1
|
Amadei A, Aschi M. Stationary and Time-Dependent Carbon Monoxide Stretching Mode Features in Carboxy Myoglobin: A Theoretical-Computational Reappraisal. J Phys Chem B 2021; 125:13624-13634. [PMID: 34904432 DOI: 10.1021/acs.jpcb.1c05815] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The stationary and time-dependent infrared spectrum (IR) of the CO stretching mode (νCO) in carboxymyoglobin (MbCO), a longstanding problem of biophysical chemistry, has been modeled through a theoretical-computational method specifically designed for simulating quantum observables in complex atomic-molecular systems and based on a combined application of long time scale molecular dynamics simulations and quantum-chemical calculations. This study is basically focused on two aspects: (i) the origin of the stationary IR substates (termed as A0, A1, and A3) and (ii) the modeling and the interpretation of the νCO energy relaxation. The results, strengthened by a more than satisfactory agreement with the experimental data, concisely indicate that (i) the conformational His64-FeCO relevant substates, i.e., characterized by the formation-disruption of the H-bond between the above moieties, are the main responsible of the presence of two distinct and well separated (A0 and A1/A3) spectroscopic regions; (ii) the characteristic bimodal shape of the A1/A3 spectral region, according to our model, is the result of the fluctuation of the electric field pattern as provided by the protein-solvent framework perturbing the bound His64-CO-Heme complex; and (iii) the electric field pattern, in conjunction with the relatively high density of MbCO vibrational states, is also the main determinant of the νCO energy relaxation, characterizing its kinetic efficiency.
Collapse
Affiliation(s)
- Andrea Amadei
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma "Tor Vergata", via della Ricerca Scientifica 1, 00 133 Roma, Italia
| | - Massimiliano Aschi
- Dipartimento di Scienze Fisiche e Chimiche, Università de l'Aquila, via Vetoio (Coppito 1), 67 010 l'Aquila, Italia
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
De Simone G, Sbardella D, Oddone F, Pesce A, Coletta M, Ascenzi P. Structural and (Pseudo-)Enzymatic Properties of Neuroglobin: Its Possible Role in Neuroprotection. Cells 2021; 10:cells10123366. [PMID: 34943874 PMCID: PMC8699588 DOI: 10.3390/cells10123366] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 12/17/2022] Open
Abstract
Neuroglobin (Ngb), the third member of the globin family, was discovered in human and murine brains in 2000. This monomeric globin is structurally similar to myoglobin (Mb) and hemoglobin (Hb) α and β subunits, but it hosts a bis-histidyl six-coordinated heme-Fe atom. Therefore, the heme-based reactivity of Ngb is modulated by the dissociation of the distal HisE7-heme-Fe bond, which reflects in turn the redox state of the cell. The high Ngb levels (~100–200 μM) present in the retinal ganglion cell layer and in the optic nerve facilitate the O2 buffer and delivery. In contrast, the very low levels of Ngb (~1 μM) in most tissues and organs support (pseudo-)enzymatic properties including NO/O2 metabolism, peroxynitrite and free radical scavenging, nitrite, hydroxylamine, hydrogen sulfide reduction, and the nitration of aromatic compounds. Here, structural and (pseudo-)enzymatic properties of Ngb, which are at the root of tissue and organ protection, are reviewed, envisaging a possible role in the protection from neuronal degeneration of the retina and the optic nerve.
Collapse
Affiliation(s)
- Giovanna De Simone
- Dipartimento di Scienze, Università Roma Tre, Viale Marconi 446, 00146 Roma, Italy;
| | | | | | - Alessandra Pesce
- Dipartimento di Fisica, Università di Genova, Via Dodecaneso 33, 16100 Genova, Italy;
| | - Massimo Coletta
- IRCCS Fondazione Bietti, 00198 Roma, Italy; (D.S.); (F.O.)
- Dipartmento di Scienze Cliniche e Medicina Traslazionale, Università di Roma “Tor Vergata”, Via Montpellier 1, 00133 Roma, Italy
- Correspondence: (M.C.); (P.A.); Tel.: +39-06-72596365 (M.C.); +39-06-57336321 (P.A.)
| | - Paolo Ascenzi
- Dipartimento di Scienze, Università Roma Tre, Viale Marconi 446, 00146 Roma, Italy;
- Accademia Nazionale dei Lincei, Via della Lungara 10, 00165 Roma, Italy
- Unità di Neuroendocrinologia, Metabolismo e Neurofarmacologia, IRCSS Fondazione Santa Lucia, 00179 Roma, Italy
- Correspondence: (M.C.); (P.A.); Tel.: +39-06-72596365 (M.C.); +39-06-57336321 (P.A.)
| |
Collapse
|
4
|
Ardiccioni C, Arcovito A, Della Longa S, van der Linden P, Bourgeois D, Weik M, Montemiglio LC, Savino C, Avella G, Exertier C, Carpentier P, Prangé T, Brunori M, Colloc’h N, Vallone B. Ligand pathways in neuroglobin revealed by low-temperature photodissociation and docking experiments. IUCRJ 2019; 6:832-842. [PMID: 31576217 PMCID: PMC6760443 DOI: 10.1107/s2052252519008157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/06/2019] [Indexed: 06/10/2023]
Abstract
A combined biophysical approach was applied to map gas-docking sites within murine neuroglobin (Ngb), revealing snapshots of events that might govern activity and dynamics in this unique hexacoordinate globin, which is most likely to be involved in gas-sensing in the central nervous system and for which a precise mechanism of action remains to be elucidated. The application of UV-visible microspectroscopy in crystallo, solution X-ray absorption near-edge spectroscopy and X-ray diffraction experiments at 15-40 K provided the structural characterization of an Ngb photolytic intermediate by cryo-trapping and allowed direct observation of the relocation of carbon monoxide within the distal heme pocket after photodissociation. Moreover, X-ray diffraction at 100 K under a high pressure of dioxygen, a physiological ligand of Ngb, unravelled the existence of a storage site for O2 in Ngb which coincides with Xe-III, a previously described docking site for xenon or krypton. Notably, no other secondary sites were observed under our experimental conditions.
