Functional metalloenzymes based on myoglobin and neuroglobin that exploit covalent interactions

Globins, such as myoglobin (Mb) and neuroglobin (Ngb), are ideal protein scaffolds for the design of functional metalloenzymes. To date, numerous approaches have been developed for enzyme design. This review presents a summary of the progress made in the design of functional metalloenzymes based on Mb and Ngb, with a focus on the exploitation of covalent interactions, including coordination bonds and covalent modifications. These include the construction of a metal-binding site, the incorporation of a non-native metal cofactor, the formation of Cys/Tyr-heme covalent links, and the design of disulfide bonds, as well as other Cys-covalent modifications. As exemplified by recent studies from our group and others, the designed metalloenzymes have potential applications in biocatalysis and bioconversions. Furthermore, we discuss the current trends in the design of functional metalloenzymes and highlight the importance of covalent interactions in the design of functional metalloenzymes.

Regulating the Heme Active Site by Covalent Modifications: Two Case Studies of Myoglobin

Using myoglobin (Mb) as a model protein, we herein developed a facial approach to modifying the heme active site. A cavity was first generated in the heme distal site by F46 C mutation, and the thiol group of Cys46 was then used for covalently linked to exogenous ligands, 1H-1,2,4-triazole-3-thiol and 1-(4-hydroxyphenyl)-1H-pyrrole-2,5-dione. The engineered proteins, termed F46C-triazole Mb and F46C-phenol Mb, respectively, were characterized by X-ray crystallography, spectroscopic and stopped-flow kinetic studies. The results showed that both the heme coordination state and the protein function such as H2 O2 activation and peroxidase activity could be efficiently regulated, which suggests that this approach might be generally applied to the design of functional heme proteins.

Application of engineered myoglobins for biosynthesis of clofazimine by integration with chemical synthesis

Significant efforts have been made in the design of artificial metalloenzymes. Myoglobin (Mb), an O2 carrier, has been engineered to exhibit different functions. Herein, we applied a series of engineered Mb mutants with peroxidase activity for biosynthesis of clofazimine (CFZ), a potential drug with a broad-spectrum antiviral activity, by integration with chemical synthesis. Two of those mutants, F43Y Mb and F43Y/T67R Mb, have been shown to efficiently catalyze the oxidative coupling of 2-N-(4-chlorophenyl) benzene-1,2-diamine (N-4-CPBDA) in the presence of H2O2, with 97% yields. The overall catalytic efficiency (kcat/Km) is 46-fold and 82-fold higher than that of WT Mb, respectively. By further combination of this reaction with chemical synthesis, the production of CFZ was accomplished with an isolated yield of 72%. These results showed that engineered Mbs containing the Tyr-heme cross-link (F43Y Mb and F43Y/T67R Mb) exhibit enhanced activity in the oxidative coupling reaction. This study also indicates that the combination of biocatalysis and chemical synthesis avoids the need for the separation of intermediate products, which offers a convenient approach for the total synthesis of the biological compound CFZ.

Dye Decolorization by a Miniaturized Peroxidase Fe-MimochromeVI*a

Oxidases and peroxidases have found application in the field of chlorine-free organic dye degradation in the paper, toothpaste, and detergent industries. Nevertheless, their widespread use is somehow hindered because of their cost, availability, and batch-to-batch reproducibility. Here, we report the catalytic proficiency of a miniaturized synthetic peroxidase, Fe-Mimochrome VI*a, in the decolorization of four organic dyes, as representatives of either the heterocyclic or triarylmethane class of dyes. Fe-Mimochrome VI*a performed over 130 turnovers in less than five minutes in an aqueous buffer at a neutral pH under mild conditions.

Biocatalysis for biorefineries: The case of dye-decolorizing peroxidases

Dye-decolorizing Peroxidases (DyPs) are heme-containing enzymes in fungi and bacteria that catalyze the reduction of hydrogen peroxide to water with concomitant oxidation of various substrates, including anthraquinone dyes, lignin-related phenolic and non-phenolic compounds, and metal ions. Investigation of DyPs has shed new light on peroxidases, one of the most extensively studied families of oxidoreductases; still, details of their microbial physiological role and catalytic mechanisms remain to be fully disclosed. They display a distinctive ferredoxin-like fold encompassing anti-parallel β-sheets and α-helices, and long conserved loops surround the heme pocket with a role in catalysis and stability. A tunnel routes H₂O₂ to the heme pocket, whereas binding sites for the reducing substrates are in cavities near the heme or close to distal aromatic residues at the surface. Variations in reactions, the role of catalytic residues, and mechanisms were observed among different classes of DyP. They were hypothetically related to the presence or absence of distal H₂O molecules in the heme pocket. The engineering of DyPs for improved properties directed their biotechnological applications, primarily centered on treating textile effluents and degradation of other hazardous pollutants, to fields such as biosensors and valorization of lignin, the most abundant renewable aromatic polymer. In this review, we track recent research contributions that furthered our understanding of the activity, stability, and structural properties of DyPs and their biotechnological applications. Overall, the study of DyP-type peroxidases has significant implications for environmental sustainability and the development of new bio-based products and materials with improved end-of-life options via biodegradation and chemical recyclability, fostering the transition to a sustainable bio-based industry in the circular economy realm.

