Nature Inspired Multienzyme Immobilization: Strategies and Concepts

Coimmobilized Dual Enzymes in a Continuous Flow Reactor for the Efficient Synthesis of Optically Pure γ/δ-Lactones

Enzyme catalysis is a promising method for producing chiral chemicals with high stereoselectivity under mild conditions. However, the traditional batch reaction suffers from low enzyme stability, low cofactor recycling, and poor enzyme reusability. Here, we present a continuous-flow method using coimmobilized dual enzymes for the synthesis of chiral γ-/δ-lactones, which are widely used in fragrances and flavors. Typically, a carbonyl reductase mutant SmCRM5 from Serratia marcescens, was coimmobilized by covalent binding with BmGDH, a glucose dehydrogenase capable of recovering and recycling the cofactor NADPH. After immobilization, SmCRM5 and BmGDH exhibited a 8.9-/8.7-fold increase in catalytic efficiency (kcat/Km) and a 57-/15-fold increase in half-life at 30 °C, respectively. We demonstrated that coimmobilized dual enzymes used in a continuous flow reactor showed a higher reaction rate and a higher space-time yield (1586 g·L-1 d-1) than free enzymes and immobilized enzymes in a batch reaction for the production of (R)-δ-decalactone. This continuous flow reactor can run continuously for more than 650 h with 99% ee and 80% conversion, and the total volume exceeds 1500 reactor volumes. The robustness of this continuous-flow immobilized enzyme system provides a green and efficient method for the synthesis of high value-added chiral chemicals.

Development of a self-assembled dual-enzyme co-display platform on the surface of the natural "chitosan beads" of yeast spores

Under starvation conditions, Saccharomyces cerevisiae diploid cells initiate meiosis to produce dormant cells called spores. When the DIT1 gene involved in assembling the outermost layer dityrosine is disrupted, the natural "chitosan beads" of yeast spores will be formed. A novel cell surface display system based on "chitosan beads" of dit1Δ yeast spores was previously established. In this study, a self-assembled dual-enzyme co-display platform on the surface of "chitosan beads" of S. cerevisiae spores was developed through the SpyTag/SpyCatcher system. As an example, two polyethylene terephthalate (PET) hydrolases, FAST-PETase (FPETase) and MHETase were self-assembled on the surface of spores. Compared with the unassembled enzymes, the assembled enzymes exhibited higher activity toward bis-hydroxyethyl terephthalate (BHET), achieving the complete degrading of 2 mM BHET within 1 h. Furthermore, the assembly of PETase and MHETase on the surface of spores demonstrated better thermostability (more than 85 % of initial activity after incubation at 30-70 °C for 12 h) and pH tolerance (approximately 80 % of original activity after incubation at pH 5.0 to 9.0 for 12 h). This study provides a novel and practical platform for the co-display and assembly of enzymes, offering a long-term stable enzyme catalyst for multi-enzyme cascade reactions especially conducted in complex environments.

Advanced applications in enzyme-induced electrospun nanofibers

Electrospun nanofibers, renowned for their high specific surface area, robust mechanical properties, and versatile chemical functionalities, offer a promising platform for enzyme immobilization. Over the past decade, significant strides have been made in developing enzyme-induced electrospun nanofibers (EIEN). This review systematically summarizes the advanced applications of EIEN which are fabricated using both non-specific immobilization methods including interfacial adsorption (direct adsorption, cross-linking, and covalent binding) and encapsulation, and specific immobilization techniques (coordination and affinity immobilization). Future research should prioritize optimizing immobilization techniques to achieve a balance between enzyme activity, stability, and cost-effectiveness, thereby facilitating the industrialization of EIEN. We elucidate the rationale behind various immobilization methods and their applications, such as wastewater treatment, biosensors, and biomedicine. We aim to provide guidelines for developing suitable EIEN immobilization techniques tailored to specific future applications.

Reinforcing thermostability and pH robustness of exo-inulinase facilitated by ReverseTag/ReverseCatcher tagging system

Enhancing protein stability is pivotal in the field of protein engineering. Protein self-cyclization using peptide a tagging system has emerged as an effective strategy for augmenting the thermostability of target proteins. In this study, we utilized a novel peptide tagging system, ReverseTag/ReverseCatcher, which leverages intramolecular ester bond formation. Initially, we employed GFP as a model to validate the feasibility of cyclization mediated by ReverseTag/ReverseCatcher in improving the protein thermostability. Cyclized GFP (cGFP) retained 30 % of its relative fluorescence after a 30-min incubation at 100 °C, while both GFP and linear GFP (lGFP) completely lost their fluorescence within 5 min. Additionally, we applied this method to exo-inulinase (EXINU), resulting in a variant named cyclized EXINU (cEXINU). The T50 and t1/2 values of cEXINU exhibited significant enhancements of 10 °C and 10 min, respectively, compared to EXINU. Furthermore, post-cyclization, EXINU demonstrated a broad operational pH range from 5 to 10 with sustained catalytic activity, and cEXINU maintained a half-life of 960 min at pH 5 and 9. Molecular dynamics simulations were conducted to elucidate the mechanisms underlying the enhanced thermostability and pH robustness of EXINU following cyclization. This study highlights that cyclization substanitially enhances the stability of both highly stable protein GFP and low-stable protein EXINU, mediated by the ReverseTag/ReverseCatcher tagging system. The ReverseTag/ReverseCatcher tagging system proves to be a potent conjugation method, with potential applications in improving thermostability, pH robustness, and other areas of protein engineering.

