1
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Freindorf M, Antonio JJ, Kraka E. Iron-histidine bonding in bishistidyl hemoproteins-A local vibrational mode study. J Comput Chem 2024; 45:574-588. [PMID: 38041830 DOI: 10.1002/jcc.27267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 12/04/2023]
Abstract
We investigated the intrinsic strength of distal and proximal FeN bonds for both ferric and ferrous oxidation states of bishistidyl hemoproteins from bacteria, animals, human, and plants, including two cytoglobins, ten hemoglobins, two myoglobins, six neuroglobins, and six phytoglobins. As a qualified measure of bond strength, we used local vibrational force constants ka (FeN) based on local mode theory developed in our group. All calculations were performed with a hybrid QM/MM ansatz. Starting geometries were taken from available x-ray structures. ka (FeN) values were correlated with FeN bond lengths and covalent bond character. We also investigated the stiffness of the axial NFeN bond angle. Our results highlight that protein effects are sensitively reflected in ka (FeN), allowing one to compare trends in diverse protein groups. Moreover, ka (NFeN) is a perfect tool to monitor changes in the axial heme framework caused by different protein environments as well as different Fe oxidation states.
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Affiliation(s)
- Marek Freindorf
- Chemistry Department, Southern Methodist University, Dallas, Texas, USA
| | - Juliana J Antonio
- Chemistry Department, Southern Methodist University, Dallas, Texas, USA
| | - Elfi Kraka
- Chemistry Department, Southern Methodist University, Dallas, Texas, USA
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2
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Hutchins GH, Noble CEM, Bunzel HA, Williams C, Dubiel P, Yadav SKN, Molinaro PM, Barringer R, Blackburn H, Hardy BJ, Parnell AE, Landau C, Race PR, Oliver TAA, Koder RL, Crump MP, Schaffitzel C, Oliveira ASF, Mulholland AJ, Anderson JLR. An expandable, modular de novo protein platform for precision redox engineering. Proc Natl Acad Sci U S A 2023; 120:e2306046120. [PMID: 37487099 PMCID: PMC10400981 DOI: 10.1073/pnas.2306046120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/20/2023] [Indexed: 07/26/2023] Open
Abstract
The electron-conducting circuitry of life represents an as-yet untapped resource of exquisite, nanoscale biomolecular engineering. Here, we report the characterization and structure of a de novo diheme "maquette" protein, 4D2, which we subsequently use to create an expanded, modular platform for heme protein design. A well-folded monoheme variant was created by computational redesign, which was then utilized for the experimental validation of continuum electrostatic redox potential calculations. This demonstrates how fundamental biophysical properties can be predicted and fine-tuned. 4D2 was then extended into a tetraheme helical bundle, representing a 7 nm molecular wire. Despite a molecular weight of only 24 kDa, electron cryomicroscopy illustrated a remarkable level of detail, indicating the positioning of the secondary structure and the heme cofactors. This robust, expressible, highly thermostable and readily designable modular platform presents a valuable resource for redox protein design and the future construction of artificial electron-conducting circuitry.
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Affiliation(s)
- George H. Hutchins
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
| | - Claire E. M. Noble
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
- BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, BristolBS8 1TQ, United Kingdom
| | - H. Adrian Bunzel
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
| | | | - Paulina Dubiel
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
| | - Sathish K. N. Yadav
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
| | - Paul M. Molinaro
- Department of Physics, The City College of New York, New York, NY10031
- Graduate Programs of Physics, Biology, Chemistry and Biochemistry, The Graduate Center of The City University of New York, New York, NY10016
| | - Rob Barringer
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
| | - Hector Blackburn
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
| | - Benjamin J. Hardy
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
| | - Alice E. Parnell
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
- BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, BristolBS8 1TQ, United Kingdom
| | - Charles Landau
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
| | - Paul R. Race
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
- BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, BristolBS8 1TQ, United Kingdom
| | | | - Ronald L. Koder
- Department of Physics, The City College of New York, New York, NY10031
- Graduate Programs of Physics, Biology, Chemistry and Biochemistry, The Graduate Center of The City University of New York, New York, NY10016
| | - Matthew P. Crump
- School of Chemistry, University of Bristol, BristolBS8 1TS, United Kingdom
| | - Christiane Schaffitzel
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
| | - A. Sofia F. Oliveira
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
- School of Chemistry, University of Bristol, BristolBS8 1TS, United Kingdom
| | - Adrian J. Mulholland
- BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, BristolBS8 1TQ, United Kingdom
- School of Chemistry, University of Bristol, BristolBS8 1TS, United Kingdom
| | - J. L. Ross Anderson
- School of Biochemistry, University of Bristol, University Walk, BristolBS8 1TD, United Kingdom
- BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, BristolBS8 1TQ, United Kingdom
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3
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Ennist NM, Stayrook SE, Dutton PL, Moser CC. Rational design of photosynthetic reaction center protein maquettes. Front Mol Biosci 2022; 9:997295. [PMID: 36213121 PMCID: PMC9532970 DOI: 10.3389/fmolb.2022.997295] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/18/2022] [Indexed: 11/20/2022] Open
Abstract
New technologies for efficient solar-to-fuel energy conversion will help facilitate a global shift from dependence on fossil fuels to renewable energy. Nature uses photosynthetic reaction centers to convert photon energy into a cascade of electron-transfer reactions that eventually produce chemical fuel. The design of new reaction centers de novo deepens our understanding of photosynthetic charge separation and may one day allow production of biofuels with higher thermodynamic efficiency than natural photosystems. Recently, we described the multi-step electron-transfer activity of a designed reaction center maquette protein (the RC maquette), which can assemble metal ions, tyrosine, a Zn tetrapyrrole, and heme into an electron-transport chain. Here, we detail our modular strategy for rational protein design and show that the intended RC maquette design agrees with crystal structures in various states of assembly. A flexible, dynamic apo-state collapses by design into a more ordered holo-state upon cofactor binding. Crystal structures illustrate the structural transitions upon binding of different cofactors. Spectroscopic assays demonstrate that the RC maquette binds various electron donors, pigments, and electron acceptors with high affinity. We close with a critique of the present RC maquette design and use electron-tunneling theory to envision a path toward a designed RC with a substantially higher thermodynamic efficiency than natural photosystems.
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Affiliation(s)
- Nathan M. Ennist
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, United States
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
- *Correspondence: Nathan M. Ennist,
| | - Steven E. Stayrook
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, United States
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, United States
- Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT, United States
| | - P. Leslie Dutton
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, United States
| | - Christopher C. Moser
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, United States
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4
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Freindorf M, Delgado AAA, Kraka E. CO bonding in hexa‐ and pentacoordinate carboxy‐neuroglobin: A quantum mechanics/molecular mechanics and local vibrational mode study. J Comput Chem 2022. [DOI: 10.1002/jcc.26973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Marek Freindorf
- Department of Chemistry Southern Methodist University Dallas Texas USA
| | | | - Elfi Kraka
- Department of Chemistry Southern Methodist University Dallas Texas USA
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5
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Exertier C, Sebastiani F, Freda I, Gugole E, Cerutti G, Parisi G, Montemiglio LC, Becucci M, Viappiani C, Bruno S, Savino C, Zamparelli C, Anselmi M, Abbruzzetti S, Smulevich G, Vallone B. Probing the Role of Murine Neuroglobin CDloop-D-Helix Unit in CO Ligand Binding and Structural Dynamics. ACS Chem Biol 2022; 17:2099-2108. [PMID: 35797699 PMCID: PMC9396615 DOI: 10.1021/acschembio.2c00172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
We produced a neuroglobin variant, namely, Ngb CDless,
with the
excised CDloop- and D-helix, directly joining the C- and E-helices.
The CDless variant retained bis-His hexacoordination, and we investigated
the role of the CDloop–D-helix unit in controlling the CO binding
and structural dynamics by an integrative approach based on X-ray
crystallography, rapid mixing, laser flash photolysis, resonance Raman
spectroscopy, and molecular dynamics simulations. Rapid mixing and
laser flash photolysis showed that ligand affinity was unchanged with
respect to the wild-type protein, albeit with increased on and off
constants for rate-limiting heme iron hexacoordination by the distal
His64. Accordingly, resonance Raman spectroscopy highlighted a more
open distal pocket in the CO complex that, in agreement with MD simulations,
likely involves His64 swinging inward and outward of the distal heme
pocket. Ngb CDless displays a more rigid overall structure with respect
to the wild type, abolishing the structural dynamics of the CDloop–D-helix
hypothesized to mediate its signaling role, and it retains ligand
binding control by distal His64. In conclusion, this mutant may represent
a tool to investigate the involvement of CDloop–D-helix in
neuroprotective signaling in a cellular or animal model.
