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Škulj S, Kožić M, Barišić A, Vega A, Biarnés X, Piantanida I, Barisic I, Bertoša B. Comparison of two peroxidases with high potential for biotechnology applications - HRP vs. APEX2. Comput Struct Biotechnol J 2024; 23:742-751. [PMID: 38298178 PMCID: PMC10828542 DOI: 10.1016/j.csbj.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 01/01/2024] [Accepted: 01/01/2024] [Indexed: 02/02/2024] Open
Abstract
Peroxidases are essential elements in many biotechnological applications. An especially interesting concept involves split enzymes, where the enzyme is separated into two smaller and inactive proteins that can dimerize into a fully active enzyme. Such split forms were developed for the horseradish peroxidase (HRP) and ascorbate peroxidase (APX) already. Both peroxidases have a high potential for biotechnology applications. In the present study, we performed biophysical comparisons of these two peroxidases and their split analogues. The active site availability is similar for all four structures. The split enzymes are comparable in stability with their native analogues, meaning that they can be used for further biotechnology applications. Also, the tertiary structures of the two peroxidases are similar. However, differences that might help in choosing one system over another for biotechnology applications were noticed. The main difference between the two systems is glycosylation which is not present in the case of APX/sAPEX2, while it has a high impact on the HRP/sHRP stability. Further differences are calcium ions and cysteine bridges that are present only in the case of HRP/sHRP. Finally, computational results identified sAPEX2 as the systems with the smallest structural variations during molecular dynamics simulations showing its dominant stability comparing to other simulated proteins. Taken all together, the sAPEX2 system has a high potential for biotechnological applications due to the lack of glycans and cysteines, as well as due to high stability.
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Affiliation(s)
- Sanja Škulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb HR-10000, Croatia
- Institute of Physiology, Pathophysiology and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Matej Kožić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb HR-10000, Croatia
| | - Antun Barišić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb HR-10000, Croatia
| | - Aitor Vega
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Xevi Biarnés
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Ivo Piantanida
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10 000 Zagreb, Croatia
| | - Ivan Barisic
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, Vienna 1210, Austria
- Eko Refugium, Crno Vrelo 2, Slunj 47240, Croatia
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb HR-10000, Croatia
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2
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Medvedev AG, Egorov PA, Mikhaylov AA, Belyaev ES, Kirakosyan GA, Gorbunova YG, Filippov OA, Belkova NV, Shubina ES, Brekhovskikh MN, Kirsanova AA, Babak MV, Lev O, Prikhodchenko PV. Synergism of primary and secondary interactions in a crystalline hydrogen peroxide complex with tin. Nat Commun 2024; 15:5758. [PMID: 38982085 DOI: 10.1038/s41467-024-50164-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 07/01/2024] [Indexed: 07/11/2024] Open
Abstract
Despite the significance of H2O2-metal adducts in catalysis, materials science and biotechnology, the nature of the interactions between H2O2 and metal cations remains elusive and debatable. This is primarily due to the extremely weak coordinating ability of H2O2, which poses challenges in characterizing and understanding the specific nature of these interactions. Herein, we present an approach to obtain H2O2-metal complexes that employs neat H2O2 as both solvent and ligand. SnCl4 effectively binds H2O2, forming a SnCl4(H2O2)2 complex, as confirmed by 119Sn and 17O NMR spectroscopy. Crystalline adducts, SnCl4(H2O2)2·H2O2·18-crown-6 and 2[SnCl4(H2O2)(H2O)]·18-crown-6, are isolated and characterized by X-ray diffraction, providing the complete characterization of the hydrogen bonding of H2O2 ligands including geometric parameters and energy values. DFT analysis reveals the synergy between a coordinative bond of H2O2 with metal cation and its hydrogen bonding with a second coordination sphere. This synergism of primary and secondary interactions might be a key to understanding H2O2 reactivity in biological systems.
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Affiliation(s)
- Alexander G Medvedev
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Pavel A Egorov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexey A Mikhaylov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Evgeny S Belyaev
- Frumkin Institute of Physical Chemistry and Electrochemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Gayane A Kirakosyan
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
- Frumkin Institute of Physical Chemistry and Electrochemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Yulia G Gorbunova
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
- Frumkin Institute of Physical Chemistry and Electrochemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Oleg A Filippov
- Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow, Russian Federation
| | - Natalia V Belkova
- Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow, Russian Federation
| | - Elena S Shubina
- Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow, Russian Federation
| | - Maria N Brekhovskikh
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Anna A Kirsanova
- Drug Discovery Lab, Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Maria V Babak
- Drug Discovery Lab, Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China.
| | - Ovadia Lev
- Casali Center of Applied Chemistry, Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Petr V Prikhodchenko
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.
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3
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Chatterjee S, Nochebuena J, Cisneros GA. Impact of an Ionic Liquid Solution on Horseradish Peroxidase Activity. J Am Chem Soc 2024; 146:13247-13257. [PMID: 38701006 DOI: 10.1021/jacs.4c01100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Horseradish peroxidase (HRP) is an enzyme that oxidizes pollutants from wastewater. A previous report indicated that peroxidases can have an enhancement in initial enzymatic activity in an aqueous solution of 0.26 M 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIm][EtSO4]) at neutral pH. However, the atomistic details remain elusive. In the enzymatic landscape of HRP, compound II (Cpd II) plays a key role and involves a histidine (H42) residue. Cpd II exists as oxoferryl (2a) or hydroxoferryl (2b(FeIV)) forms, where 2a is the predominantly observed form in experimental studies. Intriguingly, the ferric 2b(FeIII) form seen in synthetic complexes has not been observed in HRP. Here, we have investigated the structure and dynamics of HRP in pure water and aqueous [EMIm][EtSO4] (0.26 M), as well as the reaction mechanism of 2a to 2b conversion using polarizable molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations. When HRP is solvated in aq [EMIm][EtSO4], the catalytic water displaces, and H42 directly orients over the ferryl moiety, allowing a direct proton transfer (PT) with a significant energy barrier reduction. Conversely, in neat water, the reaction of 2a to 2b follows the previously reported mechanism. We further investigated the deprotonated form of H42. Analysis of the electric fields at the active site indicates that the aq [EMIm][EtSO4] medium facilitates the reaction by providing a more favorable environment compared with the system solvated in neat water. Overall, the atomic level supports the previous experimental observations and underscores the importance of favorable electric fields in the active site to promote catalysis.
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Affiliation(s)
- Shubham Chatterjee
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Jorge Nochebuena
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - G Andrés Cisneros
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, United States
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4
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Freitas CDT, Costa JH, Germano TA, de O Rocha R, Ramos MV, Bezerra LP. Class III plant peroxidases: From classification to physiological functions. Int J Biol Macromol 2024; 263:130306. [PMID: 38387641 DOI: 10.1016/j.ijbiomac.2024.130306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 02/14/2024] [Accepted: 02/18/2024] [Indexed: 02/24/2024]
Abstract
Peroxidases (EC 1.11.1.7) are involved in a wide range of physiological processes, hence their broad distribution across biological systems. These proteins can be classified as haem or non-haem enzymes. According to the RedOxiBase database, haem peroxidases are approximately 84 % of all known peroxidase enzymes. Class III plant peroxidases are haem-enzymes that share similar three-dimensional structures and a common catalytic mechanism for hydrogen peroxide degradation. They exist as large multigene families and are involved in metabolizing Reactive Oxygen Species (ROS), hormone synthesis and decomposition, fruit growth, defense, and cell wall synthesis and maintenance. As a result, plant peroxidases gained attention in research and became one of the most extensively studied groups of enzymes. This review provides an update on the database, classification, phylogeny, mechanism of action, structure, and physiological functions of class III plant peroxidases.
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Affiliation(s)
- Cleverson D T Freitas
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Campus do Pici, Fortaleza, Ceará CEP 60451-970, Brazil.
| | - José H Costa
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Campus do Pici, Fortaleza, Ceará CEP 60451-970, Brazil
| | - Thais A Germano
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Campus do Pici, Fortaleza, Ceará CEP 60451-970, Brazil
| | - Raquel de O Rocha
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven 06511, CT, USA
| | - Márcio V Ramos
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Campus do Pici, Fortaleza, Ceará CEP 60451-970, Brazil
| | - Leandro P Bezerra
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Campus do Pici, Fortaleza, Ceará CEP 60451-970, Brazil
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5
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Munzone A, Eijsink VGH, Berrin JG, Bissaro B. Expanding the catalytic landscape of metalloenzymes with lytic polysaccharide monooxygenases. Nat Rev Chem 2024; 8:106-119. [PMID: 38200220 DOI: 10.1038/s41570-023-00565-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2023] [Indexed: 01/12/2024]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) have an essential role in global carbon cycle, industrial biomass processing and microbial pathogenicity by catalysing the oxidative cleavage of recalcitrant polysaccharides. Despite initially being considered monooxygenases, experimental and theoretical studies show that LPMOs are essentially peroxygenases, using a single copper ion and H2O2 for C-H bond oxygenation. Here, we examine LPMO catalysis, emphasizing key studies that have shaped our comprehension of their function, and address side and competing reactions that have partially obscured our understanding. Then, we compare this novel copper-peroxygenase reaction with reactions catalysed by haem iron enzymes, highlighting the different chemistries at play. We conclude by addressing some open questions surrounding LPMO catalysis, including the importance of peroxygenase and monooxygenase reactions in biological contexts, how LPMOs modulate copper site reactivity and potential protective mechanisms against oxidative damage.
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Affiliation(s)
- Alessia Munzone
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, Marseille, France
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Jean-Guy Berrin
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, Marseille, France
| | - Bastien Bissaro
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, Marseille, France.
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6
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López-Gómez P, Buezo J, Urra M, Cornejo A, Esteban R, Fernández de Los Reyes J, Urarte E, Rodríguez-Dobreva E, Chamizo-Ampudia A, Eguaras A, Wolf S, Marino D, Martínez-Merino V, Moran JF. A new oxidative pathway of nitric oxide production from oximes in plants. MOLECULAR PLANT 2024; 17:178-198. [PMID: 38102832 DOI: 10.1016/j.molp.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 09/06/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
Nitric oxide (NO) is an essential reactive oxygen species and a signal molecule in plants. Although several studies have proposed the occurrence of oxidative NO production, only reductive routes for NO production, such as the nitrate (NO-3) -upper-reductase pathway, have been evidenced to date in land plants. However, plants grown axenically with ammonium as the sole source of nitrogen exhibit contents of nitrite and NO3-, evidencing the existence of a metabolic pathway for oxidative production of NO. We hypothesized that oximes, such as indole-3-acetaldoxime (IAOx), a precursor to indole-3-acetic acid, are intermediate oxidation products in NO synthesis. We detected the production of NO from IAOx and other oximes catalyzed by peroxidase (POD) enzyme using both 4-amino-5-methylamino-2',7'-difluorescein fluorescence and chemiluminescence. Flavins stimulated the reaction, while superoxide dismutase inhibited it. Interestingly, mouse NO synthase can also use IAOx to produce NO at a lower rate than POD. We provided a full mechanism for POD-dependent NO production from IAOx consistent with the experimental data and supported by density functional theory calculations. We showed that the addition of IAOx to extracts from Medicago truncatula increased the in vitro production of NO, while in vivo supplementation of IAOx and other oximes increased the number of lateral roots, as shown for NO donors, and a more than 10-fold increase in IAOx dehydratase expression. Furthermore, we found that in vivo supplementation of IAOx increased NO production in Arabidopsis thaliana wild-type plants, while prx33-34 mutant plants, defective in POD33-34, had reduced production. Our data show that the release of NO by IAOx, as well as its auxinic effect, explain the superroot phenotype. Collectively, our study reveals that plants produce NO utilizing diverse molecules such as oximes, POD, and flavins, which are widely distributed in the plant kingdom, thus introducing a long-awaited oxidative pathway to NO production in plants. This knowledge has essential implications for understanding signaling in biological systems.
