1
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Kanematsu Y, Kondo HX, Takano Y. Computational Exploration of Minimum Energy Reaction Pathway of N 2O Formation from Intermediate I of P450nor Using an Active Center Model. Int J Mol Sci 2023; 24:17172. [PMID: 38139001 PMCID: PMC10743073 DOI: 10.3390/ijms242417172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
P450nor is a heme-containing enzyme that catalyzes the conversion of nitric oxide (NO) to nitrous oxide (N2O). Its catalytic mechanism has attracted attention in chemistry, biology, and environmental engineering. The catalytic cycle of P450nor is proposed to consist of three major steps. The reaction mechanism for the last step, N2O generation, remains unknown. In this study, the reaction pathway of the N2O generation from the intermediate I was explored with the B3LYP calculations using an active center model after the examination of the validity of the model. In the validation, we compared the heme distortions between P450nor and other oxidoreductases, suggesting a small effect of protein environment on the N2O generation reaction in P450nor. We then evaluated the electrostatic environment effect of P450nor on the hydride affinity to the active site with quantum mechanics/molecular mechanics (QM/MM) calculations, confirming that the affinity was unchanged with or without the protein environment. The active center model for P450nor showed that the N2O generation process in the enzymatic reaction undergoes a reasonable barrier height without protein environment. Consequently, our findings strongly suggest that the N2O generation reaction from the intermediate I depends sorely on the intrinsic reactivity of the heme cofactor bound on cysteine residue.
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Affiliation(s)
- Yusuke Kanematsu
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima 739-8527, Japan
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan;
| | - Hiroko X. Kondo
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan;
- Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami 090-8507, Japan
| | - Yu Takano
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan;
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2
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Baeza Cinco MÁ, Wu G, Hayton TW. Photolytic C-Diazeniumdiolate Disassembly in the β-Diketiminate Complexes [ MeLM(O 2N 2CPh 3)] (M = Fe, Co, Cu). Inorg Chem 2023; 62:14064-14071. [PMID: 37584511 DOI: 10.1021/acs.inorgchem.3c02188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
The reaction of [K(18-crown-6)][O2N2CPh3] with [MeLCo(μ-Br)2Li(OEt2)] (MeL = {(2,6-iPr2C6H3)NC(Me)}2CH) generates the trityl diazeniumdiolate complex, [MeLCo(O2N2CPh3)] (1), in moderate yield. Similar metathesis reactions result in the formation of the Fe and Cu analogues, [MeLM(O2N2CPh3)] (Fe, 2; Cu, 3), which can also be isolated in moderate yields. Complexes 1-3 were characterized by ultraviolet-visible (UV-vis) spectroscopy, and their solid-state structures were determined by X-ray crystallography. These complexes were further characterized via 1H NMR spectroscopy (in the case of 1 and 2) or EPR spectroscopy (in the case of 3). Irradiation of complexes 1 and 2 with 371 nm light generates the known dinitrosyl complexes, [MeLM(NO)2] (M = Co, 4; Fe, 5), along with Ph3CH and 9-phenylfluorene. We propose that 4 and 5 are formed via the putative hyponitrite intermediates, [MeLM(κ2-O,O-ONNO)], which are formed by photoinduced homolysis of the C-N bond of the [O2N2CPh3] ligand. In contrast, irradiation of complex 3 with 371 nm light, in the presence of 1 equiv of PPh3, led to the formation of the Cu(I) complexes, [MeLCu(PPh3)], [(ArNCMeC(NO)CMeNAr)Cu(PPh3)] (6), and [(ArNCMeC(NO)CMeNAr)Cu]2 (7), of which the latter two are products of γ-nitrosation of the β-diketiminiate ligand. Also formed in this transformation are Ph3CN(H)OCPh3, Ph3PO, and N2O, along with trace amounts of NO.
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Affiliation(s)
- Miguel Á Baeza Cinco
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Guang Wu
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Trevor W Hayton
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
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3
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Takeda H, Shimba K, Horitani M, Kimura T, Nomura T, Kubo M, Shiro Y, Tosha T. Trapping of a Mononitrosyl Nonheme Intermediate of Nitric Oxide Reductase by Cryo-Photolysis of Caged Nitric Oxide. J Phys Chem B 2023; 127:846-854. [PMID: 36602896 DOI: 10.1021/acs.jpcb.2c05852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Characterization of short-lived reaction intermediates is essential for elucidating the mechanism of the reaction catalyzed by metalloenzymes. Here, we demonstrated that the photolysis of a caged compound under cryogenic temperature followed by thermal annealing is an invaluable technique for trapping of short-lived reaction intermediates of metalloenzymes through the study of membrane-integrated nitric oxide reductase (NOR) that catalyzes reductive coupling of two NO molecules to N2O at its heme/nonheme FeB binuclear center. Although NO produced by the photolysis of caged NO did not react with NOR under cryogenic temperature, annealing to ∼160 K allowed NO to diffuse and react with NOR, which was evident from the appearance of EPR signals assignable to the S = 3/2 state. This indicates that the nonheme FeB-NO species can be trapped as the intermediate. Time-resolved IR spectroscopy with the use of the photolysis of caged NO as a reaction trigger showed that the intermediate formed at 10 μs gave the NO stretching frequency at 1683 cm-1 typical of nonheme Fe-NO, confirming that the combination of the cryo-photolysis of caged NO and annealing enabled us to trap the reaction intermediate. Thus, the cryo-photolysis of the caged compound has great potential for the characterization of short-lived reaction intermediates.
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Affiliation(s)
- Hanae Takeda
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan.,RIKEN SPring-8 center, Sayo, Hyogo 679-5148, Japan
| | - Kanji Shimba
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan.,RIKEN SPring-8 center, Sayo, Hyogo 679-5148, Japan
| | - Masaki Horitani
- Department of Applied Biochemistry & Food Science, Saga University, Saga 840-8502, Japan.,The United Graduate School of Agricultural Science, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Tetsunari Kimura
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Takashi Nomura
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan
| | - Minoru Kubo
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan
| | - Yoshitsugu Shiro
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan
| | - Takehiko Tosha
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan.,RIKEN SPring-8 center, Sayo, Hyogo 679-5148, Japan
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4
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Bhadra M, Albert T, Franke A, Josef V, Ivanović-Burmazović I, Swart M, Moënne-Loccoz P, Karlin KD. Reductive Coupling of Nitric Oxide by Cu(I): Stepwise Formation of Mono- and Dinitrosyl Species En Route to a Cupric Hyponitrite Intermediate. J Am Chem Soc 2023; 145:2230-2242. [PMID: 36652374 PMCID: PMC10122266 DOI: 10.1021/jacs.2c09874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Transition-metal-mediated reductive coupling of nitric oxide (NO(g)) to nitrous oxide (N2O(g)) has significance across the fields of industrial chemistry, biochemistry, medicine, and environmental health. Herein, we elucidate a density functional theory (DFT)-supplemented mechanism of NO(g) reductive coupling at a copper-ion center, [(tmpa)CuI(MeCN)]+ (1) {tmpa = tris(2-pyridylmethyl)amine}. At -110 °C in EtOH (<-90 °C in MeOH), exposing 1 to NO(g) leads to a new binuclear hyponitrite intermediate [{(tmpa)CuII}2(μ-N2O22-)]2+ (2), exhibiting temperature-dependent irreversible isomerization to the previously characterized κ2-O,O'-trans-[(tmpa)2Cu2II(μ-N2O22-)]2+ (OOXray) complex. Complementary stopped-flow kinetic analysis of the reaction in MeOH reveals an initial mononitrosyl species [(tmpa)Cu(NO)]+ (1-(NO)) that binds a second NO molecule, forming a dinitrosyl species [(tmpa)CuII(NO)2] (1-(NO)2). The decay of 1-(NO)2 requires an available starting complex 1 to form a dicopper-dinitrosyl species hypothesized to be [{(tmpa)Cu}2(μ-NO)2]2+ (D) bearing a diamond-core motif, en route to the formation of hyponitrite intermediate 2. In contrast, exposing 1 to NO(g) in 2-MeTHF/THF (v/v 4:1) at <-80 °C leads to the newly observed transient metastable dinitrosyl species [(tmpa)CuII(NO)2] (1-(NO)2) prior to its disproportionation-mediated transformation to the nitrite product [(tmpa)CuII(NO2)]+. Our study furnishes a near-complete profile of NO(g) activation at a reduced Cu site with tripodal tetradentate ligation in two distinctly different solvents, aided by detailed spectroscopic characterization of metastable intermediates, including resonance Raman characterization of the new dinitrosyl and hyponitrite species detected.
