Enzyme Immobilization on Graphite Oxide (GO) Surface via One-Pot Synthesis of GO/Metal-Organic Framework Composites for Large-Substrate Biocatalysis

Protein and peptide confinement within metal-organic materials

Metal-organic materials (MOMs), including both discrete metal-organic cages (MOCs) and metal-organic frameworks (MOFs), are emerging as promising materials for peptide and protein immobilisation. In particular, the ease of synthesis of MOMs alongside their well-defined and modular internal void spaces makes them appealing when considering routes to immobilise and stabilise peptides and proteins outside of biological environments whilst retaining their native activity. Here we review recent advances made in understanding the conformation of peptidic materials confined within MOMs and the enzymes@MOF constructs which show the best enzymatic performance. We highlight opportunities for further advancement in each of these areas and proposed that complementary approaches taken by the MOC and MOF communities might be fruitfully combined to advance our understanding and the development of peptide/protein@MOM applications.

Isolation of marine bacteria with potential for polyhydroxyalkanoate degradation and optimization for enzyme production

Plastic materials are widely used because of their strength, light weight, durability, and environmental resistance. However, their decomposition rates are significantly slower than their typical lifespans. The rapid and continuous increase in plastic consumption has caused severe environmental impacts due to the accumulation of plastic waste. We identified potential polyhydroxyalkanoate (PHA)-degrading bacteria from marine environments capable of producing extracellular PHA depolymerases crucial for biodegrading PHAs. Marine debris was collected to screen poly [(R)-3-hydroxybutyric acid] (P(3HB))-degrading bacteria. Six isolates showed the ability to produce clear zones surrounding their colonies by degrading the bioplastic P(3HB). The isolate SS1-2, exhibiting the greatest degradation index of 1.44, was chosen for optimization through the statistical technique. The results indicated that NH4Cl was the best nitrogen source for enzyme production, and the response surface methodology (RSM) suggested that the greatest P(3HB) depolymerase production could be achieved when the concentrations of substrate loading and NH4Cl both set at 0.5%. Analysis of the 16S rRNA sequence of isolate SS1-2 revealed similarity to Pseudooceanicola antarcticus CGMCC 1.12662 (97.81% similarity). The findings of this study indicate the potential for further exploitation of this depolymerase in enzyme kinetics studies and its application in PHA degradation experiments.

State-of-the-Art, Insights, and Perspectives for MOFs-Nanocomposites and MOF-Derived (Nano)Materials

Composite structures created from metal‒organic framework (MOF) matrices are reviewed in this work. Depending on the nature of the second component apart from the MOF platform, several synergistic properties may arise; at the same time, the initial features of the single constituent materials are usually maintained, and individual shortcomings are mitigated. Currently, timely energy and environmental challenges necessitate the quest for more advanced materials and technologies. Significant developments in MOF-nanocomposites have enabled their application across a wide range of modern and traditional fields. This review demonstrates in an exhaustive and critical way a broad range of MOF-based nanocomposites, namely, MOF/perovskite nanoparticles (NPs), MOF/metal (non-iron) oxide NPs, MOF/Fe3O4 NPs, MOF/metal chalcogenide NPs, MOF/metal NPs, and MOF/carbon-based materials, as well as nanocomposites of MOFs with other semiconductor NPs. Key points related to the synthesis, characterization, and applications of these materials are provided. Depending on their configuration, the composites under discussion can be applied in domains such as photoelectrochemical sensing, antibiotic/dye degradation, optoelectronics, photovoltaics, catalysis, solar cells, supercapacitors, batteries, water remediation, and drug loading. Sometimes, MOFs can undergo certain processes (e.g. pyrolysis) and act as precursors for composite materials with appealing characteristics. Therefore, a special section in the manuscript is devoted to MOF-derived NP composites. Toward the end of the text, we conclude while also describing the challenges and possibilities for further investigations in the umbrella of material categories analyzed herein. Despite the progress achieved, key questions remain to be answered regarding the relationships among the morphology, properties, and polyvalent activity of these materials. The present work aims to shed light on most of their aspects and innovative prospects, facilitating a deeper comprehension of the underlying phenomena, functionality, and mechanistic insights governing their behavior.

Redefining Metal Organic Frameworks in Biosensors: Where Are We Now?

As a broad class of porous nanomaterials, metal organic frameworks (MOFs) exhibit unique properties, such as broad tunability, high stability, atomically well-defined structure, and ordered uniform porosity. These features facilitate the rational design of MOFs as an outstanding nanomaterial candidate in biosensing, therapeutics delivery, and catalysis applications. Recently, novel modifications of the MOF nanoarchitecture and incorporation of synergistic guest materials have been investigated to achieve well-tailored functional design, gradually bridging the fundamental gap between structure and targeted activity. Specifically, the burgeoning studies of MOF-based high-performance biosensors have aimed to achieve high sensitivity, selectivity, and stability for a large variety of analytes in different sensing matrices. In this review, we elaborate the key roles of MOF nanomaterials in biosensors, including their high stability as a protective framework for biomolecules, their intrinsic sensitivity-enhancing functionalities, and their contribution of catalytic activity as a nanozyme. By examining the main structures of MOFs, we further identify varied structural engineering approaches, such as precursor tuning and guest molecule incorporation, that elucidate the concept of the structure-activity relationship of MOFs. Furthermore, we highlight the unique applications of MOF nanomaterials in electrochemical and optical biosensors for enhanced sensor performances. Finally, the challenges and future perspectives of developing next-generation MOF nanomaterials for biosensor applications are discussed.