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Affiliation(s)
- Pedro López-Gómez
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Department of Sciences, Public University of Navarre (UPNA), Avda. de Pamplona 123, 31192 Mutilva, Spain
| | - Javier Buezo
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Department of Sciences, Public University of Navarre (UPNA), Avda. de Pamplona 123, 31192 Mutilva, Spain
| | - Marina Urra
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Department of Sciences, Public University of Navarre (UPNA), Avda. de Pamplona 123, 31192 Mutilva, Spain
| | - Alfonso Cornejo
- Institute for Advanced Materials and Mathematics (INAMAT2), Department of Sciences, Public University of Navarre (UPNA), Campus de Arrosadía, 31006 Pamplona, Spain
| | - Raquel Esteban
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Sarriena s/n, Apdo. 644, 48080 Bilbao, Spain
| | - Jorge Fernández de Los Reyes
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Department of Sciences, Public University of Navarre (UPNA), Avda. de Pamplona 123, 31192 Mutilva, Spain
| | - Estibaliz Urarte
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Department of Sciences, Public University of Navarre (UPNA), Avda. de Pamplona 123, 31192 Mutilva, Spain
| | - Estefanía Rodríguez-Dobreva
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Department of Sciences, Public University of Navarre (UPNA), Avda. de Pamplona 123, 31192 Mutilva, Spain
| | - Alejandro Chamizo-Ampudia
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Department of Sciences, Public University of Navarre (UPNA), Avda. de Pamplona 123, 31192 Mutilva, Spain
| | - Alejandro Eguaras
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Department of Sciences, Public University of Navarre (UPNA), Avda. de Pamplona 123, 31192 Mutilva, Spain
| | - Sebastian Wolf
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Geschwister-Scholl-Platz, 72074 Tübingen, Germany
| | - Daniel Marino
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Sarriena s/n, Apdo. 644, 48080 Bilbao, Spain
| | - Victor Martínez-Merino
- Institute for Advanced Materials and Mathematics (INAMAT2), Department of Sciences, Public University of Navarre (UPNA), Campus de Arrosadía, 31006 Pamplona, Spain.
| | - Jose F Moran
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Department of Sciences, Public University of Navarre (UPNA), Avda. de Pamplona 123, 31192 Mutilva, Spain.
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Du P, Xu S, Wu H, Liu Y, Wang ZG. Histidine-Based Supramolecular Nanoassembly Exhibiting Dual Enzyme-Mimetic Functions: Altering the Tautomeric Preference of Histidine to Tailor Oxidative/Hydrolytic Catalysis. NANO LETTERS 2023; 23:11461-11468. [PMID: 38079506 DOI: 10.1021/acs.nanolett.3c02934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Challenges persist in replicating enzyme-like active sites with functional group arrangements in supramolecular catalysis. In this study, we present a supramolecular material comprising Fmoc-modified histidine and copper. We also investigated the impact of noncanonical amino acids (δmH and εmH), isomers of histidine, on the catalytic process. The Fmoc-δmH-based nanoassembly exhibits an approximately 15-fold increase in oxidative activity and an ∼50-fold increase in hydrolytic activity compared to Fmoc-εmH (kcat/Km). This distinction arises from differences in basicity and ligation properties between the ε- and δ-nitrogen of histidine. The addition of guanosine monophosphate further enhances the oxidative activity of the histidine- and methylated histidine-based catalysts. The Fmoc-δmH/Cu2+-based nanoassembly catalyzes the oxidation/hydrolysis cascade of 2',7'-dichlorofluorescein diacetate, benefiting from the synergistic effect between the copper center and the nonligating ε-nitrogen of histidine. These findings advance the biomimetic catalyst design and provide insights into the mechanistic role of essential residues in natural systems.
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Affiliation(s)
- Peidong Du
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Shichao Xu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Haifeng Wu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yuanxi Liu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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8
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Podgorski MN, Lee JHZ, Harbort JS, Nguyen GTH, Doherty DZ, Donald WA, Harmer JR, Bruning JB, Bell SG. Characterisation of the heme aqua-ligand coordination environment in an engineered peroxygenase cytochrome P450 variant. J Inorg Biochem 2023; 249:112391. [PMID: 37837941 DOI: 10.1016/j.jinorgbio.2023.112391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/30/2023] [Accepted: 10/02/2023] [Indexed: 10/16/2023]
Abstract
The cytochrome P450 enzymes (CYPs) are heme-thiolate monooxygenases that catalyse the insertion of an oxygen atom into the C-H bonds of organic molecules. In most CYPs, the activation of dioxygen by the heme is aided by an acid-alcohol pair of residues located in the I-helix of the enzyme. Mutation of the threonine residue of this acid-alcohol pair of CYP199A4, from the bacterium Rhodospeudomonas palustris HaA2, to a glutamate residue induces peroxygenase activity. In the X-ray crystal structures of this variant an interaction of the glutamate side chain and the distal aqua ligand of the heme was observed and this results in this ligand not being readily displaced in the peroxygenase mutant on the addition of substrate. Here we use a range of bulky hydrophobic and nitrogen donor containing ligands in an attempt to displace the distal aqua ligand of the T252E mutant of CYP199A4. Ligand binding was assessed by UV-visible absorbance spectroscopy, native mass spectrometry, electron paramagnetic resonance and X-ray crystallography. None of the ligands tested, even the nitrogen donor ligands which bind directly to the iron in the wild-type enzyme, resulted in displacement of the aqua ligand. Therefore, modification of the I-helix threonine residue to a glutamate residue results in a significant strengthening of the ferric distal aqua ligand. This ligand was not displaced using any of the ligands during this study and this provides a rationale as to why this mutant can shutdown the monooxygenase pathway of this enzyme and switch to peroxygenase activity.
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Affiliation(s)
- Matthew N Podgorski
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - Joel H Z Lee
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - Joshua S Harbort
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, QLD 4072, Australia
| | - Giang T H Nguyen
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Daniel Z Doherty
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Jeffrey R Harmer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, QLD 4072, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, SA 5005, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia.
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9
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Costa GJ, Liang R. Understanding the Multifaceted Mechanism of Compound I Formation in Unspecific Peroxygenases through Multiscale Simulations. J Phys Chem B 2023; 127:8809-8824. [PMID: 37796883 DOI: 10.1021/acs.jpcb.3c04589] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Unspecific peroxygenases (UPOs) can selectively oxyfunctionalize unactivated hydrocarbons by using peroxides under mild conditions. They circumvent the oxygen dilemma faced by cytochrome P450s and exhibit greater stability than the latter. As such, they hold great potential for industrial applications. A thorough understanding of their catalysis is needed to improve their catalytic performance. However, it remains elusive how UPOs effectively convert peroxide to Compound I (CpdI), the principal oxidizing intermediate in the catalytic cycle. Previous computational studies of this process primarily focused on heme peroxidases and P450s, which have significant differences in the active site from UPOs. Additionally, the roles of peroxide unbinding in the kinetics of CpdI formation, which is essential for interpreting existing experiments, have been understudied. Moreover, there has been a lack of free energy characterizations with explicit sampling of protein and hydration dynamics, which is critical for understanding the thermodynamics of the proton transport (PT) events involved in CpdI formation. To bridge these gaps, we employed multiscale simulations to comprehensively characterize the CpdI formation in wild-type UPO from Agrocybe aegerita (AaeUPO). Extensive free energy and potential energy calculations were performed in a quantum mechanics/molecular mechanics setting. Our results indicate that substrate-binding dehydrates the active site, impeding the PT from H2O2 to a nearby catalytic base (Glu196). Furthermore, the PT is coupled with considerable hydrogen bond network rearrangements near the active site, facilitating subsequent O-O bond cleavage. Finally, large unbinding free energy barriers kinetically stabilize H2O2 at the active site. These findings reveal a delicate balance among PT, hydration dynamics, hydrogen bond rearrangement, and cosubstrate unbinding, which collectively enable efficient CpdI formation. Our simulation results are consistent with kinetic measurements and offer new insights into the CpdI formation mechanism at atomic-level details, which can potentially aid the design of next-generation biocatalysts for sustainable chemical transformations of feedstocks.
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Affiliation(s)
- Gustavo J Costa
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Ruibin Liang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
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10
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Li J, Tan W, Li X, Zhang P, Jin P, Fan J, Li K. Silver Ion-Facilitated Singular Poulos-Kraut Mechanism of O-O Heterolysis to Enhance the Light Activation of H 2O 2 over Peroxidase-Mimicking Photonanozymes. Anal Chem 2023; 95:12435-12442. [PMID: 37566745 DOI: 10.1021/acs.analchem.3c02095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
Abstract
The Poulos-Kraut heterolytic O-O cleavage mechanism is essential for natural peroxidases to activate H2O2. Current existing peroxidase-mimicking nanozymes, including photonanozymes (PNZs), however, are generally believed to prefer the Fenton-type mechanism of O-O homolysis, which produces •OH radicals. Here, Ag+ ions are introduced into TiO2 PNZs to boost the hot hole-driven O-O heterolysis for the expedited H2O2 activation in the peroxidase-like photonanozymatic reaction while inhibiting the Fenton-type O-O homolysis. The Ag+-facilitated Poulos-Kraut heterolytic O-O cleavage mechanism for H2O2 activation is explicated in terms of the speedy capture and exhaustion of photogenerated electrons by Ag+ and the dissociation of the peroxo-oxygen bridge in Ti-O-OH promoted by accumulated hot holes. Moreover, the enhanced photonanozymatic activity of TiO2 PNZs enables the construction of a rapid colorimetric sensing platform for Ag+ determination. This work provides valuable insights into the mechanism of H2O2 activation and exemplifies a novel photoregulation strategy for controlling reaction pathways in nanozymes.
