationship. These findings demonstrate that targeted motif substitution can effectively control the physical properties of artificial spider silk, facilitating the development of sustainable biomaterials with tailored mechanical properties for diverse industrial applications.

Clickable, Thermally Responsive Hydrogels Enabled by Recombinant Spider Silk Protein and Spy Chemistry for Sustained Neurotrophin Delivery

The ability to deliver protein therapeutics in a minimally invasive, safe, and sustained manner, without resorting to viral delivery systems, will be crucial for treating a wide range of chronic injuries and diseases. Among these challenges, achieving axon regeneration and functional recovery post-injury or disease in the central nervous system remains elusive to most clinical interventions, constantly calling for innovative solutions. Here, a thermally responsive hydrogel system utilizing recombinant spider silk protein (spidroin) is developed. The protein solution undergoes rapid sol-gel transition at an elevated temperature (37 °C) following brief sonication. This thermally triggered gelation confers injectability to the system. Leveraging SpyTag/SpyCatcher chemistry, the hydrogel, composed of SpyTag-fusion spidroin, can be functionalized with diverse SpyCatcher-fusion bioactive motifs, such as neurotrophic factors (e.g., ciliary neurotrophic factor) and cell-binding ligands (e.g., laminin), rendering it well-suited for neuronal culturing. More importantly, the intravitreous injection of the protein materials decorated with SpyCatcher-fusion CNTF into the vitreous body after optic nerve injury leads to prolonged JAK/STAT3 signaling, increased neuronal survival, and enhanced axon regeneration. This study illustrates a generalizable material system for injectable and sustained delivery of protein therapeutics for neuroprotection and regeneration, with the potential for extension to other chronic diseases and injuries.

Calcium ion-triggered liquid-liquid phase separation of silk fibroin and spinning through acidification and shear stress

Many studies try to comprehend and replicate the natural silk spinning process due to its energy-efficient and eco-friendly process. In contrast to spider silk, the mechanisms of how silkworm silk fibroin (SF) undergoes liquid-liquid phase separation (LLPS) concerning the various environmental factors in the silk glands or how the SF coacervates transform into fibers remain unexplored. Here, we show that calcium ions, among the most abundant metal ions inside the silk glands, induce LLPS of SF under macromolecular crowded conditions by increasing both hydrophobic and electrostatic interactions between SF. Furthermore, SF coacervates assemble and further develop into fibrils under acidification and shear force. Finally, we prepare SF fiber using a pultrusion-based dry spinning, mirroring the natural silk spinning system. Unlike previous artificial spinning methods requiring concentrated solutions or harsh solvents, our process uses a less concentrated aqueous SF solution and minimal shear force, offering a biomimetic approach to fiber production.

Recombinant silk protein condensates show widely different properties depending on the sample background

There is an increasing understanding that condensation is a crucial intermediate step in the assembly of biological materials and for a multitude of cellular processes. To apply and to understand these mechanisms, in vitro biophysical characterisation techniques are central. The formation and biophysical properties of protein condensates depend on a multitude of factors, such as protein concentration, pH, temperature, salt concentration, and presence of other biomolecules as well as protein purification and storage conditions. Here we show how critical the procedures for preparing protein samples for in vitro studies are. We compare two purification methods of the recombinant spider silk protein CBM-AQ12-CBM and study the effect of background molecules, such as DNA, on the formation and properties of the condensates. We characterize the condensates using aggregation induced emitters (AIEs), coalescence studies, and micropipette aspiration. The condensated sample containing background molecules exhibit a lower threshold concentration for condensate formation accompanied by a lower surface tension and longer coalescence time when compared to the pure protein condensates. Furthermore, the partitioning of small AIEs is enhanced in the presence of background molecules. Our results highlight that the purification method and remaining background molecules strongly affect the biophysical properties of spider silk condensates. Using the acquired knowledge about spider silk protein purification we derive guidelines for reproducible condensate formation that will foster the use of spider silk proteins as adhesives or carriers for biomedical applications.

Liquid-liquid crystalline phase separation of spider silk proteins

Liquid-liquid phase separation (LLPS) of proteins can be considered an intermediate solubility regime between disperse solutions and solid fibers. While LLPS has been described for several pathogenic amyloids, recent evidence suggests that it is similarly relevant for functional amyloids. Here, we review the evidence that links spider silk proteins (spidroins) and LLPS and its role in the spinning process. Major ampullate spidroins undergo LLPS mediated by stickers and spacers in their repeat regions. During spinning, the spidroins droplets shift from liquid to crystalline states. Shear force, altered ion composition, and pH changes cause micelle-like spidroin assemblies to form an increasingly ordered liquid-crystalline phase. Interactions between polyalanine regions in the repeat regions ultimately yield the characteristic β-crystalline structure of mature dragline silk fibers. Based on these findings, we hypothesize that liquid-liquid crystalline phase separation (LLCPS) can describe the molecular and macroscopic features of the phase transitions of major ampullate spidroins during spinning and speculate whether other silk types may use a similar mechanism to convert from liquid dope to solid fiber.

