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Pagliaro P, Weber NC, Femminò S, Alloatti G, Penna C. Gasotransmitters and noble gases in cardioprotection: unraveling molecular pathways for future therapeutic strategies. Basic Res Cardiol 2024; 119:509-544. [PMID: 38878210 DOI: 10.1007/s00395-024-01061-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 08/13/2024]
Abstract
Despite recent progress, ischemic heart disease poses a persistent global challenge, driving significant morbidity and mortality. The pursuit of therapeutic solutions has led to the emergence of strategies such as ischemic preconditioning, postconditioning, and remote conditioning to shield the heart from myocardial ischemia/reperfusion injury (MIRI). These ischemic conditioning approaches, applied before, after, or at a distance from the affected organ, inspire future therapeutic strategies, including pharmacological conditioning. Gasotransmitters, comprising nitric oxide, hydrogen sulfide, sulfur dioxide, and carbon monoxide, play pivotal roles in physiological and pathological processes, exhibiting shared features such as smooth muscle relaxation, antiapoptotic effects, and anti-inflammatory properties. Despite potential risks at high concentrations, physiological levels of gasotransmitters induce vasorelaxation and promote cardioprotective effects. Noble gases, notably argon, helium, and xenon, exhibit organ-protective properties by reducing cell death, minimizing infarct size, and enhancing functional recovery in post-ischemic organs. The protective role of noble gases appears to hinge on their modulation of molecular pathways governing cell survival, leading to both pro- and antiapoptotic effects. Among noble gases, helium and xenon emerge as particularly promising in the field of cardioprotection. This overview synthesizes our current understanding of the roles played by gasotransmitters and noble gases in the context of MIRI and cardioprotection. In addition, we underscore potential future developments involving the utilization of noble gases and gasotransmitter donor molecules in advancing cardioprotective strategies.
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Affiliation(s)
- Pasquale Pagliaro
- Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10, 10043, Orbassano, TO), Italy.
- National Institute for Cardiovascular Research (INRC), 40126, Bologna, Italy.
| | - Nina C Weber
- Department of Anesthesiology, Laboratory of Experimental Intensive Care and Anesthesiology-L.E.I.C.A, Amsterdam University Medical Centers, Amsterdam Cardiovascular Science (ACS), Amsterdam, The Netherlands
| | - Saveria Femminò
- Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10, 10043, Orbassano, TO), Italy
| | | | - Claudia Penna
- Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10, 10043, Orbassano, TO), Italy
- National Institute for Cardiovascular Research (INRC), 40126, Bologna, Italy
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Carpentier P, van der Linden P, Mueller-Dieckmann C. The High-Pressure Freezing Laboratory for Macromolecular Crystallography (HPMX), an ancillary tool for the macromolecular crystallography beamlines at the ESRF. Acta Crystallogr D Struct Biol 2024; 80:80-92. [PMID: 38265873 PMCID: PMC10836400 DOI: 10.1107/s2059798323010707] [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: 07/25/2023] [Accepted: 12/13/2023] [Indexed: 01/26/2024] Open
Abstract
This article describes the High-Pressure Freezing Laboratory for Macromolecular Crystallography (HPMX) at the ESRF, and highlights new and complementary research opportunities that can be explored using this facility. The laboratory is dedicated to investigating interactions between macromolecules and gases in crystallo, and finds applications in many fields of research, including fundamental biology, biochemistry, and environmental and medical science. At present, the HPMX laboratory offers the use of different high-pressure cells adapted for helium, argon, krypton, xenon, nitrogen, oxygen, carbon dioxide and methane. Important scientific applications of high pressure to macromolecules at the HPMX include noble-gas derivatization of crystals to detect and map the internal architecture of proteins (pockets, tunnels and channels) that allows the storage and diffusion of ligands or substrates/products, the investigation of the catalytic mechanisms of gas-employing enzymes (using oxygen, carbon dioxide or methane as substrates) to possibly decipher intermediates, and studies of the conformational fluctuations or structure modifications that are necessary for proteins to function. Additionally, cryo-cooling protein crystals under high pressure (helium or argon at 2000 bar) enables the addition of cryo-protectant to be avoided and noble gases can be employed to produce derivatives for structure resolution. The high-pressure systems are designed to process crystals along a well defined pathway in the phase diagram (pressure-temperature) of the gas to cryo-cool the samples according to the three-step `soak-and-freeze method'. Firstly, crystals are soaked in a pressurized pure gas atmosphere (at 294 K) to introduce the gas and facilitate its interactions within the macromolecules. Samples are then flash-cooled (at 100 K) while still under pressure to cryo-trap macromolecule-gas complexation states or pressure-induced protein modifications. Finally, the samples are recovered after depressurization at cryo-temperatures. The final section of this publication presents a selection of different typical high-pressure experiments carried out at the HPMX, showing that this technique has already answered a wide range of scientific questions. It is shown that the use of different gases and pressure conditions can be used to probe various effects, such as mapping the functional internal architectures of enzymes (tunnels in the haloalkane dehalogenase DhaA) and allosteric sites on membrane-protein surfaces, the interaction of non-inert gases with proteins (oxygen in the hydrogenase ReMBH) and pressure-induced structural changes of proteins (tetramer dissociation in urate oxidase). The technique is versatile and the provision of pressure cells and their application at the HPMX is gradually being extended to address new scientific questions.
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Affiliation(s)
- Philippe Carpentier
- Université Grenoble Alpes CEA CNRS, IRIG–LCBM UMR 5249, 17 Avenue des Martyrs, 38000 Grenoble, France
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Peter van der Linden
- ESRF, PSCM (Partnership for Soft Condensed Matter), 71 Avenue des Martyrs, 38000 Grenoble, France
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Dalecki M, Steinberg F, Beurskens R. Rapid Dual-Task Decrements After a Brief Period of Manual Tracking in Simulated Weightlessness by Water Submersion. HUMAN FACTORS 2023; 65:1001-1013. [PMID: 34861791 DOI: 10.1177/00187208211051804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
OBJECTIVE Investigating dual-task (DT) performance during simulated weightlessness by water submersion, using a manual tracking and a choice reaction task. In contrast to previous work, we focus on performance changes over time. BACKGROUND Previous research showed motor tracking and choice reaction impairments under DT and single-task (ST) conditions in shallow water submersion. Recent research analyzed performance as average across task time, neglecting potential time-related changes or fluctuations of task-performance. METHOD An unstable tracking and a choice reaction task was performed for one minute under ST and DT conditions in 5 m water submersion and on dry land in 43 participants. Tracking and choice reaction time performance for both tasks were analyzed in blocks of 10 seconds. RESULTS Tracking performance deteriorated underwater compared to dry land conditions during the second half while performing one minute in DT conditions. Choice reaction time increased underwater as well, but independent of task time and type. CONCLUSION Tracking error increased over time when performing unstable tracking and choice reaction together. Potentially, physiological and psychological alterations under shallow submersion further strain the human system during DT operations, exceeding available recourse capacities such that DT performance deteriorated over time. APPLICATION Humans operating in simulated weightlessness underwater should be aware of substantial performance declines that can occur within a short amount of time during DT situations that include continuous tracking.