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Affiliation(s)
- Jinzhao Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Wenlong Tan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Xu Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Pei Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Peng Jin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Jinsong Fan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
| | - Kun Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P. R. China
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11
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Xu S, Wu H, Liu S, Du P, Wang H, Yang H, Xu W, Chen S, Song L, Li J, Shi X, Wang ZG. A supramolecular metalloenzyme possessing robust oxidase-mimetic catalytic function. Nat Commun 2023; 14:4040. [PMID: 37419896 PMCID: PMC10328989 DOI: 10.1038/s41467-023-39779-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/23/2023] [Indexed: 07/09/2023] Open
Abstract
Enzymes fold into unique three-dimensional structures to distribute their reactive amino acid residues, but environmental changes can disrupt their essential folding and lead to irreversible activity loss. The de novo synthesis of enzyme-like active sites is challenging due to the difficulty of replicating the spatial arrangement of functional groups. Here, we present a supramolecular mimetic enzyme formed by self-assembling nucleotides with fluorenylmethyloxycarbonyl (Fmoc)-modified amino acids and copper. This catalyst exhibits catalytic functions akin those of copper cluster-dependent oxidases, and catalytic performance surpasses to date-reported artificial complexes. Our experimental and theoretical results reveal the crucial role of periodic arrangement of amino acid components, enabled by fluorenyl stacking, in forming oxidase-mimetic copper clusters. Nucleotides provide coordination atoms that enhance copper activity by facilitating the formation of a copper-peroxide intermediate. The catalyst shows thermophilic behavior, remaining active up to 95 °C in an aqueous environment. These findings may aid the design of advanced biomimetic catalysts and offer insights into primordial redox enzymes.
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Affiliation(s)
- Shichao Xu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Haifeng Wu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Siyuan Liu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Peidong Du
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Hui Wang
- Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China.
| | - Haijun Yang
- Department of Chemistry, Tsinghua University, Beijing, 10084, China
| | - Wenjie Xu
- National Synchrotron Radiation Laboratory, CAS Center for Excellence in Nanoscience, University of Science and Technology of China, Hefei, 230029, China
| | - Shuangming Chen
- National Synchrotron Radiation Laboratory, CAS Center for Excellence in Nanoscience, University of Science and Technology of China, Hefei, 230029, China
| | - Li Song
- National Synchrotron Radiation Laboratory, CAS Center for Excellence in Nanoscience, University of Science and Technology of China, Hefei, 230029, China
| | - Jikun Li
- Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing, 100190, China
| | - Xinghua Shi
- Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
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12
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Cao YC, Liao RZ. QM Calculations Revealed that Outer-Sphere Electron Transfer Boosted O-O Bond Cleavage in the Multiheme-Dependent Cytochrome bd Oxygen Reductase. Inorg Chem 2023; 62:4066-4075. [PMID: 36857027 DOI: 10.1021/acs.inorgchem.2c03742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The cytochrome bd oxygen reductase catalyzes the four-electron reduction of dioxygen to two water molecules. The structure of this enzyme reveals three heme molecules in the active site, which differs from that of heme-copper cytochrome c oxidase. The quantum chemical cluster approach was used to uncover the reaction mechanism of this intriguing metalloenzyme. The calculations suggested that a proton-coupled electron transfer reduction occurs first to generate a ferrous heme b595. This is followed by the dioxygen binding at the heme d center coupled with an outer-sphere electron transfer from the ferrous heme b595 to the dioxygen moiety, affording a ferric ion superoxide intermediate. A second proton-coupled electron transfer produces a heme d ferric hydroperoxide, which undergoes efficient O-O bond cleavage facilitated by an outer-sphere electron transfer from the ferrous heme b595 to the O-O σ* orbital and an inner-sphere proton transfer from the heme d hydroxyl group to the leaving hydroxide. The synergistic benefits of the two types of hemes rationalize the highly efficient oxygen reduction repertoire for the multi-heme-dependent cytochrome bd oxygen reductase family.
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Affiliation(s)
- Yu-Chen Cao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
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13
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Fang W, Feng S, Jiang Z, Liang W, Li P, Wang B. Understanding the Key Roles of pH Buffer in Accelerating Lignin Degradation by Lignin Peroxidase. JACS AU 2023; 3:536-549. [PMID: 36873691 PMCID: PMC9976348 DOI: 10.1021/jacsau.2c00649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 06/18/2023]
Abstract
pH buffer plays versatile roles in both biology and chemistry. In this study, we unravel the critical role of pH buffer in accelerating degradation of the lignin substrate in lignin peroxidase (LiP) using QM/MM MD simulations and the nonadiabatic electron transfer (ET) and proton-coupled electron transfer (PCET) theories. As a key enzyme involved in lignin degradation, LiP accomplishes the oxidation of lignin via two consecutive ET reactions and the subsequent C-C cleavage of the lignin cation radical. The first one involves ET from Trp171 to the active species of Compound I, while the second one involves ET from the lignin substrate to the Trp171 radical. Differing from the common view that pH = 3 may enhance the oxidizing power of Cpd I via protonation of the protein environment, our study shows that the intrinsic electric fields have minor effects on the first ET step. Instead, our study shows that the pH buffer of tartaric acid plays key roles during the second ET step. Our study shows that the pH buffer of tartaric acid can form a strong H-bond with Glu250, which can prevent the proton transfer from the Trp171-H•+ cation radical to Glu250, thereby stabilizing the Trp171-H•+ cation radical for the lignin oxidation. In addition, the pH buffer of tartaric acid can enhance the oxidizing power of the Trp171-H•+ cation radical via both the protonation of the proximal Asp264 and the second-sphere H-bond with Glu250. Such synergistic effects of pH buffer facilitate the thermodynamics of the second ET step and reduce the overall barrier of lignin degradation by ∼4.3 kcal/mol, which corresponds to a rate acceleration of 103-fold that agrees with experiments. These findings not only expand our understanding on pH-dependent redox reactions in both biology and chemistry but also provide valuable insights into tryptophan-mediated biological ET reactions.
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Affiliation(s)
- Wenhan Fang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering and Innovation Laboratory
for Sciences and Technologies of Energy Materials of Fujian Province
(IKKEM), Xiamen University, Xiamen361005, P. R. China
| | - Shishi Feng
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering and Innovation Laboratory
for Sciences and Technologies of Energy Materials of Fujian Province
(IKKEM), Xiamen University, Xiamen361005, P. R. China
| | - Zhihui Jiang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering and Innovation Laboratory
for Sciences and Technologies of Energy Materials of Fujian Province
(IKKEM), Xiamen University, Xiamen361005, P. R. China
| | - Wanzhen Liang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering and Innovation Laboratory
for Sciences and Technologies of Energy Materials of Fujian Province
(IKKEM), Xiamen University, Xiamen361005, P. R. China
| | - Pengfei Li
- Department
of Chemistry and Biochemistry, Loyola University
Chicago, 1068 W. Sheridan Rd., Chicago, Illinois60660, United States
| | - Binju Wang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering and Innovation Laboratory
for Sciences and Technologies of Energy Materials of Fujian Province
(IKKEM), Xiamen University, Xiamen361005, P. R. China
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14
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Collins DP, Johnson E, Coulter ED, Beharry Z, Ballou DP, Dawson JH. Caught in the act: Monitoring OO bond cleavage in Acylperoxoferric cytochrome P450cam to form compound I in real time. J Inorg Biochem 2022; 236:111949. [PMID: 36028338 DOI: 10.1016/j.jinorgbio.2022.111949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 07/25/2022] [Indexed: 12/15/2022]
Abstract
While monitoring the reaction of ferric cytochrome P450cam (Cyp101) with substituted peroxybenzoic acids using rapid-scanning, stopped-flow (RSSF) spectroscopy, an intermediate appears en route to formation of the high-valent moiety known as Compound I [Fe(IV)=O/porphyrin radical cation] that is thought to be the key catalytic species for O-atom transfer to substrate. We have previously suggested (Spolitak, T., Dawson, J.H., Ballou, D.P., J. Biol. Chem.2005, 280, 20,300-20,309) that this species is an acylperoxo-ferric heme adduct that subsequently undergoes OO bond cleavage to generate Compound I. Singular value decomposition analysis of the RSSF data for formation of this intermediate shows that the energy of its Soret absorption peak is sensitive to the electron donor properties of the aryl substituents on the peracid. A linear Hammett correlation plot is seen for the energy of the Soret absorption peak vs. the Hammett σ constant. This correlation requires that the aryl substituents remain as part of the ligand bound to the heme iron, providing direct evidence that the adduct is indeed a ferric acylperoxo derivative. Linear Hammett correlation plots are also seen for both the rate of formation of the intermediate as well as for its conversion to Compound I. It is proposed that the electron donating/withdrawing properties of the aryl-bound substituents affect the electrophilic nature for binding substrate, changing the observed rate of formation for the acylperoxo intermediate, as well as the propensity and stability of the substituted benzoic acid to serve as the leaving group during OO bond cleavage yielding Compound I.
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Affiliation(s)
- Daniel P Collins
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Emily Johnson
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Eric D Coulter
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Zanna Beharry
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - David P Ballou
- Department of Biological Chemistry, Medical School, University of Michigan, Ann Arbor, MI 48109, USA.
| | - John H Dawson
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA.
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15
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Teng Q, Wu H, Sun H, Liu Y, Wang H, Wang ZG. Switchable Enzyme-mimicking catalysts Self-Assembled from de novo designed peptides and DNA G-quadruplex/hemin complex. J Colloid Interface Sci 2022; 628:1004-1011. [PMID: 35970126 DOI: 10.1016/j.jcis.2022.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/25/2022] [Accepted: 08/01/2022] [Indexed: 01/02/2023]
Abstract
Reconstruction of enzymatic active site in an artificial system is key to achieving high catalytic efficiency. Herein, we report the self-assembly of the lysine-containing peptides with guanine-rich DNA and hemin to form peroxidase-mimicking active sites and catalytic nanoparticles. The DNA strand self-folds into a G-quadruplex structure that provides a supramolecular scaffold and a potential axial ligand for hemin. The β-sheet forming capability of the lysine-containing peptides is found to affect the catalytic synergy between the G-quadruplex DNA and the peptide. It is hypothesized that the β-sheet formation of the peptides results in the enrichment of the lysine residues, which distribute on the distal side of hemin to promote the formation of Compound I, like distal arginine residue in natural heme pocket. Incorporation of the histidine residues into the lysine-containing peptides further enhanced the hemin activities, indicating the cooperation between the lysine and histidine. Furthermore, the peptide/DNA/hemin complexes can be switched between active and inactive state by reversible formation and deformation of the DNA G-quadruplex, which was attributed to the peptides-promoted conformational changes of the DNA components. This work opens an avenue to mimic the catalytic residues and their spatial distribution in the natural enzymes, and shed light on the design of the smart biocatalysts that can respond to the environmental stimuli.
