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Chen ZY, Yuan H, Wang H, Sun LJ, Yu L, Gao SQ, Tan X, Lin YW. Regulating the Heme Active Site by Covalent Modifications: Two Case Studies of Myoglobin. Chembiochem 2024; 25:e202300678. [PMID: 38015421 DOI: 10.1002/cbic.202300678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/12/2023] [Accepted: 11/28/2023] [Indexed: 11/29/2023]
Abstract
Using myoglobin (Mb) as a model protein, we herein developed a facial approach to modifying the heme active site. A cavity was first generated in the heme distal site by F46 C mutation, and the thiol group of Cys46 was then used for covalently linked to exogenous ligands, 1H-1,2,4-triazole-3-thiol and 1-(4-hydroxyphenyl)-1H-pyrrole-2,5-dione. The engineered proteins, termed F46C-triazole Mb and F46C-phenol Mb, respectively, were characterized by X-ray crystallography, spectroscopic and stopped-flow kinetic studies. The results showed that both the heme coordination state and the protein function such as H2 O2 activation and peroxidase activity could be efficiently regulated, which suggests that this approach might be generally applied to the design of functional heme proteins.
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Affiliation(s)
- Ze-Yuan Chen
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, 421001, China
| | - Hong Yuan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai, 200433, China
| | - Huamin Wang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, 421001, China
| | - Li-Juan Sun
- Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Lu Yu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui, 230031, China
| | - Shu-Qin Gao
- Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai, 200433, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, 421001, China
- Hengyang Medical School, University of South China, Hengyang, 421001, China
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2
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Williams MD, Ragireddy V, Dent MR, Tejero J. Engineering neuroglobin nitrite reductase activity based on myoglobin models. Biochem Biophys Rep 2023; 36:101560. [PMID: 37929291 PMCID: PMC10623171 DOI: 10.1016/j.bbrep.2023.101560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 10/13/2023] [Indexed: 11/07/2023] Open
Abstract
Neuroglobin is a hemoprotein expressed in several nervous system cell lineages with yet unknown physiological functions. Neuroglobin presents a very similar structure to that of the related globins hemoglobin and myoglobin, but shows an hexacoordinate heme as compared to the pentacoordinated heme of myoglobin and hemoglobin. While several reactions of neuroglobin have been characterized in vitro, the relative importance of most of those reactions in vivo is yet undefined. Neuroglobin, like other heme proteins, can reduce nitrite to nitric oxide, providing a possible route to generate nitric oxide in vivo in low oxygen conditions. The reaction kinetics are highly dependent on the nature of the distal residue, and replacement of the distal histidine His64(E7) can increase the reaction rate constants by several orders of magnitude. However, mutation of other distal pocket positions such as Phe28(B10) or Val68(E11) has more limited impact on the rates. Computational analysis using myoglobin as template, guided by the structure of dedicated nitrite reductases like cytochrome cd1 nitrite reductase, has pointed out that combined mutations of the residues B10 and CD1 could increase the nitrite reductase activity of myoglobin, by mimicking the environment of the distal heme pocket in cytochrome cd1 nitrite reductase. As neuroglobin shows high sequence and structural homology with myoglobin, we hypothesized that such mutations (F28H and F42Y in neuroglobin) could also modify the nitrite reductase activity of neuroglobin. Here we study the effect of these mutations. Unfortunately, we do not observe in any case an increase in the nitrite reduction rates. Our results provide some further indications of nitrite reductase regulation in neuroglobin and highlight the minor but critical differences between the structure of penta- and hexacoordinate globins.
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Affiliation(s)
- Mark D. Williams
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Venkata Ragireddy
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Matthew R. Dent
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Jesús Tejero
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, 15260, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
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3
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Van Brempt N, Sgammato R, Beirinckx Q, Hammerschmid D, Sobott F, Dewilde S, Moens L, Herrebout W, Johannessen C, Van Doorslaer S. The effect of pH and nitrite on the haem pocket of GLB-33, a globin-coupled neuronal transmembrane receptor of Caenorhabditis elegans. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140913. [PMID: 37004900 DOI: 10.1016/j.bbapap.2023.140913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/25/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]
Abstract
Out of the 34 globins in Caenorhabditis elegans, GLB-33 is a putative globin-coupled transmembrane receptor with a yet unknown function. The globin domain (GD) contains a particularly hydrophobic haem pocket, that rapidly oxidizes to a low-spin hydroxide-ligated haem state at physiological pH. Moreover, the GD has one of the fastest nitrite reductase activity ever reported for globins. Here, we use a combination of electronic circular dichroism, resonance Raman and electron paramagnetic resonance (EPR) spectroscopy with mass spectrometry to study the pH dependence of the ferric form of the recombinantly over-expressed GD in the presence and absence of nitrite. The competitive binding of nitrite and hydroxide is examined as well as nitrite-induced haem modifications at acidic pH. Comparison of the spectroscopic results with data from other haem proteins allows to deduce the important effect of Arg at position E10 in stabilization of exogenous ligands. Furthermore, continuous-wave and pulsed EPR indicate that ligation of nitrite occurs in a nitrito mode at pH 5.0 and above. At pH 4.0, an additional formation of a nitro-bound haem form is observed along with fast formation of a nitri-globin.
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Affiliation(s)
- Niels Van Brempt
- Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, 2610 Antwerp, Belgium
| | - Roberta Sgammato
- Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium
| | - Quinten Beirinckx
- Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium
| | | | - Frank Sobott
- Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, 2610 Antwerp, Belgium
| | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, 2610 Antwerp, Belgium
| | - Wouter Herrebout
- Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium
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4
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Powell SM, Prather KY, Nguyen N, Thomas LM, Richter-Addo GB. Interactions of metronidazole and chloramphenicol with myoglobin: Crystal structure of a Mb-acetamide product. J PORPHYR PHTHALOCYA 2023; 27:1142-1147. [PMID: 37868702 PMCID: PMC10588810 DOI: 10.1142/s1088424623500700] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Nitroorganics present a general concern for a safe environment due to their health hazards. However, some nitroorganics such as metronidazole (Mtz) and chloramphenicol (CAM) also possess medicinal value. Mtz and CAM can undergo reductive bioactivation presumably via their nitroso derivatives. We show, using UV-vis spectroscopy, that sperm whale myoglobin (swMb) and its distal pocket mutants retaining H-bonding capacity react with Mtz in the presence of dithionite to generate products with spectra suggestive of the Fe-bound nitroso (Fe-RNO; λmax ~420 nm) forms. We have crystallized and solved the X-ray crystal structure of an H64Q swMb-acetamide compound to 1.76 Å resolution; formation of this compound results from the serendipitous crystallographic trapping, by the heme center, of acetamide from the reductive decomposition of Mtz. Only one of the swMb proteins, namely H64Q swMb with a relatively flexible Gln64 residue, reacted with CAM presumably due to the bulky nature of CAM that generally may restrict its access to the heme site.