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Affiliation(s)
- Marc Dalecki
- School of Kinesiology, Louisiana State University, Baton Rouge, LA, USA
| | - Fabian Steinberg
- School of Kinesiology, Louisiana State University, Baton Rouge, LA, USA
| | - Rainer Beurskens
- Fachhochschule des Mittelstandes, University of Applied Sciences, Bielefeld, Germany
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McGuigan S, Marie DJ, O'Bryan LJ, Flores FJ, Evered L, Silbert B, Scott DA. The cellular mechanisms associated with the anesthetic and neuroprotective properties of xenon: a systematic review of the preclinical literature. Front Neurosci 2023; 17:1225191. [PMID: 37521706 PMCID: PMC10380949 DOI: 10.3389/fnins.2023.1225191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction Xenon exhibits significant neuroprotection against a wide range of neurological insults in animal models. However, clinical evidence that xenon improves outcomes in human studies of neurological injury remains elusive. Previous reviews of xenon's method of action have not been performed in a systematic manner. The aim of this review is to provide a comprehensive summary of the evidence underlying the cellular interactions responsible for two phenomena associated with xenon administration: anesthesia and neuroprotection. Methods A systematic review of the preclinical literature was carried out according to the PRISMA guidelines and a review protocol was registered with PROSPERO. The review included both in vitro models of the central nervous system and mammalian in vivo studies. The search was performed on 27th May 2022 in the following databases: Ovid Medline, Ovid Embase, Ovid Emcare, APA PsycInfo, and Web of Science. A risk of bias assessment was performed utilizing the Office of Health Assessment and Translation tool. Given the heterogeneity of the outcome data, a narrative synthesis was performed. Results The review identified 69 articles describing 638 individual experiments in which a hypothesis was tested regarding the interaction of xenon with cellular targets including: membrane bound proteins, intracellular signaling cascades and transcription factors. Xenon has both common and subtype specific interactions with ionotropic glutamate receptors. Xenon also influences the release of inhibitory neurotransmitters and influences multiple other ligand gated and non-ligand gated membrane bound proteins. The review identified several intracellular signaling pathways and gene transcription factors that are influenced by xenon administration and might contribute to anesthesia and neuroprotection. Discussion The nature of xenon NMDA receptor antagonism, and its range of additional cellular targets, distinguishes it from other NMDA antagonists such as ketamine and nitrous oxide. This is reflected in the distinct behavioral and electrophysiological characteristics of xenon. Xenon influences multiple overlapping cellular processes, both at the cell membrane and within the cell, that promote cell survival. It is hoped that identification of the underlying cellular targets of xenon might aid the development of potential therapeutics for neurological injury and improve the clinical utilization of xenon. Systematic review registration https://www.crd.york.ac.uk/prospero/, identifier: 336871.
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Affiliation(s)
- Steven McGuigan
- Department of Anesthesia and Acute Pain Medicine, St. Vincent's Hospital, Melbourne, VIC, Australia
- Department of Critical Care, University of Melbourne, Melbourne, VIC, Australia
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Boston, MA, United States
| | - Daniel J. Marie
- Department of Anesthesia and Acute Pain Medicine, St. Vincent's Hospital, Melbourne, VIC, Australia
| | - Liam J. O'Bryan
- Department of Anesthesia and Acute Pain Medicine, St. Vincent's Hospital, Melbourne, VIC, Australia
| | - Francisco J. Flores
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Boston, MA, United States
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Lisbeth Evered
- Department of Anesthesia and Acute Pain Medicine, St. Vincent's Hospital, Melbourne, VIC, Australia
- Department of Critical Care, University of Melbourne, Melbourne, VIC, Australia
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, United States
| | - Brendan Silbert
- Department of Anesthesia and Acute Pain Medicine, St. Vincent's Hospital, Melbourne, VIC, Australia
- Department of Critical Care, University of Melbourne, Melbourne, VIC, Australia
| | - David A. Scott
- Department of Anesthesia and Acute Pain Medicine, St. Vincent's Hospital, Melbourne, VIC, Australia
- Department of Critical Care, University of Melbourne, Melbourne, VIC, Australia
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High-pressure crystallography shows noble gas intervention into protein-lipid interaction and suggests a model for anaesthetic action. Commun Biol 2022; 5:360. [PMID: 35422073 PMCID: PMC9010423 DOI: 10.1038/s42003-022-03233-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 02/22/2022] [Indexed: 11/09/2022] Open
Abstract
In this work we examine how small hydrophobic molecules such as inert gases interact with membrane proteins (MPs) at a molecular level. High pressure atmospheres of argon and krypton were used to produce noble gas derivatives of crystals of three well studied MPs (two different proton pumps and a sodium light-driven ion pump). The structures obtained using X-ray crystallography showed that the vast majority of argon and krypton binding sites were located on the outer hydrophobic surface of the MPs – a surface usually accommodating hydrophobic chains of annular lipids (which are known structural and functional determinants for MPs). In conformity with these results, supplementary in silico molecular dynamics (MD) analysis predicted even greater numbers of argon and krypton binding positions on MP surface within the bilayer. These results indicate a potential importance of such interactions, particularly as related to the phenomenon of noble gas-induced anaesthesia. Noble gases are known to interact with proteins and can be good anaesthetics in hyperbaric conditions. This study identifies argon and krypton binding sites on membrane proteins and proposes as a hypothesis that noble gases, by altering protein/lipid contacts, may affect protein function.
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At least three xenon binding sites in the glycine binding domain of the N-methyl D-aspartate receptor. Arch Biochem Biophys 2022; 724:109265. [DOI: 10.1016/j.abb.2022.109265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 11/21/2022]
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Wiebelhaus N, Singh N, Zhang P, Craig SL, Beratan DN, Fitzgerald MC. Discovery of the Xenon-Protein Interactome Using Large-Scale Measurements of Protein Folding and Stability. J Am Chem Soc 2022; 144:3925-3938. [PMID: 35213151 PMCID: PMC10166008 DOI: 10.1021/jacs.1c11900] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The intermolecular interactions of noble gases in biological systems are associated with numerous biochemical responses, including apoptosis, inflammation, anesthesia, analgesia, and neuroprotection. The molecular modes of action underlying these responses are largely unknown. This is in large part due to the limited experimental techniques to study protein-gas interactions. The few techniques that are amenable to such studies are relatively low-throughput and require large amounts of purified proteins. Thus, they do not enable the large-scale analyses that are useful for protein target discovery. Here, we report the application of stability of proteins from rates of oxidation (SPROX) and limited proteolysis (LiP) methodologies to detect protein-xenon interactions on the proteomic scale using protein folding stability measurements. Over 5000 methionine-containing peptides and over 5000 semi-tryptic peptides, mapping to ∼1500 and ∼950 proteins, respectively, in the yeast proteome, were assayed for Xe-interacting activity using the SPROX and LiP techniques. The SPROX and LiP analyses identified 31 and 60 Xe-interacting proteins, respectively, none of which were previously known to bind Xe. A bioinformatics analysis of the proteomic results revealed that these Xe-interacting proteins were enriched in those involved in ATP-driven processes. A fraction of the protein targets that were identified are tied to previously established modes of action related to xenon's anesthetic and organoprotective properties. These results enrich our knowledge and understanding of biologically relevant xenon interactions. The sample preparation protocols and analytical methodologies developed here for xenon are also generally applicable to the discovery of a wide range of other protein-gas interactions in complex biological mixtures, such as cell lysates.
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Affiliation(s)
- Nancy Wiebelhaus
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Niven Singh
- Program in Computational Biology and Bioinformatics, Center for Genomics and Computational Biology, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Stephen L. Craig
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - David N. Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Program in Computational Biology and Bioinformatics, Center for Genomics and Computational Biology, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Michael C. Fitzgerald
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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McGregor L, Földes T, Bui S, Moulin M, Coquelle N, Blakeley MP, Rosta E, Steiner RA. Joint neutron/X-ray crystal structure of a mechanistically relevant complex of perdeuterated urate oxidase and simulations provide insight into the hydration step of catalysis. IUCRJ 2021; 8:46-59. [PMID: 33520242 PMCID: PMC7792999 DOI: 10.1107/s2052252520013615] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/12/2020] [Indexed: 06/12/2023]
Abstract
Cofactor-independent urate oxidase (UOX) is an ∼137 kDa tetrameric enzyme essential for uric acid (UA) catabolism in many organisms. UA is first oxidized by O2 to de-hydro-isourate (DHU) via a peroxo intermediate. DHU then undergoes hydration to 5-hy-droxy-isourate (5HIU). At different stages of the reaction both catalytic O2 and water occupy the 'peroxo hole' above the organic substrate. Here, high-resolution neutron/X-ray crystallographic analysis at room temperature has been integrated with molecular dynamics simulations to investigate the hydration step of the reaction. The joint neutron/X-ray structure of perdeuterated Aspergillus flavus UOX in complex with its 8-azaxanthine (8AZA) inhibitor shows that the catalytic water molecule (W1) is present in the peroxo hole as neutral H2O, oriented at 45° with respect to the ligand. It is stabilized by Thr57 and Asn254 on different UOX protomers as well as by an O-H⋯π interaction with 8AZA. The active site Lys10-Thr57 dyad features a charged Lys10-NH3 + side chain engaged in a strong hydrogen bond with Thr57OG1, while the Thr57OG1-HG1 bond is rotationally dynamic and oriented toward the π system of the ligand, on average. Our analysis offers support for a mechanism in which W1 performs a nucleophilic attack on DHUC5 with Thr57HG1 central to a Lys10-assisted proton-relay system. Room-temperature crystallography and simulations also reveal conformational heterogeneity for Asn254 that modulates W1 stability in the peroxo hole. This is proposed to be an active mechanism to facilitate W1/O2 exchange during catalysis.
