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Hoff SE, Zinke M, Izadi-Pruneyre N, Bonomi M. Bonds and bytes: The odyssey of structural biology. Curr Opin Struct Biol 2024; 84:102746. [PMID: 38101027 DOI: 10.1016/j.sbi.2023.102746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/20/2023] [Accepted: 11/24/2023] [Indexed: 12/17/2023]
Abstract
Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of structural biology, no single method comprehensively reveals the behavior of biological systems across various spatiotemporal scales. Instead, we have a versatile toolkit of techniques, each contributing a piece to the overall puzzle. Integrative structural biology combines different techniques to create accurate and precise multi-scale models that expand our understanding of complex biological systems. This review outlines recent advancements in computational and experimental methods in structural biology, with special focus on recent Artificial Intelligence techniques, emphasizes integrative approaches that combine different types of data for precise spatiotemporal modeling, and provides an outlook into future directions of this field.
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Affiliation(s)
- S E Hoff
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Structural Bioinformatics Unit, Paris, France
| | - M Zinke
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Bacterial Transmembrane Systems Unit, Paris, France. https://twitter.com/ZinkeMaximilian
| | - N Izadi-Pruneyre
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Bacterial Transmembrane Systems Unit, Paris, France.
| | - M Bonomi
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Structural Bioinformatics Unit, Paris, France.
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2
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Zinke M, Lejeune M, Mechaly A, Bardiaux B, Boneca IG, Delepelaire P, Izadi-Pruneyre N. Ton motor conformational switch and peptidoglycan role in bacterial nutrient uptake. Nat Commun 2024; 15:331. [PMID: 38184686 PMCID: PMC10771500 DOI: 10.1038/s41467-023-44606-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 12/20/2023] [Indexed: 01/08/2024] Open
Abstract
Active nutrient uptake is fundamental for survival and pathogenicity of Gram-negative bacteria, which operate a multi-protein Ton system to transport essential nutrients like metals and vitamins. This system harnesses the proton motive force at the inner membrane to energize the import through the outer membrane, but the mechanism of energy transfer remains enigmatic. Here, we study the periplasmic domain of ExbD, a crucial component of the proton channel of the Ton system. We show that this domain is a dynamic dimer switching between two conformations representing the proton channel's open and closed states. By in vivo phenotypic assays we demonstrate that this conformational switch is essential for the nutrient uptake by bacteria. The open state of ExbD triggers a disorder to order transition of TonB, enabling TonB to supply energy to the nutrient transporter. We also reveal the anchoring role of the peptidoglycan layer in this mechanism. Herein, we propose a mechanistic model for the Ton system, emphasizing ExbD duality and the pivotal catalytic role of peptidoglycan. Sequence analysis suggests that this mechanism is conserved in other systems energizing gliding motility and membrane integrity. Our study fills important gaps in understanding bacterial motor mechanism and proposes novel antibacterial strategies.
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Affiliation(s)
- Maximilian Zinke
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015, Paris, France
| | - Maylis Lejeune
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015, Paris, France
| | - Ariel Mechaly
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Crystallography Platform, F-75015, Paris, France
| | - Benjamin Bardiaux
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015, Paris, France
| | - Ivo Gomperts Boneca
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, INSERM U1306, Unité de Biologie et génétique de la paroi bactérienne, F-75015, Paris, France
| | - Philippe Delepelaire
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université Paris Cité, UMR7099 CNRS, F-75005, Paris, France
- Institut de Biologie Physico-Chimique, F-75005, Paris, France
| | - Nadia Izadi-Pruneyre
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015, Paris, France.
