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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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2
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A Pathfinder in High-Pressure Bioscience: In Memoriam of Gaston Hui Bon Hoa. BIOLOGY 2021; 10:biology10080778. [PMID: 34440010 PMCID: PMC8389544 DOI: 10.3390/biology10080778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 11/23/2022]
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3
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Daane JM, Giordano D, Coppola D, di Prisco G, Detrich HW, Verde C. Adaptations to environmental change: Globin superfamily evolution in Antarctic fishes. Mar Genomics 2019; 49:100724. [PMID: 31735579 DOI: 10.1016/j.margen.2019.100724] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 10/27/2019] [Accepted: 11/01/2019] [Indexed: 02/08/2023]
Abstract
The ancient origins and functional versatility of globins make them ideal subjects for studying physiological adaptation to environmental change. Our goals in this review are to describe the evolution of the vertebrate globin gene superfamily and to explore the structure/function relationships of hemoglobin, myoglobin, neuroglobin and cytoglobin in teleost fishes. We focus on the globins of Antarctic notothenioids, emphasizing their adaptive features as inferred from comparisons with human proteins. We dedicate this review to Guido di Prisco, our co-author, colleague, friend, and husband of C.V. Ever thoughtful, creative, and enthusiastic, Guido spearheaded study of the structure, function, and evolution of the hemoglobins of polar fishes - this review is testimony to his wide-ranging contributions. Throughout his career, Guido inspired younger scientists to embrace polar biological research, and he challenged researchers of all ages to explore evolutionary adaptation in the context of global climate change. Beyond his scientific contributions, we will miss his warmth, his culture, and his great intellect. Guido has left an outstanding legacy, one that will continue to inspire us and our research.
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Affiliation(s)
- Jacob M Daane
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA 01908, USA
| | - Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, 80131 Napoli, Italy; Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Daniela Coppola
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, 80131 Napoli, Italy; Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Guido di Prisco
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - H William Detrich
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA 01908, USA
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, 80131 Napoli, Italy; Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy.
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4
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Colloc'h N, Carpentier P, Montemiglio LC, Vallone B, Prangé T. Mapping Hydrophobic Tunnels and Cavities in Neuroglobin with Noble Gas under Pressure. Biophys J 2017; 113:2199-2206. [PMID: 29108649 DOI: 10.1016/j.bpj.2017.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/12/2017] [Accepted: 10/06/2017] [Indexed: 01/27/2023] Open
Abstract
Internal cavities are crucial for conformational flexibility of proteins and can be mapped through noble gas diffusion and docking. Here we investigate the hydrophobic cavities and tunnel network in neuroglobin (Ngb), a hexacoordinated heme protein likely to be involved in neuroprotection, using crystallography under noble gas pressure, mostly at room temperature. In murine Ngb, a large internal cavity is involved in the heme sliding mechanism to achieve binding of gaseous ligands through coordination to the heme iron. In this study, we report that noble gases are hosted by two major sites within the internal cavity. We propose that these cavities could store oxygen and allow its relay in the heme proximity, which could correspond to NO location in the nitrite-reductase function of Ngb. Thanks to a recently designed pressurization cell using krypton at high pressure, a new gas binding site has been characterized that reveals an alternate pathway for gaseous ligands. A new gas binding site on the proximal side of the heme has also been characterized, using xenon pressure on a Ngb mutant (V140W) that binds CO with a similar rate and affinity to the wild-type, despite a reshaping of the internal cavity. Moreover, this study, to our knowledge, provides new insights into the determinants of the heme sliding mechanism, suggesting that the shift at the beginning of helix G precedes and drives this process.
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Affiliation(s)
- Nathalie Colloc'h
- ISTCT CNRS UNICAEN CEA Normandie University, CERVOxy Team, Centre Cyceron, Caen, France.
