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De Simone G, di Masi A, Sbardella D, Ascenzi P, Coletta M. Nitric Oxide Binding Geometry in Heme-Proteins: Relevance for Signal Transduction. Antioxidants (Basel) 2024; 13:666. [PMID: 38929104 PMCID: PMC11201058 DOI: 10.3390/antiox13060666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
Nitric oxide (NO) synthesis, signaling, and scavenging is associated to relevant physiological and pathological events. In all tissues and organs, NO levels and related functions are regulated at different levels, with heme proteins playing pivotal roles. Here, we focus on the structural changes related to the different binding modes of NO to heme-Fe(II), as well as the modulatory effects of this diatomic messenger on heme-protein functions. Specifically, the ability of heme proteins to bind NO at either the distal or proximal side of the heme and the transient interchanging of the binding site is reported. This sheds light on the regulation of O2 supply to tissues with high metabolic activity, such as the retina, where a precise regulation of blood flow is necessary to meet the demand of nutrients.
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Affiliation(s)
- Giovanna De Simone
- Dipartimento di Scienze, Università degli Studi Roma Tre, 00146 Rome, Italy; (G.D.S.); (A.d.M.)
| | - Alessandra di Masi
- Dipartimento di Scienze, Università degli Studi Roma Tre, 00146 Rome, Italy; (G.D.S.); (A.d.M.)
- Centro Linceo Interdisciplinare “Beniamino Segre”, Accademia dei Lincei, 00165 Rome, Italy
| | | | - Paolo Ascenzi
- Dipartimento di Scienze, Università degli Studi Roma Tre, 00146 Rome, Italy; (G.D.S.); (A.d.M.)
- Accademia Nazionale dei Lincei, 00165 Rome, Italy
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2
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Zhai Y, Abe H, Wang HC, Hayakawa T, Kumura H, Wakamatsu JI. Dissociation of ferriheme from oxidized heme proteins and re-reduction of ferriheme to ferroheme are crucial for the formation of zinc protoporphyrin IX in nitrite/nitrate-free dry-cured meat products. Food Chem 2023; 427:136755. [PMID: 37399643 DOI: 10.1016/j.foodchem.2023.136755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/19/2023] [Accepted: 06/27/2023] [Indexed: 07/05/2023]
Abstract
Zinc protoporphyrin IX (ZnPP) is the dominant red pigment in nitrate/nitrite-free dry-cured meat products such as Parma ham, and it is considered to be a potential alternative to nitrite/nitrate for reddening dry-cured meat products. Ferroheme and ferriheme dissociated from heme proteins in meat were proposed as substrates to form ZnPP. To elucidate their specific formation mechanism, nitric oxide, carbon monoxide, and azide were used to stable heme in heme proteins. The exogenous hemoglobin derivatives bound with these ligands showed lower heme dissociation compared with exogenous oxyhemoglobin and did not contribute to ZnPP formation. Meanwhile, azide inhibited almost all ZnPP formation by binding to ferriheme, indicating ferriheme dissociation from oxidized heme proteins, predominantly for ZnPP formation. Free ferriheme could not be converted to ZnPP unless it was reduced to ferroheme. Overall, ferriheme dissociated from oxidized heme proteins was the dominant substrate for conversion to ZnPP after re-reduction to ferroheme.
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Affiliation(s)
- Yang Zhai
- Laboratory of Applied Food Science, Graduate School of Agriculture, Hokkaido University, Japan
| | - Haruka Abe
- Laboratory of Applied Food Science, Graduate School of Agriculture, Hokkaido University, Japan
| | - Hung-Cheng Wang
- Laboratory of Applied Food Science, Graduate School of Agriculture, Hokkaido University, Japan
| | - Toru Hayakawa
- Laboratory of Applied Food Science, Graduate School of Agriculture, Hokkaido University, Japan
| | - Haruto Kumura
- Laboratory of Applied Food Science, Graduate School of Agriculture, Hokkaido University, Japan
| | - Jun-Ichi Wakamatsu
- Laboratory of Applied Food Science, Graduate School of Agriculture, Hokkaido University, Japan.
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3
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Valianti VK, Tselios C, Pinakoulaki E. Reversible thermally induced spin crossover in the myoglobin-nitrito adduct directly monitored by resonance Raman spectroscopy. RSC Adv 2023; 13:9020-9025. [PMID: 36950070 PMCID: PMC10025812 DOI: 10.1039/d3ra00225j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/12/2023] [Indexed: 03/24/2023] Open
Abstract
Myoglobin has been demonstrated to function as a nitrite reductase to produce nitric oxide during hypoxia. One of the most intriguing aspects of the myoglobin/nitrite interactions revealed so far is the unusual O-binding mode of nitrite to the ferric heme iron, although conflicting data have been reported for the electronic structure of this complex also raising the possibility of linkage isomerism. In this work, we applied resonance Raman spectroscopy in a temperature-dependent approach to investigate the binding of nitrite to ferric myoglobin and the properties of the formed adduct from ambient to low temperatures (293 K to 153 K). At ambient temperature the high spin state of the ferric heme Fe-O-N[double bond, length as m-dash]O species is present and upon decreasing the temperature the low spin state is populated, demonstrating that a thermally-induced spin crossover phenomenon takes place analogous to what has been observed in many transition metal complexes. The observed spin crossover is fully reversible and is not due to linkage isomerism, since the O-binding mode is retained upon the spin transition. The role of the heme pocket environment in controlling the nitrite binding mode and spin transition is discussed.
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Affiliation(s)
| | - Charalampos Tselios
- Department of Chemistry, University of Cyprus 2109 Aglantzia Cyprus
- Department of Chemical Engineering, Cyprus University of Technology Lemesos Cyprus
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4
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Zheng Y, Deng W, Liu D, Li Y, Peng K, Lorimer GH, Wang J. Redox and spectroscopic properties of mammalian nitrite reductase-like hemoproteins. J Inorg Biochem 2022; 237:111982. [PMID: 36116154 DOI: 10.1016/j.jinorgbio.2022.111982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 01/18/2023]
Abstract
Besides the canonical pathway of L-arginine oxidation to produce nitric oxide (NO) in vivo, the nitrate-nitrite-NO pathway has been widely accepted as another source for circulating NO in mammals, especially under hypoxia. To date, there have been at least ten heme-containing nitrite reductase-like proteins discovered in mammals with activities mainly identified in vitro, including four globins (hemoglobin, myoglobin, neuroglobin (Ngb), cytoglobin (Cygb)), three mitochondrial respiratory chain enzymes (cytochrome c oxidase, cytochrome bc1, cytochrome c), and three other heme proteins (endothelial nitric oxide synthase, cytochrome P450 and indoleamine 2,3-dioxygenase 1 (IDO1)). The pathophysiological functions of these proteins are closely related to their redox and spectroscopic properties, as well as their protein structure, although the physiological roles of Ngb, Cygb and IDO1 remain unclear. So far, comprehensive summaries of the redox and spectroscopic properties of these nitrite reductase-like hemoproteins are still lacking. In this review, we have mainly summarized the published data on the application of ultraviolet-visible, electron paramagnetic resonance, circular dichroism and resonance Raman spectroscopies, and X-ray crystallography in studying nitrite reductase-like activity of these 10 proteins, in order to sort out the relationships among enzymatic function, structure and spectroscopic characterization, which might help in understanding their roles in redox biology and medicine.
