Solenoid architecture of HUWE1 contributes to ligase activity and substrate recognition.

HECT ubiquitin ligases play essential roles in metazoan development and physiology. The HECT ligase HUWE1 is central to the cellular stress response by mediating degradation of key death or survival factors, including Mcl1, p53, DDIT4, and Myc. Although mutations in HUWE1 and related HECT ligases are widely implicated in human disease, our molecular understanding remains limited. Here we present a comprehensive investigation of full-length HUWE1, deepening our understanding of this class of enzymes. The N-terminal ∼3,900 amino acids of HUWE1 are indispensable for proper ligase function, and our cryo-EM structures of HUWE1 offer a complete molecular picture of this large HECT ubiquitin ligase. HUWE1 forms an alpha solenoid-shaped assembly with a central pore decorated with protein interaction modules. Structures of HUWE1 variants linked to neurodevelopmental disorders as well as of HUWE1 bound to a model substrate link the functions of this essential enzyme to its three-dimensional organization.

Modular Assembled Localized Hybridization Chain Reaction for In Situ mRNA Amplified Imaging.

As a nonenzymatic DNA signal amplification technique, localized hybridization chain reaction (LHCR) was designed to improve the limitations in response speed and low sensitivity of conventional free diffusional HCR (hybridization chain reaction). However, it is still confronted with the challenges of complicated DNA scaffolds with low loading capacity and a time-consuming process of diffusion. Herein, we introduced modular assembly of a DNA minimal scaffold for coassembly of DNA hairpins for amplified fluorescence imaging of mRNA in situ. DNA hairpins were spatially bound to two Y-shaped modules to form H-shaped DNA modules, and then multiple H-shaped DNA modules can further assemble into an H-module-based hairpin scaffold (HHS). Benefiting from highly spatial localization and high loading capacity, the HHS system showed higher sensitivity and faster speed. It has also been proven to work perfectly in vitro and in vivo, which could provide a promising bioanalysis system for low abundance biomolecule detection.

Modular Assembly of Ordered Hydrophilic Proteins Improve Salinity Tolerance in Escherichia coli.

Most late embryogenesis abundant group 3 (G3LEA) proteins are highly hydrophilic and disordered, which can be transformed into ordered α-helices to play an important role in responding to diverse stresses in numerous organisms. Unlike most G3LEA proteins, DosH derived from Dinococcus radiodurans is a naturally ordered G3LEA protein, and previous studies have found that the N-terminal domain (position 1-103) of DosH protein is the key region for its folding into an ordered secondary structure. Synthetic biology provides the possibility for artificial assembling ordered G3LEA proteins or their analogues. In this report, we used the N-terminal domain of DosH protein as module A (named DS) and the hydrophilic domains (DrHD, BnHD, CeHD, and YlHD) of G3LEA protein from different sources as module B, and artificially assembled four non-natural hydrophilic proteins, named DS + DrHD, DS + BnHD, DS + CeHD, and DS + YlHD, respectively. Circular dichroism showed that the four hydrophile proteins were highly ordered proteins, in which the α-helix contents were DS + DrHD (56.1%), DS + BnHD (53.7%), DS + CeHD (49.1%), and DS + YLHD (64.6%), respectively. Phenotypic analysis showed that the survival rate of recombinant Escherichia coli containing ordered hydrophilic protein was more than 10% after 4 h treatment with 1.5 M NaCl, which was much higher than that of the control group. Meanwhile, in vivo enzyme activity results showed that they had higher activities of superoxide dismutase, catalase, lactate dehydrogenase and less malondialdehyde production. Based on these results, the N-terminal domain of DosH protein can be applied in synthetic biology due to the fact that it can change the order of hydrophilic domains, thus increasing stress resistance.

Porphyrinic MOF Film for Multifaceted Electrochemical Sensing.

