1
|
Verde C, Giordano D, Bruno S. NO and Heme Proteins: Cross-Talk between Heme and Cysteine Residues. Antioxidants (Basel) 2023; 12:antiox12020321. [PMID: 36829880 PMCID: PMC9952723 DOI: 10.3390/antiox12020321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/19/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
Heme proteins are a diverse group that includes several unrelated families. Their biological function is mainly associated with the reactivity of the heme group, which-among several other reactions-can bind to and react with nitric oxide (NO) and other nitrogen compounds for their production, scavenging, and transport. The S-nitrosylation of cysteine residues, which also results from the reaction with NO and other nitrogen compounds, is a post-translational modification regulating protein activity, with direct effects on a variety of signaling pathways. Heme proteins are unique in exhibiting this dual reactivity toward NO, with reported examples of cross-reactivity between the heme and cysteine residues within the same protein. In this work, we review the literature on this interplay, with particular emphasis on heme proteins in which heme-dependent nitrosylation has been reported and those for which both heme nitrosylation and S-nitrosylation have been associated with biological functions.
Collapse
Affiliation(s)
- Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn (SZN), Villa Comunale, 80121 Napoli, Italy
| | - Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn (SZN), Villa Comunale, 80121 Napoli, Italy
| | - Stefano Bruno
- Department of Food and Drug, University of Parma, 43124 Parma, Italy
- Biopharmanet-TEC, University of Parma, 43124 Parma, Italy
- Correspondence:
| |
Collapse
|
2
|
Pech-Santiago EO, Argüello-García R, Vázquez C, Saavedra E, González-Hernández I, Jung-Cook H, Rafferty SP, Ortega-Pierres MG. Giardia duodenalis: Flavohemoglobin is involved in drug biotransformation and resistance to albendazole. PLoS Pathog 2022; 18:e1010840. [PMID: 36166467 PMCID: PMC9514659 DOI: 10.1371/journal.ppat.1010840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/28/2022] [Indexed: 12/12/2022] Open
Abstract
Giardia duodenalis causes giardiasis, a major diarrheal disease in humans worldwide whose treatment relies mainly on metronidazole (MTZ) and albendazole (ABZ). The emergence of ABZ resistance in this parasite has prompted studies to elucidate the molecular mechanisms underlying this phenomenon. G. duodenalis trophozoites convert ABZ into its sulfoxide (ABZSO) and sulfone (ABZSOO) forms, despite lacking canonical enzymes involved in these processes, such as cytochrome P450s (CYP450s) and flavin-containing monooxygenases (FMOs). This study aims to identify the enzyme responsible for ABZ metabolism and its role in ABZ resistance in G. duodenalis. We first determined that the iron-containing cofactor heme induces higher mRNA expression levels of flavohemoglobin (gFlHb) in Giardia trophozoites. Molecular docking analyses predict favorable interactions of gFlHb with ABZ, ABZSO and ABZSOO. Spectral analyses of recombinant gFlHb in the presence of ABZ, ABZSO and ABZSOO showed high affinities for each of these compounds with Kd values of 22.7, 19.1 and 23.8 nM respectively. ABZ and ABZSO enhanced gFlHb NADH oxidase activity (turnover number 14.5 min-1), whereas LC-MS/MS analyses of the reaction products showed that gFlHb slowly oxygenates ABZ into ABZSO at a much lower rate (turnover number 0.01 min-1). Further spectroscopic analyses showed that ABZ is indirectly oxidized to ABZSO by superoxide generated from the NADH oxidase activity of gFlHb. In a similar manner, the superoxide-generating enzyme xanthine oxidase was able to produce ABZSO in the presence of xanthine and ABZ. Interestingly, we find that gFlHb mRNA expression is lower in albendazole-resistant clones compared to those that are sensitive to this drug. Furthermore, all albendazole-resistant clones transfected to overexpress gFlHb displayed higher susceptibility to the drug than the parent clones. Collectively these findings indicate a role for gFlHb in ABZ conversion to its sulfoxide and that gFlHb down-regulation acts as a passive pharmacokinetic mechanism of resistance in this parasite.
Collapse
Affiliation(s)
- Edar O. Pech-Santiago
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Raúl Argüello-García
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Citlali Vázquez
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Iliana González-Hernández
- Laboratorio de Neuropsicofarmacología, Instituto Nacional de Neurología y Neurocirugía, Manuel Velasco Suárez, Ciudad de México, México
| | - Helgi Jung-Cook
- Laboratorio de Neuropsicofarmacología, Instituto Nacional de Neurología y Neurocirugía, Manuel Velasco Suárez, Ciudad de México, México
| | | | - M. Guadalupe Ortega-Pierres
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
- * E-mail:
| |
Collapse
|
3
|
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.
Collapse
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.)
| |
Collapse
|
4
|
De Simone G, di Masi A, Fattibene P, Ciaccio C, Platas-Iglesias C, Coletta M, Pesce A, Ascenzi P. Oxygen-mediated oxidation of ferrous nitrosylated nitrobindins. J Inorg Biochem 2021; 224:111579. [PMID: 34479003 DOI: 10.1016/j.jinorgbio.2021.111579] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/23/2021] [Accepted: 08/10/2021] [Indexed: 01/25/2023]
Abstract
The O2-mediated oxidation of all-β-barrel ferrous nitrosylated nitrobindin from Arabidopsis thaliana (At-Nb(II)-NO), Mycobacterium tuberculosis (Mt-Nb(II)-NO), and Homo sapiens (Hs-Nb(II)-NO) to ferric derivative (At-Nb(III), Mt-Nb(III), and Hs-Nb(III), respectively) has been investigated at pH 7.0 and 20.0 °C. Unlike ferrous nitrosylated horse myoglobin, human serum heme-albumin and human hemoglobin, the process in Nb(II)-NO is mono-exponential and linearly dependent on the O2 concentration, displaying a bimolecular behavior, characterized by kon = (6.3 ± 0.8) × 103 M-1 s-1, (1.4 ± 0.2) × 103 M-1 s-1, and (3.9 ± 0.5) × 103 M-1 s-1 for At-Nb(II)-NO, Mt-Nb(II)-NO, and Hs-Nb(II)-NO, respectively. No intermediate is detected, indicating that the O2 reaction with Nb(II)-NO is the rate-limiting step and that the subsequent conversion of the heme-Fe(III)-N(O)OO- species (i.e., N-bound peroxynitrite to heme-Fe(III)) to heme-Fe(III) and NO3- is much faster. A similar mechanism can be invoked for ferrous nitrosylated human neuroglobin and rabbit hemopexin, in which the heme-Fe(III)-N(O)OO- species is formed as well, although the rate-limiting step seems represented by the reshaping of the six-coordinated heme-Fe(III) complex. Although At-Nb(II)-NO and Mt-Nb(II)-NO are partially (while Hs-Nb(II)-NO is almost completely) penta-coordinated, density functional theory (DFT) calculations rule out that the cleavage of the proximal heme-Fe-His bond in Nb(II)-NO is responsible for the more stable heme-Fe(III)-N(O)OO- species. Moreover, the oxidation of the penta-coordinated heme-Fe(II)-NO adduct does not depend on O2 binding at the proximal side of the metal center. These features may instead reflect the peculiarity of Nb folding and of the heme environment, with a reduced steric constraint for the formation of the heme-Fe(III)-N(O)OO- complex.
Collapse
Affiliation(s)
- Giovanna De Simone
- Department of Sciences, Roma Tre University, Viale Guglielmo Marconi 446, 00146 Roma, Italy
| | - Alessandra di Masi
- Department of Sciences, Roma Tre University, Viale Guglielmo Marconi 446, 00146 Roma, Italy
| | - Paola Fattibene
- Technical Scientific Service and Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
| | - Chiara Ciaccio
- Department of Clinical Sciences and Translational Medicine, University of Roma "Tor Vergata", Via Montpellier 1, I-00133 Roma, Italy
| | - Carlos Platas-Iglesias
- Centro de Investigatiòns Cientìficas Avanzadas (CIA), Departamento de Quìmica, Facultade de Ciencias, Universidad da Coruña, 15071 A Coruña, Galicia, Spain
| | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma "Tor Vergata", Via Montpellier 1, I-00133 Roma, Italy
| | - Alessandra Pesce
- Department of Physics, University of Genova, Via Dodecaneso 33, 16100 Genova, Italy
| | - Paolo Ascenzi
- Department of Sciences, Roma Tre University, Viale Guglielmo Marconi 446, 00146 Roma, Italy; Interdepartmental Laboratory of Electron Microscopy, Roma Tre University, Via della Vasca Navale 79, I-00146 Roma, Italy.
| |
Collapse
|
5
|
Gardner AM, Gardner PR. Allostery in the nitric oxide dioxygenase mechanism of flavohemoglobin. J Biol Chem 2020; 296:100186. [PMID: 33310705 PMCID: PMC7948479 DOI: 10.1074/jbc.ra120.016637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022] Open
Abstract
The substrates O2 and NO cooperatively activate the NO dioxygenase function of Escherichia coli flavohemoglobin. Steady-state and transient kinetic measurements support a structure-based mechanistic model in which O2 and NO movements and conserved amino acids at the E11, G8, E2, E7, B10, and F7 positions within the globin domain control activation. In the cooperative and allosteric mechanism, O2 migrates to the catalytic heme site via a long hydrophobic tunnel and displaces LeuE11 away from the ferric iron, which forces open a short tunnel to the catalytic site gated by the ValG8/IleE15 pair and LeuE11. NO permeates this tunnel and leverages upon the gating side chains triggering the CD loop to furl, which moves the E and F-helices and switches an electron transfer gate formed by LysF7, GlnE7, and water. This allows FADH2 to reduce the ferric iron, which forms the stable ferric–superoxide–TyrB10/GlnE7 complex. This complex reacts with internalized NO with a bimolecular rate constant of 1010 M−1 s−1 forming nitrate, which migrates to the CD loop and unfurls the spring-like structure. To restart the cycle, LeuE11 toggles back to the ferric iron. Actuating electron transfer with O2 and NO movements averts irreversible NO poisoning and reductive inactivation of the enzyme. Together, structure snapshots and kinetic constants provide glimpses of intermediate conformational states, time scales for motion, and associated energies.