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Affiliation(s)
- Yunlong Zheng
- Hubei University of Technology Autism & Depression Diagnosis and Intervention Institute, Hubei University of Technology, Wuhan, Hubei, China; International Joint Research Center for General Health, Precision Medicine & Nutrition, Hubei University of Technology, Wuhan, Hubei, China; Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, Hubei, China
| | - Wenwen Deng
- Hubei University of Technology Autism & Depression Diagnosis and Intervention Institute, Hubei University of Technology, Wuhan, Hubei, China; International Joint Research Center for General Health, Precision Medicine & Nutrition, Hubei University of Technology, Wuhan, Hubei, China; Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, Hubei, China
| | - Di Liu
- Hubei University of Technology Autism & Depression Diagnosis and Intervention Institute, Hubei University of Technology, Wuhan, Hubei, China; International Joint Research Center for General Health, Precision Medicine & Nutrition, Hubei University of Technology, Wuhan, Hubei, China; Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, Hubei, China
| | - Youheng Li
- Hubei University of Technology Autism & Depression Diagnosis and Intervention Institute, Hubei University of Technology, Wuhan, Hubei, China; International Joint Research Center for General Health, Precision Medicine & Nutrition, Hubei University of Technology, Wuhan, Hubei, China; Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, Hubei, China
| | - Kang Peng
- Hubei University of Technology Autism & Depression Diagnosis and Intervention Institute, Hubei University of Technology, Wuhan, Hubei, China; International Joint Research Center for General Health, Precision Medicine & Nutrition, Hubei University of Technology, Wuhan, Hubei, China; Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, Hubei, China
| | | | - Jun Wang
- Hubei University of Technology Autism & Depression Diagnosis and Intervention Institute, Hubei University of Technology, Wuhan, Hubei, China; International Joint Research Center for General Health, Precision Medicine & Nutrition, Hubei University of Technology, Wuhan, Hubei, China; Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, Hubei, China.
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5
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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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Serra I, Schmidt D, Pfanzagl V, Mlynek G, Hofbauer S, Djinović-Carugo K, Furtmüller PG, García-Rubio I, Van Doorslaer S, Obinger C. Impact of the dynamics of the catalytic arginine on nitrite and chlorite binding by dimeric chlorite dismutase. J Inorg Biochem 2021; 227:111689. [PMID: 34922158 DOI: 10.1016/j.jinorgbio.2021.111689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/15/2021] [Accepted: 12/03/2021] [Indexed: 01/04/2023]
Abstract
Chlorite dismutases (Clds) are heme b containing oxidoreductases able to decompose chlorite to chloride and molecular oxygen. This work analyses the impact of the distal, flexible and catalytic arginine on the binding of anionic angulate ligands like nitrite and the substrate chlorite. Dimeric Cld from Cyanothece sp. PCC7425 was used as a model enzyme. We have investigated wild-type CCld having the distal catalytic R127 hydrogen-bonded to glutamine Q74 and variants with R127 (i) being arrested in a salt-bridge with a glutamate (Q74E), (ii) being fully flexible (Q74V) or (iii) substituted by either alanine (R127A) or lysine (R127K). We present the electronic and spectral signatures of the high-spin ferric proteins and the corresponding low-spin nitrite complexes elucidated by UV-visible, circular dichroism and electron paramagnetic resonance spectroscopies. Furthermore, we demonstrate the impact of the dynamics of R127 on the thermal stability of the respective nitrite adducts and present the X-ray crystal structures of the nitrite complexes of wild-type CCld and the variants Q74V, Q74E and R127A. In addition, the molecular dynamics (MD) and the binding modi of nitrite and chlorite to the ferric wild-type enzyme and the mutant proteins and the interaction of the oxoanions with R127 have been analysed by MD simulations. The findings are discussed with respect to the role(s) of R127 in ligand and chlorite binding and substrate degradation.
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Affiliation(s)
- Ilenia Serra
- BIMEF Laboratory, Department of Chemistry, University of Antwerp, Belgium
| | - Daniel Schmidt
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Vera Pfanzagl
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Georg Mlynek
- Core Facility Biomolecular & Cellular Analysis, University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, A-1190 Vienna, Austria; Department of Structural and Computational Biology, Max Perutz Laboratories, A-1030, Vienna, Austria
| | - Stefan Hofbauer
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Kristina Djinović-Carugo
- Department of Structural and Computational Biology, Max Perutz Laboratories, A-1030, Vienna, Austria; Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 5, SI-1000 Ljubljana, Slovenia
| | - Paul G Furtmüller
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Inés García-Rubio
- Department of Condensed Matter Physics, Faculty of Sciences, University of Zaragoza, 50009 Zaragoza, Spain; Centro Universitario de la Defensa, 50090 Zaragoza, Spain
| | | | - Christian Obinger
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria.
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7
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Kroneck PMH. Nature's nitrite-to-ammonia expressway, with no stop at dinitrogen. J Biol Inorg Chem 2021; 27:1-21. [PMID: 34865208 PMCID: PMC8840924 DOI: 10.1007/s00775-021-01921-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022]
Abstract
Since the characterization of cytochrome c552 as a multiheme nitrite reductase, research on this enzyme has gained major interest. Today, it is known as pentaheme cytochrome c nitrite reductase (NrfA). Part of the NH4+ produced from NO2- is released as NH3 leading to nitrogen loss, similar to denitrification which generates NO, N2O, and N2. NH4+ can also be used for assimilatory purposes, thus NrfA contributes to nitrogen retention. It catalyses the six-electron reduction of NO2- to NH4+, hosting four His/His ligated c-type hemes for electron transfer and one structurally differentiated active site heme. Catalysis occurs at the distal side of a Fe(III) heme c proximally coordinated by lysine of a unique CXXCK motif (Sulfurospirillum deleyianum, Wolinella succinogenes) or, presumably, by the canonical histidine in Campylobacter jejeuni. Replacement of Lys by His in NrfA of W. succinogenes led to a significant loss of enzyme activity. NrfA forms homodimers as shown by high resolution X-ray crystallography, and there exist at least two distinct electron transfer systems to the enzyme. In γ-proteobacteria (Escherichia coli) NrfA is linked to the menaquinol pool in the cytoplasmic membrane through a pentaheme electron carrier (NrfB), in δ- and ε-proteobacteria (S. deleyianum, W. succinogenes), the NrfA dimer interacts with a tetraheme cytochrome c (NrfH). Both form a membrane-associated respiratory complex on the extracellular side of the cytoplasmic membrane to optimize electron transfer efficiency. This minireview traces important steps in understanding the nature of pentaheme cytochrome c nitrite reductases, and discusses their structural and functional features.
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Affiliation(s)
- Peter M H Kroneck
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.
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8
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Influence of the heme distal pocket on nitrite binding orientation and reactivity in Sperm Whale myoglobin. Biochem J 2021; 478:927-942. [PMID: 33543749 PMCID: PMC7925009 DOI: 10.1042/bcj20200596] [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: 07/31/2020] [Revised: 01/30/2021] [Accepted: 02/05/2021] [Indexed: 12/05/2022]
Abstract
Nitrite binding to recombinant wild-type Sperm Whale myoglobin (SWMb) was studied using a combination of spectroscopic methods including room-temperature magnetic circular dichroism. These revealed that the reactive species is free nitrous acid and the product of the reaction contains a nitrite ion bound to the ferric heme iron in the nitrito- (O-bound) orientation. This exists in a thermal equilibrium with a low-spin ground state and a high-spin excited state and is spectroscopically distinct from the purely low-spin nitro- (N-bound) species observed in the H64V SWMb variant. Substitution of the proximal heme ligand, histidine-93, with lysine yields a novel form of myoglobin (H93K) with enhanced reactivity towards nitrite. The nitrito-mode of binding to the ferric heme iron is retained in the H93K variant again as a thermal equilibrium of spin-states. This proximal substitution influences the heme distal pocket causing the pKa of the alkaline transition to be lowered relative to wild-type SWMb. This change in the environment of the distal pocket coupled with nitrito-binding is the most likely explanation for the 8-fold increase in the rate of nitrite reduction by H93K relative to WT SWMb.