Efficient Degradation of Tetracycline Antibiotics by Engineered Myoglobin with High Peroxidase Activity

Tetracyclines are one class of widely used antibiotics. Meanwhile, due to abuse and improper disposal, they are often detected in wastewater, which causes a series of environmental problems and poses a threat to human health and safety. As an efficient and environmentally friendly method, enzymatic catalysis has attracted much attention. In previous studies, we have designed an efficient peroxidase (F43Y/P88W/F138W Mb, termed YWW Mb) based on the protein scaffold of myoglobin (Mb), an O₂ carrier, by modifying the heme active center and introducing two Trp residues. In this study, we further applied it to degrade the tetracycline antibiotics. Both UV-Vis and HPLC studies showed that the triple mutant YWW Mb was able to catalyze the degradation of tetracycline, oxytetracycline, doxycycline, and chlortetracycline effectively, with a degradation rate of ~100%, ~98%, ~94%, and ~90%, respectively, within 5 min by using H₂O₂ as an oxidant. These activities are much higher than those of wild-type Mb and other heme enzymes such as manganese peroxidase. As further analyzed by UPLC-ESI-MS, we identified multiple degradation products and thus proposed possible degradation mechanisms. In addition, the toxicity of the products was analyzed by using in vitro antibacterial experiments of E. coli. Therefore, this study indicates that the engineered heme enzyme has potential applications for environmental remediation by degradation of tetracycline antibiotics.

Converting cytochrome c into a DyP-like metalloenzyme

Dye-decolorizing peroxidase (DyP), which can degrade anthraquinone dyes using H₂O₂, is an attractive prospect for potential biotechnological applications for environmental purification. We previously designed an artificial DyP with an optimal pH for reactive blue 19 (RB19) degradation shifting from pH 4.5 to 6.5. We then attempted to degrade RB19 using Escherichia coli expressing this mutant, but RB19 was degraded equally compared with bacteria expressing wild-type (WT) DyP because most DyP was expressed in a heme-free form. In this study, we attempted to design an artificial peroxidase based on cytochrome c (cyt c), whose heme is covalently bound to the protein. We found that cyt c can degrade RB19, but its ability at pH 7.0 was ∼60% of that of DyP from Vibrio cholerae at pH 4.5. To enhance this activity we constructed several mutants using three approaches. Initially, to improve reactivity with H₂O₂, Met80 was replaced with a noncoordinating residue, Ala or Val, but catalytic efficiency (k_cat/K_m) was increased by only ∼1.5-fold. To enhance the substrate binding affinity we introduced an additional Trp by replacing Pro76 (P76W). The catalytic efficiency of this mutant was ∼3-fold greater than that of WT cyt c. Finally, to form a hydrogen bond to axial histidine Gly29 was replaced with Asp (G29D). This mutant exhibited an ∼80-fold greater dye-decolorizing activity. Escherichia coli expressing the G29D mutant was unable to degrade RB19 in solution due to degradation of heme itself, but this study provides new insights into the design of artificial DyPs.

Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere

Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.

Engineering globins for efficient biodegradation of malachite green: two case studies of myoglobin and neuroglobin

Engineered globins such as H64D Mb and A15C/H64D Ngb were efficient in the degradation of malachite green, with activities much higher than those of some native enzymes.

