Enzyme Catalyst Engineering toward the Integration of Biocatalysis and Chemocatalysis

Rational design of GH11 xylanase to balance the activity-stability trade-off

Enhancements of enzyme stability often compromise activity; thus, achieving an optimal balance between stability and activity poses a significant challenge in enzyme engineering. Our study investigated the stability-activity trade-off using the GH11 xylanase XynII as a model. A rational design strategy integrating crystal structure analysis and molecular dynamics simulations was used to distinguish regions important for structural stability and catalytic activity. Structural stability and activity were significantly enhanced by the introduction of two disulfide bonds involving four residues (T2C/T28C/R81C/T168C), which conferred a 75 % increase in activity, a 12.1 °C increase in Tm, and an 80-fold improvement in half-life compared to the wild-type enzyme. The incorporation of two additional mutations (Q125A/I129S) was shown to increase the catalytic activity by 30 % by enhancing the dynamics of the active site. Our results illustrate a successful strategy for simultaneously increasing activity and stability by optimizing the dynamics of the catalytic region and the rigidity of the noncatalytic region.

An Enhanced Ratiometric Fluorescence Immunosensor for Rapid Detection of AFB1 Based on the Dual-Enzyme Synergistic Co-Catalytic Effect of Natural Enzymes and Nanozymes

Aflatoxin B1 (AFB1) is considered a critical analyte in food safety testing due to its widespread contamination and high toxicity. In this study, a ratiometric fluorescent immunosensor with synergistic catalysis by natural enzymes and nanozymes (N-N-RF-immunosensor) was constructed for the rapid detection of AFB1. Copper oxide and zeolitic imidazolate framework composite nanomaterials (CuO/ZIF-8 NCM) with peroxidase and oxidase activities were prepared. A ratiometric fluorescence signal was generated through the synergistic cocatalytic effect of the CuO/ZIF-8 NCM and alkaline phosphatase, in response to the competition interaction between the anti-idiotypic nanobody-alkaline phosphatase fusion protein (Nb2-5-AP) and AFB1. The assay could detect aflatoxins within 140 min, exhibiting a half maximal inhibitory concentration (IC50) of 0.032 ng/mL, a limit of detection (LOD) of 2.4 pg/mL, and a linear range of 0.0024-1.043 ng/mL. Compared with the traditional enzyme-linked immunosorbent assay (ELISA), the sensitivity was enhanced 25-fold, while the detection parameter was shortened by 1/3. Furthermore, the immunosensor was successfully applied in the actual samples, with recoveries ranging from 81 to 127%. The N-N-RF-immunosensor shows great potential for rapid and sensitive detection of aflatoxins.

Mining Highly Active Oleate Hydratases by Structure Clustering, Sequence Clustering, and Ancestral Sequence Reconstruction

Oleate hydratases (Ohys) catalyze the conversion of oleic acid (OA) to 10-(R)-hydroxystearic acid (10-HSA), a compound widely used in the chemical industry. However, the limited activity of Ohys has hindered their broader applications. To address this limitation, we propose a novel strategy for mining highly active Ohys through structure clustering, sequence clustering, and ancestral sequence reconstruction (SSA strategy). Structure clustering via AI-driven protein structure prediction followed by classification enhanced the ability to mine target Ohys. Ancestral enzyme reconstruction was carried out based on mining results from both structure and sequence clustering. This strategy significantly reduces the time and cost of the discovery process. Among the 1304 Ohys screened via SSA, 13 candidates were selected. Seven candidates demonstrated high activity. Ohy 64, identified through structure clustering, exhibited the highest activity. Ancestral enzymes that were reconstructed from structure clustering targets were 3 times more likely to exhibit high catalytic activity than those identified through sequence clustering. Four critical, hydrophobic residues were identified through structure and sequence comparisons between StOhy and targets mined by SSA. Site-directed mutagenesis revealed that these hydrophobic residues conferred varying levels of enzyme activity, confirming that increased hydrophobicity at these positions enhances cofactor FAD binding, thus improving enzyme catalytic efficiency.

Valorization of tomato processing by-products: Predictive modeling and optimization for ultrasound-assisted lycopene extraction

Lycopene is a carotenoid highly valuable to the food, pharmaceutical, dye, and cosmetic industries, present in ripe tomatoes and other fruits with a distinctive red color. The main source of lycopene is tomato crops. This bioactive component can be successfully isolated from tomato processing waste, commonly called tomato pomace, mostly made from tomato skins, seeds, and some residual tomato tissue. The main investigative focus in this work was the application of green engineering principles in each stage of the optimized ultrasound-assisted extraction (UAE) of enzymatically treated tomato skins to obtain functional extracts rich in lycopene. The experimental plan was designed to determine the influence of studied operating parameters: enzymatic reaction time (60, 120, and 180 min), extraction time (0, 5, 10, 15, 30, 60, and 120 min), and temperature (25, 35 and 45 ℃) on lycopene yield. Process optimization was performed based on the yield of lycopene [1018, 1067, and 1120 mg/kg] achieved at optimal operating conditions. An artificial neural network (ANN) model was developed and trained for predictive modeling of the closed extraction system, with operating parameters used as input neurons and experimentally obtained values for lycopene content defined as the output neural layer. Applied ANN architecture provided a high correlation of experimental output with ANN-generated data (R=0.99914) with a model deviation error for the entire data set of RMSE=5.3 mg/kg. The k-Nearest Neighbor algorithm was introduced to predict lycopene yield using experimental key features: operating temperature, extraction time, and time of enzymatic treatment, split into training and testing sets with an 85/15 ratio. The model interpretation was conducted through the SHAP (SHapley Additive exPlanations) methodology.