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Affiliation(s)
- Cécile Exertier
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, Piazzale A. Moro 5, I-00185 Rome, Italy
| | - Federico Sebastiani
- Dipartimento di Chimica ″Ugo Schiff″, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Ida Freda
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, Piazzale A. Moro 5, I-00185 Rome, Italy
| | - Elena Gugole
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, Piazzale A. Moro 5, I-00185 Rome, Italy
| | - Gabriele Cerutti
- Zuckerman Mind Brain Behavior Institute, Columbia University, 3227 Broadway, New York, New York 10027, United States
| | - Giacomo Parisi
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena, 291, I-00161 Rome, Italy
| | - Linda Celeste Montemiglio
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Maurizio Becucci
- Dipartimento di Chimica ″Ugo Schiff″, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Cristiano Viappiani
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze, 7/A, I-43124 Parma, Italy
| | - Stefano Bruno
- Department of Food and Drugs, University of Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Carlotta Zamparelli
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, Piazzale A. Moro 5, I-00185 Rome, Italy
| | - Massimiliano Anselmi
- Theoretical Physics and Center for Biophysics, Saarland University, Campus E2 6, 66123 Saarbrücken, Germany
| | - Stefania Abbruzzetti
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze, 7/A, I-43124 Parma, Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica ″Ugo Schiff″, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Beatrice Vallone
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, Piazzale A. Moro 5, I-00185 Rome, Italy
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6
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Exertier C, Montemiglio LC, Freda I, Gugole E, Parisi G, Savino C, Vallone B. Neuroglobin, clues to function and mechanism. Mol Aspects Med 2021; 84:101055. [PMID: 34876274 DOI: 10.1016/j.mam.2021.101055] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 12/19/2022]
Abstract
Neuroglobin is expressed in vertebrate brain and belongs to a branch of the globin family that diverged early in evolution. Sequence conservation and presence in nervous cells of several taxa suggests a relevant role in the nervous system, with tight structural restraints. Twenty years after its discovery, a rich scientific literature provides convincing evidence of the involvement of neuroglobin in sustaining neuron viability in physiological and pathological conditions however, a full and conclusive picture of its specific function, or set of functions is still lacking. The difficulty of unambiguously assigning a precise mechanism and biochemical role to neuroglobin might arise from the participation to one or more cell mechanism that redundantly guarantee the functioning of the highly specialized and metabolically demanding central nervous system of vertebrates. Here we collect findings and hypotheses arising from recent biochemical, biophysical, structural, in cell and in vivo experimental work on neuroglobin, aiming at providing an overview of the most recent literature. Proteins are said to have jobs and hobbies, it is possible that, in the case of neuroglobin, evolution has selected for it more than one job, and support to cover for its occasional failings. Disentangling the mechanisms and roles of neuroglobin is thus a challenging task that might be achieved by considering data from different disciplines and experimental approaches.
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Affiliation(s)
- Cécile Exertier
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, P.le A. Moro 5, 00185, Rome, Italy
| | - Linda Celeste Montemiglio
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185, Rome, Italy
| | - Ida Freda
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, P.le A. Moro 5, 00185, Rome, Italy
| | - Elena Gugole
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, P.le A. Moro 5, 00185, Rome, Italy
| | - Giacomo Parisi
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, 00161, Rome, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185, Rome, Italy.
| | - Beatrice Vallone
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, P.le A. Moro 5, 00185, Rome, Italy.
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7
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De Simone G, Sbardella D, Oddone F, Pesce A, Coletta M, Ascenzi P. Structural and (Pseudo-)Enzymatic Properties of Neuroglobin: Its Possible Role in Neuroprotection. Cells 2021; 10:cells10123366. [PMID: 34943874 PMCID: PMC8699588 DOI: 10.3390/cells10123366] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 12/17/2022] Open
Abstract
Neuroglobin (Ngb), the third member of the globin family, was discovered in human and murine brains in 2000. This monomeric globin is structurally similar to myoglobin (Mb) and hemoglobin (Hb) α and β subunits, but it hosts a bis-histidyl six-coordinated heme-Fe atom. Therefore, the heme-based reactivity of Ngb is modulated by the dissociation of the distal HisE7-heme-Fe bond, which reflects in turn the redox state of the cell. The high Ngb levels (~100–200 μM) present in the retinal ganglion cell layer and in the optic nerve facilitate the O2 buffer and delivery. In contrast, the very low levels of Ngb (~1 μM) in most tissues and organs support (pseudo-)enzymatic properties including NO/O2 metabolism, peroxynitrite and free radical scavenging, nitrite, hydroxylamine, hydrogen sulfide reduction, and the nitration of aromatic compounds. Here, structural and (pseudo-)enzymatic properties of Ngb, which are at the root of tissue and organ protection, are reviewed, envisaging a possible role in the protection from neuronal degeneration of the retina and the optic nerve.
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Affiliation(s)
- Giovanna De Simone
- Dipartimento di Scienze, Università Roma Tre, Viale Marconi 446, 00146 Roma, Italy;
| | | | | | - Alessandra Pesce
- Dipartimento di Fisica, Università di Genova, Via Dodecaneso 33, 16100 Genova, Italy;
| | - Massimo Coletta
- IRCCS Fondazione Bietti, 00198 Roma, Italy; (D.S.); (F.O.)
- Dipartmento di Scienze Cliniche e Medicina Traslazionale, Università di Roma “Tor Vergata”, Via Montpellier 1, 00133 Roma, Italy
- Correspondence: (M.C.); (P.A.); Tel.: +39-06-72596365 (M.C.); +39-06-57336321 (P.A.)
| | - Paolo Ascenzi
- Dipartimento di Scienze, Università Roma Tre, Viale Marconi 446, 00146 Roma, Italy;
- Accademia Nazionale dei Lincei, Via della Lungara 10, 00165 Roma, Italy
- Unità di Neuroendocrinologia, Metabolismo e Neurofarmacologia, IRCSS Fondazione Santa Lucia, 00179 Roma, Italy
- Correspondence: (M.C.); (P.A.); Tel.: +39-06-72596365 (M.C.); +39-06-57336321 (P.A.)
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8
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Solar Fernandez V, Marino M, Fiocchetti M. Neuroglobin in Retinal Neurodegeneration: A Potential Target in Therapeutic Approaches. Cells 2021; 10:cells10113200. [PMID: 34831423 PMCID: PMC8621852 DOI: 10.3390/cells10113200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/09/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022] Open
Abstract
Retinal neurodegeneration affects an increasing number of people worldwide causing vision impairments and blindness, reducing quality of life, and generating a great economic challenge. Due to the complexity of the tissue, and the diversity of retinal neurodegenerative diseases in terms of etiology and clinical presentation, so far, there are no cures and only a few early pathological markers have been identified. Increasing efforts have been made to identify and potentiate endogenous protective mechanisms or to abolish detrimental stress responses to preserve retinal structure and function. The discovering of the intracellular monomeric globin neuroglobin (NGB), found at high concentration in the retina, has opened new possibilities for the treatment of retinal disease. Indeed, the NGB capability to reversibly bind oxygen and its neuroprotective function against several types of insults including oxidative stress, ischemia, and neurodegenerative conditions have raised the interest in the possible role of the globin as oxygen supplier in the retina and as a target for retinal neurodegeneration. Here, we provide the undercurrent knowledge on NGB distribution in retinal layers and the evidence about the connection between NGB level modulation and the functional outcome in terms of retinal neuroprotection to provide a novel therapeutic/preventive target for visual pathway degenerative disease.
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Affiliation(s)
- Virginia Solar Fernandez
- Department of Science, University Roma Tre, Viale G. Marconi, 00146 Rome, Italy; (V.S.F.); (M.M.)
- Neuroendocrinology, Metabolism, and Neuropharmacology Unit, IRCCS Santa Lucia Foundation, 00143 Rome, Italy
| | - Maria Marino
- Department of Science, University Roma Tre, Viale G. Marconi, 00146 Rome, Italy; (V.S.F.); (M.M.)
- Neuroendocrinology, Metabolism, and Neuropharmacology Unit, IRCCS Santa Lucia Foundation, 00143 Rome, Italy
| | - Marco Fiocchetti
- Department of Science, University Roma Tre, Viale G. Marconi, 00146 Rome, Italy; (V.S.F.); (M.M.)