Collapse
Affiliation(s)
- Chiara Ardiccioni
- Department of Life and Environmental Sciences, New York–Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Ancona, Italy
| | - Alessandro Arcovito
- Istituto di Biochimica e Biochimica Clinica, Universitá Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy
- Fondazione Policlinico Universitario Agostino Gemelli–IRCCS, Largo Francesco Vito 1, 00168 Rome, Italy
| | - Stefano Della Longa
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Peter van der Linden
- European Synchrotron Radiation Facility (ESRF), 38043 Grenoble, France
- Partnership for Soft Condensed Matter (PSCM), 38043 Grenoble, France
| | | | - Martin Weik
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Linda Celeste Montemiglio
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Istituto Pasteur–Fondazione Cenci Bolognetti, Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Giovanna Avella
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Chemistry Department, Merck Serono S.p.A., Via Casilina 125, 00176 Rome, Italy
| | - Cécile Exertier
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Philippe Carpentier
- European Synchrotron Radiation Facility (ESRF), 38043 Grenoble, France
- CEA/DRF/BIG/CBM/BioCat LCBM CNRS UMR 5249, Université Grenoble Alpes, 38000 Grenoble, France
| | - Thierry Prangé
- CiTeCoM UMR 8038 CNRS, Université Paris Descartes, Paris, France
| | - Maurizio Brunori
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Nathalie Colloc’h
- ISTCT UMR 6030 CNRS Université de Caen Normandie CEA, CERVOxy Team, Centre Cyceron, Caen, France
| | - Beatrice Vallone
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Istituto Pasteur–Fondazione Cenci Bolognetti, Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| |
Collapse
|
5
|
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.
Collapse
|
6
|
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]
|
7
|
Chillemi G, Anselmi M, Sanna N, Padrin C, Balducci L, Cammarata M, Pace E, Chergui M, Benfatto M. Dynamic multiple-scattering treatment of X-ray absorption: Parameterization of a new molecular dynamics force field for myoglobin. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2018; 5:054101. [PMID: 30246048 PMCID: PMC6135643 DOI: 10.1063/1.5031806] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 07/09/2018] [Indexed: 06/08/2023]
Abstract
We present a detailed analysis of the X-ray absorption near-edge structure (XANES) data on the Fe K-edge of CO Myoglobin based on a combined procedure of Molecular Dynamics (MD) calculations and MXAN (Minuit XANes) data analysis that we call D-MXAN. The ability of performing quantitative XANES data analysis allows us to refine classical force field MD parameters, thus obtaining a reliable tool for the atomic investigation of this important model system for biological macromolecules. The iterative procedure here applied corrects the greatest part of the structural discrepancy between classical MD sampling and experimental determinations. Our procedure, moreover, is able to discriminate between different heme conformational basins visited during the MD simulation, thus demonstrating the necessity of a sampling on the order of tens of nanoseconds, even for an application such X-ray absorption spectroscopy data analysis.
Collapse
Affiliation(s)
- Giovanni Chillemi
- Authors to whom correspondence should be addressed: , Telephone: +39 06 44486 706 and , Telephone: +39–06-9403–2884
| | - Massimiliano Anselmi
- Institute for Microbiology and Genetics, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | | | - Cristiano Padrin
- CINECA, SuperComputing Applications and Innovation Department, Via dei Tizii 6, 00185 Roma, Italy
| | - Lodovico Balducci
- Université de Rennes 1, CNRS, Univ. Bretagne Loire, Institut de Physique de Rennes, UMR 6251, Rennes F-35042, France
| | - Marco Cammarata
- Université de Rennes 1, CNRS, Univ. Bretagne Loire, Institut de Physique de Rennes, UMR 6251, Rennes F-35042, France
| | - Elisabetta Pace
- Laboratori Nazionali di Frascati, INFN- Via E. Fermi 44, 00044 Frascati, Italy
| | - Majed Chergui
- Lab. of Ultrafast Spectroscopy (LSU) and Lausanne Centre for Ultrafast Science (LACUS), Ecole Polytechnique Fédérale de Lausanne, ISIC, FSB, Station 6, CH-1015 Lausanne, Switzerland
| | - Maurizio Benfatto
- Laboratori Nazionali di Frascati, INFN- Via E. Fermi 44, 00044 Frascati, Italy
| |
Collapse
|
8
|
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
| |
Collapse
|
9
|
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]
|
10
|
Zhao C, Du W. Dynamic features of carboxy cytoglobin distal mutants investigated by molecular dynamics simulations. J Biol Inorg Chem 2016; 21:251-61. [DOI: 10.1007/s00775-016-1334-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 01/04/2016] [Indexed: 01/08/2023]
|
11
|
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.