Collapse
Affiliation(s)
- Anne M Gardner
- Research and Development Division, Miami Valley Biotech, Dayton, Ohio, USA; Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Paul R Gardner
- Research and Development Division, Miami Valley Biotech, Dayton, Ohio, USA; Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA; Chemistry and Biochemistry Department, University of Dayton, Dayton, Ohio, USA.
| |
Collapse
|
6
|
Giordano D, Pesce A, Vermeylen S, Abbruzzetti S, Nardini M, Marchesani F, Berghmans H, Seira C, Bruno S, Javier Luque F, di Prisco G, Ascenzi P, Dewilde S, Bolognesi M, Viappiani C, Verde C. Structural and functional properties of Antarctic fish cytoglobins-1: Cold-reactivity in multi-ligand reactions. Comput Struct Biotechnol J 2020; 18:2132-2144. [PMID: 32913582 PMCID: PMC7451756 DOI: 10.1016/j.csbj.2020.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/10/2020] [Accepted: 08/05/2020] [Indexed: 12/11/2022] Open
Abstract
While the functions of the recently discovered cytoglobin, ubiquitously expressed in vertebrate tissues, remain uncertain, Antarctic fish provide unparalleled models to study novel protein traits that may arise from cold adaptation. We report here the spectral, ligand-binding and enzymatic properties (peroxynitrite isomerization, nitrite-reductase activity) of cytoglobin-1 from two Antarctic fish, Chaenocephalus aceratus and Dissostichus mawsoni, and present the crystal structure of D. mawsoni cytoglobin-1. The Antarctic cytoglobins-1 display high O2 affinity, scarcely compatible with an O2-supply role, a slow rate constant for nitrite-reductase activity, and do not catalyze peroxynitrite isomerization. Compared with mesophilic orthologues, the cold-adapted cytoglobins favor binding of exogenous ligands to the hexa-coordinated bis-histidyl species, a trait related to their higher rate constant for distal-His/heme-Fe dissociation relative to human cytoglobin. At the light of a remarkable 3D-structure conservation, the observed differences in ligand-binding kinetics may reflect Antarctic fish cytoglobin-1 specific features in the dynamics of the heme distal region and of protein matrix cavities, suggesting adaptation to functional requirements posed by the cold environment. Taken together, the biochemical and biophysical data presented suggest that in Antarctic fish, as in humans, cytoglobin-1 unlikely plays a role in O2 transport, rather it may be involved in processes such as NO detoxification.
Collapse
Key Words
- C.aceCygb-1*, Mutant of C.aceCygb-1
- C.aceCygb-1, Cytoglobin-1 of C. aceratus
- CO, Carbon monoxide
- CYGB, Human Cygb
- Cold-adaptation
- Cygb, Cytoglobin
- Cygb-1, Cytoglobin 1
- Cygb-2, Cytoglobin 2
- Cygbh, Hexa-coordinated bis-histidyl species
- Cygbp, Penta-coordinated Cygb
- Cytoglobin
- D.mawCygb-1*, Mutant of D.mawCygb-1
- D.mawCygb-1, Cytoglobin-1 of D. mawsoni
- DTT, Dithiothreitol
- Hb, Hemoglobin
- Ligand properties
- MD, Molecular Dynamics
- Mb, Myoglobin
- NGB, Human neuroglobin
- NO dioxygenase
- NO, Nitric oxide
- RNS, Reactive Nitrogen Species
- ROS, Reactive Oxygen Species
- X-ray structure
- p50, O2 partial pressure required to achieve half saturation
- rms, Root-mean square
Collapse
Affiliation(s)
- Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111 80131 Napoli, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Alessandra Pesce
- Department of Physics, University of Genova, Via Dodecaneso 33, I-16121 Genova, Italy
| | - Stijn Vermeylen
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Stefania Abbruzzetti
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7A, 43124 Parma, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Via Celoria 26, I-20133 Milano, Italy
| | - Francesco Marchesani
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 23A, 43124, Parma, Italy
| | - Herald Berghmans
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Constantí Seira
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Science, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, Av. Prat de la Riba 171, Santa Coloma de Gramenet E-08921, Spain
| | - Stefano Bruno
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 23A, 43124, Parma, Italy
| | - F Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Science, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, Av. Prat de la Riba 171, Santa Coloma de Gramenet E-08921, Spain
| | - Guido di Prisco
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111 80131 Napoli, Italy
| | - Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, Via della Vasca Navale 79, I-00146 Roma, Italy
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Martino Bolognesi
- Department of Biosciences, University of Milano, Via Celoria 26, I-20133 Milano, Italy
| | - Cristiano Viappiani
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7A, 43124 Parma, Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111 80131 Napoli, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| |
Collapse
|
7
|
Ardiccioni C, Arcovito A, Della Longa S, van der Linden P, Bourgeois D, Weik M, Montemiglio LC, Savino C, Avella G, Exertier C, Carpentier P, Prangé T, Brunori M, Colloc’h N, Vallone B. Ligand pathways in neuroglobin revealed by low-temperature photodissociation and docking experiments. IUCRJ 2019; 6:832-842. [PMID: 31576217 PMCID: PMC6760443 DOI: 10.1107/s2052252519008157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/06/2019] [Indexed: 06/10/2023]
Abstract
A combined biophysical approach was applied to map gas-docking sites within murine neuroglobin (Ngb), revealing snapshots of events that might govern activity and dynamics in this unique hexacoordinate globin, which is most likely to be involved in gas-sensing in the central nervous system and for which a precise mechanism of action remains to be elucidated. The application of UV-visible microspectroscopy in crystallo, solution X-ray absorption near-edge spectroscopy and X-ray diffraction experiments at 15-40 K provided the structural characterization of an Ngb photolytic intermediate by cryo-trapping and allowed direct observation of the relocation of carbon monoxide within the distal heme pocket after photodissociation. Moreover, X-ray diffraction at 100 K under a high pressure of dioxygen, a physiological ligand of Ngb, unravelled the existence of a storage site for O2 in Ngb which coincides with Xe-III, a previously described docking site for xenon or krypton. Notably, no other secondary sites were observed under our experimental conditions.
Collapse
Affiliation(s)
- Chiara Ardiccioni
- Department of Life and Environmental Sciences, New York–Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Ancona, Italy
| | - Alessandro Arcovito
- Istituto di Biochimica e Biochimica Clinica, Universitá Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy
- Fondazione Policlinico Universitario Agostino Gemelli–IRCCS, Largo Francesco Vito 1, 00168 Rome, Italy
| | - Stefano Della Longa
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Peter van der Linden
- European Synchrotron Radiation Facility (ESRF), 38043 Grenoble, France
- Partnership for Soft Condensed Matter (PSCM), 38043 Grenoble, France
| | | | - Martin Weik
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Linda Celeste Montemiglio
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Istituto Pasteur–Fondazione Cenci Bolognetti, Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Giovanna Avella
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Chemistry Department, Merck Serono S.p.A., Via Casilina 125, 00176 Rome, Italy
| | - Cécile Exertier
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Philippe Carpentier
- European Synchrotron Radiation Facility (ESRF), 38043 Grenoble, France
- CEA/DRF/BIG/CBM/BioCat LCBM CNRS UMR 5249, Université Grenoble Alpes, 38000 Grenoble, France
| | - Thierry Prangé
- CiTeCoM UMR 8038 CNRS, Université Paris Descartes, Paris, France
| | - Maurizio Brunori
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Nathalie Colloc’h
- ISTCT UMR 6030 CNRS Université de Caen Normandie CEA, CERVOxy Team, Centre Cyceron, Caen, France
| | - Beatrice Vallone
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Istituto Pasteur–Fondazione Cenci Bolognetti, Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| |
Collapse
|
8
|
Tangar A, Derrien V, Lei R, Santiago Estevez MJ, Sebban P, Bernad S, Miksovska J. Utility of fluorescent heme analogue ZnPPIX to monitor conformational heterogeneity in vertebrate hexa-coordinated globins. Metallomics 2019; 11:906-913. [PMID: 30734813 DOI: 10.1039/c8mt00332g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here, we report the preparation and photo-physical characterization of hexa-coordinated vertebrate globins, human neuroglobin (hNgb) and cytoglobin (hCygb), with the native iron protoporphyrin IX (FePPIX) cofactor replaced by a fluorescent isostructural analogue, zinc protoporphyrin IX (ZnPPIX). To facilitate insertion of ZnPPIX into hexa-coordinated globins, apoproteins prepared via butanone extraction were unfolded by the addition of GuHCl and subsequently slowly refolded in the presence of ZnPPIX. The absorption/emission spectra of ZnPPIX reconstituted hCygb are similar to those observed for ZnPPIX reconstituted myoglobin whereas the absorption and emission spectra of ZnPPIX reconstituted hNgb are blue shifted by ∼2 nm. Different steady state absorption and emission properties of ZnPPIX incorporated in hCygb and hNgb are consistent with distinct hydrogen bonding interactions between ZnPPIX and the globin matrix. The fluorescence lifetime of ZnPPIX in hexa-coordinated globins is bimodal pointing towards increased heterogeneity of the heme binding cavity in hCygb and hNgb. ZnPPIX reconstituted Ngb binds to cytochrome c with the same affinity as reported for the native protein, suggesting that fluorescent analogues of Cygb and Ngb can be readily employed to monitor interactions between vertebrate hexa-coordinated globins and other proteins.