| | - Philippe Carpentier
- CEA/DRF/BIG/CBM/BioCat LCBM CNRS UMR 5249, Université Grenoble Alpes, Grenoble, France; European Synchrotron Radiation Facility, Grenoble, France
| | - Laura C Montemiglio
- Instituto Pasteur-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Roma, Italy
| | - Beatrice Vallone
- Instituto Pasteur-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Roma, Italy
| | - Thierry Prangé
- LCRB, UMR 8015 CNRS Université Paris Descartes, Paris, France
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5
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Gell DA. Structure and function of haemoglobins. Blood Cells Mol Dis 2017; 70:13-42. [PMID: 29126700 DOI: 10.1016/j.bcmd.2017.10.006] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 10/29/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022]
Abstract
Haemoglobin (Hb) is widely known as the iron-containing protein in blood that is essential for O2 transport in mammals. Less widely recognised is that erythrocyte Hb belongs to a large family of Hb proteins with members distributed across all three domains of life-bacteria, archaea and eukaryotes. This review, aimed chiefly at researchers new to the field, attempts a broad overview of the diversity, and common features, in Hb structure and function. Topics include structural and functional classification of Hbs; principles of O2 binding affinity and selectivity between O2/NO/CO and other small ligands; hexacoordinate (containing bis-imidazole coordinated haem) Hbs; bacterial truncated Hbs; flavohaemoglobins; enzymatic reactions of Hbs with bioactive gases, particularly NO, and protection from nitrosative stress; and, sensor Hbs. A final section sketches the evolution of work on the structural basis for allosteric O2 binding by mammalian RBC Hb, including the development of newer kinetic models. Where possible, reference to historical works is included, in order to provide context for current advances in Hb research.
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Affiliation(s)
- David A Gell
- School of Medicine, University of Tasmania, TAS 7000, Australia.
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6
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Colloc'h N, Sacquin-Mora S, Avella G, Dhaussy AC, Prangé T, Vallone B, Girard E. Determinants of neuroglobin plasticity highlighted by joint coarse-grained simulations and high pressure crystallography. Sci Rep 2017; 7:1858. [PMID: 28500341 PMCID: PMC5431840 DOI: 10.1038/s41598-017-02097-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/20/2017] [Indexed: 11/09/2022] Open
Abstract
Investigating the effect of pressure sheds light on the dynamics and plasticity of proteins, intrinsically correlated to functional efficiency. Here we detail the structural response to pressure of neuroglobin (Ngb), a hexacoordinate globin likely to be involved in neuroprotection. In murine Ngb, reversible coordination is achieved by repositioning the heme more deeply into a large internal cavity, the “heme sliding mechanism”. Combining high pressure crystallography and coarse-grain simulations on wild type Ngb as well as two mutants, one (V101F) with unaffected and another (F106W) with decreased affinity for CO, we show that Ngb hinges around a rigid mechanical nucleus of five hydrophobic residues (V68, I72, V109, L113, Y137) during its conformational transition induced by gaseous ligand, that the intrinsic flexibility of the F-G loop appears essential to drive the heme sliding mechanism, and that residue Val 101 may act as a sensor of the interaction disruption between the heme and the distal histidine.
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Affiliation(s)
- Nathalie Colloc'h
- ISTCT CNRS UNICAEN CEA Normandie Univ., CERVOxy team, centre Cyceron, 14000, Caen, France.
| | - Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, CNRS UPR9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Giovanna Avella
- Instituto Pasteur-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, 5 piazzale Aldo Moro, 00185, Roma, Italy.,BIOGEM Research Institute, Ariano Irpino, Italy
| | - Anne-Claire Dhaussy
- CRISTMAT UMR 6508 CNRS ENSICAEN UNICAEN Normandie Univ., 6 bd du Maréchal Juin, 14050, Caen, France
| | - Thierry Prangé
- LCRB, UMR 8015 CNRS Université Paris Descartes, 4 avenue de l'Observatoire, 75270, Paris, France
| | - Beatrice Vallone
- Instituto Pasteur-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, 5 piazzale Aldo Moro, 00185, Roma, Italy
| | - Eric Girard
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France.
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7
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Preimesberger MR, Majumdar A, Lecomte JTJ. Dynamics of Lysine as a Heme Axial Ligand: NMR Analysis of the Chlamydomonas reinhardtii Hemoglobin THB1. Biochemistry 2017; 56:551-569. [DOI: 10.1021/acs.biochem.6b00926] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matthew R. Preimesberger
- T.
C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ananya Majumdar
- Biomolecular
NMR Center, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Juliette T. J. Lecomte
- T.
C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
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8
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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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9
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Hamdane D, Bou-Nader C, Cornu D, Hui-Bon-Hoa G, Fontecave M. Flavin-Protein Complexes: Aromatic Stacking Assisted by a Hydrogen Bond. Biochemistry 2015; 54:4354-64. [PMID: 26120776 DOI: 10.1021/acs.biochem.5b00501] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enzyme-catalyzed reactions often rely on a noncovalently bound cofactor whose reactivity is tuned by its immediate environment. Flavin cofactors, the most versatile catalyst encountered in biology, are often maintained within the protein throughout numbers of complex ionic and aromatic interactions. Here, we have investigated the role of π-π stacking and hydrogen bond interactions between a tyrosine and the isoalloxazine moiety of the flavin adenine dinucleotide (FAD) in an FAD-dependent RNA methyltransferase. Combining several static and time-resolved spectroscopies as well as biochemical approaches, we showed that aromatic stacking is assisted by a hydrogen bond between the phenol group and the amide of an adjacent active site loop. A mechanism of recognition and binding of the redox cofactor is proposed.