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Affiliation(s)
- Samantha M. Powell
- Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, and Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, U.S.A. 73019
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Batelle Blvd, Richland, WA, U.S.A. 99352
| | - Kiana Y. Prather
- Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, and Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, U.S.A. 73019
- University of Oklahoma College of Medicine, 800 Stanton L. Young Blvd, Oklahoma City, OK 73117
| | - Nancy Nguyen
- Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, and Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, U.S.A. 73019
- University of Oklahoma College of Medicine, 800 Stanton L. Young Blvd, Oklahoma City, OK 73117
| | - Leonard M. Thomas
- Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, and Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, U.S.A. 73019
| | - George B. Richter-Addo
- Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, and Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, U.S.A. 73019
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5
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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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6
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Explainabilty Comparison between Random Forests and Neural Networks—Case Study of Amino Acid Volume Prediction. INFORMATION 2022. [DOI: 10.3390/info14010021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
As explainability seems to be the driver for a wiser adoption of Artificial Intelligence in healthcare and in critical applications, in general, a comprehensive study of this field is far from being completed. On one hand, a final definition and theoretical measurements of explainability have not been assessed, yet, on the other hand, some tools and frameworks for the practical evaluation of this feature are now present. This paper aims to present a concrete experience in using some of these explainability-related techniques in the problem of predicting the size of amino acids in real-world protein structures. In particular, the feature importance calculation embedded in Random Forest (RF) training is compared with the results of the Eli-5 tool applied to the Neural Network (NN) model. Both the predictors are trained on the same dataset, which is extracted from Protein Data Bank (PDB), considering 446 myoglobins structures and process it with several tools to implement a geometrical model and perform analyses on it. The comparison between the two models draws different conclusions about the residues’ geometry and their biological properties.
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7
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Bhattacharya S, Margheritis EG, Takahashi K, Kulesha A, D'Souza A, Kim I, Yoon JH, Tame JRH, Volkov AN, Makhlynets OV, Korendovych IV. NMR-guided directed evolution. Nature 2022; 610:389-393. [PMID: 36198791 PMCID: PMC10116341 DOI: 10.1038/s41586-022-05278-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 08/25/2022] [Indexed: 11/09/2022]
Abstract
Directed evolution is a powerful tool for improving existing properties and imparting completely new functionalities to proteins1-4. Nonetheless, its potential in even small proteins is inherently limited by the astronomical number of possible amino acid sequences. Sampling the complete sequence space of a 100-residue protein would require testing of 20100 combinations, which is beyond any existing experimental approach. In practice, selective modification of relatively few residues is sufficient for efficient improvement, functional enhancement and repurposing of existing proteins5. Moreover, computational methods have been developed to predict the locations and, in certain cases, identities of potentially productive mutations6-9. Importantly, all current approaches for prediction of hot spots and productive mutations rely heavily on structural information and/or bioinformatics, which is not always available for proteins of interest. Moreover, they offer a limited ability to identify beneficial mutations far from the active site, even though such changes may markedly improve the catalytic properties of an enzyme10. Machine learning methods have recently showed promise in predicting productive mutations11, but they frequently require large, high-quality training datasets, which are difficult to obtain in directed evolution experiments. Here we show that mutagenic hot spots in enzymes can be identified using NMR spectroscopy. In a proof-of-concept study, we converted myoglobin, a non-enzymatic oxygen storage protein, into a highly efficient Kemp eliminase using only three mutations. The observed levels of catalytic efficiency exceed those of proteins designed using current approaches and are similar with those of natural enzymes for the reactions that they are evolved to catalyse. Given the simplicity of this experimental approach, which requires no a priori structural or bioinformatic knowledge, we expect it to be widely applicable and to enable the full potential of directed enzyme evolution.
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Affiliation(s)
| | - Eleonora G Margheritis
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Katsuya Takahashi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Alona Kulesha
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - Areetha D'Souza
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - Inhye Kim
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - Jennifer H Yoon
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - Jeremy R H Tame
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Alexander N Volkov
- VIB Centre for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium.
- Jean Jeener NMR Centre, Vrije Universiteit Brussel (VUB), Brussels, Belgium.
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8
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Kaliszuk SJ, Morgan NI, Ayers TN, Sparacino Watkins CE, DeMartino AW, Bocian K, Ragireddy V, Tong Q, Tejero J. Regulation of nitrite reductase and lipid binding properties of cytoglobin by surface and distal histidine mutations. Nitric Oxide 2022; 125-126:12-22. [PMID: 35667547 PMCID: PMC9283305 DOI: 10.1016/j.niox.2022.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/21/2022] [Accepted: 06/01/2022] [Indexed: 12/30/2022]
Abstract
Cytoglobin is a hemoprotein widely expressed in fibroblasts and related cell lineages with yet undefined physiological function. Cytoglobin, as other heme proteins, can reduce nitrite to nitric oxide (NO) providing a route to generate NO in vivo in low oxygen conditions. In addition, cytoglobin can also bind lipids such as oleic acid and cardiolipin with high affinity. These two processes are potentially relevant to cytoglobin function. Little is known about how specific amino acids contribute to nitrite reduction and lipid binding. Here we investigate the role of the distal histidine His81 (E7) and several surface residues on the regulation of nitrite reduction and lipid binding. We observe that the replacement of His81 (E7) greatly increases heme reactivity towards nitrite, with nitrite reduction rate constants of up to 1100 M-1s-1 for the His81Ala mutant. His81 (E7) mutation causes a small decrease in lipid binding affinity, however experiments on the presence of imidazole indicate that His81 (E7) does not compete with the lipid for the binding site. Mutations of the surface residues Arg84 and Lys116 largely impair lipid binding. Our results suggest that dissociation of His81 (E7) from the heme mediates the formation of a hydrophobic cavity in the proximal heme side that can accommodate the lipid, with important contributions of the hydrophobic patch around residues Thr91, Val105, and Leu108, whereas the positive charges from Arg84 and Lys116 stabilize the carboxyl group of the fatty acid. Gain and loss-of-function mutations described here can serve as tools to study in vivo the physiological role of these putative cytoglobin functions.
