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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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2
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Taborda A, Frazão T, Rodrigues MV, Fernández-Luengo X, Sancho F, Lucas MF, Frazão C, Melo EP, Ventura MR, Masgrau L, Borges PT, Martins LO. Mechanistic insights into glycoside 3-oxidases involved in C-glycoside metabolism in soil microorganisms. Nat Commun 2023; 14:7289. [PMID: 37963862 PMCID: PMC10646112 DOI: 10.1038/s41467-023-42000-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 09/27/2023] [Indexed: 11/16/2023] Open
Abstract
C-glycosides are natural products with important biological activities but are recalcitrant to degradation. Glycoside 3-oxidases (G3Oxs) are recently identified bacterial flavo-oxidases from the glucose-methanol-coline (GMC) superfamily that catalyze the oxidation of C-glycosides with the concomitant reduction of O2 to H2O2. This oxidation is followed by C-C acid/base-assisted bond cleavage in two-step C-deglycosylation pathways. Soil and gut microorganisms have different oxidative enzymes, but the details of their catalytic mechanisms are largely unknown. Here, we report that PsG3Ox oxidizes at 50,000-fold higher specificity (kcat/Km) the glucose moiety of mangiferin to 3-keto-mangiferin than free D-glucose to 2-keto-glucose. Analysis of PsG3Ox X-ray crystal structures and PsG3Ox in complex with glucose and mangiferin, combined with mutagenesis and molecular dynamics simulations, reveal distinctive features in the topology surrounding the active site that favor catalytically competent conformational states suitable for recognition, stabilization, and oxidation of the glucose moiety of mangiferin. Furthermore, their distinction to pyranose 2-oxidases (P2Oxs) involved in wood decay and recycling is discussed from an evolutionary, structural, and functional viewpoint.
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Grants
- EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
- Fundação para a Ciência e Tecnologia, Portugal, grants 2022.02027.PTDC, UIDB/04612/2020 and UIDP/04612/2020, LA/P/0087/2020, PTDC/BII-BBF/29564/2017, and AAC 01/SAICT/2016 Fundação para a Ciência e Tecnologia, Portugal, Ph.D. fellowships 2020.07928, 2022.13872, and 2022.09426 Ministry of Science and Innovation, Spain, grant PID2021-126897NB-I00 and fellowship PRE2019-088412, funded by the MCIN/AEI/10.13039/501100011033/ FEDER, EU
- Fundação para a Ciência e Tecnologia (FCT), Portugal, grants UIDB/04326/2020, UIDP/043226/2020 and LA/P/0101/2020
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Affiliation(s)
- André Taborda
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
| | - Tomás Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
| | - Miguel V Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
| | | | - Ferran Sancho
- Zymvol Biomodeling, C/ Pau Claris, 94, 3B, 08010, Barcelona, Spain
| | | | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
| | - Eduardo P Melo
- Centro de Ciências do Mar, Universidade do Algarve, 8005-139, Faro, Portugal
| | - M Rita Ventura
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
| | - Laura Masgrau
- Department of Chemistry, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
- Zymvol Biomodeling, C/ Pau Claris, 94, 3B, 08010, Barcelona, Spain
| | - Patrícia T Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal
| | - Lígia O Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157, Oeiras, Portugal.
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3
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Hancock JT. Are Protein Cavities and Pockets Commonly Used by Redox Active Signalling Molecules? PLANTS (BASEL, SWITZERLAND) 2023; 12:2594. [PMID: 37514209 PMCID: PMC10383989 DOI: 10.3390/plants12142594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/23/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023]
Abstract
It has been well known for a long time that inert gases, such as xenon (Xe), have significant biological effects. As these atoms are extremely unlikely to partake in direct chemical reactions with biomolecules such as proteins, lipids, and nucleic acids, there must be some other mode of action to account for the effects reported. It has been shown that the topology of proteins allows for cavities and hydrophobic pockets, and it is via an interaction with such protein structures that inert gases are thought to have their action. Recently, it has been mooted that the relatively inert gas molecular hydrogen (H2) may also have its effects via such a mechanism, influencing protein structures and actions. H2 is thought to also act via interaction with redox active compounds, particularly the hydroxyl radical (·OH) and peroxynitrite (ONOO-), but not nitric oxide (NO·), superoxide anions (O2·-) or hydrogen peroxide (H2O2). However, instead of having a direct interaction with H2, is there any evidence that these redox compounds can also interact with Xe pockets and cavities in proteins, either having an independent effect on proteins or interfering with the action of inert gases? This suggestion will be explored here.