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Affiliation(s)
- Djemel Hamdane
- †Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, France 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Charles Bou-Nader
- †Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, France 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - David Cornu
- ‡INSERM U779, 78 Rue du Général Leclerc, 94275 Le Kremlin-Bicêtre, France
| | - Gaston Hui-Bon-Hoa
- §Plateforme IMAGIF, Centre de Recherche de Gif, Centre National de la Recherche Scientifique, 1 avenue de le terrasse, 91191 Gif Sur Yvette, France
| | - Marc Fontecave
- †Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, France 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
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10
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Giordano D, Coppola D, Russo R, Tinajero-Trejo M, di Prisco G, Lauro F, Ascenzi P, Verde C. The globins of cold-adapted Pseudoalteromonas haloplanktis TAC125: from the structure to the physiological functions. Adv Microb Physiol 2014; 63:329-89. [PMID: 24054800 DOI: 10.1016/b978-0-12-407693-8.00008-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Evolution allowed Antarctic microorganisms to grow successfully under extreme conditions (low temperature and high O2 content), through a variety of structural and physiological adjustments in their genomes and development of programmed responses to strong oxidative and nitrosative stress. The availability of genomic sequences from an increasing number of cold-adapted species is providing insights to understand the molecular mechanisms underlying crucial physiological processes in polar organisms. The genome of Pseudoalteromonas haloplanktis TAC125 contains multiple genes encoding three distinct truncated globins exhibiting the 2/2 α-helical fold. One of these globins has been extensively characterised by spectroscopic analysis, kinetic measurements and computer simulation. The results indicate unique adaptive structural properties that enhance the overall flexibility of the protein, so that the structure appears to be resistant to pressure-induced stress. Recent results on a genomic mutant strain highlight the involvement of the cold-adapted globin in the protection against the stress induced by high O2 concentration. Moreover, the protein was shown to catalyse peroxynitrite isomerisation in vitro. In this review, we first summarise how cold temperatures affect the physiology of microorganisms and focus on the molecular mechanisms of cold adaptation revealed by recent biochemical and genetic studies. Next, since only in a very few cases the physiological role of truncated globins has been demonstrated, we also discuss the structural and functional features of the cold-adapted globin in an attempt to put into perspective what has been learnt about these proteins and their potential role in the biology of cold-adapted microorganisms.
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11
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Guimarães BG, Hamdane D, Lechauve C, Marden MC, Golinelli-Pimpaneau B. The crystal structure of wild-type human brain neuroglobin reveals flexibility of the disulfide bond that regulates oxygen affinity. ACTA ACUST UNITED AC 2014; 70:1005-14. [PMID: 24699645 DOI: 10.1107/s1399004714000078] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 01/02/2014] [Indexed: 11/10/2022]
Abstract
Neuroglobin plays an important function in the supply of oxygen in nervous tissues. In human neuroglobin, a cysteine at position 46 in the loop connecting the C and D helices of the globin fold is presumed to form an intramolecular disulfide bond with Cys55. Rupture of this disulfide bridge stabilizes bi-histidyl haem hexacoordination, causing an overall decrease in the affinity for oxygen. Here, the first X-ray structure of wild-type human neuroglobin is reported at 1.74 Å resolution. This structure provides a direct observation of two distinct conformations of the CD region containing the intramolecular disulfide link and highlights internal cavities that could be involved in ligand migration and/or are necessary to enable the conformational transition between the low and high oxygen-affinity states following S-S bond formation.
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Affiliation(s)
- Beatriz G Guimarães
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, 91190 Gif-sur-Yvette, France
| | - Djemel Hamdane
- Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, 1 Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Christophe Lechauve
- Inserm U779, Université Paris XI, 78 Rue du Général Leclerc, 94275 Le Kremlin-Bicêtre, France
| | - Michael C Marden
- Inserm U779, Université Paris XI, 78 Rue du Général Leclerc, 94275 Le Kremlin-Bicêtre, France
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, 1 Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
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12
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Abbruzzetti S, Spyrakis F, Bidon-Chanal A, Luque FJ, Viappiani C. Ligand migration through hemeprotein cavities: insights from laser flash photolysis and molecular dynamics simulations. Phys Chem Chem Phys 2013; 15:10686-701. [PMID: 23733145 DOI: 10.1039/c3cp51149a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The presence of cavities and tunnels in the interior of proteins, in conjunction with the structural plasticity arising from the coupling to the thermal fluctuations of the protein scaffold, has profound consequences on the pathways followed by ligands moving through the protein matrix. In this perspective we discuss how quantitative analysis of experimental rebinding kinetics from laser flash photolysis, trapping of unstable conformational states by embedding proteins within the nanopores of silica gels, and molecular simulations can synergistically converge to gain insight into the migration mechanism of ligands. We show how the evaluation of the free energy landscape for ligand diffusion based on the outcome of computational techniques can assist the definition of sound reaction schemes, leading to a comprehensive understanding of the broad range of chemical events and time scales that encompass the transport of small ligands in hemeproteins.
