1
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Silva JM, Cerofolini L, Carvalho AL, Ravera E, Fragai M, Parigi G, Macedo AL, Geraldes CFGC, Luchinat C. Elucidating the concentration-dependent effects of thiocyanate binding to carbonic anhydrase. J Inorg Biochem 2023; 244:112222. [PMID: 37068394 DOI: 10.1016/j.jinorgbio.2023.112222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/28/2023] [Accepted: 04/09/2023] [Indexed: 04/19/2023]
Abstract
Many proteins naturally carry metal centers, with a large share of them being in the active sites of several enzymes. Paramagnetic effects are a powerful source of structural information and, therefore, if the native metal is paramagnetic, or it can be functionally substituted with a paramagnetic one, paramagnetic effects can be used to study the metal sites, as well as the overall structure of the protein. One notable example is cobalt(II) substitution for zinc(II) in carbonic anhydrase. In this manuscript we investigate the effects of sodium thiocyanate on the chemical environment of the metal ion of the human carbonic anhydrase II. The electron paramagnetic resonance (EPR) titration of the cobalt(II) protein with thiocyanate shows that the EPR spectrum changes from A-type to C-type on passing from 1:1 to 1:1000-fold ligand excess. This indicates the occurrence of a change in the electronic structure, which may reflect a sizable change in the metal coordination environment in turn caused by a modification of the frozen solvent glass. However, paramagnetic nuclear magnetic resonance (NMR) data indicate that the metal coordination cage remains unperturbed even in 1:1000-fold ligand excess. This result proves that the C-type EPR spectrum observed at large ligand concentration should be ascribed to the low temperature at which EPR measurements are performed, which impacts on the structure of the protein when it is destabilized by a high concentration of a chaotropic agent.
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Affiliation(s)
- José Malanho Silva
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy; UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
| | - Ana Luísa Carvalho
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, 50019, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, 50019, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, 50019, Italy
| | - Anjos L Macedo
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
| | - Carlos F G C Geraldes
- Department of Life Sciences, Faculty of Science and Technology, 3000-393 Coimbra, Portugal; Coimbra Chemistry Center- Institute of Molecular Sciences (CCC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, 50019, Italy; Giotto Biotech, S.R.L, Sesto Fiorentino, Florence 50019, Italy.
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2
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GLB-3: A resilient, cysteine-rich, membrane-tethered globin expressed in the reproductive and nervous system of Caenorhabditis elegans. J Inorg Biochem 2023; 238:112063. [PMID: 36370505 DOI: 10.1016/j.jinorgbio.2022.112063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/31/2022] [Accepted: 10/31/2022] [Indexed: 11/05/2022]
Abstract
The popular genetic model organism Caenorhabditis elegans (C. elegans) encodes 34 globins, whereby the few that are well-characterized show divergent properties besides the typical oxygen carrier function. Here, we present a biophysical characterization and expression analysis of C. elegans globin-3 (GLB-3). GLB-3 is predicted to exist in two isoforms and is expressed in the reproductive and nervous system. Knockout of this globin causes a 99% reduction in fertility and reduced motility. Spectroscopic analysis reveals that GLB-3 exists as a bis-histidyl-ligated low-spin form in both the ferrous and ferric heme form. A function in binding of diatomic gases is excluded on the basis of the slow CO-binding kinetics. Unlike other globins, GLB-3 is also not capable of reacting with H2O2, H2S, and nitrite. Intriguingly, not only does GLB-3 contain a high number of cysteine residues, it is also highly stable under harsh conditions (pH = 2 and high concentrations of H2O2). The resilience diminishes when the N- and C-terminal extensions are removed. Redox potentiometric measurements reveal a slightly positive redox potential (+8 ± 19 mV vs. SHE), suggesting that the heme iron may be able to oxidize cysteines. Electron paramagnetic resonance shows that formation of an intramolecular disulphide bridge, involving Cys70, affects the heme-pocket region. The results suggest an involvement of the globin in (cysteine) redox chemistry.
