In vitro Production of Hemin-Based Artificial Metalloenzymes

Developing enzyme alternatives is pivotal to improving and enabling new processes in biotechnology and industry. Artificial metalloenzymes (ArMs) are combinations of protein scaffolds with metal elements, such as metal nanoclusters or metal-containing molecules with specific catalytic properties, which can be customized. Here, we engineered an ArM based on the consensus tetratricopeptide repeat (CTPR) scaffold by introducing a unique histidine residue to coordinate the hemin cofactor. Our results show that this engineered system exhibits robust peroxidase-like catalytic activity driven by the hemin. The expression of the scaffold and subsequent coordination of hemin was achieved by recombinant expression in bulk and through in vitro transcription and translation systems in water-in-oil drops. The ability to synthesize this system in emulsio paves the way to improve its properties by means of droplet microfluidic screenings, facilitating the exploration of the protein combinatorial space to discover improved or novel catalytic activities.

In silico approaches to investigate enzyme immobilization: a comprehensive systematic review

Enzymes are popular catalysts with many applications, especially in industry. Biocatalyst usage on a large scale is facing some limitations, such as low operational stability, low recyclability, and high enzyme cost. Enzyme immobilization is a beneficial strategy to solve these problems. Bioinformatics tools can often correctly predict immobilization outcomes, resulting in a cost-effective experimental phase with the least time consumed. This study provides an overview of in silico methods predicting immobilization processes via a comprehensive systematic review of published articles till 11 December 2022. It also mentions the strengths and weaknesses of the processes and explains the computational analyses in each method that are required for immobilization assessment. In this regard, Web of Science and Scopus databases were screened to gain relevant publications. After screening the gathered documents (n = 3873), 60 articles were selected for the review. The selected papers have applied in silico procedures including only molecular dynamics (MD) simulations (n = 20), parallel tempering Monte Carlo (PTMC) and MD simulations (n = 3), MD and docking (n = 1), density functional theory (DFT) and MD (n = 1), only docking (n = 11), metal ion binding site prediction (MIB) server and docking (n = 2), docking and DFT (n = 1), docking and analysis of enzyme surfaces (n = 1), only DFT (n = 1), only MIB server (n = 2), analysis of an enzyme structure and surface (n = 12), rational design of immobilized derivatives (RDID) software (n = 3), and dissipative particle dynamics (DPD; n = 2). In most included studies (n = 51), enzyme immobilization was investigated experimentally in addition to in silico evaluation.

Ferritin nanocages: a versatile platform for nanozyme design

Nanozymes are a class of nanomaterials with enzyme-like activities and have attracted increasing attention due to their potential applications in biomedicine. However, nanozyme design incorporating the desired properties remains challenging. Natural or genetically engineered protein scaffolds, such as ferritin nanocages, have emerged as a promising platform for nanozyme design due to their unique protein structure, natural biomineralization capacity, self-assembly properties, and high biocompatibility. In this review, we highlight the intrinsic properties of ferritin nanocages, especially for nanozyme design. We also discuss the advantages of genetically engineered ferritin in the versatile design of nanozymes over natural ferritin. Additionally, we summarize the bioapplications of ferritin-based nanozymes based on their enzyme-mimicking activities. In this perspective, we mainly provide potential insights into the utilization of ferritin nanocages for nanozyme design.

Protein encapsulation of nanocatalysts: A feasible approach to facilitate catalytic theranostics

Enzyme-mimicking nanocatalysts, also termed nanozymes, have attracted much attention in recent years. They are considered potential alternatives to natural enzymes due to their multiple catalytic activities and high stability. However, concerns regarding the colloidal stability, catalytic specificity, efficiency and biosafety of nanomaterials in biomedical applications still need to be addressed. Proteins are biodegradable macromolecules that exhibit superior biocompatibility and inherent bioactivities; hence, the protein modification of nanocatalysts is expected to improve their bioavailability to match clinical needs. The diversity of amino acid residues in proteins provides abundant functional groups for the conjugation or encapsulation of nanocatalysts. Moreover, protein encapsulation can not only improve the overall performance of nanocatalysts in biological systems, but also bestow materials with new features, such as targeting and retention in pathological sites. This review aims to report the recent developments and perspectives of protein-encapsulated catalysts in their functional improvements, modification methods and applications in biomedicine.