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Affiliation(s)
- Stefania Abbruzzetti
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Parma, viale delle Scienze 7A, 43124, Parma, Italy
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13
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Russo R, Giordano D, di Prisco G, Hui Bon Hoa G, Marden MC, Verde C, Kiger L. Ligand-rebinding kinetics of 2/2 hemoglobin from the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1932-8. [PMID: 23429181 DOI: 10.1016/j.bbapap.2013.02.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 02/01/2013] [Accepted: 02/06/2013] [Indexed: 11/16/2022]
Abstract
Kinetic studies were performed on ligand rebinding to a cold-adapted globin of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 (Ph-2/2HbO). This 2/2 hemoglobin displays a rapid spectroscopic phase that is independent of CO concentration, followed by the standard bimolecular recombination. While the geminate recombination usually occurs on a ns timescale, Ph-2/2HbO displays a component of about 1μs that accounts for half of the geminate phase at 8°C, indicative of a relatively slow internal ligand binding. The O2 binding kinetics were measured in competition with CO to allow a short-time exposure of the deoxy hemes to O2 before CO replacement. Indeed Ph-2/2HbO is readily oxidised in the presence of O2, probably due to a superoxide character of the FeO2 bond induced by of a hydrogen-bond donor amino-acid residue. Upon O2 release or iron oxidation a distal residue (probably Tyr) is able to reversibly bind to the heme and as such to compete for binding with an external ligand. The transient hexacoordinated ferrous His-Fe-Tyr conformation after O2 dissociation could initiate the electron transfer from the iron toward its final acceptor, molecular O2 under our conditions. The hexacoordination via the distal Tyr is only partial, indicating a weak interaction between Tyr and the heme under atmospheric pressure. Hydrostatic high pressure enhances the hexacoordination indicating a flexible globin that allows structural changes. The O2 binding affinity for Ph-2/2HbO, poorly affected by the competition with Tyr, is about 1Torr at 8°C, pH7.0, which is compatible for an in vivo O2 binding function; however, this globin is more likely involved in a redox reaction associating diatomic ligands and their derived oxidative species. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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14
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Hamdane D, Argentini M, Cornu D, Myllykallio H, Skouloubris S, Hui-Bon-Hoa G, Golinelli-Pimpaneau B. Insights into folate/FAD-dependent tRNA methyltransferase mechanism: role of two highly conserved cysteines in catalysis. J Biol Chem 2011; 286:36268-80. [PMID: 21846722 DOI: 10.1074/jbc.m111.256966] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The flavoprotein TrmFO methylates specifically the C5 carbon of the highly conserved uridine 54 in tRNAs. Contrary to most methyltransferases, the 1-carbon unit transferred by TrmFO derives from 5,10-methylenetetrahydrofolate and not from S-adenosyl-L-methionine. The enzyme also employs the FAD hydroquinone as a reducing agent of the C5 methylene U54-tRNA intermediate in vitro. By analogy with the catalytic mechanism of thymidylate synthase ThyA, a conserved cysteine located near the FAD isoalloxazine ring was proposed to act as a nucleophile during catalysis. Here, we mutated this residue (Cys-53 in Bacillus subtilis TrmFO) to alanine and investigated its functional role. Biophysical characterization of this variant demonstrated the major structural role of Cys-53 in maintaining both the integrity and plasticity of the flavin binding site. Unexpectedly, gel mobility shift assays showed that, like the wild-type enzyme, the inactive C53A variant was capable of forming a covalent complex with a 5-fluorouridine-containing mini-RNA. This result confirms the existence of a covalent intermediate during catalysis but rules out a nucleophilic role for Cys-53. To identify the actual nucleophile, two other strictly conserved cysteines (Cys-192 and Cys-226) that are relatively far from the active site were replaced with alanine, and a double mutant C53A/C226A was generated. Interestingly, only mutations that target Cys-226 impeded TrmFO from forming a covalent complex and methylating tRNA. Altogether, we propose a revised mechanism for the m(5)U54 modification catalyzed by TrmFO, where Cys-226 attacks the C6 atom of the uridine, and Cys-53 plays the role of the general base abstracting the C5 proton.