- Neuroendocrinology, Metabolism, and Neuropharmacology Unit, IRCCS Santa Lucia Foundation, 00143 Rome, Italy
- Correspondence: ; Tel.: +39-06-5733-6455; Fax: +39-06-5733-6321
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9
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Adameyko KI, Kravchuk OI, Finoshin AD, Bonchuk AN, Georgiev AA, Mikhailov VS, Gornostaev NG, Mikhailov KV, Bacheva AV, Indeykina MI, Bugrova AE, Gazizova GR, Kozlova OS, Gusev OA, Shagimardanova EI, Lyupina YV. Structure of Neuroglobin from Cold-Water Sponge Halisarca dujardinii. Mol Biol 2020. [DOI: 10.1134/s0026893320030036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Milazzo L, Exertier C, Becucci M, Freda I, Montemiglio LC, Savino C, Vallone B, Smulevich G. Lack of orientation selectivity of the heme insertion in murine neuroglobin revealed by resonance Raman spectroscopy. FEBS J 2020; 287:4082-4097. [PMID: 32034988 DOI: 10.1111/febs.15241] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/30/2020] [Accepted: 02/05/2020] [Indexed: 01/17/2023]
Abstract
Different murine neuroglobin variants showing structural and dynamic alterations that are associated with perturbation of ligand binding have been studied: the CD loop mutants characterized by an enhanced flexibility (Gly-loop40-48 and Gly-loop44-47 ), the F106A mutant, and the double Gly-loop44-47 /F106A mutant. Their ferric resonance Raman spectra in solution and in crystals are almost identical. In the high-frequency region, the identification of a double set of core size marker bands indicates the presence of two 6-coordinate low spin species. The resonance Raman data, together with the corresponding crystal structures, indicate the presence of two neuroglobin conformers with a reversed (A conformer) or a canonical (B conformer) heme insertion orientation. With the identification of the marker bands corresponding to each conformer, the data indicate that the B conformer increases at the expense of the A form, predominantly in the Gly-loop44-47 /F106A double mutant, as confirmed by X-ray crystallography. This is the first time that a reversed heme insertion has been identified by resonance Raman in a native 6-coordinate low-spin heme protein. This diagnostic tool could be extended to other heme proteins in order to detect heme orientational disorder, which are likely to be correlated to functionally relevant heme dynamics. DATABASE: Crystallographic structure: structural data are deposited in the Protein Data Bank under the 6RA6 PDB entry.
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Affiliation(s)
- Lisa Milazzo
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Florence, Italy
| | - Cécile Exertier
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Italy.,Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza, Università di Roma, Italy
| | - Maurizio Becucci
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Florence, Italy.,European Laboratory for Non-Linear Spectroscopy - LENS, Florence, Italy
| | - Ida Freda
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Italy.,Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza, Università di Roma, Italy
| | - Linda Celeste Montemiglio
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Italy.,Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza, Università di Roma, Italy.,CNR Institute of Molecular Biology and Pathology, Rome, Italy
| | | | - Beatrice Vallone
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Italy.,Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza, Università di Roma, Italy.,CNR Institute of Molecular Biology and Pathology, Rome, Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Florence, Italy
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11
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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.
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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
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12
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Fiocchetti M, Fernandez VS, Montalesi E, Marino M. Neuroglobin: A Novel Player in the Oxidative Stress Response of Cancer Cells. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:6315034. [PMID: 31354909 PMCID: PMC6636438 DOI: 10.1155/2019/6315034] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 06/11/2019] [Indexed: 12/18/2022]
Abstract
Reactive oxygen species (ROS) result from intracellular aerobic metabolism and/or extracellular stimuli. Although endogenous antioxidant systems exquisitely balance ROS production, an excess of ROS production, commonly found in diverse human degenerative pathologies including cancer, gives rise to the oxidative stress. Increased oxidative stress in cancer is related to the sustained proliferation and metabolism of cancer cells. However, cancer cells show an intrinsic higher antioxidant capacity with respect to the normal counterpart as well as an ability to cope with oxidative stress-induced cell death by establishing mechanisms of adaptation, which define a selective advantage against the adverse oxidative stress environment. The identification of survival factors and adaptive pathways, set up by cancer cells against oxidative stress, provides multiple targets for the therapeutic intervention against cancer. Neuroglobin (NGB), a globin primarily described in neurons as an oxidative stress sensor and cytoprotective factor against redox imbalance, has been recently recognized as a novel tumor-associated protein. In this review, the involvement of NGB in the cancer cell adaptation and resistance to oxidative stress will be discussed highlighting the globin role in the regulation of both the stress-induced apoptotic pathway and antioxidant systems activated by cancer cells.
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Affiliation(s)
- Marco Fiocchetti
- Department of Science, University Roma Tre, Viale Guglielmo Marconi 446, I-00146 Roma, Italy
| | | | - Emiliano Montalesi
- Department of Science, University Roma Tre, Viale Guglielmo Marconi 446, I-00146 Roma, Italy
| | - Maria Marino
- Department of Science, University Roma Tre, Viale Guglielmo Marconi 446, I-00146 Roma, Italy
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13
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Neuroglobin Expression Models as a Tool to Study Its Function. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:5728129. [PMID: 31320982 PMCID: PMC6607734 DOI: 10.1155/2019/5728129] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 05/12/2019] [Indexed: 01/13/2023]
Abstract
Neuroglobin (Ngb) is an evolutionary conserved member of the globin family with a primary expression in neurons of which the exact functions remain elusive. A plethora of in vivo and in vitro model systems has been generated to this day to determine the functional biological roles of Ngb. Here, we provide a comprehensive overview and discussion of the different Ngb models, covering animal and cellular models of both overexpression and knockout strategies. Intriguingly, an in-depth literature search of available Ngb expression models revealed crucial discrepancies in the outcomes observed in different models. Not only does the level of Ngb expression—either physiologically, overexpressed, or downregulated—alter its functional properties, the experimental setup, being in vitro or in vivo, does impact the functional outcome as well and, hence, whether or not a physiological and/or therapeutic role is ascribed to Ngb. These differences could highlight either technical or biological adaptations and should be considered until elucidation of the Ngb biology.
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14
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Proximal and distal control for ligand binding in neuroglobin: role of the CD loop and evidence for His64 gating. Sci Rep 2019; 9:5326. [PMID: 30926858 PMCID: PMC6441039 DOI: 10.1038/s41598-019-41780-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 03/13/2019] [Indexed: 11/24/2022] Open
Abstract
Neuroglobin (Ngb) is predominantly expressed in neurons of the central and peripheral nervous systems and it clearly seems to be involved in neuroprotection. Engineering Ngb to observe structural and dynamic alterations associated with perturbation in ligand binding might reveal important structural determinants, and could shed light on key features related to its mechanism of action. Our results highlight the relevance of the CD loop and of Phe106 as distal and proximal controls involved in ligand binding in murine neuroglobin. We observed the effects of individual and combined mutations of the CD loop and Phe106 that conferred to Ngb higher CO binding velocities, which we correlate with the following structural observations: the mutant F106A shows, upon CO binding, a reduced heme sliding hindrance, with the heme present in a peculiar double conformation, whereas in the CD loop mutant “Gly-loop”, the original network of interactions between the loop and the heme was abolished, enhancing binding via facilitated gating out of the distal His64. Finally, the double mutant, combining both mutations, showed a synergistic effect on CO binding rates. Resonance Raman spectroscopy and MD simulations support our findings on structural dynamics and heme interactions in wild type and mutated Ngbs.
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15
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Kim J, Fukuda Y, Inoue T. Crystal structure of Kumaglobin: a hexacoordinated heme protein from an anhydrobiotic tardigrade,
Ramazzottius varieornatus. FEBS J 2018; 286:1287-1304. [DOI: 10.1111/febs.14713] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 09/28/2018] [Accepted: 11/29/2018] [Indexed: 01/05/2023]
Affiliation(s)
- JeeEun Kim
- Department of Applied Chemistry Graduate School of Engineering Osaka University Suita Japan
| | - Yohta Fukuda
- Department of Applied Chemistry Graduate School of Engineering Osaka University Suita Japan
| | - Tsuyoshi Inoue
- Department of Applied Chemistry Graduate School of Engineering Osaka University Suita Japan
- Graduate School of Pharmaceutical Science Suita Japan
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16
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Ascenzi P, De Simone G, Ciaccio C, Santucci R, Coletta M. Hydroxylamine-induced oxidation of ferrous CO-bound carboxymethylated-cytochrome c. J PORPHYR PHTHALOCYA 2018. [DOI: 10.1142/s1088424618501055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The hexa-coordinated metal center of horse heart cyt[Formula: see text] (cyt[Formula: see text] is at the root of its low reactivity. In contrast, carboxymethylated cyt[Formula: see text] (CM-cyt[Formula: see text] displays myoglobin-like properties. Herein, kinetics of CO binding to ferrous CM-cyt[Formula: see text] (CM-cyt[Formula: see text](II)) and of the irreversible oxidation of ferrous carbonylated CM-cyt[Formula: see text] (CM-cyt[Formula: see text](II)-CO) by hydroxylamine (HA), at pH 5.8 and 20.0 [Formula: see text]C, are reported. HA irreversibly oxidizes CM-cyt[Formula: see text](II)-CO with the 1:2 stoichiometry leading to the formation of the ferric species (CM-cyt[Formula: see text](III)) without the observation of intermediates. Present data indicate that: (i) the rate of CO dissociation from CM-cyt[Formula: see text](II)-CO represents the rate-limiting step of HA-mediated oxidation of the carbonylated metal center, (ii) the fast oxidation of CM-cyt[Formula: see text](II)-CO from HA reflects the penta-coordination of the transient CM-cyt[Formula: see text](II) species, (iii) the HA-catalyzed conversion of CM-cyt[Formula: see text](II)-CO to CM-cyt[Formula: see text](III) could proceed via the geminate mechanism, (iv) values of the second-order rate constants for the carbonylation and the HA-mediated oxidation of ferrous heme-proteins are linearly correlated reflecting the penta- or hexa-coordination of the metal center, the free energy for the in-plane positioning of the heme-Fe atom in the unliganded species, and the arrangement of the distal portion of the heme pocket that affects ligand and/or electron transfer.