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9
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Amanullah S, Saha P, Nayek A, Ahmed ME, Dey A. Biochemical and artificial pathways for the reduction of carbon dioxide, nitrite and the competing proton reduction: effect of 2nd sphere interactions in catalysis. Chem Soc Rev 2021; 50:3755-3823. [DOI: 10.1039/d0cs01405b] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Reduction of oxides and oxoanions of carbon and nitrogen are of great contemporary importance as they are crucial for a sustainable environment.
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Affiliation(s)
- Sk Amanullah
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Paramita Saha
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Abhijit Nayek
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Md Estak Ahmed
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Abhishek Dey
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
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10
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Dissanayake DMMM, Petel BE, Brennessel WW, Bren KL, Matson EM. Hydrogen bonding promotes diversity in nitrite coordination modes at a single iron(II) center. J COORD CHEM 2020. [DOI: 10.1080/00958972.2020.1821373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | - Brittney E. Petel
- Department of Chemistry, University of Rochester, Rochester, NY, USA
| | | | - Kara L. Bren
- Department of Chemistry, University of Rochester, Rochester, NY, USA
| | - Ellen M. Matson
- Department of Chemistry, University of Rochester, Rochester, NY, USA
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11
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Fini H, Kerman K. Revisiting the nitrite reductase activity of hemoglobin with differential pulse voltammetry. Anal Chim Acta 2019; 1104:38-46. [PMID: 32106955 DOI: 10.1016/j.aca.2019.12.071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 11/25/2019] [Accepted: 12/27/2019] [Indexed: 12/30/2022]
Abstract
Nitric oxide (NO) is an omnipresent signalling molecule in all vertebrates. NO modulates blood flow and neural activity. Nitrite anion is one of the most important sources of NO. Nitrite is reduced to NO by various physiological mechanisms including reduction by hemoglobin in vascular system. In this study, nitrite reductase activity (NRA) of hemoglobin is reported using cyclic voltammetry (CV) and differential pulse voltammetry (DPV) in a wide potential window from +0.3 V to -1.3 V (vs. Ag/AgCl). To the best of our knowledge, a detailed look into NRA of hemoglobin is proposed here for the first time. Our results indicated two different regimes for reduction of nitrite by hemoglobin in its Fe(II) and Fe(I) states. Both reactions showed a reversible behaviour in the time scale of the experiments. The first reduction displayed a normal redox behaviour, while the latter one had the characteristics of a catalytic electro-reduction/oxidation. The reduction in Fe(II) state was selected as a tool for comparing the NRA of hemoglobin (Hb) and hemoglobin-S (Hb-S) under native-like conditions in a didodecyldimethyl ammonium bromide (DDAB) liquid crystal film. These investigations lay the prospects and guidelines for understanding the direct electrochemistry of hemoglobin utilizing a simplified mediator-free platform.
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Affiliation(s)
- Hamid Fini
- Dept. of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, M1C 1A4, ON, Canada
| | - Kagan Kerman
- Dept. of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, M1C 1A4, ON, Canada.
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12
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Dybas J, Berkowicz P, Proniewski B, Dziedzic-Kocurek K, Stanek J, Baranska M, Chlopicki S, Marzec KM. Spectroscopy-based characterization of Hb-NO adducts in human red blood cells exposed to NO-donor and endothelium-derived NO. Analyst 2019; 143:4335-4346. [PMID: 30109873 DOI: 10.1039/c8an00302e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The work presents the complementary approach to characterize the formation of various Hb species inside isolated human RBCs exposed to NO, with a focus on the formed Hb-NO adducts. This work presents a complementary approach based on Resonance Raman Spectroscopy (RRS) supported by Blood Gas Analysis, Electron Paramagnetic Resonance Spectroscopy, UV-Vis Absorption Spectroscopy and Mössbauer Spectroscopy to characterize the formation of various Hb species, with a focus on the Hb-NO adducts formed inside isolated human RBCs exposed to NO, under the experimental conditions of low and high levels of oxygen Hb saturation. In the present work, we induced Hb-NO adducts using PAPA-NONOate, a NO-donor with known chemistry and kinetics of NO release, and confirmed the formation of Hb-NO adducts in RBCs incubated with Human Aortic Endothelial Cells (HAECs) stimulated to produce NO. Our results provide a new insight into the formation of Hb-NO adducts after the exposure of RBCs with high oxyHb content to exogenous NO with special attention to the formation of LSHbIIINO in addition to LSHbIINO and metHb (HS/LSHbIIIH2O). We also point out that reliable characterization of Hb-NO adducts requires complementary techniques. Among them, RRS, as a label-free and non-destructive tool, appears to be an important discrimination technique in the studies of Hb-NO adducts inside intact RBCs.
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Affiliation(s)
- Jakub Dybas
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
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13
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Costa Gouveia TL, Campos RB, Ribeiro RR, Nunes FS. DFT analysis of the linkage isomerism in penta(ammine)ruthenium(II/III) complexes of benzotriazole: Natural bond orbital method approach and a comprehensive energy decomposition analysis. J Comput Chem 2019; 40:1593-1598. [DOI: 10.1002/jcc.25810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/08/2019] [Accepted: 02/10/2019] [Indexed: 11/08/2022]
Affiliation(s)
| | - Renan Borsoi Campos
- Departamento Acadêmico de Química e BiologiaUniversidade Tecnológica Federal do Paraná 81280‐340, Curitiba PR Brazil
| | - Ronny Rocha Ribeiro
- Departamento de QuímicaUniversidade Federal do Paraná Cx. Postal 19081, 81531‐980, Curitiba PR Brazil
| | - Fábio Souza Nunes
- Departamento de QuímicaUniversidade Federal do Paraná Cx. Postal 19081, 81531‐980, Curitiba PR Brazil
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14
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DeMartino AW, Kim‐Shapiro DB, Patel RP, Gladwin MT. Nitrite and nitrate chemical biology and signalling. Br J Pharmacol 2019; 176:228-245. [PMID: 30152056 PMCID: PMC6295445 DOI: 10.1111/bph.14484] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/31/2018] [Accepted: 08/06/2018] [Indexed: 12/13/2022] Open
Abstract
Inorganic nitrate (NO3 - ), nitrite (NO2 - ) and NO are nitrogenous species with a diverse and interconnected chemical biology. The formation of NO from nitrate and nitrite via a reductive 'nitrate-nitrite-NO' pathway and resulting in vasodilation is now an established complementary route to traditional NOS-derived vasodilation. Nitrate, found in our diet and abundant in mammalian tissues and circulation, is activated via reduction to nitrite predominantly by our commensal oral microbiome. The subsequent in vivo reduction of nitrite, a stable vascular reserve of NO, is facilitated by a number of haem-containing and molybdenum-cofactor proteins. NO generation from nitrite is enhanced during physiological and pathological hypoxia and in disease states involving ischaemia-reperfusion injury. As such, modulation of these NO vascular repositories via exogenously supplied nitrite and nitrate has been evaluated as a therapeutic approach in a number of diseases. Ultimately, the chemical biology of nitrate and nitrite is governed by local concentrations, reaction equilibrium constants, and the generation of transient intermediates, with kinetic rate constants modulated at differing physiological pH values and oxygen tensions. LINKED ARTICLES: This article is part of a themed section on Nitric Oxide 20 Years from the 1998 Nobel Prize. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v176.2/issuetoc.
