Editorial

3 pages, 183 KiB

Open AccessEditorial

Natural, Designed and Engineered Metalloenzymes: Structure, Catalytic Mechanisms and Applications

by Linda Leone, Flavia Nastri and Angela Lombardi

Int. J. Mol. Sci. 2023, 24(18), 14255; https://doi.org/10.3390/ijms241814255 - 19 Sep 2023

Cited by 2 | Viewed by 632

Bioinorganic chemists have become engaged in the challenge of elucidating the molecular mechanisms that govern how protein scaffolds modulate the properties of metal cofactors [...] Full article

(This article belongs to the Special Issue Natural, Designed and Engineered Metalloenzymes: Structure, Catalytic Mechanisms and Applications)

Research

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12 pages, 6070 KiB

Open AccessArticle

A De Novo Designed Trimeric Metalloprotein as a Ni_p Model of the Acetyl-CoA Synthase

by Dhanashree Selvan and Saumen Chakraborty

Int. J. Mol. Sci. 2023, 24(12), 10317; https://doi.org/10.3390/ijms241210317 - 19 Jun 2023

Cited by 1 | Viewed by 927

Abstract

We present a Ni_p site model of acetyl coenzyme-A synthase (ACS) within a de novo-designed trimer peptide that self-assembles to produce a homoleptic Ni(Cys)₃ binding motif. Spectroscopic and kinetic studies of ligand binding demonstrate that Ni binding stabilizes the peptide assembly [...] Read more.

We present a Ni_p site model of acetyl coenzyme-A synthase (ACS) within a de novo-designed trimer peptide that self-assembles to produce a homoleptic Ni(Cys)₃ binding motif. Spectroscopic and kinetic studies of ligand binding demonstrate that Ni binding stabilizes the peptide assembly and produces a terminal Ni^I-CO complex. When the CO-bound state is reacted with a methyl donor, a new species is quickly produced with new spectral features. While the metal-bound CO is albeit unactivated, the presence of the methyl donor produces an activated metal-CO complex. Selective outer sphere steric modifications demonstrate that the physical properties of the ligand-bound states are altered differently depending on the location of the steric modification above or below the Ni site. Full article

(This article belongs to the Special Issue Natural, Designed and Engineered Metalloenzymes: Structure, Catalytic Mechanisms and Applications)

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17 pages, 3683 KiB

Open AccessArticle

Selective Oxidation of Halophenols Catalyzed by an Artificial Miniaturized Peroxidase

by Daniele D’Alonzo, Maria De Fenza, Vincenzo Pavone, Angela Lombardi and Flavia Nastri

Int. J. Mol. Sci. 2023, 24(9), 8058; https://doi.org/10.3390/ijms24098058 - 29 Apr 2023

Cited by 4 | Viewed by 1156

Abstract

The development of artificial enzymes for application in sustainable technologies, such as the transformation of environmental pollutants or biomass, is one of the most challenging goals in metalloenzyme design. In this work, we describe the oxidation of mono-, di-, tri- and penta-halogenated phenols [...] Read more.

The development of artificial enzymes for application in sustainable technologies, such as the transformation of environmental pollutants or biomass, is one of the most challenging goals in metalloenzyme design. In this work, we describe the oxidation of mono-, di-, tri- and penta-halogenated phenols catalyzed by the artificial metalloenzyme Fe-MC6*a. It promoted the dehalogenation of 4-fluorophenol into the corresponding 1,4-benzoquinone, while under the same experimental conditions, 4-chloro, 4-bromo and 4-iodophenol were selectively converted into higher molecular weight compounds. Analysis of the 4-chlorophenol oxidation products clarified that oligomers based on C-O bonds were exclusively formed in this case. All results show that Fe-MC6*a holds intriguing enzymatic properties, as it catalyzes halophenol oxidation with substrate-dependent chemoselectivity. Full article

(This article belongs to the Special Issue Natural, Designed and Engineered Metalloenzymes: Structure, Catalytic Mechanisms and Applications)

