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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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Microbial diversity and adaptation to high hydrostatic pressure in deep-sea hydrothermal vents prokaryotes. Extremophiles 2015; 19:721-40. [DOI: 10.1007/s00792-015-0760-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/26/2015] [Indexed: 12/15/2022]
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Fourme R, Girard E, Akasaka K. High-pressure macromolecular crystallography and NMR: status, achievements and prospects. Curr Opin Struct Biol 2012; 22:636-42. [PMID: 22959123 DOI: 10.1016/j.sbi.2012.07.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 07/08/2012] [Accepted: 07/09/2012] [Indexed: 10/27/2022]
Abstract
Biomacromolecules are thermodynamic entities that exist in general as an equilibrium mixture of the basic folded state and various higher-energy substates including all functionally relevant ones. Under physiological conditions, however, the higher-energy substates are usually undetectable on spectroscopy, as their equilibrium populations are extremely low. Hydrostatic pressure gives a general solution to this problem. As proteins generally have smaller partial molar volumes in higher-energy states than in the basic folded state, pressure can shift the equilibrium toward the former substantially, and allows their direct detection and analysis with X-ray crystallography or NMR spectroscopy at elevated pressures. These techniques are now mature, and their status and selected applications are presented with future prospects.
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Affiliation(s)
- Roger Fourme
- Synchrotron Soleil, BP48 Saint Aubin, 91192 Gif sur Yvette, France.
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Demco DE, Utiu L, Tillmann W, Blümich B, Popescu C. Morphology and molecular dynamics of hard α-keratin under pressure by 1H and 13C solid-state NMR. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Girard E, Marchal S, Perez J, Finet S, Kahn R, Fourme R, Marassio G, Dhaussy AC, Prangé T, Giffard M, Dulin F, Bonneté F, Lange R, Abraini JH, Mezouar M, Colloc'h N. Structure-function perturbation and dissociation of tetrameric urate oxidase by high hydrostatic pressure. Biophys J 2010; 98:2365-73. [PMID: 20483346 DOI: 10.1016/j.bpj.2010.01.058] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 01/26/2010] [Accepted: 01/28/2010] [Indexed: 10/19/2022] Open
Abstract
Structure-function relationships in the tetrameric enzyme urate oxidase were investigated using pressure perturbation. As the active sites are located at the interfaces between monomers, enzyme activity is directly related to the integrity of the tetramer. The effect of hydrostatic pressure on the enzyme was investigated by x-ray crystallography, small-angle x-ray scattering, and fluorescence spectroscopy. Enzymatic activity was also measured under pressure and after decompression. A global model, consistent with all measurements, discloses structural and functional details of the pressure-induced dissociation of the tetramer. Before dissociating, the pressurized protein adopts a conformational substate characterized by an expansion of its substrate binding pocket at the expense of a large neighboring hydrophobic cavity. This substate should be adopted by the enzyme during its catalytic mechanism, where the active site has to accommodate larger intermediates and product. The approach, combining several high-pressure techniques, offers a new (to our knowledge) means of exploring structural and functional properties of transient states relevant to protein mechanisms.
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Affiliation(s)
- Eric Girard
- Institut de Biologie Structurale J.-P. Ebel UMR 5075 CEA CNRS UJF, Grenoble, France
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Girard E, Fourme R, Ciurko R, Joly J, Bouis F, Legrand P, Jacobs J, Dhaussy AC, Ferrer JL, Mezouar M, Kahn R. Macromolecular crystallography at high pressure with pneumatic diamond anvil cells handled by a six-axis robotic arm. J Appl Crystallogr 2010. [DOI: 10.1107/s0021889810016146] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A new pneumatic diamond anvil cell has been constructed, generating continuous pressure and temperature variations in the range 0–2.5 GPa and 293–393 K. The cell is designed mainly for high-pressure macromolecular crystallography and should facilitate pressure and temperature annealing of the sample. The analysis is reported of several diffraction data sets of tetragonal hen egg-white lysozyme crystals loaded either in the new cell or in a currently used membrane-based cell. These experiments were performed on beamline FIP-BM30A at the ESRF, Grenoble, a macromolecular crystallography beamline on a bending magnet. Cells were handled and automatically centred by a six-axis robotic arm that was used as a goniometer for data collection by the oscillation method.
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Ascone I, Savino C, Kahn R, Fourme R. Flexibility of the Cu,Zn superoxide dismutase structure investigated at 0.57 GPa. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:654-63. [DOI: 10.1107/s0907444910012321] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Accepted: 04/01/2010] [Indexed: 11/11/2022]
Abstract
The 2 Å resolution crystal structure of bovine erythrocyte Cu,Zn superoxide dismutase (CuZnSOD) has been determined by X-ray diffraction at high pressure (0.57 GPa) and room temperature. At 0.57 GPa the secondary, tertiary and quaternary structures are similar to other previously determined bovine erythrocyte CuZnSOD structures. Nevertheless, pressure has a localized impact on the atomic coordinates of Cαatoms and on side chains. The compression of the crystal and of the protein backbone is anisotropic. This anisotropy is discussed, taking into account intermolecular contacts and protein conformation. Pressure perturbation highlights the more flexible zones in the protein such as the electrostatic loop. At 0.57 GPa, a global shift of the dimetallic sites in both subunits and changes in the oxidation state of Cu were observed. The flexibility of the electrostatic loop may be useful for the interaction of different metal carriers in the copper-uptake process, whereas the flexibility of the metal sites involved in the activity of the protein could contribute to explaining the ubiquitous character of CuZnSODs, which are found in organisms living in very different conditions, including the deep-sea environment. This work illustrates the potential of combining X-ray crystallography with high pressure to promote and stabilize higher energy conformational substates.