Phase separation drives the folding of recombinant collagen

Recombinantly produced collagens present a sustainable, ethical, and safe substitute for collagens derived from natural sources. However, controlling the folding of the recombinant collagens, crucial for replicating the mechanical properties of natural materials, remains a formidable task. Collagen-like proteins from willow sawfly are relatively small and contain no hydroxyprolines, presenting an attractive alternative to the large and post-translationally modified mammalian collagens. Utilizing CD spectroscopy and analytical ultracentrifugation, we demonstrate that recombinant willow sawfly collagen assembles into collagen triple helices in a concentration-dependent manner. Interestingly, we observed that the lower concentration threshold for the folding can be overcome by freezing or adding crowding agents. Microscopy data show that both freezing and the addition of crowding agents induce phase separation. We propose that the increase in local protein concentration during phase separation drives the nucleation-step of collagen folding. Finally, we show that freezing also induces the folding of recombinant human collagen fragments and accelerates the folding of natural bovine collagen, indicating the potential to apply phase separation as a universal mechanism to control the folding of recombinant collagens. We anticipate that the results provide a method to induce the nucleation of collagen folding without any requirements for genetic engineering or crosslinking.

Phosphate-Driven Interfacial Self-Assembly of Silk Fibroin for Continuous Noncovalent Growth of Nanothin Defect-Free Coatings

Silk fibroin is a fiber-forming protein derived from the thread of Bombyx mori silkworm cocoons. This biocompatible protein, under the kosmotropic influence of potassium phosphate, can undergo supramolecular self-assembly driven by a random coil to β-sheet secondary structure transition. By leveraging concurrent nonspecific adsorption and self-assembly of silk fibroin, we demonstrate an interfacial phenomenon that yields adherent, defect-free nanothin protein coatings that grow continuously in time, without observable saturation in mass deposition. This noncovalent growth of silk fibroin coatings is a departure from traditionally studied protein adsorption phenomena, which generally yield adsorbed layers that saturate in mass with time and often do not completely cover the surface. Here, we explore the fundamental mechanisms of coating growth by examining the effects of coating solution parameters that promote or inhibit silk fibroin self-assembly. Results show a strong dependence of coating kinetics and structure on solution pH, salt species, and salt concentration. Moreover, coating growth was observed to occur in two stages: an early stage driven by protein-surface interactions and a late stage driven by protein-protein interactions. To describe this phenomenon, we developed a kinetic adsorption model with Langmuir-like behavior at early times and a constant steady-state growth rate at later times. Structural analysis by FTIR and photoinduced force microscopy show that small β-sheet-rich structures serve as anchoring sites for absorbing protein nanoaggregates, which is critical for coating formation. Additionally, β-sheets are preferentially located at the interface between protein nanoaggregates in the coating, suggesting their role in forming stable, robust coatings.

Silk Proteins: Designs from Nature with Multipurpose Utility and Infinite Future Possibilities

This is a Perspective on nature as a story-teller, where inputs of evolution drove the remarkable protein designs found in silks. This selection process has resulted in silk materials with novel chemistry and properties to support organism survival in nature, yet with newfound utility in everything from comic books and automobiles to medicine. With growing global concerns related to environmental health, silks also serve as an invaluable instructional guide to the future of sustainable material designs.

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.

Effects of Mini-Spidroin Repeat Region on the Mechanical Properties of Artificial Spider Silk Fibers

Spiders can produce up to seven different types of silk, each with unique mechanical properties that stem from variations in the repetitive regions of spider silk proteins (spidroins). Artificial spider silk can be made from mini-spidroins in an all-aqueous-based spinning process, but the strongest fibers seldom reach more than 25% of the strength of native silk fibers. With the aim to improve the mechanical properties of silk fibers made from mini-spidroins and to understand the relationship between the protein design and the mechanical properties of the fibers, we designed 16 new spidroins, ranging from 31.7 to 59.5 kDa, that feature the globular spidroin N- and C-terminal domains, but harbor different repetitive sequences. We found that more than 50% of these constructs could be spun by extruding them into low-pH aqueous buffer and that the best fibers were produced from proteins whose repeat regions were derived from major ampullate spidroin 4 (MaSp4) and elastin. The mechanical properties differed between fiber types but did not correlate with the expected properties based on the origin of the repeats, suggesting that additional factors beyond protein design impact the properties of the fibers.