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Affiliation(s)
- Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, I-00146 Roma, Italy
| | | | - Chiara Ciaccio
- Department of Clinical Sciences and Translational Medicine, University of Roma “Tor Vergata”, I-00133 Roma, Italy
- Interuniversity Consortium for the Research on Chemistry of Metals in Biological Systems, I-70126 Bari, Italy
| | - Roberto Santucci
- Department of Clinical Sciences and Translational Medicine, University of Roma “Tor Vergata”, I-00133 Roma, Italy
| | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma “Tor Vergata”, I-00133 Roma, Italy
- Interuniversity Consortium for the Research on Chemistry of Metals in Biological Systems, I-70126 Bari, Italy
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17
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Impact of A90P, F106L and H64V mutations on neuroglobin stability and ligand binding kinetics. J Biol Inorg Chem 2018; 24:39-52. [DOI: 10.1007/s00775-018-1625-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/08/2018] [Indexed: 12/22/2022]
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18
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The nitrite reductase activity of ferrous human hemoglobin:haptoglobin 1-1 and 2-2 complexes. J Inorg Biochem 2018; 187:116-122. [DOI: 10.1016/j.jinorgbio.2018.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/14/2018] [Accepted: 07/17/2018] [Indexed: 12/16/2022]
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19
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Rydzewski J, Nowak W. Photoinduced transport in an H64Q neuroglobin antidote for carbon monoxide poisoning. J Chem Phys 2018; 148:115101. [DOI: 10.1063/1.5013659] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- J. Rydzewski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun, Poland
| | - W. Nowak
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun, Poland
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20
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Neuroglobin boosts axon regeneration during ischemic reperfusion via p38 binding and activation depending on oxygen signal. Cell Death Dis 2018; 9:163. [PMID: 29416029 PMCID: PMC5833339 DOI: 10.1038/s41419-017-0260-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/17/2017] [Accepted: 12/21/2017] [Indexed: 11/08/2022]
Abstract
Cerebral ischemia causes severe cell death or injury including axon breakdown or retraction in the brain. Axon regeneration is crucial for the functional recovery of injured neurons or brains after ischemia/reperfusion (I/R); however, this process has been proved extremely difficult in adult brains and there is still no effective therapy for it. Here we reported that neuroglobin (Ngb), a novel oxygen-binding or sensor protein existing predominantly in neurons or brains, functions as a driving factor for axon regeneration during I/R. Ngb was upregulated and accumulated in growth cones of ischemic neurons in primary cultures, rat, and human brains, correlating positively to the elevation of axon-regeneration markers GAP43, neurofilament-200, and Tau-1. Ngb overexpression promoted while Ngb knockdown suppressed axon regeneration as well as GAP43 expression in neurons during oxygen-glucose deprivation/reoxygenation (OGD/Re). By using specific pharmacological inhibitors, we identified p38 MAPK as the major downstream player of Ngb-induced axon regeneration during OGD/Re. Mechanistically, Ngb directly bound to and activated p38 in neurons upon OGD/Re. Serial truncation and point mutation of Ngb revealed that the 7-105 aa fragment of Ngb was required and the oxygen-binding site (His64) of Ngb was the major regulatory site for its p38 interaction/activation. Finally, administration of exogenous TAT-Ngb peptides significantly enhanced axon regeneration in cultured neurons upon OGD/Re. Taken together, Ngb promotes axon regeneration via O2-Ngb-p38-GAP43 signaling during I/R. This novel mechanism suggests potential therapeutic applications of Ngb for ischemic stroke and other related axonopathy.
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21
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Bellei M, Bortolotti CA, Di Rocco G, Borsari M, Lancellotti L, Ranieri A, Sola M, Battistuzzi G. The influence of the Cys46/Cys55 disulfide bond on the redox and spectroscopic properties of human neuroglobin. J Inorg Biochem 2018; 178:70-86. [DOI: 10.1016/j.jinorgbio.2017.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/21/2017] [Accepted: 10/09/2017] [Indexed: 12/21/2022]
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22
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Colloc'h N, Carpentier P, Montemiglio LC, Vallone B, Prangé T. Mapping Hydrophobic Tunnels and Cavities in Neuroglobin with Noble Gas under Pressure. Biophys J 2017; 113:2199-2206. [PMID: 29108649 DOI: 10.1016/j.bpj.2017.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/12/2017] [Accepted: 10/06/2017] [Indexed: 01/27/2023] Open
Abstract
Internal cavities are crucial for conformational flexibility of proteins and can be mapped through noble gas diffusion and docking. Here we investigate the hydrophobic cavities and tunnel network in neuroglobin (Ngb), a hexacoordinated heme protein likely to be involved in neuroprotection, using crystallography under noble gas pressure, mostly at room temperature. In murine Ngb, a large internal cavity is involved in the heme sliding mechanism to achieve binding of gaseous ligands through coordination to the heme iron. In this study, we report that noble gases are hosted by two major sites within the internal cavity. We propose that these cavities could store oxygen and allow its relay in the heme proximity, which could correspond to NO location in the nitrite-reductase function of Ngb. Thanks to a recently designed pressurization cell using krypton at high pressure, a new gas binding site has been characterized that reveals an alternate pathway for gaseous ligands. A new gas binding site on the proximal side of the heme has also been characterized, using xenon pressure on a Ngb mutant (V140W) that binds CO with a similar rate and affinity to the wild-type, despite a reshaping of the internal cavity. Moreover, this study, to our knowledge, provides new insights into the determinants of the heme sliding mechanism, suggesting that the shift at the beginning of helix G precedes and drives this process.
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Affiliation(s)
- Nathalie Colloc'h
- ISTCT CNRS UNICAEN CEA Normandie University, CERVOxy Team, Centre Cyceron, Caen, France.
| | - Philippe Carpentier
- CEA/DRF/BIG/CBM/BioCat LCBM CNRS UMR 5249, Université Grenoble Alpes, Grenoble, France; European Synchrotron Radiation Facility, Grenoble, France
| | - Laura C Montemiglio
- Instituto Pasteur-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Roma, Italy
| | - Beatrice Vallone
- Instituto Pasteur-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Roma, Italy
| | - Thierry Prangé
- LCRB, UMR 8015 CNRS Université Paris Descartes, Paris, France
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23
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Alekseeva OS, Grigor’ev IP, Korzhevskii DE. Neuroglobin, an oxygen-binding protein in the mammalian nervous system (localization and putative functions). J EVOL BIOCHEM PHYS+ 2017. [DOI: 10.1134/s0022093017040019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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24
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Ascenzi P, Bocedi A, Gioia M, Fanali G, Fasano M, Coletta M. Warfarin inhibits allosterically the reductive nitrosylation of ferric human serum heme-albumin. J Inorg Biochem 2017; 177:63-75. [PMID: 28926756 DOI: 10.1016/j.jinorgbio.2017.08.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 08/30/2017] [Indexed: 12/31/2022]
Abstract
Human serum heme-albumin (HSA-heme-Fe) displays heme-based ligand binding and (pseudo-)enzymatic properties. Here, the effect of the prototypical drug warfarin on kinetics and thermodynamics of NO binding to ferric and ferrous HSA-heme-Fe (HSA-heme-Fe(III) and HSA-heme-Fe(II), respectively) and on the NO-mediated reductive nitrosylation of the heme-Fe atom is reported; data were obtained between pH5.5 and 9.5 at 20.0°C. Since warfarin is a common drug, its effect on the reactivity of HSA-heme-Fe represents a relevant issue in the pharmacological therapy management. The inhibition of NO binding to HSA-heme-Fe(III) and HSA-heme-Fe(II) as well as of the NO-mediated reductive nitrosylation of the heme-Fe(III) atom by warfarin has been ascribed to drug binding to the fatty acid binding site 2 (FA2), shifting allosterically the penta-to-six coordination equilibrium of the heme-Fe atom toward the low reactive species showing the six-coordinated metal center by His146 and Tyr161 residues. These data: (i) support the role of HSA-heme-Fe in trapping NO, (ii) highlight the modulation of the heme-Fe-based reactivity by drugs, and (iii) could be relevant for the modulation of HSA functions by drugs in vivo.