Electrochemical sensors are indispensable in clinical diagnosis, biochemical detection and environmental monitoring, thanks to their ability to detect analytes in real-time with direct electronic readout. However, electrochemical sensors are challenged by sensitivity-the need to detect low concentrations, and selectivity-to detect specific analytes in multicomponent systems. Herein, a porphyrinic metal-organic framework (PP-MOF), Mn-PCN-222 is deposited on a conductive indium tin oxide (ITO) surface. It affords Mn-PCN-222/ITO, a versatile voltammetric sensor able to detect redox-active analytes such as inorganic ions, organic hazardous substances and pollutants, including nitroaromatics, phenolic and quinone-hydroquinone toxins, heavy metal ions, biological species, as well as azo dyes. As a working electrode, the high surface area of Mn-PCN-222/ITO enables high currents, and therefore leverages highly sensitive analysis. The metalloporphyrin centre facilitates analyte-specific redox catalysis to simultaneously detect more than one analyte in binary and ternary systems allowing for detection of a wide array of trace pollutants under real-world conditions, most with high sensitivity.

High-Throughput Fabrication and Modular Assembly of 3D Heterogeneous Microscale Tissues.

3D hydrogel microstructures that encapsulate cells have been used in broad applications in microscale tissue engineering, personalized drug screening, and regenerative medicine. Recent technological advances in microstructure assembly, such as bioprinting, magnetic assembly, microfluidics, and acoustics, have enabled the construction of designed 3D tissue structures with spatially organized cells in vitro. However, a bottleneck exists that still hampers the application of microtissue structures, due to a lack of techniques that combined high-throughput fabrication and flexible assembly. Here, a versatile method for fabricating customized microstructures and reorganizing building blocks composed of functional components into a combined single geometric shape is demonstrated. The arbitrary microstructures are dynamically synthesized in a microfluidic device and then transferred to an optically induced electrokinetics chip for manipulation and assembly. Moreover, building blocks containing different cells can be arranged into a desired geometry with specific shape and size, which can be used for microscale tissue engineering.

Modular assembly of synthetic proteins that span the plasma membrane in mammalian cells.

BACKGROUND: To achieve synthetic control over how a cell responds to other cells or the extracellular environment, it is important to reliably engineer proteins that can traffic and span the plasma membrane. Using a modular approach to assemble proteins, we identified the minimum necessary components required to engineer such membrane-spanning proteins with predictable orientation in mammalian cells. RESULTS: While a transmembrane domain (TM) fused to the N-terminus of a protein is sufficient to traffic it to the endoplasmic reticulum (ER), an additional signal peptidase cleavage site downstream of this TM enhanced sorting out of the ER. Next, a second TM in the synthetic protein helped anchor and accumulate the membrane-spanning protein on the plasma membrane. The orientation of the components of the synthetic protein were determined through measuring intracellular Ca2+ signaling using the R-GECO biosensor and through measuring extracellular quenching of yellow fluorescent protein variants by saturating acidic and salt conditions. CONCLUSIONS: This work forms the basis of engineering novel proteins that span the plasma membrane to potentially control intracellular responses to extracellular conditions.

An Antibiotic Nanobomb Constructed from pH-Responsive Chemical Bonds in Metal-Phenolic Network Nanoparticles for Biofilm Eradication and Corneal Ulcer Healing.

In the treatment of refractory corneal ulcers caused by Pseudomonas aeruginosa, antibacterial drugs delivery faces the drawbacks of low permeability and short ocular surface retention time. Hence, novel positively-charged modular nanoparticles (NPs) are developed to load tobramycin (TOB) through a one-step self-assembly method based on metal-phenolic network and Schiff base reaction using 3,4,5-trihydroxybenzaldehyde (THBA), ε-poly-ʟ-lysine (EPL), and Cu2+ as matrix components. In vitro antibacterial test demonstrates that THBA-Cu-TOB NPs exhibit efficient instantaneous sterilization owing to the rapid pH responsiveness to bacterial infections. Notably, only 2.6 µg mL-1 TOP is needed to eradicate P. aeruginosa biofilm in the nano-formed THBA-Cu-TOB owing to the greatly enhanced penetration, which is only 1.6% the concentration of free TOB (160 µg mL-1). In animal experiments, THBA-Cu-TOB NPs show significant advantages in ocular surface retention, corneal permeability, rapid sterilization, and inflammation elimination. Based on molecular biology analysis, the toll-like receptor 4 and nuclear factor kappa B signaling pathways are greatly downregulated as well as the reduction of inflammatory cytokines secretions. Such a simple and modular strategy in constructing nano-drug delivery platform offers a new idea for toxicity reduction, physiological barrier penetration, and intelligent drug delivery.