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Affiliation(s)
- Stefan J Kaliszuk
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Natasha I Morgan
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Taylor N Ayers
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Courtney E Sparacino Watkins
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA; Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Anthony W DeMartino
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Kaitlin Bocian
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Venkata Ragireddy
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Qin Tong
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Jesús Tejero
- Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA; Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA; Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, 15260, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
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Penjweini R, Roarke B, Alspaugh G, Link KA, Andreoni A, Mori MP, Hwang PM, Sackett DL, Knutson JR. Intracellular imaging of metmyoglobin and oxygen using new dual purpose probe EYFP-Myoglobin-mCherry. JOURNAL OF BIOPHOTONICS 2022; 15:e202100166. [PMID: 34689421 PMCID: PMC8901566 DOI: 10.1002/jbio.202100166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 10/04/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
The biological relevance of nitric oxide (NO) and reactive oxygen species (ROS) in signaling, metabolic regulation, and disease treatment has become abundantly clear. The dramatic change in NO/ROS processing that accompanies a changing oxygen landscape calls for new imaging tools that can provide cellular details about both [O2 ] and the production of reactive species. Myoglobin oxidation to the met state by NO/ROS is a known sensor with absorbance changes in the visible range. We previously employed Förster resonance energy transfer to read out the deoxygenation/oxygenation of myoglobin, creating the subcellular [O2 ] sensor Myoglobin-mCherry. We now add the fluorescent protein EYFP to this sensor to create a novel probe that senses both met formation, a proxy for ROS/NO exposure, and [O2 ]. Since both proteins are present in the construct, it can also relieve users from the need to measure fluorescence lifetime, making [O2 ] sensing available to a wider group of laboratories.
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Affiliation(s)
- Rozhin Penjweini
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1412
| | - Branden Roarke
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1412
| | - Greg Alspaugh
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1412
| | - Katie A. Link
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1412
| | - Alessio Andreoni
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1412
- Laboratory of Optical Neurophysiology, Department of Biochemistry and Molecular Medicine, University of California Davis, Tupper Hall, Davis, CA 95616
| | - Mateus P. Mori
- Laboratory of Cardiovascular and Cancer Genetics, NHLBI, NIH, Bethesda, MD 20892-1412
| | - Paul M. Hwang
- Laboratory of Cardiovascular and Cancer Genetics, NHLBI, NIH, Bethesda, MD 20892-1412
| | - Dan L. Sackett
- Cytoskeletal Dynamics Group, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda MD, 20892-0924
| | - Jay R. Knutson
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892-1412
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10
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Peng R, Wang L, Yu P, Carrier AJ, Oakes KD, Zhang X. Exacerbated Protein Oxidation and Tyrosine Nitration through Nitrite-Enhanced Fenton Chemistry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:353-359. [PMID: 34963286 DOI: 10.1021/acs.jafc.1c04591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nitrite is a common additive used during meat curing to prevent microbial contamination and retain an attractive red color in the product. However, the effects of nitrite on Fenton reactions catalyzed by free iron in meat products are not well understood, although such processes can induce protein oxidation and nitration, affecting the nutritional and aesthetic quality of meat products. This contribution reveals the mechanism through which nitrite affects Fenton reactions that generate reactive nitrogen and oxygen species by increasing the availability of Fe3+, facilitating its reduction and stabilizing Fe2+, and accelerating Fe3+/Fe2+ cycling, leading to exacerbated oxidative and nitrosative stress on proteins, with implications not only for meat processing but also in many biological and environmental processes due to the ubiquitous presence of iron, hydrogen peroxide, and nitrite in nature.
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Affiliation(s)
- Rui Peng
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Li Wang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Pinting Yu
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Andrew J Carrier
- Department of Chemistry, Cape Breton University, Sydney, Nova Scotia B1P 6L2, Canada
| | - Ken D Oakes
- Department of Biology, Cape Breton University, Sydney, Nova Scotia B1P 6L2, Canada
| | - Xu Zhang
- Department of Chemistry, Cape Breton University, Sydney, Nova Scotia B1P 6L2, Canada
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11
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Penjweini R, Mori MP, Hwang PM, Sackett DL, Knutson JR. Fluorescence lifetime imaging of metMyoglobin formation due to nitric oxide stress. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2022; 11965:119650H. [PMID: 35463920 PMCID: PMC9022600 DOI: 10.1117/12.2608888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Myoglobin is a protein that is expressed quite unevenly among different cell types. Nevertheless, it has been widely acknowledged that the Fe3+ state of myoglobin, metmyoglobin (metMb) has a broad functional role in metabolism, oxidative/nitrative regulation and gene networks. Accordingly, real-time monitoring of oxygenated, deoxygenated and metMb proportions- or, more broadly, of the mechanisms by which metMb is formed, presents a promising line of research. We had previously introduced a Förster resonance energy transfer (FRET) method to read out the deoxygenation/oxygenation states of myoglobin, by creating the targetable oxygen (O2) sensor Myoglobin-mCherry. In this sensor, changes in myoglobin absorbance features that occur with lost O2 occupancy -or upon metMb production- control the FRET rate from the fluorescent protein to myoglobin. When O2 is bound, mCherry fluorescence is only slightly quenched, but if either O2 is released or met is produced, FRET will increase- and this rate competing with emission reduces both emission yield and lifetime. Nitric oxide (NO) is an important signal (but also a toxic molecule) that can oxidize myoglobin to metMb with absorbance increases in the red visible range. mCherry thus senses both met and deoxygenated myoglobin, which cannot be easily separated at hypoxia. In order to dissect this, we treat cells with NO and investigate how the Myoglobin-mCherry lifetime is affected by generating metMb. More discriminatory power is then achieved when the fluorescent protein EYFP is added to Myoglobin-mCherry, creating a sandwich probe whose lifetime can selectively respond to metMb while being indifferent to O2 occupancy.