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Affiliation(s)
- Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, I-00146 Roma, Italy.
| | - Alessio Bocedi
- Department of Chemical Sciences and Technology, University of Roma "Tor Vergata", I-00133 Roma, Italy
| | - Magda Gioia
- Department of Clinical Sciences and Translational Medicine, University of Roma "Tor Vergata", I-00133 Roma, Italy; Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, I-70126 Bari, Italy
| | | | - Mauro Fasano
- Department of Science and High Technology, University of Insubria, I-21052 Busto Arsizio, VA, Italy; Neuroscience Research Center, University of Insubria, I-21052 Busto Arsizio, VA, Italy
| | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma "Tor Vergata", I-00133 Roma, Italy; Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, I-70126 Bari, Italy
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25
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Adam S, Knapp-Mohammady M, Yi J, Bondar AN. Revised CHARMM force field parameters for iron-containing cofactors of photosystem II. J Comput Chem 2017; 39:7-20. [PMID: 28850168 DOI: 10.1002/jcc.24918] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 07/05/2017] [Accepted: 08/03/2017] [Indexed: 01/25/2023]
Abstract
Photosystem II is a complex protein-cofactor machinery that splits water molecules into molecular oxygen, protons, and electrons. All-atom molecular dynamics simulations have the potential to contribute to our general understanding of how photosystem II works. To perform reliable all-atom simulations, we need accurate force field parameters for the cofactor molecules. We present here CHARMM bonded and non-bonded parameters for the iron-containing cofactors of photosystem II that include a six-coordinated heme moiety coordinated by two histidine groups, and a non-heme iron complex coordinated by bicarbonate and four histidines. The force field parameters presented here give water interaction energies and geometries in good agreement with the quantum mechanical target data. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Suliman Adam
- Theoretical Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, Berlin D-14195, Germany
| | - Michaela Knapp-Mohammady
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 580, Heidelberg D-69120, Germany
| | - Jun Yi
- Department of Biological Engineering, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu Province 210094, China
| | - Ana-Nicoleta Bondar
- Theoretical Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, Berlin D-14195, Germany
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26
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Fiocchetti M, Cipolletti M, Brandi V, Polticelli F, Ascenzi P. Neuroglobin and friends. J Mol Recognit 2017; 30. [DOI: 10.1002/jmr.2654] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 06/05/2017] [Accepted: 06/14/2017] [Indexed: 01/02/2023]
Affiliation(s)
| | | | | | - Fabio Polticelli
- Dipartimento di Scienze; Università Roma Tre; Rome Italy
- Istituto Nazionale di Fisica Nucleare; Sezione dell'Università Roma Tre; Rome Italy
| | - Paolo Ascenzi
- Laboratorio Interdipartimentale di Microscopia Elettronica; Università Roma Tre; Rome Italy
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27
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Colloc'h N, Sacquin-Mora S, Avella G, Dhaussy AC, Prangé T, Vallone B, Girard E. Determinants of neuroglobin plasticity highlighted by joint coarse-grained simulations and high pressure crystallography. Sci Rep 2017; 7:1858. [PMID: 28500341 PMCID: PMC5431840 DOI: 10.1038/s41598-017-02097-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/20/2017] [Indexed: 11/09/2022] Open
Abstract
Investigating the effect of pressure sheds light on the dynamics and plasticity of proteins, intrinsically correlated to functional efficiency. Here we detail the structural response to pressure of neuroglobin (Ngb), a hexacoordinate globin likely to be involved in neuroprotection. In murine Ngb, reversible coordination is achieved by repositioning the heme more deeply into a large internal cavity, the “heme sliding mechanism”. Combining high pressure crystallography and coarse-grain simulations on wild type Ngb as well as two mutants, one (V101F) with unaffected and another (F106W) with decreased affinity for CO, we show that Ngb hinges around a rigid mechanical nucleus of five hydrophobic residues (V68, I72, V109, L113, Y137) during its conformational transition induced by gaseous ligand, that the intrinsic flexibility of the F-G loop appears essential to drive the heme sliding mechanism, and that residue Val 101 may act as a sensor of the interaction disruption between the heme and the distal histidine.
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Affiliation(s)
- Nathalie Colloc'h
- ISTCT CNRS UNICAEN CEA Normandie Univ., CERVOxy team, centre Cyceron, 14000, Caen, France.
| | - Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, CNRS UPR9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Giovanna Avella
- Instituto Pasteur-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, 5 piazzale Aldo Moro, 00185, Roma, Italy.,BIOGEM Research Institute, Ariano Irpino, Italy
| | - Anne-Claire Dhaussy
- CRISTMAT UMR 6508 CNRS ENSICAEN UNICAEN Normandie Univ., 6 bd du Maréchal Juin, 14050, Caen, France
| | - Thierry Prangé
- LCRB, UMR 8015 CNRS Université Paris Descartes, 4 avenue de l'Observatoire, 75270, Paris, France
| | - Beatrice Vallone
- Instituto Pasteur-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, 5 piazzale Aldo Moro, 00185, Roma, Italy
| | - Eric Girard
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France.
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28
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Butcher D, Bernad S, Derrien V, Sebban P, Miksovska J. Role of Ionic Strength and pH in Modulating Thermodynamic Profiles Associated with CO Escape from Rice Nonsymbiotic Hemoglobin 1. J Phys Chem B 2017; 121:351-364. [PMID: 28072536 DOI: 10.1021/acs.jpcb.6b06933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Type 1 nonsymbiotic hemoglobins are found in a wide variety of land plants and exhibit very high affinities for exogenous gaseous ligands. These proteins are presumed to have a role in protecting plant cells from oxidative stress under etiolated/hypoxic conditions through NO dioxygenase activity. In this study we have employed photoacoustic calorimetry, time-resolved absorption spectroscopy, and classical molecular dynamics simulations in order to elucidate thermodynamics, kinetics, and ligand migration pathways upon CO photodissociation from WT and a H73L mutant of type 1 nonsymbiotic hemoglobin from Oryza sativa (rice). We observe a temperature dependence of the resolved thermodynamic parameters for CO photodissociation from CO-rHb1 which we attribute to temperature dependent formation of a network of electrostatic interactions in the vicinity of the heme propionate groups. We also observe slower ligand escape from the protein matrix under mildly acidic conditions in both the WT and H73L mutant (τ = 134 ± 19 and 90 ± 15 ns). Visualization of transient hydrophobic channels within our classical molecular dynamics trajectories allows us to attribute this phenomenon to a change in the ligand migration pathway which occurs upon protonation of the distal His73, His117, and His152. Protonation of these residues may be relevant to the functioning of the protein in vivo given that etiolation/hypoxia can cause a decrease in intracellular pH in plant cells.
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Affiliation(s)
- David Butcher
- Department of Chemistry and Biochemistry, Florida International University , Miami Florida 33199, United States
| | - Sophie Bernad
- Laboratoire de Chimie Physique, Université Paris-Sud 11 , 91405 Orsay, France
| | - Valerie Derrien
- Laboratoire de Chimie Physique, Université Paris-Sud 11 , 91405 Orsay, France
| | - Pierre Sebban
- Laboratoire de Chimie Physique, Université Paris-Sud 11 , 91405 Orsay, France
| | - Jaroslava Miksovska
- Department of Chemistry and Biochemistry, Florida International University , Miami Florida 33199, United States.,Biomolecular Sciences Institute, Florida International University , Miami, Florida 33199, United States
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Ascenzi P, di Masi A, Leboffe L, Fiocchetti M, Nuzzo MT, Brunori M, Marino M. Neuroglobin: From structure to function in health and disease. Mol Aspects Med 2016; 52:1-48. [DOI: 10.1016/j.mam.2016.10.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 10/27/2016] [Accepted: 10/27/2016] [Indexed: 01/01/2023]
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Guidolin D, Tortorella C, Marcoli M, Maura G, Agnati LF. Neuroglobin, a Factor Playing for Nerve Cell Survival. Int J Mol Sci 2016; 17:ijms17111817. [PMID: 27809238 PMCID: PMC5133818 DOI: 10.3390/ijms17111817] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/14/2016] [Accepted: 10/26/2016] [Indexed: 12/17/2022] Open
Abstract
Cell death represents the final outcome of several pathological conditions of the central nervous system and available evidence suggests that in both acute injuries and neurodegenerative diseases it is often associated with mitochondrial dysfunction. Thus, the possibility to prevent mitochondrial events involved in cell death might represent efficient tools to limit neuronal damage. In recent years, increased attention has been paid to the endogenous protein neuroglobin, since accumulating evidence showed that its high expression was associated with preserved mitochondrial function and to an increased survival of nerve cells in vitro and in vivo in a variety of experimental models of cell insult. The biological and structural features of neuroglobin and the mitochondria-related mechanisms of neuroglobin-induced neuroprotection will be here briefly discussed. In this respect, the inhibition of the intrinsic pathway of apoptosis emerges as a key neuroprotective effect induced by the protein. These findings could open the possibility to develop efficient neuroglobin-mediated therapeutic strategies aimed at minimizing the neuronal cell death occurring in impacting neurological pathologies like stroke and neurodegenerative diseases.
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Affiliation(s)
- Diego Guidolin
- Department of Neuroscience, University of Padova, Padova 35122, Italy.
| | - Cinzia Tortorella
- Department of Neuroscience, University of Padova, Padova 35122, Italy.
| | - Manuela Marcoli
- Department of Pharmacy and Center of Excellence for Biomedical Research, University of Genova, Genova 16126, Italy.
| | - Guido Maura
- Department of Pharmacy and Center of Excellence for Biomedical Research, University of Genova, Genova 16126, Italy.
| | - Luigi F Agnati
- Department of Biomedical Sciences, University of Modena and Reggio Emilia, Modena 41121, Italy.