Collapse
Affiliation(s)
- Antonija Tangar
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | | | | | | | | | | | | |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Structural Plasticity in Globins: Role of Protein Dynamics in Defining Ligand Migration Pathways. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2016; 105:59-80. [PMID: 27567484 DOI: 10.1016/bs.apcsb.2016.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Globins are a family of proteins characterized by the presence of the heme prosthetic group and involved in variety of biological functions in the cell. Due to their biological relevance and widespread distribution in all kingdoms of life, intense research efforts have been devoted to disclosing the relationships between structural features, protein dynamics, and function. Particular attention has been paid to the impact of differences in amino acid sequence on the topological features of docking sites and cavities and to the influence of conformational flexibility in facilitating the migration of small ligands through these cavities. Often, tunnels are carved in the interior of globins, and ligand exchange is regulated by gating residues. Understanding the subtle intricacies that relate the differences in sequence with the structural and dynamical features of globins with the ultimate aim of rationalizing the thermodynamics and kinetics of ligand binding continues to be a major challenge in the field. Due to the evolution of computational techniques, significant advances into our understanding of these questions have been made. In this review we focus our attention on the analysis of the ligand migration pathways as well as the function of the structural cavities and tunnels in a series of representative globins, emphasizing the synergy between experimental and theoretical approaches to gain a comprehensive knowledge into the molecular mechanisms of this diverse family of proteins.
Collapse
|
11
|
Frezzato D, Saielli G. Distribution and Dynamic Properties of Xenon Dissolved in the Ionic Smectic Phase of [C16mim][NO3]: MD Simulation and Theoretical Model. J Phys Chem B 2016; 120:2578-85. [DOI: 10.1021/acs.jpcb.5b12470] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Diego Frezzato
- Department
of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Giacomo Saielli
- CNR
Institute on Membrane Technology, Unit of Padova, Via Marzolo 1, 35131 Padova, Italy
| |
Collapse
|
12
|
Zhao C, Du W. Dynamic features of carboxy cytoglobin distal mutants investigated by molecular dynamics simulations. J Biol Inorg Chem 2016; 21:251-61. [DOI: 10.1007/s00775-016-1334-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 01/04/2016] [Indexed: 01/08/2023]
|
13
|
Cytoglobin ligand binding regulated by changing haem-co-ordination in response to intramolecular disulfide bond formation and lipid interaction. Biochem J 2015; 465:127-37. [PMID: 25327890 DOI: 10.1042/bj20140827] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cytoglobin (Cygb) is a hexa-co-ordinate haem protein from the globin superfamily with a physiological function that is unclear. We have previously reported that the haem co-ordination is changed in the presence of lipids, potentially transforming the redox properties of the protein and hence the function of Cygb in vivo. Recent research suggests that the protein can exist in a number of states depending on the integrity and position of disulfide bonds. In the present study, we show that the monomeric protein with an internal disulfide bond between the two cysteine residues Cys38 and Cys83, interacts with lipids to induce a change in haem co-ordination. The dimeric protein with intermolecular disulfide bonds and monomeric protein without an intramolecular disulfide bond does not exhibit these changes in haem co-ordination. Furthermore, monomeric Cygb with an intramolecular disulfide bond has significantly different properties, oxidizing lipid membranes and binding ligands more rapidly as compared with the other forms of the protein. The redox state of these cysteine residues in vivo is therefore highly significant and may be a mechanism to modulate the biochemical properties of the haem under conditions of stress.
Collapse
|
14
|
Norquay G, Leung G, Stewart NJ, Tozer GM, Wolber J, Wild JM. Relaxation and exchange dynamics of hyperpolarized129Xe in human blood. Magn Reson Med 2014; 74:303-11. [DOI: 10.1002/mrm.25417] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 07/25/2014] [Accepted: 07/29/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Graham Norquay
- Unit of Academic Radiology, Department of Cardiovascular Science; University of Sheffield; Sheffield South Yorkshire UK
| | - General Leung
- Unit of Academic Radiology, Department of Cardiovascular Science; University of Sheffield; Sheffield South Yorkshire UK
| | - Neil J. Stewart
- Unit of Academic Radiology, Department of Cardiovascular Science; University of Sheffield; Sheffield South Yorkshire UK
| | - Gillian M. Tozer
- Department of Oncology; University of Sheffield; Sheffield South Yorkshire UK
| | - Jan Wolber
- Unit of Academic Radiology, Department of Cardiovascular Science; University of Sheffield; Sheffield South Yorkshire UK
- GE Healthcare; Amersham Buckinghamshire UK
| | - Jim M. Wild
- Unit of Academic Radiology, Department of Cardiovascular Science; University of Sheffield; Sheffield South Yorkshire UK
| |
Collapse
|
15
|
Thakur N, Gupta S, Hade MD, Dikshit KL. Type I flavohemoglobin of mycobacterium smegmatis is a functional nitric oxide dioxygenase. IUBMB Life 2014; 66:396-404. [PMID: 24861678 DOI: 10.1002/iub.1275] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/06/2014] [Indexed: 12/12/2022]
Abstract
Two flavohemoglobins, type I and type II, displaying distinct structural features and cofactor binding sites coexist in Mycobacterium smegmatis; however, none of these flavohemeproteins are characterized so far. We have cloned and expressed type I flavohemoglobin (FHb1) of Mycobacterium smegmatis, encoded by MSMEG_1336, and characterized its spectral and functional properties. FHb1 exists as a monomer and displays spectral and functional characteristics similar to HMP of E. coli. Specific NO dioxygenase (NOD) activity of FHb1 was estimated to be 63.5 nmol heme(-1) sec(-1) , which was nearly eightfold higher than the HbN of M. tuberculosis and matched closely to the HMP of E. coli on the basis of cellular heme content. FHb1 preferred NADH for the NO dioxygenation and exhibited rapid reduction of flavin adenine dinucleotide and heme iron using NADH as electron donor. Level of FHb1 transcript increased significantly in M. smegmatis in the presence of acidified nitrite, and a nitric oxide-responsive transcriptional regulator of Rrf2 family exists together with the FHb1 under the same operon. These results suggested that FHb1 of M. smegmatis is a functional NOD and may be involved in the stress management of its host toward nitric oxide and nitrosative stress.
Collapse
Affiliation(s)
- Naveen Thakur
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
| | | | | | | |
Collapse
|
16
|
Affiliation(s)
- Luisa B. Maia
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - José J. G. Moura
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| |
Collapse
|
17
|
Colloc'h N, Prangé T. Functional relevance of the internal hydrophobic cavity of urate oxidase. FEBS Lett 2014; 588:1715-9. [PMID: 24657440 DOI: 10.1016/j.febslet.2014.03.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 03/10/2014] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
Abstract
Urate oxidase from Aspergillus flavus is a 135 kDa homo-tetramer which has a hydrophobic cavity buried within each monomer and located close to its active site. Crystallographic studies under moderate gas pressure and high hydrostatic pressure have shown that both gas presence and high pressure would rigidify the cavity leading to an inhibition of the catalytic activity. Analysis of the cavity volume variations and functional modifications suggest that the flexibility of the cavity would be an essential parameter for the active site efficiency. This cavity would act as a connecting vessel to give flexibility to the neighboring active site, and its expansion under pure oxygen pressure reveals that it might serve as a transient reservoir on its pathway to the active site.