Design and Engineering of an Efficient Peroxidase Using Myoglobin for Dye Decolorization and Lignin Bioconversion

The treatment of environmental pollutants such as synthetic dyes and lignin has received much attention, especially for biotechnological treatments using both native and artificial metalloenzymes. In this study, we designed and engineered an efficient peroxidase using the O₂ carrier myoglobin (Mb) as a protein scaffold by four mutations (F43Y/T67R/P88W/F138W), which combines the key structural features of natural peroxidases such as the presence of a conserved His-Arg pair and Tyr/Trp residues close to the heme active center. Kinetic studies revealed that the quadruple mutant exhibits considerably enhanced peroxidase activity, with the catalytic efficiency (k_cat/K_m) comparable to that of the most efficient natural enzyme, horseradish peroxidase (HRP). Moreover, the designed enzyme can effectively decolorize a variety of synthetic organic dyes and catalyze the bioconversion of lignin, such as Kraft lignin and a model compound, guaiacylglycerol-β-guaiacyl ether (GGE). As analyzed by HPLC and ESI-MS, we identified several bioconversion products of GGE, as produced via bond cleavage followed by dimerization or trimerization, which illustrates the mechanism for lignin bioconversion. This study indicates that the designed enzyme could be exploited for the decolorization of textile wastewater contaminated with various dyes, as well as for the bioconversion of lignin to produce more value-added products.

Dye Decoloring Peroxidase Structure, Catalytic Properties and Applications: Current Advancement and Futurity

Dye decoloring peroxidases (DyPs) were named after their high efficiency to decolorize and degrade a wide range of dyes. DyPs are a type of heme peroxidase and are quite different from known heme peroxidases in terms of amino acid sequences, protein structure, catalytic residues, and physical and chemical properties. DyPs oxidize polycyclic dyes and phenolic compounds. Thus they find high application potentials in dealing with environmental problems. The structure and catalytic characteristics of DyPs of different families from the amino acid sequence, protein structure, and enzymatic properties, and analyzes the high-efficiency degradation ability of some DyPs in dye and lignin degradation, which vary greatly among DyPs classes. In addition, application prospects of DyPs in biomedicine and other fields are also discussed briefly. At the same time, the research strategy based on genetic engineering and synthetic biology in improving the stability and catalytic activity of DyPs are summarized along with the important industrial applications of DyPs and associated challenges. Moreover, according to the current research findings, bringing DyPs to the industrial level may require improving the catalytic efficiency of DyP, increasing production, and enhancing alkali resistance and toxicity.

Applications of isothermal titration calorimetry in pure and applied research from 2016 to 2020

The last 5 years have seen a series of advances in the application of isothermal titration microcalorimetry (ITC) and interpretation of ITC data. ITC has played an invaluable role in understanding multiprotein complex formation including proteolysis-targeting chimeras (PROTACS), and mitochondrial autophagy receptor Nix interaction with LC3 and GABARAP. It has also helped elucidate complex allosteric communication in protein complexes like trp RNA-binding attenuation protein (TRAP) complex. Advances in kinetics analysis have enabled the calculation of kinetic rate constants from pre-existing ITC data sets. Diverse strategies have also been developed to study enzyme kinetics and enzyme-inhibitor interactions. ITC has also been applied to study small molecule solvent and solute interactions involved in extraction, separation, and purification applications including liquid-liquid separation and extractive distillation. Diverse applications of ITC have been developed from the analysis of protein instability at different temperatures, determination of enzyme kinetics in suspensions of living cells to the adsorption of uremic toxins from aqueous streams.

Efficient biodegradation of malachite green by an artificial enzyme designed in myoglobin

Synthetic dyes such as malachite green (MG) have a wide range of applications. Meanwhile, they bring great challenges for environmental security and cause potential damages to human health. Compared with traditional approaches, enzymatic catalysis is an emerging technique for wastewater treatment. As alternatives to natural enzymes, artificial enzymes have received much attention for potential applications. In previous studies, we have rationally designed artificial enzymes based on myoglobin (Mb), such as by introducing a distal histidine (F43H mutation) and creating a channel to the heme pocket (H64A mutation). We herein show that the artificial enzyme of F43H/H64A Mb can be successfully applied for efficient biodegradation of MG under weak acid conditions. The degradation efficiency is much higher than those of natural enzymes, such as dye-decolorizing peroxidase and laccase (13-18-fold). The interaction of MG and F43H/H64A Mb was investigated by using both experimental and molecular docking studies, and the biodegradation products of MG were also revealed by UPLC-ESI-MS analysis. Based on these results, we proposed a plausible biodegradation mechanism of MG. With the high-yield of overexpression in E. coli cells, this study suggests that the artificial enzyme has potential applications in the biodegradation of MG in fisheries and textile industries.

Bioinspired design of an artificial peroxidase: introducing key residues of native peroxidases into F43Y myoglobin with a Tyr-heme cross-link

Inspired by the structural features of native peroxidases, an artificial peroxidase was rationally designed using F43Y myoglobin with a Tyr-heme cross-link by further introduction of key residues, including both a distal Arg and a Trp close to the heme group, which exhibits an enhanced peroxidase activity similar to the most efficient native horseradish peroxidase. This study provides a simple approach for design of artificial heme enzymes by the combination of catalytic elements of native enzymes with the post-translational modifications of heme proteins.