Dimerization and liquid-liquid phase separation of the nonrepetitive domains of pyriform spidroin 1 controls the pyriform silk formation

Spiders spin high performance silks with diverse mechanical properties for specific biological functions. Of these spider silk types, pyriform silk stands out as a unique combination of wet glue and dry fibers. Investigation of self-assembly process of spider silk proteins is necessary for elucidating the silk formation mechanism. However, the functions of nonrepetitive domains in the silk formation of pyriform spidroins from liquid proteins to solid fibers are still unclear, making it difficult to achieve efficient biomimetic preparations of pyriform silk with good mechanical properties. In this study, we investigate the roles of the N-linker repeat (NLR) and both terminal domains of pyriform spidroin 1 (PySp1) in the silk formation. We demonstrate for the first time that the PySp1 NLR alone is sufficient to self-assemble into high strength fibers. Moreover, we showed that the ability to promote the pyriform silk formation by the addition of the NLR. We also found that the pH-sensitive dimerization property for N-terminal domain and the liquid-liquid phase separation (LLPS) coupled with acidification triggers the self-assembly mediated by the C-terminal domain. Overall, our results provide new insight into the role of nonrepetitive domains in the pyriform silk formation mechanism and the basis for producing new protein-based materials derived from spider pyriform silk.

Disentangling the Web: An Interdisciplinary Review on the Potential and Feasibility of Spider Silk Bioproduction

The remarkable material properties of spider silk, such as its high toughness and tensile strength combined with its low density, make it a highly sought-after material with myriad applications. In addition, the biological nature of spider silk makes it a promising, potentially sustainable alternative to many toxic or petrochemical-derived materials. Therefore, interest in the heterologous production of spider silk proteins has greatly increased over the past few decades, making recombinant spider silk an important frontier in biomanufacturing. This has resulted in a diversity of potential host organisms, a large space for sequence design, and a variety of downstream processing techniques and product applications for spider silk production. Here, we highlight advances in each of these technical aspects as well as white spaces therein, still ripe for further investigation and discovery. Additionally, industry landscaping, patent analyses, and interviews with Key Opinion Leaders help define both the research and industry landscapes. In particular, we found that though textiles dominated the early products proposed by companies, the versatile nature of spider silk has opened up possibilities in other industries, such as high-performance materials in automotive applications or biomedical therapies. While continuing enthusiasm has imbued scientists and investors alike, many technical and business considerations still remain unsolved before spider silk can be democratized as a high-performance product. We provide insights and strategies for overcoming these initial hurdles, and we highlight the importance of collaboration between academia, industry, and policy makers. Linking technical considerations to business and market entry strategies highlights the importance of a holistic approach for the effective scale-up and commercial viability of spider silk bioproduction.

Metal ions guide the production of silkworm silk fibers

Silk fibers' unique mechanical properties have made them desirable materials, yet their formation mechanism remains poorly understood. While ions are known to support silk fiber production, their exact role has thus far eluded discovery. Here, we use cryo-electron microscopy coupled with elemental analysis to elucidate the changes in the composition and spatial localization of metal ions during silk evolution inside the silk gland. During the initial protein secretion and storage stages, ions are homogeneously dispersed in the silk gland. Once the fibers are spun, the ions delocalize from the fibroin core to the sericin-coating layer, a process accompanied by protein chain alignment and increased feedstock viscosity. This change makes the protein more shear-sensitive and initiates the liquid-to-solid transition. Selective metal ion doping modifies silk fibers' mechanical performance. These findings enhance our understanding of the silk fiber formation mechanism, laying the foundations for developing new concepts in biomaterial design.

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.

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.

Dual-Mode Arginine Assay Based on the Conformation Switch of a Ferrocene-Grafted Polypeptide

Both controllable regulation of the conformational structure of a polypeptide and specific recognition of an amino acid are still arduous challenges. Here, a novel dual-mode (electrochemical and colorimetric) biosensor was built for arginine (Arg) recognition based on a conformation switch, utilizing controllable and synergistic self-assembly of a ferrocene-grafted hexadecapeptide (P16Fc) with gold nanoparticles (AuNPs). Benefiting from the flexibility and unique topological structure of P16Fc formed nanospheres, the assembly and disassembly can undergo a conformation transition induced by Arg through controlling the distance and number of Fc detached from the gold surface, producing on-off electrical signals. Also, they can induce aggregation and dispersion of AuNPs in solution, causing a color change. The mechanism of Arg recognition with polypeptide conformation regulation was well explored by combining microstructure characterizations with molecular mechanics calculations. The electrochemical and colorimetric assays for Arg were successfully established in sensitive and selective manner, not only obtaining a very low detection limit, but also effectively eliminating the interference from other amino acids and overcoming the limitation of AuNP aggregation. Notably, the conformational change-based assay with the peptide regulated by the target will make a powerful tool for the amino acid biosensing and health diagnosis.