Nb2CTx-supported bimetallic NPs@ZIF-8 nanohybrid as ECL signal amplifier and peroxidase mimics for chromogranin a immunosensing in human serum and saliva

Niobium carbide (Nb2CTx), a key component of the MXene family renowned for its utilization in lithium-ion batteries and supercapacitors, remains largely underutilized in biosensing applications. This study introduces a notably sensitive and label-free dual-mode electrochemiluminescence (ECL) and colorimetric immunosensor to specifically detect chromogranin A (CgA) in biological fluids. Initially, AuAg bimetallic nanoparticles (BiMNPs) were synthesized using Nb2CTx as a reducing and supporting material. Furthermore, a promising approach has been put forward to increase the efficacy of the ECL of [Ru (bpy)3]2+ system by integrating the combined use of the zeolitic imidazolate framework-8 (ZIF-8) and the Nb2CTx coated bimetallic NPs. Incorporation produces a significant ~165-fold increase in electrochemical signals and a 4-fold improvement in ECL signals. In particular, BiMNPs@ZIF-8 nanohybrid exhibited significantly enhanced peroxidase-like activity compared to bare BiMNPs, demonstrating synergistic peroxidase enzyme mimicry. This improved activity makes it a potent catalyst for the H₂O₂-mediated oxidation of 3,3,5,5, tetramethylbenzidine (TMB), generating the characteristic blue color. Furthermore, the ECL method achieved a detection range of 0.001 to 1000 pg/mL with LOD of 0.11 fg/mL, while the colorimetric method achieved a LOD of 100 pg/mL and a linear range of 0.1 to 4000 ng/mL. The practical applicability of the sensor was validated by analyzing CgA levels in human serum and saliva samples.

Exploring enzyme-immobilized MOFs and their application potential: biosensing, biocatalysis, targeted drug delivery and cancer therapy

Enzymes are indispensable in several applications including biosensing and degradation of pollutants and in the drug industry. However, adverse conditions restrict enzymes' utility in biocatalysis due to their inherent limitations. Metal-organic frameworks (MOFs), with their robust structure, offer an innovative avenue for enzyme immobilization, enhancing their resilience against harsh solvents and temperatures. This advancement is pivotal for application in bio-sensing, bio-catalysis, and specifically, targeted drug delivery in cancer therapy, where enzyme-MOF composites enable precise therapeutic localization, minimizing the side effects of traditional treatment. The adaptable nature of MOFs enhances drug biocompatibility and availability, significantly improving therapeutic outcomes. Moreover, the integration of enzyme-immobilized MOFs into bio-sensing represents a leap forward in the rapid and accurate identification of biomarkers, facilitating early diagnosis and disease monitoring. In bio-catalysis, this synergy promotes efficient and environmentally safe chemical synthesis, enhancing reaction rates and yields and broadening the scope of enzyme application in pharmaceutical and bio-fuel production. This review article explores the immobilization techniques and their biomedical applications, specifically focusing on drug delivery in cancer therapy and bio-sensing. Additionally, it addresses the challenges faced in this expanding field.

Copper-Based Bio-MOF/GO with Lewis Basic Sites for CO2 Fixation into Cyclic Carbonates and C-C Bond-Forming Reactions

Several measures, including crude oil recovery improvement and carbon dioxide (CO2) conversion into valuable chemicals, have been considered to decrease the greenhouse effect and ensure a sustainable low-carbon future. The Knoevenagel condensation and CO2 fixation have been introduced as two principal solutions to these challenges. In the present study for the first time, bio-metal-organic frameworks (MOF)(Cu)/graphene oxide (GO) nanocomposites have been used as catalytic agents for these two reactions. In view of the attendance of amine groups, biological MOFs with NH2 functional groups as Lewis base sites protruding on the channels' internal surface were used. The bio-MOF(Cu)/20%GO performs efficaciously in CO2 fixation, leading to more than 99.9% conversion with TON = 525 via a solvent-free reaction under a 1 bar CO2 atmosphere. It has been shown that these frameworks are highly catalytic due to the Lewis basic sites, i.e., NH2, pyrimidine, and C═O groups. Besides, the Lewis base active sites exert synergistic effects and render bio-MOF(Cu)/10%GO nanostructures as highly efficient catalysts, significantly accelerating Knoevenagel condensation reactions of aldehydes and malononitrile as substrates, thanks to the high TOF (1327 h-1) and acceptable reusability. Bio-MOFs can be stabilized in reactions using GO with oxygen-containing functional groups that contribute as efficient substitutes, leading to an expeditious reaction speed and facilitating substrate absorption.