Collapse
Affiliation(s)
- Nathalie Colloc'h
- CERVoxy Team, ISTCT UMR 6301, CNRS, Centre Cyceron, Caen, France; ISTCT UMR 6301, CEA, DSV/I2BM, Caen, France; ISTCT UMR 6301, Université de Caen Basse-Normandie, Normandie Université, Caen, France.
| | - Thierry Prangé
- LCRB UMR 8015, CNRS, Université Paris Descartes, Faculté de Pharmacie, 4 Avenue de l'Observatoire, 75006 Paris, France
| |
Collapse
|
18
|
Astudillo L, Bernad S, Derrien V, Sebban P, Miksovska J. Reduction of the internal disulfide bond between Cys 38 and 83 switches the ligand migration pathway in cytoglobin. J Inorg Biochem 2013; 129:23-9. [DOI: 10.1016/j.jinorgbio.2013.08.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 08/09/2013] [Accepted: 08/09/2013] [Indexed: 11/16/2022]
|
19
|
Tanwar AS, Goyal VD, Choudhary D, Panjikar S, Anand R. Importance of hydrophobic cavities in allosteric regulation of formylglycinamide synthetase: insight from xenon trapping and statistical coupling analysis. PLoS One 2013; 8:e77781. [PMID: 24223728 PMCID: PMC3815217 DOI: 10.1371/journal.pone.0077781] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 09/12/2013] [Indexed: 11/19/2022] Open
Abstract
Formylglycinamide ribonucleotide amidotransferase (FGAR-AT) is a 140 kDa bi-functional enzyme involved in a coupled reaction, where the glutaminase active site produces ammonia that is subsequently utilized to convert FGAR to its corresponding amidine in an ATP assisted fashion. The structure of FGAR-AT has been previously determined in an inactive state and the mechanism of activation remains largely unknown. In the current study, hydrophobic cavities were used as markers to identify regions involved in domain movements that facilitate catalytic coupling and subsequent activation of the enzyme. Three internal hydrophobic cavities were located by xenon trapping experiments on FGAR-AT crystals and further, these cavities were perturbed via site-directed mutagenesis. Biophysical characterization of the mutants demonstrated that two of these three voids are crucial for stability and function of the protein, although being ∼20 Å from the active centers. Interestingly, correlation analysis corroborated the experimental findings, and revealed that amino acids lining the functionally important cavities form correlated sets (co-evolving residues) that connect these regions to the amidotransferase active center. It was further proposed that the first cavity is transient and allows for breathing motion to occur and thereby serves as an allosteric hotspot. In contrast, the third cavity which lacks correlated residues was found to be highly plastic and accommodated steric congestion by local adjustment of the structure without affecting either stability or activity.
Collapse
Affiliation(s)
- Ajay Singh Tanwar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
| | - Venuka Durani Goyal
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
| | - Deepanshu Choudhary
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
| | - Santosh Panjikar
- Australian Synchrotron, Clayton, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Victoria, Australia
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
- * E-mail:
| |
Collapse
|
20
|
Pietra F. On the pathways of biologically relevant diatomic gases through proteins. Dioxygen and heme oxygenase from the perspective of molecular dynamics. Chem Biodivers 2013; 10:556-68. [PMID: 23576342 DOI: 10.1002/cbdv.201200434] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Indexed: 11/07/2022]
Abstract
This work deals with dioxygen (O2 ) binding sites and pathways through inducible human heme oxygenase (HO-1). The experimentally known distal binding site 1, and sites 2-3 above it, could be reproduced by means of non-deterministic random-acceleration molecular-dynamics (RAMD) simulations. In addition, RAMD revealed the proximal binding site 5, a deeply-seated binding site 4, which lies behind heme, as well as a few gates communicating with the external medium. In getting from site 1 to the main gate, which lies on the protein front opposed to site 4, O2 follows chiefly the shortest direct pathway. Less frequently, O2 visits intermediate sites 2, 4, or 5 along longer pathways. A similarity between HO-1, myoglobin, and cytoglobin in using, for diatomic gas delivery, the direct shortest pathway from the heme center to the surrounding medium, is emphasized. Otherwise, comparing other proteins and diatomic gases, each system reveals its peculiarities as to sites, gates, and pathways. Thus, relating these properties to the physiological functions of the proteins remains in general a challenge for future studies.
Collapse
Affiliation(s)
- Francesco Pietra
- Accademia Lucchese di Scienze, Lettere e Arti, Classe di Scienze, Palazzo Ducale, I-55100 Lucca.
| |
Collapse
|
21
|
Zhao C, Zhang B, Du W. Effects of distal mutation on the dynamic properties of carboxycytoglobin: a molecular dynamics simulation study. J Biol Inorg Chem 2013; 18:947-55. [DOI: 10.1007/s00775-013-1041-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 08/26/2013] [Indexed: 11/29/2022]
|
22
|
Pesce A, Tilleman L, Donné J, Aste E, Ascenzi P, Ciaccio C, Coletta M, Moens L, Viappiani C, Dewilde S, Bolognesi M, Nardini M. Structure and haem-distal site plasticity in Methanosarcina acetivorans protoglobin. PLoS One 2013; 8:e66144. [PMID: 23776624 PMCID: PMC3680402 DOI: 10.1371/journal.pone.0066144] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 05/01/2013] [Indexed: 12/04/2022] Open
Abstract
Protoglobin from Methanosarcina acetivorans C2A (MaPgb), a strictly anaerobic methanogenic Archaea, is a dimeric haem-protein whose biological role is still unknown. As other globins, protoglobin can bind O2, CO and NO reversibly in vitro, but it displays specific functional and structural properties within members of the hemoglobin superfamily. CO binding to and dissociation from the haem occurs through biphasic kinetics, which arise from binding to (and dissociation from) two distinct tertiary states in a ligation-dependent equilibrium. From the structural viewpoint, protoglobin-specific loops and a N-terminal extension of 20 residues completely bury the haem within the protein matrix. Thus, access of small ligand molecules to the haem is granted by two apolar tunnels, not common to other globins, which reach the haem distal site from locations at the B/G and B/E helix interfaces. Here, the roles played by residues Trp(60)B9, Tyr(61)B10 and Phe(93)E11 in ligand recognition and stabilization are analyzed, through crystallographic investigations on the ferric protein and on selected mutants. Specifically, protein structures are reported for protoglobin complexes with cyanide, with azide (also in the presence of Xenon), and with more bulky ligands, such as imidazole and nicotinamide. Values of the rate constant for cyanide dissociation from ferric MaPgb-cyanide complexes have been correlated to hydrogen bonds provided by Trp(60)B9 and Tyr(61)B10 that stabilize the haem-Fe(III)-bound cyanide. We show that protoglobin can strikingly reshape, in a ligand-dependent way, the haem distal site, where Phe(93)E11 acts as ligand sensor and controls accessibility to the haem through the tunnel system by modifying the conformation of Trp(60)B9.
Collapse
Affiliation(s)
| | - Lesley Tilleman
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Joke Donné
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Elisa Aste
- Department of Physics, University of Genova, Genova, Italy
| | - Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy, University Roma Tre, Roma, Italy
- Institute of Protein Biochemistry, National Research Council (CNR), Napoli, Italy
| | - Chiara Ciaccio
- Department of Clinical Sciences and Translational Medicine, University of Roma “Tor Vergata”, Roma, Italy
- Interuniversity Consortium for the Research on Chemistry of Metals in Biological Systems, Bari, Italy
| | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma “Tor Vergata”, Roma, Italy
- Interuniversity Consortium for the Research on Chemistry of Metals in Biological Systems, Bari, Italy
| | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Martino Bolognesi
- Department of Bioscience, University of Milano, Milano, Italy
- National Research Council-Biophysical Institute (CNR-IBF) and Interdisciplinary Centre for Nanostructured Materials and Interfaces (CIMaINa), University of Milano, Milano, Italy
| | - Marco Nardini
- Department of Bioscience, University of Milano, Milano, Italy
- * E-mail:
| |
Collapse
|
23
|
Pietra F. On the Pathways for CO Egress from Carboxy Human Cytoglobin. A Molecular-Dynamics Investigation. Chem Biodivers 2013; 10:86-95. [DOI: 10.1002/cbdv.201200374] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Indexed: 11/07/2022]
|
24
|
Gabba M, Abbruzzetti S, Spyrakis F, Forti F, Bruno S, Mozzarelli A, Luque FJ, Viappiani C, Cozzini P, Nardini M, Germani F, Bolognesi M, Moens L, Dewilde S. CO rebinding kinetics and molecular dynamics simulations highlight dynamic regulation of internal cavities in human cytoglobin. PLoS One 2013; 8:e49770. [PMID: 23308092 PMCID: PMC3537629 DOI: 10.1371/journal.pone.0049770] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 10/12/2012] [Indexed: 12/03/2022] Open
Abstract
Cytoglobin (Cygb) was recently discovered in the human genome and localized in different tissues. It was suggested to play tissue-specific protective roles, spanning from scavenging of reactive oxygen species in neurons to supplying oxygen to enzymes in fibroblasts. To shed light on the functioning of such versatile machinery, we have studied the processes supporting transport of gaseous heme ligands in Cygb. Carbon monoxide rebinding shows a complex kinetic pattern with several distinct reaction intermediates, reflecting rebinding from temporary docking sites, second order recombination, and formation (and dissociation) of a bis-histidyl heme hexacoordinated reaction intermediate. Ligand exit to the solvent occurs through distinct pathways, some of which exploit temporary docking sites. The remarkable change in energetic barriers, linked to heme bis-histidyl hexacoordination by HisE7, may be responsible for active regulation of the flux of reactants and products to and from the reaction site on the distal side of the heme. A substantial change in both protein dynamics and inner cavities is observed upon transition from the CO-liganded to the pentacoordinated and bis-histidyl hexacoordinated species, which could be exploited as a signalling state. These findings are consistent with the expected versatility of the molecular activity of this protein.