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Affiliation(s)
- Rozhin Penjweini
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Building 10, Room 5D14, Bethesda, MD 20892-1412
| | - Mateus P Mori
- Laboratory of Cardiovascular and Cancer Genetics, NHLBI, NIH, Bethesda, MD 20892-1412
| | - Paul M Hwang
- Laboratory of Cardiovascular and Cancer Genetics, NHLBI, NIH, Bethesda, MD 20892-1412
| | - Dan L Sackett
- Cytoskeletal Dynamics Group, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Building 9, Room 1E129, Bethesda MD, 20892-0924
| | - Jay R Knutson
- Laboratory of Advanced Microscopy and Biophotonics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Building 10, Room 5D14, Bethesda, MD 20892-1412
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12
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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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13
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Dent MR, DeMartino AW, Tejero J, Gladwin MT. Endogenous Hemoprotein-Dependent Signaling Pathways of Nitric Oxide and Nitrite. Inorg Chem 2021; 60:15918-15940. [PMID: 34313417 PMCID: PMC9167621 DOI: 10.1021/acs.inorgchem.1c01048] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Interdisciplinary research at the interface of chemistry, physiology, and biomedicine have uncovered pivotal roles of nitric oxide (NO) as a signaling molecule that regulates vascular tone, platelet aggregation, and other pathways relevant to human health and disease. Heme is central to physiological NO signaling, serving as the active site for canonical NO biosynthesis in nitric oxide synthase (NOS) enzymes and as the highly selective NO binding site in the soluble guanylyl cyclase receptor. Outside of the primary NOS-dependent biosynthetic pathway, other hemoproteins, including hemoglobin and myoglobin, generate NO via the reduction of nitrite. This auxiliary hemoprotein reaction unlocks a "second axis" of NO signaling in which nitrite serves as a stable NO reservoir. In this Forum Article, we highlight these NO-dependent physiological pathways and examine complex chemical and biochemical reactions that govern NO and nitrite signaling in vivo. We focus on hemoprotein-dependent reaction pathways that generate and consume NO in the presence of nitrite and consider intermediate nitrogen oxides, including NO2, N2O3, and S-nitrosothiols, that may facilitate nitrite-based signaling in blood vessels and tissues. We also discuss emergent therapeutic strategies that leverage our understanding of these key reaction pathways to target NO signaling and treat a wide range of diseases.
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Affiliation(s)
- Matthew R Dent
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Anthony W DeMartino
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Jesús Tejero
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Mark T Gladwin
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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14
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Galinato MGI, Trail AM, Steinbeck OR, Si Z, Rodland AM, Gowen J. Influence of heme propionates on the nitrite reductase activity of myoglobin. J Inorg Biochem 2021; 226:111630. [PMID: 34688205 DOI: 10.1016/j.jinorgbio.2021.111630] [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: 07/12/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 11/20/2022]
Abstract
The heme propionates in myoglobin (Mb) form a H-bonding network among several residues within its second-sphere coordination, providing a key structural role towards Mb's functional properties. Our work aims to understand the role of the heme propionates on the nitrite reductase (NiR) activity (e.g. reduction of NO2- to NO) of this globin by studying an artificial dimethylester heme-substituted horse heart Mb (DME-Mb). The minor structural change brought about by esterification of the heme propionates causes the NiR rate to increase by more than over two-fold (5.6 ± 0.1 M-1 s-1) relative to wildtype (wt) Mb (2.3 ± 0.1 M-1 s-1). The lower pKa observed in DME-Mb may enhance the tendency of His64 towards protonation, therefore increasing the NiR rate. In addition, the nitrite binding constant (Knitrite) for DME-MbIII is greater than wt MbIII (350 M-1 versus 120 M-1). The disparity in the NiR activity correlates with the differences in electrostatic behavior, which influences the system's reactivity towards the approaching NO2- ion, and thus the formation of the FeII-NO2- intermediate.
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Affiliation(s)
- Mary Grace I Galinato
- School of Science-Chemistry, Penn State Behrend, Erie, PA 16563, United States of America.
| | - Aaron M Trail
- School of Science-Chemistry, Penn State Behrend, Erie, PA 16563, United States of America
| | - Olivia R Steinbeck
- School of Science-Chemistry, Penn State Behrend, Erie, PA 16563, United States of America
| | - Zhuoyan Si
- School of Science-Chemistry, Penn State Behrend, Erie, PA 16563, United States of America
| | - Anthony M Rodland
- School of Science-Chemistry, Penn State Behrend, Erie, PA 16563, United States of America
| | - Jaclyn Gowen
- School of Science-Chemistry, Penn State Behrend, Erie, PA 16563, United States of America
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15
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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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16
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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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17
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Affiliation(s)
- James P. Shanahan
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, Michigan 48109, United States
| | - Nathaniel K. Szymczak
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, Michigan 48109, United States
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18
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Distinctive structural properties of THB11, a pentacoordinate Chlamydomonas reinhardtii truncated hemoglobin with N- and C-terminal extensions. J Biol Inorg Chem 2020; 25:267-283. [PMID: 32048044 PMCID: PMC7082302 DOI: 10.1007/s00775-020-01759-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/14/2020] [Indexed: 12/20/2022]
Abstract
Hemoglobins (Hbs) utilize heme b as a cofactor and are found in all kingdoms of life. The current knowledge reveals an enormous variability of Hb primary sequences, resulting in topological, biochemical and physiological individuality. As Hbs appear to modulate their reactivities through specific combinations of structural features, predicting the characteristics of a given Hb is still hardly possible. The unicellular green alga Chlamydomonas reinhardtii contains 12 genes encoding diverse Hbs of the truncated lineage, several of which possess extended N- or C-termini of unknown function. Studies on some of the Chlamydomonas Hbs revealed yet unpredictable structural and biochemical variations, which, along with a different expression of their genes, suggest diverse physiological roles. Chlamydomonas thus represents a promising system to analyze the diversification of Hb structure, biochemistry and physiology. Here, we report the crystal structure, resolved to 1.75 Å, of the heme-binding domain of cyanomet THB11 (Cre16.g662750), one of the pentacoordinate algal Hbs, which offer a free Fe-coordination site in the reduced state. The overall fold of THB11 is conserved, but individual features such as a kink in helix E, a tilted heme plane and a clustering of methionine residues at a putative tunnel exit appear to be unique. Both N- and C-termini promote the formation of oligomer mixtures, and the absence of the C terminus results in reduced nitrite reduction rates. This work widens the structural and biochemical knowledge on the 2/2Hb family and suggests that the N- and C-terminal extensions of the Chlamydomonas 2/2Hbs modulate their reactivity by intermolecular interactions.
