Atomistic Simulation of Protein Encapsulation in Metal–Organic Frameworks

Enhancing Multi-Enzyme Cascade Activity in Metal-Organic Frameworks via Controlled Enzyme Encapsulation

To position multi-enzymes in a core-shell structure, the conventional layer-by-layer approach is often used. However, this method is time-consuming and complex, requiring multiple steps and the isolation of intermediates at each stage. To address this challenge, a sequential strategy is introduced for the controlled encapsulation of multi-enzymes within metal-organic frameworks (MOFs), achieving a core-shell structure without the need for intermediate isolation. Synchrotron Terahertz-Far-Infrared (THz-Far-IR) spectroscopy is employed to monitor this encapsulation process. The results revealed that the first enzyme is co-precipitated within the MOFs, followed by biomineralization upon the addition of a second enzyme, achieving distinct enzyme positioning. This approach is applicable to both two-enzyme and three-enzyme cascade systems. The results demonstrate that multi-enzyme cascade activity is significantly enhanced compared to conventional one-pot and layer-by-layer approaches, owing to optimal spatial arrangement, increased surface area, and improved enzyme conformation. Furthermore, the encapsulated enzymes exhibit strong resistance to high temperatures, proteolysis, and organic solvents, along with excellent reusability, making this method highly promising for industrial biocatalytic applications.

Unraveling the orientation of an enzyme adsorbed onto a metal-organic framework

Bio-conversion of lignocellulosic biomass to bioethanol fuel is a highly desirable yet challenging objective because of the low catalytic activity and high cost of β-glucosidase (BGL). Recently, ZIF-8, an emerging organic porous material, has been proposed as a promising candidate for enzyme immobilization to improve associated activity and stability. However, the underlying interaction mechanism of binding BGL on the ZIF-8 surface is yet to be clarified. Here, the adsorption of BGL onto ZIF-8 is explored for the first time by molecular dynamics simulations. The results show that BGL adsorbs on the ZIF-8 surface with a "back-on" orientation. The adsorption free energy analysis shows that the adsorption process is enthalpy driven. In addition, the electrostatic interaction between negatively charged residues and Zn2+ on the surface of ZIF-8 is found to play a decisive role in surface binding, which accounts for 98% of the total interaction energy. The secondary structure of BGL is not affected despite the strong adsorption, suggesting the good biocompatibility of ZIF-8. This study not only provides a reliable theoretical insight into understanding the interaction mechanism between BGL and ZIF-8, but also helps the rational design of ZIF-8-based materials for bio-related applications.

Lab-on-the-Needles: A Microneedle Patch-Based Mobile Unit for Highly Sensitive Ex Vivo and In Vivo Detection of Protein Biomarkers

Detection of biomarkers associated with physiological conditions provides critical insights into healthcare and disease management. However, challenges in sampling and analysis complicate the detection and quantification of protein biomarkers within the epidermal layer of the skin and in viscous liquid biopsy samples. Here, we present the "Lab-on-the-Needles" concept, utilizing a microneedle patch-based sensing box (MNP-based SenBox) for mobile healthcare applications. This system facilitates the rapid capture of protein biomarkers directly from the in situ epidermal layer of skin or liquid biopsies, followed by on-needle analysis for immediate assessment. The integration of horseradish peroxidase-incorporated zeolitic imidazolate framework-8 (HRP@ZIF-8) as a sensitive and stable signal probe, the detection limit for anti-SARS-CoV-2 NP IgA antibodies and various SARS-CoV-2 S1P mutant strains improves by at least 1,000-fold compared to FDA-approved commercial saliva lateral flow immune rapid tests. Additionally, the MNP-based SenBox demonstrated minimally invasive monitoring and rapid quantification of inflammatory cytokine levels (TNF-α and IL-1β) in rats within 30 min using a portable ColorReader. This study highlights the potential of the MNP-based SenBox for the minimally invasive collection and analysis of protein biomarkers directly from in situ epidermal layers of skin or liquid biopsies that might facilitate mobile healthcare diagnostics and longitudinal monitoring.