- Department of Neuroscience, Karolinska Institutet, Stockholm 17177, Sweden.
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Abstract
If life without heme-Fe were at all possible, it would definitely be different. Indeed this complex and versatile iron-porphyrin macrocycle upon binding to different “globins” yields hemeproteins crucial to sustain a variety of vital functions, generally classified, for convenience, in a limited number of functional families. Over-and-above the array of functions briefly outlined below, the spectacular progress in molecular genetics seen over the last 30 years led to the discovery of many hitherto unknown novel hemeproteins in prokaryotes and eukaryotes. Here, we highlight a few basic aspects of the chemistry of the hemeprotein universe, in particular those that are relevant to the control of heme-Fe reactivity and specialization, as sculpted by a variety of interactions with the protein moiety.
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Affiliation(s)
- Paolo Ascenzi
- Dipartimento di Scienze, Università Roma Tre, Viale Marconi 446, I-00146 Roma, Italy
| | - Maurizio Brunori
- Dipartimento di Scienze Biochimiche “Alessandro Rossi Fanelli” and Istituto Pasteur — Fondazione Cenci, Bolognetti, Sapienza Università di Roma, Piazzale Aldo Moro 5, I-00185 Roma, Italy
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32
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Residues in the Distal Heme Pocket of Arabidopsis Non-Symbiotic Hemoglobins: Implication for Nitrite Reductase Activity. Int J Mol Sci 2016; 17:ijms17050640. [PMID: 27136534 PMCID: PMC4881466 DOI: 10.3390/ijms17050640] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/13/2016] [Accepted: 04/19/2016] [Indexed: 02/08/2023] Open
Abstract
It is well-established that plant hemoglobins (Hbs) are involved in nitric oxide (NO) metabolism via NO dioxygenase and/or nitrite reductase activity. The ferrous-deoxy Arabidopsis Hb1 and Hb2 (AHb1 and AHb2) have been shown to reduce nitrite to NO under hypoxia. Here, to test the hypothesis that a six- to five-coordinate heme iron transition might mediate the control of the nitrite reduction rate, we examined distal pocket mutants of AHb1 and AHb2 for nitrite reductase activity, NO production and spectroscopic features. Absorption spectra of AHbs distal histidine mutants showed that AHb1 mutant (H69L) is a stable pentacoordinate high-spin species in both ferrous and ferric states, whereas heme iron in AHb2 mutant (H66L) is hexacoordinated low-spin with Lys69 as the sixth ligand. The bimolecular rate constants for nitrite reduction to NO were 13.3 ± 0.40, 7.3 ± 0.5, 10.6 ± 0.8 and 171.90 ± 9.00 M−1·s−1 for AHb1, AHb2, AHb1 H69L and AHb2 H66L, respectively, at pH 7.4 and 25 °C. Consistent with the reductase activity, the amount of NO detected by chemiluminescence was significantly higher in the AHb2 H66L mutant. Our data indicate that nitrite reductase activity is determined not only by heme coordination, but also by a unique distal heme pocket in each AHb.
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33
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The nitrite reductase activity of horse heart carboxymethylated-cytochrome c is modulated by cardiolipin. J Biol Inorg Chem 2016; 21:421-32. [DOI: 10.1007/s00775-016-1351-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/28/2016] [Indexed: 10/22/2022]
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Danielsson J, Meuwly M. Atomistic Simulation of Adiabatic Reactive Processes Based on Multi-State Potential Energy Surfaces. J Chem Theory Comput 2015; 4:1083-93. [PMID: 26636362 DOI: 10.1021/ct800066q] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The adiabatic reactive molecular dynamics (ARMD) method provides a framework to study chemical reactions using molecular dynamics simulations with minimal computational overhead. Here, ARMD is generalized to an arbitrary reactive process between two states in which reactants and products can be treated by an atomistic force field. The implementation is described, and the method is applied to two systems: the kinetics of NO rebinding to myoglobin (Mb) as a validation system and the conformational transition in neuroglobin (Ngb) which explores the full functionality of ARMD. For MbNO, the nonexponential kinetics observed both in experiment and earlier ARMD studies is reproduced. Furthermore, the sensitivity of the results with respect to the asymptotic separation between the two potential energy surfaces (NO bound and unbound) is studied.
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Affiliation(s)
- Jonas Danielsson
- Chemistry Department, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Chemistry Department, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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35
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Ascenzi P, Sbardella D, Fiocchetti M, Santucci R, Coletta M. NO2−-mediated nitrosylation of ferrous microperoxidase-11. J Inorg Biochem 2015; 153:121-127. [DOI: 10.1016/j.jinorgbio.2015.06.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 06/03/2015] [Accepted: 06/30/2015] [Indexed: 11/29/2022]
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36
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De Henau S, Tilleman L, Vangheel M, Luyckx E, Trashin S, Pauwels M, Germani F, Vlaeminck C, Vanfleteren JR, Bert W, Pesce A, Nardini M, Bolognesi M, De Wael K, Moens L, Dewilde S, Braeckman BP. A redox signalling globin is essential for reproduction in Caenorhabditis elegans. Nat Commun 2015; 6:8782. [PMID: 26621324 PMCID: PMC4686822 DOI: 10.1038/ncomms9782] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 10/02/2015] [Indexed: 12/17/2022] Open
Abstract
Moderate levels of reactive oxygen species (ROS) are now recognized as redox signalling molecules. However, thus far, only mitochondria and NADPH oxidases have been identified as cellular sources of ROS in signalling. Here we identify a globin (GLB-12) that produces superoxide, a type of ROS, which serves as an essential signal for reproduction in C. elegans. We find that GLB-12 has an important role in the regulation of multiple aspects in germline development, including germ cell apoptosis. We further describe how GLB-12 displays specific molecular, biochemical and structural properties that allow this globin to act as a superoxide generator. In addition, both an intra- and extracellular superoxide dismutase act as key partners of GLB-12 to create a transmembrane redox signal. Our results show that a globin can function as a driving factor in redox signalling, and how this signal is regulated at the subcellular level by multiple control layers.
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Affiliation(s)
- Sasha De Henau
- Department of Biology, Ghent University, Ghent B-9000, Belgium
| | - Lesley Tilleman
- Department of Biomedical Sciences, University of Antwerp, Antwerp B-2000, Belgium
| | | | - Evi Luyckx
- Department of Biomedical Sciences, University of Antwerp, Antwerp B-2000, Belgium
| | - Stanislav Trashin
- Department of Chemistry, University of Antwerp, Antwerp B-2000, Belgium
| | - Martje Pauwels
- Department of Chemistry, University of Antwerp, Antwerp B-2000, Belgium
| | - Francesca Germani
- Department of Biomedical Sciences, University of Antwerp, Antwerp B-2000, Belgium
| | | | | | - Wim Bert
- Department of Biology, Ghent University, Ghent B-9000, Belgium
| | - Alessandra Pesce
- Department of Physics, University of Genova, Genova I-16146, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Milano I-20133, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milano, Milano I-20133, Italy
- CNR-IBF and CIMAINA, University of Milano, Milano I-20133, Italy
| | - Karolien De Wael
- Department of Chemistry, University of Antwerp, Antwerp B-2000, Belgium
| | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, Antwerp B-2000, Belgium
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Antwerp B-2000, Belgium
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Open and Lys-His Hexacoordinated Closed Structures of a Globin with Swapped Proximal and Distal Sites. Sci Rep 2015; 5:11407. [PMID: 26094577 PMCID: PMC4476040 DOI: 10.1038/srep11407] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 05/22/2015] [Indexed: 11/24/2022] Open
Abstract
Globins are haem-binding proteins with a conserved fold made up of α-helices and can possess diverse properties. A putative globin-coupled sensor from Methylacidiphilum infernorum, HGbRL, contains an N-terminal globin domain whose open and closed structures reveal an untypical dimeric architecture. Helices E and F fuse into an elongated helix, resulting in a novel site-swapped globin fold made up of helices A–E, hence the distal site, from one subunit and helices F–H, the proximal site, from another. The open structure possesses a large cavity binding an imidazole molecule, while the closed structure forms a unique Lys–His hexacoordinated species, with the first turn of helix E unravelling to allow Lys52(E10) to bind to the haem. Ligand binding induces reorganization of loop CE, which is stabilized in the closed form, and helix E, triggering a large conformational movement in the open form. These provide a mechanical insight into how a signal may be relayed between the globin domain and the C-terminal domain of HGbRL, a Roadblock/LC7 domain. Comparison with HGbI, a closely related globin, further underlines the high degree of structural versatility that the globin fold is capable of, enabling it to perform a diversity of functions.