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Takahashi N, Watanabe S, Wakasugi K. Crucial roles of Glu60 in human neuroglobin as a guanine nucleotide dissociation inhibitor and neuroprotective agent. PLoS One 2013; 8:e83698. [PMID: 24376733 PMCID: PMC3871547 DOI: 10.1371/journal.pone.0083698] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 11/15/2013] [Indexed: 11/18/2022] Open
Abstract
Mammalian neuroglobin (Ngb) protects neuronal cells under conditions of oxidative stress. We previously showed that human Ngb acts as a guanine nucleotide dissociation inhibitor (GDI) for the α-subunits of heterotrimeric Gi/o proteins and inhibits reductions in cAMP concentration, leading to protection against cell death. In the present study, we created human E60Q Ngb mutant and clarified that Glu60 of human Ngb is a crucial residue for its GDI and neuroprotective activities. Moreover, we investigated structural and functional properties of several human Ngb mutants and demonstrated that the neuroprotective effect of human Ngb is due to its GDI activity and not due to its scavenging activity against reactive oxygen species.
Collapse
Affiliation(s)
- Nozomu Takahashi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Seiji Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Keisuke Wakasugi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
- * E-mail:
| |
Collapse
|
14
|
Glyceride Lipid Formulations: Molecular Dynamics Modeling of Phase Behavior During Dispersion and Molecular Interactions Between Drugs and Excipients. Pharm Res 2013; 30:3238-53. [DOI: 10.1007/s11095-013-1206-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2013] [Accepted: 09/12/2013] [Indexed: 10/26/2022]
|
15
|
Zhao C, Zhang B, Du W. Effects of distal mutation on the dynamic properties of carboxycytoglobin: a molecular dynamics simulation study. J Biol Inorg Chem 2013; 18:947-55. [DOI: 10.1007/s00775-013-1041-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 08/26/2013] [Indexed: 11/29/2022]
|
16
|
Choi JH, Kwak KW, Cho M. Computational infrared and two-dimensional infrared photon echo spectroscopy of both wild-type and double mutant myoglobin-CO proteins. J Phys Chem B 2013; 117:15462-78. [PMID: 23869523 DOI: 10.1021/jp405210s] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The CO stretching mode of both wild-type and double mutant ( T67R / S92D ) MbCO (carbonmonoxymyoglobin) proteins is an ideal infrared (IR) probe for studying the local electrostatic environment inside the myoglobin heme pocket. Recently, to elucidate the conformational switching dynamics between two distinguishable states, extensive IR absorption, IR pump-probe, and two-dimensional (2D) IR spectroscopic studies for various mutant MbCO's have been performed by the Fayer group. They showed that the 2D IR spectroscopy of the double mutant, which has a peroxidase enzyme activity, reveals a rapid chemical exchange between two distinct states, whereas that of the wild-type does not. Despite the fact that a few simulation studies on these systems were already performed and reported, such complicated experimental results have not been fully reproduced nor described in terms of conformational state-to-state transition processes. Here, we first develop a distributed vibrational solvatochromic charge model for describing the CO stretch frequency shift reflecting local electric potential changes. Then, by carrying out molecular dynamic simulations of the two MbCO's and examining their CO frequency trajectories, it becomes possible to identify a proper reaction coordinate consisting of His64 imidazole ring rotation and its distance to the CO ligand. From the 2D surfaces of the resulting potential of mean forces, the spectroscopically distinguished A1 and A3 states of the wild-type as well as two more substates of the double mutant are identified and their vibrational frequencies and distributions are separately examined. Our simulated IR absorption and 2D IR spectra of the two MbCO's are directly compared with the previous experimental results reported by the Fayer group. The chemical exchange rate constants extracted from the two-state kinetic analyses of the simulated 2D IR spectra are in excellent agreement with the experimental values. On the basis of the quantitative agreement between the simulated spectra and experimental ones, we further examine the conformational differences in the heme pockets of the two proteins and show that the double mutation, T67R / S92D , suppresses the A1 population, restricts the imidazole ring rotation, and increases hydrogen-bond strength between the imidazole Nε-H and the oxygen atom of the CO ligand. It is believed that such delicate change of distal His64 imidazole ring dynamics induced by the double mutation may be responsible for its enhanced peroxidase catalytic activity as compared to the wild-type myoglobin.
Collapse
Affiliation(s)
- Jun-Ho Choi
- Department of Chemistry, Korea University , Seoul 136-713, Korea
| | | | | |
Collapse
|
17
|
Pietra F. From Dioxygen Storing to Dioxygen Sensing with Neuroglobins: An Insight from Molecular Mechanics. Chem Biodivers 2013; 10:963-75. [DOI: 10.1002/cbdv.201300060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Indexed: 11/06/2022]
|
18
|
Noise-induced alterations in cochlear mechanics, electromotility, and cochlear amplification. Pflugers Arch 2012; 465:907-17. [DOI: 10.1007/s00424-012-1198-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 11/19/2012] [Accepted: 12/02/2012] [Indexed: 11/25/2022]
|
19
|
Watanabe S, Takahashi N, Uchida H, Wakasugi K. Human neuroglobin functions as an oxidative stress-responsive sensor for neuroprotection. J Biol Chem 2012; 287:30128-38. [PMID: 22787149 DOI: 10.1074/jbc.m112.373381] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mammalian neuroglobin (Ngb) protects neuronal cells under conditions of oxidative stress. The mechanism underlying this function is only partly understood. Here, we report that human Ngb exists in lipid rafts only during oxidative stress and that lipid rafts are crucial for neuroprotection by Ngb. The ferrous oxygen-bound form of Ngb, which exists under normoxia, is converted to the ferric bis-His conformation during oxidative stress, inducing large tertiary structural changes. We clarified that ferric bis-His Ngb, but not ferrous ligand-bound Ngb, specifically binds to flotillin-1, a lipid raft microdomain-associated protein, as well as to α-subunits of heterotrimeric G proteins (Gα(i/o)). Moreover, we found that human ferric bis-His Ngb acts as a guanine nucleotide dissociation inhibitor for Gα(i/o) that has been modified by oxidative stress. In addition, our data shows that Ngb inhibits the decrease in cAMP concentration that occurs under oxidative stress, leading to protection against cell death. Furthermore, by using a mutated Ngb protein that cannot form the bis-His conformation, we demonstrate that the oxidative stress-induced structural changes of human Ngb are essential for its neuroprotective activity.