Collapse
Affiliation(s)
- Matteo Gabba
- Institute of Complex Systems - Molekulare Biophysik (ICS-5) Forschungszentrum Jülich, Jülich, Germany
| | - Stefania Abbruzzetti
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Parma, Parma, Italy
| | - Francesca Spyrakis
- Dipartimento di Scienze degli Alimenti, Università degli Studi di Parma, Parma, Italy
- INBB, Biostructures and Biosystems National Institute, Rome, Italy
| | - Flavio Forti
- Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
| | - Stefano Bruno
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma, Italy
| | - Andrea Mozzarelli
- Dipartimento di Farmacia, Università degli Studi di Parma, Parma, Italy
| | - F. Javier Luque
- Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
| | - Cristiano Viappiani
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Parma, Parma, Italy
- NEST, Istituto Nanoscienze-CNR, Pisa, Italy
- * E-mail:
| | - Pietro Cozzini
- Dipartimento di Scienze degli Alimenti, Università degli Studi di Parma, Parma, Italy
- INBB, Biostructures and Biosystems National Institute, Rome, Italy
| | - Marco Nardini
- Dipartimento di BioScienze, CNR-IBF, and CIMAINA, Università degli Studi di Milano, Milano, Italy
| | - Francesca Germani
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Martino Bolognesi
- Dipartimento di BioScienze, CNR-IBF, and CIMAINA, Università degli Studi di Milano, Milano, Italy
| | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| |
Collapse
|
25
|
Luna VM, Fee JA, Deniz AA, Stout CD. Mobility of Xe atoms within the oxygen diffusion channel of cytochrome ba(3) oxidase. Biochemistry 2012; 51:4669-76. [PMID: 22607023 DOI: 10.1021/bi3003988] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We use a form of "freeze-trap, kinetic crystallography" to explore the migration of Xe atoms away from the dinuclear heme a(3)/Cu(B) center in Thermus thermophilus cytochrome ba(3) oxidase. This enzyme is a member of the heme-copper oxidase superfamily and is thus crucial for dioxygen-dependent life. The mechanisms involved in the migration of oxygen, water, electrons, and protons into and/or out of the specialized channels of the heme-copper oxidases are generally not well understood. Pressurization of crystals with Xe gas previously revealed a O(2) diffusion channel in cytochrome ba(3) oxidase that is continuous, Y-shaped, 18-20 Å in length and comprised of hydrophobic residues, connecting the protein surface within the bilayer to the a(3)-Cu(B) center in the active site. To understand movement of gas molecules within the O(2) channel, we performed crystallographic analysis of 19 Xe laden crystals freeze-trapped in liquid nitrogen at selected times between 0 and 480 s while undergoing outgassing at room temperature. Variation in Xe crystallographic occupancy at five discrete sites as a function of time leads to a kinetic model revealing relative degrees of mobility of Xe atoms within the channel. Xe egress occurs primarily through the channel formed by the Xe1 → Xe5 → Xe3 → Xe4 sites, suggesting that ingress of O(2) is likely to occur by the reverse of this process. The channel itself appears not to undergo significant structural changes during Xe migration, thereby indicating a passive role in this important physiological function.
Collapse
Affiliation(s)
- V Mitch Luna
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | | | | | | |
Collapse
|
26
|
McRonald FE, Risk JM, Hodges NJ. Protection from intracellular oxidative stress by cytoglobin in normal and cancerous oesophageal cells. PLoS One 2012; 7:e30587. [PMID: 22359545 PMCID: PMC3281032 DOI: 10.1371/journal.pone.0030587] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 12/22/2011] [Indexed: 01/09/2023] Open
Abstract
Cytoglobin is an intracellular globin of unknown function that is expressed mostly in cells of a myofibroblast lineage. Possible functions of cytoglobin include buffering of intracellular oxygen and detoxification of reactive oxygen species. Previous work in our laboratory has demonstrated that cytoglobin affords protection from oxidant-induced DNA damage when over expressed in vitro, but the importance of this in more physiologically relevant models of disease is unknown. Cytoglobin is a candidate for the tylosis with oesophageal cancer gene, and its expression is strongly down-regulated in non-cancerous oesophageal biopsies from patients with TOC compared with normal biopsies. Therefore, oesophageal cells provide an ideal experimental model to test our hypothesis that downregulation of cytoglobin expression sensitises cells to the damaging effects of reactive oxygen species, particularly oxidative DNA damage, and that this could potentially contribute to the TOC phenotype. In the current study, we tested this hypothesis by manipulating cytoglobin expression in both normal and oesophageal cancer cell lines, which have normal physiological and no expression of cytoglobin respectively. Our results show that, in agreement with previous findings, over expression of cytoglobin in cancer cell lines afforded protection from chemically-induced oxidative stress but this was only observed at non-physiological concentrations of cytoglobin. In addition, down regulation of cytoglobin in normal oesophageal cells had no effect on their sensitivity to oxidative stress as assessed by a number of end points. We therefore conclude that normal physiological concentrations of cytoglobin do not offer cytoprotection from reactive oxygen species, at least in the current experimental model.
Collapse
Affiliation(s)
- Fiona E. McRonald
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, United Kingdom
- School of Dentistry, The University of Liverpool, Liverpool, United Kingdom
| | - Janet M. Risk
- School of Dentistry, The University of Liverpool, Liverpool, United Kingdom
| | - Nikolas J. Hodges
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, United Kingdom
| |
Collapse
|
27
|
Zhang B, Xu J, Li Y, Du W, Fang W. Molecular dynamics simulation of carboxy and deoxy human cytoglobin in solution. J Inorg Biochem 2011; 105:949-56. [DOI: 10.1016/j.jinorgbio.2011.03.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 03/28/2011] [Accepted: 03/28/2011] [Indexed: 11/30/2022]
|
28
|
Bocahut A, Bernad S, Sebban P, Sacquin-Mora S. Frontier Residues Lining Globin Internal Cavities Present Specific Mechanical Properties. J Am Chem Soc 2011; 133:8753-61. [DOI: 10.1021/ja202587a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anthony Bocahut
- Laboratoire de Biochimie Théorique, UMR 9080 CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Sophie Bernad
- Laboratoire de Chimie Physique, CNRS UMR8000, Bât. 350, Université Paris-sud, 91405 Orsay, France
| | - Pierre Sebban
- Laboratoire de Chimie Physique, CNRS UMR8000, Bât. 350, Université Paris-sud, 91405 Orsay, France
- Université des Sciences et des Technologies de Hanoi, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, UMR 9080 CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| |
Collapse
|
29
|
de Serrano V, Franzen S. Structural evidence for stabilization of inhibitor binding by a protein cavity in the dehaloperoxidase-hemoglobin from Amphitrite ornata. Biopolymers 2011; 98:27-35. [DOI: 10.1002/bip.21674] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 04/13/2011] [Accepted: 04/18/2011] [Indexed: 01/23/2023]
|
30
|
Forti F, Boechi L, Estrin DA, Marti MA. Comparing and combining implicit ligand sampling with multiple steered molecular dynamics to study ligand migration processes in heme proteins. J Comput Chem 2011; 32:2219-31. [DOI: 10.1002/jcc.21805] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Revised: 01/18/2011] [Accepted: 03/06/2011] [Indexed: 12/30/2022]
|
31
|
Pesce A, Nardini M, Dewilde S, Capece L, Martí MA, Congia S, Salter MD, Blouin GC, Estrin DA, Ascenzi P, Moens L, Bolognesi M, Olson JS. Ligand migration in the apolar tunnel of Cerebratulus lacteus mini-hemoglobin. J Biol Chem 2010; 286:5347-58. [PMID: 21147768 DOI: 10.1074/jbc.m110.169045] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The large apolar tunnel traversing the mini-hemoglobin from Cerebratulus lacteus (CerHb) has been examined by x-ray crystallography, ligand binding kinetics, and molecular dynamic simulations. The addition of 10 atm of xenon causes loss of diffraction in wild-type (wt) CerHbO(2) crystals, but Leu-86(G12)Ala CerHbO(2), which has an increased tunnel volume, stably accommodates two discrete xenon atoms: one adjacent to Leu-86(G12) and another near Ala-55(E18). Molecular dynamics simulations of ligand migration in wt CerHb show a low energy pathway through the apolar tunnel when Leu or Ala, but not Phe or Trp, is present at the 86(G12) position. The addition of 10-15 atm of xenon to solutions of wt CerHbCO and L86A CerHbCO causes 2-3-fold increases in the fraction of geminate ligand recombination, indicating that the bound xenon blocks CO escape. This idea was confirmed by L86F and L86W mutations, which cause even larger increases in the fraction of geminate CO rebinding, 2-5-fold decreases in the bimolecular rate constants for ligand entry, and large increases in the computed energy barriers for ligand movement through the apolar tunnel. Both the addition of xenon to the L86A mutant and oxidation of wt CerHb heme iron cause the appearance of an out Gln-44(E7) conformer, in which the amide side chain points out toward the solvent and appears to lower the barrier for ligand escape through the E7 gate. However, the observed kinetics suggest little entry and escape (≤ 25%) through the E7 pathway, presumably because the in Gln-44(E7) conformer is thermodynamically favored.