Peptide-Driven Assembly of Magnetic Beads for Potentiometric Sensing of Bacterial Enzyme at a Subcellular Level

Bacterial enzymes with different subcellular localizations play a critical ecological role in biogeochemical processing. However, precisely quantifying enzymes localized at certain subcellular levels, such as extracellular enzymes, has not yet been fully realized due to the complexity and dynamism of the bacterial outer membrane. Here we present a magneto-controlled potentiometric sensing platform for the specific detection of extracellular enzymatic activity. Alkaline phosphatase (ALP), which is one of the crucial hydrolytic enzymes in the ocean, was selected as the target enzyme. Magnetic beads functionalized with an ALP-responsive self-assembled peptide (GGGGGFFFpYpYEEE, MBs-peptides) prevent negatively charged peptides from entering the bacterial outer membrane, thereby enabling direct potentiometric sensing of extracellular ALP both attached to the bacterial cell surface and released into the surrounding environment. The dephosphorylation-triggered assembly of peptide-coupled magnetic beads can be directly and sensitively measured by using a magneto-controlled sensor. In this study, extracellular ALP activity of Pseudomonas aeruginosa at concentrations ranging from 10 to 1.0 × 105 CFU mL-1 was specifically and sensitively monitored. Moreover, this magneto-controlled potentiometric method enabled a simple and accurate assay of ALP activity across different subcellular localizations.

Nature-Inspired Strategies for Sustainable Degradation of Synthetic Plastics

Synthetic plastics have become integral to our daily lives, yet their escalating production, limited biodegradability, and inadequate waste management contribute to environmental contamination. Biological plastic degradation is one promising strategy to address this pollution. The inherent chemical and physical properties of synthetic plastics, however, pose challenges for microbial enzymes, hindering the effective degradation and the development of a sustainable biological recycling process. This Perspective explores alternative, nature-inspired strategies designed to overcome some key limitations in currently available plastic-degrading enzymes. Nature's refined degradation pathways for natural polymers, such as cellulose, present a compelling framework for the development of efficient technologies for enzymatic plastic degradation. By drawing insights from nature, we propose a general strategy of employing substrate binding domains to improve targeting and multienzyme scaffolds to overcome enzymatic efficiency limitations. As one potential application, we outline a multienzyme pathway to upcycle polyethylene into alkenes. Employing nature-inspired strategies can present a path toward sustainable solution to the environmental impact of synthetic plastics.

Cascade enzymatic synthesis of a statin side chain precursor - the role of reaction engineering in process optimization

Statins are an important class of drugs used to lower blood cholesterol levels and are often used to combat cardiovascular disease. In view of the importance of safe and reliable supply and production of statins in modern medicine and the global need for sustainable processes, various biocatalytic strategies for their synthesis have been investigated. In this work, a novel biocatalytic route to a statin side chain precursor was investigated in a one-pot cascade reaction starting from the protected alcohol N-(3-hydroxypropyl)-2-phenylacetamide, which is oxidized to the corresponding aldehyde in the first reaction step, and then reacts with two equivalents of acetaldehyde to form the final product N-(2-((2S,4S,6S)-4,6-dihydroxytetrahydro-2H-pyran-2-yl)ethyl)-2-phenylacetamide (phenylacetamide-lactol). To study this complex reaction, an enzyme reaction engineering approach was used, i.e. the kinetics of all reactions occurring in the cascade (including side reactions) were determined. The obtained kinetic model together with the simulations gave an insight into the system and indicated the best reactor mode for the studied reaction, which was fed-batch with acetaldehyde feed to minimize its negative effect on the enzyme activity during the reaction. The mathematical model of the process was developed and used to simulate different scenarios and to find the reaction conditions (enzyme and coenzyme concentration, substrate feed concentration and flow rate) at which the highest yield of phenylacetamide-lactol (75%) can be obtained. In the end, our goal was to show that this novel cascade route is an interesting alternative for the synthesis of the statin side chain precursor and that is why we also calculated an initial estimate of the potential value addition.

Coupling protein scaffold and biosilicification: A sustainable and recyclable approach for d-mannitol production via one-step purification and immobilization of multienzymes

Enzymatic synthesis of biochemicals in vitro is vital in synthetic biology for its efficiency, minimal by-products, and easy product separation. However, challenges like enzyme preparation, stability, and reusability persist. Here, we introduced a protein scaffold and biosilicification coupled system, providing a singular process for the purification and immobilization of multiple enzymes. Using d-mannitol as a model, we initially constructed a self-assembling EE/KK protein scaffold for the co-immobilization of glucose dehydrogenase and mannitol dehydrogenase. Under an enzyme-to-scaffold ratio of 1:8, a d-mannitol yield of 0.692 mol/mol was achieved within 4 h, 2.16-fold higher than the free enzymes. The immobilized enzymes retained 70.9 % of the initial joint activity while the free ones diminished nearly to inactivity after 8 h. Furthermore, we incorporated the biosilicification peptide CotB into the EE/KK scaffold, inducing silica deposition, which enabled the one-step purification and immobilization process assisted by Spy/Snoop protein-peptide pairs. The coupled system demonstrated a comparable d-mannitol yield to that of EE/KK scaffold and 1.34-fold higher remaining activities after 36 h. Following 6 cycles of reaction, the immobilized system retained the capability to synthesize 56.4 % of the initial d-mannitol titer. The self-assembly co-immobilization platform offers an effective approach for enzymatic synthesis of d-mannitol and other biochemicals.

