Catcher/Tag Toolbox: Biomolecular Click-Reactions For Protein Engineering Beyond Genetics

Manipulating protein architectures beyond genetic control has attracted widespread attention. Catcher/Tag systems enable highly specific conjugation of proteins in vivo and in vitro via an isopeptide-bond. They provide efficient, robust, and irreversible strategies for protein conjugation and are simple yet powerful tools for a variety of applications in enzyme industry, vaccines, biomaterials, and cellular applications. Here we summarize recent development of the Catcher/Tag toolbox with a particular emphasis on the design of Catcher/Tag pairs targeted for specific applications. We cover the current limitations of the Catcher/Tag systems and discuss the pH sensitivity of the reactions. Finally, we conclude some of the future directions in the development of this versatile protein conjugation method and envision that improved control over inducing the ligation reaction will further broaden the range of applications.

Biomimetic Structural Proteins: Modular Assembly and High Mechanical Performance

Protein-based biomaterials attract growing interests due to their encoded and programmable robust mechanical properties, superelasticity, plasticity, shape adaptability, excellent interfacial behavior, etc., derived from sequence-guided backbone structures, particularly compared to chemically synthetic counterparts in materials science and biomedical engineering. For example, protein materials have been successfully fabricated as (1) artificial implants (man-made tendons, cartilages, or dental tissues), due to programmable chemistry and biocompatibility; (2) smart biodevices with temperature/light-response and self-healing effects; and (3) impact resistance materials having great mechanical performance due to biomimetics. However, the existing method of regenerating protein materials from natural sources has two critical issues, low yield and structural damage, making it unable to meet demands. Therefore, it is crucial to develop an alternative strategy for fabricating protein materials. Heterologous expression of natural proteins with a modular assembly approach is an effective strategy for material preparation. Standardized, easy-to-assemble protein modules with specific structures and functions are developed through experimental and computational tools based on natural functional protein sequences. Through recombination and heterologous expression, these artificial protein modules become keys to material fabrication. Undergoing an assembly process similar to supramolecular self-assembly of proteins in cells, biomimetic modules can be fabricated for formation of macroscopic materials such as fibers and adhesives. This strategy inspired by synthetic biology and supramolecular chemistry is important for improving target protein yields and assembly integrity. It also preserves and optimizes the mechanical functions of structural proteins, accelerating the design and fabrication of artificial protein materials.In this Account, we overview recent studies on fabricating biomimetic protein materials to elucidate the concept of modular assembly. We discuss the design of biomimetic structural proteins at the molecular level, providing a wealth of details determining the bulk properties of materials. Additinally, we describe the modular self-assembly and assembly driven by inducing molecules, and mechanical properties and applications of resulting fibers. We used these strategies to develop fiber materials with high tensile strength, high toughness, and properties such as anti-icing and high-temperature resistance. We also extended this approach to design protein-based adhesives with ultra-strong adhesion, biocompatibility, and biodegradability for surgical applications such as wound sealing and healing. Other protein materials, including films and hydrogels, have been developed through chemical assembly routes. Finally, we describe exploiting synthetic biology and chemistry to overcome bottlenecks in structural protein modular design, biosynthesis, and material assembly and our perspectives for future development in structural biomaterials.

Recent developments and challenges in uranium extraction from seawater through amidoxime-functionalized adsorbents

As per statistical estimations, we have only around 100 years of uranium life in terrestrial ores. In contrast, seawater has viable uranium resources that can secure the future of energy. However, to achieve this, environmental challenges need to be overcome, such as low uranium concentration (3.3 ppb), fouling of adsorbents, uranium speciation, oceanic temperature, and competition between elements for the active site of adsorbent (such as vanadium which has a significant influence on uranium adsorption). Furthermore, the deployability of adsorbent under seawater conditions is a gigantic challenge; hence, leaching-resistant stable adsorbents with good reusability and high elution rates are extremely needed. Powdered (nanostructured) adsorbents available today have limitations in fulfilling these requirements. An increase in the grafting density of functional ligands keeping in view economic sustainability is also a major obstacle but a necessity for high uranium uptake. To cope with these challenges, researchers reported hundreds of adsorbents of different kinds, but amidoxime-based polymeric adsorbents have shown some remarkable advantages and are considered the benchmark in uranium extraction history; they have a high affinity for uranium because of electron donors in their structure, and their amphoteric nature is responsible for effective uranium chelation under a wide range of pH. In this review, we have mainly focused on recent developments in uranium extraction from seawater through amidoxime-based adsorbents, their comparative analysis, and problematic factors that are needed to be considered for future research.