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3
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De Simone G, Sbardella D, Oddone F, Pesce A, Coletta M, Ascenzi P. Structural and (Pseudo-)Enzymatic Properties of Neuroglobin: Its Possible Role in Neuroprotection. Cells 2021; 10:cells10123366. [PMID: 34943874 PMCID: PMC8699588 DOI: 10.3390/cells10123366] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 12/17/2022] Open
Abstract
Neuroglobin (Ngb), the third member of the globin family, was discovered in human and murine brains in 2000. This monomeric globin is structurally similar to myoglobin (Mb) and hemoglobin (Hb) α and β subunits, but it hosts a bis-histidyl six-coordinated heme-Fe atom. Therefore, the heme-based reactivity of Ngb is modulated by the dissociation of the distal HisE7-heme-Fe bond, which reflects in turn the redox state of the cell. The high Ngb levels (~100–200 μM) present in the retinal ganglion cell layer and in the optic nerve facilitate the O2 buffer and delivery. In contrast, the very low levels of Ngb (~1 μM) in most tissues and organs support (pseudo-)enzymatic properties including NO/O2 metabolism, peroxynitrite and free radical scavenging, nitrite, hydroxylamine, hydrogen sulfide reduction, and the nitration of aromatic compounds. Here, structural and (pseudo-)enzymatic properties of Ngb, which are at the root of tissue and organ protection, are reviewed, envisaging a possible role in the protection from neuronal degeneration of the retina and the optic nerve.
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Affiliation(s)
- Giovanna De Simone
- Dipartimento di Scienze, Università Roma Tre, Viale Marconi 446, 00146 Roma, Italy;
| | | | | | - Alessandra Pesce
- Dipartimento di Fisica, Università di Genova, Via Dodecaneso 33, 16100 Genova, Italy;
| | - Massimo Coletta
- IRCCS Fondazione Bietti, 00198 Roma, Italy; (D.S.); (F.O.)
- Dipartmento di Scienze Cliniche e Medicina Traslazionale, Università di Roma “Tor Vergata”, Via Montpellier 1, 00133 Roma, Italy
- Correspondence: (M.C.); (P.A.); Tel.: +39-06-72596365 (M.C.); +39-06-57336321 (P.A.)
| | - Paolo Ascenzi
- Dipartimento di Scienze, Università Roma Tre, Viale Marconi 446, 00146 Roma, Italy;
- Accademia Nazionale dei Lincei, Via della Lungara 10, 00165 Roma, Italy
- Unità di Neuroendocrinologia, Metabolismo e Neurofarmacologia, IRCSS Fondazione Santa Lucia, 00179 Roma, Italy
- Correspondence: (M.C.); (P.A.); Tel.: +39-06-72596365 (M.C.); +39-06-57336321 (P.A.)
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4
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Chen JH, Yu LJ, Boussac A, Wang-Otomo ZY, Kuang T, Shen JR. Properties and structure of a low-potential, penta-heme cytochrome c 552 from a thermophilic purple sulfur photosynthetic bacterium Thermochromatium tepidum. PHOTOSYNTHESIS RESEARCH 2019; 139:281-293. [PMID: 29691716 DOI: 10.1007/s11120-018-0507-y] [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: 02/28/2018] [Accepted: 03/30/2018] [Indexed: 06/08/2023]
Abstract
The thermophilic purple sulfur bacterium Thermochromatium tepidum possesses four main water-soluble redox proteins involved in the electron transfer behavior. Crystal structures have been reported for three of them: a high potential iron-sulfur protein, cytochrome c', and one of two low-potential cytochrome c552 (which is a flavocytochrome c) have been determined. In this study, we purified another low-potential cytochrome c552 (LPC), determined its N-terminal amino acid sequence and the whole gene sequence, characterized it with absorption and electron paramagnetic spectroscopy, and solved its high-resolution crystal structure. This novel cytochrome was found to contain five c-type hemes. The overall fold of LPC consists of two distinct domains, one is the five heme-containing domain and the other one is an Ig-like domain. This provides a representative example for the structures of multiheme cytochromes containing an odd number of hemes, although the structures of multiheme cytochromes with an even number of hemes are frequently seen in the PDB database. Comparison of the sequence and structure of LPC with other proteins in the databases revealed several characteristic features which may be important for its functioning. Based on the results obtained, we discuss the possible intracellular function of this LPC in Tch. tepidum.
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Affiliation(s)
- Jing-Hua Chen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20, Nanxincun, Xiangshan, Beijing, 100093, China
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
- University of Chinese Academy of Sciences, Yuquan Rd, Shijingshan District, Beijing, 100049, China
| | - Long-Jiang Yu
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Alain Boussac
- I2BC, SB2SM, CNRS UMR 9198, CEA Saclay, 91191, Gif-sur-Yvette, France
| | | | - Tingyun Kuang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20, Nanxincun, Xiangshan, Beijing, 100093, China
| | - Jian-Ren Shen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20, Nanxincun, Xiangshan, Beijing, 100093, China.
- Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan.