Constrained Origami Artificial Muscle-Driven Robotic Manipulator Capable of Coordinating Twisting and Grasping Motions for Object Manipulation.

Grasping and twisting motions are vital when manipulating objects due to their fundamental role in enabling precision, adaptability, and effective interaction. However, few studies in soft robotics exploiting artificial muscles have achieved object manipulation in situ through the coordination of twisting and grasping motions akin to our forearm and hand's capabilities. Especially, when using the same artificial muscle module to achieve these two motions will greatly simplify the manufacturing and control complexity. Here, we introduce identical origami artificial muscle modules (OAMMs) subjected to distinct end constraints into the design of the robotic manipulator, allowing it to achieve independent grasping and twisting motions to achieve effective, precise object manipulation. Applying different end constraints to the identical OAMMs yields distinct motions at their ends, where utilizing a fixed end and a sliding end realizes pure translation, while opting for a fixed end and a rotating end enables pure rotation. The differentially constrained OAMMs then serve as soft actuators for the manipulator's torsional mechanism and grasping mechanism to accomplish independent, controllable twisting and grasping motions. The coordination of twisting and grasping motions finally enables the manipulator to complete various tasks, including installing a light bubble, pouring the water from a lidded bottle into a cup, and sorting and stacking puzzle blocks. Our study pioneers the utilization of OAMMs for precise and versatile object manipulation through the coordination of independent twisting and grasping motions.

Spy&IAC enables specific capture of SpyTagged proteins for rapid assembly of plug-and-display nanoparticle vaccines.

From modular vaccine production to protein assembly on nanoparticles, the SpyCatcher/SpyTag system provides a convenient plug-and-display procedure. Here, we established a general-purpose immunoaffinity chromatography (IAC) method for SpyTagged proteins (Spy&IAC). SpyTags are displayed on the surface of nanoparticles to induce high-affinity monoclonal antibodies, allowing the specific capture of the target protein. Taking the key core antigenic regions of two coronaviruses that are currently more threatened in the field of human and animal diseases, the nucleocapsid (N) protein of SARS-CoV-2 and the COE protein of porcine epidemic diarrhea virus (PEDV) as model proteins, a purification model with SpyTag at the N-terminal or C-terminal expressed in E. coli or mammalian cells was constructed. After the efficient elution of Spy&IAC, the final yield of several proteins is about 3.5-15 mg/L culture, and the protein purity is above 90 %. Purification also preserves the assembly function and immunogenicity of the protein to support subsequent modular assembly and immunization programs. This strategy provides a general tool for the efficient purification of SpyTagged proteins from different expression sources and different tag positions, enabling the production of modular vaccines at lower cost and in a shorter time, which will prepare the public health field for potential pandemic threats.

Magnetically Driven Modular Mechanical Metamaterials with High Programmability, Reconfigurability, and Multiple Applications.

Shape transformation and motion guidance are emerging research hotspots of mechanical metamaterials. In this case, the key issue is how to improve the programmability and reconfigurability of metamaterials. The magnetically driven method enables materials to accomplish remote, fast, and reversible deformation, so it is desired for improving the programmability and reconfigurability of metamaterials. However, conventional magnetically driven materials are often pure elastomer materials. Their magnetic programming method is single, and their overall shape is unchangeable after fabrication, which limits their programmability and reconfigurability. Herein, this article proposes a kind of magnetically driven, programmable, and reconfigurable modular mechanical metamaterial based on origami and kirigami design mechanisms. The motion and deformation were designed to follow the predefined creases and incisions that could be transformed into each other. This metamaterial enabled more discrete motion and force transmission and integrated the fold of origami, the rotation of kirigami, and the fold guided by cuts. Such designs laid the foundation for complex, three-dimensional structures which could be quickly reassembled and constructed to deal with complex situations. This paper also demonstrated applications of this metamaterial in information storage and manifestation, mechanical logic computing, reconfigurable robotics, deployable mechanisms, and so on. The results indicated that the high programmability and reconfigurability expanded the application potential of the metamaterial for broader needs.