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3
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Zinke M, Lejeune M, Mechaly A, Bardiaux B, Boneca IG, Delepelaire P, Izadi-Pruneyre N. Ton Motor Conformational Switch and Peptidoglycan Role in Bacterial Nutrient Uptake. bioRxiv 2023:2023.08.11.552980. [PMID: 37609138 PMCID: PMC10441417 DOI: 10.1101/2023.08.11.552980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Active nutrient uptake is fundamental for survival and pathogenicity of Gram-negative bacteria, which operate a multi-protein Ton system to transport essential nutrients like metals and vitamins. This system harnesses the proton motive force at the inner membrane to energize the import through the outer membrane, but the mechanism of energy transfer remains enigmatic. Here, we study the periplasmic domain of ExbD, a crucial component of the proton channel of the Ton system. We show that this domain is a dynamic dimer switching between two conformations representing the proton channel's open and closed states. By in vivo phenotypic assays we demonstrate that this conformational switch is essential for the nutrient uptake by bacteria. The open state of ExbD triggers a disorder to order transition of TonB, enabling TonB to supply energy to the nutrient transporter. We also reveal the anchoring role of the peptidoglycan layer in this mechanism. Herein, we propose a mechanistic model for the Ton system, emphasizing ExbD duality and the pivotal catalytic role of peptidoglycan. Sequence analysis suggests that this mechanism is conserved in other systems energizing gliding motility and membrane integrity. Our study fills important gaps in understanding bacterial motor mechanism and proposes novel antibacterial strategies.
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Affiliation(s)
- Maximilian Zinke
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015 Paris, France
| | - Maylis Lejeune
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015 Paris, France
| | - Ariel Mechaly
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Crystallography Platform, F-75015 Paris, France
| | - Benjamin Bardiaux
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015 Paris, France
| | - Ivo Gomperts Boneca
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, INSERM U1306, Unité de Biologie et génétique de la paroi bactérienne F-75015, Paris, France
| | - Philippe Delepelaire
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université Paris Cité, UMR7099 CNRS, F-75005, Paris, France
- Institut de Biologie Physico-Chimique, F-75005, Paris, France
| | - Nadia Izadi-Pruneyre
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015 Paris, France
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Finkenwirth F, Sippach M, Pecina SN, Gäde M, Ruta J, Ricke A, Bondarenko E, Klare JP, Zinke M, Lange S, Lange A, Steinhoff HJ, Eitinger T. Dynamic interactions of CbiN and CbiM trigger activity of a cobalt energy-coupling-factor transporter. Biochim Biophys Acta Biomembr 2019; 1862:183114. [PMID: 31666178 DOI: 10.1016/j.bbamem.2019.183114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/01/2019] [Accepted: 10/08/2019] [Indexed: 11/26/2022]
Abstract
Energy-coupling factor (ECF) transporters for uptake of vitamins and transition-metal ions into prokaryotic cells share a common architecture consisting of a substrate-specific integral membrane protein (S), a transmembrane coupling protein (T) and two cytoplasmic ATP-binding-cassette-family ATPases. S components rotate within the membrane to expose their binding pockets alternately to the exterior and the cytoplasm. In contrast to vitamin transporters, metal-specific systems rely on additional proteins with essential but poorly understood functions. CbiN, a membrane protein composed of two transmembrane helices tethered by an extracytoplasmic loop of 37 amino-acid residues represents the auxiliary component that temporarily interacts with the CbiMQO2 Co2+ transporter. CbiN was previously shown to induce significant Co2+ transport activity in the absence of CbiQO2 in cells producing the S component CbiM plus CbiN or a Cbi(MN) fusion. Here we analyzed the mode of interaction between the two protein domains. Any deletion in the CbiN loop abolished transport activity. In silico predicted protein-protein contacts between segments of the CbiN loop and loops in CbiM were confirmed by cysteine-scanning mutagenesis and crosslinking. Likewise, an ordered structure of the CbiN loop was observed by electron paramagnetic resonance analysis after site-directed spin labeling. The N-terminal loop of CbiM containing three of four metal ligands was partially immobilized in wild-type Cbi(MN) but completely immobile in inactive variants with CbiN loop deletions. Decreased dynamics of the inactive form was also detected by solid-state nuclear magnetic resonance of isotope-labeled protein in proteoliposomes. In conclusion, CbiM-CbiN loop-loop interactions facilitate metal insertion into the binding pocket.