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5
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Bellei M, Bortolotti CA, Di Rocco G, Borsari M, Lancellotti L, Ranieri A, Sola M, Battistuzzi G. The influence of the Cys46/Cys55 disulfide bond on the redox and spectroscopic properties of human neuroglobin. J Inorg Biochem 2018; 178:70-86. [DOI: 10.1016/j.jinorgbio.2017.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/21/2017] [Accepted: 10/09/2017] [Indexed: 12/21/2022]
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6
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Van Doorslaer S, Cuypers B. Electron paramagnetic resonance of globin proteins – a successful match between spectroscopic development and protein research. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1392629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Bert Cuypers
- Department of Physics, University of Antwerp, Antwerp, Belgium
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7
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Ascenzi P, di Masi A, Leboffe L, Fiocchetti M, Nuzzo MT, Brunori M, Marino M. Neuroglobin: From structure to function in health and disease. Mol Aspects Med 2016; 52:1-48. [DOI: 10.1016/j.mam.2016.10.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 10/27/2016] [Accepted: 10/27/2016] [Indexed: 01/01/2023]
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8
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Guidolin D, Tortorella C, Marcoli M, Maura G, Agnati LF. Neuroglobin, a Factor Playing for Nerve Cell Survival. Int J Mol Sci 2016; 17:ijms17111817. [PMID: 27809238 PMCID: PMC5133818 DOI: 10.3390/ijms17111817] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/14/2016] [Accepted: 10/26/2016] [Indexed: 12/17/2022] Open
Abstract
Cell death represents the final outcome of several pathological conditions of the central nervous system and available evidence suggests that in both acute injuries and neurodegenerative diseases it is often associated with mitochondrial dysfunction. Thus, the possibility to prevent mitochondrial events involved in cell death might represent efficient tools to limit neuronal damage. In recent years, increased attention has been paid to the endogenous protein neuroglobin, since accumulating evidence showed that its high expression was associated with preserved mitochondrial function and to an increased survival of nerve cells in vitro and in vivo in a variety of experimental models of cell insult. The biological and structural features of neuroglobin and the mitochondria-related mechanisms of neuroglobin-induced neuroprotection will be here briefly discussed. In this respect, the inhibition of the intrinsic pathway of apoptosis emerges as a key neuroprotective effect induced by the protein. These findings could open the possibility to develop efficient neuroglobin-mediated therapeutic strategies aimed at minimizing the neuronal cell death occurring in impacting neurological pathologies like stroke and neurodegenerative diseases.
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Affiliation(s)
- Diego Guidolin
- Department of Neuroscience, University of Padova, Padova 35122, Italy.
| | - Cinzia Tortorella
- Department of Neuroscience, University of Padova, Padova 35122, Italy.
| | - Manuela Marcoli
- Department of Pharmacy and Center of Excellence for Biomedical Research, University of Genova, Genova 16126, Italy.
| | - Guido Maura
- Department of Pharmacy and Center of Excellence for Biomedical Research, University of Genova, Genova 16126, Italy.
| | - Luigi F Agnati
- Department of Biomedical Sciences, University of Modena and Reggio Emilia, Modena 41121, Italy.
- Department of Neuroscience, Karolinska Institutet, Stockholm 17177, Sweden.
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9
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Trashin S, de Jong M, Luyckx E, Dewilde S, De Wael K. Electrochemical Evidence for Neuroglobin Activity on NO at Physiological Concentrations. J Biol Chem 2016; 291:18959-66. [PMID: 27402851 DOI: 10.1074/jbc.m116.730176] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Indexed: 11/06/2022] Open
Abstract
The true function of neuroglobin (Ngb) and, particularly, human Ngb (NGB) has been under debate since its discovery 15 years ago. It has been expected to play a role in oxygen binding/supply, but a variety of other functions have been put forward, including NO dioxygenase activity. However, in vitro studies that could unravel these potential roles have been hampered by the lack of an Ngb-specific reductase. In this work, we used electrochemical measurements to investigate the role of an intermittent internal disulfide bridge in determining NO oxidation kinetics at physiological NO concentrations. The use of a polarized electrode to efficiently interconvert the ferric (Fe(3+)) and ferrous (Fe(2+)) forms of an immobilized NGB showed that the disulfide bridge both defines the kinetics of NO dioxygenase activity and regulates appearance of the free ferrous deoxy-NGB, which is the redox active form of the protein in contrast to oxy-NGB. Our studies further identified a role for the distal histidine, interacting with the hexacoordinated iron atom of the heme, in oxidation kinetics. These findings may be relevant in vivo, for example, in blocking apoptosis by reduction of ferric cytochrome c, and gentle tuning of NO concentration in the tissues.