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15 pages, 3462 KiB

Open AccessArticle

Photocatalytic Hydrogen Production and Carbon Dioxide Reduction Catalyzed by an Artificial Cobalt Hemoprotein

by Guillermo A. Oliveira Udry, Laura Tiessler-Sala, Eva Pugliese, Agathe Urvoas, Zakaria Halime, Jean-Didier Maréchal, Jean-Pierre Mahy and Rémy Ricoux

Int. J. Mol. Sci. 2022, 23(23), 14640; https://doi.org/10.3390/ijms232314640 - 24 Nov 2022

Cited by 4 | Viewed by 2025

Abstract

The covalent insertion of a cobalt heme into the cavity of an artificial protein named alpha Rep (αRep) leads to an artificial cobalt hemoprotein that is active as a catalyst not only for the photo-induced production of H₂, but also for [...] Read more.

The covalent insertion of a cobalt heme into the cavity of an artificial protein named alpha Rep (αRep) leads to an artificial cobalt hemoprotein that is active as a catalyst not only for the photo-induced production of H₂, but also for the reduction of CO₂ in a neutral aqueous solution. This new artificial metalloenzyme has been purified and characterized by Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS), circular dichroism, and UltraViolet–Visible spectroscopy. Using theoretical experiments, the structure of this biohybrid and the positioning of the residues near the metal complex were examined, which made it possible to complete the coordination of the cobalt ion by an axial glutamine Gln283 ligand. While the Co(III)–porphyrin catalyst alone showed weak catalytic activity for both reactions, 10 times more H₂ and four times more CO₂ were produced when the Co(III)–porphyrin complex was buried in the hydrophobic cavity of the protein. This study thus provides a solid basis for further improvement of these biohybrids using well-designed modifications of the second and outer coordination sphere by site-directed mutagenesis of the host protein. Full article

(This article belongs to the Special Issue Natural, Designed and Engineered Metalloenzymes: Structure, Catalytic Mechanisms and Applications)

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12 pages, 7013 KiB

Open AccessArticle

Reactivity of Myoglobin Reconstituted with Cobalt Corrole toward Hydrogen Peroxide

by Koji Oohora, Hirotaka Tomoda and Takashi Hayashi

Int. J. Mol. Sci. 2022, 23(9), 4829; https://doi.org/10.3390/ijms23094829 - 27 Apr 2022

Cited by 4 | Viewed by 1876

Abstract

The protein matrix of natural metalloenzymes regulates the reactivity of metal complexes to establish unique catalysts. We describe the incorporation of a cobalt complex of corrole (CoCor), a trianionic porphyrinoid metal ligand, into an apo-form of myoglobin to provide a reconstituted protein (rMb(CoCor)). [...] Read more.

The protein matrix of natural metalloenzymes regulates the reactivity of metal complexes to establish unique catalysts. We describe the incorporation of a cobalt complex of corrole (CoCor), a trianionic porphyrinoid metal ligand, into an apo-form of myoglobin to provide a reconstituted protein (rMb(CoCor)). This protein was characterized by UV-vis, EPR, and mass spectroscopic measurements. The reaction of rMb(CoCor) with hydrogen peroxide promotes an irreversible oxidation of the CoCor cofactor, whereas the same reaction in the presence of a phenol derivative yields the cation radical form of CoCor. Detailed kinetic investigations indicate the formation of a transient hydroperoxo complex of rMb(CoCor) which promotes the oxidation of the phenol derivatives. This mechanism is significantly different for native heme-dependent peroxidases, which generate a metal-oxo species as an active intermediate in a reaction with hydrogen peroxide. The present findings of unique reactivity will contribute to further design of artificial metalloenzymes. Full article

(This article belongs to the Special Issue Natural, Designed and Engineered Metalloenzymes: Structure, Catalytic Mechanisms and Applications)

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18 pages, 3079 KiB

Open AccessArticle

Functional Conversion of Acetyl-Coenzyme a Synthase to a Nickel Superoxide Dismutase via Rational Design of Coordination Microenvironment for the Ni_d-Site

by Yaozhu Wei, Yajun Zhou, Hong Yuan, Yi Liu, Ying-Wu Lin, Jihu Su and Xiangshi Tan