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Affiliation(s)
- Anthony W DeMartino
- Heart, Lung, Blood, and Vascular Medicine InstituteUniversity of PittsburghPittsburghPAUSA
| | - Daniel B. Kim‐Shapiro
- Department of PhysicsWake Forest UniversityWinston‐SalemNCUSA
- Translational Science CenterWake Forest UniversityWinston‐SalemNCUSA
| | - Rakesh P Patel
- Department of Pathology and Center for Free Radical BiologyUniversity of Alabama at BirminghamBirminghamALUSA
| | - Mark T Gladwin
- Heart, Lung, Blood, and Vascular Medicine InstituteUniversity of PittsburghPittsburghPAUSA
- Division of Pulmonary, Allergy, and Critical Care MedicineUniversity of PittsburghPittsburghPAUSA
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15
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Wang B, Shi Y, Tejero J, Powell SM, Thomas LM, Gladwin MT, Shiva S, Zhang Y, Richter-Addo GB. Nitrosyl Myoglobins and Their Nitrite Precursors: Crystal Structural and Quantum Mechanics and Molecular Mechanics Theoretical Investigations of Preferred Fe -NO Ligand Orientations in Myoglobin Distal Pockets. Biochemistry 2018; 57:4788-4802. [PMID: 29999305 PMCID: PMC6474360 DOI: 10.1021/acs.biochem.8b00542] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The globular dioxygen binding heme protein myoglobin (Mb) is present in several species. Its interactions with the simple nitrogen oxides, namely, nitric oxide (NO) and nitrite, have been known for decades, but the physiological relevance has only recently become more fully appreciated. We previously reported the O-nitrito mode of binding of nitrite to ferric horse heart wild-type (wt) MbIII and human hemoglobin. We have expanded on this work and report the interactions of nitrite with wt sperm whale (sw) MbIII and its H64A, H64Q, and V68A/I107Y mutants whose dissociation constants increase in the following order: H64Q < wt < V68A/I107Y < H64A. We also report their X-ray crystal structures that reveal the O-nitrito mode of binding of nitrite to these derivatives. The MbII-mediated reductions of nitrite to NO and structural data for the wt and mutant MbII-NOs are described. We show that their FeNO orientations vary with distal pocket identity, with the FeNO moieties pointing toward the hydrophobic interiors when the His64 residue is present but toward the hydrophilic exterior when this His64 residue is absent in this set of mutants. This correlates with the nature of H-bonding to the bound NO ligand (nitrosyl O vs N atom). Quantum mechanics and hybrid quantum mechanics and molecular mechanics calculations help elucidate the origin of the experimentally preferred NO orientations. In a few cases, the calculations reproduce the experimentally observed orientations only when the whole protein is taken into consideration.
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Affiliation(s)
- Bing Wang
- Price Family Foundation Institute of Structural Biology, and Department of Chemistry and Biochemistry,
University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019
| | - Yelu Shi
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Castle Point on Hudson,
Hoboken, NJ 07030
| | - Jesús Tejero
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh School of Medicine, 3550 Terrace
Street, Pittsburgh, PA 15261
| | - Samantha M. Powell
- Price Family Foundation Institute of Structural Biology, and Department of Chemistry and Biochemistry,
University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019
| | - Leonard M. Thomas
- Price Family Foundation Institute of Structural Biology, and Department of Chemistry and Biochemistry,
University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019
| | - Mark T. Gladwin
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh School of Medicine, 3550 Terrace
Street, Pittsburgh, PA 15261
| | - Sruti Shiva
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, 200 Lothrop Street, Pittsburgh, PA
15213
| | - Yong Zhang
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Castle Point on Hudson,
Hoboken, NJ 07030
| | - George B. Richter-Addo
- Price Family Foundation Institute of Structural Biology, and Department of Chemistry and Biochemistry,
University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019
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16
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Nilsson ZN, Mandella BL, Sen K, Kekilli D, Hough MA, Moenne-Loccoz P, Strange RW, Andrew CR. Distinguishing Nitro vs Nitrito Coordination in Cytochrome c' Using Vibrational Spectroscopy and Density Functional Theory. Inorg Chem 2017; 56:13205-13213. [PMID: 29053273 PMCID: PMC5677563 DOI: 10.1021/acs.inorgchem.7b01945] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nitrite coordination to heme cofactors is a key step in the anaerobic production of the signaling molecule nitric oxide (NO). An ambidentate ligand, nitrite has the potential to coordinate via the N- (nitro) or O- (nitrito) atoms in a manner that can direct its reactivity. Distinguishing nitro vs nitrito coordination, along with the influence of the surrounding protein, is therefore of particular interest. In this study, we probed Fe(III) heme-nitrite coordination in Alcaligenes xylosoxidans cytochrome c' (AXCP), an NO carrier that excludes anions in its native state but that readily binds nitrite (Kd ∼ 0.5 mM) following a distal Leu16 → Gly mutation to remove distal steric constraints. Room-temperature resonance Raman spectra (407 nm excitation) identify ν(Fe-NO2), δ(ONO), and νs(NO2) nitrite ligand vibrations in solution. Illumination with 351 nm UV light results in photoconversion to {FeNO}6 and {FeNO}7 states, enabling FTIR measurements to distinguish νs(NO2) and νas(NO2) vibrations from differential spectra. Density functional theory calculations highlight the connections between heme environment, nitrite coordination mode, and vibrational properties and confirm that nitrite binds to L16G AXCP exclusively through the N atom. Efforts to obtain the nitrite complex crystal structure were hampered by photochemistry in the X-ray beam. Although low dose crystal structures could be modeled with a mixed nitrite (nitro)/H2O distal population, their photosensitivity and partial occupancy underscores the value of the vibrational approach. Overall, this study sheds light on steric determinants of heme-nitrite binding and provides vibrational benchmarks for future studies of heme protein nitrite reactions.
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Affiliation(s)
- Zach N. Nilsson
- Department of Chemistry and Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
| | - Brian L. Mandella
- Department of Chemistry and Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
| | - Kakali Sen
- School of Biological Sciences, University of Essex, Colchester Essex, CO4 3SQ, United Kingdom
- Scientific Computing Department, STFC Daresbury Laboratory, Warrington, Cheshire WA4 4AD, United Kingdom
| | - Demet Kekilli
- School of Biological Sciences, University of Essex, Colchester Essex, CO4 3SQ, United Kingdom
| | - Michael A Hough
- School of Biological Sciences, University of Essex, Colchester Essex, CO4 3SQ, United Kingdom
| | - Pierre Moenne-Loccoz
- Division of Environmental and Biomolecular Systems, Oregon Health and Science University, Portland, Oregon 97239, United States
| | - Richard W. Strange
- School of Biological Sciences, University of Essex, Colchester Essex, CO4 3SQ, United Kingdom
| | - Colin R. Andrew
- Department of Chemistry and Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
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17
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Van Doorslaer S, Cuypers B. Electron paramagnetic resonance of globin proteins – a successful match between spectroscopic development and protein research. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1392629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Bert Cuypers
- Department of Physics, University of Antwerp, Antwerp, Belgium
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18
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Vitvitsky V, Yadav PK, An S, Seravalli J, Cho US, Banerjee R. Structural and Mechanistic Insights into Hemoglobin-catalyzed Hydrogen Sulfide Oxidation and the Fate of Polysulfide Products. J Biol Chem 2017; 292:5584-5592. [PMID: 28213526 DOI: 10.1074/jbc.m117.774943] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/15/2017] [Indexed: 11/06/2022] Open
Abstract
Hydrogen sulfide is a cardioprotective signaling molecule but is toxic at elevated concentrations. Red blood cells can synthesize H2S but, lacking organelles, cannot dispose of H2S via the mitochondrial sulfide oxidation pathway. We have recently shown that at high sulfide concentrations, ferric hemoglobin oxidizes H2S to a mixture of thiosulfate and iron-bound polysulfides in which the latter species predominates. Here, we report the crystal structure of human hemoglobin containing low spin ferric sulfide, the first intermediate in heme-catalyzed sulfide oxidation. The structure provides molecular insights into why sulfide is susceptible to oxidation in human hemoglobin but is stabilized against it in HbI, a specialized sulfide-carrying hemoglobin from a mollusk adapted to life in a sulfide-rich environment. We have also captured a second sulfide bound at a postulated ligand entry/exit site in the α-subunit of hemoglobin, which, to the best of our knowledge, represents the first direct evidence for this site being used to access the heme iron. Hydrodisulfide, a postulated intermediate at the junction between thiosulfate and polysulfide formation, coordinates ferric hemoglobin and, in the presence of air, generated thiosulfate. At low sulfide/heme iron ratios, the product distribution between thiosulfate and iron-bound polysulfides was approximately equal. The iron-bound polysulfides were unstable at physiological glutathione concentrations and were reduced with concomitant formation of glutathione persulfide, glutathione disulfide, and H2S. Hence, although polysulfides are unlikely to be stable in the reducing intracellular milieu, glutathione persulfide could serve as a persulfide donor for protein persulfidation, a posttranslational modification by which H2S is postulated to signal.