Biocatalytic approach for the synthesis of chiral alcohols for the development of pharmaceutical intermediates and other industrial applications: A review

Biocatalysis has emerged as a strong tool for the synthesis of active pharmaceutical ingredients (APIs). In the early twentieth century, whole cell biocatalysis was used to develop the first industrial biocatalytic processes, and the precise work of enzymes was unknown. Biocatalysis has evolved over the years into an essential tool for modern, cost-effective, and sustainable pharmaceutical manufacturing. Meanwhile, advances in directed evolution enable the rapid production of process-stable enzymes with broad substrate scope and high selectivity. Large-scale synthetic pathways incorporating biocatalytic critical steps towards >130 APIs of authorized pharmaceuticals and drug prospects are compared in terms of steps, reaction conditions, and scale with the corresponding chemical procedures. This review is designed on the functional group developed during the reaction forming alcohol functional groups. Some important biocatalyst sources, techniques, and challenges are described. A few APIs and their utilization in pharmaceutical drugs are explained here in this review. Biocatalysis has provided shorter, more efficient, and more sustainable alternative pathways toward existing small molecule APIs. Furthermore, non-pharmaceutical applications of biocatalysts are also mentioned and discussed. Finally, this review includes the future outlook and challenges of biocatalysis. In conclusion, Further research and development of promising enzymes are required before they can be used in industry.

Boosting Fructosyl Transferase's Thermostability and Catalytic Performance for Highly Efficient Fructooligosaccharides (FOS) Production

Achieving enzymatic food processing at high substrate concentrations can significantly enhance production efficiency; however, related studies are notably insufficient. This study focused on the enzymatic synthesis of fructooligosaccharides (FOS) at high temperature and high substrate concentration. Results revealed that increased viscosity and limited substrate solubility in high-concentration systems could be alleviated by raising the reaction temperature, provided it aligned with the enzyme's thermostability. Further analysis of enzyme thermostability in real sucrose solutions demonstrates that the enzyme's thermostability was remarkedly improved at higher sucrose concentrations, evidenced by a 10.3 °C increase in melting temperature (Tm) in an 800 g/L sucrose solution. Building upon these findings, we developed a novel method for enzymatic FOS synthesis at elevated temperatures and high sucrose concentrations. Compared to existing commercial methods, the initial transglycosylation rate and volumetric productivity for FOS synthesis increased by 155.9% and 113.5%, respectively, at 65 °C in an 800 g/L sucrose solution. This study underscores the pivotal role of substrate concentration, incubation temperature, and the enzyme's actual status in advancing enzyme-catalyzed processes and demonstrates the potential of enzymatic applications in enhancing food processing technologies, providing innovative strategies for the food industry.

Surface Au-H Species as Self-Generated Prosthetic Groups of a Formate Dehydrogenase-like Au Nanozyme to Engineer Multienzymatic Activities

Although the past decade has witnessed a rapid development of oxidoreductase-mimicking nanozymes, the mimicry of cofactors that play key roles in mediating electron and proton transfer remains limited. This study explores how surface Au-H species conjugated to Au nanoparticles (NPs) that imitate formate dehydrogenase (FDH) can serve as cofactors, analogous to NADH in natural enzymes, offering diverse possibilities for FDH-mimicking Au nanozymes to mimic various enzymes. Once O2 is present, Au-H species assist Au NPs to complete the on-demand H2O2 generation for cascade reactions. Alternatively, when oxidizing organic molecules are introduced as substrates, Au-H species confer nitro reductase- and aldehyde reductase-like activities on Au NPs under anaerobic conditions. Furthermore, similar to the dehydrogenase-NADH complex, Au NPs possessing Au-H species are gifted with esterase-like activity for ester hydrolysis. By revealing that Au-H species are prosthetic groups for FDH-mimicking Au nanozymes, this work may inspire explorations into future self-generated cofactor mimics for nanozymes, thereby circumventing the need for exogenous cofactors.

Valorization of food waste: A comprehensive review of individual technologies for producing bio-based products

BACKGROUND

The escalating global concerns about food waste and the imperative need for sustainable practices have fuelled a burgeoning interest in the valorization of food waste. This comprehensive review delves into various technologies employed for converting food waste into valuable bio-based products. The article surveys individual technologies, ranging from traditional to cutting-edge methods, highlighting their respective mechanisms, advantages, and challenges.

SCOPE AND APPROACH

The exploration encompasses enzymatic processes, microbial fermentation, anaerobic digestion, and emerging technologies such as pyrolysis and hydrothermal processing. Each technology's efficacy in transforming food waste into bio-based products such as biofuels, enzymes, organic acids, prebiotics, and biopolymers is critically assessed. The review also considers the environmental and economic implications of these technologies, shedding light on their sustainability and scalability. The article discusses the role of technological integration and synergies in creating holistic approaches for maximizing the valorization potential of food waste. Key finding and conclusion: This review consolidates current knowledge on the valorization of food waste, offering a comprehensive understanding of individual technologies and their contributions to the sustainable production of bio-based products. The synthesis of information presented here aims to guide researchers, policymakers, and industry stakeholders in making informed decisions to address the global challenge of food waste while fostering a circular and eco-friendly economy.

Discovery and mechanism explanation of a novel green biocatalyst esterase Bur01 from Burkholderia ambifaria for ester synthesis under aqueous phase

Biocatalyst catalyzing the synthesis of esters under aqueous phase is an alternative with green and sustainable characteristics. Here, a biocatalyst esterase Bur01 was identified through genome sequencing and gene library construction from a Burkholderia ambifaria BJQ0010 with efficient ester synthesis property under aqueous phase for the first time. Bur01 was soluble expressed and the purified enzyme showed the highest activity at pH 4.0 and 40 °C. It had a broad substrate spectrum, especially for ethyl esters. The structure of Bur01 was categorized as a member of α/β fold hydrolase superfamily. The easier opening of lid under aqueous phase and the hydrophobicity of substrate channel contribute to easier access to the active center for substrate. Molecular docking and site-directed mutation demonstrated that the oxyanion hole Ala22, Met112 and π-bond stacking between His24 and Phe217 played essential roles in catalytic function. The mutants V149A, V149I, L159I and F137I enhanced enzyme activity to 1.42, 1.14, 1.32 and 2.19 folds due to reduced spatial resistance and increased hydrophobicity of channel and ethyl octanoate with the highest conversion ratio of 68.28 % was obtained for F137I. These results provided new ideas for developing green catalysts and catalytic basis of mechanistic studies for ester synthetase under aqueous phase.