Int. J. Mol. Sci. 2022, 23(5), 2652; https://doi.org/10.3390/ijms23052652 - 28 Feb 2022

Cited by 2 | Viewed by 1376

Abstract

The Ni_d site coordination microenvironment of a truncated acetyl-coenzyme A synthase has been designed systematically for functional conversion to a Ni-SOD-like enzyme. To this end, the first strategy is to introduce an axial histidine ligand, using mutations F598H, S594H and S594H-GP individually. [...] Read more.

The Ni_d site coordination microenvironment of a truncated acetyl-coenzyme A synthase has been designed systematically for functional conversion to a Ni-SOD-like enzyme. To this end, the first strategy is to introduce an axial histidine ligand, using mutations F598H, S594H and S594H-GP individually. The resulting three mutants obtained Ni-SOD-like activity successfully, although the catalytic activity was about 10-fold lower than in native Ni-SOD. The second strategy is to mimic the H-bond network in the second sphere coordination microenvironment of the native Ni-SOD. Two mutations based on F598H (EFG-F598H and YGP-F598H) were designed. The successful EFG-F598H exhibited ~3-fold Ni-SOD-like activity of F598H. These designed Ni-SOD-like metalloproteins were characterized by UV/Vis, EPR and Cyclic voltammetry while F598H was also characterized by X-ray protein crystallography. The pH titrations were performed to reveal the source of the two protons required for forming H₂O₂ in the SOD catalytic reaction. Based on all of the results, a proposed catalytic mechanism for the Ni-SOD-like metalloproteins is presented. Full article

(This article belongs to the Special Issue Natural, Designed and Engineered Metalloenzymes: Structure, Catalytic Mechanisms and Applications)

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19 pages, 3774 KiB

Open AccessArticle

In Silico and Experimental ADAM17 Kinetic Modeling as Basis for Future Screening System for Modulators

by Marian Bienstein, Dmitriy Minond, Ulrich Schwaneberg, Mehdi D. Davari and Daniela Yildiz

Int. J. Mol. Sci. 2022, 23(3), 1368; https://doi.org/10.3390/ijms23031368 - 25 Jan 2022

Cited by 5 | Viewed by 3045

Abstract

Understanding the mechanisms of modulators’ action on enzymes is crucial for optimizing and designing pharmaceutical substances. The acute inflammatory response, in particular, is regulated mainly by a disintegrin and metalloproteinase (ADAM) 17. ADAM17 processes several disease mediators such as TNFα and APP, releasing [...] Read more.

Understanding the mechanisms of modulators’ action on enzymes is crucial for optimizing and designing pharmaceutical substances. The acute inflammatory response, in particular, is regulated mainly by a disintegrin and metalloproteinase (ADAM) 17. ADAM17 processes several disease mediators such as TNFα and APP, releasing their soluble ectodomains (shedding). A malfunction of this process leads to a disturbed inflammatory response. Chemical protease inhibitors such as TAPI-1 were used in the past to inhibit ADAM17 proteolytic activity. However, due to ADAM17′s broad expression and activity profile, the development of active-site-directed ADAM17 inhibitor was discontinued. New ‘exosite’ (secondary substrate binding site) inhibitors with substrate selectivity raised the hope of a substrate-selective modulation as a promising approach for inflammatory disease therapy. This work aimed to develop a high-throughput screen for potential ADAM17 modulators as therapeutic drugs. By combining experimental and in silico methods (structural modeling and docking), we modeled the kinetics of ADAM17 inhibitor. The results explain ADAM17 inhibition mechanisms and give a methodology for studying selective inhibition towards the design of pharmaceutical substances with higher selectivity. Full article

(This article belongs to the Special Issue Natural, Designed and Engineered Metalloenzymes: Structure, Catalytic Mechanisms and Applications)