Biofabrication of Modular Spheroids as Tumor-Scale Microenvironments for Drug Screening.

To streamline the drug discovery pipeline, there is a pressing need for preclinical models which replicate the complexity and scale of native tumors. While there have been advancements in the formation of microscale tumor units, these models are cell-line dependent, time-consuming and have not improved clinical trial success rates. In this study, two methods for generating 3D tumor microenvironments are compared, rapidly fabricated hydrogel microspheres and traditional cell-dense spheroids. These modules are then bioassembled into 3D printed thermoplastic scaffolds, using an automated biofabrication process, to form tumor-scale models. Modules are formed with SKOV3 and HFF cells as monocultures and cocultures, and the fabrication efficiency, cell architecture, and drug response profiles are characterized, both as single modules and as multimodular constructs. Cell-encapsulated Gel-MA microspheres are fabricated with high-reproducibility and dimensions necessary for automated tumor-scale bioassembly regardless of cell type, however, only cocultured spheroids form compact modules suitable for bioassembly. Chemosensitivity assays demonstrate the reduced potency of doxorubicin in coculture bioassembled constructs and a ≈five-fold increase in drug resistance of cocultured cells in 3D modules compared with 2D monolayers. This bioassembly system is efficient and tailorable so that a variety of relevant-sized tumor constructs could be developed to study tumorigenesis and modernize drug discovery.

A boronate-based modular assembly nanosystem to block the undesirable crosstalk between hepatic stellate cells and Kupffer cells.

Crosstalk between Kupffer cells (KCs) and hepatic stellate cells (HSCs) plays an important role in multiple liver disease conditions, including the formation of liver fibrosis in alcohol-associated liver disease (AALD). Therapeutic targeting of the KC-HSC crosstalk is a prime target for therapeutic interventions. Herein, a novel modular nanosystem was designed and prepared through the self-assembly utilizing boric acid and catechol interactions to prepare polymers modified with a CXCR4-inhibiting moieties. The polymers were used to encapsulate anti-miR-155 and to block the undesirable crosstalk between HSCs and KCs by downregulating miR-155 expression in KCs with the parallel inhibition of CXCR4 signaling in activated HSCs. The combined inhibition of miR-155 and CXCR4 at two different liver cell types achieved improved antifibrosis effects in a mouse model of AALD fibrosis. Our finding highlights the key role that blocking the undesirable crosstalk between HSCs and KCs plays in reversing AALD fibrosis as well as demonstrates a proof-of-concept approach for designing and constructing multifunctional delivery nanosystems using orthogonal functional modules based on the understanding of disease mechanisms.

Parallel and four-step synthesis of natural-product-inspired scaffolds through modular assembly and divergent cyclization.

By emulating the universal biosynthetic strategy, which employs modular assembly and divergent cyclizations, we have developed a four-step synthetic process to yield a collection of natural-product-inspired scaffolds. Modular assembly of building blocks onto a piperidine-based manifold 6, having a carboxylic acid group, was achieved through Ugi condensation, N-acetoacetylation and diazotransfer, leading to cyclization precursors. The rhodium-catalyzed tandem cyclization and divergent cycloaddition gave rise to tetracyclic and hexacyclic scaffolds by the appropriate choice of dipolarophiles installed at modules 3 and 4. A different piperidine-based manifold 15 bearing an amino group was successfully applied to demonstrate the flexibility and scope of the unified four-step process for the generation of structural diversity in the fused scaffolds. Evaluation of in vitro antitrypanosomal activities of the collections and preliminary structure-activity relationship (SAR) studies were also undertaken.

