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

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.

Unravelling the Potential of Crude Enzyme Extracts for Biocatalyst Entrapment in Metal-Organic Frameworks

To bolster the applicability of enzymes as catalysts, it is imperative not only to address their inherent fragility, particularly when used under harsh organic-synthetic reaction conditions, but also to mitigate deactivation during purification and enable applicability in a broad range of organic-synthetic transformations. Currently, the process of purification of crude enzyme extracts and subsequent heterogenization to obtain immobilized biocatalysts often leads to partial enzyme deactivation and represents, at least in part, a resource-intensive process that is driving up the overall production efforts. To tackle both the enzyme fragility and deactivation during purification and immobilization, we propose the direct use of crude enzyme extracts obtained from cell lysis instead of pure enzymes and their entrapment in metal-organic framework (MOF) structures. We focus on three enzyme types with varying sensitivities: aldoxime dehydratase, imine reductase, and lipase. We evaluate the effects of different metal sources (Al, Fe, Co, Ni, Cu, and Zn), their oxidation state and counterions, and MOF synthesis parameters on enzyme stability and activity during their entrapment in the MOF structures. Based on this, we optimize protocols for enzyme entrapment in Fe-MIL-88A, Fe-MIL-100, Zn-MOF-74, and Zn-ZIF-8 and develop a fast-aqueous room temperature synthesis of Al-MIL-53. Investigation of the biocatalytic performance of the enzyme@MOF biocomposites suggests that enzyme entrapment in MOFs using crude enzyme extracts can effectively maintain enzyme activity and stability in various catalytic reactions, offering a perspective for an efficient pathway for industrial applications.

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.

One-step biomineralization to synthesize reusable CRL@ZnCo-MOF for boosting lipase stability and sustainable dibutyl phthalate removal

Adsorption and biodegradation are two important means to remove the pollutants from the environment, but how to combine them and improve the catalytic performance and stability of free enzyme are facing great challenges. Herein, lipase from Candida rugosa (CRL) was immobilized into bimetallic ZnCo-MOF by biomineralization, which not only significantly improved the catalytic activity and stability of CRL but also endowed it with excellent reusability. Furthermore, CRL@ZnCo-MOF established a synergetic system of combined adsorption and enzymatic degradation for the sustainable removal of dibutyl phthalate (DBP) in actual water environment. The adsorption of DBP by CRL@ZnCo-MOF with mesoporous structure is mainly carried out by the monolayer adsorption via chemical adsorption, wherein the interaction between them is predominantly mediated by the hydrogen bonds and coordination bonds of MOF and DBP. Moreover, due to the ester bond cleavage ability of CRL, the DBP was degradated to less toxic monobutyl phthalate (MBP) and phthalic acid (PA) by CRL@ZnCo-MOF. Therefore, this study provides new insights into the development of novel approaches for the treatment of pollutants using enzyme@MOF biocomposite through the integration of adsorption-biodegradation effect.

Screening of Aluminum-Based MOFs for Effective In Situ Immobilization of Biomolecules

An effective approach for the immobilization and protection of biological entities is their encapsulation via the in situ synthesis of metal-organic frameworks (MOFs). To ensure the preservation of the bioentities, mild synthetic conditions, including aqueous media and ambient conditions (temperature and pressure), are preferred. In this study, we investigated the synthesis of various aluminum polycarboxylate-based MOFs, including the fumarate, terephthalate, amino-terephthalate, and muconate forms of MIL-53(Al), as well as the MIL-110 and MIL-160 MOF types. The potential as immobilization matrices was then assessed using bovine serum albumin (BSA). Finally, MIL-53(Al)-fum was selected for the encapsulation of a mixture of polysaccharides and more structurally complex bioentities (viruses).

Confinement-Induced Biocatalytic Activity Enhancement of Light- and Thermoresponsive Polymer@Enzyme@MOF Composites