Collapse of carbon nanotubes due to local high-pressure from van der Waals encapsulation

Van der Waals (vdW) assembly of low-dimensional materials has proven the capability of creating structures with on-demand properties. It is predicted that the vdW encapsulation can induce a local high-pressure of a few GPa, which will strongly modify the structure and property of trapped materials. Here, we report on the structural collapse of carbon nanotubes (CNTs) induced by the vdW encapsulation. By simply covering CNTs with a hexagonal boron nitride flake, most of the CNTs (≈77%) convert from a tubular structure to a collapsed flat structure. Regardless of their original diameters, all the collapsed CNTs exhibit a uniform height of ≈0.7 nm, which is roughly the thickness of bilayer graphene. Such structural collapse is further confirmed by Raman spectroscopy, which shows a prominent broadening and blue shift in the Raman G-peak. The vdW encapsulation-induced collapse of CNTs is fully captured by molecular dynamics simulations of the local vdW pressure. Further near-field optical characterization reveals a metal-semiconductor transition in accompany with the CNT structural collapse. Our study provides not only a convenient approach to generate local high-pressure for fundamental research, but also a collapsed-CNT semiconductor for nanoelectronic applications.

Nitrile-synthesizing enzymes and biocatalytic synthesis of volatile nitrile compounds: A review

Nitriles (R-CN) comprise a broad group of chemicals industrially produced and used in fine chemicals, pharmaceuticals, and bulk applications, polymer chemistry, solvents, etc. Nitriles are important starting materials for producing carboxylic acids, amides, amines, and several other compounds. In addition, some volatile nitriles have been evaluated for their potential as ingredients in fragrance and flavor formulations. However, many nitrile synthesis methods have drawbacks, such as drastic reaction conditions, limited substrate scope, lack of readily available reagents, poor yields, and long reaction times. In contrast to chemical synthesis, biocatalytic approaches using enzymes can produce nitriles without harsh conditions, such as high temperatures and pressures, or toxic compounds. In this review, we summarize the nitrile-synthesizing enzymes from microorganisms, plants, and animals. Furthermore, we introduce several examples of biocatalytic synthesis of volatile nitrile compounds, particularly those using aldoxime dehydratase.

Recent Progress and Future Prospects of Laccase Immobilization on MOF Supports for Industrial Applications

Laccase is a multicopper oxidoreductase enzyme that can oxidize organics such as phenolic compounds. Laccases appear to be unstable at room temperature, and their conformation often changes in a strongly acidic or alkaline environment, making them less effective. Therefore, rationally linking enzymes with supports can effectively improve the stability and reusability of native enzymes and add important industrial value. However, in the process of immobilization, many factors may lead to a decrease in enzymatic activity. Therefore, the selection of a suitable support can ensure the activity and economic utilization of immobilized catalysts. Metal-organic frameworks (MOFs) are porous and simple hybrid support materials. Moreover, the characteristics of the metal ion ligand of MOFs can enable a potential synergistic effect with the metal ions of the active center of metalloenzymes, enhancing the catalytic activity of such enzymes. Therefore, in addition to summarizing the biological characteristics and enzymatic properties of laccase, this article reviews laccase immobilization using MOF supports, as well as the application prospects of immobilized laccase in many fields.

Preparation of polyhydroxyalkanoate-based magnetic microspheres for carbonyl reductase purification and immobilization

A polyhydroxyalkanoate (PHA) magnetic microsphere was designed for one-step purification and immobilization of a novel carbonyl reductase (RLSR5) from recombinant Escherichia coli lysate. The hydrophobic core of this microsphere was composed of a highly biocompatible polymer, poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBHHx), in which magnetic Fe3O4 particles were embedded during solvent evaporation. The hydrophilic shell of the fusion protein formed by PHA particle-binding protein (PhaP) and RLSR5 (PR) was expressed in recombinant E. coli. The magnetic core of Fe3O4@PHBHHx directly purified the hydrophilic shell from the E. coli lysate, and the two self-assembled to form Fe3O4@PHBHHx-PR through hydrophobic and hydrophilic interactions, eliminating the separation of the fusion protein. The microstructure, magnetic properties, morphology, size, and dispersion of Fe3O4@PHBHHx-PR were investigated by XRD, VSM, SEM, TEM, elemental mapping and DLS. It was found that Fe3O4@PHBHHx-PR correctly assembled, with a well dispersed spherical structure at the nanoscale and superparamagnetism properties. The amount of RLSR5 immobilized on PHA microspheres reached 121.9 mg/g. The Fe3O4@PHBHHx-PR was employed to synthesize (R)-tolvaptan with 99 % enantiomeric excess and 97 % bioconversion efficiency, and the catalyst maintained 78.6 % activity after 10 recovery cycles. These PHA magnetic microspheres are versatile carriers for enzyme immobilization and demonstrate improved stability and reusability of the free enzyme.

Enhanced Bioactivity of Enzyme/MOF Biocomposite via Host Framework Engineering

This study reports the successful development of a sustainable synthesis protocol for a phase-pure metal azolate framework (MAF-6) and its application in enzyme immobilization. An esterase@MAF-6 biocomposite was synthesized, and its catalytic performance was compared with that of esterase@ZIF-8 and esterase@ZIF-90 in transesterification reactions. Esterase@MAF-6, with its large pore aperture, showed superior enzymatic performance compared to esterase@ZIF-8 and esterase@ZIF-90 in catalyzing transesterification reactions using both n-propanol and benzyl alcohol as reactants. The hydrophobic nature of the MAF-6 platform was shown to activate the immobilized esterase into its open-lid conformation, which exhibited a 1.5- and 4-times enzymatic activity as compared to free esterase in catalyzing transesterification reaction using n-propanol and benzyl alcohol, respectively. The present work offers insights into the potential of MAF-6 as a promising matrix for enzyme immobilization and highlights the need to explore MOF matrices with expanded pore apertures to broaden their practical applications in biocatalysis.

Characterization of an isolated lactase enzyme produced by Bacillus licheniformis ALSZ2 as a potential pharmaceutical supplement for lactose intolerance

Introduction

Lactose intolerance is a widespread problem that affects people of many different races all over the world. The following pharmacological supplements can improve the lives of those who suffer from this issue.

Methods

This work focused on lactase producer isolation and statistical design (Plackett-Burman, and BOX-Behnken) to maximize the effectiveness of environmental factors. A lactase-producing bacterium was chosen from a discovery of 100 strains in soil that had previously been polluted with dairy products. Plackett-Burman investigated fifteen variables.