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Affiliation(s)
- John T Hancock
- School of Applied Sciences, University of the West of England, Bristol BS16 1QY, UK
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4
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Gomari MM, Rostami N, Faradonbeh DR, Asemaneh HR, Esmailnia G, Arab S, Farsimadan M, Hosseini A, Dokholyan NV. Evaluation of pH change effects on the HSA folding and its drug binding characteristics, a computational biology investigation. Proteins 2022; 90:1908-1925. [DOI: 10.1002/prot.26386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Mohammad Mahmoudi Gomari
- Student Research Committee, Iran University of Medical Sciences Tehran Iran
- Department of Medical Biotechnology, Faculty of Allied Medicine Iran University of Medical Sciences Tehran Iran
| | - Neda Rostami
- Department of Chemical Engineering, Faculty of Engineering Arak University Arak Iran
| | - Davood Rabiei Faradonbeh
- Department of Medical Biotechnology School of Advanced Technologies in Medicine, Tehran University of Medical Sciences Tehran Iran
| | - Hamid Reza Asemaneh
- Polymer Research Center, Department of Chemical Engineering Razi University Kermanshah Iran
| | - Giti Esmailnia
- Department of Medical Biotechnology, Faculty of Allied Medicine Iran University of Medical Sciences Tehran Iran
| | - Shahriar Arab
- Department of Biophysics School of Biological Sciences, Tarbiat Modares University Tehran Iran
| | - Marziye Farsimadan
- Department of Biology, Faculty of Sciences University of Guilan Rasht Iran
| | - Arshad Hosseini
- Department of Medical Biotechnology, Faculty of Allied Medicine Iran University of Medical Sciences Tehran Iran
| | - Nikolay V. Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology Pennsylvania State University College of Medicine Hershey Pennsylvania USA
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5
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Hammami I, Farjot G, Naveau M, Rousseaud A, Prangé T, Katz I, Colloc'h N. Method for the Identification of Potentially Bioactive Argon Binding Sites in Protein Families. J Chem Inf Model 2022; 62:1318-1327. [PMID: 35179902 DOI: 10.1021/acs.jcim.2c00071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Argon belongs to the group of chemically inert noble gases, which display a remarkable spectrum of clinically useful biological properties. In an attempt to better understand noble gases, notably argon's mechanism of action, we mined a massive noble gas modeling database which lists all possible noble gas binding sites in the proteins from the Protein Data Bank. We developed a method of analysis to identify among all predicted noble gas binding sites the potentially relevant ones within protein families which are likely to be modulated by Ar. Our method consists in determining within structurally aligned proteins the conserved binding sites whose shape, localization, hydrophobicity, and binding energies are to be further examined. This method was applied to the analysis of two protein families where crystallographic noble gas binding sites have been experimentally determined. Our findings indicate that among the most conserved binding sites, either the most hydrophobic one and/or the site which has the best binding energy corresponds to the crystallographic noble gas binding sites with the best occupancies, therefore the best affinity for the gas. This method will allow us to predict relevant noble gas binding sites that have potential pharmacological interest and thus potential Ar targets that will be prioritized for further studies including in vitro validation.