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Affiliation(s)
| | | | - Evi Luyckx
- Biomedical Sciences, University of Antwerp, 2010 Antwerp, Belgium
| | - Sylvia Dewilde
- Biomedical Sciences, University of Antwerp, 2010 Antwerp, Belgium
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10
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Kleingardner JG, Bowman SEJ, Bren KL. The influence of heme ruffling on spin densities in ferricytochromes c probed by heme core 13C NMR. Inorg Chem 2013; 52:12933-46. [PMID: 24187968 DOI: 10.1021/ic401250d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The heme in cytochromes c undergoes a conserved out-of-plane distortion known as ruffling. For cytochromes c from the bacteria Hydrogenobacter thermophilus and Pseudomonas aeruginosa , NMR and EPR spectra have been shown to be sensitive to the extent of heme ruffling and to provide insights into the effect of ruffling on the electronic structure. Through the use of mutants of each of these cytochromes that differ in the amount of heme ruffling, NMR characterization of the low-spin (S = ½) ferric proteins has confirmed and refined the developing understanding of how ruffling influences the spin distribution on heme. The chemical shifts of the core heme carbons were obtained through site-specific labeling of the heme via biosynthetic incorporation of (13)C-labeled 5-aminolevulinic acid derivatives. Analysis of the contact shifts of these core heme carbons allowed Fermi contact spin densities to be estimated and changes upon ruffling to be evaluated. The results allow a deconvolution of the contributions to heme hyperfine shifts and a test of the influence of heme ruffling on the electronic structure and hyperfine shifts. The data indicate that as heme ruffling increases, the spin densities on the β-pyrrole carbons decrease while the spin densities on the α-pyrrole carbons and meso carbons increase. Furthermore, increased ruffling is associated with stronger bonding to the heme axial His ligand.
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Affiliation(s)
- Jesse G Kleingardner
- Department of Chemistry, University of Rochester , Rochester, New York 14627-0216, United States
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11
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Van Leuven W, Cuypers B, Desmet F, Giordano D, Verde C, Moens L, Van Doorslaer S, Dewilde S. Is the heme pocket region modulated by disulfide-bridge formation in fish and amphibian neuroglobins as in humans? BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1757-63. [PMID: 23403147 DOI: 10.1016/j.bbapap.2013.01.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 01/25/2013] [Accepted: 01/29/2013] [Indexed: 12/17/2022]
Abstract
Neuroglobin, a globin characterized by a bis-histidine ligation of the heme iron, has been identified in mammalian and non-mammalian vertebrates, including fish, amphibians and reptiles. In human neuroglobin, the presence of an internal disulfide bond in the CD loop (CD7-D5) is found to modulate the ligand binding through a change in the heme pocket structure. Although the neuroglobin sequences mostly display conserved Cys at positions CD7, D5 and G18/19, a number of exceptions are known. In this study, neuroglobins from amphibian (Xenopus tropicalis) and fish (Chaenocephalus aceratus, Dissostichus mawsoni and Danio rerio) are investigated using electron paramagnetic resonance and optical absorption spectroscopy. All these neuroglobins differ from human neuroglobin in their Cys-positions. It is demonstrated that if disulfide bonds are formed in fish and amphibian neuroglobins, the reduction of these bonds does not result in alteration of the heme pocket in these globins. Furthermore, it is shown that mutagenesis of the Cys residues of X. tropicalis neuroglobin influences the protein structure. The amphibian neuroglobin is also found to be more resistant to H2O2-induced denaturation than the other neuroglobins under study, although all show an overall large stability in high concentrations of this oxidant. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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Affiliation(s)
- Wendy Van Leuven
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
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12
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Bocahut A, Derrien V, Bernad S, Sebban P, Sacquin-Mora S, Guittet E, Lescop E. Heme orientation modulates histidine dissociation and ligand binding kinetics in the hexacoordinated human neuroglobin. J Biol Inorg Chem 2012; 18:111-22. [PMID: 23135388 PMCID: PMC3535368 DOI: 10.1007/s00775-012-0956-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 10/21/2012] [Indexed: 11/05/2022]
Abstract
Neuroglobin (Ngb) is a globin present in the brain and retina of mammals. This hexacoordinated hemoprotein binds small diatomic molecules, albeit with lower affinity compared with other globins. Another distinctive feature of most mammalian Ngb is their ability to form an internal disulfide bridge that increases ligand affinity. As often seen for prosthetic heme b containing proteins, human Ngb exhibits heme heterogeneity with two alternative heme orientations within the heme pocket. To date, no details are available on the impact of heme orientation on the binding properties of human Ngb and its interplay with the cysteine oxidation state. In this work, we used 1H NMR spectroscopy to probe the cyanide binding properties of different Ngb species in solution, including wild-type Ngb and the single (C120S) and triple (C46G/C55S/C120S) mutants. We demonstrate that in the disulfide-containing wild-type protein cyanide ligation is fivefold faster for one of the two heme orientations (the A isomer) compared with the other isomer, which is attributed to the lower stability of the distal His64–iron bond and reduced steric hindrance at the bottom of the cavity for heme sliding in the A conformer. We also attribute the slower cyanide reactivity in the absence of a disulfide bridge to the tighter histidine–iron bond. More generally, enhanced internal mobility in the CD loop bearing the disulfide bridge hinders access of the ligand to heme iron by stabilizing the histidine–iron bond. The functional impact of heme disorder and cysteine oxidation state on the properties of the Ngb ligand is discussed.