DNA-induced assembly of biocatalytic nanocompartments for sensitive and selective aptasensing of aflatoxin B1

Enzyme cascade with high specificity and catalytic efficiency has significant applications for developing efficient bioanalysis methods. In this work, a sensitive and selective aptasensor was constructed based on the DNA-induced assembly of biocatalytic nanocompartments. Different from the conventional co-immobilization in one pot, the cascade enzymes of glucose oxidase (GOX) and horseradish peroxidase (HRP) were separately encapsulated in ZIF-90 nanoparticles. After conjugating complementary DNA or aptermer on enzyme@ZIF-90, DNA hybridization drove enzyme@ZIF-90 connected into clusters or linked on other DNA modified biocatalytic nanocompartment (such as invertase loaded Fe3O4@SiO2). Owing to the shortened distance between enzymes, the catalytic efficiency of connected clusters was significantly enhanced. However, the specifically interaction between the substrate molecule and aptermer sequence would lead to the disassembly of DNA duplexes, resulting in the gradual "switching-off" of cascade reactions. With aflatoxin B1 (AFB1) as the model substrate, the compartmentalized three-enzyme nanoreactors showed good analytical performance in the linear range from 0.01 ng mL-1 to 50 ng mL-1 with a low detection limit (3.3 pg mL-1). In addition, the proposed aptasensor was applied to detect AFB1 in corn oil and wheat powder samples with total recoveries ranging from 94 % to 109 %. As a result, this DNA-induced strategy for enzyme cascade nanoreactors opens new avenues for stimuli-responsive applications in biosensing.

Comparative oil extraction from mutt (Myliobatis goodei) liver by enzymatic hydrolysis: free versus immobilized biocatalyst

BACKGROUND

The development and fine-tuning of biotechnological processes for fish oil extraction constitute a very important focus to contribute to the development of a food industry based on fish consumption. This work lies in a comparative analysis of the oil extraction yield of Myliobatis goodei livers using free and immobilized enzymes.

RESULTS

An immobilized biocatalyst was designed from the cell-free extract of a Bacillus sp. Mcn4. A complete factorial design was used to study the components of the bacterial culture medium and select the condition with the highest titers of extracellular enzymatic activities. Wheat bran had a significant effect on the culture medium composition for enzymatic production. The immobilized biocatalyst was designed by covalent binding of the proteins present in the cocktail retaining a percentage of different types of enzymatic activities (Mult.Enz@MgFe2 O4 ). Among the biocatalyst used, Alcalase® 2.4 L and Purazyme® AS 60 L (free commercial proteases) showed extraction yields of 87.39% and 84.25%, respectively, while Mult.Enz@MgFe2 O4 achieved a better one of 89.97%. The oils obtained did not show significant differences in their physical-chemical properties while regarding the fatty acid content, the oil extracted with Purazyme® AS 60 L showed a comparatively lower proportion of polyunsaturated fatty acids.

CONCLUSIONS

Our results suggest that the use of by-products of M. goodei is a valid alternative and encourages the use of immobilized multienzyme biocatalysts for the treatment of complex substrates in the fishing industry. © 2023 Society of Chemical Industry.

Enzymes Immobilized into Starch- and Gelatin-Based Hydrogels: Properties and Application in Inhibition Assay

The present work is a review of the research on using hydrogels based on natural biodegradable polymers, starch, and gelatin for enzyme immobilization. This review addresses the main properties of starch and gelatin that make them promising materials in biotechnology for producing enzyme preparations stable during use and storage and insensitive to chemical and physical impacts. The authors summarize their achievements in developing the preparations of enzymes immobilized in starch and gelatin gels and assess their activity, stability, and sensitivity for use as biorecognition elements of enzyme inhibition-based biosensors.

Recent Advances on Key Enzymes of Microbial Origin in the Lycopene Biosynthesis Pathway

Lycopene is a common carotenoid found mainly in ripe red fruits and vegetables that is widely used in the food industry due to its characteristic color and health benefits. Microbial synthesis of lycopene is gradually replacing the traditional methods of plant extraction and chemical synthesis as a more economical and productive manufacturing strategy. The biosynthesis of lycopene is a typical multienzyme cascade reaction, and it is important to understand the characteristics of each key enzyme involved and how they are regulated. In this paper, the catalytic characteristics of the key enzymes involved in the lycopene biosynthesis pathway and related studies are first discussed in detail. Then, the strategies applied to the key enzymes of lycopene synthesis, including fusion proteins, enzyme screening, combinatorial engineering, CRISPR/Cas9-based gene editing, DNA assembly, and scaffolding technologies are purposefully illustrated and compared in terms of both traditional and emerging multienzyme regulatory strategies. Finally, future developments and regulatory options for multienzyme synthesis of lycopene and similar secondary metabolites are also discussed.

Bactericidal and biocatalytic temperature responsive microgel based self-cleaning membranes for water purification

The present study focuses on creating an antimicrobial and biocatalytic smart gating membrane by synthesizing unique core-shell microgels. The core-shell microgels are synthesized by grafting short chains of poly(ethylenimine) (PEI) onto a poly((N-isopropyl acrylamide)-co-glycidyl methacrylate)) (P(NIPAm-co-GMA)) core. Subsequently, the produced microgels are utilized as a substrate for synthesizing and stabilizing silver nanoparticles (Ag NPs) through an in-situ approach. These Ag NPs immobilized microgels are then suction filtered over a polyethylene terephthalate (PET) track-etched support to create cross-linked composite microgel membranes (CMMs). After structural and permeation characterization of the prepared CMMs, the laccase enzyme is then covalently grafted to the surface of the membrane and tested for its effectiveness in degrading Reactive red-120 dye. The laccase immobilized biocatalytic CMMs show effective degradation of the Reactive red-120 by 71%, 48%, and 34% at pH 3, 4, and 5, respectively. Furthermore, the immobilized laccase enzyme showed better activity and stability in terms of thermal, pH, and storage compared to the free laccase, leading to increased reusability. The unique combination of Ag NPs and laccase on a thermoresponsive microgel support resulted in a responsive self-cleaning membrane with excellent antimicrobial and dye degradation capabilities for environmentally friendly separation technology.