Collapse
Affiliation(s)
- Seiji Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Tokyo 153-8902, Japan
| | | | | | | |
Collapse
|
20
|
Drummond ML, Wilson AK, Cundari TR. Carbon Dioxide Migration Pathways in Proteins. J Phys Chem Lett 2012; 3:830-833. [PMID: 26286405 DOI: 10.1021/jz3001085] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Some of the most important biological processes, such as carbon fixation, are dependent on protein-gas interactions. The motion of CO2 through the enzyme phosphoenolpyruvate carboxykinase was investigated using extensive all-atom molecular dynamics simulations. Three discrete migration pathways were located, suggesting the protein directs the movement of CO2. The chemical nature of these pathways is discussed, as are their biotechnological ramifications.
Collapse
Affiliation(s)
- Michael L Drummond
- Center for Advanced Scientific Computing and Modeling (CASCaM), Department of Chemistry, University of North Texas, Denton, Texas 76203-5070, United States
| | - Angela K Wilson
- Center for Advanced Scientific Computing and Modeling (CASCaM), Department of Chemistry, University of North Texas, Denton, Texas 76203-5070, United States
| | - Thomas R Cundari
- Center for Advanced Scientific Computing and Modeling (CASCaM), Department of Chemistry, University of North Texas, Denton, Texas 76203-5070, United States
| |
Collapse
|
21
|
Boron I, Russo R, Boechi L, Cheng CHC, di Prisco G, Estrin DA, Verde C, Nadra AD. Structure and dynamics of Antarctic fish neuroglobin assessed by computer simulations. IUBMB Life 2011; 63:206-13. [PMID: 21445852 DOI: 10.1002/iub.444] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Neuroglobin (Ngb) is a heme protein, highly conserved along evolution, predominantly found in the nervous system. It is upregulated by hypoxia and ischemia and may have a neuroprotective role under hypoxic stress. Although many other roles have been proposed, the physiological function is still unclear. Antarctic icefishes lack hemoglobin and some species also lack myoglobin, but all have Ngb and thus may help the elucidation of Ngb function. We present the first theoretically derived structure of fish Ngb and describe its behavior using molecular dynamics simulations. Specifically, we sequenced and analyzed Ngbs from a colorless-blooded Antarctic icefish species Chaenocephalus aceratus and a related red-blooded species (Dissostichus mawsoni). Both fish Ngbs are 6-coordinated but have some peculiarities that differentiate them from mammalian counterparts: they have extensions in the N and C termini that can interact with the EF loop, and a gap in the alignment that changes the CD-region structure/dynamics that has been found to play a key role in human neuroglobin. Our results suggest that a single mutation between both fish Ngbs is responsible for significant difference in the behavior of the proteins. The functional role of these characteristics is discussed.
Collapse
Affiliation(s)
- Ignacio Boron
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | | | | | | | | | | | | | | |
Collapse
|
22
|
Zhang B, Xu J, Li Y, Du W, Fang W. Molecular dynamics simulation of carboxy and deoxy human cytoglobin in solution. J Inorg Biochem 2011; 105:949-56. [DOI: 10.1016/j.jinorgbio.2011.03.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 03/28/2011] [Accepted: 03/28/2011] [Indexed: 11/30/2022]
|
23
|
Bocahut A, Bernad S, Sebban P, Sacquin-Mora S. Frontier Residues Lining Globin Internal Cavities Present Specific Mechanical Properties. J Am Chem Soc 2011; 133:8753-61. [DOI: 10.1021/ja202587a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anthony Bocahut
- Laboratoire de Biochimie Théorique, UMR 9080 CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Sophie Bernad
- Laboratoire de Chimie Physique, CNRS UMR8000, Bât. 350, Université Paris-sud, 91405 Orsay, France
| | - Pierre Sebban
- Laboratoire de Chimie Physique, CNRS UMR8000, Bât. 350, Université Paris-sud, 91405 Orsay, France
- Université des Sciences et des Technologies de Hanoi, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, UMR 9080 CNRS, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| |
Collapse
|
24
|
Anselmi M, Di Nola A, Amadei A. Kinetics of carbon monoxide migration and binding in solvated neuroglobin as revealed by molecular dynamics simulations and quantum mechanical calculations. J Phys Chem B 2011; 115:2436-46. [PMID: 21332165 DOI: 10.1021/jp110833v] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Neuroglobin (Ngb) is a globular protein that reversibly binds small ligands at the six coordination position of the heme. With respect to other globins similar to myoglobin, Ngb displays some peculiarities as the topological reorganization of the internal cavities coupled to the sliding of the heme, or the binding of the endogenous distal histidine to the heme in the absence of an exogenous ligand. In this Article, by using multiple (independent) molecular dynamics trajectories (about 500 ns in total), the migration pathways of photolized carbon monoxide (CO) within solvated Ngb were analyzed, and a quantitative description of CO migration and corresponding kinetics was obtained. MD results, combined with quantum mechanical calculations on the CO-heme binding-unbinding reaction step in Ngb, allowed construction of a quantitative model representing the relevant steps of CO migration and rebinding.