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Affiliation(s)
- Qiao Teng
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Haifeng Wu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hao Sun
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yuanxi Liu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hui Wang
- Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, CAS Key Laboratory of Nanophotonic Materials and Devices, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
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16
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Aboelnga MM. Mechanistic insights into the chemistry of compound I formation in heme peroxidases: quantum chemical investigations of cytochrome c peroxidase. RSC Adv 2022; 12:15543-15554. [PMID: 35685178 PMCID: PMC9125774 DOI: 10.1039/d2ra01073a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/17/2022] [Indexed: 11/21/2022] Open
Abstract
Peroxidases are heme containing enzymes that catalyze peroxide-dependant oxidation of a variety of substrates through forming key ferryl intermediates, compounds I and II. Cytochrome c peroxidase (Ccp1) has served for decades as a chemical model toward understanding the chemical biology of this heme family of enzymes. It is known to feature a distinctive electronic behaviour for its compound I despite significant structural similarity to other peroxidases. A water-assisted mechanism has been proposed over a dry one for the formation of compound I in similar peroxidases. To better identify the viability of these mechanisms, we employed quantum chemistry calculations for the heme pocket of Ccp1 in three different spin states. We provided comparative energetic and structural results for the six possible pathways that suggest the preference of the dry mechanism energetically and structurally. The doublet state is found to be the most preferable spin state for the mechanism to proceed and for the formation of the Cpd I ferryl-intermediate irrespective of the considered dielectric constant used to represent the solvent environment. The nature of the spin state has negligible effects on the calculated structures but great impact on the energetics. Our analysis was also expanded to explain the major contribution of key residues to the peroxidase activity of Ccp1 through exploring the mechanism at various in silico generated Ccp1 variants. Overall, we provide valuable findings toward solving the current ambiguity of the exact mechanism in Ccp1, which could be applied to peroxidases with similar heme pockets. Discerning the feasibility of a no-water peroxidase mechanism in the doublet spin state irrespective of the environment surrounding the heme pocket.![]()
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Affiliation(s)
- Mohamed M Aboelnga
- Chemistry Department, Faculty of Science, Damietta University New Damietta 34517 Egypt
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17
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Nayek A, Ahmed ME, Samanta S, Dinda S, Patra S, Dey SG, Dey A. Bioinorganic Chemistry on Electrodes: Methods to Functional Modeling. J Am Chem Soc 2022; 144:8402-8429. [PMID: 35503922 DOI: 10.1021/jacs.2c01842] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
One of the major goals of bioinorganic chemistry has been to mimic the function of elegant metalloenzymes. Such functional modeling has been difficult to attain in solution, in particular, for reactions that require multiple protons and multiple electrons (nH+/ne-). Using a combination of heterogeneous electrochemistry, electrode and molecule design one may control both electron transfer (ET) and proton transfer (PT) of these nH+/ne- reactions. Such control can allow functional modeling of hydrogenases (H+ + e- → 1/2 H2), cytochrome c oxidase (O2 + 4 e- + 4 H+ → 2 H2O), monooxygenases (RR'CH2 + O2 + 2 e- + 2 H+ → RR'CHOH + H2O) and dioxygenases (S + O2 → SO2; S = organic substrate) in aqueous medium and at room temperatures. In addition, these heterogeneous constructs allow probing unnatural bioinspired reactions and estimation of the inner- and outer-sphere reorganization energy of small molecules and proteins.
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Affiliation(s)
- Abhijit Nayek
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Md Estak Ahmed
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Soumya Samanta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Souvik Dinda
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Suman Patra
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Somdatta Ghosh Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
| | - Abhishek Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India 700032
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18
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Roy M, Nath AK, Pal I, Dey SG. Second Sphere Interactions in Amyloidogenic Diseases. Chem Rev 2022; 122:12132-12206. [PMID: 35471949 DOI: 10.1021/acs.chemrev.1c00941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amyloids are protein aggregates bearing a highly ordered cross β structural motif, which may be functional but are mostly pathogenic. Their formation, deposition in tissues and consequent organ dysfunction is the central event in amyloidogenic diseases. Such protein aggregation may be brought about by conformational changes, and much attention has been directed toward factors like metal binding, post-translational modifications, mutations of protein etc., which eventually affect the reactivity and cytotoxicity of the associated proteins. Over the past decade, a global effort from different groups working on these misfolded/unfolded proteins/peptides has revealed that the amino acid residues in the second coordination sphere of the active sites of amyloidogenic proteins/peptides cause changes in H-bonding pattern or protein-protein interactions, which dramatically alter the structure and reactivity of these proteins/peptides. These second sphere effects not only determine the binding of transition metals and cofactors, which define the pathology of some of these diseases, but also change the mechanism of redox reactions catalyzed by these proteins/peptides and form the basis of oxidative damage associated with these amyloidogenic diseases. The present review seeks to discuss such second sphere modifications and their ramifications in the etiopathology of some representative amyloidogenic diseases like Alzheimer's disease (AD), type 2 diabetes mellitus (T2Dm), Parkinson's disease (PD), Huntington's disease (HD), and prion diseases.
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Affiliation(s)
- Madhuparna Roy
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Arnab Kumar Nath
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Ishita Pal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Somdatta Ghosh Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
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19
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Podgorski MN, Harbort JS, Lee JHZ, Nguyen GT, Bruning JB, Donald WA, Bernhardt PV, Harmer JR, Bell SG. An Altered Heme Environment in an Engineered Cytochrome P450 Enzyme Enables the Switch from Monooxygenase to Peroxygenase Activity. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05877] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Matthew N. Podgorski
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Joshua S. Harbort
- Center for Advanced Imaging, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Joel H. Z. Lee
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Giang T.H. Nguyen
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - John B. Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - William A. Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Paul V. Bernhardt
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jeffrey R. Harmer
- Center for Advanced Imaging, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Stephen G. Bell
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
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20
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Škulj S, Barišić A, Mutter N, Spadiut O, Barišić I, Bertoša B. Effect of N-glycosylation on horseradish peroxidase structural and dynamical properties. Comput Struct Biotechnol J 2022; 20:3096-3105. [PMID: 35782731 PMCID: PMC9233188 DOI: 10.1016/j.csbj.2022.06.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/03/2022] [Accepted: 06/04/2022] [Indexed: 11/03/2022] Open
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21
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Mukherjee M, Dey A. Rejigging Electron and Proton Transfer to Transition between Dioxygenase, Monooxygenase, Peroxygenase, and Oxygen Reduction Activity: Insights from Bioinspired Constructs of Heme Enzymes. JACS AU 2021; 1:1296-1311. [PMID: 34604840 PMCID: PMC8479764 DOI: 10.1021/jacsau.1c00100] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Indexed: 05/10/2023]
Abstract
Nature has employed heme proteins to execute a diverse set of vital life processes. Years of research have been devoted to understanding the factors which bias these heme enzymes, with all having a heme cofactor, toward distinct catalytic activity. Among them, axial ligation, distal super structure, and substrate binding pockets are few very vividly recognized ones. Detailed mechanistic investigation of these heme enzymes suggested that several of these enzymes, while functionally divergent, use similar intermediates. Furthermore, the formation and decay of these intermediates depend on proton and electron transfer processes in the enzyme active site. Over the past decade, work in this group, using in situ surface enhanced resonance Raman spectroscopy of synthetic and biosynthetic analogues of heme enzymes, a general idea of how proton and electron transfer rates relate to the lifetime of different O2 derived intermediates has been developed. These findings suggest that the enzymatic activities of all these heme enzymes can be integrated into one general cycle which can be branched out to different catalytic pathways by regulating the lifetime and population of each of these intermediates. This regulation can further be achieved by tuning the electron and proton transfer steps. By strategically populating one of these intermediates during oxygen reduction, one can navigate through different catalytic processes to a desired direction by altering proton and electron transfer steps.
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Affiliation(s)
- Manjistha Mukherjee
- School of Chemical Science, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India, 700032
| | - Abhishek Dey
- School of Chemical Science, Indian Association for the Cultivation of Science, 2A Raja SC Mullick Road, Kolkata, WB India, 700032
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22
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Tian G, Hao G, Chen X, Liu Y. Tyrosyl Radical-Mediated Sequential Oxidative Decarboxylation of Coproporphyrinogen III through PCET: Theoretical Insights into the Mechanism of Coproheme Decarboxylase ChdC. Inorg Chem 2021; 60:13539-13549. [PMID: 34382397 DOI: 10.1021/acs.inorgchem.1c01864] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The peroxide-dependent coproheme decarboxylase ChdC from Geobacillus stearothermophilus catalyzes two key steps in the synthesis of heme b, i.e., two sequential oxidative decarboxylations of coproporphyrinogen III (coproheme III) at propionate groups P2 and P4. In the binding site of coproheme III, P2 and P4 are anchored by different residues (Tyr144, Arg217, and Ser222 for P2 and Tyr113, Lys148, and Trp156 for P4); however, strong experimental evidence supports that the generated Tyr144 radical acts as an unique intermediary for hydrogen atom transfer (HAT) from both reactive propionates. So far, the reaction details are still unclear. Herein, we carried out quantum mechanics/molecular mechanics calculations to explore the decarboxylation mechanism of coproheme III. In our calculations, the coproheme Cpd I, Fe(IV) = O coupled to a porphyrin radical cation (por•+) with four propionate groups, was used as a reactant model. Our calculations reveal that Tyr144 is directly involved in the decarboxylation of propionate group P2. First, the proton-coupled electron transfer (PCET) occurs from Tyr144 to P2, generating a Tyr144 radical, which then abstracts a hydrogen atom from the Cβ of P2. The β-H extraction was calculated to be the rate-limiting step of decarboxylation. It is the porphyrin radical cation (por•+) that makes the PCET from Tyr144 to P2 to be quite easy to initiate the decarboxylation. Finally, the electron transfers from the Cβ• through the porphyrin to the iron center, leading to the decarboxylation of P2. Importantly, the decarboxylation of P4 mediated by Lys148 was calculated to be very difficult, which suggests that after the P2 decarboxylation, the generated harderoheme III intermediate should rebind or rotate in the active site so that the propionate P4 occupies the binding site of P2, and Tyr144 again mediates the decarboxylation of P4. Thus, our calculations support the fact that Tyr144 is responsible for the decarboxylation of both P2 and P4.