Results

The most critical variables that lead to increased lactase synthesis are glucose, peptone, and magnesium sulfate (MgSO4). The ideal process conditions for the creation of lactase yield among the stated variables were then determined using a BOX-Benken design. To establish a polynomial quadratic relationship between the three variables and lactase activity, the Box-Behnken design level was used. The EXCEL-solver nonlinear optimization technique was used to predict the best form for lactase production. The ideal temperature and pH levels have been determined, both before and after the lactase purification process, to achieve the highest performance of isolated lactase.

Conclusion

According to this study, Bacillus licheniformis is a perfect supply of the lactase enzyme (β -Galactosidase), It can be used as a product to assist people who have health issues due to lactose intolerance.

Conversion of Similar Xenochemicals to Dissimilar Products: Exploiting Competing Reactions in Whole-Cell Catalysis

Many enzymes have latent activities that can be used in the conversion of non-natural reactants for novel organic conversions. A classic example is the conversion of benzaldehyde to a phenylacetyl carbinol, a precursor for ephedrine manufacture. It is often tacitly assumed that purified enzymes are more promising catalysts than whole cells, despite the lower cost and easier maintenance of the latter. Competing substrates inside the cell have been known to elicit currently hard-to-predict selectivities that are not easily measured inside the living cell. We employ NMR spectroscopic assays to rationally combine isomers for selective reactions in commercial S. cerevisiae. This approach uses internal competition between alternative pathways of aldehyde clearance in yeast, leading to altered selectivities compared to catalysis with the purified enzyme. In this manner, 4-fluorobenzyl alcohol and 2-fluorophenylacetyl carbinol can be formed with selectivities in the order of 90%. Modification of the cellular redox state can be used to tune product composition further. Hyperpolarized NMR shows that the cellular reaction and pathway usage are affected by the xenochemical. Overall, we find that the rational construction of ternary or more complex substrate mixtures can be used for in-cell NMR spectroscopy to optimize the upgrading of similar xenochemicals to dissimilar products with cheap whole-cell catalysts.

Diversity-Oriented Biosynthesis Yields l-Kynurenine Derivative-Based Neurological Drug Candidate Collection

Natural product libraries with a remarkable range of biological activities play pivotal roles in drug discoveries due to their extraordinary structural complexity and immense diversity. l-Kynurenine (l-Kyn)-based derivatives are privileged pharmacophores that exhibit diverse therapeutic implications in neurological disorders. However, the difficulty in obtaining l-Kyn analogues with different skeletal structures has recently led to a decline in its medicinal research. Herein, we report a two-step, one-pot protocol for diversity-oriented biosynthesis of a collection of previously intractable l-Kyn-like compounds. The success of these challenging transformations mainly depends on unlocking the new catalytic scope of tryptophan 2,3-dioxygenases, followed by rational site-directed mutagenesis to modify the substrate domains further. As a result, 18 kynurenine analogues with diverse molecular scaffolds can be rapidly assembled in a predictable manner with 20-83% isolated yields, which not only fill the voids of the catalytic profile of tryptophan 2,3-dioxygenases with an array of substituent groups (e.g., F, Cl, Br, I, CH₃, OCH₃, and NO₂) but also update the current understanding of its substrate spectrum. Our work highlights the great potential of existing enzymes in addressing long-standing synthetic challenges for facilitating the development or discovery of new drug candidates. Furthermore, our approach enables translating the reaction parameters from Eppendorf tubes to 1 L scale, affording l-4-Cl-Kyn and l-5-Cl-Kyn both on a gram scale with more than 80% isolated yields, and provides a promising alternative to further industrial applications.

Immobilization of Enzymes on Cyclodextrin-Anchored Dehiscent Mesoporous TiO2 for Efficient Photoenzymatic Hydroxylation

A three-in-one heterogeneous catalyst (UPO@dTiO₂-CD) was fabricated by grafting cyclodextrins (CDs) on the dehiscent TiO₂ (dTiO₂) surface and subsequently immobilizing unspecific peroxygenase (rAaeUPO), which exhibited double enhanced electron/mass transfer in photo-enzymatic enantioselective hydroxylation of the C-H bond. The tunable anatase/rutile phase ratio and dehiscent mesoporous architectures of dTiO₂ and the electron donor feature and hydrophobic inner cavity of the CDs are independently responsible for accelerating both electron and mass transfer. The coordination of the photocatalytic and enzymatic steps was achieved by structural and compositional regulation. The optimized UPO@dTiO₂-CD not only displayed high catalytic efficiency (turnover number and turnover frequency of rAaeUPO up to >65,000 and 91 min^-1, respectively) but also exhibited high stability and reusability.

Enzyme-Polymer Conjugates for Tuning, Enhancing, and Expanding Biocatalytic Activity

Combining polymers with functional proteins is an approach that has brought several successful stories in the field of biomedicine with PEGylated therapeutic proteins. The latest advances in polymer chemistry have facilitated the expansion of protein-polymer hybrids to other research areas such as biocatalysis. Polymers can impart stability and novel functionalities to the enzyme of interest, thereby improving the catalytic performance of a given reaction. In this review, we have revisited the main methodologies currently used for the synthesis of enzyme-polymer hybrids, unveiling the interplay between the configuration and the composition of the assembled structure and the eventual traits of the hybrid. Finally, the latest advances, such as the assembly of polymer-based chemoenzymatic nanoreactors and the use of deep learning methodologies to achieve the most suitable polymer compositions for catalysis, are discussed.

Bioinspired Coassembly of Copper Ions and Nicotinamide Adenine Dinucleotides for Single-Site Nanozyme with Dual Catalytic Functions

Nanozymes can imitate the catalytic properties of natural enzymes while overcoming the limitations of natural enzymes such as high cost, poor robustness, and difficulty in recycling. However, rational design and facile preparation of nanozymes are still in demand. Inspired by the chemical structure of laccase, we report an amorphous metal-organic coordination nanocomposite named CuNAD, which is composed of copper ions and nicotinamide adenine dinucleotide (NAD⁺) via a simple coordinating coassembly process. As a single-site nanozyme, CuNAD exhibits excellent robustness under extreme conditions, significantly stronger catalytic activity for phenolic compounds, and 4.02-fold higher sensitivity for epinephrine detection than laccase. Furthermore, by breaking through the functional constraints of laccase, CuNAD is also able to activate H₂O₂ at neutral pH, benefiting a one-step chromogenic detection platform for cholesterol. This facile approach demonstrates the potential to develop single-site nanozymes by biomimicking natural enzymes and may boost more insights into the structure-function relationship of nanozymes.