Collapse
Affiliation(s)
- Alessandra Pesce
- Department of Physics, University of Genova, Via Dodecaneso 33, 16146 Genova, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
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]
|
33
|
Arroyo-Mañez P, Bikiel DE, Boechi L, Capece L, Di Lella S, Estrin DA, Martí MA, Moreno DM, Nadra AD, Petruk AA. Protein dynamics and ligand migration interplay as studied by computer simulation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:1054-64. [PMID: 20797453 DOI: 10.1016/j.bbapap.2010.08.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 08/12/2010] [Accepted: 08/13/2010] [Indexed: 10/19/2022]
Abstract
Since proteins are dynamic systems in living organisms, the employment of methodologies contemplating this crucial characteristic results fundamental to allow revealing several aspects of their function. In this work, we present results obtained using classical mechanical atomistic simulation tools applied to understand the connection between protein dynamics and ligand migration. Firstly, we will present a review of the different sampling schemes used in the last years to obtain both ligand migration pathways and the thermodynamic information associated with the process. Secondly, we will focus on representative examples in which the schemes previously presented are employed, concerning the following: i) ligand migration, tunnels, and cavities in myoglobin and neuroglobin; ii) ligand migration in truncated hemoglobin members; iii) NO escape and conformational changes in nitrophorins; iv) ligand selectivity in catalase and hydrogenase; and v) larger ligand migration: the P450 and haloalkane dehalogenase cases. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
Collapse
Affiliation(s)
- Pau Arroyo-Mañez
- Departamento de Química Inorgánica, Analítica y Química-Física (INQUIMAE-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Savino C, Miele AE, Draghi F, Johnson KA, Sciara G, Brunori M, Vallone B. Pattern of cavities in globins: The case of human hemoglobin. Biopolymers 2009; 91:1097-107. [DOI: 10.1002/bip.21201] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
35
|
Moschetti T, Mueller U, Schulze J, Brunori M, Vallone B. The structure of neuroglobin at high Xe and Kr pressure reveals partial conservation of globin internal cavities. Biophys J 2009; 97:1700-8. [PMID: 19751675 PMCID: PMC2741589 DOI: 10.1016/j.bpj.2009.05.059] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Revised: 05/13/2009] [Accepted: 05/14/2009] [Indexed: 10/20/2022] Open
Abstract
Neuroglobin (Ngb) is a hexacoordinate globin expressed in the brain of vertebrates. Ferrous Ngb binds dioxygen with high affinity and the O(2) adduct is able to scavenge NO. Convincing in vitro and in vivo data indicate that Ngb is involved in neuroprotection during hypoxia and ischemia. The 3D structure of Ngb reveals the presence of a wide internal cavity connecting its heme active site with the bulk. To explore the role of this "tunnel" in the control of ligand binding, we determined the structure of metNgb and NgbCO equilibrated with Xe or Kr. We show four docking sites for Xe (only two for Kr); two of the four Xe sites are within the large cavity. They are only partially conserved in globins, since the two proximal Xe sites identified in myoglobin (Xe1 and Xe2) are absent in Ngb, as well as in cytoglobin. The Xe docking sites in Ngb map a pathway within the protein matrix, leading to the heme, which becomes more accessible in the ligand-bound species. This may be of significance in connection with the redox chemistry that may be the primary function of this hexacoordinate globin.
Collapse
Affiliation(s)
- Tommaso Moschetti
- Department of Biochemical Sciences “A.Rossi-Fanelli”, University of Rome “La Sapienza”, Rome, Italy
| | - Uwe Mueller
- Macromolecular Crystallography Group, Helmholtz Zentrum Berlin für Materialien und Energie, BESSY-II, Berlin, Germany
| | - Jörg Schulze
- Macromolecular Crystallography Group, Helmholtz Zentrum Berlin für Materialien und Energie, BESSY-II, Berlin, Germany
| | - Maurizio Brunori
- Department of Biochemical Sciences “A.Rossi-Fanelli”, University of Rome “La Sapienza”, Rome, Italy
| | - Beatrice Vallone
- Department of Biochemical Sciences “A.Rossi-Fanelli”, University of Rome “La Sapienza”, Rome, Italy
| |
Collapse
|
36
|
Teilum K, Olsen JG, Kragelund BB. Functional aspects of protein flexibility. Cell Mol Life Sci 2009; 66:2231-47. [PMID: 19308324 PMCID: PMC11115794 DOI: 10.1007/s00018-009-0014-6] [Citation(s) in RCA: 157] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Revised: 02/24/2009] [Accepted: 03/04/2009] [Indexed: 12/29/2022]
Abstract
Proteins are dynamic entities, and they possess an inherent flexibility that allows them to function through molecular interactions within the cell, among cells and even between organisms. Appreciation of the non-static nature of proteins is emerging, but to describe and incorporate this into an intuitive perception of protein function is challenging. Flexibility is of overwhelming importance for protein function, and the changes in protein structure during interactions with binding partners can be dramatic. The present review addresses protein flexibility, focusing on protein-ligand interactions. The thermodynamics involved are reviewed, and examples of structure-function studies involving experimentally determined flexibility descriptions are presented. While much remains to be understood about protein flexibility, it is clear that it is encoded within their amino acid sequence and should be viewed as an integral part of their structure.
Collapse
Affiliation(s)
- Kaare Teilum
- Structural Biology and NMR Laboratory (SBiN-Lab), Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Johan G. Olsen
- Structural Biology and NMR Laboratory (SBiN-Lab), Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Birthe B. Kragelund
- Structural Biology and NMR Laboratory (SBiN-Lab), Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| |
Collapse
|
37
|
Shigematsu A, Adachi Y, Matsubara J, Mukaide H, Koike-Kiriyama N, Minamino K, Shi M, Yanai S, Imamura M, Taketani S, Ikehara S. Analyses of expression of cytoglobin by immunohistochemical studies in human tissues. Hemoglobin 2008; 32:287-96. [PMID: 18473245 DOI: 10.1080/03630260802017261] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Cytoglobin (Cygb) is a recently discovered member of the vertebrate globin family, which includes probably most extensively studied proteins, hemoglobin (Hb), myoglobin (Mb) and neuroglobin (Ngb). It has been reported that Cygb is expressed ubiquitously at the mRNA or protein level. However, details of the distribution of Cygb in the various tissues have hitherto been unclear. In this experiment, we clarified the distribution of Cygb in various human tissues by immunohistochemical staining. First, we prepared a rabbit anti human Cygb polyclonal antibody. Using the antibody, we stained a tissue array slide containing 60 normal tissues from 40 human organs. We confirmed the staining patterns of the antibodies in these various tissues using autopsy samples from our university. In general, Cygb is positive in the epithelial cells, hepatocytes, pancreatic acinar cells, cardiomyocytes and skeletal muscle but rarely so in cells in the interstitial tissues. Cytoglobin is usually positive in the cytoplasm, but is also positive in the nucleus in some hepatocytes. In contrast, Cygb is negative in the smooth muscle. The distribution of Cygb could suggest its roles.
Collapse
Affiliation(s)
- Akio Shigematsu
- First Department of Pathology, Kansai Medical University, Moriguchi City, Osaka, Japan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Reactions of ferrous neuroglobin and cytoglobin with nitrite under anaerobic conditions. J Inorg Biochem 2008; 102:1777-82. [PMID: 18599123 DOI: 10.1016/j.jinorgbio.2008.05.008] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2008] [Revised: 05/01/2008] [Accepted: 05/19/2008] [Indexed: 11/19/2022]
Abstract
Recent evidence suggests that the reaction of nitrite with deoxygenated hemoglobin and myoglobin contributes to the generation of nitric oxide and S-nitrosothiols in vivo under conditions of low oxygen availability. We have investigated whether ferrous neuroglobin and cytoglobin, the two hexacoordinate globins from vertebrates expressed in brain and in a variety of tissues, respectively, also react with nitrite under anaerobic conditions. Using absorption spectroscopy, we find that ferrous neuroglobin and nitrite react with a second-order rate constant similar to that of myoglobin, whereas the ferrous heme of cytoglobin does not react with nitrite. Deconvolution of absorbance spectra shows that, in the course of the reaction of neuroglobin with nitrite, ferric Fe(III) heme is generated in excess of nitrosyl Fe(II)-NO heme as due to the low affinity of ferrous neuroglobin for nitric oxide. By using ferrous myoglobin as scavenger for nitric oxide, we find that nitric oxide dissociates from ferrous neuroglobin much faster than previously appreciated, consistently with the decay of the Fe(II)-NO product during the reaction. Both neuroglobin and cytoglobin are S-nitrosated when reacting with nitrite, with neuroglobin showing higher levels of S-nitrosation. The possible biological significance of the reaction between nitrite and neuroglobin in vivo under brain hypoxia is discussed.