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Affiliation(s)
- Lindsay McGregor
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, United Kingdom
- Large Scale Structures Group, Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Tamás Földes
- Department of Chemistry, King’s College London, London SE1 1DB, United Kingdom
- Department of Physics and Astronomy, University College, London WC1E 6BT, United Kingdom
| | - Soi Bui
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, United Kingdom
| | - Martine Moulin
- Life Sciences Group, Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Nicolas Coquelle
- Large Scale Structures Group, Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Matthew P. Blakeley
- Large Scale Structures Group, Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France
| | - Edina Rosta
- Department of Chemistry, King’s College London, London SE1 1DB, United Kingdom
- Department of Physics and Astronomy, University College, London WC1E 6BT, United Kingdom
| | - Roberto A. Steiner
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, United Kingdom
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Wang J, Yuan K, Wang X, Zhang L, Hu J. Influence of Krypton Gas Nanobubbles on the Activity of Pepsin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:14070-14075. [PMID: 33179933 DOI: 10.1021/acs.langmuir.0c02635] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The fact that biologically inert gases can significantly affect the biological function of proteins still lacks a full understanding because they are usually chemically stable and weakly absorbed by biological molecules. Recently, nanobubbles were proposed to play an important role in the activity of a protein (Scientific reports 2013, 3; Scientific reports 2017, 7, 10176). In this study, we developed a controllable method to produce high-concentration krypton (Kr) gas nanobubbles in pure water and measured the concentration influence of those Kr nanobubbles on pepsin protein activity. By combining high-sensitivity synchrotron radiation X-ray fluorescence techniques with a nanoparticle tracking analysis technology, we provided strong evidence that the observed "nanoparticles" were indeed Kr nanobubbles. Activity measurements showed that the activity would be inhibited by the existence of Kr nanobubbles and could be recovered by degassing. More importantly, the inhibition extent of pepsin activity was dominated by the number of nanobubbles in solution. More nanobubbles would cause more inhibition of pepsin activity. Furthermore, the structures of pepsin could be changed by nanobubbles, which might be the reason for inhabitation of activity. Our results would provide a further understanding of the mechanisms of the biological effects of inert gases.
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Affiliation(s)
- Jing Wang
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201204, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaiwei Yuan
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xingya Wang
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Lijuan Zhang
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Jun Hu
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201204, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Jayapaul J, Schröder L. Molecular Sensing with Host Systems for Hyperpolarized 129Xe. Molecules 2020; 25:E4627. [PMID: 33050669 PMCID: PMC7587211 DOI: 10.3390/molecules25204627] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/27/2020] [Accepted: 09/30/2020] [Indexed: 12/12/2022] Open
Abstract
Hyperpolarized noble gases have been used early on in applications for sensitivity enhanced NMR. 129Xe has been explored for various applications because it can be used beyond the gas-driven examination of void spaces. Its solubility in aqueous solutions and its affinity for hydrophobic binding pockets allows "functionalization" through combination with host structures that bind one or multiple gas atoms. Moreover, the transient nature of gas binding in such hosts allows the combination with another signal enhancement technique, namely chemical exchange saturation transfer (CEST). Different systems have been investigated for implementing various types of so-called Xe biosensors where the gas binds to a targeted host to address molecular markers or to sense biophysical parameters. This review summarizes developments in biosensor design and synthesis for achieving molecular sensing with NMR at unprecedented sensitivity. Aspects regarding Xe exchange kinetics and chemical engineering of various classes of hosts for an efficient build-up of the CEST effect will also be discussed as well as the cavity design of host molecules to identify a pool of bound Xe. The concept is presented in the broader context of reporter design with insights from other modalities that are helpful for advancing the field of Xe biosensors.
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Affiliation(s)
| | - Leif Schröder
- Molecular Imaging, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany;
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Denesyuk AI, Permyakov SE, Johnson MS, Denessiouk K, Permyakov EA. System Approach for Building of Calcium-Binding Sites in Proteins. Biomolecules 2020; 10:biom10040588. [PMID: 32290360 PMCID: PMC7226230 DOI: 10.3390/biom10040588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 11/16/2022] Open
Abstract
We introduce five new local metal cation (first of all, Ca2+) recognition units in proteins: Clampn,(n−2), Clampn,(n−1), Clampn,n, Clampn,(n+1) and Clampn,(n+2). In these units, the backbone oxygen atom of a residue in position “n” of an amino acid sequence and side-chain oxygen atom of a residue in position “n + i” (i = −2 to +2) directly interact with a metal cation. An analysis of the known “Ca2+-bound niches” in proteins has shown that a system approach based on the simultaneous use of the Clamp units and earlier proposed One-Residue (OR)/Three-Residue (TR) units significantly improves the results of constructing metal cation-binding sites in proteins.
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Affiliation(s)
- Alexander I. Denesyuk
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino 142290, Russia; (S.E.P.); (E.A.P.)
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, Turku 20520, Finland; (M.S.J.); (K.D.)
- Correspondence: ; Tel.: +358-2-215-4006
| | - Sergei E. Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino 142290, Russia; (S.E.P.); (E.A.P.)
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, Turku 20520, Finland; (M.S.J.); (K.D.)
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, Turku 20520, Finland; (M.S.J.); (K.D.)
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, Turku 20520, Finland
| | - Eugene A. Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino 142290, Russia; (S.E.P.); (E.A.P.)
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Jayapaul J, Schröder L. Probing Reversible Guest Binding with Hyperpolarized 129Xe-NMR: Characteristics and Applications for Cucurbit[ n]urils. Molecules 2020; 25:E957. [PMID: 32093412 PMCID: PMC7070628 DOI: 10.3390/molecules25040957] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 01/01/2023] Open
Abstract
Cucurbit[n]urils (CB[n]s) are a family of macrocyclic host molecules that find various applications in drug delivery, molecular switching, and dye displacement assays. The CB[n]s with n = 5-7 have also been studied with 129Xe-NMR. They bind the noble gas with a large range of exchange rates. Starting with insights from conventional direct detection of bound Xe, this review summarizes recent achievements with chemical exchange saturation transfer (CEST) detection of efficiently exchanging Xe in various CB[n]-based supramolecular systems. Unprecedented sensitivity has been reached by combining the CEST method with hyperpolarized Xe, the production of which is also briefly described. Applications such as displacement assays for enzyme activity detection and rotaxanes as emerging types of Xe biosensors are likewise discussed in the context of biomedical applications and pinpoint future directions for translating this field to preclinical studies.
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Affiliation(s)
| | - Leif Schröder
- Molecular Imaging, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany;
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Hong S, Na S, Kim OH, Jeong S, Oh BC, Ha NC. High-resolution structures of annexin A5 in a two-dimensional array. J Struct Biol 2019; 209:107401. [PMID: 31605770 DOI: 10.1016/j.jsb.2019.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 08/26/2019] [Accepted: 10/04/2019] [Indexed: 11/15/2022]
Abstract
Annexins are soluble cytosolic proteins that bind to cell membranes. Annexin A5 self-assembles into a two-dimensional (2D) array and prevents cell rupture by attaching to damaged membranes. However, this process is not fully understood at the molecular level. In this study, we determined the crystal structures of annexin A5 with and without calcium (Ca2+) and confirmed the Ca2+-dependent outward motion of a tryptophan residue. Strikingly, the two structures exhibited the same crystal packing and 2D arrangement into a p3 lattice, which agrees well with the results of low-resolution structural imaging. High-resolution structures indicated that a three-fold interaction near the tryptophan residue is important for mediating the formation of the p3 lattice. A hypothesis on the promotion of p3 lattice formation by phosphatidyl serine (PS) is also suggested. This study provides molecular insight into how annexins modulate the physical properties of cell membranes as a function of Ca2+ concentration and the phospholipid composition of the membrane.
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Affiliation(s)
- Seokho Hong
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Seoul National University, Seoul 08826, Republic of Korea
| | - Soohui Na
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Seoul National University, Seoul 08826, Republic of Korea
| | - Ok-Hee Kim
- Department of Physiology, Lee Gil Ya Cancer and Diabetes Institute, Gachon University College of Medicine, Incheon 21999, Republic of Korea
| | - Soyeon Jeong
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Seoul National University, Seoul 08826, Republic of Korea
| | - Byung-Chul Oh
- Department of Physiology, Lee Gil Ya Cancer and Diabetes Institute, Gachon University College of Medicine, Incheon 21999, Republic of Korea
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Seoul National University, Seoul 08826, Republic of Korea.