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Affiliation(s)
- Ge Tian
- School of Life Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, Shandong 271000, China.,School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Gangping Hao
- School of Life Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, Shandong 271000, China
| | - Xiaohua Chen
- National-Municipal Joint Engineering Laboratory for Chemical Process Intensification and Reaction, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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23
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Product Distributions of Cytochrome P450 OleT JE with Phenyl-Substituted Fatty Acids: A Computational Study. Int J Mol Sci 2021; 22:ijms22137172. [PMID: 34281222 PMCID: PMC8269385 DOI: 10.3390/ijms22137172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 11/17/2022] Open
Abstract
There are two types of cytochrome P450 enzymes in nature, namely, the monooxygenases and the peroxygenases. Both enzyme classes participate in substrate biodegradation or biosynthesis reactions in nature, but the P450 monooxygenases use dioxygen, while the peroxygenases take H2O2 in their catalytic cycle instead. By contrast to the P450 monooxygenases, the P450 peroxygenases do not require an external redox partner to deliver electrons during the catalytic cycle, and also no external proton source is needed. Therefore, they are fully self-sufficient, which affords them opportunities in biotechnological applications. One specific P450 peroxygenase, namely, P450 OleTJE, reacts with long-chain linear fatty acids through oxidative decarboxylation to form hydrocarbons and, as such, has been implicated as a suitable source for the biosynthesis of biofuels. Unfortunately, the reactions were shown to produce a considerable amount of side products originating from Cα and Cβ hydroxylation and desaturation. These product distributions were found to be strongly dependent on whether the substrate had substituents on the Cα and/or Cβ atoms. To understand the bifurcation pathways of substrate activation by P450 OleTJE leading to decarboxylation, Cα hydroxylation, Cβ hydroxylation and Cα–Cβ desaturation, we performed a computational study using 3-phenylpropionate and 2-phenylbutyrate as substrates. We set up large cluster models containing the heme, the substrate and the key features of the substrate binding pocket and calculated (using density functional theory) the pathways leading to the four possible products. This work predicts that the two substrates will react with different reaction rates due to accessibility differences of the substrates to the active oxidant, and, as a consequence, these two substrates will also generate different products. This work explains how the substrate binding pocket of P450 OleTJE guides a reaction to a chemoselectivity.
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24
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Zhang X, Jiang Y, Chen Q, Dong S, Feng Y, Cong Z, Shaik S, Wang B. H-Bonding Networks Dictate the Molecular Mechanism of H2O2 Activation by P450. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02068] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xuan Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Yiping Jiang
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, People’s Republic of China
| | - Qianqian Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Sheng Dong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, People’s Republic of China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, People’s Republic of China
| | - Zhiqi Cong
- CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, People’s Republic of China
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, 9190407 Jerusalem, Israel
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
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25
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Liu Q, Wan K, Shang Y, Wang ZG, Zhang Y, Dai L, Wang C, Wang H, Shi X, Liu D, Ding B. Cofactor-free oxidase-mimetic nanomaterials from self-assembled histidine-rich peptides. NATURE MATERIALS 2021; 20:395-402. [PMID: 33257794 DOI: 10.1038/s41563-020-00856-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 10/14/2020] [Indexed: 05/21/2023]
Abstract
Natural oxidases mainly rely on cofactors and well-arranged amino acid residues for catalysing electron-transfer reactions but suffer from non-recovery of their activity upon externally induced protein unfolding. However, it remains unknown whether residues at the active site can catalyse similar reactions in the absence of the cofactor. Here, we describe a series of self-assembling, histidine-rich peptides, as short as a dipeptide, with catalytic function similar to that of haem-dependent peroxidases. The histidine residues of the peptide chains form periodic arrays that are able to catalyse H2O2 reduction reactions efficiently through the formation of reactive ternary complex intermediates. The supramolecular catalyst exhibiting the highest activity could be switched between inactive and active states without loss of activity for ten cycles of heating/cooling or acidification/neutralization treatments, demonstrating the reversible assembly/disassembly of the active residues. These findings may aid the design of advanced biomimetic catalytic materials and provide a model for primitive cofactor-free enzymes.
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Affiliation(s)
- Qing Liu
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, People's Republic of China
| | - Kaiwei Wan
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, People's Republic of China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, People's Republic of China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic-Inorganic Composites, Key Laboratory of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing, China.
| | - Yiyang Zhang
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, China
| | - Luru Dai
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, People's Republic of China
| | - Chen Wang
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, People's Republic of China
- University of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Hui Wang
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, People's Republic of China.
| | - Xinghua Shi
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, People's Republic of China
- University of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, People's Republic of China.
- University of the Chinese Academy of Sciences, Beijing, People's Republic of China.
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26
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Ghatak A, Bhunia S, Dey A. Effect of Pendant Distal Residues on the Rate and Selectivity of Electrochemical Oxygen Reduction Reaction Catalyzed by Iron Porphyrin Complexes. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02836] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Arnab Ghatak
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
| | - Sarmistha Bhunia
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
| | - Abhishek Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
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27
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Mukherjee S, Nayek A, Bhunia S, Dey SG, Dey A. A Single Iron Porphyrin Shows pH Dependent Switch between "Push" and "Pull" Effects in Electrochemical Oxygen Reduction. Inorg Chem 2020; 59:14564-14576. [PMID: 32970430 DOI: 10.1021/acs.inorgchem.0c02408] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The "push-pull" effects associated with heme enzymes manifest themselves through highly evolved distal amino acid environments and axial ligands to the heme. These conserved residues enhance their reactivities by orders of magnitude relative to small molecules that mimic the primary coordination. An instance of a mononuclear iron porphyrin with covalently attached pendent phenanthroline groups is reported which exhibit reactivity indicating a pH dependent "push" to "pull" transition in the same molecule. The pendant phenanthroline residues provide proton transfer pathways into the iron site, ensuring selective 4e-/4H+ reduction of O2 to water. The protonation of these residues at lower pH mimics the pull effect of peroxidases, and a coordination of an axial hydroxide ligand at high pH emulates the push effect of P450 monooxygenases. Both effects enhance the rate of O2 reduction by orders of magnitude over its value at neutral pH while maintaining exclusive selectivity for 4e-/4H+ oxygen reduction reaction.
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Affiliation(s)
- Sudipta Mukherjee
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Abhijit Nayek
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Sarmistha Bhunia
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Somdatta Ghosh Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Abhishek Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
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28
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Shen X, Wang Z, Gao X, Zhao Y. Density Functional Theory-Based Method to Predict the Activities of Nanomaterials as Peroxidase Mimics. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03426] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Xiaomei Shen
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, China
| | - Zhenzhen Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Xingfa Gao
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, China
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
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29
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Bhunia S, Rana A, Dey SG, Ivancich A, Dey A. A designed second-sphere hydrogen-bond interaction that critically influences the O-O bond activation for heterolytic cleavage in ferric iron-porphyrin complexes. Chem Sci 2020; 11:2681-2695. [PMID: 34084327 PMCID: PMC8157560 DOI: 10.1039/c9sc04388h] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 01/26/2020] [Indexed: 12/18/2022] Open
Abstract
Heme hydroperoxidases catalyze the oxidation of substrates by H2O2. The catalytic cycle involves the formation of a highly oxidizing species known as Compound I, resulting from the two-electron oxidation of the ferric heme in the active site of the resting enzyme. This high-valent intermediate is formed upon facile heterolysis of the O-O bond in the initial FeIII-OOH complex. Heterolysis is assisted by the histidine and arginine residues present in the heme distal cavity. This chemistry has not been successfully modeled in synthetic systems up to now. In this work, we have used a series of iron(iii) porphyrin complexes (FeIIIL2(Br), FeIIIL3(Br) and FeIIIMPh(Br)) with covalently attached pendent basic groups (pyridine and primary amine) mimicking the histidine and arginine residues in the distal-pocket of natural heme enzymes. The presence of pendent basic groups, capable of 2nd sphere hydrogen bonding interactions, leads to almost 1000-fold enhancement in the rate of Compound I formation from peracids relative to analogous complexes without these residues. The short-lived Compound I intermediate formed at cryogenic temperatures could be detected using UV-vis electronic absorption spectroscopy and also trapped to be unequivocally identified by 9 GHz EPR spectroscopy at 4 K. The broad (2000 G) and axial EPR spectrum of an exchange-coupled oxoferryl-porphyrin radical species, [FeIV[double bond, length as m-dash]O Por˙+] with g eff ⊥ = 3.80 and g eff ‖ = 1.99, was observed upon a reaction of the FeIIIL3(Br) porphyrin complex with m-CPBA. The characterization of the reactivity of the FeIII porphyrin complexes with a substrate in the presence of an oxidant like m-CPBA by UV-vis electronic absorption spectroscopy showed that they are capable of oxidizing two equivalents of inorganic and organic substrate(s) like ferrocene, 2,4,6-tritertiary butyl phenol and o-phenylenediamine. These oxidations are catalytic with a turnover number (TON) as high as 350. Density Functional Theory (DFT) calculations show that the mechanism of O-O bond activation by 2nd sphere hydrogen bonding interaction from these pendent basic groups, which are protonated by a peracid, involves polarization of the O-O σ-bond, leading to lowering of the O-O σ*-orbital allowing enhanced back bonding from the iron center. These results demonstrate how inclusion of 2nd sphere hydrogen bonding interaction can play a critical role in O-O bond heterolysis.
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Affiliation(s)
- Sarmistha Bhunia
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science Kolkata 700032 India
| | - Atanu Rana
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science Kolkata 700032 India
| | - Somdatta Ghosh Dey
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science Kolkata 700032 India
| | - Anabella Ivancich
- CNRS, Aix-Marseille Univ, Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479 Marseille France
| | - Abhishek Dey
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science Kolkata 700032 India
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30
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Abstract
Lytic polysaccharide monooxygenases (LPMOs) are a recently discovered class of monocopper enzymes broadly distributed across the tree of life. Recent reports indicate that LPMOs can use H2O2 as an oxidant and thus carry out a novel type of peroxygenase reaction involving unprecedented copper chemistry. Here, we present a combined computational and experimental analysis of the H2O2-mediated reaction mechanism. In silico studies, based on a model of the enzyme in complex with a crystalline substrate, suggest that a network of hydrogen bonds, involving both the enzyme and the substrate, brings H2O2 into a strained reactive conformation and guides a derived hydroxyl radical toward formation of a copper-oxyl intermediate. The initial cleavage of H2O2 and subsequent hydrogen atom abstraction from chitin by the copper-oxyl intermediate are the main energy barriers. Stopped-flow fluorimetry experiments demonstrated that the priming reduction of LPMO-Cu(II) to LPMO-Cu(I) is a fast process compared to the reoxidation reactions. Using conditions resulting in single oxidative events, we found that reoxidation of LPMO-Cu(I) is 2,000-fold faster with H2O2 than with O2, the latter being several orders of magnitude slower than rates reported for other monooxygenases. The presence of substrate accelerated reoxidation by H2O2, whereas reoxidation by O2 became slower, supporting the peroxygenase paradigm. These insights into the peroxygenase nature of LPMOs will aid in the development and application of enzymatic and synthetic copper catalysts and contribute to a further understanding of the roles of LPMOs in nature, varying from biomass conversion to chitinolytic pathogenesis-defense mechanisms.