A novel olfactory biosensor based on ZIF-8@SWCNT integrated with nanosome-AuNPs/Prussian blue for sensitive detection of hexanal

Hexanal is considered as an important volatile compound indicator for the assessment of freshness and maturity of foods. Therefore, sensitive and stable monitoring of hexanal is highly desired. Herein, an efficient receptor immobilization strategy based on ZIF-8@ Single-walled carbon nanotube (SWCNT) and nanosomes-AuNPs/Prussian blue (PB) was proposed for the development of olfactory biosensors. ZIF-8@SWCNT as dual support materials provided a high density of active sites for nanosomes loading. Moreover, the co-electrodeposition of nanosomes-AuNPs and PB on the sensor interface effectively amplified the electrochemical signal and maintained the activity of the receptor. The combination of ZIF-8@SWCNT with AuNPs/PB imparts excellent sensing performance of the biosensor with a wide detection range of 10-16-10-9 M, a low detection limit of 10-16 M for hexanal, and a long storage stability of 15 days. These results indicate that our biosensor can be a powerful tool for versatile applications in food and other related industries.

Boosting one-step degradation of shrimp shell waste to produce chitin oligosaccharides at smart nanoscale enzyme reactor with liquid-solid system

Chitin oligosaccharides (CTOS) possess potential applications in food, medicine, and agriculture. However, lower mass transfer and catalytic efficiency are the main kinetic limitations for the production of CTOS from shrimp shell waste (SSW) and crystalline chitin. Chemical or physical methods are usually used for pretreatment to improve chitinase hydrolysis efficiency, but this is not eco-friendly and cost-effective. To address this challenge, a chitinase nanoreactor with the liquid-solid system (BcChiA1@ZIF-8) was manufactured to boost the one-step degradation of SSW and crystalline chitin. Compared with free enzyme, the catalytic efficiency of BcChiA1@ZIF-8 on colloidal chitin was significantly improved to 142 %. SSW and crystalline chitin can be directly degraded by BcChiA1@ZIF-8 without any pretreatments. The yield of N, N'-diacetylchitobiose [(GlcNAc)2] from SSW and N-acetyl-D-glucosamine (GlcNAc) from crystalline chitin was 2 times and 3.1 times than that of free enzyme, respectively. The reason was that BcChiA1@ZIF-8 with a liquid-solid system enlarged the interface area, increased the collision frequency between enzyme and substrate, and improved the large-substrates binding activity of chitinase. Moreover, the biphasic system exhibited excellent stability, and the design showed universal applicability. This strategy provided novel guidance for other polysaccharide biosynthesis and the conversion of environmental waste into carbohydrates.

Magnetic Multienzyme@Metal-Organic Material for Sustainable Biodegradation of Insoluble Biomass

Biodegradation of insoluble biomass such as cellulose via carbohydrase enzymes is an effective approach to break down plant cell walls and extract valuable materials therein. Yet, the high cost and poor reusability of enzymes are practical concerns. We recently proved that immobilizing multiple digestive enzymes on metal-organic materials (MOMs) allows enzymes to be reused via gravimetric separation, improving the cost efficiency of cereal biomass degradation [ACS Appl. Mater. Interfaces 2021, 13, 36, 43085-43093]. However, this strategy cannot be adapted for enzymes whose substrates or products are insoluble (e.g., cellulose crystals). Recently, we described an alternative approach based on magnetic metal-organic frameworks (MOFs) using model enzymes/substrates [ACS Appl. Mater. Interfaces 2020, 12, 37, 41794-41801]. Here, we aim to prove the effectiveness of combining these two strategies in cellulose degradation. We immobilized multiple carbohydrase enzymes that cooperate in cellulose degradation via cocrystallization with Ca2+, a carboxylate ligand (BDC) in the absence and presence of magnetic nanoparticles (MNPs). We then compared the separation efficiency and enzyme reusability of the resultant multienzyme@Ca-BDC and multienzyme@MNP-Ca-BDC composites via gravimetric and magnetic separation, respectively, and found that, although both composites were effective in cellulose degradation in the first round, the multienzyme@MNP-Ca-BDC composites displayed significantly enhanced reusability. This work provides the first experimental demonstration of using magnetic solid supports to immobilize multiple carbohydrase enzymes simultaneously and degrade cellulose and promotes green/sustainable chemistry in three ways: (1) reusing the enzymes saves energy/sources to prepare them, (2) the synthetic conditions are "green" without generating unwanted wastes, and (3) using our composites to degrade cellulose is the first step of extracting valuable materials from sustainable biomasses such as plants whose growth does not rely on nonregeneratable resources.

A Protocol for Custom Biomineralization of Enzymes in Metal-Organic Frameworks (MOFs)

Enzyme immobilization offers a number of advantages that improve biocatalysis; however, finding a proper way to immobilize enzymes is often a challenging task. Implanting enzymes in metal-organic frameworks (MOFs) via co-crystallization, also known as biomineralization, provides enhanced reusability and stability with minimal perturbation and substrate selectivity to the enzyme. Currently, there are limited metal-ligand combinations with a proper protocol guiding the experimental procedures. We have recently explored 10 combinations that allow custom immobilization of enzymes according to enzyme stability and activity in different metals/ligands. Here, as a follow-up of that work, we present a protocol for how to carry out custom immobilization of enzymes using the available combinations of metal ions and ligands. Detailed procedures to prepare metal ions, ligands, and enzymes for their co-crystallization, together with characterization and assessment, are discussed. Precautions for each experimental step and result analysis are highlighted as well. This protocol is important for enzyme immobilization in various research and industrial fields. Key features • A wide selection of metal ions and ligands allows for the immobilization of enzymes in metal-organic frameworks (MOFs) via co-crystallization. • Step-by-step enzyme immobilization procedure via co-crystallization of metal ions, organic linkers, and enzymes. • Practical considerations and experimental conditions to synthesize the enzyme@MOF biocomposites are discussed. • The demonstrated method can be generalized to immobilize other enzymes and find other metal ion/ligand combinations to form MOFs in water and host enzymes.