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14
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Roose BW, Zemerov SD, Dmochowski IJ. Xenon-Protein Interactions: Characterization by X-Ray Crystallography and Hyper-CEST NMR. Methods Enzymol 2018; 602:249-272. [PMID: 29588032 DOI: 10.1016/bs.mie.2018.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The physiological activity of xenon has long been recognized, though the exact nature of its interactions with biomolecules remains poorly understood. Xe is an inert noble gas, but can act as a general anesthetic, most likely by binding internal hydrophobic cavities within proteins. Understanding Xe-protein interactions, therefore, can provide crucial insight regarding the mechanism of Xe anesthesia and potentially other general anesthetic agents. Historically, Xe-protein interactions have been studied primarily through X-ray crystallography and nuclear magnetic resonance (NMR). In this chapter, we first describe our methods for preparing Xe derivatives of protein crystals and identifying Xe-binding sites. Second, we detail our procedure for 129Xe hyper-CEST NMR spectroscopy, a versatile NMR technique well suited for characterizing the weak, transient nature of Xe-protein interactions.
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15
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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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16
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Miao J, Gao Y. The switch of the binding behaviours between Xe and π system induced by the change of oxidation state of Cu ion. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1334884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Junjian Miao
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, P.R. China
| | - Yi Gao
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, P.R. China
- Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, China
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17
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Xenon for tunnelling analysis of the efflux pump component OprN. PLoS One 2017; 12:e0184045. [PMID: 28886086 PMCID: PMC5590881 DOI: 10.1371/journal.pone.0184045] [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: 04/28/2017] [Accepted: 08/17/2017] [Indexed: 12/02/2022] Open
Abstract
Tripartite efflux pumps are among the main actors responsible for antibiotics resistance in Gram-negative bacteria. In the last two decades, structural studies gave crucial information about the assembly interfaces and the mechanistic motions. Thus rigidifying the assembly seems to be an interesting way to hamper the drug efflux. In this context, xenon is a suitable probe for checking whether small ligands could act as conformational lockers by targeting hydrophobic cavities. Here we focus on OprN, the outer membrane channel of the MexEF efflux pump from Pseudomonas aeruginosa. After exposing OprN crystals to xenon gas pressure, 14 binding sites were observed using X-ray crystallography. These binding sites were unambiguously characterized in hydrophobic cavities of OprN. The major site is observed in the sensitive iris-like region gating the channel at the periplasmic side, built by the three key-residues Leu 405, Asp 109, and Arg 412. This arrangement defines along the tunnel axis a strong hydrophobic/polar gradient able to enhance the passive efflux mechanism of OprN. The other xenon atoms reveal strategic hydrophobic regions of the channel scaffold to target, with the aim to freeze the dynamic movements responsible of the open/close conformational equilibrium in OprN.
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18
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Steinberg F, Doppelmayr M. Executive Functions of Divers Are Selectively Impaired at 20-Meter Water Depth. Front Psychol 2017; 8:1000. [PMID: 28676772 PMCID: PMC5476772 DOI: 10.3389/fpsyg.2017.01000] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/31/2017] [Indexed: 11/13/2022] Open
Abstract
Moving and acting underwater within recreational or occupational activities require intact executive functions, since they subserve higher cognitive functions such as successful self-regulation, coping with novel situations, and decision making; all of which could be influenced by nitrogen narcosis due to elevated partial pressure under water. However, specific executive functions that could provide a differentiated view on humans' cognitive performance ability have not yet been systematically analyzed in full-water immersion, which is a research gap addressed within this approach to contribute to a better understanding of nitrogen narcosis. In this study, 20 young, healthy, and certified recreational divers participated and performed three different executive-function tests: the Stroop test (Inhibition), the Number/Letter test (Task switching), the 2-back test (Updating/Working memory), and a simple reaction time test (Psychomotor performance). These tests were performed once on land, at 5-meter (m) water depth, and at 20-meter (m) water depth of an indoor diving facility in standardized test conditions (26°C in all water depths). A water-proofed and fully operational tablet computer was used to present visual stimuli and to register reaction times. Performance of the simple reaction time test was not different between underwater and land testing, suggesting that reaction times were not biased by the utilization of the tablet in water immersion. Executive functions were not affected by the shallow water immersion of 5-m water depth. However, performance scores in 20-m water depth revealed a decreased performance in the incongruent test condition (i.e., an index of inhibitory control ability) of the Stroop test, while all other tests were unaffected. Even though only one out of the three tested cognitive domains was affected, the impairment of inhibitory control ability even in relatively shallow water of 20-m is a critical component that should be considered for diver's safety, since inhibition is required in self-control requiring situations where impulsive and automatic behavior must be inhibited. Our interpretation of these selective impairments is based on a discussion suggesting that different neural networks within the central nervous system, which process specific executive functions, are affected differently by nitrogen narcosis.
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Affiliation(s)
- Fabian Steinberg
- Department of Sport Psychology, Institute of Sport Science, Johannes Gutenberg University MainzMainz, Germany
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19
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Rostain JC, Lavoute C. Neurochemistry of Pressure-Induced Nitrogen and Metabolically Inert Gas Narcosis in the Central Nervous System. Compr Physiol 2016; 6:1579-90. [PMID: 27347903 DOI: 10.1002/cphy.c150024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Gases that are not metabolized by the organism are thus chemically inactive under normal conditions. Such gases include the "noble gases" of the Periodic Table as well as hydrogen and nitrogen. At increasing pressure, nitrogen induces narcosis at 4 absolute atmospheres (ATAs) and more in humans and at 11 ATA and more in rats. Electrophysiological and neuropharmacological studies suggest that the striatum is a target of nitrogen narcosis. Glutamate and dopamine release from the striatum in rats are decreased by exposure to nitrogen at a pressure of 31 ATA (75% of the anesthetic threshold). Striatal dopamine levels decrease during exposure to compressed argon, an inert gas more narcotic than nitrogen, or to nitrous oxide, an anesthetic gas. Inversely, striatal dopamine levels increase during exposure to compressed helium, an inert gas with a very low narcotic potency. Exposure to nitrogen at high pressure does not change N-methyl-d-aspartate (NMDA) glutamate receptor activities in Substantia Nigra compacta and striatum but enhances gama amino butyric acidA (GABAA) receptor activities in Substantia Nigra compacta. The decrease in striatal dopamine levels in response to hyperbaric nitrogen exposure is suppressed by recurrent exposure to nitrogen narcosis, and dopamine levels increase after four or five exposures. This change, the lack of improvement of motor disturbances, the desensitization of GABAA receptors on dopamine cells during recurrent exposures and the long-lasting decrease of glutamate coupled with the higher sensitivity of NMDA receptors, suggest a nitrogen toxicity induced by repetitive exposures to narcosis. These differential changes in different neurotransmitter receptors would support the binding protein theory. © 2016 American Physiological Society. Compr Physiol 6:1579-1590, 2016.
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Affiliation(s)
- Jean-Claude Rostain
- UMR-MD2 Disoxie et Suractivité, Aix-Marseille University, Institut de Recherche Biomédicale des Armées (IRBA), Faculté de Médecine Nord, Marseille, France
| | - Cécile Lavoute
- UMR-MD2 Disoxie et Suractivité, Aix-Marseille University, Institut de Recherche Biomédicale des Armées (IRBA), Faculté de Médecine Nord, Marseille, France
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20
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21
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Sauguet L, Fourati Z, Prangé T, Delarue M, Colloc'h N. Structural Basis for Xenon Inhibition in a Cationic Pentameric Ligand-Gated Ion Channel. PLoS One 2016; 11:e0149795. [PMID: 26910105 PMCID: PMC4765991 DOI: 10.1371/journal.pone.0149795] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/04/2016] [Indexed: 12/15/2022] Open
Abstract
GLIC receptor is a bacterial pentameric ligand-gated ion channel whose action is inhibited by xenon. Xenon has been used in clinical practice as a potent gaseous anaesthetic for decades, but the molecular mechanism of interactions with its integral membrane receptor targets remains poorly understood. Here we characterize by X-ray crystallography the xenon-binding sites within both the open and "locally-closed" (inactive) conformations of GLIC. Major binding sites of xenon, which differ between the two conformations, were identified in three distinct regions that all belong to the trans-membrane domain of GLIC: 1) in an intra-subunit cavity, 2) at the interface between adjacent subunits, and 3) in the pore. The pore site is unique to the locally-closed form where the binding of xenon effectively seals the channel. A putative mechanism of the inhibition of GLIC by xenon is proposed, which might be extended to other pentameric cationic ligand-gated ion channels.