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Affiliation(s)
- Anthony Bocahut
- Laboratoire de Chimie Physique, UMR 8000, CNRS, Université Paris-Sud 11, Bât. 350, 91405 Orsay, France
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13
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Chen Y, Naik SG, Krzystek J, Shin S, Nelson WH, Xue S, Yang JJ, Davidson VL, Liu A. Role of calcium in metalloenzymes: effects of calcium removal on the axial ligation geometry and magnetic properties of the catalytic diheme center in MauG. Biochemistry 2012; 51:1586-97. [PMID: 22320333 DOI: 10.1021/bi201575f] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
MauG is a diheme enzyme possessing a five-coordinate high-spin heme with an axial His ligand and a six-coordinate low-spin heme with His-Tyr axial ligation. A Ca(2+) ion is linked to the two hemes via hydrogen bond networks, and the enzyme activity depends on its presence. Removal of Ca(2+) altered the electron paramagnetic resonance (EPR) signals of each ferric heme such that the intensity of the high-spin heme was decreased and the low-spin heme was significantly broadened. Addition of Ca(2+) back to the sample restored the original EPR signals and enzyme activity. The molecular basis for this Ca(2+)-dependent behavior was studied by magnetic resonance and Mössbauer spectroscopy. The results show that in the Ca(2+)-depleted MauG the high-spin heme was converted to a low-spin heme and the original low-spin heme exhibited a change in the relative orientations of its two axial ligands. The properties of these two hemes are each different than those of the heme in native MauG and are now similar to each other. The EPR spectrum of Ca(2+)-free MauG appears to describe one set of low-spin ferric heme signals with a large g(max) and g anisotropy and a greatly altered spin relaxation property. Both EPR and Mössbauer spectroscopic results show that the two hemes are present as unusual highly rhombic low-spin hemes in Ca(2+)-depleted MauG, with a smaller orientation angle between the two axial ligand planes. These findings provide insight into the correlation of enzyme activity with the orientation of axial heme ligands and describe a role for the calcium ion in maintaining this structural orientation that is required for activity.
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Affiliation(s)
- Yan Chen
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
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14
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Ioanitescu AI, Doorslaer SV, Dewilde S, Endeward B, Moens L. Probing the heme-pocket structure of the paramagnetic forms of cytoglobin and a distal histidine mutant using electron paramagnetic resonance. Mol Phys 2010. [DOI: 10.1080/00268970701616030] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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15
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Structure and reactivity of hexacoordinate hemoglobins. Biophys Chem 2010; 152:1-14. [PMID: 20933319 DOI: 10.1016/j.bpc.2010.08.008] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 08/20/2010] [Accepted: 08/21/2010] [Indexed: 01/07/2023]
Abstract
The heme prosthetic group in hemoglobins is most often attached to the globin through coordination of either one or two histidine side chains. Those proteins with one histidine coordinating the heme iron are called "pentacoordinate" hemoglobins, a group represented by red blood cell hemoglobin and most other oxygen transporters. Those with two histidines are called "hexacoordinate hemoglobins", which have broad representation among eukaryotes. Coordination of the second histidine in hexacoordinate Hbs is reversible, allowing for binding of exogenous ligands like oxygen, carbon monoxide, and nitric oxide. Research over the past several years has produced a fairly detailed picture of the structure and biochemistry of hexacoordinate hemoglobins from several species including neuroglobin and cytoglobin in animals, and the nonsymbiotic hemoglobins in plants. However, a clear understanding of the physiological functions of these proteins remains an elusive goal.