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38
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Yang Y, Allemand F, Guca E, Vallone B, Delbecq S, Roumestand C. (1)H, (15)N and (13)C backbone resonance assignments of murine met-neuroglobin, free and in complex with cyanide. BIOMOLECULAR NMR ASSIGNMENTS 2015; 9:153-156. [PMID: 24830543 DOI: 10.1007/s12104-014-9563-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/06/2014] [Indexed: 06/03/2023]
Abstract
Neuroglobin is a globin present in the brain and retina of mammals. This hexacoordinated hemoprotein binds small diatomic molecules, albeit with lower affinity compared with other globins. We report here the resonance assignment of murine met-Neuroglobine, free and in complex with cyanide.
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Affiliation(s)
- Yinshan Yang
- CNRS UMR 5048, Centre de Biochimie Structurale, Université de Montpellier I and II, 29 rue de Navacelles, 34090, Montpellier Cedex, France
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39
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Engineered chimeras reveal the structural basis of hexacoordination in globins: A case study of neuroglobin and myoglobin. Biochim Biophys Acta Gen Subj 2015; 1850:169-77. [DOI: 10.1016/j.bbagen.2014.10.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 09/12/2014] [Accepted: 10/06/2014] [Indexed: 11/18/2022]
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40
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Crystallographic Studies with Xenon and Nitrous Oxide Provide Evidence for Protein-dependent Processes in the Mechanisms of General Anesthesia. Anesthesiology 2014; 121:1018-27. [DOI: 10.1097/aln.0000000000000435] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Abstract
Background:
The mechanisms by which general anesthetics, including xenon and nitrous oxide, act are only beginning to be discovered. However, structural approaches revealed weak but specific protein–gas interactions.
Methods:
To improve knowledge, we performed x-ray crystallography studies under xenon and nitrous oxide pressure in a series of 10 binding sites within four proteins.
Results:
Whatever the pressure, we show (1) hydrophobicity of the gas binding sites has a screening effect on xenon and nitrous oxide binding, with a threshold value of 83% beyond which and below which xenon and nitrous oxide, respectively, binds to their sites preferentially compared to each other; (2) xenon and nitrous oxide occupancies are significantly correlated respectively to the product and the ratio of hydrophobicity by volume, indicating that hydrophobicity and volume are binding parameters that complement and oppose each other’s effects; and (3) the ratio of occupancy of xenon to nitrous oxide is significantly correlated to hydrophobicity of their binding sites.
Conclusions:
These data demonstrate that xenon and nitrous oxide obey different binding mechanisms, a finding that argues against all unitary hypotheses of narcosis and anesthesia, and indicate that the Meyer–Overton rule of a high correlation between anesthetic potency and solubility in lipids of general anesthetics is often overinterpreted. This study provides evidence that the mechanisms of gas binding to proteins and therefore of general anesthesia should be considered as the result of a fully reversible interaction between a drug ligand and a receptor as this occurs in classical pharmacology.
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41
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Ascenzi P, di Masi A, Tundo GR, Pesce A, Visca P, Coletta M. Nitrosylation mechanisms of Mycobacterium tuberculosis and Campylobacter jejuni truncated hemoglobins N, O, and P. PLoS One 2014; 9:e102811. [PMID: 25051055 PMCID: PMC4106858 DOI: 10.1371/journal.pone.0102811] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 06/23/2014] [Indexed: 01/19/2023] Open
Abstract
Truncated hemoglobins (trHbs) are widely distributed in bacteria and plants and have been found in some unicellular eukaryotes. Phylogenetic analysis based on protein sequences shows that trHbs branch into three groups, designated N (or I), O (or II), and P (or III). Most trHbs are involved in the O2/NO chemistry and/or oxidation/reduction function, permitting the survival of the microorganism in the host. Here, a detailed comparative analysis of kinetics and/or thermodynamics of (i) ferrous Mycobacterium tubertulosis trHbs N and O (Mt-trHbN and Mt-trHbO, respectively), and Campylobacter jejuni trHb (Cj-trHbP) nitrosylation, (ii) nitrite-mediated nitrosylation of ferrous Mt-trHbN, Mt-trHbO, and Cj-trHbP, and (iii) NO-based reductive nitrosylation of ferric Mt-trHbN, Mt-trHbO, and Cj-trHbP is reported. Ferrous and ferric Mt-trHbN and Cj-trHbP display a very high reactivity towards NO; however, the conversion of nitrite to NO is facilitated primarily by ferrous Mt-trHbN. Values of kinetic and/or thermodynamic parameters reflect specific trHb structural features, such as the ligand diffusion pathways to/from the heme, the heme distal pocket structure and polarity, and the ligand stabilization mechanisms. In particular, the high reactivity of Mt-trHbN and Cj-trHbP reflects the great ligand accessibility to the heme center by two protein matrix tunnels and the E7-path, respectively, and the penta-coordination of the heme-Fe atom. In contrast, the heme-Fe atom of Mt-trHbO the ligand accessibility to the heme center of Mt-trHbO needs large conformational readjustments, thus limiting the heme-based reactivity. These results agree with different roles of Mt-trHbN, Mt-trHbO, and Cj-trHbP in vivo.
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Affiliation(s)
- Paolo Ascenzi
- Interdepartmental Laboratory of Electron Microscopy, University Roma Tre, Roma, Italy
- * E-mail:
| | - Alessandra di Masi
- Interdepartmental Laboratory of Electron Microscopy, University Roma Tre, Roma, Italy
- Department of Sciences, University Roma Tre, Roma, Italy
| | - Grazia R. Tundo
- Department of Clinical Sciences and Translational Medicine, University of Roma “Tor Vergata”, Roma, Italy
- Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, Bari, Italy
| | | | - Paolo Visca
- Interdepartmental Laboratory of Electron Microscopy, University Roma Tre, Roma, Italy
| | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma “Tor Vergata”, Roma, Italy
- Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, Bari, Italy
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42
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Morozov AN, Roach JP, Kotzer M, Chatfield DC. A possible mechanism for redox control of human neuroglobin activity. J Chem Inf Model 2014; 54:1997-2003. [PMID: 24855999 PMCID: PMC4114473 DOI: 10.1021/ci5002108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Neuroglobin (Ngb) promotes neuron survival under hypoxic/ischemic conditions. In vivo and in vitro assays provide evidence for redox-regulated functioning of Ngb. On the basis of X-ray crystal structures and our MD simulations, a mechanism for redox control of human Ngb (hNgb) activity via the influence of the CD loop on the active site is proposed. We provide evidence that the CD loop undergoes a strand-to-helix transition when the external environment becomes sufficiently oxidizing, and that this CD loop conformational transition causes critical restructuring of the active site. We postulate that the strand-to-helix mechanics of the CD loop allows hNgb to utilize the lability of Cys46/Cys55 disulfide bonding and of the Tyr44/His64/heme propionate interaction network for redox-controlled functioning of hNgb.
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Affiliation(s)
- Alexander N Morozov
- Department of Chemistry and Biochemistry, Florida International University , Miami, Florida 33199, United States
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43
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Avella G, Ardiccioni C, Scaglione A, Moschetti T, Rondinelli C, Montemiglio LC, Savino C, Giuffrè A, Brunori M, Vallone B. Engineering the internal cavity of neuroglobin demonstrates the role of the haem-sliding mechanism. ACTA ACUST UNITED AC 2014; 70:1640-8. [DOI: 10.1107/s1399004714007032] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 03/29/2014] [Indexed: 11/10/2022]
Abstract
Neuroglobin is a member of the globin family involved in neuroprotection; it is primarily expressed in the brain and retina of vertebrates. Neuroglobin belongs to the heterogeneous group of hexacoordinate globins that have evolved in animals, plants and bacteria, endowed with the capability of reversible intramolecular coordination, allowing the binding of small gaseous ligands (O2, NO and CO). In a unique fashion among haemoproteins, ligand-binding events in neuroglobin are dependent on the sliding of the haem itself within a preformed internal cavity, as revealed by the crystal structure of its CO-bound derivative. Point mutants of the neuroglobin internal cavity have been engineered and their functional and structural characterization shows that hindering the haem displacement leads to a decrease in CO affinity, whereas reducing the cavity volume without interfering with haem sliding has negligible functional effects.
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44
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Yu ZL, Qiu S, Chen XC, Dai ZH, Huang YC, Li YN, Cai RH, Lei HT, Gu HY. Neuroglobin - a potential biological marker of retinal damage induced by LED light. Neuroscience 2014; 270:158-67. [PMID: 24747803 DOI: 10.1016/j.neuroscience.2014.04.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Revised: 04/05/2014] [Accepted: 04/09/2014] [Indexed: 01/16/2023]
Abstract
Neuroglobin (NGB), a protein highly expressed in the retina, has been shown to be up-regulated to protect neurons from hypoxic and ischemic injuries. It exhibits neuroprotective functions and plays an important role in the survival of neurons. Recent studies show that light-emitting diode (LED) white light emitted significant amounts of blue light (short-wavelength), which may be harmful to retinal cells, but the studies about biomarkers for evaluating the damage from LED white light are still insufficient. In our study, we found that NGB levels in the retina showed a twofold increase and peaked at 1h after a 1-h exposure to blue light (453 nm) which did not cause damage to the retina. However, retinal damage was observed after 2h of blue-light irradiation, which induced an approximate sevenfold increase of NGB levels as confirmed by Western blot and RT-PCR analysis. Immunofluorescence study demonstrated that NGB was predominantly up-regulated in the ganglion cell layer (GCL), plexiform layer (PL) and photoreceptor layer (PRL). We also examined Ngb mRNA and protein expression in the damaged retina induced by light of other wavelengths given equal photon fluxes. The LED red light (625 nm), green light (527 nm) and blue light (453 nm) increased the expression of NGB and caused TdT-mediated dUTP nick-end labeling-positive cells, especially in the blue-light group. In addition, a negative correlation between NGB and rhodopsin was observed. These findings suggested that there was a correlation between NGB expression and the severity of the retinal damage, indicating NGB's potential function as a biological marker of retinal damage induced by LED light.