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

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

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.

Liquid-Liquid Phase Separation-Mediated Photocatalytic Subcellular Hybrid System for Highly Efficient Hydrogen Production

Plant chloroplasts have a highly compartmentalized interior, essential for executing photocatalytic functions. However, the construction of a photocatalytic reaction compartment similar to chloroplasts in inorganic-biological hybrid systems (IBS) has not been reported. Drawing inspiration from the compartmentalized chloroplast and the phenomenon of liquid-liquid phase separation, herein, a new strategy is first developed for constructing a photocatalytic subcellular hybrid system through liquid-liquid phase separation technology in living cells. Photosensitizers and in vivo expressed hydrogenases are designed to coassemble within the cell to create subcellular compartments for synergetic photocatalysis. This compartmentalization facilitates efficient electron transfer and light energy utilization, resulting in highly effective H2 production. The subcellular compartments hybrid system (HM/IBSCS) exhibits a nearly 87-fold increase in H2 production compared to the bare bacteria/hybrid system. Furthermore, the intracellular compartments of the photocatalytic reactor enhance the system's stability obviously, with the bacteria maintaining approximately 81% of their H2 production activity even after undergoing five cycles of photocatalytic hydrogen production. The research brings forward visionary prospects for the field of semi-artificial photosynthesis, offering new possibilities for advancements in areas such as renewable energy, biomanufacturing, and genetic engineering.

Nanoassembly of spider silk protein mediated by intrinsically disordered regions

Spider silk is the self-assembling product of silk proteins each containing multiple repeating units. Each repeating unit is entirely intrinsically disordered or contains a small disordered domain. The role of the disordered domain/unit in conferring silk protein storage and self-assembly is not fully understood yet. Here, we used biophysical and biochemical techniques to investigate the self-assembly of a miniature version of a minor ampullate spidroin (denoted as miniMiSp). miniMiSp consists of two identical intrinsically disordered domains, one folded repetitive domain, and two folded terminal domains. Our data indicated that miniMiSp self-assembles into oligomers and further into liquid droplets. The oligomerization is attributed to the aggregation-prone property of both the disordered domains and the folded repetitive domain. Our results support the model of micellar structure for silk proteins at high protein concentrations. The disordered domain is indispensable for liquid droplet formation via liquid-liquid phase separation, and tyrosine residues located in the disordered domain make dominant contributions to stability of the liquid droplets. As the same tyrosine residues are also critical to fibrillation, the liquid droplets are likely an intermediate state between the solution state and the fiber state. Additionally, the terminal domains contribute to the pH- and salt-dependent self-assembly properties.

In-situ observation of silk nanofibril assembly via graphene plasmonic infrared sensor

Silk nanofibrils (SNFs), the fundamental building blocks of silk fibers, endow them with exceptional properties. However, the intricate mechanism governing SNF assembly, a process involving both protein conformational transitions and protein molecule conjunctions, remains elusive. This lack of understanding has hindered the development of artificial silk spinning techniques. In this study, we address this challenge by employing a graphene plasmonic infrared sensor in conjunction with multi-scale molecular dynamics (MD). This unique approach allows us to probe the secondary structure of nanoscale assembly intermediates (0.8-6.2 nm) and their morphological evolution. It also provides insights into the dynamics of silk fibroin (SF) over extended molecular timeframes. Our novel findings reveal that amorphous SFs undergo a conformational transition towards β-sheet-rich oligomers on graphene. These oligomers then connect to evolve into SNFs. These insights provide a comprehensive picture of SNF assembly, paving the way for advancements in biomimetic silk spinning.

Liquid-liquid phase separation-inspired design of biomaterials

Liquid-liquid phase separation (LLPS) is a crucial biological process that governs biomolecular condensation, assembly, and functionality within phase-separated aqueous environments. This phenomenon serves as a source of inspiration for the creation of artificial designs in both structured and functional biomaterials, presenting novel strategies for manipulating the structures of functional protein aggregates in a wide range of biomedical applications. This mini review summarizes my past research endeavors, offering a panoramic overview of LLPS-inspired biomaterials utilized in the design of structured materials, the development of cell mimetics, and the advancement of intelligent biomaterials.