HP35 Protein in the Mesopore of MIL-101(Cr) MOF: A Model to Study Cotranslocational Unfolding

The immobilization of enzymes in metal-organic framework (MOF) cages is important in biotechnology. In this context, the mechanism of translocation of proteins through the cavities of the MOF and the roles played by confinement and MOF chemistry in giving rise to stable protein intermediates that are otherwise transiently populated in the physiological environment are important questions to be addressed. These unexplored aspects are examined with villin headpiece (HP35) as a model protein confined within a mesopore of MIL-101(Cr) using molecular dynamics simulations. At equilibrium, the protein is located farther from the center of the cavity and closer to the MOF surface. Molecular interactions with the MOF partially unfold helix-1 at its N-terminus. Umbrella sampling simulations inform the range of conformations that HP35 undertakes during translocation from one cavity to another and associated changes in free energy. Relative to its equilibrium state within the cavity, the free energy barrier for the unfolded protein at the cage window is estimated to be 16 kcal/mol. This study of MOF-based protein conformation can also be a general approach to observing intermediates in folding-unfolding pathways.

In-silico study of drug delivery to atherosclerosis in the human carotid artery using metal-organic frameworks based on adhesion of nanocarriers

This study investigates nanocarriers (NCs) for drug delivery targeting carotid artery atherosclerosis. This targeted drug delivery mechanism is based on ligand-receptor bindings facilitated by coating NCs with P-selectin aptamers, which exhibit high affinities for P-selectin plaque receptors. Recognizing the significant advantages of metal-organic frameworks (MOFs), such as their high drug-loading percentages, we chose them as nanocarriers for this research. Our evaluation considers critical factors: NC surface density (the number of attached nanocarriers per unit of plaque area), toxicity (percentage of NCs missing the target), and efficient drug transfer to plaque tissue. Employing molecular dynamics (MD) for drug loading calculations via van der Waals interactions and computational fluid dynamics (CFD) for toxicity, surface density, and drug transfer assessments, we achieve a comprehensive analysis. A cardiac cycle-based metric guides optimal MOF release conditions, establishing an ideal dosage of 600 NCs per cycle. MOF-801 exhibits outstanding drug delivery performance, particularly in plaque targeting. While a magnetic field enhances NC adhesion, its impact on drug transfer is limited, emphasizing the need for further optimization in magnetic targeting for NC-based therapies. This study provides crucial insights into NC drug delivery performance in carotid artery atherosclerosis, advancing the field of targeted drug delivery for atherosclerosis treatment.

Reticular Synthesis of Highly Crystalline Three-Dimensional Mesoporous Covalent-Organic Frameworks for Lipase Inclusion

The synthesis and application of three-dimensional (3D) mesoporous covalent-organic frameworks (COFs) are still to be developed. Herein, two mesoporous 3D COFs with an stp topology were synthesized in a highly crystalline form with aniline as the modulator. The chemical composition of these COFs was confirmed by Fourier transform infrared (FT-IR) and 13C cross-polarization magic angle spinning nuclear magnetic resonance (NMR) spectroscopies. These 3D mesoporous COFs were highly crystalline and exhibited permanent porosity and good chemical stability in both aqueous and organic media. The space group and unit cell parameters of COF HFPTP-TAE were verified by powder X-ray diffraction (PXRD), small-angle X-ray scattering, and three-dimensional electron diffraction (3D ED). The appropriate pore size of the COF HFPTP-TAE facilitated the inclusion of enzyme lipase PS with a loading amount of 0.28 g g-1. The lipase⊂HFPTP-TAE (⊂ refers to "include in") composite exhibited high catalytic activity, good thermal stability, and a wide range of solvent tolerance. Specifically, it could catalyze the alcoholysis of aspirin methyl ester (AME) with high catalytic efficiency. Oriented one-dimensional (1D) channel mesopores in HFPTP-TAE accommodated lipase, meanwhile preventing them from aggregation, while windows on the wall of the 1D channel favored molecular diffusion; thus, this COF-enzyme design outperformed its amorphous isomer, two-dimensional (2D) mesoporous COF, 3D mesoporous COF with limited crystallinity, and mesoporous silica as an enzyme host.

Locking the Ultrasound-Induced Active Conformation of Metalloenzymes in Metal-Organic Frameworks

Enhancing the enzymatic activity inside metal-organic frameworks (MOFs) is a critical challenge in chemical technology and bio-technology, which, if addressed, will broaden their scope in energy, food, environmental, and pharmaceutical industries. Here, we report a simple yet versatile and effective strategy to optimize biocatalytic activity by using MOFs to rapidly "lock" the ultrasound (US)-activated but more fragile conformation of metalloenzymes. The results demonstrate that up to 5.3-fold and 9.3-fold biocatalytic activity enhancement of the free and MOF-immobilized enzymes could be achieved compared to those without US pretreatment, respectively. Using horseradish peroxidase as a model, molecular dynamics simulation demonstrates that the improved activity of the enzyme is driven by an opened gate conformation of the heme active site, which allows more efficient substrate binding to the enzyme. The intact heme active site is confirmed by solid-state UV-vis and electron paramagnetic resonance, while the US-induced enzyme conformation change is confirmed by circular dichroism spectroscopy and Fourier-transform infrared spectroscopy. In addition, the improved activity of the biocomposites does not compromise their stability upon heating or exposure to organic solvent and a digestion cocktail. This rapid locking and immobilization strategy of the US-induced active enzyme conformation in MOFs gives rise to new possibilities for the exploitation of highly efficient biocatalysts for diverse applications.