Use of an Artificial Miniaturized Enzyme in Hydrogen Peroxide Detection by Chemiluminescence

Advanced oxidation processes represent a viable alternative in water reclamation for potable reuse. Sensing methods of hydrogen peroxide are, therefore, needed to test both process progress and final quality of the produced water. Several bio-based assays have been developed so far, mainly relying on peroxidase enzymes, which have the advantage of being fast, efficient, reusable, and environmentally safe. However, their production/purification and, most of all, batch-to-batch consistency may inherently prevent their standardization. Here, we provide evidence that a synthetic de novo miniaturized designed heme-enzyme, namely Mimochrome VI*a, can be proficiently used in hydrogen peroxide assays. Furthermore, a fast and automated assay has been developed by using a lab-bench microplate reader. Under the best working conditions, the assay showed a linear response in the 10.0-120 μM range, together with a second linearity range between 120 and 500 μM for higher hydrogen peroxide concentrations. The detection limit was 4.6 μM and quantitation limits for the two datasets were 15.5 and 186 μM, respectively. In perspective, Mimochrome VI*a could be used as an active biological sensing unit in different sensor configurations.

Sphingomyelin-induced structural modification of native human hemoglobin and its chemically and thermally disrupted secondary structure: A photophysical exploration

Sphingomyelin-induced structural modification of Human Hemoglobin (Hb) has been investigated in its native and unfolded conformers that are partially denatured in presence of ∼ 4 M urea, completely denatured in ∼ 8 M urea and thermally disrupted (at ∼ 65 °C) state. The absorption studies unveil ground state complexation between Hb and SM. From steady-state fluorescence and quenching studies alteration of the micro-environments around Trp residues of Hb in above mentioned different cases has been determined. Moreover, lesser exposure of Trp residues to SM in thermally disrupted Hb can be accounted for the exceptionally interesting outcomes in other experiments. The alterations in the time-resolved decay profiles of native Hb, partially and totally chemically denatured as well as thermally disrupted Hb with gradual addition of SM also affirm the amendment of the proteinous micro-environment surrounding Trp residues in a view of FRET between Trp residues and heme group. Wavelength-sensitive emission spectral studies reveal that the protein shows red edge effect in its different conformations in presence and absence of SM. Interestingly, the wavelength-responsive time-resolved study at a constant excitation wavelength demonstrates that with addition of lipid the increment of the average fluorescence lifetime signifies a considerable modulation of solvation dynamics of the fluorescent Trp residues in their excited state being greatest in case of thermally disrupted Hb. Nevertheless, the loss of α-helicity of Hb at its various conformers with addition of SM has been portrayed thoroughly by means of far-UV CD spectral studies in a view of disruption of secondary structure of the protein.

Rational Design of Artificial Metalloproteins and Metalloenzymes with Metal Clusters

Metalloproteins and metalloenzymes play important roles in biological systems by using the limited metal ions, complexes, and clusters that are associated with the protein matrix. The design of artificial metalloproteins and metalloenzymes not only reveals the structure and function relationship of natural proteins, but also enables the synthesis of artificial proteins and enzymes with improved properties and functions. Acknowledging the progress in rational design from single to multiple active sites, this review focuses on recent achievements in the design of artificial metalloproteins and metalloenzymes with metal clusters, including zinc clusters, cadmium clusters, iron-sulfur clusters, and copper-sulfur clusters, as well as noble metal clusters and others. These metal clusters were designed in both native and de novo protein scaffolds for structural roles, electron transfer, or catalysis. Some synthetic metal clusters as functional models of native enzymes are also discussed. These achievements provide valuable insights for deep understanding of the natural proteins and enzymes, and practical clues for the further design of artificial enzymes with functions comparable or even beyond those of natural counterparts.

Green and efficient biosynthesis of indigo from indole by engineered myoglobins

Myoglobin (Mb) was redesigned to a green and efficient biocatalysts for the biosynthesis of indigo from indole, exhibiting improved yield, catalytic efficiency and chemoselectivity (as high as ∼80%).

Regulation of both the structure and function by a de novo designed disulfide bond: a case study of heme proteins in myoglobin

The V21C/V66C/F46S myoglobin mutant, with a de novo designed intramolecular disulfide bond resembling that in cytoglobin without structural evidence, exhibits a dehalogenation activity exceeding that of a native dehaloperoxidase.