Biohydrogenation of 1,3-Butadiene to 1-Butene under Acetogenic Conditions by Acetobacterium wieringae

The environmental fate and transformation mechanism(s) of 1,3-butadiene (BD) under anoxic conditions remain largely unexplored. Anaerobic consortia that can biohydrogenate BD to stoichiometric amounts of 1-butene at a maximum rate of 205.7 ± 38.6 μM day^-1 were derived from freshwater river sediment. The formation of 1-butene occurred only in the presence of both H₂ and CO₂ with concomitant acetate production, suggesting the dependence of BD biohydrogenation on acetogenesis. The 16S rRNA gene-targeted amplicon sequencing revealed the enrichment and dominance of a novel Acetobacterium wieringae population, designated as strain N, in the BD-biohydrogenating community. Multiple genes encoding putative ene-reductases, candidate catalysts for the hydrogenation of the C═C bond in diene compounds, were annotated on the metagenome-assembled genome of strain N, and thus attributed the BD biohydrogenation activity to strain N. Our findings emphasize an essential but overlooked role of certain Acetobacterium members (e.g., strain N) contributing to the natural attenuation of BD in contaminated subsurface environments (e.g., sediment and groundwater). Future efforts to identify and characterize the ene-reductase(s) responsible for BD biohydrogenation in strain N hold promise for the development of industrial biocatalysts capable of stereoselective conversion of BD to 1-butene.

Effective Production of Selected Dioxolanes by Sequential Bio- and Chemocatalysis Enabled by Adapted Solvent Switching

Most combinations of chemo- and biocatalysis take place in aqueous media or require a solvent change with complex intermediate processing. Using enzymes in the same organic solvent as the chemocatalyst eliminates this need. Here, it was shown that a complete chemoenzymatic cascade to form dioxolanes could be carried out in a purely organic environment. The result, including downstream processing, was compared with a classical mode, shifting solvent. First, a two-step enzyme cascade starting from aliphatic aldehydes to chiral diols (3,4-hexanediol and 4,5-octanediol) was run either in an aqueous buffer or in the potentially biobased solvent cyclopentyl methyl ether. Subsequently, a ruthenium molecular catalyst enabled the conversion to dioxolanes [e. g., (4S,5S)-dipropyl-1,3-dioxolane]. Importantly, the total synthesis of this product was not only highly stereoselective but also based on the combination of biomass, CO₂ , and hydrogen, thus providing an important example of a bio-hybrid chemical.

Discovery of a highly efficient TylF methyltransferase via random mutagenesis for improving tylosin production

Macrolides are currently a class of extensively used antibiotics in human and animal medicine. Tylosin is not only one of the most important veterinary macrolides but also an indispensable material for the bio- and chemo-synthesis of new generations of macrolide antibiotics. Thus, improving its production yield is of great value. As the key rate-limiting enzyme catalyzing the terminal step of tylosin biosynthesis in Streptomyces fradiae (S. fradiae), TylF methyltransferase's catalytic activity directly affects tylosin yield. In this study, a tylF mutant library of S. fradiae SF-3 was constructed based on error-prone PCR technology. After two steps of screening in 24-well plates and conical flask fermentation and enzyme activity assay, a mutant strain was identified with higher TylF activity and tylosin yield. The mutation of tyrosine to phenylalanine is localized at the 139th amino acid residue on TylF (TylF^Y139F), and protein structure simulations demonstrated that this mutation changed the protein structure of TylF. Compared with wild-type protein TylF, TylF^Y139F exhibited higher enzymatic activity and thermostability. More importantly, the Y139 residue in TylF is a previously unidentified position required for TylF activity and tylosin production in S. fradiae, indicating the further potential to engineer the enzyme. These findings provide helpful information for the directed molecular evolution of this important enzyme and the genetic modification of tylosin-producing bacteria.

Surface Modification of Magnetic ZIF-90 Nanoparticles Improves the Microenvironment of Immobilized Lipase and Its Application in Esterification

Interactions of enzymes with supports significantly affect the activity and stability of immobilized enzymes. Herein, amino-functionalized ionic liquid (IL)-grafted magnetic zeolitic imidazolate framework-90 (MZIF-90) was prepared and used to immobilize porcine pancreatic lipase (PPL). The nanocomposites were fully characterized; meanwhile, the interactions between ILs and ZIF-90 were calculated based on density functional theory. The prepared biocatalyst (PPL-ILs/MZIF-90) had a lipase loading of 178.3 mg/g and hydrolysis activity up to 287.5 U/g. When the biocatalyst was used to synthesize isoamyl acetate, the reaction media, molar ratio of alcohol/acid, temperature, and reaction time were optimized. Under the optimized reaction conditions (in hexane, alcohol/acid = 3:1, under 45 °C, reacted for 9 h), the ester yield reached 85.5%. The results of the stability test showed that PPL-ILs/MZIF-90 retained 88.7% of the initial activity after storing for 35 days and 92.5% of the initial activity after reusing for seven cycles for synthesizing isoamyl acetate. Moreover, the secondary structure analysis showed that the synthesized supports protected the active conformation of immobilized lipase, which lead to the enhanced catalytic performance. Additionally, the biocatalyst can be easily separated with a magnet, which facilitated the reusability. This study provides insights regarding the application of metal organic framework composites in the field of enzyme catalysis.