Collapse
|
25
|
Time resolved thermodynamics associated with ligand photorelease in heme peroxidases and globins: Open access channels versus gated ligand release. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1065-76. [PMID: 21278003 DOI: 10.1016/j.bbapap.2011.01.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 01/14/2011] [Accepted: 01/17/2011] [Indexed: 10/18/2022]
Abstract
Heme proteins represent a diverse class of biomolecules responsible for an extremely diverse array of physiological functions including electron transport, monooxygenation, ligand transport and storage, cellular signaling, respiration, etc. An intriguing aspect of these proteins is that such functional diversity is accomplished using a single type of heme macrocycle based upon iron protoporphyrin IX. The functional diversity originates from a delicate balance of inter-molecular interactions within the protein matrix together with well choreographed dynamics that modulate the heme electronic structure as well as ligand entry/exit pathways from the bulk solvent to the active site. Of particular interest are the dynamics and energetics associated with the entry/exit of ligands as this process plays a significant role in regulating the rates of heme protein activity. Time-resolved photoacoustic calorimetry (PAC) has emerged as a powerful tool through which to probe the underlying energetics associated with small molecule dissociation and release to the bulk solvent in heme proteins on time scales from tens of nanoseconds to several microseconds. In this review, the results of PAC studies on various classes of heme proteins are summarized highlighting how different protein structures affect the thermodynamics of ligand migration. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
Collapse
|
26
|
Bagchi S, Nebgen BT, Loring RF, Fayer MD. Dynamics of a myoglobin mutant enzyme: 2D IR vibrational echo experiments and simulations. J Am Chem Soc 2010; 132:18367-76. [PMID: 21142083 PMCID: PMC3033732 DOI: 10.1021/ja108491t] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Myoglobin (Mb) double mutant T67R/S92D displays peroxidase enzymatic activity in contrast to the wild type protein. The CO adduct of T67R/S92D shows two CO absorption bands corresponding to the A(1) and A(3) substates. The equilibrium protein dynamics for the two distinct substates of the Mb double mutant are investigated by using two-dimensional infrared (2D IR) vibrational echo spectroscopy and molecular dynamics (MD) simulations. The time-dependent changes in the 2D IR vibrational echo line shapes for both of the substates are analyzed using the center line slope (CLS) method to obtain the frequency-frequency correlation function (FFCF). The results for the double mutant are compared to those from the wild type Mb. The experimentally determined FFCF is compared to the FFCF obtained from molecular dynamics simulations, thereby testing the capacity of a force field to determine the amplitudes and time scales of protein structural fluctuations on fast time scales. The results provide insights into the nature of the energy landscape around the free energy minimum of the folded protein structure.
Collapse
Affiliation(s)
- Sayan Bagchi
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | | | | | | |
Collapse
|
27
|
Xu J, Yin G, Du W. Distal mutation modulates the heme sliding in mouse neuroglobin investigated by molecular dynamics simulation. Proteins 2010; 79:191-202. [DOI: 10.1002/prot.22872] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
28
|
D’Angelo P, Della Longa S, Arcovito A, Anselmi M, Di Nola A, Chillemi G. Dynamic Investigation of Protein Metal Active Sites: Interplay of XANES and Molecular Dynamics Simulations. J Am Chem Soc 2010; 132:14901-9. [DOI: 10.1021/ja1056533] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paola D’Angelo
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy, Department of Experimental Medicine, University of L’Aquila, 67100 L’Aquila, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, and CASPUR, Consortium for Supercomputing Applications, Via dei Tizii 6b, 00185 Rome, Italy
| | - Stefano Della Longa
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy, Department of Experimental Medicine, University of L’Aquila, 67100 L’Aquila, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, and CASPUR, Consortium for Supercomputing Applications, Via dei Tizii 6b, 00185 Rome, Italy
| | - Alessandro Arcovito
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy, Department of Experimental Medicine, University of L’Aquila, 67100 L’Aquila, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, and CASPUR, Consortium for Supercomputing Applications, Via dei Tizii 6b, 00185 Rome, Italy
| | - Massimiliano Anselmi
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy, Department of Experimental Medicine, University of L’Aquila, 67100 L’Aquila, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, and CASPUR, Consortium for Supercomputing Applications, Via dei Tizii 6b, 00185 Rome, Italy
| | - Alfredo Di Nola
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy, Department of Experimental Medicine, University of L’Aquila, 67100 L’Aquila, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, and CASPUR, Consortium for Supercomputing Applications, Via dei Tizii 6b, 00185 Rome, Italy
| | - Giovanni Chillemi
- Department of Chemistry, University of Rome “La Sapienza”, P.le Aldo Moro 5, 00185 Rome, Italy, Department of Experimental Medicine, University of L’Aquila, 67100 L’Aquila, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, and CASPUR, Consortium for Supercomputing Applications, Via dei Tizii 6b, 00185 Rome, Italy
| |
Collapse
|
29
|
Arcovito A, Ardiccioni C, Cianci M, D’Angelo P, Vallone B, Della Longa S. Polarized X-ray Absorption Near-Edge Structure Spectroscopy of Neuroglobin and Myoglobin Single Crystals. J Phys Chem B 2010; 114:13223-31. [DOI: 10.1021/jp104395g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alessandro Arcovito