Protein-Based Hydrogels and Their Biomedical Applications

Hydrogels made from proteins are attractive materials for diverse medical applications, as they are biocompatible, biodegradable, and amenable to chemical and biological modifications. Recent advances in protein engineering, synthetic biology, and material science have enabled the fine-tuning of protein sequences, hydrogel structures, and hydrogel mechanical properties, allowing for a broad range of biomedical applications using protein hydrogels. This article reviews recent progresses on protein hydrogels with special focus on those made of microbially produced proteins. We discuss different hydrogel formation strategies and their associated hydrogel properties. We also review various biomedical applications, categorized by the origin of protein sequences. Lastly, current challenges and future opportunities in engineering protein-based hydrogels are discussed. We hope this review will inspire new ideas in material innovation, leading to advanced protein hydrogels with desirable properties for a wide range of biomedical applications.

Uranium extraction from seawater: material design, emerging technologies and marine engineering

Uranium extraction from seawater (UES), a potential approach to securing the long-term uranium supply and sustainability of nuclear energy, has experienced significant progress in the past decade. Promising adsorbents with record-high capacities have been developed by diverse innovative synthetic strategies, and scale-up marine field tests have been put forward by several countries. However, significant challenges remain in terms of the adsorbents' properties in complex marine environments, deployment methods, and the economic viability of current UES systems. This review presents an up-to-date overview of the latest advancements in the UES field, highlighting new insights into the mechanistic basis of UES and the methodologies towards the function-oriented development of uranium adsorbents with high adsorption capacity, selectivity, biofouling resistance, and durability. A distinctive emphasis is placed on emerging electrochemical and photochemical strategies that have been employed to develop efficient UES systems. The most recent achievements in marine tests by the major countries are summarized. Challenges and perspectives related to the fundamental, technical, and engineering aspects of UES are discussed. This review is envisaged to inspire innovative ideas and bring technical solutions towards the development of technically and economically viable UES systems.

Genetically engineered materials: Proteins and beyond

Information-rich molecules provide opportunities for evolution. Genetically engineered materials are superior in that their properties are coded within genetic sequences and could be fine-tuned. In this review, we elaborate the concept of genetically engineered materials (GEMs) using examples ranging from engineered protein materials to engineered living materials. Protein-based materials are the materials of choice by nature. Recent progress in protein engineering has led to opportunities to tune their sequences for optimal material performance. Proteins also play a central role in living materials where they act in concert with other biological components as well as nonbiological cofactors, giving rise to living features. While the existing GEMs are often limited to those constructed by building blocks of biological origin, being genetically engineerable does not preclude nonbiologic or synthetic materials, the latter of which have yet to be fully explored.

Bioengineered Microbes for Soil Health Restoration - Present Status and Future

According to the United Nations Environment Programme (UNEP), soil health is declining over the decades and it has an adverse impact on human health and food security. Hence, soil health restoration is a need of the hour. It is known that microorganisms play a vital role in remediation of soil pollutants like heavy metals, pesticides, hydrocarbons, etc. However, the indigenous microbes have a limited capacity to degrade these pollutants and it will be a slow process. Genetically modified organisms (GMOs) can catalyze the degradation process as their altered metabolic pathways lead to hypersecretions of various biomolecules that favor the bioremediation process. This review provides an overview on the application of bioengineered microorganisms for the restoration of soil health by degradation of various pollutants. It also sheds light on the challenges of using GMOs in environmental application as their introduction may affect the normal microbial community in soil. Since soil health also refers to the potential of native organisms to survive, the possible changes in the native microbial community with the introduction of GMOs are also discussed. Finally, the future prospects of using bioengineered microorganisms in environmental engineering applications to make the soil fertile and healthy have been deciphered. With the alarming rates of soil health loss, the treatment of soil and soil health restoration need to be fastened to a greater pace and the combinatorial efforts unifying GMOs, plant growth-promoting rhizobacteria, and other soil amendments will provide an effective solution to soil heath restoration ten years ahead.