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Affiliation(s)
- Friedrich Finkenwirth
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Michael Sippach
- Fachbereich Physik, Universität Osnabrück, 49076 Osnabrück, Germany
| | - Sinah N Pecina
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Mario Gäde
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Julia Ruta
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Adrian Ricke
- Fachbereich Physik, Universität Osnabrück, 49076 Osnabrück, Germany
| | - Elena Bondarenko
- Fachbereich Physik, Universität Osnabrück, 49076 Osnabrück, Germany
| | - Johann P Klare
- Fachbereich Physik, Universität Osnabrück, 49076 Osnabrück, Germany
| | - Maximilian Zinke
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Sascha Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | | | - Thomas Eitinger
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany.
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Zinke M, Fricke P, Lange S, Zinn‐Justin S, Lange A. Protein-Protein Interfaces Probed by Methyl Labeling and Proton-Detected Solid-State NMR Spectroscopy. Chemphyschem 2018; 19:2457-2460. [PMID: 29917302 PMCID: PMC6220863 DOI: 10.1002/cphc.201800542] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Indexed: 12/18/2022]
Abstract
Proton detection and fast magic-angle spinning have advanced biological solid-state NMR, allowing for the backbone assignment of complex protein assemblies with high sensitivity and resolution. However, so far no method has been proposed to detect intermolecular interfaces in these assemblies by proton detection. Herein, we introduce a concept based on methyl labeling that allows for the assignment of these moieties and for the study of protein-protein interfaces at atomic resolution.
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Affiliation(s)
- Maximilian Zinke
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Pascal Fricke
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Sascha Lange
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Sophie Zinn‐Justin
- Institute for Integrative Biology of the Cell (I2BC) CEA, CNRSUniversité Paris-Sud Université Paris-SaclayGif-sur-Yvette CedexFrance
| | - Adam Lange
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
- Institut für BiologieHumboldt-Universität zu BerlinBerlinGermany
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6
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Hanff E, Zinke M, Böhmer A, Niebuhr J, Maassen M, Endeward V, Maassen N, Tsikas D. GC-MS determination of nitrous anhydrase activity of bovine and human carbonic anhydrase II and IV. Anal Biochem 2018; 550:132-136. [PMID: 29729279 DOI: 10.1016/j.ab.2018.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/30/2018] [Accepted: 05/01/2018] [Indexed: 12/21/2022]
Abstract
The most widely recognized activity of the large family of the metalloenzyme carbonic anhydrases (CAs) is the diffusion-controlled hydration of CO2 to HCO3- and one proton, and the less rapid dehydration of HCO3- to CO2: CO2 + H2O ⇆ HCO3- + H+. CAs also catalyze the reaction of water with other electrophiles such as aromatic esters, sulfates and phosphates, thus contributing to lending to CAs esterase, sulfatase and phosphatase activity, respectively. Renal CAII and CAIV are involved in the reabsorption of nitrite, the autoxidation product of the signalling molecule nitric oxide (NO): 4 NO + O2 + 2 H2O → 4 ONO- + 4 H+. Bovine and human CAII and CAIV have been reported to exert nitrite reductase and nitrous anhydride activity: 2 NO2- + 2 H+ ⇆ [2 HONO] ⇆ N2O3 + H2O. In the presence of L-cysteine, NO may be formed. In the literature, these issues are controversial, mainly due to analytical shortcomings, i.e., the inability to detect authentic HONO and N2O3. Here, we present a gas chromatography-mass spectrometry (GC-MS) assay to unambiguously detect and quantify the nitrous anhydrase activity of CAs. The assay is based on the hydrolysis of N2O3 in H218O to form ON18O- and 18ON18O-. After pentafluorobenzyl bromide derivatization and electron capture negative-ion chemical ionization of the pentafluorobenzyl nitro derivatives, quantification is performed by selected-ion monitoring of the anions with mass-to-charge (m/z) ratios of 46 (ONO-), m/z 48 (ON18O- and 18ONO-), m/z 50 (18ON18O-) and m/z 47 (O15NO-, internal standard).