Impact of Crystallinity on Enzyme Orientation and Dynamics upon Biomineralization in Metal-Organic Frameworks

Aqueous-phase co-crystallization (also known as biomimetic mineralization or biomineralization) is a unique way to encapsulate large enzymes, enzyme clusters, and enzymes with large substrates in metal-organic frameworks (MOFs), broadening the application of MOFs as enzyme carriers. The crystallinity of resultant enzyme@MOF biocomposites, however, can be low, raising a concern about how MOF crystal packing quality affects enzyme performance upon encapsulation. The challenges to overcome this concern are (1) the limited database of enzyme performance upon biomineralization in different aqueous MOFs and (2) the difficulty in probing enzyme restriction and motion in the resultant MOF scaffolds, which are related to the local crystal packing quality/density, under the interference of the MOF backgrounds. We have discovered several new aqueous MOFs for enzyme biomineralization with varied crystallinity [Jordahl, D.; Armstrong, Z.; Li, Q.; Gao, R.; Liu, W.; Johnson, K.; Brown, W.; Scheiwiller, A.; Feng, L.; Ugrinov, A.; Mao, H.; Chen, B.; Quadir, M.; Pan, Y.; Li, H.; Yang, Z. Expanding the Library of Metal-Organic Frameworks (MOFs) for Enzyme Biomineralization. ACS Appl. Mater. Interfaces 2022, 14 (46), 51619-51629, DOI: 10.1021/acsami.2c12998]. Here, we address the second challenge by probing enzyme dynamics/restriction in these MOFs at the residue level via site-directed spin labeling (SDSL)-electron paramagnetic resonance (EPR) spectroscopy, a unique approach to determine protein backbone motions regardless of the background complexity. We encapsulated a model large-substrate enzyme, lysozyme, in eight newly discovered MOFs, which possess various degrees of crystallization, via aqueous-phase co-crystallization. Through the EPR study and simulations, we found rough connections between (a) enzyme mobility/dynamics and MOF crystal properties (packing quality and density) and (b) enzyme areas exposed above each MOF and their catalytic performance. This work suggests that protein SDSL and EPR can serve as an indicator of MOF crystal packing quality/density when biomineralized in MOFs. The method can be generalized to probing the dynamics of other enzymes on other solid surfaces/interfaces and guide the rational design of solid platforms (ca. MOFs) to customize enzyme immobilization.

An Up-to-Date Review on the Remediation of Dyes and Phenolic Compounds from Wastewaters Using Enzymes Immobilized on Emerging and Nanostructured Materials: Promises and Challenges

Addressing the critical issue of water pollution, this review article emphasizes the need to remove hazardous dyes and phenolic compounds from wastewater. These pollutants pose severe risks due to their toxic, mutagenic, and carcinogenic properties. The study explores various techniques for the remediation of organic contaminants from wastewater, including an enzymatic approach. A significant challenge in enzymatic wastewater treatment is the loss of enzyme activity and difficulty in recovery post-treatment. To mitigate these issues, this review examines the strategy of immobilizing enzymes on newly developed nanostructured materials like graphene, carbon nanotubes (CNTs), and metal-organic frameworks (MOFs). These materials offer high surface areas, excellent porosity, and ample anchoring sites for effective enzyme immobilization. The review evaluates recent research on enzyme immobilization on these supports and their applications in biocatalytic nanoparticles. It also analyzes the impact of operational factors (e.g., time, pH, and temperature) on dye and phenolic compound removal from wastewater using these enzymes. Despite promising outcomes, this review acknowledges the challenges for large-scale implementation and offers recommendations for future research to tackle these obstacles. This review concludes by suggesting that enzyme immobilization on these emerging materials could present a sustainable, environmentally friendly solution to the escalating water pollution crisis.

Multipoint Immobilization at Inert Center of Papain on Homo-Functional Diazo-Activated Silica Support: A Way of Restoring "Above Room-Temperature" Bio-Catalytic Sustainability

Although enzymes play a significant role in industrial applications, their potential usage at high-level efficiency, particularly above room temperature, has not yet been fully harnessed. It brings above room-temperature catalytic sustainability of an immobilized (imm.) bio-catalyst as a long pending issue to improve enzyme stability, activity, specificity, or selectivity, particularly the enantio-selectivity over the native-enzymes. At this juncture, in a robust methodology, a heterogeneous solid phase bio-catalyst, {Si(OSi)₄(H₂O)_1.03}_n=328{OSi(CH₃)₂-NH-C₆H₄-N═N}₄{papain}(H₂O)₂₅₁, has efficiently been prepared by immobilizing papain on homo-functionalized SG (silica-gel) via multipoint covalent attachment. The bio-catalyst is easy to be recovered and reused multiple times. The homo-functional -N═N⁺, which appears on the SG-surface, makes the multipoint diazo-links with the inert center of the tyrosine-moiety to couple the enzyme where all the amino, thiol, phenol, and so forth, groups of the protein, including those that belong to the active-site, remain intact. The immobilized enzyme (13.9 μmol g^-1) swims in pore-water within the pore-channel, remains stable up to 70 ± 5 °C, and exhibits wider temperature adaptability in performing its hydrolyzing activities. The relative activity, 78 ± 2% at 27 °C, remains quantitative for 60 days and can be reused for 60 cycles with 53% activity at room-temperature. The thermal (relative activity: 87%; incubated at 70 ± 5 °C for 24 h) and mechanical (relative activity: 92%; incubated at 2500 rpm for 2 h at 27 °C) stability was outstanding.