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Affiliation(s)
- Mayukh Bhadra
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Therese Albert
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Alicja Franke
- Department of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nuremberg, 91058 Erlangen, Germany
- Department of Chemistry, Ludwig-Maximilians University, Munich, 81377 Munich, Germany
| | - Verena Josef
- Department of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nuremberg, 91058 Erlangen, Germany
| | - Ivana Ivanović-Burmazović
- Department of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nuremberg, 91058 Erlangen, Germany
- Department of Chemistry, Ludwig-Maximilians University, Munich, 81377 Munich, Germany
| | - Marcel Swart
- IQCC & Departament de Química, Universitat de Girona, Campus Montilivi (Ciencies), 17003 Girona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Pierre Moënne-Loccoz
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Kenneth D Karlin
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
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5
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Tao W, Carter S, Trevino R, Zhang W, Shafaat HS, Zhang S. Reductive NO Coupling at Dicopper Center via a [Cu 2(NO) 2] 2+ Diamond-Core Intermediate. J Am Chem Soc 2022; 144:22633-22640. [PMID: 36469729 DOI: 10.1021/jacs.2c09523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Treatment of a dicopper(I,I) complex with excess amounts of NO leads to the formation of a dicopper dinitrosyl [Cu2(NO)2]2+ complex capable of (i) releasing two equivalents of NO reversibly in 90% yield and (ii) reacting with another equivalent of NO to afford N2O and dicopper nitrosyl oxo species [Cu2(NO)(O)]2+. Resonance Raman characterization of the [Cu2(NO)2]2+ complex shows a 15N-sensitive N═O stretch at 1527.6 cm-1 and two Cu-N stretches at 390.6 and 414.1 cm-1, supporting a symmetric diamond-core structure with bis-μ-NO ligands. The conversion of [Cu2(NO)2]2+ to [Cu2(NO)O]2+ occurs via a rate-limiting reaction with NO and bypasses the dicopper oxo intermediate, a mechanism distinct from that of diFe-mediated NO reduction to N2O.
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Affiliation(s)
- Wenjie Tao
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Samantha Carter
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Regina Trevino
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Weiyao Zhang
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Hannah S Shafaat
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Shiyu Zhang
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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6
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Matsumura H, Faponle AS, Hagedoorn PL, Tosha T, de Visser SP, Moënne-Loccoz P. Mechanism of substrate inhibition in cytochrome-c dependent NO reductases from denitrifying bacteria (cNORs). J Inorg Biochem 2022; 231:111781. [DOI: 10.1016/j.jinorgbio.2022.111781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 12/24/2022]
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7
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Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
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Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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8
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Lichtenberg M, Line L, Schrameyer V, Jakobsen TH, Rybtke ML, Toyofuku M, Nomura N, Kolpen M, Tolker-Nielsen T, Kühl M, Bjarnsholt T, Jensen PØ. Nitric-oxide-driven oxygen release in anoxic Pseudomonas aeruginosa. iScience 2021; 24:103404. [PMID: 34849468 PMCID: PMC8608891 DOI: 10.1016/j.isci.2021.103404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 09/29/2021] [Accepted: 11/03/2021] [Indexed: 11/19/2022] Open
Abstract
Denitrification supports anoxic growth of Pseudomonas aeruginosa in infections. Moreover, denitrification may provide oxygen (O2) resulting from dismutation of the denitrification intermediate nitric oxide (NO) as seen in Methylomirabilis oxyfera. To examine the prevalence of NO dismutation we studied O2 release by P. aeruginosa in airtight vials. P. aeruginosa rapidly depleted O2 but NO supplementation generated peaks of O2 at the onset of anoxia, and we demonstrate a direct role of NO in the O2 release. However, we were not able to detect genetic evidence for putative NO dismutases. The supply of endogenous O2 at the onset of anoxia could play an adaptive role when P. aeruginosa enters anaerobiosis. Furthermore, O2 generation by NO dismutation may be more widespread than indicated by the reports on the distribution of homologues genes. In general, NO dismutation may allow removal of nitrate by denitrification without release of the very potent greenhouse gas, nitrous oxide. Pseudomonas aeruginosa was found to release O2 at the onset of anoxia Peaks of O2 were amplified in a nitric oxide reductase (NOR) mutant The O2 release was mediated by nitric oxide (NO)
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Affiliation(s)
- Mads Lichtenberg
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Laura Line
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Verena Schrameyer
- Marine Biological Section, Department of Biology, University of Copenhagen, 3000 Helsingør, Denmark
| | - Tim Holm Jakobsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Morten Levin Rybtke
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Masanori Toyofuku
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, 305-8577 Tsukuba, Japan
| | - Nobuhiko Nomura
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba, 305-8577 Tsukuba, Japan
| | - Mette Kolpen
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, 3000 Helsingør, Denmark
| | - Thomas Bjarnsholt
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Peter Østrup Jensen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark
- Center for Rheumatology and Spine Diseases, Institute for Inflammation Research, Rigshospitalet, 2100 Copenhagen, Denmark
- Corresponding author
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9
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Lin S, He C. Development of Nonheme {FeNO} 7 Complexes Based on the Pyrococcus furiosus Rubredoxin for Red-Light-Controllable Nitric Oxide Release. Inorg Chem 2021; 60:14364-14370. [PMID: 34503329 DOI: 10.1021/acs.inorgchem.1c02089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nitric oxide (NO) is an essential biological messenger, contributing a significant role in a diverse range of physiological processes. The light-controllable NO releasers are of great interest because of their potential as agents for NO-related research and therapeutics. Herein, we developed a pair of red-light-controllable NO releasers, pfRd-C9A-{FeNO}7 and pfRd-C42A-{FeNO}7 (pfRd = Pyrococcus furiosus rubredoxin), by constructing a nonheme {FeNO}7 center within the redesigned iron-sulfur protein scaffolds. While shown to be both air and thermally stable, these complexes are highly sensitive to red-light irradiation with temporal precision, which was confirmed by electron paramagnetic resonance spin trapping and Griess assay. The temporally controlled NO release from these complexes was also demonstrated in DNA cleavage assay. Overall, this study demonstrates that such a protein-based nonheme iron nitrosyl system could be a viable chemical tool for precise NO administration.
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Affiliation(s)
- Shaomin Lin
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Chunmao He
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, China
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10
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Blomberg MRA. The importance of exact exchange-A methodological investigation of NO reduction in heme-copper oxidases. J Chem Phys 2021; 154:055103. [PMID: 33557557 DOI: 10.1063/5.0035634] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Significant improvements of the density functional theory (DFT) methodology during the past few decades have made DFT calculations a powerful tool in studies of enzymatic reaction mechanisms. For metalloenzymes, however, there are still concerns about the reliability in the DFT-results. Therefore, a systematic study is performed where the fraction of exact exchange in a hybrid DFT functional is used as a parameter. By varying this parameter, a set of different but related functionals are obtained. The various functionals are applied to one of the reactions occurring in the enzyme family heme-copper oxidases, the reduction of nitric oxide (NO) to nitrous oxide (N2O) and water. The results show that, even though certain parts of the calculated energetics exhibit large variations, the qualitative pictures of the reaction mechanisms are quite stable. Furthermore, it is found that the functional with 15% exact exchange (B3LYP*) gives the best agreement with experimental data for the particular reactions studied. An important aspect of the procedure used is that the computational results are carefully combined with a few more general experimental data to obtain a complete description of the entire catalytic cycle of the reactions studied.