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31
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Mubarak MQE, Visser SP. Computational Study on the Catalytic Reaction Mechanism of Heme Haloperoxidase Enzymes. Isr J Chem 2019. [DOI: 10.1002/ijch.201900099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- M. Qadri E. Mubarak
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science The University of Manchester 131 Princess Street Manchester M1 7DN United Kingdom
| | - Sam P. Visser
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science The University of Manchester 131 Princess Street Manchester M1 7DN United Kingdom
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32
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Ghatak A, Bhakta S, Bhunia S, Dey A. Influence of the distal guanidine group on the rate and selectivity of O 2 reduction by iron porphyrin. Chem Sci 2019; 10:9692-9698. [PMID: 32055338 PMCID: PMC6993607 DOI: 10.1039/c9sc02711d] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/28/2019] [Indexed: 12/20/2022] Open
Abstract
The O2 reduction reaction (ORR) catalysed by iron porphyrins with covalently attached pendant guanidine groups is reported. The results show a clear enhancement in the rate and selectivity for the 4e-/4H+ ORR. In situ resonance Raman investigations show that the rate determining step (rds) is O2 binding to ferrous porphyrins in contrast to the case of mononuclear iron porphyrins and heme/Cu analogues where the O-O bond cleavage of a heme peroxide is the rds. The selectivity is further enhanced when an axial imidazole ligand is introduced. Thus, the combination of the axial imidazole ligand and pendant guanidine ligand, analogous to the active site of peroxidases, is determined to be very effective in enabling a facile and selective 4e-/4H+ ORR.
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Affiliation(s)
- Arnab Ghatak
- School of Chemical Sciences , Indian Association for the Cultivation of Science , 2A & 2B Raja S. C. Mullick Road, Jadavpur , Kolkata , 700032 , India .
| | - Snehadri Bhakta
- School of Chemical Sciences , Indian Association for the Cultivation of Science , 2A & 2B Raja S. C. Mullick Road, Jadavpur , Kolkata , 700032 , India .
| | - Sarmistha Bhunia
- School of Chemical Sciences , Indian Association for the Cultivation of Science , 2A & 2B Raja S. C. Mullick Road, Jadavpur , Kolkata , 700032 , India .
| | - Abhishek Dey
- School of Chemical Sciences , Indian Association for the Cultivation of Science , 2A & 2B Raja S. C. Mullick Road, Jadavpur , Kolkata , 700032 , India .
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33
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Shinomiya R, Araki H, Momotake A, Kotani H, Kojima T, Yamamoto Y. Identification of Intermediates in Peroxidase Catalytic Cycle of a DNAzyme Possessing Heme. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20190157] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ryosuke Shinomiya
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Haruka Araki
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Atsuya Momotake
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Hiroaki Kotani
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Takahiko Kojima
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
- Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
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34
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Pal I, Nath AK, Roy M, Seal M, Ghosh C, Dey A, Dey SG. Formation of compound I in heme bound Aβ-peptides relevant to Alzheimer's disease. Chem Sci 2019; 10:8405-8410. [PMID: 31803419 PMCID: PMC6844219 DOI: 10.1039/c9sc01679a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/22/2019] [Indexed: 12/02/2022] Open
Abstract
Proteolysis of Amyloid Precursor Protein, APP, results in the formation of amyloid β (Aβ) peptides, which have been associated with Alzheimer's disease (AD). Recently the failure of therapeutic agents that prohibit Aβ aggregation and sequester Cu/Zn in providing symptomatic relief to AD patients has questioned the amyloid and metal ion hypothesis. Alternatively, abnormal heme homeostasis and reduced levels of neurotransmitters in the brain are hallmark features of AD. Heme can bind Aβ peptides forming a peroxidase type active site which can oxidatively degrade neurotransmitters like serotonin. To date the reactive species responsible for this activity has not been identified. Using rapid kinetics and freeze quenching, we show that heme bound Aβ forms a highly reactive intermediate, compound I. Thus, compound I provides a basis for elucidating the oxidative degradation of neurotransmitters like serotonin, resulting in abnormal neurotransmission, a key pathological feature of AD. Site directed mutants indicate that the Arg5 and Tyr10 residues, unique to human Aβ, affect the rates of formation and decay of compound I providing insight into their roles in the oxidative degradation of neurotransmitters. Tyr10 can potentially play a natural protective role against the highly reactive oxidant, compound I, in AD.
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Affiliation(s)
- Ishita Pal
- Indian Association for the Cultivation of Science , 2A & 2B, Raja S. C. Mullick Road, Jadavpur , Kolkata 700032 , India .
| | - Arnab Kumar Nath
- Indian Association for the Cultivation of Science , 2A & 2B, Raja S. C. Mullick Road, Jadavpur , Kolkata 700032 , India .
| | - Madhuparna Roy
- Indian Association for the Cultivation of Science , 2A & 2B, Raja S. C. Mullick Road, Jadavpur , Kolkata 700032 , India .
| | - Manas Seal
- Indian Association for the Cultivation of Science , 2A & 2B, Raja S. C. Mullick Road, Jadavpur , Kolkata 700032 , India .
| | - Chandradeep Ghosh
- Indian Association for the Cultivation of Science , 2A & 2B, Raja S. C. Mullick Road, Jadavpur , Kolkata 700032 , India .
| | - Abhishek Dey
- Indian Association for the Cultivation of Science , 2A & 2B, Raja S. C. Mullick Road, Jadavpur , Kolkata 700032 , India .
| | - Somdatta Ghosh Dey
- Indian Association for the Cultivation of Science , 2A & 2B, Raja S. C. Mullick Road, Jadavpur , Kolkata 700032 , India .
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35
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Bhakta S, Nayek A, Roy B, Dey A. Induction of Enzyme-like Peroxidase Activity in an Iron Porphyrin Complex Using Second Sphere Interactions. Inorg Chem 2019; 58:2954-2964. [DOI: 10.1021/acs.inorgchem.8b02707] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Snehadri Bhakta
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Abhijit Nayek
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Bijan Roy
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
| | - Abhishek Dey
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
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36
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Zhang J, Tang M, Chen D, Lin B, Zhou Z, Liu Q. Horizontal and Vertical Push Effects in Saddled Zinc Porphyrin Complexes: Implications for Heme Distortion. Inorg Chem 2019; 58:2627-2636. [DOI: 10.1021/acs.inorgchem.8b03219] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Jinjin Zhang
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules, Ministry of Education, and School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Min Tang
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules, Ministry of Education, and School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Dilong Chen
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules, Ministry of Education, and School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Binghua Lin
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules, Ministry of Education, and School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Zaichun Zhou
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules, Ministry of Education, and School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Qiuhua Liu
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules, Ministry of Education, and School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
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37
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Bohn A, Chinaux-Chaix C, Cheaib K, Guillot R, Herrero C, Sénéchal-David K, Rebilly JN, Banse F. Base-controlled mechanistic divergence between iron(iv)-oxo and iron(iii)-hydroperoxo in the H2O2 activation by a nonheme iron(ii) complex. Dalton Trans 2019; 48:17045-17051. [DOI: 10.1039/c9dt03487k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
An FeII complex reacts with excess H2O2 in the presence of sub-stoichiometric NEt3 to give FeIV(O) and FeIII(OOH) reactive species following a base-dependent and a base-independent pathway, respectively.
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Affiliation(s)
- Antoine Bohn
- Institut de Chimie Moléculaire et des Matériaux d'Orsay
- Univ. Paris-Sud
- Univ. Paris-Saclay
- CNRS
- 91405 Orsay cedex
| | - Clémence Chinaux-Chaix
- Institut de Chimie Moléculaire et des Matériaux d'Orsay
- Univ. Paris-Sud
- Univ. Paris-Saclay
- CNRS
- 91405 Orsay cedex
| | - Khaled Cheaib
- Institut de Chimie Moléculaire et des Matériaux d'Orsay
- Univ. Paris-Sud
- Univ. Paris-Saclay
- CNRS
- 91405 Orsay cedex
| | - Régis Guillot
- Institut de Chimie Moléculaire et des Matériaux d'Orsay
- Univ. Paris-Sud
- Univ. Paris-Saclay
- CNRS
- 91405 Orsay cedex
| | - Christian Herrero
- Institut de Chimie Moléculaire et des Matériaux d'Orsay
- Univ. Paris-Sud
- Univ. Paris-Saclay
- CNRS
- 91405 Orsay cedex
| | - Katell Sénéchal-David
- Institut de Chimie Moléculaire et des Matériaux d'Orsay
- Univ. Paris-Sud
- Univ. Paris-Saclay
- CNRS
- 91405 Orsay cedex
| | - Jean-Noël Rebilly
- Institut de Chimie Moléculaire et des Matériaux d'Orsay
- Univ. Paris-Sud
- Univ. Paris-Saclay
- CNRS
- 91405 Orsay cedex
| | - Frédéric Banse
- Institut de Chimie Moléculaire et des Matériaux d'Orsay
- Univ. Paris-Sud
- Univ. Paris-Saclay
- CNRS
- 91405 Orsay cedex
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38
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Cheaib K, Mubarak MQE, Sénéchal-David K, Herrero C, Guillot R, Clémancey M, Latour JM, de Visser SP, Mahy JP, Banse F, Avenier F. Selective Formation of an FeIV
O or an FeIII
OOH Intermediate From Iron(II) and H2
O2
: Controlled Heterolytic versus Homolytic Oxygen-Oxygen Bond Cleavage by the Second Coordination Sphere. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201812724] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Khaled Cheaib
- Institut de Chimie Moléculaire et des matériaux d'Orsay (UMR 8182) Univ Paris Sud; Université Paris Saclay; 91405 Orsay cedex France
| | - M. Qadri E. Mubarak
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Katell Sénéchal-David
- Institut de Chimie Moléculaire et des matériaux d'Orsay (UMR 8182) Univ Paris Sud; Université Paris Saclay; 91405 Orsay cedex France
| | - Christian Herrero
- Institut de Chimie Moléculaire et des matériaux d'Orsay (UMR 8182) Univ Paris Sud; Université Paris Saclay; 91405 Orsay cedex France
| | - Régis Guillot
- Institut de Chimie Moléculaire et des matériaux d'Orsay (UMR 8182) Univ Paris Sud; Université Paris Saclay; 91405 Orsay cedex France
| | - Martin Clémancey
- LCBM/PMB and CEA/BIG/CBM/ and CNRS UMR 5249; Université Grenoble Alpes; Grenoble 38054 France
| | - Jean-Marc Latour
- LCBM/PMB and CEA/BIG/CBM/ and CNRS UMR 5249; Université Grenoble Alpes; Grenoble 38054 France
| | - Sam P. de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science; The University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Jean-Pierre Mahy
- Institut de Chimie Moléculaire et des matériaux d'Orsay (UMR 8182) Univ Paris Sud; Université Paris Saclay; 91405 Orsay cedex France
| | - Frédéric Banse
- Institut de Chimie Moléculaire et des matériaux d'Orsay (UMR 8182) Univ Paris Sud; Université Paris Saclay; 91405 Orsay cedex France
| | - Frédéric Avenier
- Institut de Chimie Moléculaire et des matériaux d'Orsay (UMR 8182) Univ Paris Sud; Université Paris Saclay; 91405 Orsay cedex France
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39
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Cheaib K, Mubarak MQE, Sénéchal-David K, Herrero C, Guillot R, Clémancey M, Latour JM, de Visser SP, Mahy JP, Banse F, Avenier F. Selective Formation of an Fe IV O or an Fe III OOH Intermediate From Iron(II) and H 2 O 2 : Controlled Heterolytic versus Homolytic Oxygen-Oxygen Bond Cleavage by the Second Coordination Sphere. Angew Chem Int Ed Engl 2018; 58:854-858. [PMID: 30485630 DOI: 10.1002/anie.201812724] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Indexed: 11/06/2022]
Abstract
We demonstrate that the devised incorporation of an alkylamine group into the second coordination sphere of an FeII complex allows to switch its reactivity with H2 O2 from the usual formation of FeIII species towards the selective generation of an FeIV -oxo intermediate. The FeIV -oxo species was characterized by UV/Vis absorption and Mössbauer spectroscopy. Variable-temperature kinetic analyses point towards a mechanism in which the heterolytic cleavage of the O-O bond is triggered by a proton transfer from the proximal to the distal oxygen atom in the FeII -H2 O2 complex with the assistance of the pendant amine. DFT studies reveal that this heterolytic cleavage is actually initiated by an homolytic O-O cleavage immediately followed by a proton-coupled electron transfer (PCET) that leads to the formation of the FeIV -oxo and release of water through a concerted mechanism.