Non-covalent binding tags for batch and flow biocatalysis

Enzyme immobilization offers considerable advantage for biocatalysis in batch and continuous flow reactions. However, many currently available immobilization methods require that the surface of the carrier is chemically modified to allow site specific interactions with their cognate enzymes, which requires specific processing steps and incurs associated costs. Two carriers (cellulose and silica) were investigated here, initially using fluorescent proteins as models to study binding, followed by assessment of industrially relevant enzyme performance (transaminases and an imine reductase/glucose oxidoreductase fusion). Two previously described binding tags, the 17 amino acid long silica-binding peptide from the Bacillus cereus CotB protein and the cellulose binding domain from the Clostridium thermocellum, were fused to a range of proteins without impairing their heterologous expression. When fused to a fluorescent protein both tags conferred high avidity specific binding with their respective carriers (low nanomolar K_d values). The CotB peptide (CotB1p) induced protein aggregation in the transaminase and imine reductase/glucose oxidoreductase fusions when incubated with the silica carrier. The Clostridium thermocellum cellulose binding domain (CBDclos) allowed immobilization of all the proteins tested, but immobilization led to loss of enzymatic activity in the transaminases (< 2-fold) and imine reductase/glucose oxidoreductase fusion (> 80%). A transaminase-CBDclos fusion was then successfully used to demonstrate the application of the binding tag in repetitive batch and a continuous-flow reactor.

Exploring the Feasibility of Cell-Free Synthesis as a Platform for Polyhydroxyalkanoate (PHA) Production: Opportunities and Challenges

The extensive utilization of traditional petroleum-based plastics has resulted in significant damage to the natural environment and ecological systems, highlighting the urgent need for sustainable alternatives. Polyhydroxyalkanoates (PHAs) have emerged as promising bioplastics that can compete with petroleum-based plastics. However, their production technology currently faces several challenges, primarily focused on high costs. Cell-free biotechnologies have shown significant potential for PHA production; however, despite recent progress, several challenges still need to be overcome. In this review, we focus on the status of cell-free PHA synthesis and compare it with microbial cell-based PHA synthesis in terms of advantages and drawbacks. Finally, we present prospects for the development of cell-free PHA synthesis.

Controlled Assembly of Fluorophores inside a Nanoliposome

Cellular compartmentalization plays an essential role in organizing the complex and multiple biochemical reactions in the cell. An artificial compartment would provide powerful strategies to develop new biochemical tools for material production and diagnosis, but it is still a great challenge to synthesize the compartments that encapsulate materials of interest while controlling their accurate locations, numbers, and stoichiometry. In this study, we evaluated chemical characteristics of a liposome-encapsulated compartment, which has great potential to locate various materials of interest with precise control of their locations and numbers in the compartment. A nanoliposome was constructed inside a ring-shaped DNA origami skeleton according to the method of Yang et al., and further equipped with a double-stranded DNA platform to assemble molecules of interest in the nanoliposome. Upon formation of the nanoliposome, a pH-sensitive fluorophore on the bridged platform showed little or no response to the pH change of the outer buffer, ensuring that the molecules assembled on the platform are effectively shielded from the outer environment. The ring-shaped DNA skeleton equipped with a double-stranded DNA platform allows spatial assembly of several functional molecules inside the nanoliposome to isolate them from the outer environment.

Convenient site-selective protein coupling from bacterial raw lysates to coenzyme A-modified tobacco mosaic virus (TMV) by Bacillus subtilis Sfp phosphopantetheinyl transferase

A facile enzyme-mediated strategy enables site-specific covalent one-step coupling of genetically tagged luciferase molecules to coenzyme A-modified tobacco mosaic virus (TMV-CoA) both in solution and on solid supports. Bacillus subtilis surfactin phosphopantetheinyl transferase Sfp produced in E. coli mediated the conjugation of firefly luciferase N-terminally extended by eleven amino acids forming a 'ybbR tag' as Sfp-selective substrate, which even worked in bacterial raw lysates. The enzymes displayed on the protein coat of the TMV nanocarriers exhibited high activity. As TMV has proven a beneficial high surface-area adapter template stabilizing enzymes in different biosensing layouts in recent years, the use of TMV-CoA for fishing ybbR-tagged proteins from complex mixtures might become an advantageous concept for the versatile equipment of miniaturized devices with biologically active proteins. It comes along with new opportunities for immobilizing multiple functionalities on TMV adapter coatings, as desired, e.g., in handheld systems for point-of-care detection.

Site-Specific and Tunable Co-immobilization of Proteins onto Magnetic Nanoparticles via Spy Chemistry

Co-immobilization of multiple proteins onto one nanosupport has large potential in mimicking natural multiprotein complexes and constructing efficient cascade biocatalytic systems. However, control of different proteins regarding their spatial arrangement and loading ratio remains a big challenge, and protein co-immobilization often requires the use of purified proteins. Herein, built upon our recently designed SpyTag-functionalized magnetic nanoparticles (MNPs), we established a modular MNP platform for site-specific, tunable, and cost-effective protein co-immobilization. SpyCatcher-fused enhanced green fluorescent protein (i.e., EGFP-SpyCatcher) and mCherry red fluorescent protein (i.e., RFP-SpyCatcher) were designed and conjugated on MNPs, and the immobilized proteins showed 3-7-fold enhancement in storage stability and greatly improved stability against the freeze-thaw process compared to free proteins. The protein-conjugated MNPs also retained desirable colloidal stability and magnetic responsiveness, enabling facile proteins' recovery. Also, one-pot co-immobilization of the two proteins could be fine-tuned with their feed ratios. In addition, MNPs could selectively and efficiently co-immobilize both SpyCatcher-fused proteins from combined cell lysates without purification, offering a convenient and cost-effective approach for multiprotein immobilization. This MNP platform provides a facile and efficient tool to construct bionano hybrid materials (i.e., protein-based MNPs) and multiprotein systems for a variety of industrial and green chemistry applications.