Multipoint Hydrogen Bonding-Based Molecular Recognition of Amino Acids and Peptide Derivatives in a Porous Metal-Macrocycle Framework: Residue-Specificity, Diastereoselectivity, and Conformational Control

Porous crystals have great potential to exert space-specific functions such as multipoint molecular recognition. In order to rationally enhance the porous function, it is necessary to precisely control molecular recognition event in the pores. Hydrogen bonding is an effective tool for controlling molecular recognition. However, multiple hydrogen bonds, which are essentially the origin of high complementarity and specificity, remain difficult to innovate in porous crystals in an intelligent way. This paper demonstrates molecular recognition of amino acid and peptide derivatives by multipoint hydrogen bonding in a porous metal-macrocycle framework revealed by single-crystal X-ray diffraction analysis. l-Serine residues are site-selectively and residue-specifically adsorbed on the pore surface via multiple hydrogen bonds. A serine derivative is diastereoselectively recognized on the (P)- or (M)-side of the enantiomeric pore surface. Moreover, the conformation of the peptide is highly regulated, incorporating a poly-l-proline type I helix-like structure into the pore. These findings will bring deep scientific knowledge to the design of new porous crystals and functions.

Metal-Organic Frameworks for Liquid Phase Applications

In the last two decades, metal-organic frameworks (MOFs) have attracted overwhelming attention. With readily tunable structures and functionalities, MOFs offer an unprecedentedly vast degree of design flexibility from enormous number of inorganic and organic building blocks or via postsynthetic modification to produce functional nanoporous materials. A large extent of experimental and computational studies of MOFs have been focused on gas phase applications, particularly the storage of low-carbon footprint energy carriers and the separation of CO2-containing gas mixtures. With progressive success in the synthesis of water- and solvent-resistant MOFs over the past several years, the increasingly active exploration of MOFs has been witnessed for widespread liquid phase applications such as liquid fuel purification, aromatics separation, water treatment, solvent recovery, chemical sensing, chiral separation, drug delivery, biomolecule encapsulation and separation. At this juncture, the recent experimental and computational studies are summarized herein for these multifaceted liquid phase applications to demonstrate the rapid advance in this burgeoning field. The challenges and opportunities moving from laboratory scale towards practical applications are discussed.

Lysozyme Adsorption on Porous Organic Cages: A Molecular Simulation Study

Recently, porous organic cages (POCs) have emerged as a novel porous material with many merits and are widely utilized in many application fields. In this work, for the first time, molecular dynamics simulations were performed to investigate the mechanism of lysozyme adsorption onto the CC3 crystal, a kind of widely studied POC material. The simulation results show that lysozyme adsorbs onto the surface of CC3 with "top end-on," "back-on," or "side-on" orientations. It is found that the van der Waals interaction is the primary contribution to the binding; the conformation of the lysozyme is well preserved during the adsorption process. This provides some evidence for its biocompatibility and feasibility in biorelated applications. Arginine plays an important role in mediating the adsorption through nonpolar aliphatic chains. More importantly, the distribution and structure of the water layer on the POC surface has a significant impact on adsorption. This study provides insights into the development of POC materials with defined morphologies for the adsorption of biomolecules and may help the rational design of biorelated systems.

Metal-organic frameworks for precise inclusion of single-stranded DNA and transfection in immune cells

Effective transfection of genetic molecules such as DNA usually relies on vectors that can reversibly uptake and release these molecules, and protect them from digestion by nuclease. Non-viral vectors meeting these requirements are rare due to the lack of specific interactions with DNA. Here, we design a series of four isoreticular metal-organic frameworks (Ni-IRMOF-74-II to -V) with progressively tuned pore size from 2.2 to 4.2 nm to precisely include single-stranded DNA (ssDNA, 11–53 nt), and to achieve reversible interaction between MOFs and ssDNA. The entire nucleic acid chain is completely confined inside the pores providing excellent protection, and the geometric distribution of the confined ssDNA is visualized by X-ray diffraction. Two MOFs in this series exhibit excellent transfection efficiency in mammalian immune cells, 92% in the primary mouse immune cells (CD4+ T cell) and 30% in human immune cells (THP-1 cell), unrivaled by the commercialized agents (Lipo and Neofect).