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Affiliation(s)
- Erik Hanff
- Institute of Toxicology, Core Unit Proteomics, Hannover Medical School, Hannover, Germany
| | - Maximilian Zinke
- Institute of Toxicology, Core Unit Proteomics, Hannover Medical School, Hannover, Germany
| | - Anke Böhmer
- Institute of Toxicology, Core Unit Proteomics, Hannover Medical School, Hannover, Germany
| | - Janine Niebuhr
- Institute of Toxicology, Core Unit Proteomics, Hannover Medical School, Hannover, Germany
| | - Mirja Maassen
- Institute of Sport Medicine, Hannover Medical School, Hannover, Germany; Institute of Sport Science, Leibniz University Hannover, Hannover, Germany
| | - Volker Endeward
- Institute of Vegetative Physiology, Hannover Medical School, Germany
| | - Norbert Maassen
- Institute of Sport Medicine, Hannover Medical School, Hannover, Germany
| | - Dimitrios Tsikas
- Institute of Toxicology, Core Unit Proteomics, Hannover Medical School, Hannover, Germany.
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Hwang S, Fricke P, Zinke M, Giller K, Wall JS, Riedel D, Becker S, Lange A. Comparison of the 3D structures of mouse and human α-synuclein fibrils by solid-state NMR and STEM. J Struct Biol 2018; 206:43-48. [PMID: 29678776 PMCID: PMC6470123 DOI: 10.1016/j.jsb.2018.04.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/05/2018] [Accepted: 04/15/2018] [Indexed: 01/23/2023]
Abstract
Intra-neuronal aggregation of α-synuclein into fibrils is the molecular basis for α-synucleinopathies, such as Parkinson's disease. The atomic structure of human α-synuclein (hAS) fibrils was recently determined by Tuttle et al. using solid-state NMR (ssNMR). The previous study found that hAS fibrils are composed of a single protofilament. Here, we have investigated the structure of mouse α-synuclein (mAS) fibrils by STEM and isotope-dilution ssNMR experiments. We found that in contrast to hAS, mAS fibrils consist of two or even three protofilaments which are connected by rather weak interactions in between them. Although the number of protofilaments appears to be different between hAS and mAS, we found that they have a remarkably similar secondary structure and protofilament 3D structure as judged by secondary chemical shifts and intra-molecular distance restraints. We conclude that the two mutant sites between hAS and mAS (positions 53 and 87) in the fibril core region are crucial for determining the quaternary structure of α-synuclein fibrils.
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Affiliation(s)
- Songhwan Hwang
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Pascal Fricke
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Maximilian Zinke
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Karin Giller
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Joseph S Wall
- Brookhaven National Laboratory, Upton, 11967 NY, USA
| | - Dietmar Riedel
- Electron Microscopy Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
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Zinke M, Fricke P, Samson C, Hwang S, Wall JS, Lange S, Zinn‐Justin S, Lange A. Bacteriophage Tail-Tube Assembly Studied by Proton-Detected 4D Solid-State NMR. Angew Chem Int Ed Engl 2017; 56:9497-9501. [PMID: 28644511 PMCID: PMC5582604 DOI: 10.1002/anie.201706060] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Indexed: 01/03/2023]
Abstract
Obtaining unambiguous resonance assignments remains a major bottleneck in solid-state NMR studies of protein structure and dynamics. Particularly for supramolecular assemblies with large subunits (>150 residues), the analysis of crowded spectral data presents a challenge, even if three-dimensional (3D) spectra are used. Here, we present a proton-detected 4D solid-state NMR assignment procedure that is tailored for large assemblies. The key to recording 4D spectra with three indirect carbon or nitrogen dimensions with their inherently large chemical shift dispersion lies in the use of sparse non-uniform sampling (as low as 2 %). As a proof of principle, we acquired 4D (H)COCANH, (H)CACONH, and (H)CBCANH spectra of the 20 kDa bacteriophage tail-tube protein gp17.1 in a total time of two and a half weeks. These spectra were sufficient to obtain complete resonance assignments in a straightforward manner without use of previous solution NMR data.