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Affiliation(s)
- Islem Hammami
- ISTCT UMR 6030 CNRS Univ. Caen Normandie, GIP Cyceron, 14074 Caen, France.,Air Liquide Santé International, Innovation Campus Paris, 78354 Les Loges-en-Josas, France
| | - Géraldine Farjot
- Air Liquide Santé International, Innovation Campus Paris, 78354 Les Loges-en-Josas, France
| | - Mikaël Naveau
- UAR 3408 US 50 CNRS INSERM Université de Caen-Normandie, GIP Cyceron, 14074 Caen, France
| | - Audrey Rousseaud
- Air Liquide Santé International, Innovation Campus Paris, 78354 Les Loges-en-Josas, France
| | - Thierry Prangé
- CiTCoM UMR 8038 CNRS Université de Paris, Faculté de Pharmacie, 75006 Paris, France
| | - Ira Katz
- Air Liquide Santé International, Innovation Campus Paris, 78354 Les Loges-en-Josas, France
| | - Nathalie Colloc'h
- ISTCT UMR 6030 CNRS Univ. Caen Normandie, GIP Cyceron, 14074 Caen, France
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6
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Prangé T, Carpentier P, Dhaussy AC, van der Linden P, Girard E, Colloc'h N. Comparative study of the effects of high hydrostatic pressure per se and high argon pressure on urate oxidase ligand stabilization. Acta Crystallogr D Struct Biol 2022; 78:162-173. [DOI: 10.1107/s2059798321012134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/15/2021] [Indexed: 11/11/2022] Open
Abstract
The stability of the tetrameric enzyme urate oxidase in complex with excess of 8-azaxanthine was investigated either under high hydrostatic pressure per se or under a high pressure of argon. The active site is located at the interface of two subunits, and the catalytic activity is directly related to the integrity of the tetramer. This study demonstrates that applying pressure to a protein–ligand complex drives the thermodynamic equilibrium towards ligand saturation of the complex, revealing a new binding site. A transient dimeric intermediate that occurs during the pressure-induced dissociation process was characterized under argon pressure and excited substates of the enzyme that occur during the catalytic cycle can be trapped by pressure. Comparison of the different structures under pressure infers an allosteric role of the internal hydrophobic cavity in which argon is bound, since this cavity provides the necessary flexibility for the active site to function.
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7
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Exertier C, Montemiglio LC, Freda I, Gugole E, Parisi G, Savino C, Vallone B. Neuroglobin, clues to function and mechanism. Mol Aspects Med 2021; 84:101055. [PMID: 34876274 DOI: 10.1016/j.mam.2021.101055] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 12/19/2022]
Abstract
Neuroglobin is expressed in vertebrate brain and belongs to a branch of the globin family that diverged early in evolution. Sequence conservation and presence in nervous cells of several taxa suggests a relevant role in the nervous system, with tight structural restraints. Twenty years after its discovery, a rich scientific literature provides convincing evidence of the involvement of neuroglobin in sustaining neuron viability in physiological and pathological conditions however, a full and conclusive picture of its specific function, or set of functions is still lacking. The difficulty of unambiguously assigning a precise mechanism and biochemical role to neuroglobin might arise from the participation to one or more cell mechanism that redundantly guarantee the functioning of the highly specialized and metabolically demanding central nervous system of vertebrates. Here we collect findings and hypotheses arising from recent biochemical, biophysical, structural, in cell and in vivo experimental work on neuroglobin, aiming at providing an overview of the most recent literature. Proteins are said to have jobs and hobbies, it is possible that, in the case of neuroglobin, evolution has selected for it more than one job, and support to cover for its occasional failings. Disentangling the mechanisms and roles of neuroglobin is thus a challenging task that might be achieved by considering data from different disciplines and experimental approaches.
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Affiliation(s)
- Cécile Exertier
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, P.le A. Moro 5, 00185, Rome, Italy
| | - Linda Celeste Montemiglio
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185, Rome, Italy
| | - Ida Freda
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, P.le A. Moro 5, 00185, Rome, Italy
| | - Elena Gugole
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, P.le A. Moro 5, 00185, Rome, Italy
| | - Giacomo Parisi
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, 00161, Rome, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185, Rome, Italy.
| | - Beatrice Vallone
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza, Università di Roma, P.le A. Moro 5, 00185, Rome, Italy.