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Affiliation(s)
- Ludovic Sauguet
- Unité de Dynamique Structurale des Macromolécules (UMR 3528 CNRS) Institut Pasteur, Paris, France
| | - Zeineb Fourati
- Unité de Dynamique Structurale des Macromolécules (UMR 3528 CNRS) Institut Pasteur, Paris, France
| | - Thierry Prangé
- Laboratoire de cristallographie et RMN biologiques (UMR 8015 CNRS), Paris, France
| | - Marc Delarue
- Unité de Dynamique Structurale des Macromolécules (UMR 3528 CNRS) Institut Pasteur, Paris, France
- * E-mail:
| | - Nathalie Colloc'h
- CNRS, UMR 6301, ISTCT CERVOxy group, GIP Cyceron, Caen, France
- UNICAEN, Normandie Univ., UMR 6301 ISTCT, Caen, France
- CEA, DSV/I2BM, UMR 6301 ISTCT, Caen, France
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22
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Miao J, Song B, Gao Y. Enhanced Aerogen-π Interaction by a Cation-π Force. Chemistry 2016; 22:2586-9. [DOI: 10.1002/chem.201504210] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Indexed: 12/19/2022]
Affiliation(s)
- Junjian Miao
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 P.R. China
| | - Bo Song
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 P.R. China
| | - Yi Gao
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 P.R. China
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23
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Abraini J, David H, Vallée N, Risso JJ. Theoretical considerations on the ultimate depth that could be reached by saturation human divers. Med Gas Res 2016; 6:119-121. [PMID: 27867478 PMCID: PMC5110125 DOI: 10.4103/2045-9912.184722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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24
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Argon blocks the expression of locomotor sensitization to amphetamine through antagonism at the vesicular monoamine transporter-2 and mu-opioid receptor in the nucleus accumbens. Transl Psychiatry 2015; 5:e594. [PMID: 26151922 PMCID: PMC5068729 DOI: 10.1038/tp.2015.27] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 01/06/2015] [Accepted: 01/20/2015] [Indexed: 01/16/2023] Open
Abstract
We investigated the effects of the noble gas argon on the expression of locomotor sensitization to amphetamine and amphetamine-induced changes in dopamine release and mu-opioid neurotransmission in the nucleus accumbens. We found (1) argon blocked the increase in carrier-mediated dopamine release induced by amphetamine in brain slices, but, in contrast, potentiated the decrease in KCl-evoked dopamine release induced by amphetamine, thereby suggesting that argon inhibited the vesicular monoamine transporter-2; (2) argon blocked the expression of locomotor and mu-opioid neurotransmission sensitization induced by repeated amphetamine administration in a short-term model of sensitization in rats; (3) argon decreased the maximal number of binding sites and increased the dissociation constant of mu-receptors in membrane preparations, thereby indicating that argon is a mu-receptor antagonist; (4) argon blocked the expression of locomotor sensitization and context-dependent locomotor activity induced by repeated administration of amphetamine in a long-term model of sensitization. Taken together, these data indicate that argon could be of potential interest for treating drug addiction and dependence.
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25
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Smit KF, Weber NC, Hollmann MW, Preckel B. Noble gases as cardioprotectants - translatability and mechanism. Br J Pharmacol 2015; 172:2062-73. [PMID: 25363501 DOI: 10.1111/bph.12994] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 10/06/2014] [Accepted: 10/21/2014] [Indexed: 01/03/2023] Open
Abstract
Several noble gases, although classified as inert substances, exert a tissue-protective effect in different experimental models when applied before organ ischaemia as an early or late preconditioning stimulus, after ischaemia as a post-conditioning stimulus or when given in combination before, during and/or after ischaemia. A wide range of organs can be protected by these inert substances, in particular cardiac and neuronal tissue. In this review we summarize the data on noble gas-induced cardioprotection, focusing on the underlying protective mechanisms. We will also look at translatability of experimental data to the clinical situation.
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Affiliation(s)
- Kirsten F Smit
- Department of Anaesthesiology, Laboratory of Experimental Intensive Care and Anaesthesiology (L.E.I.C.A), Academic Medical Centre (AMC), Amsterdam, The Netherlands
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26
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Laletin V, Bykov Y. General anesthetics as a factor of effective neuroprotection in ischemic stroke models. ACTA ACUST UNITED AC 2015; 61:440-8. [DOI: 10.18097/pbmc20156104440] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Stroke is the second leading cause of death in the world. Unfortunately, only a few drugs have been proved in clinical trials. Drug development of the last decade has been focused substantially on a promising and heterogeneous group of neuroprotective drugs. Hundreds of compounds were suggested as new putative neuroprotectors, which effectiveness was confirmed in preclinical trials only. At the present time discrepancy between results of preclinical studies and clinical trials requires careful analysis. One of the least evaluated and probably the most noticeable reasons is general anesthesia - an obligatory component of an overwhelming majority of existing animal stroke models. The aim of the review is to describe known mechanisms of common general anesthetics influence on ionotropic and metabotropic plasma membrane receptors, and key signal pathways involved in neuronal hypoxic-ischemic injury and survival
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Affiliation(s)
- V.S. Laletin
- Irkutsk State Medical University, Irkutsk, Russia
| | - Y.N. Bykov
- Irkutsk State Medical University, Irkutsk, Russia
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27
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Meersman F, McMillan PF. High hydrostatic pressure: a probing tool and a necessary parameter in biophysical chemistry. Chem Commun (Camb) 2014; 50:766-75. [PMID: 24286104 DOI: 10.1039/c3cc45844j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
High pressures extending up to several thousands of atmospheres provide extreme conditions for biological organisms to survive. Recent studies are investigating the survival mechanisms and biological function of microorganisms under natural and laboratory conditions extending into the GigaPascal range, with applications to understanding the Earth's deep biosphere and food technology. High pressure has also emerged as a useful tool and physical parameter for probing changes in the structure and functional properties of biologically important macromolecules and polymers encountered in soft matter science. Here we highlight some areas of current interest in high pressure biophysics and physical chemistry that are emerging at the frontier of this cross-disciplinary field.
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Affiliation(s)
- Filip Meersman
- Department of Chemistry, University College London, 20 Gordon St., London WC1H 0AJ, UK.
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28
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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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29
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Mottarella SE, Beglov D, Beglova N, Nugent MA, Kozakov D, Vajda S. Docking server for the identification of heparin binding sites on proteins. J Chem Inf Model 2014; 54:2068-78. [PMID: 24974889 PMCID: PMC4184157 DOI: 10.1021/ci500115j] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Many proteins of widely differing functionality and structure are capable of binding heparin and heparan sulfate. Since crystallizing protein-heparin complexes for structure determination is generally difficult, computational docking can be a useful approach for understanding specific interactions. Previous studies used programs originally developed for docking small molecules to well-defined pockets, rather than for docking polysaccharides to highly charged shallow crevices that usually bind heparin. We have extended the program PIPER and the automated protein-protein docking server ClusPro to heparin docking. Using a molecular mechanics energy function for scoring and the fast Fourier transform correlation approach, the method generates and evaluates close to a billion poses of a heparin tetrasaccharide probe. The docked structures are clustered using pairwise root-mean-square deviations as the distance measure. It was shown that clustering of heparin molecules close to each other but having different orientations and selecting the clusters with the highest protein-ligand contacts reliably predicts the heparin binding site. In addition, the centers of the five most populated clusters include structures close to the native orientation of the heparin. These structures can provide starting points for further refinement by methods that account for flexibility such as molecular dynamics. The heparin docking method is available as an advanced option of the ClusPro server at http://cluspro.bu.edu/ .