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Affiliation(s)
- Khaled Cheaib
- Institut de Chimie Moléculaire et des matériaux d'Orsay (UMR 8182) Univ Paris Sud, Université Paris Saclay, 91405, Orsay cedex, France
| | - M Qadri E Mubarak
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Katell Sénéchal-David
- Institut de Chimie Moléculaire et des matériaux d'Orsay (UMR 8182) Univ Paris Sud, Université Paris Saclay, 91405, Orsay cedex, France
| | - Christian Herrero
- Institut de Chimie Moléculaire et des matériaux d'Orsay (UMR 8182) Univ Paris Sud, Université Paris Saclay, 91405, Orsay cedex, France
| | - Régis Guillot
- Institut de Chimie Moléculaire et des matériaux d'Orsay (UMR 8182) Univ Paris Sud, Université Paris Saclay, 91405, Orsay cedex, France
| | - Martin Clémancey
- LCBM/PMB and CEA/BIG/CBM/ and CNRS UMR 5249, Université Grenoble Alpes, Grenoble, 38054, France
| | - Jean-Marc Latour
- LCBM/PMB and CEA/BIG/CBM/ and CNRS UMR 5249, Université Grenoble Alpes, Grenoble, 38054, France
| | - Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Jean-Pierre Mahy
- Institut de Chimie Moléculaire et des matériaux d'Orsay (UMR 8182) Univ Paris Sud, Université Paris Saclay, 91405, Orsay cedex, France
| | - Frédéric Banse
- Institut de Chimie Moléculaire et des matériaux d'Orsay (UMR 8182) Univ Paris Sud, Université Paris Saclay, 91405, Orsay cedex, France
| | - Frédéric Avenier
- Institut de Chimie Moléculaire et des matériaux d'Orsay (UMR 8182) Univ Paris Sud, Université Paris Saclay, 91405, Orsay cedex, France
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40
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Enhancing the peroxidase-like activity of ficin via heme binding and colorimetric detection for uric acid. Talanta 2018; 185:433-438. [DOI: 10.1016/j.talanta.2018.04.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/27/2018] [Accepted: 04/01/2018] [Indexed: 12/19/2022]
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41
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Bhunia S, Rana A, Roy P, Martin DJ, Pegis ML, Roy B, Dey A. Rational Design of Mononuclear Iron Porphyrins for Facile and Selective 4e -/4H + O 2 Reduction: Activation of O-O Bond by 2nd Sphere Hydrogen Bonding. J Am Chem Soc 2018; 140:9444-9457. [PMID: 29975839 DOI: 10.1021/jacs.8b02983] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Facile and selective 4e-/4H+ electrochemical reduction of O2 to H2O in aqueous medium has been a sought-after goal for several decades. Elegant but synthetically demanding cytochrome c oxidase mimics have demonstrated selective 4e-/4H+ electrochemical O2 reduction to H2O is possible with rate constants as fast as 105 M-1 s-1 under heterogeneous conditions in aqueous media. Over the past few years, in situ mechanistic investigations on iron porphyrin complexes adsorbed on electrodes have revealed that the rate and selectivity of this multielectron and multiproton process is governed by the reactivity of a ferric hydroperoxide intermediate. The barrier of O-O bond cleavage determines the overall rate of O2 reduction and the site of protonation determines the selectivity. In this report, a series of mononuclear iron porphyrin complexes are rationally designed to achieve efficient O-O bond activation and site-selective proton transfer to effect facile and selective electrochemical reduction of O2 to water. Indeed, these crystallographically characterized complexes accomplish facile and selective reduction of O2 with rate constants >107 M-1 s-1 while retaining >95% selectivity when adsorbed on electrode surfaces (EPG) in water. These oxygen reduction reaction rate constants are 2 orders of magnitude faster than all known heme/Cu complexes and these complexes retain >90% selectivity even under rate determining electron transfer conditions that generally can only be achieved by installing additional redox active groups in the catalyst.
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Affiliation(s)
- Sarmistha Bhunia
- Department of Inorganic Chemistry , Indian Association for the Cultivation of Science , 2A Raja SC Mullick Road , Kolkata , West Bengal 700032 , India
| | - Atanu Rana
- Department of Inorganic Chemistry , Indian Association for the Cultivation of Science , 2A Raja SC Mullick Road , Kolkata , West Bengal 700032 , India
| | - Pronay Roy
- Department of Inorganic Chemistry , Indian Association for the Cultivation of Science , 2A Raja SC Mullick Road , Kolkata , West Bengal 700032 , India
| | - Daniel J Martin
- Department of Chemistry , Yale University , New Haven , Connecticut 06520 , United States
| | - Michael L Pegis
- Department of Chemistry , Yale University , New Haven , Connecticut 06520 , United States.,Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Bijan Roy
- Department of Inorganic Chemistry , Indian Association for the Cultivation of Science , 2A Raja SC Mullick Road , Kolkata , West Bengal 700032 , India
| | - Abhishek Dey
- Department of Inorganic Chemistry , Indian Association for the Cultivation of Science , 2A Raja SC Mullick Road , Kolkata , West Bengal 700032 , India
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42
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Wang ZG, Wang H, Liu Q, Duan F, Shi X, Ding B. Designed Self-Assembly of Peptides with G-Quadruplex/Hemin DNAzyme into Nanofibrils Possessing Enzyme-Mimicking Active Sites and Catalytic Functions. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00896] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhen-Gang Wang
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
| | - Hui Wang
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
| | - Qing Liu
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
| | - Fangyuan Duan
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
| | - Xinghua Shi
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
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43
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Huang XL. Hydrolysis of Phosphate Esters Catalyzed by Inorganic Iron Oxide Nanoparticles Acting as Biocatalysts. ASTROBIOLOGY 2018; 18:294-310. [PMID: 29489387 DOI: 10.1089/ast.2016.1628] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Phosphorus ester hydrolysis is one of the key chemical processes in biological systems, including signaling, free-energy transaction, protein synthesis, and maintaining the integrity of genetic material. Hydrolysis of this otherwise kinetically stable phosphoester and/or phosphoanhydride bond is induced by enzymes such as purple acid phosphatase. Here, I report that, as in previously reported aged inorganic iron ion solutions, the iron oxide nanoparticles in the solution, which are trapped in a dialysis membrane tube filled with the various iron oxides, significantly promote the hydrolysis of the various phosphate esters, including the inorganic polyphosphates, with enzyme-like kinetics. This observation, along with those of recent studies of iron oxide, vanadium pentoxide, and molybdenum trioxide nanoparticles that behave as mimics of peroxidase, bromoperoxidase, and sulfite oxidase, respectively, indicates that the oxo-metal bond in the oxide nanoparticles is critical for the function of these corresponding natural metalloproteins. These inorganic biocatalysts challenge the traditional concept of replicator-first scenarios and support the metabolism-first hypothesis. As biocatalysts, these inorganic nanoparticles with enzyme-like activity may work in natural terrestrial environments and likely were at work in early Earth environments as well. They may have played an important role in the C, H, O, S, and P metabolic pathway with regard to the emergence and early evolution of life. Key Words: Enzyme-Hydrolysis-Iron oxide-Nanoparticles-Origin of life-Phosphate ester. Astrobiology 18, 294-310.
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Abstract
Aerobic organisms have evolved to activate oxygen from the atmosphere, which allows them to catalyze the oxidation of different kinds of substrates. This activation of oxygen is achieved by a metal center (usually iron or copper) buried within a metalloprotein. In the case of iron-containing heme enzymes, the activation of oxygen is achieved by formation of transient iron-oxo (ferryl) intermediates; these intermediates are called Compound I and Compound II. The Compound I and II intermediates were first discovered in the 1930s in horseradish peroxidase, and it is now known that these same species are used across the family of heme enzymes, which include all of the peroxidases, the heme catalases, the P450s, cytochrome c oxidase, and NO synthase. Many years have passed since the first observations, but establishing the chemical nature of these transient ferryl species remains a fundamental question that is relevant to the reactivity, and therefore the usefulness, of these species in biology. This Account summarizes experiments that were conceived and conducted at Leicester and presents our ideas on the chemical nature, stability, and reactivity of these ferryl heme species. We begin by briefly summarizing the early milestones in the field, from the 1940s and 1950s. We present comparisons between the nature and reactivity of the ferryl species in horseradish peroxidase, cytochrome c peroxidase, and ascorbate peroxidase; and we consider different modes of electron delivery to ferryl heme, from different substrates in different peroxidases. We address the question of whether the ferryl heme is best formulated as an (unprotonated) FeIV═O or as a (protonated) FeIV-OH species. A range of spectroscopic approaches (EXAFS, resonance Raman, Mossbauer, and EPR) have been used over many decades to examine this question, and in the last ten years, X-ray crystallography has also been employed. We describe how information from all of these studies has blended together to create an overall picture, and how the recent application of neutron crystallography has directly identified protonation states and has helped to clarify the precise nature of the ferryl heme in cytochrome c peroxidase and ascorbate peroxidase. We draw comparisons between the Compound I and Compound II species that we have observed in peroxidases with those found in other heme systems, notably the P450s, highlighting possible commonality across these heme ferryl systems. The identification of proton locations from neutron structures of these ferryl species opens the door for understanding the proton translocations that need to occur during O-O bond cleavage.