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Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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11
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Blomberg MRA. Activation of O 2 and NO in heme-copper oxidases - mechanistic insights from computational modelling. Chem Soc Rev 2021; 49:7301-7330. [PMID: 33006348 DOI: 10.1039/d0cs00877j] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Heme-copper oxidases are transmembrane enzymes involved in aerobic and anaerobic respiration. The largest subgroup contains the cytochrome c oxidases (CcO), which reduce molecular oxygen to water. A significant part of the free energy released in this exergonic process is conserved as an electrochemical gradient across the membrane, via two processes, electrogenic chemistry and proton pumping. A deviant subgroup is the cytochrome c dependent NO reductases (cNOR), which reduce nitric oxide to nitrous oxide and water. This is also an exergonic reaction, but in this case none of the released free energy is conserved. Computational studies applying hybrid density functional theory to cluster models of the bimetallic active sites in the heme-copper oxidases are reviewed. To obtain a reliable description of the reaction mechanisms, energy profiles of the entire catalytic cycles, including the reduction steps have to be constructed. This requires a careful combination of computational results with certain experimental data. Computational studies have elucidated mechanistic details of the chemical parts of the reactions, involving cleavage and formation of covalent bonds, which have not been obtainable from pure experimental investigations. Important insights regarding the mechanisms of energy conservation have also been gained. The computational studies show that the reduction potentials of the active site cofactors in the CcOs are large enough to afford electrogenic chemistry and proton pumping, i.e. efficient energy conservation. These results solve a conflict between different types of experimental data. A mechanism for the proton pumping, involving a specific and crucial role for the active site tyrosine, conserved in all CcOs, is suggested. For the cNORs, the calculations show that the low reduction potentials of the active site cofactors are optimized for fast elimination of the toxic NO molecules. At the same time, the low reduction potentials lead to endergonic reduction steps with high barriers. To prevent even higher barriers, which would lead to a too slow reaction, when the electrochemical gradient across the membrane is present, the chemistry must occur in a non-electrogenic manner. This explains why there is no energy conservation in cNOR.
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Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden.
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12
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Reed CJ, Lam QN, Mirts EN, Lu Y. Molecular understanding of heteronuclear active sites in heme-copper oxidases, nitric oxide reductases, and sulfite reductases through biomimetic modelling. Chem Soc Rev 2021; 50:2486-2539. [PMID: 33475096 PMCID: PMC7920998 DOI: 10.1039/d0cs01297a] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Heme-copper oxidases (HCO), nitric oxide reductases (NOR), and sulfite reductases (SiR) catalyze the multi-electron and multi-proton reductions of O2, NO, and SO32-, respectively. Each of these reactions is important to drive cellular energy production through respiratory metabolism and HCO, NOR, and SiR evolved to contain heteronuclear active sites containing heme/copper, heme/nonheme iron, and heme-[4Fe-4S] centers, respectively. The complexity of the structures and reactions of these native enzymes, along with their large sizes and/or membrane associations, make it challenging to fully understand the crucial structural features responsible for the catalytic properties of these active sites. In this review, we summarize progress that has been made to better understand these heteronuclear metalloenzymes at the molecular level though study of the native enzymes along with insights gained from biomimetic models comprising either small molecules or proteins. Further understanding the reaction selectivity of these enzymes is discussed through comparisons of their similar heteronuclear active sites, and we offer outlook for further investigations.
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Affiliation(s)
- Christopher J Reed
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA.
| | - Quan N Lam
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA
| | - Evan N Mirts
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA. and Department of Biochemistry, University of Illinois at Urbana-Champaign, Urban, IL 61801, USA and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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13
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Tosha T, Yamagiwa R, Sawai H, Shiro Y. NO Dynamics in Microbial Denitrification System. CHEM LETT 2021. [DOI: 10.1246/cl.200629] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Takehiko Tosha
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Raika Yamagiwa
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Hitomi Sawai
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Yoshitsugu Shiro
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
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14
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Takeda H, Kimura T, Nomura T, Horitani M, Yokota A, Matsubayashi A, Ishii S, Shiro Y, Kubo M, Tosha T. Timing of NO Binding and Protonation in the Catalytic Reaction of Bacterial Nitric Oxide Reductase as Established by Time-Resolved Spectroscopy. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20200038] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Hanae Takeda
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Tetsunari Kimura
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Takashi Nomura
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Masaki Horitani
- Department of Applied Biochemistry & Food Science, Saga University, Saga 840-8502, Japan
| | - Azusa Yokota
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Akiko Matsubayashi
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Shoko Ishii
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Yoshitsugu Shiro
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Minoru Kubo
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Takehiko Tosha
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
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15
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Ferousi C, Majer SH, DiMucci IM, Lancaster KM. Biological and Bioinspired Inorganic N-N Bond-Forming Reactions. Chem Rev 2020; 120:5252-5307. [PMID: 32108471 PMCID: PMC7339862 DOI: 10.1021/acs.chemrev.9b00629] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The metallobiochemistry underlying the formation of the inorganic N-N-bond-containing molecules nitrous oxide (N2O), dinitrogen (N2), and hydrazine (N2H4) is essential to the lifestyles of diverse organisms. Similar reactions hold promise as means to use N-based fuels as alternative carbon-free energy sources. This review discusses research efforts to understand the mechanisms underlying biological N-N bond formation in primary metabolism and how the associated reactions are tied to energy transduction and organismal survival. These efforts comprise studies of both natural and engineered metalloenzymes as well as synthetic model complexes.
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Affiliation(s)
- Christina Ferousi
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Sean H Majer
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Ida M DiMucci
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Kyle M Lancaster
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
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16
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Wu W, Liaw W. Nitric oxide reduction forming hyponitrite triggered by metal‐containing complexes. J CHIN CHEM SOC-TAIP 2020. [DOI: 10.1002/jccs.201900473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Wun‐Yan Wu
- Department of Chemistry and Frontier Research Center of Fundamental and Applied Science of MattersNational Tsing Hua University Hsinchu, Taiwan Republic of China
| | - Wen‐Feng Liaw
- Department of Chemistry and Frontier Research Center of Fundamental and Applied Science of MattersNational Tsing Hua University Hsinchu, Taiwan Republic of China
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17
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Sun C, Zhang Y, Qu Z, Zhou J. Effects of cobalt-histidine absorbent on aerobic denitrification by Paracoccus versutus LYM. AMB Express 2019; 9:202. [PMID: 31848761 PMCID: PMC6917670 DOI: 10.1186/s13568-019-0927-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 12/03/2019] [Indexed: 11/10/2022] Open
Abstract
To overcome the problem that ferrous complexes are easily oxidized by O2 and then lose NO binding ability in the chemical absorption-biological reduction (CABR) process, cobalt(II)-histidine [Co(II)His] was proposed as an alternative. To evaluate the applicability of Co(II)His, the effects of CoHis absorbent on the aerobic denitrification by Paracoccus versutus LYM were investigated. Results indicated that His significantly promoted nitrite reduction. The inhibition effects of CoHis absorbent could be substantially alleviated by increasing the initial His/Co2+ to 4 or higher. CoHis with concentrations of 4, 8, 12, 16 and 20 mM presented no distinct effect on nitrite reduction, but slightly inhibited the reduction of nitrate, resulting in longer lag of nitrate reduction, and obviously promoted the growth of strain LYM. In the presence of 5, 10, 15 and 20 mM CoHis absorbent, the main denitrification product was N2 (not less than 95.0%). This study is of significance in verifying the applicability of Co(II)His in the CABR process, and provides a referable CoHis absorbent concentration as 20 mM with an initial His/Co2+ of 4 for the future experiments.