Co-Enzymes with Dissimilar Stabilities: A Discussion of the Likely Biocatalyst Performance Problems and Some Potential Solutions

Enzymes have several excellent catalytic features, and the last few years have seen a revolution in biocatalysis, which has grown from using one enzyme to using multiple enzymes in cascade reactions, where the product of one enzyme reaction is the substrate for the subsequent one. However, enzyme stability remains an issue despite the many benefits of using enzymes in a catalytic system. When enzymes are exposed to harsh process conditions, deactivation occurs, which changes the activity of the enzyme, leading to an increase in reaction time to achieve a given conversion. Immobilization is a well-known strategy to improve many enzyme properties, if the immobilization is properly designed and controlled. Enzyme co-immobilization is a further step in the complexity of preparing a biocatalyst, whereby two or more enzymes are immobilized on the same particle or support. One crucial problem when designing and using co-immobilized enzymes is the possibility of using enzymes with very different stabilities. This paper discusses different scenarios using two co-immobilized enzymes of the same or differing stability. The effect on operational performance is shown via simple simulations using Michaelis–Menten equations to describe kinetics integrated with a deactivation term. Finally, some strategies for overcoming some of these problems are discussed.

Engineering Self-Assembled Endolysin Nanoparticles against Antibiotic-Resistant Bacteria

Antibiotic resistance represents a serious global health concern and has stimulated the development of antimicrobial nanomaterials to combat resistant bacteria. Protein-based nanoparticles combining characteristics of both proteins and nanoparticles offer advantages including high biocompatibility, attractive biodegradability, enhanced bioavailability and functional versatility. They have played an increasing role as promising candidates for broad applications ranging from biocatalysts and drug delivery to vaccine development to cancer therapeutics. However, their application as antibacterial biomaterials to address challenging antibiotic-resistance problems has not been explicitly pursued. Herein, we describe engineering protein-only nanoparticles against resistant Gram-positive bacteria. A self-assembling peptide (P114) enables the assembly of a phage lytic enzyme (P128) into nanoparticles in response to pH reduction. Compared to native P128 and monomeric P114-P128, P128 nanoparticles (P128NANO) demonstrated a stronger bactericidal ability with high potency at lower concentrations (2-3-fold lower), particularly for methicillin-resistant Staphylococcus aureus strains. In addition, P128NANO showed an enhanced thermal (up to 65 °C) and storage stability and elicited extensive damages to bacterial cell walls. These remarkable antibacterial abilities are likely due to the P128NANO nanostructure, mediating multivalent interactions with bacterial cell walls at increased local concentrations of endolysin. The engineered endolysin nanoparticles offer a promising antimicrobial alternative to conventional antibiotics.

Mechanistic Aspects for the Modulation of Enzyme Reactions on the DNA Scaffold

Cells have developed intelligent systems to implement the complex and efficient enzyme cascade reactions via the strategies of organelles, bacterial microcompartments and enzyme complexes. The scaffolds such as the membrane or protein in the cell are believed to assist the co-localization of enzymes and enhance the enzymatic reactions. Inspired by nature, enzymes have been located on a wide variety of carriers, among which DNA scaffolds attract great interest for their programmability and addressability. Integrating these properties with the versatile DNA–protein conjugation methods enables the spatial arrangement of enzymes on the DNA scaffold with precise control over the interenzyme distance and enzyme stoichiometry. In this review, we survey the reactions of a single type of enzyme on the DNA scaffold and discuss the proposed mechanisms for the catalytic enhancement of DNA-scaffolded enzymes. We also review the current progress of enzyme cascade reactions on the DNA scaffold and discuss the factors enhancing the enzyme cascade reaction efficiency. This review highlights the mechanistic aspects for the modulation of enzymatic reactions on the DNA scaffold.

Self-Assembly of Functional Protein Nanosheets from Thermoresponsive Bolaamphiphiles

Nanosheets are two-dimensional materials, less than 100 nm thick, that can be used for separations, biosensing, and biocatalysis. Nanosheets can be made from inorganic and organic materials such as graphene, polymers, and proteins. Here, we report the self-assembly of nanosheets under aqueous conditions from functional proteins. The nanosheets are synthesized from two fusion proteins held together by high-affinity interactions of two leucine zippers to form bolaamphiphiles. The hydrophobic domain, Z_R-ELP-Z_R, contains the thermoresponsive elastin-like peptide (ELP) flanked by arginine-rich leucine zippers (Z_R), each of which binds the hydrophilic fusion protein, globule-Z_E, via the glutamate-rich leucine zipper (Z_E) fused to a functional, globular protein. Nanosheets form when the proteins are mixed at 4 °C in aqueous solutions and then heated to 25 °C as the container is rotated end-over-end causing expansion and contraction of the air-water interface. The nanosheets are robust with respect to the choice of globular protein and can incorporate small fluorescent proteins that are less than 30 kDa as well as large enzymes, such as 80 kDa malate synthase G. Upon incorporation into nanosheets, enzymes retain more than 70% of their original activity, demonstrating the potential of protein nanosheets to be used for biosensing or biocatalytic applications.