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Affiliation(s)
- Victor Vitvitsky
- From the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109 and
| | - Pramod K Yadav
- From the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109 and
| | - Sojin An
- From the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109 and
| | - Javier Seravalli
- the Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588
| | - Uhn-Soo Cho
- From the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109 and
| | - Ruma Banerjee
- From the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109 and
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19
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Nitrite coordination in myoglobin. J Inorg Biochem 2017; 166:49-54. [DOI: 10.1016/j.jinorgbio.2016.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 10/07/2016] [Accepted: 10/13/2016] [Indexed: 12/16/2022]
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20
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Marzec KM, Dybas J, Chlopicki S, Baranska M. Resonance Raman in Vitro Detection and Differentiation of the Nitrite-Induced Hemoglobin Adducts in Functional Human Red Blood Cells. J Phys Chem B 2016; 120:12249-12260. [PMID: 27934219 DOI: 10.1021/acs.jpcb.6b08359] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This work presents in vitro studies of the functional, isolated human red blood cells (RBCs) treated with various concentrations of Na14NO2 and Na15NO2 with the use of resonance Raman spectroscopy (RRS) at two different laser excitations supported by absorption spectrophotometry (UV-vis). The products of the reaction between oxyhemoglobin (oxyHb) in isolated RBCs with NaNO2 were analyzed and identified in situ. The metHb-H2O was found to be the major product of this reaction; however, additional adducts were also clearly observed. Vibrational analysis allowed identification of various Hb3+NO2 species (Fe3+-O-N=O with O-binding mode of nitrite ion to the Fe3+ core and nitrovinyl adducts with 2-vinyl nitration favored over 4-vinyl nitration) as well as the Fe3+-NO adduct. In addition, we were able to visualize in situ the Hb-NO2 species inside functional RBCs with the use of Raman imaging.
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Affiliation(s)
- Katarzyna M Marzec
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University , Bobrzynskiego 14, Krakow 30-348, Poland
| | - Jakub Dybas
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University , Bobrzynskiego 14, Krakow 30-348, Poland.,Faculty of Chemistry, Jagiellonian University , Ingardena 3, Krakow 30-060, Poland
| | - Stefan Chlopicki
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University , Bobrzynskiego 14, Krakow 30-348, Poland.,Department of Experimental Pharmacology, Jagiellonian University Medical College , Grzegorzecka 16, Krakow 31-531, Poland
| | - Malgorzata Baranska
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University , Bobrzynskiego 14, Krakow 30-348, Poland.,Faculty of Chemistry, Jagiellonian University , Ingardena 3, Krakow 30-060, Poland
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21
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Kia R, Safari F. Synthesis, spectral and structural characterization and computational studies of rhenium(I)-tricarbonyl nitrito complexes of 2,2′-bipyridine and 2,9-dimethylphenanthroline ligands: π-Accepting character of the diimine ligands. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.08.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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22
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He C, Ogata H, Lubitz W. Elucidation of the heme active site electronic structure affecting the unprecedented nitrite dismutase activity of the ferriheme b proteins, the nitrophorins. Chem Sci 2016; 7:5332-5340. [PMID: 30155185 PMCID: PMC6020753 DOI: 10.1039/c6sc01019a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/23/2016] [Indexed: 12/14/2022] Open
Abstract
Nitrophorins (NPs) catalyze the nitrite dismutation reaction that is unprecedented in ferriheme proteins. Despite progress in studying the reaction mechanism, fundamental issues regarding the correlation of the structural features with the nitrite dismutase activity of NPs remain elusive. On the other hand, it has been shown that the nitrite complexes of NPs are unique among those of the ferriheme proteins since some of their electron paramagnetic resonance (EPR) spectra show significant highly anisotropic low spin (HALS) signals with large gmax values over 3.2. The origin of HALS signals in ferriheme proteins or models is not well understood, especially in cases where axial ligands other than histidine are present. In this study several mutations were introduced in NP4. The related nitrite coordination and dismutation reaction were investigated. As a result, the EPR spectra of the NP-nitrite complexes were found to be tightly correlated with the extent of heme ruffling and protonation state of the proximal His ligand-dictated by an extended H-bonding network at the heme active site. Furthermore, it is established that the two factors are essential in determining the nitrite dismutase activity of NPs. These results may provide a valuable guide for identifying or designing novel heme proteins with similar activity.
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Affiliation(s)
- Chunmao He
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , D-45470 , Mülheim an der Ruhr , Germany . ;
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , D-45470 , Mülheim an der Ruhr , Germany . ;
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion , Stiftstrasse 34-36 , D-45470 , Mülheim an der Ruhr , Germany . ;
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23
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Galinato MGI, Fogle RS, Stetz A, Galan JF. Modulating the nitrite reductase activity of globins by varying the heme substituents: Utilizing myoglobin as a model system. J Inorg Biochem 2015; 154:7-20. [PMID: 26544504 DOI: 10.1016/j.jinorgbio.2015.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 10/08/2015] [Accepted: 10/19/2015] [Indexed: 11/18/2022]
Abstract
Globins, such as hemoglobin (Hb) and myoglobin (Mb), have gained attention for their ability to reduce nitrite (NO2(-)) to nitric oxide (NO). The molecular interactions that regulate this chemistry are not fully elucidated, therefore we address this issue by investigating one part of the active site that may control this reaction. Here, the effects of the 2,4-heme substituents on the nitrite reductase (NiR) reaction, and on the structures and energies of the ferrous nitrite intermediates, are investigated using Mb as a model system. This is accomplished by studying Mbs with hemes that have different 2,4-R groups, namely diacetyldeuteroMb (-acetyl), protoMb (wild-type (wt) Mb, -vinyl), deuteroMb (-H), and mesoMb (-ethyl). While trends on the natural charge on Fe and O-atom of bound nitrite are observed among the series of Mbs, the Fe(II)-NPyr (Pyr=pyrrole) and Fe(II)-NHis93 (His=histidine) bond lengths do not significantly change. Kinetic analysis shows increasing NiR activity as follows: diacetyldeuteroMb<wt Mb<deuteroMb<mesoMb. Nitrite binding energy calculations of the different Mb(II)-nitrite conformations demonstrate the N-bound complexes to be more stable than the O-bound complexes for all the different types of heme structures, with diacetyldeuteroMb having the greatest nitrite binding affinity. Spectral deconvolution on the final product generated from the reaction between Mb(II) and NO2(-) for the reconstituted Mbs indicates the formation of 1:1 Mb(III) and Mb(II)-NO. The electronic changes induced by the -R groups on the 2,4-positions do not alter the stoichiometric ratio of the products, resembling wt Mb.