Aligned Magnetic Nanocomposites for Modularized and Recyclable Soft Microrobots.

Creating reconfigurable and recyclable soft microrobots that can execute multimodal locomotion has been a challenge due to the difficulties in material processing and structure engineering at a small scale. Here, we propose a facile technique to manufacture diverse soft microrobots (∼100 µm in all dimensions) by mechanically assembling modular magnetic microactuators into different three-dimensional (3D) configurations. The module is composed of a cubic micropillar supported on a square substrate, both made of elastomer matrix embedded with prealigned magnetic nanoparticle chains. By directionally bonding the sides or backs of identical modules together, we demonstrate that assemblies from only two and four modules can execute a wide range of locomotion, including gripping microscale objects, crawling and crossing solid obstacles, swimming within narrow and tortuous microchannels, and rolling along flat and inclined surfaces, upon applying proper magnetic fields. The assembled microrobots can additionally perform pick-transfer-place and cargo-release tasks at the microscale. More importantly, like the game of block-building, the microrobots can be disassembled back to separate modules and then reassembled to other configurations as demanded. The present study not only provides a versatile and economic manufacturing technique for reconfigurable and recyclable soft microrobots, enabling unlimited design space for diverse robotic locomotion from limited materials and module structures, but also extends the functionality and dexterity of existing soft robots to microscale that should facilitate practical applications at such small scale.

Engineered meatballs via scalable skeletal muscle cell expansion and modular micro-tissue assembly using porous gelatin micro-carriers.

The emerging field of cultured meat faces several technical hurdles, including the scale-up production of quality muscle and adipose progenitor cells, and the differentiation and bioengineering of these cellular materials into large, meat-like tissue. Here, we present edible, 3D porous gelatin micro-carriers (PoGelat-MCs), as efficient cell expansion scaffolds, as well as modular tissue-engineering building blocks for lab-grown meat. PoGelat-MC culture in spinner flasks, not only facilitated the scalable expansion of porcine skeletal muscle satellite cells and murine myoblasts, but also triggered their spontaneous myogenesis, in the absence of myogenic reagents. Using 3D-printed mold and transglutaminase, we bio-assembled pork muscle micro-tissues into centimeter-scale meatballs, which exhibited similar mechanical property and higher protein content compared to conventional ground pork meatballs. PoGelat-MCs also supported the expansion and differentiation of 3T3L1 murine pre-adipocytes into mature adipose micro-tissues, which could be used as modular assembly unit for engineered fat-containing meat products. Together, our results highlight PoGelat-MCs, in combination with dynamic bioreactors, as a scalable culture system to produce large quantity of highly-viable muscle and fat micro-tissues, which could be further bio-assembled into ground meat analogues.

Modular assembly of bioprinted perfusable blood vessel and tracheal epithelium for studying inflammatory respiratory diseases.

In vitroorgan models allow for the creation of precise preclinical models that mimic organ physiology. During a pandemic of a life-threatening acute respiratory disease, an improved trachea model (TM) is required. We fabricated a modular assembly of the blood vessel and TMs using 3D bioprinting technology. First, decellularized extracellular matrix (dECM) were prepared using the porcine trachea and blood vessels. A trachea module was fabricated based on the tracheal mucosa-derived dECM and microporous membrane. Further, a blood vessel module was manufactured using the prepared vascular-tissue-derived dECM. By assembling each manufactured module, a perfusable vascularized TM simulating the interface between the tracheal epithelium and blood vessels was fabricated. This assembled model was manufactured with efficient performance, and it offered respiratory symptoms, such as inflammatory response and allergen-induced asthma exacerbation. These characteristics indicate the possibility of manufacturing a highly functional organ model that mimics a complex organ environment in the future.

Multifunctional PEG Carrier by Chemoenzymatic Synthesis for Drug Delivery Systems: In Memory of Professor Andrzej Dworak.