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18
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Lehnert N, Fujisawa K, Camarena S, Dong HT, White CJ. Activation of Non-Heme Iron-Nitrosyl Complexes: Turning Up the Heat. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03219] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Kiyoshi Fujisawa
- Department of Chemistry, Ibaraki University, Mito 310-8512, Japan
| | - Stephanie Camarena
- Department of Chemistry and Department of Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Hai T. Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Corey J. White
- Department of Chemistry and Department of Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
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19
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Zhou G, Wang YS, Peng H, Shen PF, Xie XB, Shi QS. Functional roles ofnorCBinPseudomonas aeruginosaATCC 9027 under aerobic conditions. J Basic Microbiol 2019; 59:1154-1162. [DOI: 10.1002/jobm.201900267] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/25/2019] [Accepted: 08/29/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Gang Zhou
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology; Guangdong Academy of Sciences; Guangzhou Guangdong China
| | - Ying-Si Wang
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology; Guangdong Academy of Sciences; Guangzhou Guangdong China
| | - Hong Peng
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology; Guangdong Academy of Sciences; Guangzhou Guangdong China
| | - Peng-Fei Shen
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology; Guangdong Academy of Sciences; Guangzhou Guangdong China
| | - Xiao-Bao Xie
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology; Guangdong Academy of Sciences; Guangzhou Guangdong China
| | - Qing-Shan Shi
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology; Guangdong Academy of Sciences; Guangzhou Guangdong China
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20
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Kahle M, Blomberg MRA, Jareck S, Ädelroth P. Insights into the mechanism of nitric oxide reductase from a Fe B -depleted variant. FEBS Lett 2019; 593:1351-1359. [PMID: 31077353 DOI: 10.1002/1873-3468.13436] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 04/29/2019] [Accepted: 05/09/2019] [Indexed: 11/06/2022]
Abstract
A key step of denitrification, the reduction of toxic nitric oxide to nitrous oxide, is catalysed by cytochrome c-dependent NO reductase (cNOR). cNOR contains four redox-active cofactors: three hemes and a nonheme iron (FeB ). Heme b3 and FeB constitute the active site, but the specific mechanism of NO-binding events and reduction is under debate. Here, we used a recently constructed, fully folded and hemylated cNOR variant that lacks FeB to investigate the role of FeB during catalysis. We show that in the FeB -less cNOR, binding of both NO and O2 to heme b3 still occurs but further reduction is impaired, although to a lesser degree for O2 than for NO. Implications for the catalytic mechanisms of cNOR are discussed.
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Affiliation(s)
- Maximilian Kahle
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
| | | | - Sascha Jareck
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
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21
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Amanullah S, Singha A, Dey A. Tailor made iron porphyrins for investigating axial ligand and distal environment contributions to electronic structure and reactivity. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.01.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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22
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Sabuncu S, Reed JH, Lu Y, Moënne-Loccoz P. Nitric Oxide Reductase Activity in Heme-Nonheme Binuclear Engineered Myoglobins through a One-Electron Reduction Cycle. J Am Chem Soc 2018; 140:17389-17393. [PMID: 30512937 DOI: 10.1021/jacs.8b11037] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
FeBMbs are structural and functional models of native bacterial nitric oxide reductases (NORs) generated through engineering of myoglobin. These biosynthetic models replicate the heme-nonheme diiron site of NORs and allow substitutions of metal centers and heme cofactors. Here, we provide evidence for multiple NOR turnover in monoformyl-heme-containing FeBMb1 proteins loaded with FeII, CoII, or ZnII metal ions at the FeB site (FeII/CoII/ZnII-FeBMb1(MF-heme)). FTIR detection of the ν(NNO) band of N2O at 2231 cm-1 provides a direct quantitative measurement of the product in solution. A maximum number of turnover is observed with FeII-FeBMb1(MF-heme), but the NOR activity is retained when the FeB site is loaded with ZnII. These data support the viability of a one-electron semireduced pathway for the reduction of NO at binuclear centers in reducing conditions.
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Affiliation(s)
- Sinan Sabuncu
- Department of Biochemistry & Molecular Biology , Oregon Health & Science University , Portland , Oregon 97239 , United States
| | - Julian H Reed
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Yi Lu
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Pierre Moënne-Loccoz
- Department of Biochemistry & Molecular Biology , Oregon Health & Science University , Portland , Oregon 97239 , United States
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23
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Beck D, Klüfers P. HN 2 O 2 - as a Ligand in Mononuclear Hydrogenhyponitrite-κ 2 -N,O Ruthenium Complexes with Bisphosphane Co-Ligands. Chemistry 2018; 24:16019-16028. [PMID: 30144196 DOI: 10.1002/chem.201803770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 01/21/2023]
Abstract
The hyponitrite anion is a tentative intermediate in the reduction of nitric oxide (NO) to nitrous oxide (N2 O) catalyzed by nitric-oxide reductase (NOR) in the process of bacterial denitrification. Owing to the considerable number of known coordination modes for the hyponitrito ligand, its actual bonding form in the enzymatic cycle is a point of current discussion. Here, we contribute to the hardly known ligand properties of a key intermediate, the monoprotonated hyponitrite anion. Three air- and water-stable ruthenium complexes with hydrogenhyponitrite as the ligand were synthesized by using commercially available bisphosphane co-ligands (1,2-bis(diphenylphosphino)ethane (dppe), 1,3-bis(diphenylphosphino)propane (dppp), 1,2-bis(diphenylphosphino)ethene (dppv)). The starting compounds [Ru(dppe)2 (tos)]BF4 (1) and [Ru(dppp)2 (tos)]BF4 (2) contained the bidentate coordinating tosylate anion (tos) as a particularly well-suited leaving group. To confirm the protonated and deprotonated species, X-ray diffraction, IR, UV/Vis spectroscopy (solution and solid state), solid-state NMR spectroscopy, and high-resolution mass spectroscopy were used. DFT calculations give insight into the bonding situation. We report on [Ru(dppe)2 (HN2 O2 )]BF4 (5), [Ru(dppp)2 (HN2 O2 )]BF4 (6), [Ru(dppv)2 (HN2 O2 )]BF4 (7), [Ru(dppp)2 (HN2 O2 )]BF4 ⋅Imi (9; Imi=imidazole) as the first mononuclear trans-hydrogenhyponitrite complexes. Isolated deprotonated analogs are [Ru(dppe)2 (N2 O2 )]⋅HImi(BF4 ) (8) and [Ru(dppv)2 (N2 O2 )] ⋅HImi(BF4 )⋅Imi (10).
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Affiliation(s)
- Daniel Beck
- Ludwig-Maximilians-Universitaet, Department of Chemistry, Butenandtstrasse 5-13, Haus D, München, 81377, Germany
| | - Peter Klüfers
- Ludwig-Maximilians-Universitaet, Department of Chemistry, Butenandtstrasse 5-13, Haus D, München, 81377, Germany
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24
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Speelman AL, White CJ, Zhang B, Alp EE, Zhao J, Hu M, Krebs C, Penner-Hahn J, Lehnert N. Non-heme High-Spin {FeNO} 6-8 Complexes: One Ligand Platform Can Do It All. J Am Chem Soc 2018; 140:11341-11359. [PMID: 30107126 DOI: 10.1021/jacs.8b06095] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Heme and non-heme iron-nitrosyl complexes are important intermediates in biology. While there are numerous examples of low-spin heme iron-nitrosyl complexes in different oxidation states, much less is known about high-spin (hs) non-heme iron-nitrosyls in oxidation states other than the formally ferrous NO adducts ({FeNO}7 in the Enemark-Feltham notation). In this study, we present a complete series of hs-{FeNO}6-8 complexes using the TMG3tren coligand. Redox transformations from the hs-{FeNO}7 complex [Fe(TMG3tren)(NO)]2+ to its {FeNO}6 and {FeNO}8 analogs do not alter the coordination environment of the iron center, allowing for detailed comparisons between these species. Here, we present new MCD, NRVS, XANES/EXAFS, and Mössbauer data, demonstrating that these redox transformations are metal based, which allows us to access hs-Fe(II)-NO-, Fe(III)-NO-, and Fe(IV)-NO- complexes. Vibrational data, analyzed by NCA, directly quantify changes in Fe-NO bonding along this series. Optical data allow for the identification of a "spectator" charge-transfer transition that, together with Mössbauer and XAS data, directly monitors the electronic changes of the Fe center. Using EXAFS, we are also able to provide structural data for all complexes. The magnetic properties of the complexes are further analyzed (from magnetic Mössbauer). The properties of our hs-{FeNO}6-8 complexes are then contrasted to corresponding, low-spin iron-nitrosyl complexes where redox transformations are generally NO centered. The hs-{FeNO}8 complex can further be protonated by weak acids, and the product of this reaction is characterized. Taken together, these results provide unprecedented insight into the properties of biologically relevant non-heme iron-nitrosyl complexes in three relevant oxidation states.