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Affiliation(s)
- Mary Grace I Galinato
- School of Science-Chemistry, Penn State Erie, The Behrend College, Erie, PA 16563, United States.
| | - Robert S Fogle
- School of Science-Chemistry, Penn State Erie, The Behrend College, Erie, PA 16563, United States
| | - Amanda Stetz
- School of Science-Chemistry, Penn State Erie, The Behrend College, Erie, PA 16563, United States
| | - Jhenny F Galan
- Dept. of Marine Sciences, Texas A&M at Galveston, 200 Seawolf Parkway, Galveston, TX 77553, United States.
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24
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Zhang TT, Liu YD, Zhong RG. Iron(II) porphyrins induced conversion of nitrite into nitric oxide: A computational study. J Inorg Biochem 2015; 150:126-32. [DOI: 10.1016/j.jinorgbio.2015.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 05/27/2015] [Accepted: 06/02/2015] [Indexed: 01/26/2023]
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25
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Sundararajan M, Neese F. Distal Histidine Modulates the Unusual O-Binding of Nitrite to Myoglobin: Evidence from the Quantum Chemical Analysis of EPR Parameters. Inorg Chem 2015; 54:7209-17. [DOI: 10.1021/acs.inorgchem.5b00557] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mahesh Sundararajan
- Theoretical Chemistry
Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Frank Neese
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
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26
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He C, Howes BD, Smulevich G, Rumpel S, Reijerse EJ, Lubitz W, Cox N, Knipp M. Nitrite Dismutase Reaction Mechanism: Kinetic and Spectroscopic Investigation of the Interaction between Nitrophorin and Nitrite. J Am Chem Soc 2015; 137:4141-50. [DOI: 10.1021/ja512938u] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Chunmao He
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Barry D. Howes
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino(Fi), Italy
| | - Giulietta Smulevich
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino(Fi), Italy
| | - Sigrun Rumpel
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Edward J. Reijerse
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Nicholas Cox
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Markus Knipp
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
- Faculty
of Chemistry and Biochemistry, Ruhr University, Universitätsstrasse 150, D-44780 Bochum, Germany
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27
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Lockwood CWJ, Burlat B, Cheesman MR, Kern M, Simon J, Clarke TA, Richardson DJ, Butt JN. Resolution of Key Roles for the Distal Pocket Histidine in Cytochrome c Nitrite Reductases. J Am Chem Soc 2015; 137:3059-68. [DOI: 10.1021/ja512941j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | | | | | - Melanie Kern
- Microbial
Energy Conversion and Biotechnology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Jörg Simon
- Microbial
Energy Conversion and Biotechnology, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
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28
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Tejero J, Sparacino-Watkins CE, Ragireddy V, Frizzell S, Gladwin MT. Exploring the mechanisms of the reductase activity of neuroglobin by site-directed mutagenesis of the heme distal pocket. Biochemistry 2015; 54:722-33. [PMID: 25554946 PMCID: PMC4410703 DOI: 10.1021/bi501196k] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Neuroglobin
(Ngb) is a six-coordinate globin that can catalyze
the reduction of nitrite to nitric oxide. Although this reaction is
common to heme proteins, the molecular interactions in the heme pocket
that regulate this reaction are largely unknown. We have shown that
the H64L Ngb mutation increases the rate of nitrite reduction by 2000-fold
compared to that of wild-type Ngb [Tiso, M., et al. (2011) J. Biol. Chem. 286, 18277–18289]. Here we explore
the effect of distal heme pocket mutations on nitrite reduction. For
this purpose, we have generated mutations of Ngb residues Phe28(B10),
His64(E7), and Val68(E11). Our results indicate a dichotomy in the
reactivity of deoxy five- and six-coordinate globins toward nitrite.
In hemoglobin and myoglobin, there is a correlation between faster
rates and more negative potentials. However, in Ngb, reaction rates
are apparently related to the distal pocket volume, and redox potential
shows a poor relationship with the rate constants. This suggests a
relationship between the nitrite reduction rate and heme accessibility
in Ngb, particularly marked for His64(E7) mutants. In five-coordinate
globins, His(E7) facilitates nitrite reduction, likely through proton
donation. Conversely, in Ngb, the reduction mechanism does not rely
on the delivery of a proton from the histidine side chain, as His64
mutants show the fastest reduction rates. In fact, the rate observed
for H64A Ngb (1120 M–1 s–1) is
to the best of our knowledge the fastest reported for a heme nitrite
reductase. These differences may be related to a differential stabilization
of the iron–nitrite complexes in five- and six-coordinate globins.
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Affiliation(s)
- Jesús Tejero
- Vascular Medicine Institute, University of Pittsburgh , Pittsburgh, Pennsylvania 15261, United States
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29
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Lambrou A, Pinakoulaki E. Resonance Raman detection of the myoglobin nitrito heme Fe–O–NO/2-nitrovinyl species: implications for helix E-helix F interactions. Phys Chem Chem Phys 2015; 17:3841-9. [DOI: 10.1039/c4cp04352a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We present resonance Raman evidence for the formation of myoglobin nitrito heme Fe–O–NO/2-nitrovinyl and propose that the species we have detected at acidic pH is the myoglobin nitrous heme Fe–(H)O–NO/2-nitrovinyl complex.
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30
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31
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Matson EM, Park YJ, Fout AR. Facile nitrite reduction in a non-heme iron system: formation of an iron(III)-oxo. J Am Chem Soc 2014; 136:17398-401. [PMID: 25470029 DOI: 10.1021/ja510615p] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Reaction of tetrabutylammonium nitrite with [N(afa(Cy))3Fe(OTf)](OTf) cleanly resulted in the formation of an iron(III)-oxo species, [N(afa(Cy))3Fe(O)](OTf), and NO(g). Formation of NO(g) as a byproduct was confirmed by reaction of the iron(II) starting material with half an equivalent of nitrite, resulting in a mixture of two products, the iron-oxo and an iron-NO species, [N(afa(Cy))3Fe(NO)](OTf)2. Formation of the latter was confirmed through independent synthesis. The results of this study provide insight into the role of hydrogen bonding in the mechanism of nitrite reduction and the binding mode of nitrite in biological heme systems.
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Affiliation(s)
- Ellen M Matson
- School of Chemical Sciences, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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Loullis A, Noor MR, Soulimane T, Pinakoulaki E. The structure of a ferrous heme-nitro species in the binuclear heme a3/CuB center of ba3-cytochrome c oxidase as determined by resonance Raman spectroscopy. Chem Commun (Camb) 2014; 51:286-9. [PMID: 25406996 DOI: 10.1039/c4cc08019j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Members of the cytochrome c oxidase family exhibit nitrite reductase activity. In this work, we have characterized a ferrous heme a3-nitro species in ba3-oxidase by resonance Raman spectroscopy. This provides the first evidence for the structure of a nitrite-bound species in the binuclear heme/copper center of cytochrome c oxidases.
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Affiliation(s)
- Andreas Loullis
- Department of Chemistry, University of Cyprus, PO Box 20537, 1678, Nicosia, Cyprus.