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15 pages, 3419 KiB

Open AccessArticle

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

by Wen-Jie Guo, Jia-Kun Xu, Sheng-Tao Wu, Shu-Qin Gao, Ge-Bo Wen, Xiangshi Tan and Ying-Wu Lin

Int. J. Mol. Sci. 2022, 23(1), 413; https://doi.org/10.3390/ijms23010413 - 30 Dec 2021

Cited by 13 | Viewed by 2612

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Natural, Designed and Engineered Metalloenzymes: Structure, Catalytic Mechanisms and Applications)

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Review

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41 pages, 6422 KiB

Open AccessReview

Enzymatic and Bioinspired Systems for Hydrogen Production

by Linda Leone, Gianmattia Sgueglia, Salvatore La Gatta, Marco Chino, Flavia Nastri and Angela Lombardi

Int. J. Mol. Sci. 2023, 24(10), 8605; https://doi.org/10.3390/ijms24108605 - 11 May 2023

Cited by 6 | Viewed by 2607

Abstract

The extraordinary potential of hydrogen as a clean and sustainable fuel has sparked the interest of the scientific community to find environmentally friendly methods for its production. Biological catalysts are the most attractive solution, as they usually operate under mild conditions and do [...] Read more.

The extraordinary potential of hydrogen as a clean and sustainable fuel has sparked the interest of the scientific community to find environmentally friendly methods for its production. Biological catalysts are the most attractive solution, as they usually operate under mild conditions and do not produce carbon-containing byproducts. Hydrogenases promote reversible proton reduction to hydrogen in a variety of anoxic bacteria and algae, displaying unparallel catalytic performances. Attempts to use these sophisticated enzymes in scalable hydrogen production have been hampered by limitations associated with their production and stability. Inspired by nature, significant efforts have been made in the development of artificial systems able to promote the hydrogen evolution reaction, via either electrochemical or light-driven catalysis. Starting from small-molecule coordination compounds, peptide- and protein-based architectures have been constructed around the catalytic center with the aim of reproducing hydrogenase function into robust, efficient, and cost-effective catalysts. In this review, we first provide an overview of the structural and functional properties of hydrogenases, along with their integration in devices for hydrogen and energy production. Then, we describe the most recent advances in the development of homogeneous hydrogen evolution catalysts envisioned to mimic hydrogenases. Full article

(This article belongs to the Special Issue Natural, Designed and Engineered Metalloenzymes: Structure, Catalytic Mechanisms and Applications)

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45 pages, 5597 KiB

Open AccessReview

Recent Theoretical Insights into the Oxidative Degradation of Biopolymers and Plastics by Metalloenzymes

by Anna Rovaletti, Luca De Gioia, Piercarlo Fantucci, Claudio Greco, Jacopo Vertemara, Giuseppe Zampella, Federica Arrigoni and Luca Bertini

Int. J. Mol. Sci. 2023, 24(7), 6368; https://doi.org/10.3390/ijms24076368 - 28 Mar 2023

Cited by 6 | Viewed by 2882

Abstract

Molecular modeling techniques have become indispensable in many fields of molecular sciences in which the details related to mechanisms and reactivity need to be studied at an atomistic level. This review article provides a collection of computational modeling works on a topic of [...] Read more.

Molecular modeling techniques have become indispensable in many fields of molecular sciences in which the details related to mechanisms and reactivity need to be studied at an atomistic level. This review article provides a collection of computational modeling works on a topic of enormous interest and urgent relevance: the properties of metalloenzymes involved in the degradation and valorization of natural biopolymers and synthetic plastics on the basis of both circular biofuel production and bioremediation strategies. In particular, we will focus on lytic polysaccharide monooxygenase, laccases, and various heme peroxidases involved in the processing of polysaccharides, lignins, rubbers, and some synthetic polymers. Special attention will be dedicated to the interaction between these enzymes and their substrate studied at different levels of theory, starting from classical molecular docking and molecular dynamics techniques up to techniques based on quantum chemistry. Full article

(This article belongs to the Special Issue Natural, Designed and Engineered Metalloenzymes: Structure, Catalytic Mechanisms and Applications)

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