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Fourme R, Girard E, Kahn R, Dhaussy AC, Ascone I. Advances in High-Pressure Biophysics: Status and Prospects of Macromolecular Crystallography. Annu Rev Biophys 2009; 38:153-71. [DOI: 10.1146/annurev.biophys.050708.133700] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A survey of the main interests of high pressure for molecular biophysics highlights the possibility of exploring the whole conformational space using pressure perturbation. A better understanding of fundamental mechanisms responsible for the effects of high pressure on biomolecules requires high-resolution molecular information. Thanks to recent instrumental and methodological progress taking advantage of the remarkable adaptation of the crystalline state to hydrostatic compression, pressure-perturbed macromolecular crystallography is now a full-fledged technique applicable to a variety of systems, including large assemblies. This versatility is illustrated by selected applications, including DNA fragments, a tetrameric protein, and a viral capsid. Binding of compressed noble gases to proteins is commonly used to solve the phase problem, but standard macromolecular crystallography would also benefit from the transfer of experimental procedures developed for high-pressure studies. Dedicated short-wavelength synchrotron radiation beamlines are unarguably required to fully exploit the various facets of high-pressure macromolecular crystallography.
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Affiliation(s)
- Roger Fourme
- Synchrotron-SOLEIL, BP48 Saint Aubin, 91192 Gif sur Yvette, France
| | - Eric Girard
- Synchrotron-SOLEIL, BP48 Saint Aubin, 91192 Gif sur Yvette, France
- Institut de Biologie Structurale, UMR 5075 CEA-CNRS-UJF-PSB, 38027 Grenoble, France
| | - Richard Kahn
- Institut de Biologie Structurale, UMR 5075 CEA-CNRS-UJF-PSB, 38027 Grenoble, France
| | | | - Isabella Ascone
- Synchrotron-SOLEIL, BP48 Saint Aubin, 91192 Gif sur Yvette, France
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Calandrini V, Hamon V, Hinsen K, Calligari P, Bellissent-Funel MC, Kneller G. Relaxation dynamics of lysozyme in solution under pressure: Combining molecular dynamics simulations and quasielastic neutron scattering. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2007.07.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Calandrini V, Kneller GR. Influence of pressure on the slow and fast fractional relaxation dynamics in lysozyme: A simulation study. J Chem Phys 2008; 128:065102. [DOI: 10.1063/1.2828769] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Boldyreva EV. High-pressure diffraction studies of molecular organic solids. A personal view. Acta Crystallogr A 2007; 64:218-31. [DOI: 10.1107/s0108767307065786] [Citation(s) in RCA: 146] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Accepted: 12/05/2007] [Indexed: 11/10/2022] Open
Abstract
This paper discusses the trends in the experimental studies of molecular organic solids at high pressures by diffraction techniques. Crystallization of liquids, crystallization from solutions and solid-state transformations are considered. Special attention is paid to the high-pressure studies of pharmaceuticals and of biomimetics.
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Colloc'h N, Girard E, Dhaussy AC, Kahn R, Ascone I, Mezouar M, Fourme R. High pressure macromolecular crystallography: the 140-MPa crystal structure at 2.3 A resolution of urate oxidase, a 135-kDa tetrameric assembly. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:391-7. [PMID: 16478683 DOI: 10.1016/j.bbapap.2006.01.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2005] [Revised: 12/07/2005] [Accepted: 01/06/2006] [Indexed: 10/25/2022]
Abstract
We report the three-dimensional structure determined by high-pressure macromolecular crystallography (HPMX) of a 135-kDa homo-tetrameric enzyme, urate oxidase from Aspergillus flavus complexed with its potent inhibitor 8-azaxanthin. Urate oxidase crystals are quite sensitive to pressure, as three-dimensional order is lost at about 180 MPa. A highly complete 2.3 A resolution data set was collected at 140 MPa, close to the critical pressure. Crystal structures at atmospheric pressure and at high pressure were refined in the orthorhombic space group I222 with final crystallographic R factors 14.1% and 16.1%, respectively. The effect of pressure on temperature factors, ordered water molecules, hydrogen bond lengths, contacts, buried surface areas as well as cavity volume was investigated. Results suggest that the onset of disruption of the tetrameric assembly by pressure has been captured in the crystalline state.
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Affiliation(s)
- Nathalie Colloc'h
- Centre CYCERON, UMR 6185 Université de Caen-CNRS, Bd Becquerel, 14074 Caen, France
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