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Sarkar A, Bhakta S, Chattopadhyay S, Dey A. Role of distal arginine residue in the mechanism of heme nitrite reductases. Chem Sci 2023; 14:7875-7886. [PMID: 37502318 PMCID: PMC10370594 DOI: 10.1039/d3sc01777j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/14/2023] [Indexed: 07/29/2023] Open
Abstract
Heme nitrite reductases reduce NO2- by 1e-/2H+ to NO or by 6e-/8H+ to NH4+ which are key steps in the global nitrogen cycle. Second-sphere residues, such as arginine (with a guanidine head group), are proposed to play a key role in the reaction by assisting substrate binding and hydrogen bonding and by providing protons to the active site for the reaction. The reactivity of an iron porphyrin with a NO2- covalently attached to a guanidinium arm in its 2nd sphere was investigated to understand the role of arginine residues in the 2nd sphere of heme nitrite reductases. The presence of the guanidinium residue allows the synthetic ferrous porphyrin to reduce NO2- and produce a ferrous nitrosyl species ({FeNO}7), where the required protons are provided by the guanidinium group in the 2nd sphere. However, in the presence of additional proton sources in solution, the reaction of ferrous porphyrin with NO2- results in the formation of ferric porphyrin and the release of NO. Spectroscopic and kinetic data indicated that re-protonation of the guanidine group in the 2nd sphere by an external proton source causes NO to dissociate from a ferric nitrosyl species ({FeNO}6) at rates similar to those observed for enzymatic sites. This re-protonation of the guanidine group mimics the proton recharge mechanism in the active site of NiR. DFT calculations indicated that the lability of the Fe-NO bond in the {FeNO}6 species is derived from the greater binding affinity of anions (e.g. NO2-) to the ferric center relative to neutral NO due to hydrogen bonding and electrostatic interaction of these bound anions with the protonated guanidium group in the 2nd sphere. The reduced {FeNO}7 species, once formed, is not affected significantly by the re-protonation of the guanidine residue. These results provide direct insight into the role of the 2nd sphere arginine residue present in the active sites of heme-based NiRs in determining the fate of NO2- reduction. Specifically, the findings using the synthetic model suggest that rapid re-protonation of these arginine residues may trigger the dissociation of NO from the {FeNO}6, which may also be the case in the protein active site.
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Affiliation(s)
- Ankita Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science 2A & 2B Raja S.C. Mullick Road Kolkata WB 700032 India
| | - Snehadri Bhakta
- School of Chemical Sciences, Indian Association for the Cultivation of Science 2A & 2B Raja S.C. Mullick Road Kolkata WB 700032 India
| | - Samir Chattopadhyay
- School of Chemical Sciences, Indian Association for the Cultivation of Science 2A & 2B Raja S.C. Mullick Road Kolkata WB 700032 India
| | - Abhishek Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science 2A & 2B Raja S.C. Mullick Road Kolkata WB 700032 India
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2
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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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3
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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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4
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Xu S, Kwon HY, Ashley DC, Chen CH, Jakubikova E, Smith JM. Intramolecular Hydrogen Bonding Facilitates Electrocatalytic Reduction of Nitrite in Aqueous Solutions. Inorg Chem 2019; 58:9443-9451. [DOI: 10.1021/acs.inorgchem.9b01274] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Song Xu
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Hyuk-Yong Kwon
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| | - Daniel C. Ashley
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| | - Chun-Hsing Chen
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Elena Jakubikova
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| | - Jeremy M. Smith
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47401, United States
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5
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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 DOI: 10.1021/acs.biochem.8b00542] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [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 , Oklahoma 73019 , United States
| | - Yelu Shi
- Department of Chemistry and Chemical Biology , Stevens Institute of Technology , Castle Point on Hudson , Hoboken , New Jersey 07030 , United States
| | - Jesús Tejero
- Heart, Lung, Blood and Vascular Medicine Institute , University of Pittsburgh School of Medicine , 3550 Terrace Street , Pittsburgh , Pennsylvania 15261 , United States
| | - Samantha M Powell