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8
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Keller TCS, Lechauve C, Keller AS, Brooks S, Weiss MJ, Columbus L, Ackerman HC, Cortese-Krott MM, Isakson BE. The role of globins in cardiovascular physiology. Physiol Rev 2021; 102:859-892. [PMID: 34486392 DOI: 10.1152/physrev.00037.2020] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Globin proteins exist in every cell type of the vasculature, from erythrocytes to endothelial cells, vascular smooth muscle cells, and peripheral nerve cells. Many globin subtypes are also expressed in muscle tissues (including cardiac and skeletal muscle), in other organ-specific cell types, and in cells of the central nervous system. The ability of each of these globins to interact with molecular oxygen (O2) and nitric oxide (NO) is preserved across these contexts. Endothelial α-globin is an example of extra-erythrocytic globin expression. Other globins, including myoglobin, cytoglobin, and neuroglobin are observed in other vascular tissues. Myoglobin is observed primarily in skeletal muscle and smooth muscle cells surrounding the aorta or other large arteries. Cytoglobin is found in vascular smooth muscle but can also be expressed in non-vascular cell types, especially in oxidative stress conditions after ischemic insult. Neuroglobin was first observed in neuronal cells, and its expression appears to be restricted mainly to the central and peripheral nervous systems. Brain and central nervous system neurons expressing neuroglobin are positioned close to many arteries within the brain parenchyma and can control smooth muscle contraction and, thus, tissue perfusion and vascular reactivity. Overall, reactions between NO and globin heme-iron contribute to vascular homeostasis by regulating vasodilatory NO signals and scaveging reactive species in cells of the mammalian vascular system. Here, we discuss how globin proteins affect vascular physiology with a focus on NO biology, and offer perspectives for future study of these functions.
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Affiliation(s)
- T C Steven Keller
- Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, United States.,Department of Molecular Physiology and Biophysics, University of Virginia School of Medicine, Charlottesville, VA, United States
| | - Christophe Lechauve
- Department of Hematology, St. Jude's Children's Research Hospital, Memphis, TN, United States
| | - Alexander S Keller
- Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, United States.,Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, United States
| | - Steven Brooks
- Physiology Unit, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, MD, United States
| | - Mitchell J Weiss
- Department of Hematology, St. Jude's Children's Research Hospital, Memphis, TN, United States
| | - Linda Columbus
- Department of Chemistry, University of Virginia, Charlottesville, VA, United States
| | - Hans C Ackerman
- Physiology Unit, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, MD, United States
| | - Miriam M Cortese-Krott
- Myocardial Infarction Research Laboratory, Department of Cardiology, Pulmunology, and Angiology, Medical Faculty, Heinrich-Heine-University of Düsseldorf, Düsseldorf, Germany.,Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Brant E Isakson
- Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, United States.,Department of Molecular Physiology and Biophysics, University of Virginia School of Medicine, Charlottesville, VA, United States
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9
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Markova K, Chmelova K, Marques SM, Carpentier P, Bednar D, Damborsky J, Marek M. Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst. Chem Sci 2020; 11:11162-11178. [PMID: 34094357 PMCID: PMC8162949 DOI: 10.1039/d0sc03367g] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/10/2020] [Indexed: 12/01/2022] Open
Abstract
Computational design of protein catalysts with enhanced stabilities for use in research and enzyme technologies is a challenging task. Using force-field calculations and phylogenetic analysis, we previously designed the haloalkane dehalogenase DhaA115 which contains 11 mutations that confer upon it outstanding thermostability (T m = 73.5 °C; ΔT m > 23 °C). An understanding of the structural basis of this hyperstabilization is required in order to develop computer algorithms and predictive tools. Here, we report X-ray structures of DhaA115 at 1.55 Å and 1.6 Å resolutions and their molecular dynamics trajectories, which unravel the intricate network of interactions that reinforce the αβα-sandwich architecture. Unexpectedly, mutations toward bulky aromatic amino acids at the protein surface triggered long-distance (∼27 Å) backbone changes due to cooperative effects. These cooperative interactions produced an unprecedented double-lock system that: (i) induced backbone changes, (ii) closed the molecular gates to the active site, (iii) reduced the volumes of the main and slot access tunnels, and (iv) occluded the active site. Despite these spatial restrictions, experimental tracing of the access tunnels using krypton derivative crystals demonstrates that transport of ligands is still effective. Our findings highlight key thermostabilization effects and provide a structural basis for designing new thermostable protein catalysts.