Deciphering the liquid-liquid phase separation induced modulation in the structure, dynamics, and enzymatic activity of an ordered protein β-lactoglobulin

Owing to the significant role in the subcellular organization of biomolecules, physiology, and the realm of biomimetic materials, studies related to biomolecular condensates formed through liquid-liquid phase separation (LLPS) have emerged as a growing area of research. Despite valuable contributions of prior research, there is untapped potential in exploring the influence of phase separation on the conformational dynamics and enzymatic activities of native proteins. Herein, we investigate the LLPS of β-lactoglobulin (β-LG), a non-intrinsically disordered protein, under crowded conditions. In-depth characterization through spectroscopic and microscopic techniques revealed the formation of dynamic liquid-like droplets, distinct from protein aggregates, driven by hydrophobic interactions. Our analyses revealed that phase separation can alter structural flexibility and photophysical properties. Importantly, the phase-separated β-LG exhibited efficient enzymatic activity as an esterase; a characteristic seemingly exclusive to β-LG droplets. The droplets acted as robust catalytic crucibles, providing an ideal environment for efficient ester hydrolysis. Further investigation into the catalytic mechanism suggested the involvement of specific amino acid residues, rather than general acid or base catalysis. Also, the alteration in conformational distribution caused by phase separation unveils the latent functionality. Our study delineates the understanding of protein phase separation and insights into the diverse catalytic strategies employed by proteins. It opens exciting possibilities for designing functional artificial compartments based on phase-separated biomolecules.

Triblock Proteins with Weakly Dimerizing Terminal Blocks and an Intrinsically Disordered Region for Rational Design of Condensate Properties

Condensates are molecular assemblies that are formed through liquid-liquid phase separation and play important roles in many biological processes. The rational design of condensate formation and their properties is central to applications, such as biosynthetic materials, synthetic biology, and for understanding cell biology. Protein engineering is used to make a triblock structure with varying terminal blocks of folded proteins on both sides of an intrinsically disordered mid-region. Dissociation constants are determined in the range of micromolar to millimolar for a set of proteins suitable for use as terminal blocks. Varying the weak dimerization of terminal blocks leads to an adjustable tendency for condensate formation while keeping the intrinsically disordered region constant. The dissociation constants of the terminal domains correlate directly with the tendency to undergo liquid-liquid phase separation. Differences in physical properties, such as diffusion rate are not directly correlated with the strength of dimerization but can be understood from the properties and interplay of the constituent blocks. The work demonstrates the importance of weak interactions in condensate formation and shows a principle for protein design that will help in fabricating functional condensates in a predictable and rational way.

Replicating shear-mediated self-assembly of spider silk through microfluidics

The development of artificial spider silk with properties similar to native silk has been a challenging task in materials science. In this study, we use a microfluidic device to create continuous fibers based on recombinant MaSp2 spidroin. The strategy incorporates ion-induced liquid-liquid phase separation, pH-driven fibrillation, and shear-dependent induction of β-sheet formation. We find that a threshold shear stress of approximately 72 Pa is required for fiber formation, and that β-sheet formation is dependent on the presence of polyalanine blocks in the repetitive sequence. The MaSp2 fiber formed has a β-sheet content (29.2%) comparable to that of native dragline with a shear stress requirement of 111 Pa. Interestingly, the polyalanine blocks have limited influence on the occurrence of liquid-liquid phase separation and hierarchical structure. These results offer insights into the shear-induced crystallization and sequence-structure relationship of spider silk and have significant implications for the rational design of artificially spun fibers.

C-Terminal Domain Controls Protein Quality and Secretion of Spider Silk in Tobacco Cells

The remarkable mechanical strength and extensibility of spider dragline silk spidroins are attributed to the major ampullate silk proteins (MaSp). Although fragmented MaSp molecules have been extensively produced in various heterologous expression platforms for biotechnological applications, complete MaSp molecules are required to achieve instinctive spinning of spidroin fibers from aqueous solutions. Here, a plant cell-based expression platform for extracellular production of the entire MaSp2 protein is developed, which exhibits remarkable self-assembly properties to form spider silk nanofibrils. The engineered transgenic Bright-yellow 2 (BY-2) cell lines overexpressing recombinant secretory MaSp2 proteins yield 0.6-1.3  µg L-1 at 22 days post-inoculation, which is four times higher than those of cytosolic expressions. However, only 10-15% of these secretory MaSp2 proteins are discharged into the culture media. Surprisingly, expression of functional domain-truncated MaSp2 proteins lacking the C-terminal domain in transgenic BY-2 cells increases recombinant protein secretion incredibly, from 0.9 to 2.8 mg L-1 per day within 7 days. These findings demonstrate significant improvement in the extracellular production of recombinant biopolymers such as spider silk spidroins using plant cells. In addition, the results reveal the regulatory roles of the C-terminal domain of MaSp2 proteins in controlling their protein quality and secretion.