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Affiliation(s)
- Djemel Hamdane
- Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.
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15
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Spyrakis F, Luque FJ, Viappiani C. Structural analysis in nonsymbiotic hemoglobins: what can we learn from inner cavities? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 181:8-13. [PMID: 21600392 DOI: 10.1016/j.plantsci.2011.03.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 03/24/2011] [Accepted: 03/29/2011] [Indexed: 05/09/2023]
Abstract
Plants contain three classes of hemoglobins which are not associated with nitrogen fixing bacteria, and have been accordingly termed nonsymbiotic hemoglobins. The function of nonsymbiotic hemoglobins is as yet mostly unknown. A NO dioxygenase activity has been proposed and demonstrated for some of them in vitro. In this context, a sound molecular mechanism that relates the structure with the biological activity is crucial to suggest a given physiological role. Insight into such a mechanism is now facilitated by recent progress made in both experimental and computational techniques. These studies have highlighted a number of key structural features implicated in the function of nonsymbiotic hemoglobins. The bis-histidyl hexacoordination of the heme in both its ferric and ferrous states provides a powerful and general tool to modulate reactivity, protein dynamics, and shape of the cavities. In addition, the specific arrangement of distal cavity residues provides effective protection against autoxidation. Inspection of the static crystal structures available for both liganded and unliganded states seems unsufficient to explain the function of these proteins. Function appears to be intimately linked with protein flexibility, which influences the dynamical behavior of inner cavities, capable of delivering apolar reactants to the reaction site, and removing charged reaction products. In this mini review, we demonstrate how the integration of information derived from experimental assays and computational studies is valuable and can shed light into the linkage between structural plasticity of nonsymbiotic hemoglobins and their biological role.
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Affiliation(s)
- Francesca Spyrakis
- Dipartimento di Chimica Generale ed Inorganica, Chimica Analitica, Chimica Fisica, Università degli Studi di Parma, Italy
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16
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Hamdane D, Kiger L, Hui-Bon-Hoa G, Marden MC. Kinetics Inside the Protein: Shape of the Geminate Kinetics in Myoglobin. J Phys Chem B 2011; 115:3919-23. [DOI: 10.1021/jp107168b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Djemel Hamdane
- Inserm U779, University Paris 11, 94275 Le Kremlin-Bicêtre, France
| | - Laurent Kiger
- Inserm U779, University Paris 11, 94275 Le Kremlin-Bicêtre, France
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17
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Zhang H, Kenaan C, Hamdane D, Hoa GHB, Hollenberg PF. Effect of conformational dynamics on substrate recognition and specificity as probed by the introduction of a de novo disulfide bond into cytochrome P450 2B1. J Biol Chem 2009; 284:25678-86. [PMID: 19605359 PMCID: PMC2757969 DOI: 10.1074/jbc.m109.032748] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Revised: 07/15/2009] [Indexed: 11/06/2022] Open
Abstract
The conformational dynamics of cytochrome P450 2B1 (CYP2B1) were investigated through the introduction of a disulfide bond to link the I- and K-helices by generation of a double Cys variant, Y309C/S360C. The consequences of the disulfide bonding were examined both experimentally and in silico by molecular dynamics simulations. Under high hydrostatic pressures, the partial inactivation volume for the Y309C/S360C variant was determined to be -21 cm3mol(-1), which is more than twice as much as those of the wild type (WT) and single Cys variants (Y309C, S360C). This result indicates that the engineered disulfide bond has substantially reduced the protein plasticity of the Y309C/S360C variant. Under steady-state turnover conditions, the S360C variant catalyzed the N-demethylation of benzphetamine and O-deethylation of 7-ethoxy-trifluoromethylcoumarin as the WT did, whereas the Y309C variant retained only 39% of the N-demethylation activity and 66% of the O-deethylation activity compared with the WT. Interestingly, the Y309C/S360C variant restored the N-demethylation activity to the same level as that of the WT but decreased the O-deethylation activity to only 19% of the WT. Furthermore, the Y309C/S360C variant showed increased substrate specificity for testosterone over androstenedione. Molecular dynamics simulations revealed that the engineered disulfide bond altered substrate access channels. Taken together, these results suggest that protein dynamics play an important role in regulating substrate entry and recognition.