Unveiling the orientation and dynamics of enzymes in unstructured artificial compartments of metal-organic frameworks (MOFs)

Confining enzymes in well-shaped MOF compartments is a promising approach to mimic the cellular environment of enzymes and determine enzyme structure-function relationship therein. Under the cellular crowding, however, enzymes can also be confined in unstructured spaces that are close to the shapes/outlines of the enzyme. Therefore, for a better understanding of enzymes in their physiological environments, it is necessary to study enzymes in these unstructured spaces. However, practically it is challenging to create compartments that are close to the outline of an enzyme and probe enzyme structural information therein. Here, for proof-of-principle, we confined a model enzyme, lysozyme, in the crystal defects of a MOF via co-crystallization, where lysozyme served as the nuclei for MOF crystal scaffolds to grow on so that unstructured spaces close to the outline of lysozyme are created, and determined enzyme relative orientation and dynamics. This effort is important for understanding enzymes in near-native environments and guiding the rational design of biocatalysts that mimic how nature confines enzymes.

Metal-Organic Materials (MOMs) Enhance Proteolytic Selectivity, Efficiency, and Reusability of Trypsin: A Time-Resolved Study on Proteolysis

Proteases are involved in essential biological functions in nature and have become drug targets recently. In spite of the promising progress, two challenges, (i) the intrinsic instability and (ii) the difficulty in monitoring the catalytic process in real time, still hinder the further understanding and engineering of protease functionalities. These challenges are caused by the lack of proper materials/approaches to stabilize proteases and monitor proteolytic products (truncated polypeptides) in real time in a highly heterogeneous reaction mixture. This work combines metal-organic materials (MOMs), site-directed spin labeling-electron paramagnetic resonance (SDSL-EPR) spectroscopy, and mass spectrometry (MS) to overcome both barriers. A model protease, trypsin, which cleaves the peptide bonds at lysine or arginine residues, was immobilized on a Ca-MOM via aqueous-phase, one-pot cocrystallization, which allows for trypsin protection and ease of separation from its proteolytic products. Time-resolved EPR and MS were employed to monitor the populations, rotational motion, and sequences of the cleaved peptide truncations of a model protein substrate as the reaction proceeded. Our data suggest a significant (at least 5-10 times) enhancement in the catalytic efficiency (kcat/km) of trypsin@Ca-MOM and excellent reusability as compared to free trypsin in solution. Surprisingly, entrapping trypsin in Ca-MOMs results in cleavage site/region selectivity against the protein substrate, as compared to the near nonselective cleavage of all lysine and arginine residues of the substrate in solution. Remarkably, immobilizing trypsin allows for the separation and, thus, MS study on the sequences of truncated peptides in real time, leading to a time-resolved "movie" of trypsin proteolysis. This work demonstrates the use of MOMs and cocrystallization to enhance the selectivity, catalytic efficiency, and stability of trypsin, suggesting the possibility of tuning the catalytic performance of a general protease using MOMs.

Advances in the One-Step Approach of Polymeric Materials Using Enzymatic Techniques

The formulation in which biochemical enzymes are administered in polymer science plays a key role in retaining their catalytic activity. The one-step synthesis of polymers with highly sequence-controlled enzymes is a strategy employed to provide enzymes with higher catalytic activity and thermostability in material sustainability. Enzyme-catalyzed chain growth polymerization reactions using activated monomers, protein-polymer complexation techniques, covalent and non-covalent interaction, and electrostatic interactions can provide means to develop formulations that maintain the stability of the enzyme during complex material processes. Multifarious applications of catalytic enzymes are usually attributed to their efficiency, pH, and temperature, thus, progressing with a critical structure-controlled synthesis of polymer materials. Due to the obvious economics of manufacturing and environmental sustainability, the green synthesis of enzyme-catalyzed materials has attracted significant interest. Several enzymes from microorganisms and plants via enzyme-mediated material synthesis have provided a viable alternative for the appropriate synthesis of polymers, effectively utilizing the one-step approach. This review analyzes more and deeper strategies and material technologies widely used in multi-enzyme cascade platforms for engineering polymer materials, as well as their potential industrial applications, to provide an update on current trends and gaps in the one-step synthesis of materials using catalytic enzymes.