This paper describes the synthesis and characterization of new bivalent folate-targeted PEGylated doxorubicin (FA2-dPEG-DOX2) made by modular chemo-enzymatic processes using Candida antarctica lipase B (CALB) as a biocatalyst. Unique features are the use of monodisperse PEG (dPEG) and the synthesis of thiol-functionalized folic acid yielding exclusive γ-conjugation of folic acid (FA) to dPEG. The polymer-based drug conjugate is built up by a series of transesterification and Michael addition reactions all catalyzed be CALB. In comparison with other methods in the literature, the modular approach with enzyme catalysis leads to selectivity, full conversion and high yield, and no transition metal catalyst residues. The intermediate product with four acrylate groups is an excellent platform for Michael-addition-type reactions for a wide variety of biologically active molecules. The chemical structures were confirmed by nuclear magnetic resonance spectroscopy (NMR). Flow cytometry analysis showed that, at 10 µM concentration, both free DOX and FA2-dPEG-DOX2 were taken up by 99.9% of triple-negative breast cancer cells in 2 h. Fluorescence was detected for 5 days after injecting compound IV into mice. Preliminary results showed that intra-tumoral injection seemed to delay tumor growth more than intravenous delivery.

Bottom-Up Design: A Modular Golden Gate Assembly Platform of Yeast Plasmids for Simultaneous Secretion and Surface Display of Distinct FAP Fusion Proteins.

A need in synthetic biology is the ability to precisely and efficiently make flexible fully designed vectors that addresses challenging cloning strategies of single plasmids that rely on combinatorial co-expression of a multitude of target and bait fusion reporters useful in projects like library screens. For these strategies, the regulatory elements and functional components need to correspond perfectly to project specific sequence elements that facilitate easy exchange of these elements. This requires systematic implementation and building on recent improvements in Golden Gate (GG) that ensures high cloning efficiency for such complex vectors. Currently, this is not addressed in the variety of molecular GG cloning techniques in synthetic biology. Here, we present the bottom-up design and plasmid synthesis to prepare 10 kb functional yeast secrete and display plasmids that uses an optimized version of GG in combination with fluorogen-activating protein reporter technology. This allowed us to demonstrate nanobody/target protein interactions in a single cell, as detected by cell surface retention of secreted target proteins by cognate nanobodies. This validates the GG constructional approach and suggests a new approach for discovering protein interactions. Our GG assembly platform paves the way for vector-based library screening and can be used for other recombinant GG platforms.

Functionalizing Ferritin Nanoparticles for Vaccine Development.

In the last decade, the interest in ferritin-based vaccines has been increasing due to their safety and immunogenicity. Candidates against a wide range of pathogens are now on Phase I clinical trials namely for influenza, Epstein-Barr, and SARS-CoV-2 viruses. Manufacturing challenges related to particle heterogeneity, improper folding of fused antigens, and antigen interference with intersubunit interactions still need to be overcome. In addition, protocols need to be standardized so that the production bioprocess becomes reproducible, allowing ferritin-based therapeutics to become readily available. In this review, the building blocks that enable the formulation of ferritin-based vaccines at an experimental stage, including design, production, and purification are presented. Novel bioengineering strategies of functionalizing ferritin nanoparticles based on modular assembly, allowing the challenges associated with genetic fusion to be circumvented, are discussed. Distinct up/down-stream approaches to produce ferritin-based vaccines and their impact on production yield and vaccine efficacy are compared. Finally, ferritin nanoparticles currently used in vaccine development and clinical trials are summarized.

Engineering Biological Tissues from the Bottom-Up: Recent Advances and Future Prospects.

Tissue engineering provides a powerful solution for current organ shortages, and researchers have cultured blood vessels, heart tissues, and bone tissues in vitro. However, traditional top-down tissue engineering has suffered two challenges: vascularization and reconfigurability of functional units. With the continuous development of micro-nano technology and biomaterial technology, bottom-up tissue engineering as a promising approach for organ and tissue modular reconstruction has gradually developed. In this article, relevant advances in living blocks fabrication and assembly techniques for creation of higher-order bioarchitectures are described. After a critical overview of this technology, a discussion of practical challenges is provided, and future development prospects are proposed.