Collapse
|
39
|
Chen L, Lyubimov AY, Brammer L, Vrielink A, Sampson NS. The binding and release of oxygen and hydrogen peroxide are directed by a hydrophobic tunnel in cholesterol oxidase. Biochemistry 2008; 47:5368-77. [PMID: 18410129 DOI: 10.1021/bi800228w] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The usage by enzymes of specific binding pathways for gaseous substrates or products is debated. The crystal structure of the redox enzyme cholesterol oxidase, determined at sub-angstrom resolution, revealed a hydrophobic tunnel that may serve as a binding pathway for oxygen and hydrogen peroxide. This tunnel is formed by a cascade of conformational rearrangements and connects the active site with the exterior surface of the protein. To elucidate the relationship between this tunnel and gas binding and release, three mutant enzymes were constructed to block the tunnel or its putative gate. Mutation of the proposed gating residue Asn485 to Asp or tunnel residue Phe359 or Gly347 to Trp or Asn reduces the catalytic efficiency of oxidation. The K mO 2 increases from 300 +/- 35 microM for the wild-type enzyme to 617 +/- 15 microM for the F359W mutant. The k cat for the F359W mutant-catalyzed reaction decreases 13-fold relative to that of the wild-type-catalyzed reaction. The N485D and G347N mutants could not be saturated with oxygen. Transfer of hydride from the sterol to the flavin prosthetic group is no longer rate-limiting for these tunnel mutants. The steady-state kinetics of both wild-type and tunnel mutant enzymes are consistent with formation of a ternary complex of steroid and oxygen during catalysis. Furthermore, kinetic cooperativity with respect to molecular oxygen is observed with the tunnel mutants, but not with the wild-type enzyme. A rate-limiting conformational change for binding and release of oxygen and hydrogen peroxide, respectively, is consistent with the cooperative kinetics. In the atomic-resolution structure of F359W, the indole ring of the tryptophan completely fills the tunnel and is observed in only a single conformation. The size of the indole is proposed to limit conformational rearrangement of residue 359 that leads to tunnel opening in the wild-type enzyme. Overall, these results substantiate the functional importance of the tunnel for substrate binding and product release.
Collapse
Affiliation(s)
- Lin Chen
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
| | | | | | | | | |
Collapse
|
40
|
Orlowski S, Nowak W. Locally enhanced sampling molecular dynamics study of the dioxygen transport in human cytoglobin. J Mol Model 2007; 13:715-23. [PMID: 17503097 DOI: 10.1007/s00894-007-0203-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Accepted: 03/20/2007] [Indexed: 11/28/2022]
Abstract
Cytoglobin (Cyg)--a new member of the vertebrate heme globin family--is expressed in many tissues of the human body but its physiological role is still unclear. It may deliver oxygen under hypoxia, serve as a scavenger of reactive species or be involved in collagen synthesis. This protein is usually six-coordinated and binds oxygen by a displacement of the distal HisE7 imidazole. In this paper, the results of 60 ns molecular dynamics (MD) simulations of dioxygen diffusion inside Cyg matrix are discussed. In addition to a classical MD trajectory, an approximate Locally Enhanced Sampling (LES) method has been employed. Classical diffusion paths were carefully analyzed, five cavities in dynamical structures were determined and at least four distinct ligand exit paths were identified. The most probable exit/entry path is connected with a large tunnel present in Cyg. Several residues that are perhaps critical for kinetics of small gaseous diffusion were discovered. A comparison of gaseous ligand transport in Cyg and in the most studied heme protein myoglobin is presented. Implications of efficient oxygen transport found in Cyg to its possible physiological role are discussed.
Collapse
Affiliation(s)
- Slawomir Orlowski
- Theoretical Molecular Biophysics Group, Institute of Physics, Nicolaus Copernicus University, ul. Grudziadzka 5, 87-100, Torun, Poland
| | | |
Collapse
|
41
|
Mouawad L, Tetreau C, Abdel-Azeim S, Perahia D, Lavalette D. CO migration pathways in cytochrome P450cam studied by molecular dynamics simulations. Protein Sci 2007; 16:781-94. [PMID: 17400927 PMCID: PMC2206643 DOI: 10.1110/ps.062374707] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Previous laser flash photolysis investigations between 100 and 300 K have shown that the kinetics of CO rebinding with cytochrome P450(cam)(camphor) consist of up to four different processes revealing a complex internal dynamics after ligand dissociation. In the present work, molecular dynamics simulations were undertaken on the ternary complex P450(cam)(cam)(CO) to explore the CO migration pathways, monitor the internal cavities of the protein, and localize the CO docking sites. One trajectory of 1 nsec with the protein in a water box and 36 trajectories of 1 nsec in the vacuum were calculated. In each trajectory, the protein contained only one CO ligand on which no constraints were applied. The simulations were performed at 200, 300, and 320 K. The results indicate the presence of seven CO docking sites, mainly hydrophobic, located in the same moiety of the protein. Two of them coincide with xenon binding sites identified by crystallography. The protein matrix exhibits eight persistent internal cavities, four of which corresponding to the ligand docking sites. In addition, it was observed that water molecules entering the protein were mainly attracted into the polar pockets, far away from the CO docking sites. Finally, the identified CO migration pathways provide a consistent interpretation of the experimental rebinding kinetics.
Collapse
Affiliation(s)
- Liliane Mouawad
- Inserm U759, Institut Curie-Recherche, Bâtiment 112, Université Paris-Sud, 91405 Orsay cedex, France.
| | | | | | | | | |
Collapse
|
42
|
Franzen S, Gilvey LB, Belyea JL. The pH dependence of the activity of dehaloperoxidase from Amphitrite ornata. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1774:121-30. [PMID: 17182294 DOI: 10.1016/j.bbapap.2006.09.019] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Revised: 09/18/2006] [Accepted: 09/29/2006] [Indexed: 11/17/2022]
Abstract
Dehaloperoxidase (DHP) from the terebellid polychaete, Amphitrite ornata, is the first hemoglobin that has peroxidase activity as part of its native function. The substrate 2,4,6-tribromophenol (TBP) is oxidatively debrominated by DHP to form 2,6-dibromoquinone (DBQ) in a two-electron process. There is a well-defined internal binding site for TBP above the heme, a feature not observed in other hemoglobins or peroxidases. A study of the pH dependence of the activity of DHP reveals a substantial difference in mechanism. From direct observation of the Soret band of the heme it is shown that the pKa for heme activation in protein DHP is 6.5. Below this pH the heme absorbance decreases in the presence of H2O2 with or without addition of substrate. The low pH data are consistent with significant heme degradation. Above pH 6.5 addition of H2O2 causes the heme to shift rapidly to a compound II spectrum and then slowly to an unidentified intermediate with an absorbance of 410 nm. However, the pKa of the substrate TBP is 6.8 and the greatest enzyme activity is observed above the pKa of TBP under conditions where the substrate is a phenolate anion (TPBO-). Although the mechanisms may differ, the data show that both neutral TBP and anionic TPBO- are converted to the quinone product. The mechanistic implications of the pH dependence are discussed by comparison other known peroxidases, which oxidize substrates at the heme edge.
Collapse
Affiliation(s)
- Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA.
| | | | | |
Collapse
|
43
|
Mammen PP, Shelton JM, Ye Q, Kanatous SB, McGrath AJ, Richardson JA, Garry DJ. Cytoglobin is a stress-responsive hemoprotein expressed in the developing and adult brain. J Histochem Cytochem 2006; 54:1349-61. [PMID: 16899760 PMCID: PMC3958125 DOI: 10.1369/jhc.6a7008.2006] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Cytoglobin (Cygb) is a novel tissue hemoprotein relatively similar to myoglobin (Mb). Because Cygb shares several structural features with Mb, we hypothesized that Cygb functions in the modulation of oxygen and nitric oxide metabolism or in scavenging free radicals within a cell. In the present study we examined the spatial and temporal expression pattern of Cygb during murine embryogenesis. Using in situ hybridization, RT-PCR, and Northern blot analyses, limited Cygb expression was observed during embryogenesis compared with Mb expression. Cygb expression was primarily restricted to the central nervous system and neural crest derivatives during the latter stages of development. In the adult mouse, Cygb is expressed in distinct regions of the brain as compared with neuroglobin (Ngb), another globin protein, and these regions are responsive to oxidative stress (i.e., hippocampus, thalamus, and hypothalamus). In contrast to Ngb, Cygb expression in the brain is induced in response to chronic hypoxia (10% oxygen). These results support the hypothesis that Cygb is an oxygen-responsive tissue hemoglobin expressed in distinct regions of thenormoxic and hypoxic brain and may play a key role in the response of the brain to ahypoxic insult.