Spider Silk Protein Forms Amyloid-Like Nanofibrils through a Non-Nucleation-Dependent Polymerization Mechanism

Amyloid fibrils-nanoscale fibrillar aggregates with high levels of order-are pathogenic in some today incurable human diseases; however, there are also many physiologically functioning amyloids in nature. The process of amyloid formation is typically nucleation-elongation-dependent, as exemplified by the pathogenic amyloid-β peptide (Aβ) that is associated with Alzheimer's disease. Spider silk, one of the toughest biomaterials, shares characteristics with amyloid. In this study, it is shown that forming amyloid-like nanofibrils is an inherent property preserved by various spider silk proteins (spidroins). Both spidroins and Aβ capped by spidroin N- and C-terminal domains, can assemble into macroscopic spider silk-like fibers that consist of straight nanofibrils parallel to the fiber axis as observed in native spider silk. While Aβ forms amyloid nanofibrils through a nucleation-dependent pathway and exhibits strong cytotoxicity and seeding effects, spidroins spontaneously and rapidly form amyloid-like nanofibrils via a non-nucleation-dependent polymerization pathway that involves lateral packing of fibrils. Spidroin nanofibrils share amyloid-like properties but lack strong cytotoxicity and the ability to self-seed or cross-seed human amyloidogenic peptides. These results suggest that spidroins´ unique primary structures have evolved to allow functional properties of amyloid, and at the same time direct their fibrillization pathways to avoid formation of cytotoxic intermediates.

A Minispidroin Guides the Molecular Design for Cellular Condensation Mechanisms in S. cerevisiae

Structural engineering of molecules for condensation is an emerging technique within synthetic biology. Liquid-liquid phase separation of biomolecules leading to condensation is a central step in the assembly of biological materials into their functional forms. Intracellular condensates can also function within cells in a regulatory manner to facilitate reaction pathways and to compartmentalize interactions. We need to develop a strong understanding of how to design molecules for condensates and how their in vivo-in vitro properties are related. The spider silk protein NT2RepCT undergoes condensation during its fiber-forming process. Using parallel in vivo and in vitro characterization, in this study, we mapped the effects of intracellular conditions for NT2RepCT and its several structural variants. We found that intracellular conditions may suppress to some extent condensation whereas molecular crowding affects both condensate properties and their formation. Intracellular characterization of protein condensation allowed experiments on pH effects and solubilization to be performed within yeast cells. The growth of intracellular NT2RepCT condensates was restricted, and Ostwald ripening was not observed in yeast cells, in contrast to earlier observations in E. coli. Our results lead the way to using intracellular condensation to screen for properties of molecular assembly. For characterizing different structural variants, intracellular functional characterization can eliminate the need for time-consuming batch purification and in vitro condensation. Therefore, we suggest that the in vivo-in vitro understanding will become useful in, e.g., high-throughput screening for molecular functions and in strategies for designing tunable intracellular condensates.

Natural spider silk nanofibrils produced by assembling molecules or disassembling fibers

Spider silk is biocompatible, biodegradable, and rivals some of the best synthetic materials in terms of strength and toughness. Despite extensive research, comprehensive experimental evidence of the formation and morphology of its internal structure is still limited and controversially discussed. Here, we report the complete mechanical decomposition of natural silk fibers from the golden silk orb-weaver Trichonephila clavipes into ≈10 nm-diameter nanofibrils, the material's apparent fundamental building blocks. Furthermore, we produced nanofibrils of virtually identical morphology by triggering an intrinsic self-assembly mechanism of the silk proteins. Independent physico-chemical fibrillation triggers were revealed, enabling fiber assembly from stored precursors "at-will". This knowledge furthers the understanding of this exceptional material's fundamentals, and ultimately, leads toward the realization of silk-based high-performance materials. STATEMENT OF SIGNIFICANCE: Spider silk is one of the strongest and toughest biomaterials, rivaling the best man-made materials. The origins of these traits are still under debate but are mostly attributed to the material's intriguing hierarchical structure. Here we fully disassembled spider silk into 10 nm-diameter nanofibrils for the first time and showed that nanofibrils of the same appearance can be produced via molecular self-assembly of spider silk proteins under certain conditions. This shows that nanofibrils are the key structural elements in silk and leads toward the production of high-performance future materials inspired by spider silk.