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Affiliation(s)
- Scott E Mottarella
- Program in Bioinformatics and ‡Department of Biomedical Engineering, Boston University , 44 Cummington Street, Boston, Massachusetts 02215, United States
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30
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Colloc'h N, Prangé T. Functional relevance of the internal hydrophobic cavity of urate oxidase. FEBS Lett 2014; 588:1715-9. [PMID: 24657440 DOI: 10.1016/j.febslet.2014.03.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 03/10/2014] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
Abstract
Urate oxidase from Aspergillus flavus is a 135 kDa homo-tetramer which has a hydrophobic cavity buried within each monomer and located close to its active site. Crystallographic studies under moderate gas pressure and high hydrostatic pressure have shown that both gas presence and high pressure would rigidify the cavity leading to an inhibition of the catalytic activity. Analysis of the cavity volume variations and functional modifications suggest that the flexibility of the cavity would be an essential parameter for the active site efficiency. This cavity would act as a connecting vessel to give flexibility to the neighboring active site, and its expansion under pure oxygen pressure reveals that it might serve as a transient reservoir on its pathway to the active site.
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Affiliation(s)
- Nathalie Colloc'h
- CERVoxy Team, ISTCT UMR 6301, CNRS, Centre Cyceron, Caen, France; ISTCT UMR 6301, CEA, DSV/I2BM, Caen, France; ISTCT UMR 6301, Université de Caen Basse-Normandie, Normandie Université, Caen, France.
| | - Thierry Prangé
- LCRB UMR 8015, CNRS, Université Paris Descartes, Faculté de Pharmacie, 4 Avenue de l'Observatoire, 75006 Paris, France
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31
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Oksanen E, Blakeley MP, El-Hajji M, Ryde U, Budayova-Spano M. The neutron structure of urate oxidase resolves a long-standing mechanistic conundrum and reveals unexpected changes in protonation. PLoS One 2014; 9:e86651. [PMID: 24466188 PMCID: PMC3900588 DOI: 10.1371/journal.pone.0086651] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 12/16/2013] [Indexed: 12/02/2022] Open
Abstract
Urate oxidase transforms uric acid to 5-hydroxyisourate without the help of cofactors, but the catalytic mechanism has remained enigmatic, as the protonation state of the substrate could not be reliably deduced. We have determined the neutron structure of urate oxidase, providing unique information on the proton positions. A neutron crystal structure inhibited by a chloride anion at 2.3 Å resolution shows that the substrate is in fact 8-hydroxyxanthine, the enol tautomer of urate. We have also determined the neutron structure of the complex with the inhibitor 8-azaxanthine at 1.9 Å resolution, showing the protonation states of the K10–T57–H256 catalytic triad. Together with X-ray data and quantum chemical calculations, these structures allow us to identify the site of the initial substrate protonation and elucidate why the enzyme is inhibited by a chloride anion.
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Affiliation(s)
- Esko Oksanen
- Institut de Biologie Structurale (IBS), Direction des Sciences du Vivant, Commissariat à l’Energie Atomique et aux Energies Alternatives, Grenoble, France, IBS, Centre National de la Recherche Scientifique, Grenoble, France, IBS, Université Grenoble Alpes, Grenoble, France
| | | | | | - Ulf Ryde
- Department of Theoretical Chemistry Lund University, Lund, Sweden
| | - Monika Budayova-Spano
- Institut de Biologie Structurale (IBS), Direction des Sciences du Vivant, Commissariat à l’Energie Atomique et aux Energies Alternatives, Grenoble, France, IBS, Centre National de la Recherche Scientifique, Grenoble, France, IBS, Université Grenoble Alpes, Grenoble, France
- * E-mail:
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Mizuno N, Makino M, Kumasaka T. A convenient tool for gas derivatization using fine-needle capillary mounting for protein crystals. JOURNAL OF SYNCHROTRON RADIATION 2013; 20:999-1002. [PMID: 24121356 PMCID: PMC3795572 DOI: 10.1107/s0909049513021584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 08/02/2013] [Indexed: 06/02/2023]
Abstract
Gas derivatization of protein crystals is useful not only to analyse gas-binding proteins but also to solve the phase problem of X-ray crystallography by using noble gases. However, the gas pressurization tools for these experiments are often elaborate and need to release the gas before flash-cooling. To simplify this step, a procedure using a fine-needle capillary to mount and flash-cool protein crystals under the pressurization of gases has been developed. After the crystals are picked up with the capillary, the capillary is sealed with an adhesive and then connected directly to a gas regulator. The quality of the diffraction data using this method is comparable with that of data from conventional pressurization procedures. The preparation of xenon-derivatives of hen egg-white lysozyme using this method was a success. In the derivatives, two new xenon binding sites were found and one of their sites vanished by releasing the gas. This observation shows the availability of flash-cooling under gas pressurization. This procedure is simple and useful for preparing gas-derivative crystals.
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Affiliation(s)
- Nobuhiro Mizuno
- Structural Biology Group, Japan Synchrotron Radiation Research Institute (JASRI/SPring-8), 1-1-1 Kouto, Sayo, Hyogo 6795198, Japan
| | - Masatomo Makino
- Structural Biology Group, Japan Synchrotron Radiation Research Institute (JASRI/SPring-8), 1-1-1 Kouto, Sayo, Hyogo 6795198, Japan
| | - Takashi Kumasaka
- Structural Biology Group, Japan Synchrotron Radiation Research Institute (JASRI/SPring-8), 1-1-1 Kouto, Sayo, Hyogo 6795198, Japan
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David HN, Haelewyn B, Risso JJ, Abraini JH. Modulation by the noble gas argon of the catalytic and thrombolytic efficiency of tissue plasminogen activator. Naunyn Schmiedebergs Arch Pharmacol 2012; 386:91-5. [PMID: 23142817 DOI: 10.1007/s00210-012-0809-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 10/30/2012] [Indexed: 11/28/2022]
Abstract
Argon has been shown to provide cortical as well as, under certain conditions, subcortical neuroprotection in all models so far (middle cerebral artery occlusion, trauma, neonatal asphyxia, etc.). This has led to the suggestion that argon could be a cost-efficient alternative to xenon, a metabolically inert gas thought to be gold standard in gas pharmacology but whose clinical development suffers its little availability and excessive cost of production. However, whether argon interacts with the thrombolytic agent tissue plasminogen activator, which is the only approved therapy of acute ischemic stroke to date, still remains unknown. This latter point is not trivial since previous data have clearly demonstrated the inhibiting effect of xenon on tPA enzymatic and thrombolytic efficiency and the critical importance of the time at which xenon is administered, during or after ischemia, in order not to block thrombolysis and to obtain neuroprotection. Here, we investigated the effect of argon on tPA enzymatic and thrombolytic efficiency using in vitro methods shown to provide reliable prediction of the in vivo effects of both oxygen and the noble inert gases on tPA-induced thrombolysis. We found that argon has a concentration-dependent dual effect on tPA enzymatic and thrombolytic efficiency. Low and high concentrations of argon of 25 and 75 vol% respectively block and increase tPA enzymatic and thrombolytic efficiency. The possible use of argon at low and high concentrations in the treatment of acute ischemic stroke if given during ischemia or after tPA-induced reperfusion is discussed as regards to its neuroprotectant action and its inhibiting and facilitating effects on tPA-induced thrombolysis. The mechanisms of argon-tPA interactions are also discussed.
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Affiliation(s)
- Hélène N David
- CSSS Alphonse-Desjardins, Centre Hospitalier Affilié Universitaire Hôtel-Dieu de Lévis, Université Laval, Lévis, QC, Canada.