- Price Family Foundation Institute of Structural Biology and Department of Chemistry and Biochemistry , University of Oklahoma , 101 Stephenson Parkway , Norman , Oklahoma 73019 , United States
| | - Leonard M Thomas
- Price Family Foundation Institute of Structural Biology and Department of Chemistry and Biochemistry , University of Oklahoma , 101 Stephenson Parkway , Norman , Oklahoma 73019 , United States
| | - Mark T Gladwin
- Heart, Lung, Blood and Vascular Medicine Institute , University of Pittsburgh School of Medicine , 3550 Terrace Street , Pittsburgh , Pennsylvania 15261 , United States
| | - Sruti Shiva
- Department of Pharmacology and Chemical Biology , University of Pittsburgh , 200 Lothrop Street , Pittsburgh , Pennsylvania 15213 , United States
| | - Yong Zhang
- Department of Chemistry and Chemical Biology , Stevens Institute of Technology , Castle Point on Hudson , Hoboken , New Jersey 07030 , United States
| | - George B Richter-Addo
- Price Family Foundation Institute of Structural Biology and Department of Chemistry and Biochemistry , University of Oklahoma , 101 Stephenson Parkway , Norman , Oklahoma 73019 , United States
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6
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Fujii H, Yamaki D, Ogura T, Hada M. The functional role of the structure of the dioxo-isobacteriochlorin in the catalytic site of cytochrome cd 1 for the reduction of nitrite. Chem Sci 2016; 7:2896-2906. [PMID: 30090283 PMCID: PMC6054029 DOI: 10.1039/c5sc04825g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 01/20/2016] [Indexed: 11/25/2022] Open
Abstract
Cytochrome cd1 is a key enzyme in bacterial denitrification and catalyzes one-electron reduction of nitrite (NO2-) to nitric oxide (NO) at the heme d1 center under anaerobic conditions. The heme d1 has a unique dioxo-isobacteriochlorin structure and is present only in cytochrome cd1. To reveal the functional role of the unique heme d1 in the catalytic nitrite reduction, we studied effect of the porphyrin macrocycle on each reaction step of the catalytic cycle of cytochrome cd1 using synthetic model complexes. The complexes investigated are iron complexes of dioxo-octaethylisobacteriochlorin (1), mono-oxo-octaethylchlorin (2) and octaethylporphyrin (3). We show here that the reduction potential for the transition from the ferric state to the ferrous state and the binding constant for binding of NO2- to the ferrous complex increases with a trend of 3 < 2 < 1. However, the reactivity of the ferrous nitrite complex with protons increases in the reversed order, 1 < 2 < 3. We also show that the iron bound NO of the ferric NO complex is readily replaced by addition of 1 equiv. of p-nitrophenolate. These results indicate that the dioxo-isobacteriochlorin structure is superior to porphyrin and mono-oxo-chlorin structures in the first iron reduction step, the second nitrite binding step, and the NO dissociation step, but inferior in the third nitrite reduction step. These results suggest that the heme d1 has evolved as the catalytic site of cytochrome cd1 to catalyze the nitrite reduction at the highest possible redox potential while maintaining its catalytic activity.
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Affiliation(s)
- Hiroshi Fujii
- Department of Chemistry, Biology and Environmental Science , Faculty of Science , Nara Women's University , Kitauoyanishi , Nara 630-8506 , Japan .
| | - Daisuke Yamaki
- Department of Chemistry , Graduate School of Science , Tokyo Metropolitan University , 1-1 Minami-Osawa , Hachioji , Tokyo 192-0397 , Japan
| | - Takashi Ogura
- Department of Life Science and Picobiology Institute , Graduate School of Life Science , University of Hyogo , RSC-UH Leading Program Center , 1-1-1 Koto, Sayo-cho, Sayo-gun , Hyogo 679-5148 , Japan
| | - Masahiko Hada
- Department of Chemistry , Graduate School of Science , Tokyo Metropolitan University , 1-1 Minami-Osawa , Hachioji , Tokyo 192-0397 , Japan
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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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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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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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Outer-sphere oxidation of Fe(II) in nitrosylmyoglobin by ferricyanide. J Biol Inorg Chem 2014; 19:805-12. [DOI: 10.1007/s00775-014-1112-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 01/22/2014] [Indexed: 10/25/2022]
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11
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Lin Y, Wang J, Lu Y. Functional tuning and expanding of myoglobin by rational protein design. Sci China Chem 2014. [DOI: 10.1007/s11426-014-5063-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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12
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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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