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Kurtikyan TS, Hayrapetyan VA, Mehrabyan MM, Ford PC. Six-coordinate nitrito and nitrato complexes of manganese porphyrin. Inorg Chem 2014; 53:11948-59. [PMID: 25369232 DOI: 10.1021/ic5014329] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reaction of small increments of NO2 gas with sublimed amorphous layers of Mn(II)(TPP) (TPP = meso-tetra-phenylporphyrinato dianion) in a vacuum cryostat leads to formation of the 5-coordinate monodentate nitrato complex Mn(III)(TPP)(η(1)-ONO2) (II). This transformation proceeds through the two distinct steps with initial formation of the five coordinate O-nitrito complex Mn(III)(TPP)(η(1)-ONO) (I) as demonstrated by the electronic absorption spectra and by FTIR spectra using differently labeled nitrogen dioxide. A plausible mechanism for the second stage of reaction is offered based on the spectral changes observed upon subsequent interaction of (15)NO2 and NO2 with the layered Mn(TPP). Low-temperature interaction of I and II with the vapors of various ligands L (L = O-, S-, and N-donors) leads to formation of the 6-coordinate O-nitrito Mn(III)(TPP)(L)(η(1)-ONO) and monodentate nitrato Mn(III)(TPP)(L)(η(1)-ONO2) complexes, respectively. Formation of the 6-coordinate O-nitrito complex is accompanied by the shifts of the ν(N═O) band to lower frequency and of the ν(N-O) band to higher frequency. The frequency difference between these bands Δν = ν(N═O) - ν(N-O) is a function of L and is smaller for the stronger bases. Reaction of excess NH3 with I leads to formation of Mn(TPP)(NH3)(η(1)-ONO) and of the cation [Mn(TPP)(NH3)2](+) plus ionic nitrite. The nitrito complexes are relatively unstable, but several of the nitrato species can be observed in the solid state at room temperature. For example, the tetrahydrofuran complex Mn(TPP)(THF)(η(1)-ONO2) is stable in the presence of THF vapors (∼5 mm), but it loses this ligand upon high vacuum pumping at RT. When L = dimethylsulfide (DMS), the nitrato complex is stable only to ∼-30 °C. Reactions of II with the N-donor ligands NH3, pyridine, or 1-methylimidazole are more complex. With these ligands, the nitrato complexes Mn(III)(TPP)(L)(η(1)-ONO2) and the cationic complexes [Mn(TPP)(L)2](+) coexist in the layer at room temperature, the latter formed as a result of NO3(-) displacement when L is in excess.
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Affiliation(s)
- T S Kurtikyan
- Molecule Structure Research Centre (MSRC) of the Scientific and Technological Centre of Organic and Pharmaceutical Chemistry NAS , 375014, Yerevan, Armenia
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Silaghi-Dumitrescu R, Svistunenko DA, Cioloboc D, Bischin C, Scurtu F, Cooper CE. Nitrite binding to globins: linkage isomerism, EPR silence and reductive chemistry. Nitric Oxide 2014; 42:32-9. [PMID: 25172022 PMCID: PMC4256065 DOI: 10.1016/j.niox.2014.08.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Revised: 07/29/2014] [Accepted: 08/18/2014] [Indexed: 12/28/2022]
Abstract
A DFT-derived barrier for nitrite linkage isomerism on heme center is reported. EPR spectra of nitrite adducts show evidence for linkage isomerism. The electronic structure of Fe(III)-nitrite heme is conformation-dependent. Certain conformations are inducive to EPR silence. Fe(II)-nitrite is undetectable on stopped-flow time scales.
The nitrite adducts of globins can potentially bind via O- or N- linkage to the heme iron. We have used EPR (electron paramagnetic resonance) and DFT (density functional theory) to explore these binding modes to myoglobin and hemoglobin. We demonstrate that the nitrite adducts of both globins have detectable EPR signals; we provide an explanation for the difficulty in detecting these EPR features, based on uniaxial state considerations. The EPR and DFT data show that both nitrite linkage isomers can be present at the same time and that the two isomers are readily interconvertible in solution. The millisecond-scale process of nitrite reduction by Hb is investigated in search of the elusive Fe(II)-nitrite adduct.
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Affiliation(s)
- Radu Silaghi-Dumitrescu
- "Babeş-Bolyai" University, 1 Mihail Kogalniceanu str., RO-400084 Cluj-Napoca, Romania; Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK.
| | - Dimitri A Svistunenko
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - Daniela Cioloboc
- "Babeş-Bolyai" University, 1 Mihail Kogalniceanu str., RO-400084 Cluj-Napoca, Romania
| | - Cristina Bischin
- "Babeş-Bolyai" University, 1 Mihail Kogalniceanu str., RO-400084 Cluj-Napoca, Romania
| | - Florina Scurtu
- "Babeş-Bolyai" University, 1 Mihail Kogalniceanu str., RO-400084 Cluj-Napoca, Romania
| | - Chris E Cooper
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
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Yi J, Soares AS, Richter-Addo GB. Crystallographic characterization of the nitric oxide derivative of R-state human hemoglobin. Nitric Oxide 2014; 39:46-50. [PMID: 24769418 DOI: 10.1016/j.niox.2014.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Accepted: 04/01/2014] [Indexed: 11/26/2022]
Abstract
Nitric oxide (NO) is a signaling agent that is biosynthesized in vivo. NO binds to the heme center in human hemoglobin (Hb) to form the HbNO adduct. This reaction of NO with Hb has been studied for many decades. Of continued interest has been the effect that the bound NO ligand has on the geometrical parameters of the resulting heme-NO active site. Although the crystal structure of a T-state human HbNO complex has been published previously, that of the high affinity R-state HbNO derivative has not been reported to date. We have crystallized and solved the three-dimensional X-ray structure of R-state human HbNO to 1.90 Å resolution. The differences in the FeNO bond parameters and H-bonding patterns between the α and β subunits contribute to understanding of the observed enhanced stability of the α(FeNO) moieties relative to the β(FeNO) moieties in human R-state HbNO.
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Affiliation(s)
- Jun Yi
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, USA; Department of Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Alexei S Soares
- Macromolecular Crystallography Research Resource, National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - George B Richter-Addo
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, USA.
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Affiliation(s)
- Luisa B. Maia
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - José J. G. Moura
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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Domínguez SE, Alborés P, Fagalde F. Photoinduced linkage isomerization in new rhenium(I) tricarbonyl complexes coordinated to N-nitrite and O-nitrite. Polyhedron 2014. [DOI: 10.1016/j.poly.2013.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Tsou CC, Yang WL, Liaw WF. Nitrite activation to nitric oxide via one-fold protonation of iron(II)-O,O-nitrito complex: relevance to the nitrite reductase activity of deoxyhemoglobin and deoxyhemerythrin. J Am Chem Soc 2013; 135:18758-61. [PMID: 24289743 DOI: 10.1021/ja4105864] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The reversible transformations [(Bim)3Fe(κ(2)-O2N)][BF4] (3) <-> [(Bim)3Fe(NO)(κ(1)-ONO)][BF4]2 (4) were demonstrated and characterized. Transformation of O,O-nitrito-containing complex 3 into [(Bim)3Fe(μ-O)(μ-OAc)Fe(Bim)3](3+) (5) along with the release of NO and H2O triggered by 1 equiv of AcOH implicates that nitrite-to-nitric oxide conversion occurs, in contrast to two protons needed to trigger nitrite reduction producing NO observed in the protonation of [Fe(II)-nitro] complexes.