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Cao Q, Andrijchenko N, Ahola AE, Domanskaya A, Räsänen M, Ermilov A, Nemukhin A, Khriachtchev L. Interaction of phenol with xenon and nitrogen: Spectroscopic and computational characterization. J Chem Phys 2012; 137:134305. [DOI: 10.1063/1.4754435] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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35
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Cao Q, Melavuori M, Lundell J, Räsänen M, Khriachtchev L. Matrix-isolation and ab initio study of the complex between formic acid and xenon. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.05.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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36
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Luna VM, Fee JA, Deniz AA, Stout CD. Mobility of Xe atoms within the oxygen diffusion channel of cytochrome ba(3) oxidase. Biochemistry 2012; 51:4669-76. [PMID: 22607023 DOI: 10.1021/bi3003988] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We use a form of "freeze-trap, kinetic crystallography" to explore the migration of Xe atoms away from the dinuclear heme a(3)/Cu(B) center in Thermus thermophilus cytochrome ba(3) oxidase. This enzyme is a member of the heme-copper oxidase superfamily and is thus crucial for dioxygen-dependent life. The mechanisms involved in the migration of oxygen, water, electrons, and protons into and/or out of the specialized channels of the heme-copper oxidases are generally not well understood. Pressurization of crystals with Xe gas previously revealed a O(2) diffusion channel in cytochrome ba(3) oxidase that is continuous, Y-shaped, 18-20 Å in length and comprised of hydrophobic residues, connecting the protein surface within the bilayer to the a(3)-Cu(B) center in the active site. To understand movement of gas molecules within the O(2) channel, we performed crystallographic analysis of 19 Xe laden crystals freeze-trapped in liquid nitrogen at selected times between 0 and 480 s while undergoing outgassing at room temperature. Variation in Xe crystallographic occupancy at five discrete sites as a function of time leads to a kinetic model revealing relative degrees of mobility of Xe atoms within the channel. Xe egress occurs primarily through the channel formed by the Xe1 → Xe5 → Xe3 → Xe4 sites, suggesting that ingress of O(2) is likely to occur by the reverse of this process. The channel itself appears not to undergo significant structural changes during Xe migration, thereby indicating a passive role in this important physiological function.
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Affiliation(s)
- V Mitch Luna
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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37
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Zierkiewicz W. Nature of multiple weak interactions between volatile anaesthetic isoflurane and apoferritin: A theoretical study. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2012.03.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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38
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David HN, Haelewyn B, Degoulet M, Colomb DG, Risso JJ, Abraini JH. Prothrombolytic action of normobaric oxygen given alone or in combination with recombinant tissue-plasminogen activator in a rat model of thromboembolic stroke. J Appl Physiol (1985) 2012; 112:2068-76. [PMID: 22492935 DOI: 10.1152/japplphysiol.00092.2012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The potential benefit of 100 vol% normobaric oxygen (NBO) for the treatment of acute ischemic stroke patients is still a matter of debate. To advance this critical question, we studied the effects of intraischemic normobaric oxygen alone or in combination with recombinant tissue-plasminogen activator (rtPA) on cerebral blood flow and ischemic brain damage and swelling in a clinically relevant rat model of thromboembolic stroke. We show that NBO provides neuroprotection by achieving cerebral blood flow restoration equivalent to 0.9 mg/kg rtPA through probable direct interaction and facilitation of the fibrinolytic properties of endogenous tPA. In contrast, combined NBO and rtPA has no neuroprotective effect on ischemic brain damage despite producing cerebral blood flow restoration. These results 1) by providing a new mechanism of action of NBO highlight together with previous findings the way by which intraischemic NBO shows beneficial action; 2) suggest that NBO could be an efficient primary care therapeutic intervention for patients eligible for rtPA therapy; 3) indicate that NBO could be an interesting alternative for patients not eligible for rtPA therapy; and 4) caution the use of NBO in combination with rtPA in acute stroke patients.
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Affiliation(s)
- H N David
- Centre de Recherche, Centre Hospitalier Affilié Universitaire Hôtel-Dieu de Lévis, Lévis, Quebec, Canada
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Mechanism of action of nitrogen pressure in controlling striatal dopamine level of freely moving rats is changed by recurrent exposures to nitrogen narcosis. Neurochem Res 2011; 37:655-64. [PMID: 22127756 DOI: 10.1007/s11064-011-0657-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 10/26/2011] [Accepted: 11/09/2011] [Indexed: 10/15/2022]
Abstract
In rats, a single exposure to 3 MPa nitrogen induces change in motor processes, a sedative action and a decrease in dopamine release in the striatum. These changes due to a narcotic effect of nitrogen have been attributed to a decrease in glutamatergic control and the facilitation of GABAergic neurotransmission involving NMDA and GABA(A) receptors, respectively. After repeated exposure to nitrogen narcosis, a second exposure to 3 MPa increased dopamine levels suggesting a change in the control of the dopaminergic pathway. We investigated the role of the nigral NMDA and GABA(A) receptors in changes in the striatal dopamine levels. Dopamine-sensitive electrodes were implanted into the striatum under general anesthesia, together with a guide-cannula for drug injections into the SNc. Dopamine level was monitored by in vivo voltammetry. The effects of NMDA/GABA(A) receptor agonists (NMDA/muscimol) and antagonists (AP7/gabazine) on dopamine levels were investigated. Rats were exposed to 3 MPa nitrogen before and after five daily exposures to 1 MPa. After these exposures to nitrogen narcosis, gabazine, NMDA and AP7 had no effect on the nitrogen-induced increase in dopamine levels. By contrast, muscimol strongly enhanced the increase in dopamine level induced by nitrogen. Our findings suggest that repeated nitrogen exposure disrupted NMDA receptor function and decreased GABAergic input by modifying GABA(A) receptor sensitivity. These findings demonstrated a change in the mechanism of action of nitrogen at pressure.
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40
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Collins MD, Kim CU, Gruner SM. High-pressure protein crystallography and NMR to explore protein conformations. Annu Rev Biophys 2011; 40:81-98. [PMID: 21275639 DOI: 10.1146/annurev-biophys-042910-155304] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
High-pressure methods for solving protein structures by X-ray crystallography and NMR are maturing. These techniques are beginning to impact our understanding of thermodynamic and structural features that define not only the protein's native conformation, but also the higher free energy conformations. The ability of high-pressure methods to visualize these mostly unexplored conformations provides new insight into protein function and dynamics. In this review, we begin with a historical discussion of high-pressure structural studies, with an eye toward early results that paved the way to mapping the multiple conformations of proteins. This is followed by an examination of several recent studies that emphasize different strengths and uses of high-pressure structural studies, ranging from basic thermodynamics to the suggestion of high-pressure structural methods as a tool for protein engineering.
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Affiliation(s)
- Marcus D Collins
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195-7290, USA
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Kier LB. Water chreodes and the mechanisms of ligand diffusion, general anesthesia, and sleep. Biochem Res Int 2011; 2011:396560. [PMID: 21804942 PMCID: PMC3144665 DOI: 10.1155/2011/396560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 05/31/2011] [Indexed: 11/18/2022] Open
Abstract
The concept of the presence of passageways, chreodes, created by the influence of the hydropathic states of amino acid side chains on the surface water of proteins, has been proposed. These chreodes facilitate and direct the diffusion of neurotransmitters through surface water, to the receptor or active site on a protein. This system of chreodes is vulnerable to the presence of some other molecules that may encounter the chreode system. This encounter and disruption has been proposed to explain the mechanism of general anesthesia. Based on much recent evidence of the similarities between anesthesia from volatile anesthetic agents and sleep, a comparable mechanism has been proposed for sleep. Since this must be an exogenous substance to be comparable to a general anesthetic agent, it was proposed that this exogenous, sleep-producing substance is elemental nitrogen. Recent evidence supports these hypotheses.
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Affiliation(s)
- Lemont B. Kier
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 842030, USA
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42
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Xenon fails to inhibit capsaicin-evoked CGRP release by nociceptors in culture. Neurosci Lett 2011; 499:124-6. [DOI: 10.1016/j.neulet.2011.05.051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 04/26/2011] [Accepted: 05/19/2011] [Indexed: 11/17/2022]
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Meersman F, Cabrera RQ, McMillan PF, Dmitriev V. Structural and mechanical properties of TTR105-115 amyloid fibrils from compression experiments. Biophys J 2011; 100:193-7. [PMID: 21190671 DOI: 10.1016/j.bpj.2010.11.052] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 11/09/2010] [Accepted: 11/29/2010] [Indexed: 10/18/2022] Open
Abstract
Amyloid fibrils, originally associated with neurodegenerative diseases, are now recognized to have interesting mechanical properties. By using synchrotron x-ray diffraction at high pressure in a diamond anvil cell we determined the bulk modulus of TTR105-115 amyloid fibrils in water and in silicone oil to be 2.6 and 8.1 GPa, respectively. The compression characteristics of the fibrils are quite different in the two media, revealing the presence of cavities along the axis of the fibrils, but not between the β-sheets, which are separated by a dry interface as in a steric zipper motif. Our results emphasize the importance of peptide packing in determining the structural and mechanical properties of amyloid fibrils.
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Affiliation(s)
- Filip Meersman
- Department of Chemistry, Katholieke Universiteit Leuven, Leuven, Belgium, UK.