Collapse
Affiliation(s)
- Pradeep P.A. Mammen
- Departments of Internal Medicine University of Texas Southwestern Medical Center, Dallas, Texas
- Donald W. Reynolds Cardiovascular Clinical Research Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - John M. Shelton
- Departments of Internal Medicine University of Texas Southwestern Medical Center, Dallas, Texas
- Donald W. Reynolds Cardiovascular Clinical Research Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Qiu Ye
- Departments of Internal Medicine University of Texas Southwestern Medical Center, Dallas, Texas
| | - Shane B. Kanatous
- Departments of Internal Medicine University of Texas Southwestern Medical Center, Dallas, Texas
| | - Amanda J. McGrath
- Departments of Internal Medicine University of Texas Southwestern Medical Center, Dallas, Texas
| | - James A. Richardson
- Pathology University of Texas Southwestern Medical Center, Dallas, Texas
- Molecular Biology University of Texas Southwestern Medical Center, Dallas, Texas
| | - Daniel J. Garry
- Departments of Internal Medicine University of Texas Southwestern Medical Center, Dallas, Texas
- Molecular Biology University of Texas Southwestern Medical Center, Dallas, Texas
- Donald W. Reynolds Cardiovascular Clinical Research Center, University of Texas Southwestern Medical Center, Dallas, Texas
| |
Collapse
|
44
|
Walker FA. The heme environment of mouse neuroglobin: histidine imidazole plane orientations obtained from solution NMR and EPR spectroscopy as compared with X-ray crystallography. J Biol Inorg Chem 2006; 11:391-7. [PMID: 16586113 DOI: 10.1007/s00775-006-0095-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2006] [Accepted: 02/22/2006] [Indexed: 12/16/2022]
Abstract
The 1H NMR chemical shifts of the heme methyl groups of the ferriheme complex of metneuroglobin (Du et al. in J. Am. Chem. Soc. 125:8080-8081, 2003) predict orientations of the axial histidine ligands (Shokhirev and Walker in J. Biol. Inorg. Chem. 3:581-594, 1998) that are not consistent with the X-ray data (Vallone et al. in Proteins Struct. Funct. Bioinf. 56:85-94, 2004), and the EPR spectrum (Vinck et al. in J. Am. Chem. Soc. 126:4516-4517, 2004) is only marginally consistent with these data. The reasons for these inconsistencies appear to be rooted in the high degree of aqueous solution exposure of the heme group and the fact that there are no strong hydrogen-bond acceptors for the histidine imidazole N-H protons provided by the protein. Similar inconsistencies may exist for other water-soluble heme proteins, and 1H NMR spectroscopy provides a simple means to verify whether the solution structure of the heme center is the same as or different from that in the crystalline state.
Collapse
Affiliation(s)
- F Ann Walker
- Department of Chemistry, The University of Arizona, PO Box 210041, Tucson, AZ 85721-0041, USA.
| |
Collapse
|
45
|
de Sanctis D, Dewilde S, Vonrhein C, Pesce A, Moens L, Ascenzi P, Hankeln T, Burmester T, Ponassi M, Nardini M, Bolognesi M. Bishistidyl Heme Hexacoordination, a Key Structural Property in Drosophila melanogaster Hemoglobin. J Biol Chem 2005; 280:27222-9. [PMID: 15917230 DOI: 10.1074/jbc.m503814200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hemoglobins at high concentration have been isolated long ago from some insect larvae living in hypoxic environments. Conversely, a monomeric hemoglobin has been discovered recently in the fruit fly Drosophila melanogaster as intracellular protein expressed both in larvae and in the adult fly. Such a finding indicates that the oxygen supply in insects may be more complex than previously thought, relying not only on O2 diffusion through the tubular tracheal system, but also on carrier-mediated transport and storage. We present here the crystal structure of recombinant D. melanogaster hemoglobin at 1.20 A resolution. Spectroscopic data show that the protein displays a hexacoordinated heme, whose axial ligands are the proximal and distal His residues. Such bis-His ligation of the heme has sizable effects on the protein local structure. Three protein matrix cavities, comparable in size but not in topological locations with those of sperm whale myoglobin, are spread through the protein matrix; one of these can host a xenon atom. Additionally, D. melanogaster hemoglobin binds one molecule of 3-(cyclohexylamino)propanesulfonic acid (CAPS) buffer at a surface pocket, next to the EF hinge. Despite the high resolution achieved, no sequence/structure features specifically supporting the heme hexa- to pentacoordination transition required for diatomic ligand binding could be recognized.
Collapse
Affiliation(s)
- Daniele de Sanctis
- Department of Physics, National Institute for the Physics of Matter (NFM), University of Genova, Genova I-16146, Italy
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Ascenzi P, Bocedi A, de Sanctis D, Pesce A, Bolognesi M, Marden MC, Dewilde S, Moens L, Hankeln T, Burmester T. Neuroglobin and cytoglobin: Two new entries in the hemoglobin superfamily*. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2004; 32:305-313. [PMID: 21706744 DOI: 10.1002/bmb.2004.494032050386] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Neuroglobin (Ngb) and cytoglobin (Cygb) are two newly discovered intracellular members of the vertebrate hemoglobin (Hb) family. Ngb, predominantly expressed in nerve cells, is of ancient evolutionary origin and is homologous to nerve-globins of invertebrates. Cygb, present in many different tissues, shares common ancestry with myoglobin (Mb) and can be traced to early vertebrate evolution. Ngb and Cygb display the classical three-on-three α-helical globin fold and are endowed with a hexa-coordinate heme Fe atom, in both their ferrous and ferric forms, having the heme distal HisE7 residue as the endogenous sixth ligand. Reversible intramolecular hexa- to penta-coordination of the heme Fe atom modulates Ngb and Cygb ligand-binding properties. In Ngb and Cygb, ligand migration to/from the heme distal site may be assisted by protein/matrix tunnel cavity systems. The physiological roles of Ngb and Cygb are poorly understood. Ngb may protect neuronal cells from hypoxic-ischemic insults, may act as oxidative stress-responsive sensor protein, and may sustain NO/O(2) scavenging and/or reactive oxygen species (ROS) detoxification. Cygb, located in the cytoplasm of fibroblasts, chondroblasts, osteoblasts, and hepatic stellate cells, has been hypothesized to be involved in collagen synthesis. In neurons, Cygb, located in both cytoplasm and nucleus, may provide O(2) for enzymatic reactions, and may be involved in a ROS (NO)-signaling pathway(s). Here, we review current knowledge on Ngb and Cygb in terms of their structure, function, and evolutionary links to the well-known human HbA and Mb.
Collapse
Affiliation(s)
- Paolo Ascenzi
- Department of Biology and the Interdepartmental Laboratory for Electron Microscopy, University "Roma Tre," I-00146 Roma, Italy; National Institute for Infectious Diseases IRCSS "Lazzaro Spallanzani," I-00149 Roma, Italy.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Fago A, Hundahl C, Dewilde S, Gilany K, Moens L, Weber RE. Allosteric regulation and temperature dependence of oxygen binding in human neuroglobin and cytoglobin. Molecular mechanisms and physiological significance. J Biol Chem 2004; 279:44417-26. [PMID: 15299006 DOI: 10.1074/jbc.m407126200] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two new globin proteins have recently been discovered in vertebrates, neuroglobin in neurons and cytoglobin in all tissues, both showing heme hexacoordination by the distal His(E7) in the absence of gaseous ligands. In analogy to hemoglobin and myoglobin, neuroglobin and cytoglobin are supposedly involved in O2 storage and delivery, although their physiological role remains to be solved. Here we report O2 equilibria of recombinant human neuroglobin (NGB) and cytoglobin (CYGB) measured under close to physiological conditions and at varying temperature and pH ranges. NGB shows both alkaline and acid Bohr effects (pH-dependent O2 affinity) and temperature-dependent enthalpy of oxygenation. O2 and CO binding equilibrium studies on neuroglobin mutants strongly suggest that the bound O2 is stabilized by interactions with His(E7) and that this residue functions as a major Bohr group in the presence of Lys(E10). As shown by the titration of free thiols with 4,4'-dithiodipyridine and by mass spectrometry, this mechanism of modulating O2 affinity is independent of formation of an internal disulfide bond under the experimental conditions used, which stabilize thiols in the reduced form. In CYGB, O2 binding is cooperative, consistent with its proposed dimeric structure. Similar to myoglobin but in contrast to NGB, O2 binding to CYGB is pH-independent and exothermic throughout the temperature range investigated. Our data support the hypothesis that CYGB may be involved in O2-requiring metabolic processes. In contrast, the lower O2 affinity in NGB does not appear compatible with a physiological role involving mitochondrial O2 supply at the low O2 tensions found within neurons.
Collapse
Affiliation(s)
- Angela Fago
- Department of Zoophysiology, Institute of Biological Sciences, C. F. Møllers Alle 131, Aarhus University, DK-8000 Aarhus C, Denmark.
| | | | | | | | | | | |
Collapse
|