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Affiliation(s)
- Amy L Speelman
- Department of Chemistry and Department of Biophysics , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Corey J White
- Department of Chemistry and Department of Biophysics , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Bo Zhang
- Department of Chemistry and Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - E Ercan Alp
- Advanced Photon Source , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Jiyong Zhao
- Advanced Photon Source , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Michael Hu
- Advanced Photon Source , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Carsten Krebs
- Department of Chemistry and Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - James Penner-Hahn
- Department of Chemistry and Department of Biophysics , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Nicolai Lehnert
- Department of Chemistry and Department of Biophysics , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
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25
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Sakurai N, Kataoka K, Sugaya N, Shimodaira T, Iwamoto M, Shoda M, Horiuchi H, Kiyono M, Ohta Y, Triwiyono B, Seo D, Sakurai T. Heterologous expression of Halomonas halodenitrificans nitric oxide reductase and its N-terminally truncated NorC subunit in Escherichia coli. J Inorg Biochem 2017; 169:61-67. [PMID: 28131879 DOI: 10.1016/j.jinorgbio.2017.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 12/30/2016] [Accepted: 01/20/2017] [Indexed: 11/29/2022]
Abstract
Halomonas halodenitrificans nitric oxide reductase (NOR) is the membrane-bound heterodimer complex of NorC, which contains a low-spin heme c center, and NorB, which contains a low-spin heme b center, a high-spin heme b3 center, and a non-heme FeB center. The soluble domain of NorC, NorC* (ΔMet1-Val37) was heterologously expressed in Escherichia coli using expression plasmids harboring the truncated norC gene deleted of its 84 5'-terminal nucleotides. Analogous scission of the N-terminal helix as the membrane anchor took place when the whole norC gene was used. NorC* exhibited spectra typical of a low-spin heme c. In addition, NorC* functioned as the acceptor of an electron from a cytochrome c isolated from the periplasm of H. halodenitrificans and small reducing reagents. The redox potential of NorC* shifted ca. 40mV in the negative direction from that of NorC. Unlike NorC, recombinant NorB was not heterologously expressed. However, recombinant NOR (rNOR) could be expressed in E. coli by using a plasmid harboring all genes in the nor operon, norCBQDX, from which the three hairpin loops (mRNA) were deleted, and by using the ccm genes for the maturation of C-type heme. rNOR exhibited the same spectroscopic properties and reactivity to NO and O2 as NOR, although its enzymatic activity toward NO was considerably decreased. These results on the expression of rNOR and NorC* will allow us to develop more profound studies on the properties of the four Fe centers and the reaction mechanism of NOR from this halophilic denitrifying bacterium.
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Affiliation(s)
- Nobuhiko Sakurai
- Division of Biological Science, Graduate School of Natural Sciences, Nagoya City University, Yamanohata 1, Mizuho, Nagoya 467-8501, Japan.
| | - Kunishige Kataoka
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Noriko Sugaya
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Takaki Shimodaira
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Mie Iwamoto
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Munehiro Shoda
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Hajime Horiuchi
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Miyuki Kiyono
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Yasuke Ohta
- Division of Biological Science, Graduate School of Natural Sciences, Nagoya City University, Yamanohata 1, Mizuho, Nagoya 467-8501, Japan
| | - Bambang Triwiyono
- Division of Biological Science, Graduate School of Natural Sciences, Nagoya City University, Yamanohata 1, Mizuho, Nagoya 467-8501, Japan
| | - Daisuke Seo
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
| | - Takeshi Sakurai
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
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26
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Blomberg MRA. Can Reduction of NO to N2O in Cytochrome c Dependent Nitric Oxide Reductase Proceed through a Trans-Mechanism? Biochemistry 2016; 56:120-131. [DOI: 10.1021/acs.biochem.6b00788] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Margareta R. A. Blomberg
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
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27
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Yi J, Campbell ALO, Richter-Addo GB. Nitric oxide coupling to generate N 2O promoted by a single-heme system as examined by density functional theory. Nitric Oxide 2016; 60:69-75. [PMID: 27646954 DOI: 10.1016/j.niox.2016.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 08/11/2016] [Accepted: 09/14/2016] [Indexed: 11/25/2022]
Abstract
Bacteria utilize a heme/non-heme enzyme system to detoxify nitric oxide (NO) to N2O. In order to probe the capacity of a single-heme system to mediate this NO-to-N2O transformation, various scenarios for addition of electrons, protons, and a second NO molecule to a heme nitrosyl to generate N2O were explored by density functional theory calculations. We describe, utilizing this single-heme system, several stepwise intermediates along pathways that enable the critical N-N bond formation step yielding the desired Fe-N2O product. We also report a hitherto unreported directional second protonation that results in either productive N2O formation with loss of water, or formation of a non-productive hyponitrous acid adduct Fe{HONNOH}.
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Affiliation(s)
- Jun Yi
- Department of Biological Engineering, Nanjing University of Science and Technology, 200 Xiao Ling Wei Road, Nanjing, Jiangsu Province, 210094, PR China; Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK, 73019, USA.
| | - Adam L O Campbell
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK, 73019, USA
| | - George B Richter-Addo
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK, 73019, USA.
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Matsumura H, Chakraborty S, Reed J, Lu Y, Moënne-Loccoz P. Effect of Outer-Sphere Side Chain Substitutions on the Fate of the trans Iron-Nitrosyl Dimer in Heme/Nonheme Engineered Myoglobins (Fe(B)Mbs): Insights into the Mechanism of Denitrifying NO Reductases. Biochemistry 2016; 55:2091-9. [PMID: 27003474 DOI: 10.1021/acs.biochem.5b01109] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Denitrifying NO reductases are transmembrane protein complexes that utilize a heme/nonheme diiron center at their active sites to reduce two NO molecules to the innocuous gas N2O. Fe(B)Mb proteins, with their nonheme iron sites engineered into the heme distal pocket of sperm whale myoglobin, are attractive models for studying the molecular details of the NO reduction reaction. Spectroscopic and structural studies of Fe(B)Mb constructs have confirmed that they reproduce the metal coordination spheres observed at the active site of the cytochrome c-dependent NO reductase from Pseudomonas aeruginosa. Exposure of Fe(B)Mb to excess NO, as examined by analytical and spectroscopic techniques, results primarily in the formation of a five-coordinate heme-nitrosyl complex without N2O production. However, substitution of the outer-sphere residue Ile107 with a glutamic acid (i.e., I107E) decreases the formation rate of the five-coordinate heme-nitrosyl complex and allows for the substoichiometric production of N2O. Here, we aim to better characterize the formation of the five-coordinate heme-nitrosyl complex and to explain why the level of N2O production increases with the I107E substitution. We follow the formation of the five-coordinate heme-nitrosyl inhibitory complex through the sequential exposure of Fe(B)Mb to different NO isotopomers using rapid-freeze-quench resonance Raman spectroscopy. The data show that the complex is formed by the displacement of the proximal histidine by a new NO molecule after the weakening of the Fe(II)-His bond in the intermediate six-coordinate low-spin (6cLS) heme-nitrosyl complex. These results lead us to explore diatomic migration within the scaffold of myoglobin and whether substitutions at residue 107 can be sufficient to control access to the proximal heme cavities. Results on a new Fe(B)Mb construct with an I107F substitution (Fe(B)Mb3) show an increased rate for the formation of the five-coordinate low-spin heme-nitrosyl complex without N2O production. Taken together, our results suggest that production of N2O from the [6cLS heme {FeNO}(7)/{Fe(B)NO}(7)] trans iron-nitrosyl dimer intermediate requires a proton transfer event facilitated by an outer-sphere residue such as E107 in Fe(B)Mb2 and E280 in P. aeruginosa cNOR.