Power to the protein: enhancing and combining activities using the Spy toolbox

Proteins span an extraordinary range of shapes, sizes and functionalities. Therefore generic approaches are needed to overcome this diversity and stream-line protein analysis or application. Here we review SpyTag technology, now used in hundreds of publications or patents, and its potential for detecting and controlling protein behaviour. SpyTag forms a spontaneous and irreversible isopeptide bond upon binding its protein partner SpyCatcher, where both parts are genetically-encoded. New variants of this pair allow reaction at a rate approaching the diffusion limit, while reversible versions allow purification of SpyTagged proteins or tuned dynamic interaction inside cells. Anchoring of SpyTag-linked proteins has been established to diverse nanoparticles or surfaces, including gold, graphene and the air/water interface. SpyTag/SpyCatcher is mechanically stable, so is widely used for investigating protein folding and force sensitivity. A toolbox of scaffolds allows SpyTag-fusions to be assembled into defined multimers, from dimers to 180-mers, or unlimited 1D, 2D or 3D networks. Icosahedral multimers are being evaluated for vaccination against malaria, HIV and cancer. For enzymes, Spy technology has increased resilience, promoted substrate channelling, and assembled hydrogels for continuous flow biocatalysis. Combinatorial increase in functionality has been achieved through modular derivatisation of antibodies, light-emitting diodes or viral vectors. In living cells, SpyTag allowed imaging of protein trafficking, retargeting of CAR-T cell killing, investigation of heart contraction, and control of nucleosome position. The simple genetic encoding and rapid irreversible reaction provide diverse opportunities to enhance protein function. We describe limitations as well as future directions.

An Ion-Crosslinked Supramolecular Hydrogel for Ultrahigh and Fast Uranium Recovery from Seawater

Large-scale uranium extraction from seawater is a crucial but challenging part of nuclear power generation. In this study, a new ion-crosslinked supramolecular Zn²⁺ -poly(amidoxime) (PAO) hydrogel that can super-efficiently adsorb uranium from seawater is explored. By simply mixing two solutions of zinc chloride and PAO, a supramolecular Zn²⁺ -PAO hydrogel is achieved via the interaction between zinc cations and amidoxime anions. In contrast with existing amidoxime-functionalized hydrogel-based adsorbents having low PAO contents and fiber-based adsorbents with weak hydrophilicity, the PAOs can be directly crosslinked using a small quantity of superhydrophilic zinc ion. Thus, a supramolecular hydrogel is formed, having both a high content of well-dispersed PAOs and good hydrophilicity. Relative to reported adsorbents, this low-cost hydrogel membrane exhibits outstanding uranium adsorption performance, reaching 1188 mg g^-1 of M_U /M_{dry gel} in 32 ppm uranium-spiked water. More importantly, after immersion in natural seawater for only 4 weeks, the uranium extraction capacity of the Zn²⁺ -PAO hydrogel membrane reaches 9.23 mg g^-1 of M_U /M_{dry gel} . This work can provide a general strategy for designing a new type of supramolecular hydrogel, crosslinked by various bivalent/multivalent cation-crosslinkers and even many other superhydrophilic supramolecular crosslinkers, for the high-efficient and massive extraction of uranium from seawater.

Probing Metal Ion Discrimination in a Protein Designed to Bind Uranyl Cation With Femtomolar Affinity

The design of metal-binding sites in proteins that combine high affinity with high selectivity for the desired metal ion remains a challenging goal. Recently, a protein designed to display femtomolar affinity for UO22+, dubbed “Super Uranyl-binding Protein” (SUP), was described, with potential applications for removing UO22+ in water. Although it discriminated most metal ions present in seawater, the protein showed a surprisingly high affinity for Cu²⁺ ions. Here, we have investigated Cu²⁺ binding to SUP using a combination of electron paramagnetic resonance, fluorescence and circular dichroism spectroscopies. Our results provide evidence for two Cu²⁺ binding sites on SUP that are distinct from the UO22+ binding site, but one of which interferes with UO22+ binding. They further suggest that in solution the protein's secondary structure changes significantly in response to binding UO22+; in contrast, the crystal structures of the apo- and holo-protein are almost superimposable. These results provide insights for further improving the selectivity of SUP for UO22+, paving the way toward protein-based biomaterials for decontamination and/or recovery of uranium.