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Affiliation(s)
- Peter C. E. Moody
- Department
of Molecular and Cell Biology and Leicester Institute of Structural
and Chemical Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, England
| | - Emma L. Raven
- Department
of Chemistry and Leicester Institute of Structural and Chemical Biology, University of Leicester, University Road, Leicester LE1 7RH, U.K
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45
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Shrestha R, Huang G, Meekins DA, Geisbrecht BV, Li P. Mechanistic Insights into Dye-Decolorizing Peroxidase Revealed by Solvent Isotope and Viscosity Effects. ACS Catal 2017; 7:6352-6364. [PMID: 29308295 PMCID: PMC5751952 DOI: 10.1021/acscatal.7b01861] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dye-decolorizing peroxidases (DyPs) are a family of H2O2-dependent heme peroxidases, which have shown potential applications in lignin degradation and valorization. However, the DyP kinetic mechanism remains underexplored. Using structural biology and solvent isotope (sKIE) and viscosity effects, many mechanistic characteristics have been uncovered for the B-class ElDyP from Enterobacter lignolyticus. Its structure revealed that a water molecule acts as the sixth axial ligand with two channels at diameters of ~3.0 and 8.0 Å leading to the heme center. A conformational change of ERS* to ERS, which have identical spectral characteristics, was proposed as the final step in DyPs' bisubstrate Ping-Pong mechanism. This step is also the rate-determining step in ABTS oxidation. The normal KIE of wild-type ElDyP with D2O2 at pH 3.5 suggested that cmpd 0 deprotonation by the distal aspartate is rate-limiting in the formation of cmpd I, which is more reactive under acidic pH than under neutral or alkaline pH. The viscosity effects and other biochemical methods implied that the reducing substrate binds with cmpd I instead of the free enzyme. The significant inverse sKIEs of kcat/KM and kERS* suggested that the aquo release in DyPs is mechanistically important and may explain the enzyme's adoption of two-electron reduction for cmpd I. The distal aspartate is catalytically more important than the distal arginine and plays key roles in determining DyPs' acidic pH optimum. The kinetic mechanism of D143H-ElDyP was also briefly studied. The results obtained will pave the way for future protein engineering to improve DyPs' lignolytic activity.
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Affiliation(s)
- Ruben Shrestha
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
| | - Gaochao Huang
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
| | - David A. Meekins
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
| | - Brian V. Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Ping Li
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
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46
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Mallick D, Shaik S. Kinetic Isotope Effect Probes the Reactive Spin State, As Well As the Geometric Feature and Constitution of the Transition State during H-Abstraction by Heme Compound II Complexes. J Am Chem Soc 2017; 139:11451-11459. [PMID: 28737390 DOI: 10.1021/jacs.7b04247] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
What do experimentally measured kinetic isotope effects (KIEs) tell us about H-abstraction reactions with multispin-state reactivity options? Using DFT calculations with tunneling corrections for experimentally studied H-abstraction reactions of porphyrin-Compound II species (Chem.-Eur. J. 2014, 20, 14437; Angew. Chem., Int. Ed. 2008, 47, 7321) with cyclohexane, dihydroanthracene (DHA), and xanthene (Xan), we show here that KIE is a selective probe that identifies the experimentally reactive spin state. At the same time, comparison of calculated and experimental KIE values permits us to determine the structural orientation of the transition states, as well as the presence/absence of an axial ligand, and the effect of porphyrin substituents. The studied compound II (Cpd II) species involve porphine, and porphyrin ligands with different meso-substituents, TPFPP (tetrakis(pentafluorophenyl)porphyrin dianion) and TMP (tetramesitylporphyrin dianion), with and without imidazole axial ligands. The DFT calculations reveal three potential pathways: quintet and triplet σ-pathways (5Hσ and 3Hσ) that possess linear transition state (TS) structures, and a triplet π -pathway (3Hπ) having a bent TS structure. Without an axial ligand, the 5Hσ pathways for these Cpd II complexes cross below the triplet states. The axial ligand raises the barriers for the quintet and triplet σ-pathways and quenches any chances for two-state reactivity, thus proceeding via the 3Hπ pathway. All of these pathways exhibit characteristic KIE values: very large for 3Hπ (48-200), small for 5Hσ (3-9), and intermediate for 3Hσ (23-51). The calculated KIEs for (TPFPP)FeIV═O without an axial ligand reveal that 3Hσ is the only pathway having a KIE that matches the experimental values, for the reactions with DHA and Xan (Angew. Chem., Int. Ed. 2008, 47, 7321). Indeed, theory shows that tunneling significantly lowers the 3Hσ barrier rendering it the sole reactive state for the reaction. A prediction is made for the reactivity and KIE of (TMP)FeIV═O complex, and a comparison is made with the analogous nonheme complexes.
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Affiliation(s)
- Dibyendu Mallick
- Institute of Chemistry and the Lise Meitner Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Sason Shaik
- Institute of Chemistry and the Lise Meitner Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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47
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Liu Q, Wang H, Shi X, Wang ZG, Ding B. Self-Assembled DNA/Peptide-Based Nanoparticle Exhibiting Synergistic Enzymatic Activity. ACS NANO 2017; 11:7251-7258. [PMID: 28657711 DOI: 10.1021/acsnano.7b03195] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Designing enzyme-mimicking active sites in artificial systems is key to achieving catalytic efficiencies rivaling those of natural enzymes and can provide valuable insight in the understanding of the natural evolution of enzymes. Here, we report the design of a catalytic hemin-containing nanoparticle with self-assembled guanine-rich nucleic acid/histidine-rich peptide components that mimics the active site and peroxidative activity of hemoproteins. The chemical complementarities between the folded nucleic acid and peptide enable the spatial arrangement of essential elements in the active site and effective activation of hemin. As a result, remarkable synergistic effects of nucleic acid and peptide on the catalytic performances were observed. The turnover number of peroxide reached the order of that of natural peroxidase, and the catalytic efficiency is comparable to that of myoglobin. These results have implications in the precise design of supramolecular enzyme mimetics, particularly those with hierarchical active sites. The assemblies we describe here may also resemble an intermediate in the evolution of contemporary enzymes from the catalytic RNA of primitive cells.
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Affiliation(s)
- Qing Liu
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology , Beijing 100190, P.R. China
- University of Chinese Academy of Sciences , Beijing 100049, P.R. China
| | - Hui Wang
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology , Beijing 100190, P.R. China
| | - Xinghua Shi
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology , Beijing 100190, P.R. China
- University of Chinese Academy of Sciences , Beijing 100049, P.R. China
| | - Zhen-Gang Wang
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology , Beijing 100190, P.R. China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology , Beijing 100190, P.R. China
- University of Chinese Academy of Sciences , Beijing 100049, P.R. China
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In Vitro Evaluation of Antileishmanial Activity of Computationally Screened Compounds against Ascorbate Peroxidase To Combat Amphotericin B Drug Resistance. Antimicrob Agents Chemother 2017; 61:AAC.02429-16. [PMID: 28461317 DOI: 10.1128/aac.02429-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 03/28/2017] [Indexed: 12/11/2022] Open
Abstract
In visceral leishmaniasis (VL), the host macrophages generate oxidative stress to destroy the pathogen, while Leishmania combats the harmful effect of radicals by redox homeostasis through its unique trypanothione cascade. Leishmania donovani ascorbate peroxidase (LdAPx) is a redox enzyme that regulates the trypanothione cascade and detoxifies the effect of H2O2 The absence of an LdAPx homologue in humans makes it an excellent drug target. In this study, the homology model of LdAPx was built, including heme, and diverse compounds were prefiltered (PAINS, ADMET, and Lipinski's rule of five) and thereafter screened against the LdAPx model. Compounds having good affinity in terms of the Glide XP (extra precision) score were clustered to select diverse compounds for experimental validation. A total of 26 cluster representatives were procured and tested on promastigote culture, yielding 12 compounds with good antileishmanial activity. Out of them, six compounds were safer on the BALB/c peritoneal macrophages and were also effective against disease-causing intracellular amastigotes. Three out of six compounds inhibited recombinant LdAPx in a noncompetitive manner and also demonstrated partial reversion of the resistance property in an amphotericin B (AmB)-resistant strain, which may be due to an increased level of reactive oxygen species (ROS) and decrease of glutathione (GSH) content. However, inhibition of LdAPx in resistant parasites enhanced annexin V staining and activation of metacaspase-like protease activity, which may help in DNA fragmentation and apoptosis-like cell death. Thus, the present study will help in the search for specific hits and templates of potential therapeutic interest and therefore may facilitate the development of new drugs for combination therapy against VL.
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Abderrahim M, Arribas SM, Condezo-Hoyos L. A novel pyrogallol red-based assay to assess catalase activity: Optimization by response surface methodology. Talanta 2017; 166:349-356. [DOI: 10.1016/j.talanta.2017.01.059] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 01/19/2017] [Accepted: 01/24/2017] [Indexed: 01/15/2023]
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Fan K, Wang H, Xi J, Liu Q, Meng X, Duan D, Gao L, Yan X. Optimization of Fe3O4 nanozyme activity via single amino acid modification mimicking an enzyme active site. Chem Commun (Camb) 2017; 53:424-427. [DOI: 10.1039/c6cc08542c] [Citation(s) in RCA: 245] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Histidine modification effectively improved the affinity of Fe3O4 nanozyme to H2O2, enhancing its catalytic efficiency by mimicking peroxidase active site.
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Affiliation(s)
- Kelong Fan
- Key Laboratory of Protein and Peptide Pharmaceuticals
- CAS-University of Tokyo Joint Laboratory of Structural Virology and Immunology
- Institute of Biophysics
- Chinese Academy of Sciences
- Beijing 100101
| | - Hui Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication
- National Centre for Nanoscience and Technology
- Beijing 100190
- China
| | - Juqun Xi
- School of Medicine
- Yangzhou University
- Yangzhou
- China
| | - Qi Liu
- School of Medicine
- Yangzhou University
- Yangzhou
- China
| | - Xiangqin Meng
- Key Laboratory of Protein and Peptide Pharmaceuticals
- CAS-University of Tokyo Joint Laboratory of Structural Virology and Immunology
- Institute of Biophysics
- Chinese Academy of Sciences
- Beijing 100101
| | - Demin Duan
- Key Laboratory of Protein and Peptide Pharmaceuticals
- CAS-University of Tokyo Joint Laboratory of Structural Virology and Immunology
- Institute of Biophysics
- Chinese Academy of Sciences
- Beijing 100101
| | - Lizeng Gao
- Key Laboratory of Protein and Peptide Pharmaceuticals
- CAS-University of Tokyo Joint Laboratory of Structural Virology and Immunology
- Institute of Biophysics
- Chinese Academy of Sciences
- Beijing 100101
| | - Xiyun Yan
- Key Laboratory of Protein and Peptide Pharmaceuticals
- CAS-University of Tokyo Joint Laboratory of Structural Virology and Immunology
- Institute of Biophysics
- Chinese Academy of Sciences
- Beijing 100101
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