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16
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Molecular modeling and dynamics simulation of a histidine-tagged cytochrome b 5. J Mol Model 2010; 17:971-8. [DOI: 10.1007/s00894-010-0795-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Accepted: 06/25/2010] [Indexed: 12/17/2022]
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17
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Chuang PY, Conley YP, Poloyac SM, Okonkwo DO, Ren D, Sherwood PR, Hravnak M, Alexander SA. Neuroglobin genetic polymorphisms and their relationship to functional outcomes after traumatic brain injury. J Neurotrauma 2010; 27:999-1006. [PMID: 20345238 PMCID: PMC2943497 DOI: 10.1089/neu.2009.1129] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Neuroglobin has shown rich neuroprotective effects against cerebral hypoxia, and therefore has the potential to impact outcomes after traumatic brain injury (TBI). However, to date an association between genetic variation within the human neuroglobin (NGB) gene and recovery post-TBI has not been reported. The purpose of this study was to explore the relationship between NGB genotypes and outcomes (as assessed by the Glasgow Outcome Scale [GOS], the Disability Rating Scale [DRS], and the Neurobehavioral Rating Scale-Revised [NRS-R]) after severe TBI. Genotyping using TaqMan allele discrimination for two tagging single nucleotide polymorphisms (tSNPs) that represent the two haplotype blocks for NGB (rs3783988 and rs10133981) was completed on DNA obtained from 196 Caucasian patients recovering from severe TBI. Patients were dichotomized based on the presence of the variant allele for each tSNP. Chi-square and Fisher's exact tests were used to compare characteristics between groups. Multivariate linear regression was used to examine NGB tSNPs and recovery from severe TBI. Subjects with the TT genotype (wild-type) for rs3783988 were more likely to have better GOS and DRS scores at 3, 6, 12, and 24 months, while rs10133981 genotype was not significantly related to functional outcome. After controlling for age, gender, and Glasgow Coma Scale (GCS) score, those subjects with the rs3783988 TT genotype had more than a 2.65-times greater likelihood of better functional outcomes than individuals with genotypes harboring a variant allele. Data suggest that the haplotype block represented by rs3783988 in NGB appears to influence recovery after severe TBI. Represented within this haplotype block of NGB is the region that codes for the oxygen-binding portion of NGB.
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Affiliation(s)
- Pei-Ying Chuang
- Acute/Tertiary Care Department, Health Promotion and Development, School of Nursing, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA.
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Xu J, Li L, Yin G, Li H, Du W. Ligand orientation of human neuroglobin obtained from solution NMR and molecular dynamics simulation as compared with X-ray crystallography. J Inorg Biochem 2009; 103:1693-701. [PMID: 19850349 DOI: 10.1016/j.jinorgbio.2009.09.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Revised: 09/17/2009] [Accepted: 09/21/2009] [Indexed: 10/20/2022]
Abstract
Neuroglobin, a new member of hemoprotein family, can reversibly bind oxygen and take part in many biological processes such as enzymatic reaction, signal transduction and the mitochondria function. Different from myoglobin and hemoglobin, it has a hexacoordinated heme environment, with histidyl imidazole of proximal His(96)(F8) and distal His(64)(E7) directly bound to the metal ion. In the present work, solution (1)H NMR spectroscopy was employed to investigate the electronic structure of heme center of wild-type met-human neuroglobin. The resonances of heme protons and key residues in the heme pocket were assigned. Two heme orientations resulting from a 180 degrees rotation about the alpha-gamma-meso axis with a population ratio about 2:1 were observed. Then the (1)H NMR chemical shifts of the ferriheme methyl groups were used to predict orientations of the axial ligand. The obtained axial ligand plane angle phi is consistent with that from the molecular dynamics simulation but not with those from the crystal data. Compared with mouse neuroglobin, the obtained average ligand orientation of human neuroglobin reflects the changeability of heme environment for the Ngb family.