Non-viral vectors are important for transfection but can be limited in the uptake, protection and release of ssDNA. Here, the authors report on the design of metal-organic-framework vectors with precisely controlled pore geometry and demonstrate the vector in the transfection of immune cells.

A facile strategy for enzyme immobilization with highly stable hierarchically porous metal-organic frameworks

Metal-organic frameworks (MOFs) have drawn extensive research interest as candidates for enzyme immobilization owing to their tunable porosity, high surface area, and excellent chemical/thermal stability. Herein, we report a facile and universal strategy for enzyme immobilization using highly stable hierarchically porous metal-organic frameworks (HP-MOFs). The HP-MOFs were stable over a wide pH range (pH = 2-11 for HP-DUT-5) and met the catalysis conditions of most enzymes. The as-prepared hierarchical micro/mesoporous MOFs with mesoporous defects showed a superior adsorption capacity towards enzymes. The maximum adsorption capacity of HP-DUT-5 for glucose oxidase (GOx) and uricase was 208 mg g^-1 and 225 mg g^-1, respectively. Furthermore, we constructed two multi-enzyme biosensors for glucose and uric acid (UA) by immobilizing GOx and uricase with horseradish peroxidase (HRP) on HP-DUT-5, respectively. These sensors were efficiently applied in the colorimetric detection of glucose and UA and showed good sensitivity, selectivity, and recyclability.

Metal-Organic Frameworks at the Biointerface: Synthetic Strategies and Applications

Many living organisms are capable of producing inorganic materials of precisely controlled structure and morphology. This ubiquitous process is termed biomineralization and is observed in nature from the macroscale (e.g., formation of exoskeletons) down to the nanoscale (e.g., mineral storage and transportation in proteins). Extensive research efforts have pursued replicating this chemistry with the overarching aims of synthesizing new materials of unprecedented physical properties and understanding the complex mechanisms that occur at the biological-inorganic interface. Recently, we demonstrated that a class of porous materials termed metal-organic frameworks (MOFs) can spontaneously form on protein-based hydrogels via a process analogous to natural matrix-mediated biomineralization. Subsequently, this strategy was extended to functional biomacromolecules, including proteins and DNA, which have been shown to seed and accelerate crystallization of MOFs. Alternative strategies exploit co-precipitating agents such as polymers to induce MOF particle formation thus facilitating protein encapsulation within the porous crystals. In these examples the rigid molecular architecture of the MOF was found to form a protective coating around the biomacromolecule offering improved stability to external environments that would normally lead to its degradation. In this way, the MOF shell mimics the protective function of a biomineralized exoskeleton. Other methodologies have also been explored to encapsulate enzymes within MOF structures, including the fabrication of polycrystalline hollow MOF microcapsules that preserve the original enzyme functionality over several batch reaction cycles. The potential to design MOFs of varied pore size and chemical functionality has underpinned studies describing the postsynthesis infiltration of enzymes into MOF pore networks and bioconjugation strategies for the decoration of the MOF outer surface, respectively. These methods and configurations allow for customized biocomposites. MOF biocomposites have been extended from simple proteins to complex biological systems including viruses, living yeast cells, and bacteria. Indeed, a noteworthy result was that cells encapsulated within a crystalline MOF shell remain viable after exposure to a medium containing lytic enzymes. Furthermore, the cells can adsorb nutrients (glucose) through the MOF shell but cease reproducing until the MOF casing is removed, at which point normal cellular activity is fully restored. The field of MOF biocomposites is expansive and rapidly developing toward different applied research fields including protection and delivery of biopharmaceuticals, biosensing, biocatalysis, biobanking, and cell and virus manipulation. This Account describes the current progress of MOFs toward biotechnological applications highlighting the different strategies for the preparation of biocomposites, the developmental milestones, the challenges, and the potential impact of MOFs to the field.

Enzyme–MOF (metal–organic framework) composites

This review summarizes the syntheses and applications of metal–organic framework (MOF)–enzyme composites with specific emphasis on the merits MOFs bring to the immobilized enzymes.

Magnetic metal–organic frameworks as scaffolds for spatial co-location and positional assembly of multi-enzyme systems enabling enhanced cascade biocatalysis

Magnetic metal–organic frameworks have been prepared as scaffolds for spatial co-location and positional assembly of multi-enzymes enabling enhanced cascade biocatalysis.