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19
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Engineering Metalloprotein Functions in Designed and Native Scaffolds. Trends Biochem Sci 2019; 44:1022-1040. [DOI: 10.1016/j.tibs.2019.06.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 12/15/2022]
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20
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Cui X, Wang T, Wang W, Wang H, Wang Z. Peroxidase from proso millet exhibits endonuclease-like activity. Acta Biochim Biophys Sin (Shanghai) 2019; 51:688-696. [PMID: 31168624 DOI: 10.1093/abbs/gmz049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Indexed: 12/28/2022] Open
Abstract
In this study, the mechanism of DNA cleavage by cationic peroxidase from proso millet (PmPOD) was investigated. PmPOD cleaved supercoiled circular DNA into both nicked circular and linear forms via a cleavage mechanism that resembles those of native endonucleases. Inhibition and ligation studies demonstrated that reactive oxygen species and the ferriprotoporphyrin IX moiety in PmPOD are not involved in PmPOD-mediated DNA cleavage. Similar to other endonucleases, Mg ions considerably enhance the DNA cleavage activity of PmPOD. Further studies suggested that PmPOD can disrupt phosphodiester bonds in DNA and mononucleotides, indicating that it is a phosphatase. The phosphatase activity of PmPOD is higher than that of horseradish peroxidase (HRP), but the peroxidase activity of PmPOD was lower than that of HRP. PmPOD-mediated hydrolytic cleavage of DNA observed in this study is different from those reported for heme proteins. This study provides valuable insights into the distinct mechanisms underlying DNA cleavage by heme proteins.
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Affiliation(s)
- Xiaodong Cui
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, China
| | - Tingfen Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, China
| | - Wenming Wang
- Institute of Molecular Science, Shanxi University, Taiyuan, China
| | - Hongfei Wang
- Institute of Molecular Science, Shanxi University, Taiyuan, China
| | - Zhuanhua Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, China
- School of Life Science, Shanxi University, Taiyuan, China
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21
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Nath AK, Ghosh C, Roy M, Seal M, Ghosh Dey S. Nitrite reductase activity of heme and copper bound Aβ peptides. Dalton Trans 2019; 48:7451-7461. [PMID: 31086893 DOI: 10.1039/c9dt00914k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A significant abundance of copper (Cu) and iron in amyloid β (Aβ) plaques, and several heme related metabolic disorders are directly correlated with Alzheimer's disease (AD), and these together with co-localization of Aβ plaques with heme rich deposits in the brains of AD sufferers indicates a possible association of the said metals with the disease. Recently, the Aβ peptides have been found to bind heme and Cu individually as well as simultaneously. Another significant finding relevant to this is the lower levels of nitrite and nitrate found in the brains of patients suffering from AD. In this study, a combination of absorption and electron paramagnetic resonance spectroscopy and kinetic assays have been used to study the interaction of nitrite with the metal bound Aβ complexes. The data indicate that heme(III)-Cu(i)-Aβ, heme(II)-Cu(i)-Aβ, heme(II)-Aβ and Cu(i)-Aβ can reduce nitrite to nitric oxide (NO), an important biological messenger also related to AD, and thus behave as nitrite reductases. However these complexes reduce nitrite at different rates with heme(III)-Cu(i)-Aβ being the fastest following an inner sphere electron transfer mechanism. The rest of the metal-Aβ adducts follow an outer sphere electron transfer mechanism during nitrite reduction. Protonation from the Arg5 residue triggering the N-O bond heterolysis in heme(III) bound nitrite with a simultaneous electron transfer from the Cu(i) center to produce NO is the rate determining step, indicating a proton transfer followed by electron transfer (PTET) mechanism.
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Affiliation(s)
- Arnab Kumar Nath
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India.
| | - Chandradeep Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India.
| | - Madhuparna Roy
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India.
| | - Manas Seal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India.
| | - Somdatta Ghosh Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India.
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22
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Liu C, Yuan H, Liao F, Wei CW, Du KJ, Gao SQ, Tan X, Lin YW. Unique Tyr-heme double cross-links in F43Y/T67R myoglobin: an artificial enzyme with a peroxidase activity comparable to that of native peroxidases. Chem Commun (Camb) 2019; 55:6610-6613. [PMID: 31119219 DOI: 10.1039/c9cc02714a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The X-ray crystal structure of F43Y/T67R myoglobin revealed unique Tyr-heme double cross-links between Tyr43 and the heme 4-vinyl group, which represents a novel post-translational modification of heme proteins. Moreover, with the feature of a distal His-Arg pair, the designed artificial enzyme exhibited a peroxidase activity comparable to that of native peroxidases, such as the most efficient horseradish peroxidase.
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Affiliation(s)
- Can Liu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Hong Yuan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Fei Liao
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Chuan-Wan Wei
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Ke-Jie Du
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China. and Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
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23
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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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24
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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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25
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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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26
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Lynch KB, Chen A, Yang Y, Lu JJ, Liu S. High-performance liquid chromatographic cartridge with gradient elution capability coupled with UV absorbance detector and mass spectrometer for peptide and protein analysis. J Sep Sci 2017; 40:2752-2758. [PMID: 28514057 DOI: 10.1002/jssc.201700185] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/05/2017] [Accepted: 05/08/2017] [Indexed: 02/05/2023]
Abstract
We discuss the construction and performance of a high-performance liquid chromatography cartridge that we developed that resulted from a culmination of previous research. We have recently developed an innovative approach to creating gradient elutions using dual electroosmotic pumps and a series of three valves. This method has been proved to be the most reproducible and robust in producing gradients compared to our previously tested methods. Using this approach, we have assembled a high-performance liquid chromatography cartridge powered and controlled via a computer. We have successfully coupled the cartridge with an ultraviolet absorbance detector and a mass spectrometer for separating complex protein/peptide samples. The cartridge is readily coupled with other detectors such as electrochemical detector and laser-induced fluorescence detector.