Nanozyme Based on Dispersion of Hemin by Graphene Quantum Dots for Colorimetric Detection of Glutathione

Compared with natural enzymes, nanozymes have the advantages of good catalytic performance, high stability, low cost, and can be used under extreme conditions. Preparation of highly active nanozymes through simple methods and their application in bioanalysis is highly desirable. In this work, a nanozyme based on dispersion of hemin by graphene quantum dot (GQD) is demonstrated, which enables colorimetric detection of glutathione (GSH). GQD was prepared by a one-step hydrothermal synthesis method. Hemin, the catalytic center of heme protein but with low solubility and easy aggregation that limits its catalytic activity, can be dispersed with GQD by simple sonication. The as-prepared Hemin/GQD nanocomplex had excellent peroxidase-like activity and can be applied as a nanozyme. In comparison with natural horseradish peroxidase (HRP), Hemin/GQD nanozyme exhibited a clearly reduced Michaelis–Menten constant (K_m) when tetramethylbenzidine (TMB) was used as the substrate. With H₂O₂ being the substrate, Hemin/GQD nanozyme exhibited a higher maximum reaction rate (V_max) than HRP. The mechanisms underlying the nanozyme activity were investigated through a free radical trapping experiment. A colorimetric platform capable of sensitive detection of GSH was developed as the proof-of-concept demonstration. The linear detection range was from 1 μM to 50 μM with a low limit of detection of 200 nM (S/N = 3). Determination of GSH in serum samples was also achieved.

Phenoxyl mediators improve enzymatic degradation of organic pollutants: Effect and mechanism

A mediation strategy can effectively overcome the low reaction activity of enzymes with nonspecific substrates. In this study, we demonstrated how phenol compounds can mitigate the substrate limitation of HRP in catalytic degradation of various organic pollutants. In a classical HRP/H₂O₂ system, phenol and natural phenolic compounds (4-HBA & pHBA), exhibited up to over 100-fold enhancement in eliminating organic dyes and persistent antibiotics while the loading is only 2-5 wt%. A combination of molecular modelling, docking and frontier orbital energy analysis was employed to elucidate the catalytic performance and mechanism. We revealed that (1) generating phenoxyl radicals required the proximity of mediators to the HRP active centre, and (2) the subsequent efficient radical transfer to pollutants was determined by the large energy gap between the SOMO energy of phenoxyl radicals and the HOMO energy of phenols. When considering phenols as pollutants, we showed a synergistic effect on catalytic degradation of phenols, dyes, and tetracycline with a removal efficiency of 71-92 %. Overall, this work not only demonstrates that phenoxyl mediators can overcome the lower efficiency and substrate-specificity limitations of the HRP/H₂O₂ system but also revealed their structure-mediation relationship, implying great potential in the biodegradation of diverse pollutants and their mixtures.

Polymeric Nanocapsule Enhances the Peroxidase-like Activity of Fe3O4 Nanozyme for Removing Organic Dyes

Peroxidase-like nanozymes are nanoscale materials that can closely mimic the activity of natural peroxidase for a range of oxidation reactions. Surface coating with polymer nanogels has been considered to prevent the aggregation of nanozymes. For a long time, the understanding of polymer coating has been largely limited to its stabilization effect on the nanozyme in aqueous media, while little is known about how polymer coating plays a role in interaction with substrates and primary oxidants to dictate the catalytic process. This work reported a facile sequential modification of Fe3O4 nanoparticles to polyacrylamide coated nanozymes, and as low as 112 mg/L samples with only 5 mg/L Fe3O4 could nearly quantitatively (99%) remove a library of organic dyes with either H2O2 or Na2S2O8 as primary oxidants. The catalytic results and molecular simulation provide both experimental and computational evidence that the hydrogen bonding interaction between the reactant and nanozymes is key for the high local concentration hence catalytic efficiency. We envision that this work, for the first time, provides some insights into the role of polymer coating in enhancing the catalytic activity of nanozyme apart from the well-known water dispersity effect.

Probing secondary coordination sphere interactions within porphyrin-cored polymer nanoparticles

A suite of zinc porphyrin-cored polymeric nanoparticles were synthesized and characterized to study secondary coordination sphere interactions. We show that with proper design these materials catalyze the reaction of cyanide with N,N-dimethylformamide.