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L. go F. Vito 1, 00168 Rome, Italy, Dipartimento di Scienze Biochimiche “A. Rossi-Fanelli”, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy, European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603, Hamburg, Germany, Dipartimento di Chimica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy, and Dipartimento di Medicina Sperimentale, Università “L’Aquila”, Via
| | - Chiara Ardiccioni
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L. go F. Vito 1, 00168 Rome, Italy, Dipartimento di Scienze Biochimiche “A. Rossi-Fanelli”, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy, European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603, Hamburg, Germany, Dipartimento di Chimica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy, and Dipartimento di Medicina Sperimentale, Università “L’Aquila”, Via
| | - Michele Cianci
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L. go F. Vito 1, 00168 Rome, Italy, Dipartimento di Scienze Biochimiche “A. Rossi-Fanelli”, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy, European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603, Hamburg, Germany, Dipartimento di Chimica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy, and Dipartimento di Medicina Sperimentale, Università “L’Aquila”, Via
| | - Paola D’Angelo
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L. go F. Vito 1, 00168 Rome, Italy, Dipartimento di Scienze Biochimiche “A. Rossi-Fanelli”, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy, European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603, Hamburg, Germany, Dipartimento di Chimica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy, and Dipartimento di Medicina Sperimentale, Università “L’Aquila”, Via
| | - Beatrice Vallone
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L. go F. Vito 1, 00168 Rome, Italy, Dipartimento di Scienze Biochimiche “A. Rossi-Fanelli”, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy, European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603, Hamburg, Germany, Dipartimento di Chimica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy, and Dipartimento di Medicina Sperimentale, Università “L’Aquila”, Via
| | - Stefano Della Longa
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L. go F. Vito 1, 00168 Rome, Italy, Dipartimento di Scienze Biochimiche “A. Rossi-Fanelli”, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy, European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603, Hamburg, Germany, Dipartimento di Chimica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy, and Dipartimento di Medicina Sperimentale, Università “L’Aquila”, Via
| |
Collapse
|
30
|
Nienhaus K, Nienhaus GU. Ligand dynamics in heme proteins observed by Fourier transform infrared-temperature derivative spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:1030-41. [PMID: 20656073 DOI: 10.1016/j.bbapap.2010.07.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 07/14/2010] [Accepted: 07/15/2010] [Indexed: 11/29/2022]
Abstract
Fourier transform infrared (FTIR) spectroscopy is a powerful tool for the investigation of protein-ligand interactions in heme proteins. Nitric oxide and carbon monoxide are attractive physiologically relevant ligands because their bond stretching vibrations give rise to strong mid-infrared absorption bands that can be measured with exquisite sensitivity and precision using photolysis difference spectroscopy at cryogenic temperatures. These stretching bands are fine-tuned by electrostatic interactions with the environment and, therefore, ligands can be utilized as local probes of structure and dynamics. Bound to the heme iron, the ligand stretching bands are susceptible to changes in the iron-ligand bond and the electric field at the active site. Upon photolysis, the vibrational bands display changes due to ligand relocation to docking sites within the protein, rotational motions of the ligand in these sites and protein conformational changes. Photolysis difference spectra taken over a wide temperature range (3-300K) using specific temperature protocols for sample photodissociation can provide detailed insights into both protein and ligand dynamics. Moreover, temperature-derivative spectroscopy (TDS) has proven to be a particularly powerful technique to study protein-ligand interactions. The FTIR-TDS technique has been extensively applied to studies of carbon monoxide binding to heme proteins, whereas measurements with nitric oxide are still scarce. Here we describe infrared cryo-spectroscopy and present a variety of applications to the study of protein-ligand interactions in heme proteins. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
Collapse
Affiliation(s)
- Karin Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics and Center for Functional Nanostructures, Wolfgang-Gaede-Str. 1, D-76131 Karlsruhe, Germany
| | | |
Collapse
|
31
|
Astudillo L, Bernad S, Derrien V, Sebban P, Miksovska J. Probing the role of the internal disulfide bond in regulating conformational dynamics in neuroglobin. Biophys J 2010; 99:L16-8. [PMID: 20643048 PMCID: PMC2905123 DOI: 10.1016/j.bpj.2010.04.033] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 04/05/2010] [Accepted: 04/19/2010] [Indexed: 11/20/2022] Open
Abstract
In this report, we demonstrate that the internal disulfide bridge in human neuroglobin modulates structural changes associated with ligand photo-dissociation from the heme active site. This is evident from time-resolved photothermal studies of CO photo-dissociation, which reveal a 13.4+/-0.9 mL mol(-1) volume expansion upon ligand photo-release from human neuroglobin, whereas the CO dissociation from rat neuroglobin leads to a significantly smaller volume change (DeltaV=4.6+/-0.3 mL mol(-1)). Reduction of the internal disulfide bond in human neuroglobin leads to conformational changes (reflected by DeltaV) nearly identical to those observed for rat Ngb. Our data favor the hypothesis that the disulfide bond between Cys46 and Cys55 modulates the functioning of human neuroglobin.