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Affiliation(s)
- Z-L Yu
- Department of Anatomy and Neurobiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - S Qiu
- Department of Anatomy and Neurobiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - X-C Chen
- Department of Anatomy and Neurobiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Z-H Dai
- Department of Anatomy and Neurobiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Y-C Huang
- Department of Anatomy and Neurobiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Y-N Li
- School of Physics and Engineering, Sun Yat-sen University, Guangzhou, China
| | - R-H Cai
- Joinmax Display Technology Co., Ltd., Guangzhou, China
| | - H-T Lei
- Women and Childern Care Center of Luoyang, Henan Province, China
| | - H-Y Gu
- Department of Anatomy and Neurobiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
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45
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Giordano D, Coppola D, Russo R, Tinajero-Trejo M, di Prisco G, Lauro F, Ascenzi P, Verde C. The globins of cold-adapted Pseudoalteromonas haloplanktis TAC125: from the structure to the physiological functions. Adv Microb Physiol 2014; 63:329-89. [PMID: 24054800 DOI: 10.1016/b978-0-12-407693-8.00008-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Evolution allowed Antarctic microorganisms to grow successfully under extreme conditions (low temperature and high O2 content), through a variety of structural and physiological adjustments in their genomes and development of programmed responses to strong oxidative and nitrosative stress. The availability of genomic sequences from an increasing number of cold-adapted species is providing insights to understand the molecular mechanisms underlying crucial physiological processes in polar organisms. The genome of Pseudoalteromonas haloplanktis TAC125 contains multiple genes encoding three distinct truncated globins exhibiting the 2/2 α-helical fold. One of these globins has been extensively characterised by spectroscopic analysis, kinetic measurements and computer simulation. The results indicate unique adaptive structural properties that enhance the overall flexibility of the protein, so that the structure appears to be resistant to pressure-induced stress. Recent results on a genomic mutant strain highlight the involvement of the cold-adapted globin in the protection against the stress induced by high O2 concentration. Moreover, the protein was shown to catalyse peroxynitrite isomerisation in vitro. In this review, we first summarise how cold temperatures affect the physiology of microorganisms and focus on the molecular mechanisms of cold adaptation revealed by recent biochemical and genetic studies. Next, since only in a very few cases the physiological role of truncated globins has been demonstrated, we also discuss the structural and functional features of the cold-adapted globin in an attempt to put into perspective what has been learnt about these proteins and their potential role in the biology of cold-adapted microorganisms.
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Affiliation(s)
- Luisa B. Maia
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - José J. G. Moura
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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Guimarães BG, Hamdane D, Lechauve C, Marden MC, Golinelli-Pimpaneau B. The crystal structure of wild-type human brain neuroglobin reveals flexibility of the disulfide bond that regulates oxygen affinity. ACTA ACUST UNITED AC 2014; 70:1005-14. [PMID: 24699645 DOI: 10.1107/s1399004714000078] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 01/02/2014] [Indexed: 11/10/2022]
Abstract
Neuroglobin plays an important function in the supply of oxygen in nervous tissues. In human neuroglobin, a cysteine at position 46 in the loop connecting the C and D helices of the globin fold is presumed to form an intramolecular disulfide bond with Cys55. Rupture of this disulfide bridge stabilizes bi-histidyl haem hexacoordination, causing an overall decrease in the affinity for oxygen. Here, the first X-ray structure of wild-type human neuroglobin is reported at 1.74 Å resolution. This structure provides a direct observation of two distinct conformations of the CD region containing the intramolecular disulfide link and highlights internal cavities that could be involved in ligand migration and/or are necessary to enable the conformational transition between the low and high oxygen-affinity states following S-S bond formation.
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Affiliation(s)
- Beatriz G Guimarães
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, 91190 Gif-sur-Yvette, France
| | - Djemel Hamdane
- Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, 1 Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Christophe Lechauve
- Inserm U779, Université Paris XI, 78 Rue du Général Leclerc, 94275 Le Kremlin-Bicêtre, France
| | - Michael C Marden
- Inserm U779, Université Paris XI, 78 Rue du Général Leclerc, 94275 Le Kremlin-Bicêtre, France
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, 1 Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
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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]
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Nicolis S, Monzani E, Pezzella A, Ascenzi P, Sbardella D, Casella L. Neuroglobin Modification by Reactive Quinone Species. Chem Res Toxicol 2013; 26:1821-31. [DOI: 10.1021/tx4001896] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Stefania Nicolis
- Dipartimento
di Chimica, Università di Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Enrico Monzani
- Dipartimento
di Chimica, Università di Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Alessandro Pezzella
- Dipartimento
di Scienze Chimiche, Università di Napoli ‘Federico II’, Via Cintia 4, 80126 Napoli, Italy
| | - Paolo Ascenzi
- Laboratorio
Interdipartimentale di Microscopia Elettronica, Università Roma Tre, Via della Vasca Navale 79, 00146 Roma, Italy
| | - Diego Sbardella
- Dipartimento
di Scienze Cliniche e Medicina Traslazionale, Università di Roma ‘Tor Vergata’, Via Montpellier 1, 00133 Roma, Italy
- Consorzio Interuniversitario per la Ricerca sulla Chimica dei Metalli nei Sistemi Biologici, Via C. Ulpiani
27, 70126 Bari, Italy
| | - Luigi Casella
- Dipartimento
di Chimica, Università di Pavia, Via Taramelli 12, 27100 Pavia, Italy
- Consorzio Interuniversitario per la Ricerca sulla Chimica dei Metalli nei Sistemi Biologici, Via C. Ulpiani
27, 70126 Bari, Italy
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Ascenzi P, Coletta A, Cao Y, Trezza V, Leboffe L, Fanali G, Fasano M, Pesce A, Ciaccio C, Marini S, Coletta M. Isoniazid inhibits the heme-based reactivity of Mycobacterium tuberculosis truncated hemoglobin N. PLoS One 2013; 8:e69762. [PMID: 23936350 PMCID: PMC3731299 DOI: 10.1371/journal.pone.0069762] [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: 03/02/2013] [Accepted: 06/12/2013] [Indexed: 11/19/2022] Open
Abstract
Isoniazid represents a first-line anti-tuberculosis medication in prevention and treatment. This prodrug is activated by a mycobacterial catalase-peroxidase enzyme called KatG in Mycobacterium tuberculosis), thereby inhibiting the synthesis of mycolic acid, required for the mycobacterial cell wall. Moreover, isoniazid activation by KatG produces some radical species (e.g., nitrogen monoxide), that display anti-mycobacterial activity. Remarkably, the ability of mycobacteria to persist in vivo in the presence of reactive nitrogen and oxygen species implies the presence in these bacteria of (pseudo-)enzymatic detoxification systems, including truncated hemoglobins (trHbs). Here, we report that isoniazid binds reversibly to ferric and ferrous M. tuberculosis trHb type N (or group I; Mt-trHbN(III) and Mt-trHbN(II), respectively) with a simple bimolecular process, which perturbs the heme-based spectroscopic properties. Values of thermodynamic and kinetic parameters for isoniazid binding to Mt-trHbN(III) and Mt-trHbN(II) are K = (1.1±0.1)×10−4 M, kon = (5.3±0.6)×103 M−1 s−1 and koff = (4.6±0.5)×10−1 s−1; and D = (1.2±0.2)×10−3 M, don = (1.3±0.4)×103 M−1 s−1, and doff = 1.5±0.4 s−1, respectively, at pH 7.0 and 20.0°C. Accordingly, isoniazid inhibits competitively azide binding to Mt-trHbN(III) and Mt-trHbN(III)-catalyzed peroxynitrite isomerization. Moreover, isoniazid inhibits Mt-trHbN(II) oxygenation and carbonylation. Although the structure of the Mt-trHbN-isoniazid complex is not available, here we show by docking simulation that isoniazid binding to the heme-Fe atom indeed may take place. These data suggest a direct role of isoniazid to impair fundamental functions of mycobacteria, e.g. scavenging of reactive nitrogen and oxygen species, and metabolism.
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Affiliation(s)
- Paolo Ascenzi
- Interdepartmental Laboratory of Electron Microscopy, University Roma Tre, Roma, Italy.
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