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Affiliation(s)
- Kyle B Lynch
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Apeng Chen
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Yu Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Joann J Lu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Shaorong Liu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
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27
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Ioannou A, Pinakoulaki E. Probing nitrite coordination in horseradish peroxidase by resonance Raman spectroscopy: Detection of two binding sites. J Inorg Biochem 2017; 169:79-85. [PMID: 28160625 DOI: 10.1016/j.jinorgbio.2017.01.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 01/04/2017] [Accepted: 01/20/2017] [Indexed: 11/15/2022]
Abstract
Nitrite is a powerful oxidant that affects the activity of peroxidases towards various substrates and leads to heme macrocycle modifications in members of the peroxidase family, such as the horseradish peroxidase (HRP). We have applied resonance Raman spectroscopy to investigate the structural properties of the species formed in the reaction of NO2- with the ferric form of HRP. Our data demonstrate that the heme nitrovinyl group is partially formed at near neutral pH, without coordination of NO2- to the heme Fe. Nitrite coordinates to the heme Fe at acidic pH in the nitro binding mode, characterized by the detection of the ν(Fe-NO2) at 563cm-1, δ(FeNO2) at 822cm-1 and νsym(NO2) at 1272cm-1. The sensitivity of the vibrations of the heme Fe-nitro complex to H/D exchange indicates H-bonding interaction of the heme-bound ligand with the distal environment that determines the NO2- binding mode. A model describing the different modes of NO2- binding in HRP is presented.
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Affiliation(s)
- Androulla Ioannou
- Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - Eftychia Pinakoulaki
- Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus.
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28
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Ioannou A, Lambrou A, Daskalakis V, Pinakoulaki E. Coupling of helix E-F motion with the O-nitrito and 2-nitrovinyl coordination in myoglobin. Biophys Chem 2017; 221:10-16. [DOI: 10.1016/j.bpc.2016.11.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/15/2016] [Accepted: 11/23/2016] [Indexed: 10/20/2022]
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29
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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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30
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Li LL, Yuan H, Liao F, He B, Gao SQ, Wen GB, Tan X, Lin YW. Rational design of artificial dye-decolorizing peroxidases using myoglobin by engineering Tyr/Trp in the heme center. Dalton Trans 2017; 46:11230-11238. [DOI: 10.1039/c7dt02302b] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Artificial dye-decolorizing peroxidases (DyPs) have been rationally designed using myoglobin (Mb) as a protein scaffold by engineering Tyr/Trp in the heme center, such as F43Y/F138 W Mb, which exhibited catalytic performance comparable to some native DyPs.
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Affiliation(s)
- Le-Le Li
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Hong Yuan
- Department of Chemistry & Institute of Biomedical Science
- Fudan University
- Shanghai 200433
- China
| | - Fei Liao
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Bo He
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function
- University of South China
- Hengyang 421001
- China
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function
- University of South China
- Hengyang 421001
- China
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science
- Fudan University
- Shanghai 200433
- China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering
- University of South China
- Hengyang 421001
- China
- Laboratory of Protein Structure and Function
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31
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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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32
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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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33
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Lambrou A, Ioannou A, Pinakoulaki E. Spin Crossover in Nitrito-Myoglobin as Revealed by Resonance Raman Spectroscopy. Chemistry 2016; 22:12176-80. [PMID: 27417111 DOI: 10.1002/chem.201601738] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Alexandra Lambrou
- Department of Chemistry; University of Cyprus, PO Box 20537; 1678 Nicosia Cyprus
| | - Androulla Ioannou
- Department of Chemistry; University of Cyprus, PO Box 20537; 1678 Nicosia Cyprus
| | - Eftychia Pinakoulaki
- Department of Chemistry; University of Cyprus, PO Box 20537; 1678 Nicosia Cyprus
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34
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Residues in the Distal Heme Pocket of Arabidopsis Non-Symbiotic Hemoglobins: Implication for Nitrite Reductase Activity. Int J Mol Sci 2016; 17:ijms17050640. [PMID: 27136534 PMCID: PMC4881466 DOI: 10.3390/ijms17050640] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/13/2016] [Accepted: 04/19/2016] [Indexed: 02/08/2023] Open
Abstract
It is well-established that plant hemoglobins (Hbs) are involved in nitric oxide (NO) metabolism via NO dioxygenase and/or nitrite reductase activity. The ferrous-deoxy Arabidopsis Hb1 and Hb2 (AHb1 and AHb2) have been shown to reduce nitrite to NO under hypoxia. Here, to test the hypothesis that a six- to five-coordinate heme iron transition might mediate the control of the nitrite reduction rate, we examined distal pocket mutants of AHb1 and AHb2 for nitrite reductase activity, NO production and spectroscopic features. Absorption spectra of AHbs distal histidine mutants showed that AHb1 mutant (H69L) is a stable pentacoordinate high-spin species in both ferrous and ferric states, whereas heme iron in AHb2 mutant (H66L) is hexacoordinated low-spin with Lys69 as the sixth ligand. The bimolecular rate constants for nitrite reduction to NO were 13.3 ± 0.40, 7.3 ± 0.5, 10.6 ± 0.8 and 171.90 ± 9.00 M−1·s−1 for AHb1, AHb2, AHb1 H69L and AHb2 H66L, respectively, at pH 7.4 and 25 °C. Consistent with the reductase activity, the amount of NO detected by chemiluminescence was significantly higher in the AHb2 H66L mutant. Our data indicate that nitrite reductase activity is determined not only by heme coordination, but also by a unique distal heme pocket in each AHb.
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35
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Wu LB, Yuan H, Gao SQ, You Y, Nie CM, Wen GB, Lin YW, Tan X. Regulating the nitrite reductase activity of myoglobin by redesigning the heme active center. Nitric Oxide 2016; 57:21-29. [PMID: 27108710 DOI: 10.1016/j.niox.2016.04.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/13/2016] [Accepted: 04/20/2016] [Indexed: 10/21/2022]
Abstract
Heme proteins perform diverse functions in living systems, of which nitrite reductase (NIR) activity receives much attention recently. In this study, to better understand the structural elements responsible for the NIR activity, we used myoglobin (Mb) as a model heme protein and redesigned the heme active center, by introducing one or two distal histidines, and by creating a channel to the heme center with removal of the native distal His64 gate (His to Ala mutation). UV-Vis kinetic studies, combined with EPR studies, showed that a single distal histidine with a suitable position to the heme iron, i.e., His43, is crucial for nitrite (NO2(-)) to nitric oxide (NO) reduction. Moreover, creation of a water channel to the heme center significantly enhanced the NIR activity compared to the corresponding mutant without the channel. In addition, X-ray crystallographic studies of F43H/H64A Mb and its complexes with NO2(-) or NO revealed a unique hydrogen-bonding network in the heme active center, as well as unique substrate and product binding models, providing valuable structural information for the enhanced NIR activity. These findings enriched our understanding of the structure and NIR activity relationship of heme proteins. The approach of creating a channel in this study is also useful for rational design of other functional heme proteins.