Where Chemocatalysis Meets Biocatalysis: In Water

Chemoenzymatic catalysis, by definition, involves the merging of sequential reactions using both chemocatalysis and biocatalysis, typically in a single reaction vessel. A major challenge, the solution to which, however, is associated with numerous advantages, is to run such one-pot processes in water: the majority of enzyme-catalyzed processes take place in water as Nature's reaction medium, thus enabling a broad synthetic diversity when using water due to the option to use virtually all types of enzymes. Furthermore, water is cheap, abundantly available, and environmentally friendly, thus making it, in principle, an ideal reaction medium. On the other hand, most chemocatalysis is routinely performed today in organic solvents (which might deactivate enzymes), thus appearing to make it difficult to combine such reactions with biocatalysis toward one-pot cascades in water. Several creative approaches and solutions that enable such combinations of chemo- and biocatalysis in water to be realized and applied to synthetic problems are presented herein, reflecting the state-of-the-art in this blossoming field. Coverage has been sectioned into three parts, after introductory remarks: (1) Chapter 2 focuses on historical developments that initiated this area of research; (2) Chapter 3 describes key developments post-initial discoveries that have advanced this field; and (3) Chapter 4 highlights the latest achievements that provide attractive solutions to the main question of compatibility between biocatalysis (used predominantly in aqueous media) and chemocatalysis (that remains predominantly performed in organic solvents), both Chapters covering mainly literature from ca. 2018 to the present. Chapters 5 and 6 provide a brief overview as to where the field stands, the challenges that lie ahead, and ultimately, the prognosis looking toward the future of chemoenzymatic catalysis in organic synthesis.

Hierarchically Structured CA@ZIF-8 Biohybrids for Carbon Dioxide Mineralization

Carbonic anhydrase (CA) is a powerful biocatalyst for carbon dioxide (CO₂) mineralization, of which immobilization is usually used for maintaining its catalytic activity against harsh external stimuli. However, the incorporated materials for CA immobilization would commonly increase the internal diffusion resistance during the catalytic process, thereby decreasing the catalytic efficiency. In our study, poly-L-glutamic acid (PLGA) as the structure regulator was used to induce the synthesis of CA@zeolitic imidazolate framework-8 (CA@ZIF-8) biohybrids. The introduction of PLGA that could coordinate with Zn²⁺ interfered the crystallization of ZIF-8, thereby changing the morphological structure of CA@ZIF-8 biohybrids. With the increase of PLGA amount from 0 to 60 mg, PLGA(x)-CA@ZIF-8 biohybrids were gradually transformed from a dodecahedron structure to a 3D lamellar nano-flower structure, which caused elevated exposed surface area. Accordingly, the loading ratio was increased from 34.6 to 49.8 mg g_cat^-1, while the catalytic activity was elevated from 20.6 to 23.4%. The CO₂ conversion rate was enhanced by nearly two folds compared to PLGA(0)-CA@ZIF-8 under the optimized condition. The final CaCO₃ yield could reach 5.6 mg mg_cat^-1, whereas the reaction system could remain above 80% of the initial reaction activity after 8 cycles.

A Statistical Analysis of the Sequence and Structure of Thermophilic and Non-Thermophilic Proteins

Thermophilic proteins have various practical applications in theoretical research and in industry. In recent years, the demand for thermophilic proteins on an industrial scale has been increasing; therefore, the engineering of thermophilic proteins has become a hot direction in the field of protein engineering. However, the exact mechanism of thermostability of proteins is not yet known, for engineering thermophilic proteins knowing the basis of thermostability is necessary. In order to understand the basis of the thermostability in proteins, we have made a statistical analysis of the sequences, secondary structures, hydrogen bonds, salt bridges, DHA (Donor-Hydrogen-Accepter) angles, and bond lengths of ten pairs of thermophilic proteins and their non-thermophilic orthologous. Our findings suggest that polar amino acids contribute to thermostability in proteins by forming hydrogen bonds and salt bridges which provide resistance against protein denaturation. Short bond length and a wider DHA angle provide greater bond stability in thermophilic proteins. Moreover, the increased frequency of aromatic amino acids in thermophilic proteins contributes to thermal stability by forming more aromatic interactions. Additionally, the coil, helix, and loop in the secondary structure also contribute to thermostability.

Confining enzymes in porous organic frameworks: from synthetic strategy and characterization to healthcare applications

Enzymes are a class of natural catalysts with high efficiency, specificity, and selectivity unmatched by their synthetic counterparts and dictate a myriad of reactions that constitute various cascades in living cells. The development of suitable supports is significant for the immobilization of structurally flexible enzymes, enabling biomimetic transformation in the extracellular environment. Accordingly, porous organic frameworks, including metal organic frameworks (MOFs), covalent organic frameworks (COFs) and hydrogen-bonded organic frameworks (HOFs), have emerged as ideal supports for the immobilization of enzymes because of their structural features including ultrahigh surface area, tailorable porosity, and versatile framework compositions. Specially, organic framework-encased enzymes have shown significant enhancement in stability and reusability, and their tailorable pore opening provides a gatekeeper-like effect for guest sieving, which is beneficial for mimicking intracellular biocatalysis processes. This immobilization technique brings new insight into the development of next-generation enzyme materials and shows huge potential in healthcare applications, such as biomarker diagnosis, biostorage, and cancer and antibacterial therapies. In this review, we describe the state-of-the-art strategies for the structural immobilization of enzymes using the well-explored MOFs and burgeoning COFs and HOFs as scaffolds, with special emphasis on how these porous framework-confined technologies can provide a favorable microenvironment for mimicking natural biocatalysis. Subsequently, advanced characterization techniques for enzyme conformation, the effect of the confined microenvironment on the activity of enzymes, and the emerging healthcare applications will be surveyed.

Advanced Strategies in Enzyme Activity Regulation for Biomedical Applications

Enzymes are important macromolecular biocatalysts that accelerate chemical and biochemical reactions in living organisms. Most human diseases are related to alterations in enzyme activity. Moreover, enzymes are potential therapeutic tools for treating different diseases, such as cancer, infections, and cardiovascular and cerebrovascular diseases. Precise remote enzyme activity regulation provides new opportunities to combat diseases. This review summarizes recent advances in the field of enzyme activity regulation, including reversible and irreversible regulation. It also discusses the mechanisms and approaches for on-demand control of these activities. Furthermore, a range of stimulus-responsive inhibitors, polymers, and nanoparticles for regulating enzyme activity and their prospective biomedical applications are summarized. Finally, the current challenges and future perspectives on enzyme activity regulation are discussed.

Coupling metal and whole-cell catalysis to synthesize chiral alcohols

BACKGROUND

The combination of metal-catalyzed reactions and enzyme catalysis has been an essential tool for synthesizing chiral pharmaceutical intermediates in the field of drug synthesis. Metal catalysis commonly enables the highly efficient synthesis of molecular scaffolds under harsh organic conditions, whereas enzymes usually catalyze reactions in mild aqueous medium to obtain high selectivity. Since the incompatibility between metal and enzyme catalysis, there are limitations on the compatibility of reaction conditions that must be overcome.