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Affiliation(s)
- Hirotoshi Matsumura
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University , Portland, Oregon 97239, United States
| | - Saumen Chakraborty
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Julian Reed
- Department of Biochemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Department of Biochemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Pierre Moënne-Loccoz
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University , Portland, Oregon 97239, United States
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Abstract
Redox active iron is utilized in biology for various electron transfer and catalytic reactions essential for life, yet this same chemistry mediates the formation of partially reduced oxygen species (PROS). Oxidative stress derived from the iron accumulated in the amyloid plaques originating from amyloid β (Aβ) peptides and neurofibrillary tangles derived from hyperphosphorylated tau proteins has been implicated in the pathogenesis of Alzheimer's disease (AD). Altered heme homeostasis leading to dysregulation of expression of heme proteins and heme deposits in the amyloid plaques are characteristic of the AD brain. However, the pathogenic significance of heme in neurodegeneration in AD has been unappreciated due to the lack of detailed understanding of the chemistry of the interaction of heme and Aβ peptides. As a result, the biochemistry and biophysics of heme complexes of Aβ peptides (heme-Aβ) remained largely unexplored. In this Account, we discuss the active site environment of heme bound Aβ complexes, which involves three amino acid residues unique in mammalian Aβ (Arg5, Tyr10, and His13) and missing in Aβ from rodents, which do not get affected by AD. The histidine residue binds heme, while the arginine and the tyrosine act as key second sphere residues of the heme-Aβ active site that play a crucial role in its reactivity. Generation of PROS, enhanced peroxidase activity, and oxidation of neurotransmitters such as serotonin (5-HT) are all found to be catalyzed by heme-Aβ in in vitro assays, and these reactivities can potentially be linked to the observed neuropathologies in AD brain. Association of Cu with heme-Aβ leads to the formation of heme-Cu-Aβ. The heme-Cu-Aβ complex produces a greater amount of PROS than reduced heme-Aβ or Cu-Aβ alone. Nitric oxide (NO), a signaling molecule, is found to ameliorate the detrimental effects of heme-Aβ and Cu bound heme-Aβ complexes by detaching heme from the heme-Aβ complex and releasing it into the environment solution. Heme-Aβ complexes show fast electron transfer with oxidized cytochrome c and rapid heme transfer with apomyoglobin and aponeuroglobin. NO, cytochrome c, and apoglobins can all lead to reduction in PROS generated by reduced heme-Aβ. Synthetic analogues of heme, offering a hydrophobic distal environment, have been used to trap oxygen bound intermediates, which provides insight into the mechanism of PROS generation by reduced heme-Aβ. Artificial constructs of Aβ on nonbiological platforms are used not only to stabilize metastable and physiologically relevant large and small amyloid aggregates but also to monitor the interaction of various drug candidates with heme and Cu bound Aβ aggregates, representing a tractable avenue for testing therapeutic agents targeting metals and cofactors in AD.
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Affiliation(s)
- Chandradeep Ghosh
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Manas Seal
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Soumya Mukherjee
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Somdatta Ghosh Dey
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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Attia AAA, Silaghi-Dumitrescu R. Bacterial nitric oxide reductase: a mechanism revisited by an ONIOM (DFT:MM) study. J Mol Model 2015; 21:130. [PMID: 25920393 DOI: 10.1007/s00894-015-2679-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 04/13/2015] [Indexed: 10/23/2022]
Abstract
Bacterial nitric oxide reductase (cNOR) is an important binuclear iron enzyme responsible for the reduction of nitric oxide to nitrous oxide in the catalytic cycle of bacterial respiration. The reaction mechanism of cNOR as well as the key reactive intermediates of the reaction are still under debate. Here, we report a computational study based on ONIOM (DFT:MM) calculations aimed at investigating the reaction mechanism of cNOR. The results suggest that the reaction proceeds via the mono-nitrosyl mechanism which starts off by the binding of an NO molecule to the heme b3 center, N-N hyponitrite bond formation as a result of the reaction with a second NO molecule was found to proceed with an exothermic energy barrier to yield a hyponitrite adduct forming an open (incomplete) ring conformation with the non-heme FeB center (O-N-N-O-FeB). N-O bond cleavage to yield N2O was shown to be the rate-limiting step with an activation barrier of 22.6 kcal mol(-1). The dinitrosyl (trans) mechanism, previously proposed by several studies, was also examined and found unfavorable due to high activation barriers of the resulting intermediates.
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Affiliation(s)
- Amr A A Attia
- Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Babeș-Bolyai University, Cluj-Napoca, Romania
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31
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Harrop TC. New Insights on {FeNO}n (n=7, 8) Systems as Enzyme Models and HNO Donors. ADVANCES IN INORGANIC CHEMISTRY 2015. [DOI: 10.1016/bs.adioch.2014.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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32
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Yang H, Gandhi H, Ostrom NE, Hegg EL. Isotopic fractionation by a fungal P450 nitric oxide reductase during the production of N2O. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:10707-10715. [PMID: 25121461 DOI: 10.1021/es501912d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas with a 100-year global warming potential approximately 300 times that of CO2. Because microbes account for over 75% of the N2O released in the U.S., understanding the biochemical processes by which N2O is produced is critical to our efforts to mitigate climate change. In the current study, we used gas chromatography-isotope ratio mass spectrometry (GC-IRMS) to measure the δ(15)N, δ(18)O, δ(15)N(α), and δ(15)N(β) of N2O generated by purified fungal nitric oxide reductase (P450nor) from Histoplasma capsulatum. The isotope values were used to calculate site preference (SP) values (difference in δ(15)N between the central (α) and terminal (β) N atoms in N2O), enrichment factors (ε), and kinetic isotope effects (KIEs). Both oxygen and N(α) displayed normal isotope effects during enzymatic NO reduction with ε values of -25.7‰ (KIE = 1.0264) and -12.6‰ (KIE = 1.0127), respectively. However, bulk nitrogen (average δ(15)N of N(α) and N(β)) and N(β) exhibited inverse isotope effects with ε values of 14.0‰ (KIE = 0.9862) and 36.1‰ (KIE = 0.9651), respectively. The observed inverse isotope effect in δ(15)N(β) is consistent with reversible binding of the first NO in the P450nor reaction mechanism. In contrast to the constant SP observed during NO reduction in microbial cultures, the site preference measured for purified H. capsulatum P450nor was not constant, increasing from ∼ 15‰ to ∼ 29‰ during the course of the reaction. This indicates that SP for microbial cultures can vary depending on the growth conditions, which may complicate source tracing during microbial denitrification.
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Affiliation(s)
- Hui Yang
- Department of Biochemistry & Molecular Biology, Michigan State University , East Lansing, Michigan 48824, United States
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33
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Duarte AG, Cordas CM, Moura JJ, Moura I. Steady-state kinetics with nitric oxide reductase (NOR): New considerations on substrate inhibition profile and catalytic mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:375-84. [DOI: 10.1016/j.bbabio.2014.01.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 12/28/2013] [Accepted: 01/02/2014] [Indexed: 10/25/2022]
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34
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Terasaka E, Okada N, Sato N, Sako Y, Shiro Y, Tosha T. Characterization of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus: enzymatic activity and active site structure. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1019-26. [PMID: 24569054 DOI: 10.1016/j.bbabio.2014.02.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 02/10/2014] [Accepted: 02/15/2014] [Indexed: 10/25/2022]
Abstract
Nitric oxide reductase (NOR) catalyzes the reduction of nitric oxide to generate nitrous oxide. We recently reported on the crystal structure of a quinol-dependent NOR (qNOR) from Geobacillus stearothermophilus [Y. Matsumoto, T. Tosha, A.V. Pisliakov, T. Hino, H. Sugimoto, S. Nagano, Y. Sugita and Y. Shiro, Nat. Struct. Mol. Biol. 19 (2012) 238-246], and suggested that a water channel from the cytoplasm, which is not observed in cytochrome c-dependent NOR (cNOR), functions as a pathway transferring catalytic protons. Here, we further investigated the functional and structural properties of qNOR, and compared the findings with those for cNOR. The pH optimum for the enzymatic reaction of qNOR was in the alkaline range, whereas Pseudomonas aeruginosa cNOR showed a higher activity at an acidic pH. The considerably slower reduction rate, and a correlation of the pH dependence for enzymatic activity and the reduction rate suggest that the reduction process is the rate-determining step for the NO reduction by qNOR, while the reduction rate for cNOR was very fast and therefore is unlikely to be the rate-determining step. A close examination of the heme/non-heme iron binuclear center by resonance Raman spectroscopy indicated that qNOR has a more polar environment at the binuclear center compared with cNOR. It is plausible that a water channel enhances the accessibility of the active site to solvent water, creating a more polar environment in qNOR. This structural feature could control certain properties of the active site, such as redox potential, which could explain the different catalytic properties of the two NORs. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
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Affiliation(s)
- Erina Terasaka
- RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan; Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Norihiro Okada
- RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan; Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Nozomi Sato
- RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan; Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshihiko Sako
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshitsugu Shiro
- RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan; Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan.
| | - Takehiko Tosha
- RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan.