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Affiliation(s)
- Klara Markova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University Kamenice 5 625 00 Brno Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno Pekarska 53 656 91 Brno Czech Republic
| | - Klaudia Chmelova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University Kamenice 5 625 00 Brno Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno Pekarska 53 656 91 Brno Czech Republic
| | - Sérgio M Marques
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University Kamenice 5 625 00 Brno Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno Pekarska 53 656 91 Brno Czech Republic
| | - Philippe Carpentier
- Université Grenoble Alpes, CNRS, CEA, Interdisciplinary Research Institute of Grenoble (IRIG), Laboratoire Chimie et Biologie des Métaux (LCBM) 17 Avenue des Martyrs 38054 Grenoble France
- European Synchrotron Radiation Facility (ESRF) 71 Avenue des Martyrs 38043 Grenoble France
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University Kamenice 5 625 00 Brno Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno Pekarska 53 656 91 Brno Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University Kamenice 5 625 00 Brno Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno Pekarska 53 656 91 Brno Czech Republic
| | - Martin Marek
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University Kamenice 5 625 00 Brno Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno Pekarska 53 656 91 Brno Czech Republic
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10
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Milazzo L, Exertier C, Becucci M, Freda I, Montemiglio LC, Savino C, Vallone B, Smulevich G. Lack of orientation selectivity of the heme insertion in murine neuroglobin revealed by resonance Raman spectroscopy. FEBS J 2020; 287:4082-4097. [PMID: 32034988 DOI: 10.1111/febs.15241] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/30/2020] [Accepted: 02/05/2020] [Indexed: 01/17/2023]
Abstract
Different murine neuroglobin variants showing structural and dynamic alterations that are associated with perturbation of ligand binding have been studied: the CD loop mutants characterized by an enhanced flexibility (Gly-loop40-48 and Gly-loop44-47 ), the F106A mutant, and the double Gly-loop44-47 /F106A mutant. Their ferric resonance Raman spectra in solution and in crystals are almost identical. In the high-frequency region, the identification of a double set of core size marker bands indicates the presence of two 6-coordinate low spin species. The resonance Raman data, together with the corresponding crystal structures, indicate the presence of two neuroglobin conformers with a reversed (A conformer) or a canonical (B conformer) heme insertion orientation. With the identification of the marker bands corresponding to each conformer, the data indicate that the B conformer increases at the expense of the A form, predominantly in the Gly-loop44-47 /F106A double mutant, as confirmed by X-ray crystallography. This is the first time that a reversed heme insertion has been identified by resonance Raman in a native 6-coordinate low-spin heme protein. This diagnostic tool could be extended to other heme proteins in order to detect heme orientational disorder, which are likely to be correlated to functionally relevant heme dynamics. DATABASE: Crystallographic structure: structural data are deposited in the Protein Data Bank under the 6RA6 PDB entry.
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Affiliation(s)
- Lisa Milazzo
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Florence, Italy
| | - Cécile Exertier
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Italy.,Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza, Università di Roma, Italy
| | - Maurizio Becucci
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Florence, Italy.,European Laboratory for Non-Linear Spectroscopy - LENS, Florence, Italy
| | - Ida Freda
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Italy.,Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza, Università di Roma, Italy
| | - Linda Celeste Montemiglio
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Italy.,Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza, Università di Roma, Italy.,CNR Institute of Molecular Biology and Pathology, Rome, Italy
| | | | - Beatrice Vallone
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Italy.,Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza, Università di Roma, Italy.,CNR Institute of Molecular Biology and Pathology, Rome, Italy
| | - Giulietta Smulevich
- Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Florence, Italy
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Engilberge S, Wagner T, Carpentier P, Girard E, Shima S. Krypton-derivatization highlights O 2-channeling in a four-electron reducing oxidase. Chem Commun (Camb) 2020; 56:10863-10866. [DOI: 10.1039/d0cc04557h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Kr-derivatization and X-ray structures indicated O2-channel and gating-loop that prevent side-reaction in reduction of O2 to water in F420H2 oxidase.