FINDINGS

We report a chemoenzymatic cascade reaction involved Palladium (Pd) catalyzed Suzuki-Miyaura coupling and whole-cell catalyzed C = O asymmetric reduction for enantioselective synthesis of value-added chiral alcohol. The cell membrane serves as a natural barrier can protect intracellular enzymes from organic solvents.

CONCLUSIONS

With dual advantages of cascade catalysis and biocompatibility, our work provides a rational strategy to harvest chiral alcohols in high yield and excellent enantioselectivity, as a channel to establish chemoenzymatic catalysis.

A review on the immobilization of pepsin: A Lys-poor enzyme that is unstable at alkaline pH values

Pepsin is a protease used in many different applications, and in many instances, it is utilized in an immobilized form to prevent contamination of the reaction product. This enzyme has two peculiarities that make its immobilization complex. The first one is related to the poor presence of primary amino groups on its surface (just one Lys and the terminal amino group). The second one is its poor stability at alkaline pH values. Both features make the immobilization of this enzyme to be considered a complicated goal, as most of the immobilization protocols utilize primary amino groups for immobilization. This review presents some of the attempts to get immobilized pepsin biocatalyst and their applications. The high density of anionic groups (Asp and Glu) make the anion exchange of the enzyme simpler, but this makes many of the strategies utilized to immobilize the enzyme (e.g., amino-glutaraldehyde supports) more related to a mixed ion exchange/hydrophobic adsorption than to real covalent immobilization. Finally, we propose some possibilities that can permit not only the covalent immobilization of this enzyme, but also their stabilization via multipoint covalent attachment.

Integration of Adenylate Kinase 1 with Its Peptide Conformational Imprint

In the present study, molecularly imprinted polymers (MIPs) were used as a tool to grasp a targeted α-helix or β-sheet of protein. During the fabrication of the hinge-mediated MIPs, elegant cavities took shape in a special solvent on quartz crystal microbalance (QCM) chips. The cavities, which were complementary to the protein secondary structure, acted as a peptide conformational imprint (PCI) for adenylate kinase 1 (AK1). We established a promising strategy to examine the binding affinities of human AK1 in conformational dynamics using the peptide-imprinting method. Moreover, when bound to AK1, PCIs are able to gain stability and tend to maintain higher catalytic activities than free AK1. Such designed fixations not only act on hinges as accelerators; some are also inhibitors. One example of PCI inhibition of AK1 catalytic activity takes place when PCI integrates with an AK1_9-23 β-sheet. In addition, conformation ties, a general MIP method derived from random-coil AK1_133-144 in buffer/acetonitrile, are also inhibitors. The inhibition may be due to the need for this peptide to execute conformational transition during catalysis.

Enhancing Enzyme Activity by the Modulation of Covalent Interactions in the Confined Channels of Covalent Organic Frameworks

Controllable regulations on the enzyme conformation to optimize catalytic performance are highly desired for the immobilized biocatalysts yet remain challenging. Covalent organic frameworks (COFs) possess confined channels with finely tunable pore environment, offering a promising platform for enzyme encapsulation. Herein, we covalently immobilized the cytochrome c (Cyt c) in the size-matched channels of COFs with different contents of anchoring site, and significant enhancement of the stability and activity (≈600 % relative activity compared with free enzyme) can be realized by optimizing the covalent interactions. Structural analyses on the immobilized Cyt c suggest that covalent bonding could induce conformational perturbation resulting in more accessible active sites. The effectiveness of the covalent interaction modulation together with the tailorable confined channels of COFs offers promise to develop high-performance biocatalysts.

The presence and role of the intermediary CO reservoir in heterogeneous electroreduction of CO2

SignificanceThe electroconversion of CO2 to value-added products is a promising path to sustainable fuels and chemicals. However, the microenvironment that is created during CO2 electroreduction near the surface of heterogeneous Cu electrocatalysts remains unknown. Its understanding can lead to the development of ways to improve activity and selectivity toward multicarbon products. This work introduces a method called on-stream substitution of reactant isotope that provides quantitative information of the CO intermediate species present on Cu surfaces during electrolysis. An intermediary CO reservoir that contains more CO molecules than typically expected in a surface adsorbed configuration was identified. Its size was shown to be a factor closely associated with the formation of multicarbon products.

Origin of Metal Cluster Tuning Enzyme Activity at the Bio-Nano Interface

Detailed understanding of how the bio-nano interface orchestrates the function of both biological components and nanomaterials remains ambiguous. Here, through a combination of experiments and molecular dynamics simulations, we investigated how the interface between Candida Antarctic lipase B and palladium (Pd) nanoparticles (NPs) tunes the structure, dynamics, and catalysis of the enzyme. Our simulations show that the metal binding to protein is a shape matching behavior and there is a transition from saturated binding to unsaturated binding along with the increase in the size of metal NPs. When we engineered the interface with the polymer, not only did the critical size of saturated binding of metal NPs become larger, but also the disturbance of the metal NPs to the enzyme function was reduced. In addition, we found that an enzyme-metal interface engineered with the polymer can boost bio-metal cascade reactions via substrate channeling. Understanding and control of the bio-nano interface at the molecular level enable us to rationally design bio-nanocomposites with prospective properties.

Construction and Application of a High-Throughput In Vivo Screening Platform for the Evolution of Nitrile Metabolism-Related Enzymes Based on a Desensitized Repressive Biosensor

Transcription factor (TF)-based biosensors are expected to serve as powerful tools for the high-throughput screening of biocatalytic systems; however, most of them respond to ligands in a narrow concentration range, which limits their application. In this study, we constructed a heterogenous niacin biosensor using the repressive TF BsNadR and its target promoters from Bacillus subtilis. The fine-tunable output of the niacin biosensor was expanded to a wide range of niacin concentrations (0-50 mM) through desensitization engineering, which was suitable for the accurate identification of differences in enzyme activity. Structural mechanism analysis indicated that weakening the affinity of BsNadR with the ligand niacin and with DNA alters its regulatory properties. Based on the desensitized niacin biosensor, a high-throughput in vivo screening platform was developed for evolving nitrile metabolism-related enzymes. The evolved nitrilase, amidase, and nitrile hydratase with 6.6-, 2.1-, and 21.3-fold improvements in activity were achieved, respectively. In addition, these mutants also exhibited elevated activity toward other cognate substrates, indicating the broad applicability of the screening platform. This study not only provided a universal high-throughput screening platform for different nitrile metabolism-related enzymes but also demonstrated the advantages of repressive biosensors and the vital role of desensitization engineering of the TF in the development of high-throughput screening platforms for enzymes.