Development of Nanoscale Graphene Oxide Models for the Adsorption of Biological Molecules

Graphene oxide (GO), a nanomaterial with promising applications that range from water purification to enzyme immobilization, is actively present in scientific research since its discovery. GO studies with computational methodologies such as molecular dynamics are frequently reported in the literature; however, the models used often rely on approximations, such as randomly placing functional groups and the use of generalized force fields. Therefore, it is important to develop new MD models that provide a more accurate description of GO structures and their interaction with an aqueous solvent and other adsorbate molecules. In this paper, we derived new force field non-bonded parameters from linear-scaling density functional theory calculations of nanoscale GO sheets with more than 10,000 atoms through an atoms-in-molecules (AIM) partitioning scheme. The resulting GAFF2-AIM force field, derived from the bonded terms of GAFF2 parameterization, reproduces the solvent structure reported in ab initio MD simulations better than the force field nowadays widely used in the literature. Additionally, we analyzed the effect of the ionic strength of the medium and of the C/O ratio on the distribution of charges surrounding the GO sheets. Finally, we simulated the adsorption of natural amino acid molecules to a GO sheet and estimated their free energy of binding, which compared very favorably to their respective experimental values, validating the force field presented in this work.

Graphene-Based Metal-Organic Framework Hybrids for Applications in Catalysis, Environmental, and Energy Technologies

Current energy and environmental challenges demand the development and design of multifunctional porous materials with tunable properties for catalysis, water purification, and energy conversion and storage. Because of their amenability to de novo reticular chemistry, metal-organic frameworks (MOFs) have become key materials in this area. However, their usefulness is often limited by low chemical stability, conductivity and inappropriate pore sizes. Conductive two-dimensional (2D) materials with robust structural skeletons and/or functionalized surfaces can form stabilizing interactions with MOF components, enabling the fabrication of MOF nanocomposites with tunable pore characteristics. Graphene and its functional derivatives are the largest class of 2D materials and possess remarkable compositional versatility, structural diversity, and controllable surface chemistry. Here, we critically review current knowledge concerning the growth, structure, and properties of graphene derivatives, MOFs, and their graphene@MOF composites as well as the associated structure-property-performance relationships. Synthetic strategies for preparing graphene@MOF composites and tuning their properties are also comprehensively reviewed together with their applications in gas storage/separation, water purification, catalysis (organo-, electro-, and photocatalysis), and electrochemical energy storage and conversion. Current challenges in the development of graphene@MOF hybrids and their practical applications are addressed, revealing areas for future investigation. We hope that this review will inspire further exploration of new graphene@MOF hybrids for energy, electronic, biomedical, and photocatalysis applications as well as studies on previously unreported properties of known hybrids to reveal potential "diamonds in the rough".

Expanding the "Library" of Metal-Organic Frameworks for Enzyme Biomineralization

Metal-organic frameworks (MOFs) are advanced platforms for enzyme immobilization. Enzymes can be entrapped via either diffusion (into pre-formed MOFs) or co-crystallization. Enzyme co-crystallization with specific metals/ligands in the aqueous phase, also known as biomineralization, minimizes the enzyme loss compared to organic phase co-crystallization, removes the size limitation on enzymes and substrates, and can potentially broaden the application of enzyme@MOF composites. However, not all enzymes are stable/functional in the presence of excess metal ions and/or ligands currently available for co-crystallization. Furthermore, most current biomineralization-based MOFs have limited (acid) pH stability, making it necessary to explore other metal-ligand combinations that can also immobilize enzymes. Here, we report our discovery on the combination of five metal ions and two ligands that can form biocomposites with two model enzymes differing in size and hydrophobicity in the aqueous phase under ambient conditions. Surprisingly, most of the formed composites are single- or multiphase crystals, even though the reaction phase is aqueous, with the rest as amorphous powders. All 20 enzyme@MOF composites showed good to excellent reusability and were stable under weakly acidic pH values. The stability under weakly basic conditions depended upon the selection of enzyme and metal-ligand combinations, yet for both enzymes, 3-4 MOFs offered decent stability under basic conditions. This work initiates the expansion of the current "library" of metal-ligand selection for encapsulating/biomineralizing large enzymes/enzyme clusters, leading to customized encapsulation of enzymes according to enzyme stability, functionality, and optimal pH.

Amphiphilic Nanointerface: Inducing the Interfacial Activation for Lipase

Graphene-based materials are widely used in the field of immobilized enzymes due to their easily tunable interfacial properties. We designed amphiphilic nanobiological interfaces between graphene oxide (GO) and lipase TL (Thermomyces lanuginosus) with tunable reduction degrees through molecular dynamics simulations and a facile chemical modulation, thus revealing the optimal interface for the interfacial activation of lipase TL and addressing the weakness of lipase TL, which exhibits weak catalytic activity due to an inconspicuous active site lid. It was demonstrated that the reduced graphene oxide (rGO) after 4 h of ascorbic acid reduction could boost the relative enzyme activity of lipase TL to reach 208%, which was 48% higher than the pristine GO and 120% higher than the rGO after 48 h of reduction. Moreover, TL-GO-4 h's tolerance against heat, organic solvent, and long-term storage environment was higher than that of free TL. The drawbacks of strong hydrophobic nanomaterials on lipase production were explored in depth with the help of molecular dynamics simulations, which explained the mechanism of enzyme activity enhancement. We demonstrated that nanomaterials with certain hydrophilicity could facilitate the lipase to undergo interfacial activation and improve its stability and protein loading rate, displaying the potential of the extensive application.

