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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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2
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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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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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4
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Liu Y, Buerk DG, Barbee KA, Jaron D. A mathematical model for the role of N 2O 3 in enhancing nitric oxide bioavailability following nitrite infusion. Nitric Oxide 2016; 60:1-9. [PMID: 27565833 PMCID: PMC5343674 DOI: 10.1016/j.niox.2016.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 05/23/2016] [Accepted: 08/22/2016] [Indexed: 12/18/2022]
Abstract
Nitrite infusion into the bloodstream has been shown to elicit vasodilation and protect against ischemia-reperfusion injury through nitric oxide (NO) release in hypoxic conditions. However, the mechanism by which nitrite-derived NO escapes scavenging by hemoglobin in the erythrocyte has not been fully elucidated, owing in part to the difficulty in measuring the reactions and transport on NO in vivo. We developed a mathematical model for an arteriole and surrounding tissue to examine the hypothesis that dinitrogen trioxide (N2O3) acts as a stable intermediate for preserving NO. Our simulations predict that with hypoxia and moderate nitrite concentrations, the N2O3 pathway can significantly preserve the NO produced by hemoglobin nitrite reductase in the erythrocyte and elevate NO reaching the smooth muscle cells. Nitrite retains its ability to increase NO bioavailability even at varying flow conditions, but there is minimal effect under normoxia or very low nitrite concentrations. Our model demonstrates a viable pathway for reconciling experimental findings of potentially beneficial effects of nitrite infusions despite previous models showing negligible NO elevation associated with hemoglobin nitrite reductase. Our results suggest that additional mechanisms may be needed to explain the efficacy of nitrite-induced vasodilation at low infusion concentrations.
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Affiliation(s)
- Yien Liu
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3140 Market St., Philadelphia, PA 19104, USA
| | - Donald G Buerk
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3140 Market St., Philadelphia, PA 19104, USA
| | - Kenneth A Barbee
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3140 Market St., Philadelphia, PA 19104, USA
| | - Dov Jaron
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3140 Market St., Philadelphia, PA 19104, USA.
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Wojdyła Z, Borowski T. DFT study of the mechanism of manganese quercetin 2,3-dioxygenase: quest for origins of enzyme unique nitroxygenase activity and regioselectivity. J Biol Inorg Chem 2016; 21:475-89. [DOI: 10.1007/s00775-016-1356-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 04/27/2016] [Indexed: 10/21/2022]
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6
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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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7
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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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8
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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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9
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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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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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Sanders BC, Rhine MA, Harrop TC. Properties of {FeNO}8 and {CoNO}9 Metal Nitrosyls in Relation to Nitroxyl Coordination Chemistry. MOLECULAR DESIGN IN INORGANIC BIOCHEMISTRY 2013. [DOI: 10.1007/430_2012_87] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Abstract
Nitrosothiols are powerful vasodilators. Although the mechanism of their formation near neutral pH is an area of intense research, neither the energetics nor the kinetics of this reaction or of subsequent reactions have been addressed. The following considerations may help to guide experiments. (1) The standard Gibbs energy for the homolysis reaction RSNO → RS(•) + NO(•)(aq) is +110 ± 5 kJ mol(-1). (2) The electrode potential of the RSNO, H(+)/RSH, NO(•)(aq) couple is -0.20 ± 0.06 V at pH 7. (3) Thiol nitrosation by NO(2)(-) is favorable by 37 ± 5 kJ mol(-1) at pH 7. (4) N(2)O(3) is not involved in in vivo nitrosation mechanisms for thermodynamic--its formation from NO(2)(-) costs 59 kJ mol(-1)--or kinetic--the reaction being second-order in NO(2)(-)--reasons. (5) Hemoglobin (Hb) cannot catalyze formation of N(2)O(3), be it via the intermediacy of the reaction of Hb[FeNO(2)](2+) with NO(•) (+81 kJ mol(-1)) or reaction of Hb[FeNO](3+) with NO(2)(-) (+88 kJ mol(-1)). (6) Energetically and kinetically viable are nitrosations that involve HNO(2) or NO(•) in the presence of an electron acceptor with an electrode potential higher than -0.20 V. These considerations are derived from existing thermochemical and kinetics data.
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Affiliation(s)
- Willem H Koppenol
- Institute of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland.
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