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Affiliation(s)
| | - Tristan Wagner
- Microbial Metabolism Group
- Max-Planck-Institut für Marine Mikrobiologie
- Celsiusstraße 1
- Bremen
- Germany
| | - Philippe Carpentier
- Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Laboratoire Chimie et Biologie des Métaux (LCBM)
- Université Grenoble Alpes, CNRS, CEA
- Grenoble
- France
- European Synchrotron Radiation Facility (ESRF)
| | - Eric Girard
- Univ. Grenoble Alpes, CEA, CNRS, IBS
- F-38000 Grenoble
- France
| | - Seigo Shima
- Microbial Protein Structure Group
- Max Planck Institute for Terrestrial Microbiology
- Karl-von-Frisch Straße 10
- 35043 Marburg
- Germany
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12
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Winkler DA, Warden AC, Prangé T, Colloc'h N, Thornton AW, Ramirez-Gil JF, Farjot G, Katz I. Massive in Silico Study of Noble Gas Binding to the Structural Proteome. J Chem Inf Model 2019; 59:4844-4854. [PMID: 31613613 DOI: 10.1021/acs.jcim.9b00640] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Noble gases are chemically inert, and it was therefore thought they would have little effect on biology. Paradoxically, it was found that they do exhibit a wide range of biological effects, many of which are target-specific and potentially useful and some of which have been demonstrated in vivo. The underlying mechanisms by which useful pharmacology, such as tissue and neuroprotection, anti-addiction effects, and analgesia, is elicited are relatively unexplored. Experiments to probe the interactions of noble gases with specific proteins are more difficult with gases than those with other chemicals. It is clearly impractical to conduct the large number of gas-protein experiments required to gain a complete picture of noble gas biology. Given the simplicity of atoms as ligands, in silico methods provide an opportunity to gain insight into which noble gas-protein interactions are worthy of further experimental or advanced computational investigation. Our previous validation studies showed that in silico methods can accurately predict experimentally determined noble gas binding sites in X-ray structures of proteins. Here, we summarize the largest reported in silico reverse docking study involving 127 854 protein structures and the five nonradioactive noble gases. We describe how these computational screening methods are implemented, summarize the main types of interactions that occur between noble gases and target proteins, describe how the massive data set that this study generated can be analyzed (freely available at group18.csiro.au), and provide the NDMA receptor as an example of how these data can be used to understand the molecular pharmacology underlying the biology of the noble gases. We encourage chemical biologists to access the data and use them to expand the knowledge base of noble gas pharmacology, and to use this information, together with more efficient delivery systems, to develop "atomic drugs" that can fully exploit their considerable and relatively unexplored potential in medicine.