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Affiliation(s)
- Haoming Zhang
- From the Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109 and
| | - Cesar Kenaan
- From the Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109 and
| | - Djemel Hamdane
- INSERM U779, 78 rue du Général Leclerc, 94275 Le Kremlin-Bicêtre, France
| | - Gaston Hui Bon Hoa
- INSERM U779, 78 rue du Général Leclerc, 94275 Le Kremlin-Bicêtre, France
| | - Paul F. Hollenberg
- From the Department of Pharmacology, University of Michigan, Ann Arbor, Michigan 48109 and
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18
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Capece L, Marti MA, Bidon-Chanal A, Nadra A, Luque FJ, Estrin DA. High pressure reveals structural determinants for globin hexacoordination: Neuroglobin and myoglobin cases. Proteins 2009; 75:885-94. [DOI: 10.1002/prot.22297] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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19
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Dordas C. Nonsymbiotic hemoglobins and stress tolerance in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2009; 176:433-40. [PMID: 26493132 DOI: 10.1016/j.plantsci.2009.01.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Revised: 01/09/2009] [Accepted: 01/09/2009] [Indexed: 05/24/2023]
Abstract
Hemoglobins (Hbs) are heme containing proteins found in most organisms including animals, bacteria, and plants. Their structure, size, and function are quite diverse among the different organisms. There are three different types of hemoglobins in plants: symbiotic (sHb), nonsymbiotic (nsHb), and truncated hemoglobins (trHb). The nonsymbiotic hemoglobins are divided into: class 1 hemoglobins (nsHb-1s), which have a very high affinity for oxygen: and class 2 hemoglobins (nsHb-2s), which have lower affinity for oxygen, are similar to the sHbs. nsHb-1s are expressed under hypoxia, osmotic stress, nutrient deprivation, cold stress, rhizobial infection, nitric oxide exposure, and fungal infection. Tolerance to stress is very important for the survival of the plant. Hemoglobins are one of many different strategies that plants have evolved to overcome stress conditions and survive. Hbs also react with NO produced under different stress conditions. Class 1 nsHbs are involved in a metabolic pathway involving NO. Those hemoglobins provide an alternative type of respiration to mitochondrial electron transport under limiting oxygen concentrations. Class 1 nsHbs in hypoxic plants act as part of a soluble, terminal, NO dioxygenase system, yielding nitrate from the reaction of oxyHb with NO. The overall reaction sequence, referred to as the nsHb/NO cycle, consumes NADH and maintains ATP levels via an as yet unknown mechanism. Class 2 nsHbs seem to scavenge NO in a similar fashion as class 1 Hbs and are involved in reducing flowering time in Arabidopsis. nsHbs also show peroxidase-like activity and NO metabolism and possibly protect against nitrosative stress in plant-pathogen interaction and in symbiotic interactions. nsHbs may be involved in other stress conditions such as osmotic, nutrient and cold stress together with NO and the function of nsHbs can be in NO metabolism and signal transduction. However, other possible functions cannot be precluded as Hbs have many different functions in other organisms.
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Affiliation(s)
- Christos Dordas
- Aristotle University of Thessaloniki, Faculty of Agriculture, Laboratory of Agronomy, 54124 Thessaloniki, Greece.
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20
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Lechauve C, Rezaei H, Celier C, Kiger L, Corral-Debrinski M, Noinville S, Chauvierre C, Hamdane D, Pato C, Marden MC. Neuroglobin and prion cellular localization: investigation of a potential interaction. J Mol Biol 2009; 388:968-77. [PMID: 19327369 DOI: 10.1016/j.jmb.2009.03.047] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Revised: 02/18/2009] [Accepted: 03/18/2009] [Indexed: 11/25/2022]
Abstract
Neuroglobin (Ngb) and the cellular prion protein (PrP(c)), proteins of unknown function in the nervous system, are known to be expressed in the retina and have been observed in different rat retinal cells. The retina is the site of the highest concentration for Ngb, a heme protein of similar size and conformation to myoglobin. In this study, we demonstrated by immunohistochemical analysis of retinal colocalization of Ngb and PrP(c) in the ganglion cell layer. Considering for these two a common protective role in relation to oxidative stress and a possible transient contact during migration of PrP(c) through the eye or upon neuronal degradation, we undertook in vitro studies of the interaction of the purified proteins. Mixing these two proteins leads to rapid aggregation, even at submicromolar concentrations. As observed with the use of dynamic light scattering, particles comprising both proteins evolve to hundreds of nanometers within several seconds, a first report showing that PrP(c) is able to form aggregates without major structural changes. The main effect would then appear to be a protein-protein interaction specific to the surface charge of the Ngb protein with PrP(c) N-terminal sequence. A dominant parameter is the solvent ionic force, which can significantly modify the final state of aggregation. PrP(c), normally anchored to the cell membrane, is toxic in the cytoplasm, where Ngb is present; this could suggest an Ngb function of scavenging proteins capable of forming deleterious aggregates considering a charge complementarity in the complex.