Collapse
Affiliation(s)
- Luisana Astudillo
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida
| | - Sophie Bernad
- University Paris-Sud, Laboratoire de Chimie-Physique, Faculté d'Orsay, Orsay cedex, France
- CNRS, Orsay, France
| | - Valérie Derrien
- University Paris-Sud, Laboratoire de Chimie-Physique, Faculté d'Orsay, Orsay cedex, France
- CNRS, Orsay, France
| | - Pierre Sebban
- University Paris-Sud, Laboratoire de Chimie-Physique, Faculté d'Orsay, Orsay cedex, France
- CNRS, Orsay, France
| | - Jaroslava Miksovska
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida
| |
Collapse
|
32
|
Bocahut A, Bernad S, Sebban P, Sacquin-Mora S. Relating the Diffusion of Small Ligands in Human Neuroglobin to Its Structural and Mechanical Properties. J Phys Chem B 2009; 113:16257-67. [DOI: 10.1021/jp906854x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anthony Bocahut
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France, Laboratoire de Chimie Physique, Université Paris-sud 11, CNRS UMR8000 Bât. 350, 91405 Orsay, France
| | - Sophie Bernad
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France, Laboratoire de Chimie Physique, Université Paris-sud 11, CNRS UMR8000 Bât. 350, 91405 Orsay, France
| | - Pierre Sebban
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France, Laboratoire de Chimie Physique, Université Paris-sud 11, CNRS UMR8000 Bât. 350, 91405 Orsay, France
| | - Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France, Laboratoire de Chimie Physique, Université Paris-sud 11, CNRS UMR8000 Bât. 350, 91405 Orsay, France
| |
Collapse
|
33
|
Ligand migration through the internal hydrophobic cavities in human neuroglobin. Proc Natl Acad Sci U S A 2009; 106:18984-9. [PMID: 19850865 DOI: 10.1073/pnas.0905433106] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Neuroglobin (Ngb), a member of the globin superfamily, was found in the brain of vertebrates and is suggested to play a neuroprotective function under hypoxic conditions by scavenging nitrogen monoxide (NO) through a dioxygenase activity. In order for such a reaction to efficiently take place and to minimize the release of reactive intermediates in the cytosol, the cosubstrates O(2) and NO and other unstable reaction intermediates should bind sequentially to docking sites in the protein matrix. We have characterized the accessibility of these sites by analyzing the geminate CO rebinding kinetics to the heme moiety observed upon nanosecond flash photolysis of the Ngb-CO complex encapsulated in silica gels. The geminate rebinding phase showed a remarkable complexity, revealing the presence of a system of secondary docking sites where ligands are stored for hundreds of microseconds. Most kinetics steps display little temperature dependence, demonstrating that ligands can easily migrate through the cavities, except for the slowest reaction intermediate, possibly reflecting a structural conformational change reshaping the system of cavities. This conformational change is unrelated with distal His E7 binding to the heme, as it persists for the HE7L mutant. Overall, data are consistent with the presence of a discrete system of docking sites, possibly acting as reservoirs for the putative cosubstrates and for other reactive species involved in the physiologically relevant reaction.
Collapse
|
34
|
Molecular dynamics simulation of a carboxy murine neuroglobin mutated on the proximal side: heme displacement and concomitant rearrangement in loop regions. J Mol Model 2009; 16:759-70. [DOI: 10.1007/s00894-009-0581-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Accepted: 08/17/2009] [Indexed: 11/26/2022]
|
35
|
Moschetti T, Mueller U, Schulze J, Brunori M, Vallone B. The structure of neuroglobin at high Xe and Kr pressure reveals partial conservation of globin internal cavities. Biophys J 2009; 97:1700-8. [PMID: 19751675 PMCID: PMC2741589 DOI: 10.1016/j.bpj.2009.05.059] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Revised: 05/13/2009] [Accepted: 05/14/2009] [Indexed: 10/20/2022] Open
Abstract
Neuroglobin (Ngb) is a hexacoordinate globin expressed in the brain of vertebrates. Ferrous Ngb binds dioxygen with high affinity and the O(2) adduct is able to scavenge NO. Convincing in vitro and in vivo data indicate that Ngb is involved in neuroprotection during hypoxia and ischemia. The 3D structure of Ngb reveals the presence of a wide internal cavity connecting its heme active site with the bulk. To explore the role of this "tunnel" in the control of ligand binding, we determined the structure of metNgb and NgbCO equilibrated with Xe or Kr. We show four docking sites for Xe (only two for Kr); two of the four Xe sites are within the large cavity. They are only partially conserved in globins, since the two proximal Xe sites identified in myoglobin (Xe1 and Xe2) are absent in Ngb, as well as in cytoglobin. The Xe docking sites in Ngb map a pathway within the protein matrix, leading to the heme, which becomes more accessible in the ligand-bound species. This may be of significance in connection with the redox chemistry that may be the primary function of this hexacoordinate globin.
Collapse
Affiliation(s)
- Tommaso Moschetti
- Department of Biochemical Sciences “A.Rossi-Fanelli”, University of Rome “La Sapienza”, Rome, Italy
| | - Uwe Mueller
- Macromolecular Crystallography Group, Helmholtz Zentrum Berlin für Materialien und Energie, BESSY-II, Berlin, Germany
| | - Jörg Schulze
- Macromolecular Crystallography Group, Helmholtz Zentrum Berlin für Materialien und Energie, BESSY-II, Berlin, Germany
| | - Maurizio Brunori
- Department of Biochemical Sciences “A.Rossi-Fanelli”, University of Rome “La Sapienza”, Rome, Italy
| | - Beatrice Vallone
- Department of Biochemical Sciences “A.Rossi-Fanelli”, University of Rome “La Sapienza”, Rome, Italy
| |
Collapse
|
36
|
Orlowski S, Nowak W. Topology and thermodynamics of gaseous ligands diffusion paths in human neuroglobin. Biosystems 2008; 94:263-6. [DOI: 10.1016/j.biosystems.2008.04.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Accepted: 04/18/2008] [Indexed: 11/15/2022]
|
37
|
Molecular dynamics simulation of the neuroglobin crystal: comparison with the simulation in solution. Biophys J 2008; 95:4157-62. [PMID: 18641072 DOI: 10.1529/biophysj.108.135855] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Neuroglobin (Ngb) is a monomeric protein that, despite the small sequence similarity with other globins, displays the typical globin fold. In the absence of exogenous ligands, the ferric and the ferrous forms of Ngb are both hexacoordinated to the distal and proximal histidines. In the ferrous form, oxygen, nitric oxide or carbon monoxide can displace the distal histidine, yielding a reversible adduct. Crystallographic data show that the binding of an exogenous ligand is associated to structural changes involving heme sliding and a topological reorganization of the internal cavities. Molecular dynamics (MD) simulations in solution show that the heme oscillates between two positions, much as the ones observed in the crystal structure, although the occupancy is different. The simulations also suggest that ligand binding in solution can affect the flexibility and conformation of residues connecting the C and D helices, referred to as the CD corner, which is coupled to the configuration adopted by the distal histidine. In this study, we report the results of 30 ns MD simulations of CO-bound Ngb in the crystal. Our goal was to compare the protein dynamical behavior in the crystal with the results supplied by the previous MD simulation of CO-bound Ngb in solution and the x-ray experimental data. The results show that the different environments (crystal or solution) affect the dynamics of the heme group and of the CD corner.