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Affiliation(s)
- Chih-Chin Tsou
- Department of Chemistry and Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University , Hsinchu, 30013, Taiwan
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Abstract
Despite its reactivity and hence toxicity to living cells, sulfite is readily converted by various microorganisms using distinct assimilatory and dissimilatory metabolic routes. In respiratory pathways, sulfite either serves as a primary electron donor or terminal electron acceptor (yielding sulfate or sulfide, respectively), and its conversion drives electron transport chains that are coupled to chemiosmotic ATP synthesis. Notably, such processes are also seen to play a general role in sulfite detoxification, which is assumed to have an evolutionary ancient origin. The diversity of sulfite conversion is reflected by the fact that the range of microbial sulfite-converting enzymes displays different cofactors such as siroheme, heme c, or molybdopterin. This chapter aims to summarize the current knowledge of microbial sulfite metabolism and focuses on sulfite catabolism. The structure and function of sulfite-converting enzymes and the emerging picture of the modular architecture of the corresponding respiratory/detoxifying electron transport chains is emphasized.
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Affiliation(s)
- Jörg Simon
- Department of Biology, Microbial Energy Conversion and Biotechnology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany.
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Roche CJ, Cassera MB, Dantsker D, Hirsch RE, Friedman JM. Generating S-nitrosothiols from hemoglobin: mechanisms, conformational dependence, and physiological relevance. J Biol Chem 2013; 288:22408-25. [PMID: 23775069 DOI: 10.1074/jbc.m113.482679] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In vitro, ferrous deoxy-hemes in hemoglobin (Hb) react with nitrite to generate nitric oxide (NO) through a nitrite reductase reaction. In vivo studies indicate Hb with nitrite can be a source of NO bioactivity. The nitrite reductase reaction does not appear to account fully for this activity because free NO is short lived especially within the red blood cell. Thus, the exporting of NO bioactivity both out of the RBC and over a large distance requires an additional mechanism. A nitrite anhydrase (NA) reaction in which N2O3, a potent S-nitrosating agent, is produced through the reaction of NO with ferric heme-bound nitrite has been proposed (Basu, S., Grubina, R., Huang, J., Conradie, J., Huang, Z., Jeffers, A., Jiang, A., He, X., Azarov, I., Seibert, R., Mehta, A., Patel, R., King, S. B., Hogg, N., Ghosh, A., Gladwin, M. T., and Kim-Shapiro, D. B. (2007) Nat. Chem. Biol. 3, 785-794) as a possible mechanism. Legitimate concerns, including physiological relevance and the nature of the mechanism, have been raised concerning the NA reaction. This study addresses these concerns demonstrating NO and nitrite with ferric hemes under near physiological conditions yield an intermediate having the properties of the purported NA heme-bound N2O3 intermediate. The results indicate that ferric heme sites, traditionally viewed as a source of potential toxicity, can be functionally significant, especially for partially oxygenated/partially met-R state Hb that arises from the NO dioxygenation reaction. In the presence of low levels of nitrite and either NO or a suitable reductant such as L-cysteine, these ferric heme sites can function as a generator for the formation of S-nitrosothiols such as S-nitrosoglutathione and, as such, should be considered as a source of RBC-derived and exportable bioactive NO.
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Affiliation(s)
- Camille J Roche
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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Small ligand-globin interactions: reviewing lessons derived from computer simulation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1722-38. [PMID: 23470499 DOI: 10.1016/j.bbapap.2013.02.038] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 02/22/2013] [Accepted: 02/26/2013] [Indexed: 11/24/2022]
Abstract
In this work we review the application of classical and quantum-mechanical atomistic computer simulation tools to the investigation of small ligand interaction with globins. In the first part, studies of ligand migration, with its connection to kinetic association rate constants (kon), are presented. In the second part, we review studies for a variety of ligands such as O2, NO, CO, HS(-), F(-), and NO2(-) showing how the heme structure, proximal effects, and the interactions with the distal amino acids can modulate protein ligand binding. The review presents mainly results derived from our previous works on the subject, in the context of other theoretical and experimental studies performed by others. The variety and extent of the presented data yield a clear example of how computer simulation tools have, in the last decade, contributed to our deeper understanding of small ligand interactions with globins. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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Ascenzi P, Leboffe L, Polticelli F. Reactivity of the human hemoglobin “Dark side”. IUBMB Life 2013; 65:121-6. [DOI: 10.1002/iub.1121] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 11/26/2012] [Indexed: 12/19/2022]
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He C, Ogata H, Knipp M. Insertion of an H-Bonding Residue into the Distal Pocket of the Ferriheme Protein Nitrophorin 4: Effect on NitriteIron Coordination and Nitrite Disproportionation. Chem Biodivers 2012; 9:1761-75. [DOI: 10.1002/cbdv.201100401] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Castiglione N, Rinaldo S, Giardina G, Stelitano V, Cutruzzolà F. Nitrite and nitrite reductases: from molecular mechanisms to significance in human health and disease. Antioxid Redox Signal 2012; 17:684-716. [PMID: 22304560 DOI: 10.1089/ars.2011.4196] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Nitrite, previously considered physiologically irrelevant and a simple end product of endogenous nitric oxide (NO) metabolism, is now envisaged as a reservoir of NO to be activated in response to oxygen (O(2)) depletion. In the first part of this review, we summarize and compare the mechanisms of nitrite-dependent production of NO in selected bacteria and in eukaryotes. Bacterial nitrite reductases, which are copper or heme-containing enzymes, play an important role in the adaptation of pathogens to O(2) limitation and enable microrganisms to survive in the human body. In mammals, reduction of nitrite to NO under hypoxic conditions is carried out in tissues and blood by an array of metalloproteins, including heme-containing proteins and molybdenum enzymes. In humans, tissues play a more important role in nitrite reduction, not only because most tissues produce more NO than blood, but also because deoxyhemoglobin efficiently scavenges NO in blood. In the second part of the review, we outline the significance of nitrite in human health and disease and describe the recent advances and pitfalls of nitrite-based therapy, with special attention to its application in cardiovascular disorders, inflammation, and anti-bacterial defence. It can be concluded that nitrite (as well as nitrate-rich diet for long-term applications) may hold promise as therapeutic agent in vascular dysfunction and ischemic injury, as well as an effective compound able to promote angiogenesis.
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Affiliation(s)
- Nicoletta Castiglione
- Department of Biochemical Sciences, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome, Italy
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Lin YW, Nie CM, Liao LF. Rational design of a nitrite reductase based on myoglobin: a molecular modeling and dynamics simulation study. J Mol Model 2012; 18:4409-15. [DOI: 10.1007/s00894-012-1451-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2011] [Accepted: 04/30/2012] [Indexed: 10/28/2022]
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47
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Yi J, Thomas LM, Richter-Addo GB. Distal Pocket Control of Nitrite Binding in Myoglobin. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201200010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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48
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Yi J, Thomas LM, Richter-Addo GB. Distal Pocket Control of Nitrite Binding in Myoglobin. Angew Chem Int Ed Engl 2012; 51:3625-7. [DOI: 10.1002/anie.201200010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2012] [Indexed: 11/09/2022]
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49
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Yi J, Richter-Addo GB. Unveiling the three-dimensional structure of the green pigment of nitrite-cured meat. Chem Commun (Camb) 2012; 48:4172-4. [DOI: 10.1039/c2cc31065a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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50
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Silaghi-Dumitrescu R, Mich M, Matyas C, Cooper CE. Nitrite and nitrate reduction by molybdenum centers of the nitrate reductase type: Computational predictions on the catalytic mechanism. Nitric Oxide 2012; 26:27-31. [DOI: 10.1016/j.niox.2011.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 10/11/2011] [Accepted: 11/17/2011] [Indexed: 11/28/2022]
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