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Affiliation(s)
- D A Winkler
- CSIRO Future Industries , Bayview Avenue , Clayton , Victoria 3168 , Australia.,Monash Institute of Pharmaceutical Sciences , Monash University , 392 Royal Parade , Parkville 3052 , Australia.,La Trobe Institute for Molecular Science , La Trobe University , Kingsbury Drive , Bundoora 3086 , Australia.,School of Pharmacy , University of Nottingham , Nottingham NG7 2QL , U.K
| | - A C Warden
- CSIRO Land and Water , Clunies Ross Street , Acton , New South Wales 2601 , Australia
| | - T Prangé
- CiTeCoM UMR 8038 CNRS University Paris Descartes , Paris 75006 , France
| | - N Colloc'h
- ISTCT UMR 6030 CNRS Université de Caen-Normandie CEA, CERVOxy Team, Centre Cyceron , Caen 14032 , France
| | - A W Thornton
- CSIRO Future Industries , Bayview Avenue , Clayton , Victoria 3168 , Australia
| | - J-F Ramirez-Gil
- Medical R&D, Healthcare World Business Line, Air Liquide Santé International , Paris Innovation Campus , Jouy-en-Josas 78354 , France
| | - G Farjot
- Medical R&D, Healthcare World Business Line, Air Liquide Santé International , Paris Innovation Campus , Jouy-en-Josas 78354 , France
| | - I Katz
- Medical R&D, Healthcare World Business Line, Air Liquide Santé International , Paris Innovation Campus , Jouy-en-Josas 78354 , France
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Ardiccioni C, Arcovito A, Della Longa S, van der Linden P, Bourgeois D, Weik M, Montemiglio LC, Savino C, Avella G, Exertier C, Carpentier P, Prangé T, Brunori M, Colloc’h N, Vallone B. Ligand pathways in neuroglobin revealed by low-temperature photodissociation and docking experiments. IUCRJ 2019; 6:832-842. [PMID: 31576217 PMCID: PMC6760443 DOI: 10.1107/s2052252519008157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/06/2019] [Indexed: 06/10/2023]
Abstract
A combined biophysical approach was applied to map gas-docking sites within murine neuroglobin (Ngb), revealing snapshots of events that might govern activity and dynamics in this unique hexacoordinate globin, which is most likely to be involved in gas-sensing in the central nervous system and for which a precise mechanism of action remains to be elucidated. The application of UV-visible microspectroscopy in crystallo, solution X-ray absorption near-edge spectroscopy and X-ray diffraction experiments at 15-40 K provided the structural characterization of an Ngb photolytic intermediate by cryo-trapping and allowed direct observation of the relocation of carbon monoxide within the distal heme pocket after photodissociation. Moreover, X-ray diffraction at 100 K under a high pressure of dioxygen, a physiological ligand of Ngb, unravelled the existence of a storage site for O2 in Ngb which coincides with Xe-III, a previously described docking site for xenon or krypton. Notably, no other secondary sites were observed under our experimental conditions.
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Affiliation(s)
- Chiara Ardiccioni
- Department of Life and Environmental Sciences, New York–Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Ancona, Italy
| | - Alessandro Arcovito
- Istituto di Biochimica e Biochimica Clinica, Universitá Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy
- Fondazione Policlinico Universitario Agostino Gemelli–IRCCS, Largo Francesco Vito 1, 00168 Rome, Italy
| | - Stefano Della Longa
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Peter van der Linden
- European Synchrotron Radiation Facility (ESRF), 38043 Grenoble, France
- Partnership for Soft Condensed Matter (PSCM), 38043 Grenoble, France
| | | | - Martin Weik
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Linda Celeste Montemiglio
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Istituto Pasteur–Fondazione Cenci Bolognetti, Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Giovanna Avella
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Chemistry Department, Merck Serono S.p.A., Via Casilina 125, 00176 Rome, Italy
| | - Cécile Exertier
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Philippe Carpentier
- European Synchrotron Radiation Facility (ESRF), 38043 Grenoble, France
- CEA/DRF/BIG/CBM/BioCat LCBM CNRS UMR 5249, Université Grenoble Alpes, 38000 Grenoble, France
| | - Thierry Prangé
- CiTeCoM UMR 8038 CNRS, Université Paris Descartes, Paris, France
| | - Maurizio Brunori
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Nathalie Colloc’h
- ISTCT UMR 6030 CNRS Université de Caen Normandie CEA, CERVOxy Team, Centre Cyceron, Caen, France
| | - Beatrice Vallone
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale Aldo Moro 5, 00185 Rome, Italy
- Istituto Pasteur–Fondazione Cenci Bolognetti, Department of Biochemical Sciences ‘A. Rossi Fanelli’, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
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