Is enzyme immobilization a mature discipline? Some critical considerations to capitalize on the benefits of immobilization

Enzyme immobilization has been developing since the 1960s and although many industrial biocatalytic processes use the technology to improve enzyme performance, still today we are far from full exploitation of the field. One clear reason is that many evaluate immobilization based on only a few experiments that are not always well-designed. In contrast to many other reviews on the subject, here we highlight the pitfalls of using incorrectly designed immobilization protocols and explain why in many cases sub-optimal results are obtained. We also describe solutions to overcome these challenges and come to the conclusion that recent developments in material science, bioprocess engineering and protein science continue to open new opportunities for the future. In this way, enzyme immobilization, far from being a mature discipline, remains as a subject of high interest and where intense research is still necessary to take full advantage of the possibilities.

Droplet Microfluidic Device for Chemoenzymatic Sensing

The rapid detection of pollutants in water can be performed with enzymatic probes, the catalytic light-emitting activity of which decreases in the presence of many types of pollutants. Herein, we present a microfluidic system for continuous chemoenzymatic biosensing that generates emulsion droplets containing two enzymes of the bacterial bioluminescent system (luciferase and NAD(P)H:FMN-oxidoreductase) with substrates required for the reaction. The developed chip generates "water-in-oil" emulsion droplets with a volume of 0.1 μL and a frequency of up to 12 drops per minute as well as provides the efficient mixing of reagents in droplets and their distancing. The bioluminescent signal from each individual droplet was measured by a photomultiplier tube with a signal-to-noise ratio of up to 3000/1. The intensity of the luminescence depended on the concentration of the copper sulfate with the limit of its detection of 5 μM. It was shown that bioluminescent enzymatic reactions could be carried out in droplet reactors in dispersed streams. The parameters and limitations required for the bioluminescent reaction to proceed were also studied. Hereby, chemoenzymatic sensing capabilities powered by a droplet microfluidics manipulation technique may serve as the basis for early-warning online water pollution systems.

Lipase immobilization via cross-linked enzyme aggregates: Problems and prospects - A review

In this review we have focused on the preparation of cross-linked enzyme aggregates (CLEAs) from lipases, as these are among the most used enzyme in bioprocesses. This immobilization method is considered very attractive due to preparation simplicity, non-use of supports and the possibility of using crude enzyme extracts. CLEAs provide lipase stabilization under extreme temperature or pH conditions or in the presence of organic solvents, in addition to preventing enzyme leaching in aqueous medium. However, it presents some problems in the preparation and limitations in their use. The problems in preparation refer mainly to the crosslinking step, and may be solved using an aminated feeder. The problems in handling have been tackled designing magnetic-CLEAs or trapping the CLEAs in particles with better mechanical properties, the substrate diffusion problems has been reduced by producing more porous-CLEAs, etc. The enzyme co-immobilization using combi-CLEAs is also a new tendency. Therefore, this review explores the CLEAs methodology aimed at lipase immobilization and its applications.

Chemical amination of immobilized enzymes for enzyme coimmobilization: Reuse of the most stable immobilized and modified enzyme

Although Lecitase and the lipase from Thermomyces lanuginosus (TLL) could be coimmobilized on octyl-agarose, the stability of Lecitase was lower than that of TLL causing the user to discard active immobilized TLL when Lecitase was inactivated. Here, we propose the chemical amination of immobilized TLL to ionically exchange Lecitase on immobilized TLL, which should be released to the medium after its inactivation by incubation at high ionic strength. Using conditions where Lecitase was only adsorbed on immobilized TLL after its amination, the combibiocatalyst was produced. Unfortunately, the release of Lecitase was not possible using just high ionic strength solutions, and if detergent was added, TLL was also released from the support. This occurred when using 0.25 M ammonium sulfate, Lecitase did not immobilize on aminated TLL. That makes the use octyl-vinylsulfone supports necessary to irreversibly immobilize TLL, and after blocking with ethylendiamine, the immobilized TLL was aminated. Lecitase immobilized and released from this biocatalyst using 0.25 M ammonium sulfate and 0.1% Triton X-100. That way, a coimmobilized TLL and Lecitase biocatalyst could be produced, and after Lecitase inactivation, it could be released and the immobilized, aminated, and fully active TLL could be utilized to build a new combibiocatalyst.

Efficient production of inulo-oligosaccharides from inulin by exo- and endo-inulinase co-immobilized onto a self-assembling protein scaffold

Inulin can be hydrolyzed by inulinases to yield inulo-oligosaccharides (IOSs), which have great application potential in the food and nutraceutical industries. However, conventional enzymatic production of IOSs is limited by long hydrolysis times and poor thermo-stability of inulinases. Here, the self-assembling protein scaffold EutM was engineered to co-immobilize exo-inulinase (EXINU) and endo-inulinase (ENINU) for synergistic hydrolysis of inulin to produce IOSs with 3 to 5 monosaccharide units (DP3-5 IOSs). The immobilization of EXINU/ENINU onto the EutM scaffold resulted in an increase of catalytic efficiency, a 65% increase of the V_max of ENINU, as well as an increase of thermo-stability, with 4.26-fold higher residual activity of EXINU after 22 h-incubation at 50 °C. After optimization, two efficient production protocols were obtained, in which the yield and productivity of DP3-5 IOSs reached 80.38% and 70.86 g·(L·h)^-1, respectively, which were at a high level in similar studies. Overall, this study provides an attractive self-assembling protein platform for the co-immobilization of inulinases, as well as optimized bioprocesses with great promise for the industrial production of DP3-5 IOSs.