Metal-organic frameworks (MOFs) are favorable hosting materials for fixing enzymes to construct enzyme@MOF composites and to expand the applications of biocatalysts. However, the rigid structure of MOFs without tunable hollow voids and a confinement effect often limits their catalytic activities. Taking advantage of the smart soft polymers to overcome the limitation, herein, a protection protocol to encapsulate the enzyme in zeolitic imidazolate framework-8 (ZIF-8) was developed using a glutathione-sensitive liposome (L) as a soft template. Glucose oxidase (GOx) and horseradish peroxidase (HRP) were first anchored on a light- and thermoresponsive porous poly(styrene-maleic anhydride-N,N-dimethylaminoethyl methacrylate-spiropyran) membrane (PSMDSP) to produce PSMDSP@GOx-HRP, which could provide a confinement effect by switching the UV irradiation or varying the temperature. Afterward, embedding PSMDSP@GOx-HRP in L and encapsulating PSMDSP@GOx-HRP@L into hollow ZIF-8 (HZIF-8) to form PSMDSP@GOx-HRP@HZIF-8 composites were performed, which proceeded during the crystallization of the framework following the removal of L by adding glutathione. Impressively, the biocatalytic activity of the composites was 4.45-fold higher than that of the free enzyme under UV irradiation at 47 °C, which could benefit from the confinement effect of PSMDSP and the conformational freedom of the enzyme in HZIF-8. The proposed composites contributed to the protection of the enzyme against harsh conditions and exhibited superior stability. Furthermore, a colorimetric assay based on the composites for the detection of serum glucose was established with a linearity range of 0.05-5.0 mM, and the calculated LOD value was 0.001 mM in a cascade reaction system. This work provides a universal design idea and a versatile technique to immobilize enzymes on soft polymer membranes that can be encapsulated in porous rigid MOF-hosts. It also holds potential for the development of smart polymer@enzyme@HMOFs biocatalysts with a tunable confinement effect and high catalytic performance.

Amino Functionality Enables Aqueous Synthesis of Carboxylic Acid-Based MOFs at Room Temperature by Biomimetic Crystallization

Enzyme immobilization within metal-organic frameworks (MOFs) is a promising solution to avoid denaturation and thereby utilize the desirable properties of enzymes outside of their native environments. The biomimetic mineralization strategy employs biomacromolecules as nucleation agents to promote the crystallization of MOFs in water at room temperature, thus overcoming pore size limitations presented by traditional postassembly encapsulation. Most biomimetic crystallization studies reported to date have employed zeolitic imidazole frameworks (ZIFs). Herein, we expand the library of MOFs suitable for biomimetic mineralization to include zinc(II) MOFs incorporating functionalized terephthalic acid linkers and study the catalytic performance of the enzyme@MOFs. Amine functionalization of terephthalic acids is shown to accelerate the formation of crystalline MOFs enabling new enzyme@MOFs to be synthesized. The structure and morphology of the enzyme@MOFs were characterized by PXRD, FTIR, and SEM-EDX, and the catalytic potential was evaluated. Increasing the linker length while retaining the amino moiety gave rise to a family of linkers; however, MOFs generated with the 2,2'-aminoterephthalic acid linker displayed the best catalytic performance. Our data also illustrate that the pH of the reaction mixture affects the crystal structure of the MOF and that this structural transformation impacts the catalytic performance of the enzyme@MOF.

Immobilized Dipeptidase in Manganese Ion-Loaded Polyethylenimine-Induced Calcium Phosphate Nanocrystals for Carnosine Synthesis

Carnosine is a natural bioactive dipeptide with important physiological functions widely used in food and medicine. Dipeptidase (PepD) from Serratia marcescens can catalyze the reverse hydrolytic reaction of β-alanine with l-histidine to synthesize carnosine in the presence of Mn2+. However, it remains challenging to practice carnosine biosynthesis due to the low activity and high cost of the enzyme. Therefore, the development of biocatalysts with high activity and stability is of significance for carnosine synthesis. Here, we proposed to chelate Mn2+ to polyethylenimine (PEI) that induced rapid formation of calcium phosphate nanocrystals (CaP), and Mn-PEI@CaP was used for PepD immobilization via electrostatic interaction. Mn-PEI@CaP as the carrier enhanced the stability of the immobilized enzyme. Moreover, Mn2+ loaded in the carrier acted as an in situ activator of the immobilized PepD for facilitating the biocatalytic process of carnosine synthesis. The as-prepared immobilized enzyme (PepD-Mn-PEI@CaP) kept similar activity with free PepD plus Mn2+ (activity recovery, 102.5%), while exhibiting elevated thermal stability and pH tolerance. Moreover, it exhibited about two times faster carnosine synthesis than the free PepD system. PepD-Mn-PEI@CaP retained 86.8% of the original activity after eight cycles of batch catalysis without the addition of free Mn2+ ions during multiple cycles. This work provides a new strategy for the co-immobilization of PepD and Mn2+, which greatly improves the operability of the biocatalysis and demonstrates the potential of the immobilized PepD system for efficient carnosine synthesis.

The Promise and Potential of Metal-Organic Frameworks and Covalent Organic Frameworks in Vaccine Nanotechnology

The immune system's complexity and ongoing evolutionary struggle against deleterious pathogens underscore the value of vaccination technologies, which have been bolstering human immunity for over two centuries. Despite noteworthy advancements over these 200 years, three areas remain recalcitrant to improvement owing to the environmental instability of the biomolecules used in vaccines─the challenges of formulating them into controlled release systems, their need for constant refrigeration to avoid loss of efficacy, and the requirement that they be delivered via needle owing to gastrointestinal incompatibility. Nanotechnology, particularly metal-organic frameworks (MOFs) and covalent organic frameworks (COFs), has emerged as a promising avenue for confronting these challenges, presenting a new frontier in vaccine development. Although these materials have been widely explored in the context of drug delivery, imaging, and cancer immunotherapy, their role in immunology and vaccine-related applications is a recent yet rapidly developing field. This review seeks to elucidate the prospective use of MOFs and COFs for biomaterial stabilization, eliminating the necessity for cold chains, enhancing antigen potency as adjuvants, and potentializing needle-free delivery of vaccines. It provides an expansive and critical viewpoint on this rapidly evolving field of research and emphasizes the vital contribution of chemists in driving further advancements.