Collapse
|
38
|
Nadra AD, Martí MA, Pesce A, Bolognesi M, Estrin DA. Exploring the molecular basis of heme coordination in human neuroglobin. Proteins 2008; 71:695-705. [PMID: 17975837 DOI: 10.1002/prot.21814] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Neuroglobin (Ngb), a recently discovered ancient heme protein, presents the typical globin fold and is around 20% identical to myoglobin (Mb). In contrast with Mb, however, its heme is hexacoordinated (6c). It is expressed in the nervous system and has been the subject of numerous investigations in the last years, but its function is still unclear. The proposed roles include oxygen transport, reactive oxygen species (ROS) detoxification, hypoxia protection, and redox state sensing. All proposed functions require distal histidine dissociation from the heme to yield a reactive iron. With the aim of understanding the 6c to 5c transition, we have performed molecular dynamics simulations for ferrous Ngb in the 6c, 5c, and oxy states. We also computed free energy profiles associated with the transition employing an advanced sampling technique. Finally, we studied the effect of the redox state of CysCD7 and CysD5, which are known to form a disulfide bridge. Our results show that protein oxidation promotes a stabilization of the pentacoordinated species, thus favoring the protein to adopt the more reactive state and supporting the existence of a molecular mechanism whereby O2 would be released under hypoxic conditions, thereby suggesting an O(2) storage function for Ngb. Taken together, our results provide structural information not available experimentally which may shed light on the protein proposed functions, particularly as a redox sensor.
Collapse
Affiliation(s)
- Alejandro D Nadra
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, Buenos Aires (C1428EHA), Argentina
| | | | | | | | | |
Collapse
|
39
|
Neuroprotective function of human neuroglobin is correlated with its guanine nucleotide dissociation inhibitor activity. Biochem Biophys Res Commun 2008; 369:695-700. [DOI: 10.1016/j.bbrc.2008.02.089] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2008] [Accepted: 02/16/2008] [Indexed: 11/18/2022]
|
40
|
Giuffrè A, Moschetti T, Vallone B, Brunori M. Neuroglobin: Enzymatic reduction and oxygen affinity. Biochem Biophys Res Commun 2008; 367:893-8. [DOI: 10.1016/j.bbrc.2008.01.021] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Accepted: 01/03/2008] [Indexed: 10/22/2022]
|
41
|
Giuffrè A, Moschetti T, Vallone B, Brunori M. Is neuroglobin a signal transducer? IUBMB Life 2008; 60:410-3. [DOI: 10.1002/iub.88] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
42
|
Ishikawa H, Kim S, Kwak K, Wakasugi K, Fayer MD. Disulfide bond influence on protein structural dynamics probed with 2D-IR vibrational echo spectroscopy. Proc Natl Acad Sci U S A 2007; 104:19309-14. [PMID: 18042705 PMCID: PMC2148286 DOI: 10.1073/pnas.0709760104] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2007] [Indexed: 11/18/2022] Open
Abstract
Intramolecular disulfide bonds are understood to play a role in regulating protein stability and activity. Because disulfide bonds covalently link different components of a protein, they influence protein structure. However, the effects of disulfide bonds on fast (subpicosecond to approximately 100 ps) protein equilibrium structural fluctuations have not been characterized experimentally. Here, ultrafast 2D-IR vibrational echo spectroscopy is used to examine the constraints an intramolecular disulfide bond places on the structural fluctuations of the protein neuroglobin (Ngb). Ngb is a globin family protein found in vertebrate brains that binds oxygen reversibly. Like myoglobin (Mb), Ngb has the classical globin fold and key residues around the heme are conserved. Furthermore, the heme-ligated CO vibrational spectra of Mb (Mb-CO) and Ngb (Ngb-CO) are virtually identical. However, in contrast to Mb, human Ngb has an intramolecular disulfide bond that affects its oxygen affinity and protein stability. By using 2D-IR vibrational echo spectroscopy, we investigated the equilibrium protein dynamics of Ngb-CO by observing the CO spectral diffusion (time dependence of the 2D-IR line shapes) with and without the disulfide bond. Despite the similarity of the linear FTIR spectra of Ngb-CO with and without the disulfide bond, 2D-IR measurements reveal that the equilibrium sampling of different protein configurations is accelerated by disruption of the disulfide bond. The observations indicate that the intramolecular disulfide bond in Ngb acts as an inhibitor of fast protein dynamics even though eliminating it does not produce significant conformational change in the protein's structure.
Collapse
Affiliation(s)
- Haruto Ishikawa
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080; and
| | - Seongheun Kim
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080; and
| | - Kyungwon Kwak
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080; and
| | - Keisuke Wakasugi
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Tokyo 153-8902, Japan
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080; and
| |
Collapse
|