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35
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Chakraborty S, Reed J, Ross M, Nilges MJ, Petrik ID, Ghosh S, Hammes-Schiffer S, Sage JT, Zhang Y, Schulz CE, Lu Y. Spectroscopic and Computational Study of a Nonheme Iron Nitrosyl Center in a Biosynthetic Model of Nitric Oxide Reductase. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201308431] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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36
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Chakraborty S, Reed J, Ross M, Nilges MJ, Petrik ID, Ghosh S, Hammes-Schiffer S, Sage JT, Zhang Y, Schulz CE, Lu Y. Spectroscopic and computational study of a nonheme iron nitrosyl center in a biosynthetic model of nitric oxide reductase. Angew Chem Int Ed Engl 2014; 53:2417-21. [PMID: 24481708 DOI: 10.1002/anie.201308431] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 11/27/2013] [Indexed: 11/07/2022]
Abstract
A major barrier to understanding the mechanism of nitric oxide reductases (NORs) is the lack of a selective probe of NO binding to the nonheme FeB center. By replacing the heme in a biosynthetic model of NORs, which structurally and functionally mimics NORs, with isostructural ZnPP, the electronic structure and functional properties of the FeB nitrosyl complex was probed. This approach allowed observation of the first S=3/2 nonheme {FeNO}(7) complex in a protein-based model system of NOR. Detailed spectroscopic and computational studies show that the electronic state of the {FeNO}(7) complex is best described as a high spin ferrous iron (S=2) antiferromagnetically coupled to an NO radical (S=1/2) [Fe(2+)-NO(.)]. The radical nature of the FeB -bound NO would facilitate N-N bond formation by radical coupling with the heme-bound NO. This finding, therefore, supports the proposed trans mechanism of NO reduction by NORs.
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Affiliation(s)
- Saumen Chakraborty
- Department of Chemistry and Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL (USA)
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37
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Sato N, Ishii S, Sugimoto H, Hino T, Fukumori Y, Sako Y, Shiro Y, Tosha T. Structures of reduced and ligand-bound nitric oxide reductase provide insights into functional differences in respiratory enzymes. Proteins 2014; 82:1258-71. [PMID: 24338896 DOI: 10.1002/prot.24492] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Revised: 11/27/2013] [Accepted: 12/09/2013] [Indexed: 11/07/2022]
Abstract
Nitric oxide reductase (NOR) catalyzes the generation of nitrous oxide (N2O) via the reductive coupling of two nitric oxide (NO) molecules at a heme/non-heme Fe center. We report herein on the structures of the reduced and ligand-bound forms of cytochrome c-dependent NOR (cNOR) from Pseudomonas aeruginosa at a resolution of 2.3-2.7 Å, to elucidate structure-function relationships in NOR, and compare them to those of cytochrome c oxidase (CCO) that is evolutionarily related to NOR. Comprehensive crystallographic refinement of the CO-bound form of cNOR suggested that a total of four atoms can be accommodated at the binuclear center. Consistent with this, binding of bulky acetaldoxime (CH3-CH=N-OH) to the binuclear center of cNOR was confirmed by the structural analysis. Active site reduction and ligand binding in cNOR induced only ∼0.5 Å increase in the heme/non-heme Fe distance, but no significant structural change in the protein. The highly localized structural change is consistent with the lack of proton-pumping activity in cNOR, because redox-coupled conformational changes are thought to be crucial for proton pumping in CCO. It also permits the rapid decomposition of cytotoxic NO in denitrification. In addition, the shorter heme/non-heme Fe distance even in the bulky ligand-bound form of cNOR (∼4.5 Å) than the heme/Cu distance in CCO (∼5 Å) suggests the ability of NOR to maintain two NO molecules within a short distance in the confined space of the active site, thereby facilitating N-N coupling to produce a hyponitrite intermediate for the generation of N2O.
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Affiliation(s)
- Nozomi Sato
- Biometal Science Laboratory, RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan; Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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38
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Pirota V, Gennarini F, Dondi D, Monzani E, Casella L, Dell'Acqua S. Dinuclear heme and non-heme metal complexes as bioinspired catalysts for oxidation reactions. NEW J CHEM 2014. [DOI: 10.1039/c3nj01279d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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39
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Shoji M, Hanaoka K, Kondo D, Sato A, Umeda H, Katsumasa Kamiya, Shiraishi K. A QM/MM study of nitric oxide reductase-catalysed N2O formation. Mol Phys 2013. [DOI: 10.1080/00268976.2013.830200] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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40
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Characterization of the nitric oxide reductase from Thermus thermophilus. Proc Natl Acad Sci U S A 2013; 110:12613-8. [PMID: 23858452 DOI: 10.1073/pnas.1301731110] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nitrous oxide (N2O) is a powerful greenhouse gas implicated in climate change. The dominant source of atmospheric N2O is incomplete biological dentrification, and the enzymes responsible for the release of N2O are NO reductases. It was recently reported that ambient emissions of N2O from the Great Boiling Spring in the United States Great Basin are high, and attributed to incomplete denitrification by Thermus thermophilus and related bacterial species [Hedlund BP, et al. (2011) Geobiology 9(6)471-480]. In the present work, we have isolated and characterized the NO reductase (NOR) from T. thermophilus. The enzyme is a member of the cNOR family of enzymes and belongs to a phylogenetic clade that is distinct from previously examined cNORs. Like other characterized cNORs, the T. thermophilus cNOR consists of two subunits, NorB and NorC, and contains a one heme c, one Ca(2+), a low-spin heme b, and an active site consisting of a high-spin heme b and FeB. The roles of conserved residues within the cNOR family were investigated by site-directed mutagenesis. The most important and unexpected result is that the glutamic acid ligand to FeB is not essential for function. The E211A mutant retains 68% of wild-type activity. Mutagenesis data and the pattern of conserved residues suggest that there is probably not a single pathway for proton delivery from the periplasm to the active site that is shared by all cNORs, and that there may be multiple pathways within the T. thermophilus cNOR.
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41
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Tosha T, Shiro Y. Crystal structures of nitric oxide reductases provide key insights into functional conversion of respiratory enzymes. IUBMB Life 2013; 65:217-26. [DOI: 10.1002/iub.1135] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Accepted: 12/25/2012] [Indexed: 11/08/2022]
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42
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Berto TC, Speelman AL, Zheng S, Lehnert N. Mono- and dinuclear non-heme iron–nitrosyl complexes: Models for key intermediates in bacterial nitric oxide reductases. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.05.007] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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43
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Ghosh C, Pramanik D, Mukherjee S, Dey A, Dey SG. Interaction of NO with Cu and heme-bound Aβ peptides associated with Alzheimer's disease. Inorg Chem 2012; 52:362-8. [PMID: 23214455 DOI: 10.1021/ic302131n] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Reduced Cu and heme has been invoked to be involved in Alzheimer's disease (AD). Recently the Aβ peptides have been demonstrated to bind heme and Cu simultaneously, and this complex produces significantly more toxic partially reduced oxygen species (PROS) than the Cu or heme-bound Aβ peptides. Here a combination of absorption, EPR, and resonance Raman spectroscopy along with kinetic assays are used to investigate the interaction of nitric oxide (NO) with the physiologically relevant form of Cu and heme-bound Aβ peptides, since a down-regulation of nitric oxide synthase activity is observed in patients suffering from AD. The data indicate that NO oxidizes the Cu(I) sites, making them less toxic toward PROS generation and releases heme from the Aβ peptides ameliorating the effects of heme binding to Aβ peptides associated with AD. This process involves a tyrosine-mediated electron transfer between the Cu and heme sites. These results provide a mechanistic pathway for the possible protective role of NO in AD.