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Affiliation(s)
- Lei-Bin Wu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Hong Yuan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China
| | - Shu-Qin Gao
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Yong You
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Chang-Ming Nie
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China
| | - Ge-Bo Wen
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China
| | - Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China; Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China.
| | - Xiangshi Tan
- Department of Chemistry & Institute of Biomedical Science, Fudan University, Shanghai 200433, China.
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36
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Zhao Y, Du KJ, Gao SQ, He B, Wen GB, Tan X, Lin YW. Distinct mechanisms for DNA cleavage by myoglobin with a designed heme active center. J Inorg Biochem 2016; 156:113-21. [DOI: 10.1016/j.jinorgbio.2016.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 12/29/2015] [Accepted: 01/07/2016] [Indexed: 12/14/2022]
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37
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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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38
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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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39
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Hematian S, Garcia-Bosch I, Karlin KD. Synthetic heme/copper assemblies: toward an understanding of cytochrome c oxidase interactions with dioxygen and nitrogen oxides. Acc Chem Res 2015; 48:2462-74. [PMID: 26244814 DOI: 10.1021/acs.accounts.5b00265] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Our long-time niche in synthetic biological inorganic chemistry has been to design ligands and generate coordination complexes of copper or iron ions or both, those reacting with dioxygen (O2) or nitrogen oxides (e.g., nitric oxide (NO(g)) and nitrite (NO2(-))) or both. As inspiration for this work, we turn to mitochondrial cytochrome c oxidase, which is responsible for dioxygen consumption and is also the predominant target for NO(g) and nitrite within mitochondria. In this Account, we highlight recent advances in studying synthetic heme/Cu complexes in two respects. First, there is the design, synthesis, and characterization of new O2 adducts whose further study will add insights into O2 reductive cleavage chemistry. Second, we describe how related heme/Cu constructs reduce nitrite ion to NO(g) or the reverse, oxidize NO(g) to nitrite. The reactions of nitrogen oxides occur as part of CcO's function, which is intimately tied to cellular O2 balance. We had first discovered that reduced heme/Cu compounds react with O2 giving μ-oxo heme-Fe(III)-O-Cu(II)(L) products; their properties are discussed. The O-atom is derived from dioxygen, and interrogations of these systems led to the construction and characterization of three distinctive classes of heme-peroxo complexes, two high-spin and one low-spin species. Recent investigations include a new approach to the synthesis of low-spin heme-peroxo-Cu complexes, employing a "naked" synthon, where the copper ligand denticity and geometric types can be varied. The result is a collection of such complexes; spectroscopic and structural features (by DFT calculations) are described. Some of these compounds are reactive toward reductants/protons effecting subsequent O-O cleavage. This points to how subtle improvements in ligand environment lead to a desired local structure and resulting optimized reactivity, as known to occur at enzyme active sites. The other sector of research is focused on heme/Cu assemblies mediating the redox interplay between nitrite and NO(g). In the nitrite reductase chemistry, the cupric center serves as a Lewis acid, while the heme is the redox active center providing the electron. The orientation of nitrite in approaching the ferrous heme center and N-atom binding are important. Also, detailed spectroscopic and kinetic studies of the NO(g) oxidase chemistry, in excellent agreement with theoretical calculations, reveal the intermediates and key mechanistic steps. Thus, we suggest that both chemical and biochemical heme/Cu-mediated nitrite reductase and NO(g) oxidase chemistry require N-atom binding to a ferrous heme along with cupric ion O-atom coordination, proceeding via a three-membered O-Fe-N chelate ring transition state. These important mechanistic features of heme/Cu systems interconverting NO(g) and nitrite are discussed for the first time.
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Affiliation(s)
- Shabnam Hematian
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21211, United States
| | - Isaac Garcia-Bosch
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21211, United States
| | - Kenneth D. Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21211, United States
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40
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Chen A, Lu JJ, Gu C, Zhang M, Lynch KB, Liu S. Combining selection valve and mixing chamber for nanoflow gradient generation: Toward developing a liquid chromatography cartridge coupled with mass spectrometer for protein and peptide analysis. Anal Chim Acta 2015; 887:230-236. [PMID: 26320807 DOI: 10.1016/j.aca.2015.06.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 06/24/2015] [Accepted: 06/26/2015] [Indexed: 01/15/2023]
Abstract
Toward developing a micro HPLC cartridge, we have recently built a high-pressure electroosmotic pump (EOP). However, we do not recommend people to use this pump to deliver an organic solvent directly, because it often makes the pump rate unstable. We have experimented several approaches to address this issue, but none of them are satisfactory. Here, we develop an innovative approach to address this issue. We first create an abruption (a dead-volume) within a fluid conduit. We then utilize an EOP to withdraw, via a selection valve, a train of eluent solutions having decreasing eluting power into the fluid conduit. When these solutions are further aspirated through the dead-volume, these solutions are partially mixed, smoothening concentration transitions between two adjacent eluent solutions. As these solutions are pushed back, through the dead-volume again, a smooth gradient profile is formed. In this work, we characterize this scheme for gradient formation, and we incorporate this approach with a high-pressure EOP, a nanoliter injection valve, and a capillary column, yielding a micro HPLC system. We then couple this micro HPLC with an electrospray ionization - mass spectrometer for peptide and protein separations and identifications.
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Affiliation(s)
- Apeng Chen
- Department of Chemistry and Biochemistry, University of Oklahoma Norman, OK 73019, USA.
| | - Joann J Lu
- Department of Chemistry and Biochemistry, University of Oklahoma Norman, OK 73019, USA.
| | - Congying Gu
- Department of Chemistry and Biochemistry, University of Oklahoma Norman, OK 73019, USA; Veritas Laboratories, LLC, Tifton, GA 31793, USA.
| | - Min Zhang
- Department of Chemistry and Biochemistry, University of Oklahoma Norman, OK 73019, USA.
| | - Kyle B Lynch
- Department of Chemistry and Biochemistry, University of Oklahoma Norman, OK 73019, USA.
| | - Shaorong Liu
- Department of Chemistry and Biochemistry, University of Oklahoma Norman, OK 73019, USA.