Emerging 3D Printing Strategies for Enzyme Immobilization: Materials, Methods, and Applications

As the strategies of enzyme immobilization possess attractive advantages that contribute to realizing recovery or reuse of enzymes and improving their stability, they have become one of the most desirable techniques in industrial catalysis, biosensing, and biomedicine. Among them, 3D printing is the emerging and most potential enzyme immobilization strategy. The main advantages of 3D printing strategies for enzyme immobilization are that they can directly produce complex channel structures at low cost, and the printed scaffolds with immobilized enzymes can be completely modified just by changing the original design graphics. In this review, a comprehensive set of developments in the fields of 3D printing techniques, materials, and strategies for enzyme immobilization and the potential applications in industry and biomedicine are summarized. In addition, we put forward some challenges and possible solutions for the development of this field and some possible development directions in the future.

Updated results on the integration of metal-organic framework with functional materials toward n-alkane for latent heat retention and reliability

Phase change composites are in high demand in thermal management systems. Various supporting materials, including nanocomposites, have been employed to develop shape-stable phase change materials (PCMs). As the reliability of most composite materials has mostly been studied right after the preparation with specific thermal cycling measurements, it is difficult to analyze the long-term leakage-resistance capability and energy retention capacity. Additionally, achieving multifunctional phase change composites is a significant challenge for single supporting materials. Herein, we provide a follow-up report on the thermal performance of hybrid material-supported n-alkane after a storage time of one year and 50 heating/cooling cycles. The interconnected hybrid material composed of a metal-organic framework (MOF) and graphite improved the shape/thermal stability of tetradecane (TD). The as-synthesized MOF/graphite/TD composites exhibited a high latent heat retention capacity of 84.2%, low leakage rate of 1.25%, and high PCM loading capacity, making them suitable for thermal management applications, such as industrial waste heat recovery systems. Furthermore, the intermolecular interactions and capillary forces between the hybrid materials and TD provided high stability and compatibility. Therefore, the as-prepared hybrid material fabricated in this study can be important in the development of multidirectional composite PCMs with comprehensive thermal characteristics.

Rapid sample preparation workflow based on enzymatic nanoreactors for potential serum biomarker discovery in pancreatic cancer

Mass spectrometry (MS)-based proteomics have been extensively applied in clinical practice to discover potential protein and peptide biomarkers. However, the traditional sample pretreatment workflow remains labor-intensive and time-consuming, which limits the application of MS-based proteomic biomarker discovery studies in a high throughput manner. In the current work, we improved the previously reported procedure of the simple and rapid sample preparation methods (RSP) by introducing macroporous ordered siliceous foams (MOSF), namely RSP-MOSF. With the aid of MOSF, we further reduced the digestion time to 10 min, facilitating the whole sample handling process within 30 min. Combining with 30 min direct data independent acquisition (DIA) of LC-MS/MS, we accomplished a serum sample analysis in 1 h. Comparing with the RSP method, the performance of protein and peptide identification, quantitation, as well as the reproducibility of RSP-MOSF is comparable or even outperformed the RSP method. We further applied this workflow to analyze serum samples for potential candidate biomarker discovery of pancreatic cancer. Overall, 576 serum proteins were detected with 41 proteins significantly changed, which could serve as potential biomarkers for pancreatic cancer. Additionally, we evaluated the performance of RSP-MOSF method in a 96-well plate format which demonstrated an excellent reproducibility of the analysis. These results indicated that RSP-MOSF method had the potential to be applied on an automatic platform for further scaled analysis.

De Novo Approach to Encapsulating Biocatalysts into Synthetic Matrixes: From Enzymes to Microbial Electrocatalysts

Biocatalysts hold great promise in chemical and electrochemical reactions. However, biocatalysts are prone to inhospitable physiochemical conditions. Encapsulating biocatalysts into a synthetic host matrix can improve their stability and activity, and broaden their operational conditions. In this Review, we summarize the emerging de novo approaches to encapsulating biocatalysts into synthetic matrixes. Here, de novo means that embedding of biocatalysts and construction of matrixes take place simultaneously. We discuss the advantages and limitations of the de novo approach. On the basis of the nature of the biocatalysts and the synthetic frameworks, we specifically focus on two aspects: (1) encapsulation of enzymes (in vitro) in metal-organic frameworks and (2) encapsulation of microbial electrocatalysts (in vivo) on the electrode. For both cases, we discuss how the encapsulation improves biocatalysts' performance (stability, viability, activity, and etc.). We also highlight the benefit of encapsulation in facilitating the transport of charge carriers in microbial electrocatalysis.

Current Status and Future Perspectives of Supports and Protocols for Enzyme Immobilization

The market for industrial enzymes has witnessed constant growth, which is currently around 7% a year, projected to reach $10.5 billion in 2024. Lipases are hydrolase enzymes naturally responsible for triglyceride hydrolysis. They are the most expansively used industrial biocatalysts, with wide application in a broad range of industries. However, these biocatalytic processes are usually limited by the low stability of the enzyme, the half-life time, and the processes required to solve these problems are complex and lack application feasibility at the industrial scale. Emerging technologies create new materials for enzyme carriers and sophisticate the well-known immobilization principles to produce more robust, eco-friendlier, and cheaper biocatalysts. Therefore, this review discusses the trending studies and industrial applications of the materials and protocols for lipase immobilization, analyzing their advantages and disadvantages. Finally, it summarizes the current challenges and potential alternatives for lipases at the industrial level.