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.

Hollow Hierarchical Porous and Antihydrolytic Spherical Zeolitic Imidazolate Frameworks for Enzyme Encapsulation and Biocatalysis

The creation of a new metal-organic framework (MOF) with a hollow hierarchical porous structure has gained significant attention in the realm of enzyme immobilization. The present work employed a novel, facile, and effective combinatorial technique to synthesize modified MOF (N-PVP/HZIF-8) with a hierarchically porous core-shell structure, allowing for the preservation of the structural integrity of the encapsulated enzyme molecules. Scanning electron microscopy, X-ray diffraction, X-ray photoelectron spectroscopy, confocal laser scanning microscopy, and other characterization tools were used to fully explore the changes of morphological structure and surface properties in different stages of the preparation of immobilization enzyme CRL-N-PVP/HZIF-8, thus showing the superiority of N-PVP/HZIF-8 as an enzyme immobilization platform and the logic of the immobilization process on the carrier. Additionally, the maximum enzyme loading was 216.3 mg mL-1, the relative activity of CRL-N-PVP/HZIF-8 increased by 15 times compared with the CRL@ZIF-8 immobilized in situ, and exhibited quite good thermal, chemical, and operational stability. With a maximal conversion of 88.8%, CRL-N-PVP/HZIF-8 demonstrated good catalytic performance in the biosynthesis of phytosterol esters as a proof of concept. It is anticipated that this work will offer fresh concepts from several perspectives for the creation of MOF-based immobilized enzymes for biotechnological uses.

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.

A Protocol to Depict the Proteolytic Processes Using a Combination of Metal-Organic Materials (MOMs), Electron Paramagnetic Resonance (EPR), and Mass Spectrometry (MS)

Proteolysis is a critical biochemical process yet a challenging field to study experimentally due to the self-degradation of a protease and the complex, dynamic degradation steps of a substrate. Mass spectrometry (MS) is the traditional way for proteolytic studies, yet it is challenging when time-resolved, step-by-step details of the degradation process are needed. We recently found a way to resolve the cleavage site, preference/selectivity of cleavage regions, and proteolytic kinetics by combining site-directed spin labeling (SDSL) of protein substrate, time-resolved two-dimensional (2D) electron paramagnetic resonance (EPR) spectroscopy, protease immobilization via metal-organic materials (MOMs), and MS. The method has been demonstrated on a model substrate and protease, yet there is a lack of details on the practical operations to carry out our strategy. Thus, this protocol summarizes the key steps and considerations when carrying out the EPR/MS study on proteolytic processes, which can be generalized to study other protein/polypeptide substrates in proteolysis. Details for the experimental operation and cautions of each step are reported with figures illustrating the concepts. This protocol provides an effective approach to understanding the proteolytic process with the advantages of offering time-resolved, residue-level resolution of structural basis underlying the process. Such information is important for revealing the cleavage site and proteolytic mechanisms of unknown proteases. The advantage of EPR, probing the target substrate regardless of the complexities caused by the proteases and their self-degradation, offers a practically effective, rapid, and easy-to-operate approach to studying proteolysis. Key features • Combining protease immobilization, EPR, spin labeling, and MS experimental methods allows for the analysis of proteolysis process in real time. • Reveals cleavage site, kinetics of product generation, and preference of cleavage regions via time-resolved SDSL-EPR. • MS confirms EPR findings and helps depict the sequences and populations of the cleaved segments in real time. • The demonstrated method can be generalized to other proteins or polypeptide substrates upon proteolysis by other proteases.

Alternative protein encapsulation with MOFs: overcoming the elusive mineralization of HKUST-1 in water

Protein encapsulation by in situ formation of MOFs is a valuable strategy to immobilise and protect these bioentities. However the required biocompatible conditions limits the scope of MOFs under investigation, particularly in the case of hydrolytically unstable MOFs such as HKUST-1. We report alternative synthetic procedures to obtain protein@HKUST-1 biocomposites from related Cu-BTC dense biocomposites. pH dependent dense phase precursors are first obtained and their transformations into HKUST-1 are characterized. Encapsulation efficiency is affected by the protein's nature, and can be modulated by the sequential or simultaneous addition of MOF precursors.

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.

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.