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Affiliation(s)
- Jia Xu
- Department of Chemistry, Renmin University of China, Beijing 100872, China
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19
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Davis MF, Gracz H, Vendeix FAP, de Serrano V, Somasundaram A, Decatur SM, Franzen S. Different Modes of Binding of Mono-, Di-, and Trihalogenated Phenols to the Hemoglobin Dehaloperoxidase from Amphitrite ornata. Biochemistry 2009; 48:2164-72. [DOI: 10.1021/bi801568s] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael F. Davis
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27606, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27606, and Chemistry Department, Oberlin College, Oberlin, Ohio 44074
| | - Hanna Gracz
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27606, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27606, and Chemistry Department, Oberlin College, Oberlin, Ohio 44074
| | - Franck A. P. Vendeix
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27606, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27606, and Chemistry Department, Oberlin College, Oberlin, Ohio 44074
| | - Vesna de Serrano
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27606, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27606, and Chemistry Department, Oberlin College, Oberlin, Ohio 44074
| | - Aswin Somasundaram
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27606, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27606, and Chemistry Department, Oberlin College, Oberlin, Ohio 44074
| | - Sean M. Decatur
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27606, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27606, and Chemistry Department, Oberlin College, Oberlin, Ohio 44074
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27606, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27606, and Chemistry Department, Oberlin College, Oberlin, Ohio 44074
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Fufezan C, Zhang J, Gunner MR. Ligand preference and orientation in b- and c-type heme-binding proteins. Proteins 2008; 73:690-704. [PMID: 18491383 DOI: 10.1002/prot.22097] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Hemes are often incorporated into designed proteins. The importance of the heme ligand type and its orientation is still a matter of debate. Here, heme ligands and ligand orientation were investigated using a nonredundant (87 structures) and a redundant (1503 structures) set of structures to compare and contrast design features of natural b- and c-type heme-binding proteins. Histidine is the most common ligand. Marked differences in ligation motifs between b- and c-type hemes are higher occurrence of His-Met in c-type heme binding motifs (16.4% vs. 1.4%) and higher occurrence of exchangeable, small molecules in b-type heme binding motifs (67.6% vs. 9.9%). Histidine ligands that are part of the c-type CXXCH heme-binding motif show a distinct asymmetric distribution of orientation. They tend to point between either the heme propionates or between the NA and NB heme nitrogens. Molecular mechanics calculations show that this asymmetry is due to the bonded constraints of the covalent attachment between the heme and the protein. In contrast, the orientations of b-type hemes histidine ligands are found evenly distributed with no preference. Observed histidine heme ligand orientations show no dominating influence of electrostatic interactions between the heme propionates and the ligands. Furthermore, ligands in bis-His hemes are found more frequently perpendicular rather than parallel to each other. These correlations support energetic constraints on ligands that can be used in designing proteins.
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Affiliation(s)
- Christian Fufezan
- Physics Department, City College of New York, New York, New York 10031, USA.
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Solution 1H NMR study of the active site structure for the double mutant H64Q/V68F cyanide complex from mouse neuroglobin. Biophys Chem 2008; 136:115-23. [DOI: 10.1016/j.bpc.2008.05.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Revised: 05/12/2008] [Accepted: 05/12/2008] [Indexed: 11/20/2022]
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Yatsunyk LA, Dawson A, Carducci MD, Nichol GS, Walker FA. Models of the cytochromes: crystal structures and EPR spectral characterization of low-spin bis-imidazole complexes of (OETPP)Fe(III) having intermediate ligand plane dihedral angles. Inorg Chem 2007; 45:5417-28. [PMID: 16813405 DOI: 10.1021/ic060283h] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The preparation, EPR spectra, and crystal structures of octaethyltetraphenylporphyrinatoiron(III) having two imidazole, N-benzylimidazole, and N-methylimidazole axial ligands are reported, [(OETPP)Fe(HIm)2]Cl, [(OETPP)Fe(N-BzIm)2]Cl, and [(OETPP)Fe(N-MeIm)2]Cl. Despite large variation in axial ligand size, the unit cell parameters for all complexes are very similar; each structure has the same basic motif, with large voids formed by the extended porphyrin framework (filled by ordered or disordered axial ligands and disordered solvent), which allows differently sized ligands to fit within the same cell dimensions. Each porphyrin core adopts a saddled conformation with absolute value(deltaC(beta)) = 1.13-1.15 A. The dihedral angles between axial ligand planes, delta phi, are far from being either ideal parallel or perpendicular: 30.1 degrees, 57.2 degrees for [(OETPP)Fe(HIm)2]Cl (molecules 1 and 2), 56.8 degrees for [(OETPP)Fe(N-BzIm)(2)]Cl, and 16.0 degrees, 44.6 degrees, 59.6 degrees, and 88.1 degrees for [(OETPP)Fe(N-MeIm)2]Cl, which has disordered axial ligands. Among the complexes of this study, an axial ligand delta phi of 56.8 degrees is found to be the largest "parallel" angle (as defined by the observation of a normal rhombic or Type II EPR signal (N-BzIm, g = 3.08, 2.19, 1.31)), while 57.2 degrees is found to be the smallest "perpendicular" delta phi (as defined by the observation of a "large gmax" or Type I EPR signal (HIm, gmax = 3.24)). From the results of this study, it is clear that the size of the largest g for Types I and II complexes varies continuously, with no break between the two. While the switch in EPR signal type, from Type II to Type I, appears to be very sharp in this study, this may be somewhat artificial based upon limited numbers of examples and the required saddle distortion of the (OETPP)Fe(III) complexes. However, in comparison to several proteins with dihedral angles near 60 degrees and Type II EPR spectra, we may conclude that the switch in EPR signal type occurs near 57 degrees +/- 3-5 degrees.