Cobalt-Cross-Linked, Redox-Responsive Spy Network Protein Hydrogels

Although assembly of recombinant proteins by SpyTag/SpyCatcher chemistry has proven to be a versatile approach for creating bioactive hydrogels, the resulting Spy networks often exhibit weak mechanics due to the poor efficiency of interchain cross-linking. Here we leverage metal/ligand (i.e., cobalt/His6-tag) coordination interactions to modulate the bulk mechanics of the protein networks. The drastic difference between the Co²⁺ and Co³⁺ complexes in thermodynamic and kinetic properties enabled us to regulate the materials' properties and to immobilize and release recombinant proteins in a redox-dependent manner. The resulting hydrogels are capable of not only supporting cell growth and proliferation, but also influencing specific cell signaling via immobilized growth factors such as leukemia inhibitory factor (LIF). The integrated use of stimuli-responsive metal coordination and SpyTag/SpyCatcher chemistry opens up a new dimension for designing bioactive protein materials.

Sunlight Polymerization of Poly(amidoxime) Hydrogel Membrane for Enhanced Uranium Extraction from Seawater

The uranium level in seawater is ≈1000 times as high as terrestrial ores and can provide potential near-infinite fuel for the nuclear energy industry. However, it is still a significant challenge to develop high-efficiency and low-cost adsorbents for massively extracting uranium from seawater. Herein, a simple and fast method through low-energy consumption sunlight polymerization to direct fabrication of a poly(amidoxime) (PAO) hydrogel membrane, which exhibits high uranium adsorption capacity, is reported. This PAO hydrogel owns semi-interpenetrating structure and a hydrophilic poly(acrylamide) 3D network of hydrogel which can disperse and fix PAOs well. As a result, the amidoxime groups of PAOs exhibit an outstanding uranium adsorption efficiency (718 ± 16.6 and 1279 ± 14.5 mg g-1 of m uranium/m PAO in 8 and 32 ppm uranium-spiked seawater, respectively) among reported hydrogel-based adsorbents. Most importantly, U-uptake capacity of this hydrogel can achieve 4.87 ± 0.38 mg g-1 of m uranium/m dry gel just after four weeks within natural seawater. Furthermore, this hydrogel can be massively produced through low-energy consumption and environmentally-friendly sunlight polymerization. This work will provide a high-efficiency and low-cost adsorbent for massive uranium extraction from seawater.

Controlling SpyTag/SpyCatcher Reactivity via Redox-Gated Conformational Restriction

Herein, we report that the reactivity of genetically encoded SpyTag/SpyCatcher chemistry can be manipulated via redox-gated conformational restriction, which facilitates the preparation of all-protein-based hydrogel with latent reactive sites for subsequent covalent functionalization.

A Genetically Encoded Protein Polymer for Uranyl Binding and Extraction Based on the SpyTag-SpyCatcher Chemistry

A defining goal of synthetic biology is to develop biomaterials with superior performance and versatility. Here we introduce a purely genetically encoded and self-assembling biopolymer based on the SpyTag-SpyCatcher chemistry. We show the application of this polymer for highly efficient uranyl binding and extraction from aqueous solutions, by embedding two functional modules-the superuranyl binding protein and the monomeric streptavidin-to the polymer via genetic fusion. We further provide a modeling strategy for predicting the polymer's physical properties, and experimentally demonstrate the autosecretion of component monomers from bacterial cells. The potential of multifunctionalization, in conjunction with the genetic design and production pipeline, underscores the advantage of the SpyTag-SpyCatcher biopolymers for applications beyond trace metal enrichment and environmental remediation.