Hemin-based cell therapy via nanoparticle-assisted uptake, intracellular reactive oxygen species generation and autophagy induction

A hemin-based colloidal nanoparticle is designed that offers an iron-based Fenton reaction inside the cell and induces cellular autophagy via oxidative stress.

Emamectin benzoate nanogel suspension constructed from poly(vinyl alcohol)-valine derivatives and lignosulfonate enhanced insecticidal efficacy

To reduce the negative impact of nanopesticide carriers of on the environment, a greener nanodelivery system is necessary. Nanogels are nontoxic and degradable carriers, however, the potential of nanogels for delivering pesticides has not been proven. In this study, poly(vinyl alcohol)-valine, an ecofriendly polymer, was synthesized and used to fabricate emamectin benzoate nanogel suspension (EB NS). The nanoformulation showed favorable stability at low temperature, high temperature or one year storage, and in water with different hardnesses. The retention of the EB NS solution on leaves was higher than that of an EB emulsifiable concentrate (EC) by approximately 9% at a concentration of 10 mg L^-1. The half-life of EB nanogels under Ultra Violet irradiation was prolonged by 3.3-fold. Moreover, the bioactivity of the EB NS against Plutella xylostella was higher than that of the EB EC. These advantages resulted in a relatively long duration of pest control. The response of nanogels to laccase, a digestive enzyme in the digestive tract of lepidopteran pests, enables pesticide release on demand. Nanogels have the advantages of being ecofriendly carriers, exhibiting higher utilization, and prolonged pest control periods, and they have a brilliant future in pesticide delivery.

Hemin-Caged Ferritin Acting as a Peroxidase-like Nanozyme for the Selective Detection of Tumor Cells

Nanozyme is a class of artificial materials that possess enzyme-like activities and can overcome limitations of natural enzymes. However, controllability of the active sites, uniformity of the particles, and dispersion in the physiological media are still challenging for nanomaterial-based nanozymes. In this work, a protein-based nanozyme has been constructed by the encapsulation of hemin into the nanocavity of a recombinant human heavy chain ferritin (Ftn), generating a monodispersed peroxidase-mimetic nanozyme (hemin@Ftn). Hemin@Ftn possesses high peroxidase catalytic activity and high tolerance to the harsh environmental conditions, such as high temperature and chemical denaturant. Remarkably, hemin@Ftn can act as a colorimetric probe for the detection of tumor cells because it can selectively catalyze reactions in tumor cells. This protein-based nanozyme bridges the gap between natural enzymes and nanomaterial-based nanozymes by the incorporation of a catalytically active prosthetic group into a highly stable Ftn.

Robust nanocarriers to engineer nanobiocatalysts for bioprocessing applications

The synergistic integration of bio-catalysis engineering with nanostructured materials, as unique multifunctional carrier matrices, has emerged as a new interface of nanobiocatalysis (NBC). NBC is an emerging innovation that offers significant considerations to expand the designing and fabrication of robust catalysts at the nanoscale with improved catalytic characteristics for multipurpose bioprocessing applications. In addition, nanostructured materials with unique structural, physical, chemical, and functional entities have manifested significant contributions in mimicking the enzyme microenvironment. A fine-tuned enzyme microenvironment with an added-value of NBC offers chemo- regio- and stereo- selectivities and specificities. Furthermore, NBC is growing rapidly and will become a powerful norm in bio-catalysis with much controlled features, such as selectivity, specificity, stability, resistivity, induce activity, reaction efficacy, multi-usability, improved mass transfer efficiency, high catalytic turnover, optimal yield, ease in recovery, and cost-effectiveness. Considering the above critics and unique structural, physicochemical, and functional attributes, herein, we present and discuss advances in NBC and its bioprocessing applications in different fields. Briefly, this review is focused on four parts, i.e., (1) NBC as a drive towards applied nanobiocatalysts (as an introduction with opportunities), (2) promising nanocarriers to develop nanobiocatalysts, (3) applications in the fields of biotransformation, biofuel production, carbohydrate hydrolysis, bio-/nanosensing, detergent formulations, and extraction and purification of value-added compounds, and (4) current challenges, concluding remarks, and future trends.