Protein Mediated Enzyme Immobilization

Enzyme immobilization is an essential technology for commercializing biocatalysis. It imparts stability, recoverability, and other valuable features that improve the effectiveness of biocatalysts. While many avenues to join an enzyme to solid phases exist, protein-mediated immobilization is rapidly developing and has many advantages. Protein-mediated immobilization allows for the binding interaction to be genetically coded, can be used to create artificial multienzyme cascades, and enables modular designs that expand the variety of enzymes immobilized. By designing around binding interactions between protein domains, they can be integrated into functional materials for protein immobilization. These materials are framed within the context of biocatalytic performance, immobilization efficiency, and stability of the materials. In this review, supports composed entirely of protein are discussed first, with systems such as cellulosomes and protein cages being discussed alongside newer technologies like spore-based biocatalysts and forizymes. Protein-composite materials such as polymersomes and protein-inorganic supraparticles are then discussed to demonstrate how protein-mediated strategies are applied to many classes of solid materials. Critical analysis and future directions of protein-based immobilization are then discussed, with a particular focus on both computational and design strategies to advance this area of research and make it more broadly applicable to many classes of enzymes.

Combining a Genetically Engineered Oxidase with Hydrogen-Bonded Organic Frameworks (HOFs) for Highly Efficient Biocomposites

Enzymes incorporated into hydrogen-bonded organic frameworks (HOFs) via bottom-up synthesis are promising biocomposites for applications in catalysis and sensing. Here, we explored synthetic incorporation of d-amino acid oxidase (DAAO) with the metal-free tetraamidine/tetracarboxylate-based BioHOF-1 in water. N-terminal enzyme fusion with the positively charged module Zbasic2 strongly boosted the loading (2.5-fold; ≈500 mg enzyme gmaterial-1 ) and the specific activity (6.5-fold; 23 U mg-1 ). The DAAO@BioHOF-1 composites showed superior activity with respect to every reported carrier for the same enzyme and excellent stability during catalyst recycling. Further, extension to other enzymes, including cytochrome P450 BM3 (used in the production of high-value oxyfunctionalized compounds), points to the versatility of genetic engineering as a strategy for the preparation of biohybrid systems with unprecedented properties.

Functional enzyme-polymer complexes

SignificanceThe use of biological enzyme catalysts could have huge ramifications for chemical industries. However, these enzymes are often inactive in nonbiological conditions, such as high temperatures, present in industrial settings. Here, we show that the enzyme PETase (polyethylene terephthalate [PET]), with potential application in plastic recycling, is stabilized at elevated temperature through complexation with random copolymers. We demonstrate this through simulations and experiments on different types of substrates. Our simulations also provide strategies for designing more enzymatically active complexes by altering polymer composition and enzyme charge distribution.

Reversible Regulating the Substrate Specificity of Enzymes in Microgels by a Phase Transition in Polymer Networks

Here, we report a distinct approach for regulating the substrate specificity of enzymes immobilized in microgels by a phase transition in polymer networks. The finding is demonstrated on glucose oxidase that is immobilized in thermoresponsive poly(N-isopropylacrylamide)-based microgels. Laser light scattering and enzymatic oxidation tests indicate that the broadened specificity appears at low temperatures, at which the gel matrix is in the relatively swollen state relative to its state at microgel synthesis temperature; upon heating to the relative higher temperatures, the gel matrix is not able to shrink further that offers a tight space in which the enzyme resides to retain high glucose specificity. It is proposed that polymer phase transition in the gel matrix mainly alter protein gates that control passage of substrates into active sites, making them open or close to a certain extent that enable reversible regulating the substrate specificity. The finding is also observed on bulk gels under a rational design, making it of potential interest in enzymatic biofuel cell applications.

Biocatalytic self-assembled synthetic vesicles and coacervates: From single compartment to artificial cells

Compartmentalization is an intrinsic feature of living cells that allows spatiotemporal control over the biochemical pathways expressed in them. Over the years, a library of compartmentalized systems has been generated, which includes nano to micrometer sized biomimetic vesicles derived from lipids, amphiphilic block copolymers, peptides, and nanoparticles. Biocatalytic vesicles have been developed using a simple bag containing enzyme design of liposomes to multienzymes immobilized multi-vesicular compartments for artificial cell generation. Additionally, enzymes were also entrapped in membrane-less coacervate droplets to mimic the cytoplasmic macromolecular crowding mechanisms. Here, we have discussed different types of single and multicompartment systems, emphasizing their recent developments as biocatalytic self-assembled structures using recent examples. Importantly, we have summarized the strategies in the development of the self-assembled structure to improvise their adaptivity and flexibility for enzyme immobilization. Finally, we have presented the use of biocatalytic assemblies in mimicking different aspects of living cells, which further carves the path for the engineering of a minimal cell.