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Affiliation(s)
- Christophe Lechauve
- INSERM U779, Universités Paris VI et XI, Hopital de Bicêtre, Le Kremlin-Bicêtre, France
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21
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Brindell M, Stawoska I, Orzeł L, Labuz P, Stochel G, van Eldik R. Application of high pressure laser flash photolysis in studies on selected hemoprotein reactions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1481-92. [PMID: 18778796 DOI: 10.1016/j.bbapap.2008.08.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Revised: 07/14/2008] [Accepted: 08/04/2008] [Indexed: 12/31/2022]
Abstract
This article focuses on the application of high pressure laser flash photolysis for studies on selected hemoprotein reactions with the objective to establish details of the underlying reaction mechanisms. In this context, particular attention is given to the reactions of small molecules such as dioxygen, carbon monoxide, and nitric oxide with selected hemoproteins (hemoglobin, myoglobin, neuroglobin and cytochrome P450(cam)), as well as to photo-induced electron transfer reactions occurring in hemoproteins (particularly in various types of cytochromes). Mechanistic conclusions based on the interpretation of the obtained activation volumes are discussed in this account.
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Affiliation(s)
- Małgorzata Brindell
- Department of Inorganic Chemistry, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
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22
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Hamdane D, Vasseur-Godbillon C, Baudin-Creuza V, Hoa GHB, Marden MC. Reversible Hexacoordination of α-Hemoglobin-stabilizing Protein (AHSP)/α-Hemoglobin Versus Pressure. J Biol Chem 2007; 282:6398-404. [PMID: 17194704 DOI: 10.1074/jbc.m610543200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Using high hydrostatic pressure or hydrogen peroxide as perturbing agents, we demonstrate a protective effect of the chaperone AHSP for the alpha-chains of Hb. High pressure induces an irreversible aggregation of the ferrous deoxy alpha-chains, whereas the AHSP/alpha-Hb complex shows reversible hexacoordination of the alpha-Hb without protein aggregation. Upon pressure release, the relaxation kinetics of the transition from the hexacoordinated to pentacoordinated form of alpha-Hb in the presence of AHSP exhibit a biphasic shape. High pressure did not induce dissociation of alpha-Hb from its chaperone, as evidenced by the ligand binding kinetics that show a unique rate for the AHSP/alpha-Hb complex. For both free alpha-Hb and the AHSP/alpha-Hb complex, the bimolecular rate constant of CO binding (k(CO)(on)) versus pressure exhibits a bell shape, attributed to the transition of the rate-determining step from the chemical barrier to the migration of CO within the protein matrix. These results reveal a plasticity of the alpha-Hb active site in the presence of the chaperone and indicate that the AHSP was still active at 300 MPa. The ferric state of the AHSP/alpha-Hb complex shows hexacoordination even at atmospheric pressures, indicating a His-Fe-His binding scheme as previously observed in neuroglobin and cytoglobin. The reaction with hydrogen peroxide of ferric alpha-Hb within the complex also demonstrates a protection against aggregation.
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Affiliation(s)
- Djemel Hamdane
- INSERM U779, University of Paris XI, 94275 Le Kremlin-Bicêtre, France
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23
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Smagghe BJ, Kundu S, Hoy JA, Halder P, Weiland TR, Savage A, Venugopal A, Goodman M, Premer S, Hargrove MS. Role of phenylalanine B10 in plant nonsymbiotic hemoglobins. Biochemistry 2006; 45:9735-45. [PMID: 16893175 DOI: 10.1021/bi060716s] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
All plants contain an unusual class of hemoglobins that display bis-histidyl coordination yet are able to bind exogenous ligands such as oxygen. Structurally homologous hexacoordinate hemoglobins (hxHbs) are also found in animals (neuroglobin and cytoglobin) and some cyanobacteria, where they are thought to play a role in free radical scavenging or ligand sensing. The plant hxHbs can be distinguished from the others because they are only weakly hexcacoordinate in the ferrous state, yet no structural mechanism for regulating hexacoordination has been articulated to account for this behavior. Plant hxHbs contain a conserved Phe at position B10 (Phe(B10)), which is near the reversibly coordinated distal His(E7). We have investigated the effects of Phe(B10) mutation on kinetic and equilibrium constants for hexacoordination and exogenous ligand binding in the ferrous and ferric oxidation states. Kinetic and equilibrium constants for hexacoordination and ligand binding along with CO-FTIR spectroscopy, midpoint reduction potentials, and the crystal structures of two key mutant proteins (F40W and F40L) reveal that Phe(B10) is an important regulatory element in hexacoordination. We show that Phe at this position is the only amino acid that facilitates stable oxygen binding to the ferrous Hb and the only one that promotes ligand binding in the ferric oxidation states. This work presents a structural mechanism for regulating reversible intramolecular coordination in plant hxHbs.