Cascade/Parallel Biocatalysis via Multi-enzyme Encapsulation on Metal-Organic Materials for Rapid and Sustainable Biomass Degradation

Multiple-enzyme cooperation simultaneously is an effective approach to biomass conversion and biodegradation. The challenge, however, lies in the interference of the involved enzymes with each other, especially when a protease is needed, and thus, the difficulty in reusing the enzymes; while extracting/synthesizing new enzymes costs energy and negative impact on the environment. Here, we present a unique approach to immobilize multiple enzymes, including a protease, on a metal-organic material (MOM) via co-precipitation in order to enhance the reusability and sustainability. We prove our strategy on the degradation of starch-containing polysaccharides (require two enzymes to degrade) and food proteins (require a protease to digest) before the quantification of total dietary fiber. As compared to the widely adopted "official" method, which requires the sequential addition of three enzymes under different conditions (pH/temperature), the three enzymes can be simultaneously immobilized on the surface of our MOM crystals to allow for contact with the large substrates (starch), while MOMs offer sufficient protection to the enzymes so that the reusability and long-term storage are improved. Furthermore, the same biodegradation can be carried out without adjusting the reaction condition, further reducing the reaction time. Remarkably, the simultaneous presence of all enzymes enhances the reaction efficiency by a factor of ∼3 as compared to the official method. To our best knowledge, this is the first experimental demonstration of using aqueous-phase co-precipitation to immobilize multiple enzymes for large-substrate biocatalysis. The significantly enhanced efficiency can potentially impact the food industry by reducing the labor requirement and enhancing enzyme cost efficiency, leading to reduced food cost. The reduced energy cost of extracting enzymes and adjusting reaction conditions minimize the negative impact on the environment. The strategy to prevent protease damage in a multi-enzyme system can be adapted to other biocatalytic reactions involving proteases.

Protocol for resolving enzyme orientation and dynamics in advanced porous materials via SDSL-EPR

Enzyme encapsulation in metal-organic frameworks (MOFs)/covalent-organic frameworks (COFs) provides advancement in biocatalysis, yet the structural basis underlying the catalytic performance is challenging to probe. Here, we present an effective protocol to determine the orientation and dynamics of enzymes in MOFs/COFs using site-directed spin labeling and electron paramagnetic resonance spectroscopy. The protocol is demonstrated using lysozyme and can be generalized to other enzymes.

For complete information on the generation and use of this protocol, please refer to Pan et al. (2021a).

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A protocol to resolve protein orientation/dynamics in porous materials is provided

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Site-directed spin labeling is combined with electron paramagnetic resonance

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Principles of protein labeling and key data acquisition steps are summarized

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Spectral simulation details with troubleshooting procedures are detailed

Metal-organic frameworks as advanced materials for sample preparation of bioactive peptides

Development of novel affinity materials and separation techniques is crucial for the progress of modern proteomics and peptidomics. Detection of peptides and proteins from complex matrices still remains a challenging task due to the highly complicated biological composition, low abundance of target molecules, and large dynamic range of proteins. As an emerging area of analytical science, metal-organic framework (MOF)-based separation of proteins and peptides is attracting growing interest. This minireview summarizes the recent advances in MOF-based affinity materials for the sample preparation of proteins and peptides. Some newly emerging MOF nanoreactors for the degradation of peptides and proteins are introduced. An update of MOF-based affinity materials for the isolation of glycopeptides, phosphopeptides and low-abundance endogenous peptides in the last two years is focused on. The separation mechanism is discussed along with the chemical structures of MOFs. Finally, the remaining challenges and future development of MOFs in analyzing peptides and proteins in complicated biological samples are discussed.

Size-Tunable Metal-Organic Framework-Coated Magnetic Nanoparticles for Enzyme Encapsulation and Large-Substrate Biocatalysis

Immobilizing enzymes on nanoparticles (NPs) enhances the cost-efficiency of biocatalysis; however, when the substrates are large, it becomes difficult to separate the enzyme@NP from the products while avoiding leaching or damage of enzymes in the reaction medium. Metal-organic framework (MOF)-coated magnetic NPs (MNPs) offer efficient magnetic separation and enhanced enzyme protection; however, the involved enzymes/substrates have to be smaller than the MOF apertures. A potential solution to these challenges is coprecipitating metal/ligand with enzymes on the MNP surface, which can partially bury (protect) the enzyme below the composite surface while exposing the rest of the enzyme to the reaction medium for catalysis of larger substrates. Here, to prove this concept, we show that using Ca²⁺ and terephthalic acid (BDC), large-substrate enzymes can be encapsulated in CaBDC-MOF layers coated on MNPs via an enzyme-friendly, aqueous-phase one-pot synthesis. Interestingly, we found that using MNPs as the nuclei of crystallization, the composite size can be tuned so that nanoscale composites were formed under low Ca²⁺/BDC concentrations, while microscale composites were formed under high Ca²⁺/BDC concentrations. While the microscale composites showed significantly enhanced reusability against a non-structured large substrate, the nanoscale composites displayed enhanced catalytic efficiency against a rigid, crystalline-like large substrate, starch, likely due to the improved diffusivity of the nanoscale composites. To our best knowledge, this is the first report on aqueous-phase one-pot synthesis of size-tunable enzyme@MOF/MNP composites for large-substrate biocatalysis. Our platform can be applied to immobilize other large-substrate enzymes with enhanced reusability and tunable sizes.