Catalyst Replacement Policy on Multienzymatic Systems: Theoretical Study in the One-Pot Sequential Batch Production of Lactofructose Syrup

One-pot systems are an interesting proposal to carry out multi-enzymatic reactions, though this strategy implies establishing an optimal balance between the activity and operability of the involved enzymes. This is crucial for enzymes with marked differences in their operational stability, such as one-pot production of lactofructose syrup from cheese whey permeate, which involves two enzymes—β-galactosidase (β-gal) and glucose isomerase (GI). The aim of this work was to study the behavior of one-pot sequential batch production of lactofructose syrup considering both enzymes immobilized individually, in order to evaluate and design a strategy of replacement of the catalysts according to their stabilities. To this end, the modelling and simulation of the process was carried out, considering simultaneously the kinetics of both reactions and the kinetics of inactivation of both enzymes. For the latter, it was also considered the modulating effect that sugars present in the medium may have on the stability of β-gal, which is the less stable enzyme. At the simulated reaction conditions of 40 °C, pH 7, and 0.46 (IUGI/IUβ-gal), the results showed that considering the stability of β-gal under non-reactive conditions, meaning in absence of the effect of modulation, it is necessary to carry out four replacements of β-gal for each cycle of use of GI. On the other hand, when considering the modulation caused by the sugars on the β-gal stability, the productivity increases up to 23% in the case of the highest modulation factor studied (η = 0.8). This work shows the feasibility of conducting a one-pot operation with immobilized enzymes of quite different operational stability, and that a proper strategy of biocatalyst replacement increases the productivity of the process.

Metabolic channeling: predictions, deductions, and evidence

With the elucidation of myriad anabolic and catabolic enzyme-catalyzed cellular pathways crisscrossing each other, an obvious question arose: how could these networks operate with maximal catalytic efficiency and minimal interference? A logical answer was the postulate of metabolic channeling, which in its simplest embodiment assumes that the product generated by one enzyme passes directly to a second without diffusion into the surrounding medium. This tight coupling of activities might increase a pathway's metabolic flux and/or serve to sequester unstable/toxic/reactive intermediates as well as prevent their access to other networks. Here, we present evidence for this concept, commencing with enzymes that feature a physical molecular tunnel, to multi-enzyme complexes that retain pathway substrates through electrostatics or enclosures, and finally to metabolons that feature collections of enzymes assembled into clusters with variable stoichiometric composition. Lastly, we discuss the advantages of reversibly assembled metabolons in the context of the purinosome, the purine biosynthesis metabolon.

Solid-Phase Assembly of Multienzyme Systems into Artificial Cellulosomes

We herein describe a bioinspired solid-phase assembly of a multienzyme system scaffolded on an artificial cellulosome. An alcohol dehydrogenase and an ω-transaminase were fused to cohesin and dockerin domains to drive their sequential and ordered coimmobilization on agarose porous microbeads. The resulting immobilized scaffolded enzymatic cellulosome was characterized through quartz crystal microbalance with dissipation and confocal laser scanning microscopy to demonstrate that both enzymes interact with each other and physically colocalize within the microbeads. Finally, the assembled multifunctional heterogeneous biocatalyst was tested for the one-pot conversion of alcohols into amines. By using the physically colocalized enzymatic system confined into porous microbeads, the yield of the corresponding amine was 1.3 and 10 times higher than the spatially segregated immobilized system and the free enzymes, respectively. This work establishes the basis of a new concept to organize multienzyme systems at the nanoscale within solid and porous immobilization carriers.

Substrate Channeling by a Rationally Designed Fusion Protein in a Biocatalytic Cascade

Substrate channeling, where an intermediate in a multistep reaction is directed toward a reaction center rather than freely diffusing, offers several advantages when employed in catalytic cascades. Here we present a fusion enzyme comprised of an alcohol and aldehyde dehydrogenase, that is computationally designed to facilitate electrostatic substrate channeling using a cationic linker bridging the two structures. Rosetta protein folding software was utilized to determine an optimal linker placement, added to the truncated termini of the proteins, which is as close as possible to the active sites of the enzymes without disrupting critical catalytic residues. With improvements in stability, product selectivity (90%), and catalyst turnover frequency, representing 500-fold increased activity compared to the unbound enzymes and nearly 140-fold for a neutral-linked fusion enzyme, this design strategy holds promise for making other multistep catalytic processes more sustainable and efficient.

Efficient Entrapment of Carbonic Anhydrase in Alginate Hydrogels Using Liposomes for Continuous-Flow Catalytic Reactions

A versatile approach to entrap relatively small enzymes in hydrogels allows their diverse biotechnological applications. In the present work, bovine carbonic anhydrase (BCA) was efficiently entrapped in calcium alginate beads with the help of liposomes. A mixture of sodium alginate (3 wt %) and carbonic anhydrase-liposome conjugates (BCALs) was dripped into a Tris-HCl buffer solution (pH = 7.5) containing 0.4 M CaCl2 to induce the gelation and curing of the dispersed alginate-rich droplets. The entrapment efficiency of BCALs, which was defined as the amount of catalysts entrapped in alginate beads relative to that initially charged, was 98.7 ± 0.2% as determined through quantifying BCALs in the filtrate being separated from the beads. When free BCA was employed, on the other hand, a significantly lower entrapment efficiency of 27.2 ± 4.1% was obtained because free BCA could pass through alginate matrices. Because the volume of a cured alginate bead (10 μL) entrapped with BCALs was about 2.5 times smaller than that of an original droplet, BCALs were densely present in the beads to give the concentrations of lipids and BCA of 4.6-8.3 mM and 1.1-1.8 mg/mL, respectively. Alginate beads entrapped with BCALs were used to catalyze the hydrolysis of 1.0 mM p-nitrophenyl acetate (p-NA) at pH = 7.5 using the wells of a microplate or 10 mL glass beakers as batch reactors. Furthermore, the beads were confined in a column for continuous-flow hydrolysis of 1.0 mM p-NA for 1 h at a mean residence time of 8.5 or 4.3 min. The results obtained demonstrate that the conjugation of BCA to liposomes gave an opportunity to achieve efficient and stable entrapment of BCA in alginate hydrogels for applying to catalytic reactions in bioreactors.