A brief review on the mechanisms and approaches of silk spinning-inspired biofabrication

Silk spinning, observed in spiders and insects, exhibits a remarkable biological source of inspiration for advanced polymer fabrications. Because of the systems design, silk spinning represents a holistic and circular approach to sustainable polymer fabrication, characterized by renewable resources, ambient and aqueous processing conditions, and fully recyclable "wastes." Also, silk spinning results in structures that are characterized by the combination of monolithic proteinaceous composition and mechanical strength, as well as demonstrate tunable degradation profiles and minimal immunogenicity, thus making it a viable alternative to most synthetic polymers for the development of advanced biomedical devices. However, the fundamental mechanisms of silk spinning remain incompletely understood, thus impeding the efforts to harness the advantageous properties of silk spinning. Here, we present a concise and timely review of several essential features of silk spinning, including the molecular designs of silk proteins and the solvent cues along the spinning apparatus. The solvent cues, including salt ions, pH, and water content, are suggested to direct the hierarchical assembly of silk proteins and thus play a central role in silk spinning. We also discuss several hypotheses on the roles of solvent cues to provide a relatively comprehensive analysis and to identify the current knowledge gap. We then review the state-of-the-art bioinspired fabrications with silk proteins, including fiber spinning and additive approaches/three-dimensional (3D) printing. An emphasis throughout the article is placed on the universal characteristics of silk spinning developed through millions of years of individual evolution pathways in spiders and silkworms. This review serves as a stepping stone for future research endeavors, facilitating the in vitro recapitulation of silk spinning and advancing the field of bioinspired polymer fabrication.

An evolutionarily nascent architecture underlying the formation and emergence of biomolecular condensates

Biomolecular condensates are implicated in core cellular processes such as gene regulation and ribosome biogenesis. Although the architecture of biomolecular condensates is thought to rely on collective interactions between many components, it is unclear how the collective interactions required for their formation emerge during evolution. Here, we show that the structure and evolution of a recently emerged biomolecular condensate, the nucleolar fibrillar center (FC), is explained by a single self-assembling scaffold, TCOF1. TCOF1 is necessary to form the FC, and it structurally defines the FC through self-assembly mediated by homotypic interactions of serine/glutamate-rich low-complexity regions (LCRs). Finally, introduction of TCOF1 into a species lacking the FC is sufficient to form an FC-like biomolecular condensate. By demonstrating that a recently emerged biomolecular condensate is built on a simple architecture determined by a single self-assembling protein, our work provides a compelling mechanism by which biomolecular condensates can emerge in the tree of life.

Factors Influencing Properties of Spider Silk Coatings and Their Interactions within a Biological Environment

Biomaterials are an indispensable part of biomedical research. However, although many materials display suitable application-specific properties, they provide only poor biocompatibility when implanted into a human/animal body leading to inflammation and rejection reactions. Coatings made of spider silk proteins are promising alternatives for various applications since they are biocompatible, non-toxic and anti-inflammatory. Nevertheless, the biological response toward a spider silk coating cannot be generalized. The properties of spider silk coatings are influenced by many factors, including silk source, solvent, the substrate to be coated, pre- and post-treatments and the processing technique. All these factors consequently affect the biological response of the environment and the putative application of the appropriate silk coating. Here, we summarize recently identified factors to be considered before spider silk processing as well as physicochemical characterization methods. Furthermore, we highlight important results of biological evaluations to emphasize the importance of adjustability and adaption to a specific application. Finally, we provide an experimental matrix of parameters to be considered for a specific application and a guided biological response as exemplarily tested with two different fibroblast cell lines.

Protein nanocondensates: the next frontier

Over the past decade, myriads of studies have highlighted the central role of protein condensation in subcellular compartmentalization and spatiotemporal organization of biological processes. Conceptually, protein condensation stands at the highest level in protein structure hierarchy, accounting for the assembly of bodies ranging from thousands to billions of molecules and for densities ranging from dense liquids to solid materials. In size, protein condensates range from nanocondensates of hundreds of nanometers (mesoscopic clusters) to phase-separated micron-sized condensates. In this review, we focus on protein nanocondensation, a process that can occur in subsaturated solutions and can nucleate dense liquid phases, crystals, amorphous aggregates, and fibers. We discuss the nanocondensation of proteins in the light of general physical principles and examine the biophysical properties of several outstanding examples of nanocondensation. We conclude that protein nanocondensation cannot be fully explained by the conceptual framework of micron-scale biomolecular condensation. The evolution of nanocondensates through changes in density and order is currently under intense investigation, and this should lead to the development of a general theoretical framework, capable of encompassing the full range of sizes and densities found in protein condensates.