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Affiliation(s)
- Chandradeep Ghosh
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata, India 700032
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44
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Electrochemical behaviour of bacterial nitric oxide reductase-evidence of low redox potential non-heme Fe(B) gives new perspectives on the catalytic mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:233-8. [PMID: 23142527 DOI: 10.1016/j.bbabio.2012.10.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 10/26/2012] [Accepted: 10/31/2012] [Indexed: 11/20/2022]
Abstract
Nitric oxide reductase (NOR) is a membrane bound enzyme involved in the metabolic denitrification pathway, reducing nitric oxide (NO) to nitrous oxide (N(2)O), subsequently promoting the formation of the NN bond. Three types of bacterial NOR are known, namely cNOR, qNOR and qCuNOR, that differ on the physiological electron donor. cNOR has been purified as a two subunit complex, the NorC, anchored to the cytoplasmic membrane, with a low-spin heme c, and the NorB subunit showing high structural homology with the HCuO subunit I, comprising a bis-histidine low-spin heme b and a binuclear iron centre. The binuclear iron centre is the catalytic site and it is formed by a heme b(3) coupled to a non-heme iron (Fe(B)) through a μ-oxo bridge. The catalytic mechanism is still under discussion and three hypotheses have been proposed: the trans-mechanism, the cis-Fe(B) and the cis-heme b(3) mechanisms. In the present work, the Pseudomonas nautica cNOR electrochemical behaviour was studied by cyclic voltammetry (CV), using a pyrolytic graphite electrode modified with the immobilised protein. The protein redox centres were observed and the formal redox potentials were determined. The binuclear iron centre presents the lowest redox potential value, and discrimination between the heme b(3) and Fe(B) redox processes was attained. Also, the number of electrons involved and correspondent surface electronic transfer rate constants were estimated. The pH dependence of the observed redox processes was determined and some new insights on the NOR catalytic mechanism are discussed.
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45
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Shiro Y, Sugimoto H, Tosha T, Nagano S, Hino T. Structural basis for nitrous oxide generation by bacterial nitric oxide reductases. Philos Trans R Soc Lond B Biol Sci 2012; 367:1195-203. [PMID: 22451105 DOI: 10.1098/rstb.2011.0310] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The crystal structure of the bacterial nitric oxide reductase (cNOR) from Pseudomonas aeruginosa is reported. Its overall structure is similar to those of the main subunit of aerobic and micro-aerobic cytochrome oxidases (COXs), in agreement with the hypothesis that all these enzymes are members of the haem-copper oxidase superfamily. However, substantial structural differences between cNOR and COX are observed in the catalytic centre and the delivery pathway of the catalytic protons, which should be reflected in functional differences between these respiratory enzymes. On the basis of the cNOR structure, we propose a possible reaction mechanism of nitric oxide reduction to nitrous oxide as a working hypothesis.
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46
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Blomberg MRA, Siegbahn PEM. Mechanism for N2O Generation in Bacterial Nitric Oxide Reductase: A Quantum Chemical Study. Biochemistry 2012; 51:5173-86. [DOI: 10.1021/bi300496e] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Margareta R. A. Blomberg
- Department of Physics, AlbaNova university
center,
and Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Per E. M. Siegbahn
- Department of Physics, AlbaNova university
center,
and Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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47
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Salomonsson L, Reimann J, Tosha T, Krause N, Gonska N, Shiro Y, Adelroth P. Proton transfer in the quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus during reduction of oxygen. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1914-20. [PMID: 22538294 DOI: 10.1016/j.bbabio.2012.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Revised: 04/04/2012] [Accepted: 04/10/2012] [Indexed: 12/17/2022]
Abstract
Bacterial nitric oxide reductases (NOR) are integral membrane proteins that catalyse the reduction of nitric oxide to nitrous oxide, often as a step in the process of denitrification. Most functional data has been obtained with NORs that receive their electrons from a soluble cytochrome c in the periplasm and are hence termed cNOR. Very recently, the structure of a different type of NOR, the quinol-dependent (q)-NOR from the thermophilic bacterium Geobacillus stearothermophilus was solved to atomic resolution [Y. Matsumoto, T. Tosha, A.V. Pisliakov, T. Hino, H. Sugimoto, S. Nagano, Y. Sugita and Y. Shiro, Nat. Struct. Mol. Biol. 19 (2012) 238-246]. In this study, we have investigated the reaction between this qNOR and oxygen. Our results show that, like some cNORs, the G. stearothermophilus qNOR is capable of O(2) reduction with a turnover of ~3electronss(-1) at 40°C. Furthermore, using the so-called flow-flash technique, we show that the fully reduced (with three available electrons) qNOR reacts with oxygen in a reaction with a time constant of 1.8ms that oxidises the low-spin heme b. This reaction is coupled to proton uptake from solution and presumably forms a ferryl intermediate at the active site. The pH dependence of the reaction is markedly different from a corresponding reaction in cNOR from Paracoccus denitrificans, indicating that possibly the proton uptake mechanism and/or pathway differs between qNOR and cNOR. This study furthermore forms the basis for investigation of the proton transfer pathway in qNOR using both variants with putative proton transfer elements modified and measurements of the vectorial nature of the proton transfer. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).
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Affiliation(s)
- Lina Salomonsson
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
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Shiro Y. Structure and function of bacterial nitric oxide reductases: nitric oxide reductase, anaerobic enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1907-13. [PMID: 22425814 DOI: 10.1016/j.bbabio.2012.03.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 03/01/2012] [Accepted: 03/01/2012] [Indexed: 10/28/2022]
Abstract
The crystal structures of bacterial nitric oxide reductases (NOR) from Pseudomonas aeruginosa and Geobacillus stearothermophilus were reported. The structural characteristics of these enzymes, especially at the catalytic site and on the pathway that catalytic protons are delivered, are compared, and the corresponding regions of aerobic and micro-aerobic cytochrome oxidases, O(2) reducing enzymes, which are evolutionarily related to NOR are discussed. On the basis of these structural comparisons, a mechanism for the reduction of NO to produce N(2)O by NOR, and the possible molecular evolution of the proton pumping ability of the respiratory enzymes is discussed. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).
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Arikawa Y, Onishi M. Reductive N–N coupling of NO molecules on transition metal complexes leading to N2O. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2011.10.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Matsumoto Y, Tosha T, Pisliakov AV, Hino T, Sugimoto H, Nagano S, Sugita Y, Shiro Y. Crystal structure of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus. Nat Struct Mol Biol 2012; 19:238-45. [PMID: 22266822 DOI: 10.1038/nsmb.2213] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 11/22/2011] [Indexed: 11/09/2022]
Abstract
The structure of quinol-dependent nitric oxide reductase (qNOR) from G. stearothermophilus, which catalyzes the reduction of NO to produce the major ozone-depleting gas N(2)O, has been characterized at 2.5 Å resolution. The overall fold of qNOR is similar to that of cytochrome c-dependent NOR (cNOR), and some structural features that are characteristic of cNOR, such as the calcium binding site and hydrophilic cytochrome c domain, are observed in qNOR, even though it harbors no heme c. In contrast to cNOR, structure-based mutagenesis and molecular dynamics simulation studies of qNOR suggest that a water channel from the cytoplasm can serve as a proton transfer pathway for the catalytic reaction. Further structural comparison of qNOR with cNOR and aerobic and microaerobic respiratory oxidases elucidates their evolutionary relationship and possible functional conversions.
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Affiliation(s)
- Yushi Matsumoto
- Biometal Science Laboratory, RIKEN SPring-8 Center, Sayo, Hyogo, Japan
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