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41
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Bykov D, Neese F. Six-Electron Reduction of Nitrite to Ammonia by Cytochrome c Nitrite Reductase: Insights from Density Functional Theory Studies. Inorg Chem 2015; 54:9303-16. [DOI: 10.1021/acs.inorgchem.5b01506] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Dmytro Bykov
- qLEAP Center
for Theoretical Chemistry, Department of Chemistry, Aarhus University, Gustav
Wieds Vej 10A, DK-8000 Aarhus C, Denmark
| | - Frank Neese
- Max-Planck Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
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42
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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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43
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Tsai ML, Tsou CC, Liaw WF. Dinitrosyl iron complexes (DNICs): from biomimetic synthesis and spectroscopic characterization toward unveiling the biological and catalytic roles of DNICs. Acc Chem Res 2015; 48:1184-93. [PMID: 25837426 DOI: 10.1021/ar500459j] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Dinitrosyl iron complexes (DNICs) have been recognized as storage and transport agents of nitric oxide capable of selectively modifying crucial biological targets via its distinct redox forms (NO(+), NO(•) and NO(-)) to initiate the signaling transduction pathways associated with versatile physiological and pathological responses. For decades, the molecular geometry and spectroscopic identification of {Fe(NO)2}(9) DNICs ({Fe(NO)x}(n) where n is the sum of electrons in the Fe 3d orbitals and NO π* orbitals based on Enemark-Feltham notation) in biology were limited to tetrahedral (CN = 4) and EPR g-value ∼2.03, respectively, due to the inadequacy of structurally well-defined biomimetic DNICs as well as the corresponding spectroscopic library accessible in biological environments. The developed synthetic methodologies expand the scope of DNICs into nonclassical square pyramidal and trigonal bipyramidal (CN = 5) and octahedral (CN = 6) {Fe(NO)2}(9) DNICs, as well as two/three accessible redox couples for mononuclear {Fe(NO)2}(9/10) and dinuclear [{Fe(NO)2}(9/10)-{Fe(NO)2}(9/10)] DNICs with biologically relevant S/O/N ligation modes. The unprecedented molecular geometries and electronic states of structurally well-defined DNIC models provide the foundation to construct a spectroscopic library for uncovering the identity of DNICs in biological environments as well as to determine the electronic structures of the {Fe(NO)2} core in qualitative and quantitative fashions by a wide range of spectroscopic methods. On the basis of (15)N NMR, electron paramagnetic resonance (EPR), IR, cyclic voltammetry (CV), superconducting quantum interference device (SQUID) magnetometry, UV-vis, single-crystal X-ray crystallography, and Fe/S K-edge X-ray absorption and Fe Kβ X-ray emission spectroscopies, the molecular geometry, ligation modes, nuclearity, and electronic states of the mononuclear {Fe(NO)2}(9/10) and dinuclear [{Fe(NO)2}(9/10)-{Fe(NO)2}(9/10)] DNICs could be characterized and differentiated. In addition, Fe/S K-edge X-ray absorption spectroscopy of tetrahedral DNICs deduced the qualitative assignment of Fe/NO oxidation states of {Fe(NO)2}(9) DNICs as a resonance hybrid of {Fe(II)((•)NO)(NO(-))}(9) and {Fe(III)(NO(-))2}(9) electronic states; the quantitative NO oxidation states of [(PhS)3Fe(NO)](-), [(PhS)2Fe(NO)2](-), and [(PhO)2Fe(NO)2](-) were further achieved by newly developed valence to core Fe Kβ X-ray emission spectroscopy as -0.58 ± 0.18, -0.77 ± 0.18, and -0.95 ± 0.18, respectively. The in-depth elaborations of electronic structures provide credible guidance to elucidate (a) the essential roles of DNICs modeling the degradation and repair of [Fe-S] clusters under the presence of NO, (b) transformation of DNIC into S-nitrosothiol (RSNO)/N-nitrosamine (R2NNO) and NO(+)/NO(•)/NO(-), (c) nitrite/nitrate activation producing NO regulated by redox shuttling of {Fe(NO)2}(9) and {Fe(NO)2}(10) DNICs, and (d) DNICs as H2S storage and cellular permeation pathway of DNIC/Roussin's red ester (RRE) for subsequent protein S-nitrosylation. The consolidated efforts on biomimetic synthesis, inorganic spectroscopy, chemical reactivity, and biological functions open avenues to the future designs of DNICs serving as stable inorganic NO(+)/NO(•)/NO(-) donors for pharmaceutical applications.
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Affiliation(s)
- Ming-Li Tsai
- Department of Chemistry and
Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chih-Chin Tsou
- Department of Chemistry and
Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Wen-Feng Liaw
- 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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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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45
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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
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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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46
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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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48
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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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49
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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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50
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Roche CJ, Talwar A, Palmer AF, Cabrales P, Gerfen G, Friedman JM. Evaluating the capacity to generate and preserve nitric oxide bioactivity in highly purified earthworm erythrocruorin: a giant polymeric hemoglobin with potential blood substitute properties. J Biol Chem 2014; 290:99-117. [PMID: 25371199 PMCID: PMC4281771 DOI: 10.1074/jbc.m114.583260] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The giant extracellular hemoglobin (erythrocruorin) from the earth worm (Lumbricus terrestris) has shown promise as a potential hemoglobin-based oxygen carrier (HBOC) in in vivo animal studies. An important beneficial characteristic of this hemoglobin (LtHb) is the large number of heme-based oxygen transport sites that helps overcome issues of osmotic stress when attempting to provide enough material for efficient oxygen delivery. A potentially important additional property is the capacity of the HBOC either to generate nitric oxide (NO) or to preserve NO bioactivity to compensate for decreased levels of NO in the circulation. The present study compares the NO-generating and NO bioactivity-preserving capability of LtHb with that of human adult hemoglobin (HbA) through several reactions including the nitrite reductase, reductive nitrosylation, and still controversial nitrite anhydrase reactions. An assignment of a heme-bound dinitrogen trioxide as the stable intermediate associated with the nitrite anhydrase reaction in both LtHb and HbA is supported based on functional and EPR spectroscopic studies. The role of the redox potential as a factor contributing to the NO-generating activity of these two proteins is evaluated. The results show that LtHb undergoes the same reactions as HbA and that the reduced efficacy for these reactions for LtHb relative to HbA is consistent with the much higher redox potential of LtHb. Evidence of functional heterogeneity in LtHb is explained in terms of the large difference in the redox potential of the isolated subunits.
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Affiliation(s)
- Camille J Roche
- From the Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Abhinav Talwar
- From the Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, Herricks High School, New Hyde Park, New York 11040
| | - Andre F Palmer
- William G. Lawrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, and
| | - Pedro Cabrales
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093-0412
| | - Gary Gerfen
- From the Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Joel M Friedman
- From the Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461,
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