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44
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Marassio G, Prangé T, David HN, Santos JSDO, Gabison L, Delcroix N, Abraini JH, Colloc'h N. Pressure-response analysis of anesthetic gases xenon and nitrous oxide on urate oxidase: a crystallographic study. FASEB J 2011; 25:2266-75. [PMID: 21421845 DOI: 10.1096/fj.11-183046] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The remarkably safe anesthetics xenon (Xe) and, to lesser extent, nitrous oxide (N(2)O) possess neuroprotective properties in preclinical studies. To investigate the mechanisms of pharmacological action of these gases, which are still poorly known, we performed both crystallography under a large range of gas pressure and biochemical studies on urate oxidase, a prototype of globular gas-binding proteins whose activity is modulated by inert gases. We show that Xe and N(2)O bind to, compete for, and expand the volume of a hydrophobic cavity located just behind the active site of urate oxidase and further inhibit urate oxidase enzymatic activity. By demonstrating a significant relationship between the binding and biochemical effects of Xe and N(2)O, given alone or in combination, these data from structure to function highlight the mechanisms by which chemically and metabolically inert gases can alter protein function and produce their pharmacological effects. Interestingly, the effects of a Xe:N(2)O equimolar mixture were found to be equivalent to those of Xe alone, thereby suggesting that gas mixtures containing Xe and N(2)O could be an alternative and efficient neuroprotective strategy to Xe alone, whose widespread clinical use is limited due to the cost of production and availability of this gas.
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Affiliation(s)
- Guillaume Marassio
- Equipe de Recherche Technologique Interne (ERTi) 1083, Centre National de la Recherche Scientifique (CNRS), Centre Cyceron, Caen, France
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45
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White JPM, Calcott G, Jenes A, Hossein M, Paule CC, Santha P, Davis JB, Ma D, Rice ASC, Nagy I. Xenon reduces activation of transient receptor potential vanilloid type 1 (TRPV1) in rat dorsal root ganglion cells and in human TRPV1-expressing HEK293 cells. Life Sci 2011; 88:141-9. [PMID: 21056583 DOI: 10.1016/j.lfs.2010.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Revised: 09/20/2010] [Accepted: 10/27/2010] [Indexed: 11/19/2022]
Abstract
AIMS Xenon provides effective analgesia in several pain states at sub-anaesthetic doses. Our aim was to examine whether xenon may mediate its analgesic effect, in part, through reducing the activity of transient receptor potential vanilloid type 1 (TRPV1), a receptor known to be involved in certain inflammatory pain conditions. MAIN METHODS We studied the effect of xenon on capsaicin-evoked cobalt uptake in rat cultured primary sensory neurons and in human TRPV1 (hTRPV1)-expressing human embryonic kidney 293 (HEK293) cells. We also examined xenon's effect on the phosphorylation of extracellular signal-regulated kinase 1/2 (ERK1/2) in the rat spinal dorsal horn evoked by hind-paw injection of capsaicin. KEY FINDINGS Xenon (75%) reduced the number of primary sensory neurons responding to the TRPV1 agonist, capsaicin (100 nM-1 μM) by ~25% to ~50%. Xenon reduced the number of heterologously-expressed hTRPV1 activated by 300 nM capsaicin by ~50%. Xenon (80%) reduced by ~40% the number of phosphorylated ERK1/2-expressing neurons in rat spinal dorsal horn resulting from hind-paw capsaicin injection. SIGNIFICANCE Xenon substantially reduces the activity of TRPV1 in response to noxious stimulation by the specific TRPV1 agonist, capsaicin, suggesting a possible role for xenon as an adjunct analgesic where hTRPV1 is an active contributor to the excitation of primary afferents which initiates the pain sensation.
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Affiliation(s)
- John P M White
- Anaesthetics, Pain Medicine and Intensive Care Section, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Chelsea and Westminster Hospital, 369, Fulham Road, London, SW10 9NH, United Kingdom
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46
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Liu LT, Xu Y, Tang P. Mechanistic insights into xenon inhibition of NMDA receptors from MD simulations. J Phys Chem B 2010; 114:9010-6. [PMID: 20560662 DOI: 10.1021/jp101687j] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Inhibition of N-methyl-D-aspartate (NMDA) receptors has been viewed as a primary cause of xenon anesthesia, yet the mechanism is unclear. Here, we investigated interactions between xenon and the ligand-binding domain (LBD) of a NMDA receptor and examined xenon-induced structural and dynamical changes that are relevant to functional changes of the NMDA receptor. Several comparative molecular dynamics simulations were performed on two X-ray structures representing the open- and closed-cleft LBD of the NMDA receptor. We identified plausible xenon action sites in the LBD, including those nearby agonist sites, in the hinge region, and at the interface between two subunits. The xenon-binding energy varies from -5.3 to -0.7 kcal/mol. Xenon's effect on the NMDA receptor is conformation-dependent and is produced through both competitive and noncompetitive mechanisms. Xenon can promote cleft opening in the absence of agonists and consequently stabilizes the closed channel. Xenon can also bind at the interface of two subunits, alter the intersubunit interaction, and lead to a reduction of the distance between two GT linkers. This reduction corresponds to a rearrangement of the channel toward a direction of pore size decreasing, implying a closed or desensitized channel. In addition to these noncompetitive actions, xenon was found to weaken the glutamate binding, which could lead to low agonist efficacy and appear as competitive inhibition.
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Affiliation(s)
- Lu Tian Liu
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
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Abstract
AbstractIn recent years, significant progress in high pressure macromolecular crystallography has been observed. It can be attributed both to the developments in experimental techniques, as well as to recognition of importance of high pressure protein studies in biochemistry and biophysics. The number of protein structures determined at pressure up to 1 GPa is growing. The unique advantages of this method can greatly improve the investigation of higher energy conformers of functional significance and our understanding of functionally important conformers, protein folding processes and the structural base of conformational diseases.
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48
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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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Dickinson R, Franks NP. Bench-to-bedside review: Molecular pharmacology and clinical use of inert gases in anesthesia and neuroprotection. Crit Care 2010; 14:229. [PMID: 20836899 PMCID: PMC2945072 DOI: 10.1186/cc9051] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In the past decade there has been a resurgence of interest in the clinical use of inert gases. In the present paper we review the use of inert gases as anesthetics and neuroprotectants, with particular attention to the clinical use of xenon. We discuss recent advances in understanding the molecular pharmacology of xenon and we highlight specific pharmacological targets that may mediate its actions as an anesthetic and neuroprotectant. We summarize recent in vitro and in vivo studies on the actions of helium and the other inert gases, and discuss their potential to be used as neuroprotective agents.
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Affiliation(s)
- Robert Dickinson
- Biophysics Section, Blackett Laboratory, Imperial College London, South Kensington, London SW7 2AZ, UK.
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50
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Gabison L, Chiadmi M, El Hajji M, Castro B, Colloc'h N, Prangé T. Near-atomic resolution structures of urate oxidase complexed with its substrate and analogues: the protonation state of the ligand. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:714-24. [DOI: 10.1107/s090744491001142x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 03/25/2010] [Indexed: 02/04/2023]
Abstract
Urate oxidase (uricase; EC 1.7.3.3; UOX) fromAspergillus flavuscatalyzes the oxidation of uric acid in the presence of molecular oxygen to 5-hydroxyisourate in the degradation cascade of purines; intriguingly, catalysis proceeds using neither a metal ion (Fe, Cuetc.) nor a redox cofactor. UOX is a tetrameric enzyme with four active sites located at the interface of two subunits; its structure was refined at atomic resolution (1 Å) using new crystal data in the presence of xanthine and at near-atomic resolution (1.3–1.7 Å) in complexes with the natural substrate (urate) and two inhibitors: 8-nitroxanthine and 8-thiouric acid. Three new features of the structural and mechanistic behaviour of the enzyme were addressed. Firstly, the high resolution of the UOX–xanthine structure allowed the solution of an old structural problem at a contact zone within the tetramer; secondly, the protonation state of the substrate was determined from both a halochromic inhibitor complex (UOX–8-nitroxanthine) and from the H-atom distribution in the active site, using the structures of the UOX–xanthine and the UOX–uric acid complexes; and thirdly, it was possible to extend the general base system, characterized by the conserved catalytic triad Thr–Lys–His, to a large water network that is able to buffer and shuttle protons back and forth between the substrate and the peroxo hole along the reaction pathway.
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