Mass Spectrometry of RNA-Binding Proteins during Liquid-Liquid Phase Separation Reveals Distinct Assembly Mechanisms and Droplet Architectures

Liquid-liquid phase separation (LLPS) of heterogeneous ribonucleoproteins (hnRNPs) drives the formation of membraneless organelles, but structural information about their assembled states is still lacking. Here, we address this challenge through a combination of protein engineering, native ion mobility mass spectrometry, and molecular dynamics simulations. We used an LLPS-compatible spider silk domain and pH changes to control the self-assembly of the hnRNPs FUS, TDP-43, and hCPEB3, which are implicated in neurodegeneration, cancer, and memory storage. By releasing the proteins inside the mass spectrometer from their native assemblies, we could monitor conformational changes associated with liquid-liquid phase separation. We find that FUS monomers undergo an unfolded-to-globular transition, whereas TDP-43 oligomerizes into partially disordered dimers and trimers. hCPEB3, on the other hand, remains fully disordered with a preference for fibrillar aggregation over LLPS. The divergent assembly mechanisms revealed by ion mobility mass spectrometry of soluble protein species that exist under LLPS conditions suggest structurally distinct complexes inside liquid droplets that may impact RNA processing and translation depending on biological context.

Glycan-Presenting Coacervates Derived from Charged Poly(active esters): Preparation, Phase Behavior, and Lectin Capture

This study presents the preparation and phase behavior of glycan-functionalized polyelectrolytes for capturing carbohydrate-binding proteins and bacteria in liquid condensate droplets. The droplets are formed by complex coacervation of poly(active ester)-derived polyanions and polycations. This approach allows for a straightforward modular introduction of charged motifs and specifically interacting units; mannose and galactose oligomers are used here as first examples. The introduction of carbohydrates has a notable effect on the phase separation and the critical salt concentration, potentially by reducing the charge density. Two mannose binding species, concanavalin A (ConA) and Escherichia coli, are shown to not only specifically bind to mannose-functionalized coacervates but also to some degree to unfunctionalized, carbohydrate-free coacervates. This suggests non-carbohydrate-specific charge-charge interactions between the protein/bacteria and the droplets. However, when mannose interactions are inhibited or when non-binding galactose-functionalized polymers are used, interactions are significantly weakened. This confirms specific mannose-mediated binding functionalization and suggests that introducing carbohydrates reduces non-specific charge-charge interactions by a so far unidentified mechanism. Overall, the presented route toward glycan-presenting polyelectrolytes enables new functional liquid condensate droplets with specific biomolecular interactions.

Liquid sculpture and curing of bio-inspired polyelectrolyte aqueous two-phase systems

Aqueous two-phase systems (ATPS) provide imperative interfaces and compartments in biology, but the sculpture and conversion of liquid structures to functional solids is challenging. Here, inspired by phase evolution of mussel foot proteins ATPS, we tackle this problem by designing poly(ionic liquids) capable of responsive condensation and phase-dependent curing. When mixed with poly(dimethyl diallyl ammonium chloride), the poly(ionic liquids) formed liquid condensates and ATPS, which were tuned into bicontinuous liquid phases under stirring. Selective, rapid curing of the poly(ionic liquids)-rich phase was facilitated under basic conditions (pH 11), leading to the liquid-to-gel conversion and structure sculpture, i.e., the evolution from ATPS to macroporous sponges featuring bead-and-string networks. This mechanism enabled the selective embedment of carbon nanotubes in the poly(ionic liquids)-rich phase, which showed exceptional stability in harsh conditions (10 wt% NaCl, 80 ^oC, 3 days) and high (2.5 kg/m²h) solar thermal desalination of concentrated salty water under 1-sun irradiation.

Liquid-Liquid Phase Separation Primes Spider Silk Proteins for Fiber Formation via a Conditional Sticker Domain

Many protein condensates can convert to fibrillar aggregates, but the underlying mechanisms are unclear. Liquid-liquid phase separation (LLPS) of spider silk proteins, spidroins, suggests a regulatory switch between both states. Here, we combine microscopy and native mass spectrometry to investigate the influence of protein sequence, ions, and regulatory domains on spidroin LLPS. We find that salting out-effects drive LLPS via low-affinity stickers in the repeat domains. Interestingly, conditions that enable LLPS simultaneously cause dissociation of the dimeric C-terminal domain (CTD), priming it for aggregation. Since the CTD enhances LLPS of spidroins but is also required for their conversion into amyloid-like fibers, we expand the stickers and spacers-model of phase separation with the concept of folded domains as conditional stickers that represent regulatory units.