Whole-cell biosynthesis of cytarabine by an unnecessary protein-reduced Escherichia coli that coexpresses purine and uracil phosphorylase

Currently, whole-cell catalysts face challenges due to the complexity of reaction systems, although they have a cost advantage over pure enzymes. In this work, cytarabine was synthesized by purified purine phosphorylase 1 (PNP1) and uracil phosphorylase (UP), and the conversion of cytarabine from adenine arabinoside reached 72.3±4.3%. However, the synthesis was unsuccessful by whole-cell catalysis due to interference from unnecessary proteins (UNPs) in cells. Thus, we carried out a large-scale gene editing involving 377 genes in the genome of Escherichia coli to reduce the negative effect of UNPs on substrate conversion and cytarabine production. Finally, the PNP1 and UP activities of the obtained mutant were increased significantly compared with the parental strain, and more importantly, the conversion rate of cytarabine by whole-cell catalysis reached 67.4±2.5%. The lack of 148 proteins and down-regulation of 783 proteins caused by gene editing were equivalent to partial purification of the enzymes within cells, and thus, we provided inspiration to solve the problem caused by UNP interference, which is ubiquitous in the field of whole-cell catalysis. This article is protected by copyright. All rights reserved.

Rational Design of Photocatalysts for Controlled Polymerization: Effect of Structures on Photocatalytic Activities

Over the past decade, the use of photocatalysts (PCs) in controlled polymerization has brought new opportunities in sophisticated macromolecular synthesis. However, the selection of PCs in these systems has been typically based on laborious trial-and-error strategies. To tackle this limitation, computer-guided rational design of PCs based on knowledge of structure-property-performance relationships has emerged. These rational strategies provide rapid and economic methodologies for tuning the performance and functionality of a polymerization system, thus providing further opportunities for polymer science. This review provides an overview of PCs employed in photocontrolled polymerization systems and summarizes their progression from early systems to the current state-of-the-art. Background theories on electronic transitions are also introduced to establish the structure-property-performance relationships from a perspective of quantum chemistry. Typical examples for each type of structure-property relationships are then presented to enlighten future design of PCs for photocontrolled polymerization.

An Insight in Developing Carrier-Free Immobilized Enzymes

Enzymes play vital roles in all organisms. The enzymatic process is progressively at its peak, mainly for producing biochemical products with a higher value. The immobilization of enzymes can sometimes tremendously improve the outcome of biocatalytic processes, making the product(s) relatively pure and economical. Carrier-free immobilized enzymes can increase the yield of the product and the stability of the enzyme in biocatalysis. Immobilized enzymes are easier to purify. Due to these varied advantages, researchers are tempted to explore carrier-free methods used for the immobilization of enzymes. In this review article, we have discussed various aspects of enzyme immobilization, approaches followed to design a process used for immobilization of an enzyme and the advantages and disadvantages of various common processes used for enzyme immobilization.

Improvement of the enzymatic detoxification activity towards mycotoxins through structure-based engineering

Mycotoxin contamination of food and feed is posing a serious threat to the global food safety and public health. Biological detoxification mediated by enzymes has emerged as a promising approach, as they can specifically degrade mycotoxins into non-toxic ones. However, the low degradation efficiency and stability limit their further application. To optimize the enzymes for mycotoxin removal, modification strategies that combine computational design with their structural data have been developed. Accordingly, this review will comprehensively summarize the recent trends in structure-based engineering to improve the enzyme catalytic efficiency, selectivity and stability in mycotoxins detoxification, which also provides perspectives in obtaining innovative and effective biocatalysts for mycotoxins degradation.

Lipase-Catalyzed Epoxy-Acid Addition and Transesterification: from Model Molecule Studies to Network Build-Up

Commercially available lipase from Pseudomonas stutzeri (lipase TL) is investigated as a biocatalyst for the formation of an acid-epoxy chemical network. Molecular model reactions are performed by reacting 2-phenyl glycidyl ether and hexanoic acid in bulk, varying two parameters: temperature and water content. Characterizations of the formed products by ¹H NMR spectroscopy and gas chromatography-mass spectrometry combined with enzymatic assays confirm that lipase TL is able to simultaneously promote acid-epoxy addition and transesterification reactions below 100 °C and solely the acid-epoxy addition after denaturation at T > 100 °C. A prototype bio-based chemical network with β-hydroxyester links was obtained using resorcinol diglycidyl ether and sebacic acid as monomers with lipase TL as catalyst. Differential scanning calorimetry, attenuated total reflection, and swelling analysis confirm gelation of the network.

Recent advances in (chemo)enzymatic cascades for upgrading bio-based resources

Developing (chemo)enzymatic cascades is very attractive for green synthesis, because they streamline multistep synthetic processes. In this Feature Article, we have summarized the recent advances in in vitro or whole-cell cascade reactions with a focus on the use of renewable bio-based resources as starting materials. This includes the synthesis of rare sugars (such as ketoses, L-ribulose, D-tagatose, myo-inositol or aminosugars) from readily available carbohydrate sources (cellulose, hemi-cellulose, starch), in vitro enzyme pathways to convert glucose to various biochemicals, cascades to convert 5-hydroxymethylfurfural and furfural obtained from lignin or xylose into novel precursors for polymer synthesis, the syntheses of phenolic compounds, cascade syntheses of aliphatic and highly reduced chemicals from plant oils and fatty acids, upgrading of glycerol or ethanol as well as cascades to transform natural L-amino acids into high-value (chiral) compounds. In several examples these processes have demonstrated their efficiency with respect to high space-time yields and low E-factors enabling mature green chemistry processes. Also, the strengths and limitations are discussed and an outlook is provided for improving the existing and developing new cascades.