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Affiliation(s)
- Liliya A Yatsunyk
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721-0041, USA
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Shokhireva TK, Weichsel A, Smith KM, Berry RE, Shokhirev NV, Balfour CA, Zhang H, Montfort WR, Walker FA. Assignment of the ferriheme resonances of the low-spin complexes of nitrophorins 1 and 4 by (1)H and (13)C NMR spectroscopy: comparison to structural data obtained from X-ray crystallography. Inorg Chem 2007; 46:2041-56. [PMID: 17290983 PMCID: PMC2587420 DOI: 10.1021/ic061408l] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work we report the assignment of the majority of the ferriheme resonances of low-spin nitrophorins (NP) 1 and 4 and compare them to those of NP2, published previously. It is found that the structure of the ferriheme complexes of NP1 and NP4, in terms of the orientation of the ligand(s), can be determined with good accuracy by NMR techniques in the low-spin forms and that angle plots proposed previously (Shokhirev, N. V.; Walker, F. A. J. Biol. Inorg. Chem. 1998, 3, 581-594) describe the angle of the effective nodal plane of the axial ligands in solution. The effective nodal plane of low-spin NP1, NP4, and NP2 complexes is in all cases of imidazole and histamine complexes quite similar to the average of the His-59 or -57 and the exogenous ligand angles seen in the X-ray crystal structures. For the cyanide complexes of the nitrophorins, however, the effective nodal plane of the axial ligand does not coincide with the actual histidine-imidazole plane orientation. This appears to be a result of the contribution of an additional source of asymmetry, the orientation of one of the zero-ruffling lines of the heme. Probably this effect exists for the imidazole and histamine complexes as well, but because the effect of asymmetry that occurs from planar exogenous axial ligands is much larger than the effect of heme ruffling the effect of the zero-ruffling line can only be detected for the cyanide complexes, where the only ligand plane is that of the proximal histidine. The three-dimensional structures of the three NP-CN complexes, including that of NP2-CN reported herein, confirm the high degree of ruffling of these complexes. There is an equilibrium between the two heme orientations (A and B) that depends on the heme cavity shape and changes somewhat with exogenous axial ligand. The A:B ratio can be much more accurately measured by NMR spectroscopy than by X-ray crystallography.
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Affiliation(s)
- Tatiana Kh Shokhireva
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, USA
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Shokhireva TK, Smith KM, Berry RE, Shokhirev NV, Balfour CA, Zhang H, Walker FA. Assignment of the ferriheme resonances of the high-spin forms of nitrophorins 1 and 4 by 1H NMR spectroscopy: comparison to structural data obtained from X-ray crystallography. Inorg Chem 2007; 46:170-8. [PMID: 17198425 PMCID: PMC2518634 DOI: 10.1021/ic061407t] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, we report the assignment of the majority of the ferriheme resonances of high-spin nitrophorins (NPs) 1 and 4 and compare them to those of NP2, published previously. It is found that the structures of the ferriheme complexes of NP1 and NP4, in terms of the orientation of the histidine imidazole ligand, can be described with good accuracy by NMR techniques and that the angle plot proposed previously for the high-spin form of the NPs (Shokhireva, T. Kh.; Shokhirev, N. V.; Walker, F. A. Biochemistry 2003, 42, 679-693) describes the angle of the effective nodal plane of the axial histidine imidazole in solution. There is an equilibrium between the two heme orientations (A and B), which depends on the heme cavity shape, which can be altered by mutation of amino acids with side chains (phenyl vs tyrosyl) near the potential position where a heme vinyl group would be in one of the isomers. The A:B ratio can be much more accurately measured by NMR spectroscopy than by X-ray crystallography.
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