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Affiliation(s)
- Benoit J Smagghe
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA
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24
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Schay G, Smeller L, Tsuneshige A, Yonetani T, Fidy J. Allosteric Effectors Influence the Tetramer Stability of Both R- and T-states of Hemoglobin A. J Biol Chem 2006; 281:25972-83. [PMID: 16822864 DOI: 10.1074/jbc.m604216200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The contribution of heterotropic effectors to hemoglobin allostery is still not completely understood. With the recently proposed global allostery model, this question acquires crucial significance, because it relates tertiary conformational changes to effector binding in both the R- and T-states. In this context, an important question is how far the induced conformational changes propagate from the binding site(s) of the allosteric effectors. We present a study in which we monitored the interdimeric interface when the effectors such as Cl-, 2,3-diphosphoglycerate, inositol hexaphosphate, and bezafibrate were bound. We studied oxy-Hb and a hybrid form (alphaFeO2)2-(betaZn)2 as the T-state analogue by monitoring heme absorption and Trp intrinsic fluorescence under hydrostatic pressure. We observed a pressure-dependent change in the intrinsic fluorescence, which we attribute to a pressure-induced tetramer to dimer transition with characteristic pressures in the 70-200-megapascal range. The transition is sensitive to the binding of allosteric effectors. We fitted the data with a simple model for the tetramer-dimer transition and determined the dissociation constants at atmospheric pressure. In the R-state, we observed a stabilizing effect by the allosteric effectors, although in the T-analogue a stronger destabilizing effect was seen. The order of efficiency was the same in both states, but with the opposite trend as inositol hexaphosphate > 2,3-diphosphoglycerate > Cl-. We detected intrinsic fluorescence from bound bezafibrate that introduced uncertainty in the comparison with other effectors. The results support the global allostery model by showing that conformational changes propagate from the effector binding site to the interdimeric interfaces in both quaternary states.
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Affiliation(s)
- Gusztáv Schay
- Department of Biophysics and Radiation Biology and Biophysics Research Group of the Hungarian Academy of Sciences, Faculty of Medicine, Semmelweis University, P. O. Box 263 H 1444 Budapest, Hungary
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25
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Dewilde S, Ebner B, Vinck E, Gilany K, Hankeln T, Burmester T, Kreiling J, Reinisch C, Vanfleteren JR, Kiger L, Marden MC, Hundahl C, Fago A, Van Doorslaer S, Moens L. The nerve hemoglobin of the bivalve mollusc Spisula solidissima: molecular cloning, ligand binding studies, and phylogenetic analysis. J Biol Chem 2005; 281:5364-72. [PMID: 16352603 DOI: 10.1074/jbc.m509486200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Members of the hemoglobin (Hb) superfamily are present in nerve tissue of several vertebrate and invertebrate species. In vertebrates they display hexacoordinate heme iron atoms and are typically expressed at low levels (microM). Their function is still a matter of debate. In invertebrates they have a hexa- or pentacoordinate heme iron, are mostly expressed at high levels (mM), and have been suggested to have a myoglobin-like function. The native Hb of the surf clam, Spisula solidissima, composed of 162 amino acids, does not show specific deviations from the globin templates. UV-visible and resonance Raman spectroscopy demonstrate a hexacoordinate heme iron. Based on the sequence analogy, the histidine E7 is proposed as a sixth ligand. Kinetic and equilibrium measurements show a moderate oxygen affinity (P(50) approximately 0.6 torr) and no cooperativity. The histidine binding affinity is 100-fold lower than in neuroglobin. Phylogenetic analysis demonstrates a clustering of the S. solidissima nerve Hb with mollusc Hbs and myoglobins, but not with the vertebrate neuroglobins. We conclude that invertebrate nerve Hbs expressed at high levels are, despite the hexacoordinate nature of their heme iron, not essentially different from other intracellular Hbs. They most likely fulfill a myoglobin-like function and enhance oxygen supply to the neurons.
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Affiliation(s)
- Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Campus Drie eiken, Universiteitsplein 1, B-2610 Antwerp, Belgium
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