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Affiliation(s)
- Maximilian Zinke
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Pascal Fricke
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Camille Samson
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRSUniversité Paris-Sud, Université Paris-SaclayGif-sur-Yvette CedexFrance
| | - Songhwan Hwang
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | | | - Sascha Lange
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Sophie Zinn‐Justin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRSUniversité Paris-Sud, Université Paris-SaclayGif-sur-Yvette CedexFrance
| | - Adam Lange
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
- Institut für BiologieHumboldt-Universität zu BerlinBerlinGermany
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9
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Zinke M, Fricke P, Samson C, Hwang S, Wall JS, Lange S, Zinn-Justin S, Lange A. Bacteriophage Tail-Tube Assembly Studied by Proton-Detected 4D Solid-State NMR. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Maximilian Zinke
- Department of Molecular Biophysics; Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP); Berlin Germany
| | - Pascal Fricke
- Department of Molecular Biophysics; Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP); Berlin Germany
| | - Camille Samson
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS; Université Paris-Sud, Université Paris-Saclay; Gif-sur-Yvette Cedex France
| | - Songhwan Hwang
- Department of Molecular Biophysics; Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP); Berlin Germany
| | | | - Sascha Lange
- Department of Molecular Biophysics; Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP); Berlin Germany
| | - Sophie Zinn-Justin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS; Université Paris-Sud, Université Paris-Saclay; Gif-sur-Yvette Cedex France
| | - Adam Lange
- Department of Molecular Biophysics; Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP); Berlin Germany
- Institut für Biologie; Humboldt-Universität zu Berlin; Berlin Germany
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10
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Samson C, Celli F, Hendriks K, Zinke M, Essawy N, Herrada I, Arteni AA, Theillet FX, Alpha-Bazin B, Armengaud J, Coirault C, Lange A, Zinn-Justin S. Emerin self-assembly mechanism: role of the LEM domain. FEBS J 2017; 284:338-352. [PMID: 27960036 DOI: 10.1111/febs.13983] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/18/2016] [Accepted: 12/05/2016] [Indexed: 01/01/2023]
Abstract
At the nuclear envelope, the inner nuclear membrane protein emerin contributes to the interface between the nucleoskeleton and the chromatin. Emerin is an essential actor of the nuclear response to a mechanical signal. Genetic defects in emerin cause Emery-Dreifuss muscular dystrophy. It was proposed that emerin oligomerization regulates nucleoskeleton binding, and impaired oligomerization contributes to the loss of function of emerin disease-causing mutants. We here report the first structural characterization of emerin oligomers. We identified an N-terminal emerin region from amino acid 1 to amino acid 132 that is necessary and sufficient for formation of long curvilinear filaments. In emerin monomer, this region contains a globular LEM domain and a fragment that is intrinsically disordered. Solid-state nuclear magnetic resonance analysis identifies the LEM β-fragment as part of the oligomeric structural core. However, the LEM domain alone does not self-assemble into filaments. Additional residues forming a β-structure are observed within the filaments that could correspond to the unstructured region in emerin monomer. We show that the delK37 mutation causing muscular dystrophy triggers LEM domain unfolding and increases emerin self-assembly rate. Similarly, inserting a disulfide bridge that stabilizes the LEM folded state impairs emerin N-terminal region self-assembly, whereas reducing this disulfide bridge triggers self-assembly. We conclude that the LEM domain, responsible for binding to the chromatin protein BAF, undergoes a conformational change during self-assembly of emerin N-terminal region. The consequences of these structural rearrangement and self-assembly events on emerin binding properties are discussed.
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Affiliation(s)
- Camille Samson
- Laboratory of Structural Biology and Radiobiology, Institute for Integrative Biology of the Cell (CEA, CNRS, University Paris South), University Paris-Saclay, Gif-sur-Yvette, France
| | - Florian Celli
- Laboratory of Structural Biology and Radiobiology, Institute for Integrative Biology of the Cell (CEA, CNRS, University Paris South), University Paris-Saclay, Gif-sur-Yvette, France
| | - Kitty Hendriks
- Department of Molecular Biophysics, Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
| | - Maximilian Zinke
- Department of Molecular Biophysics, Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
| | - Nada Essawy
- Center for Research in Myology (INSERM, CNRS), Université Pierre et Marie Curie Paris 06, Sorbonne Universités, France
| | - Isaline Herrada
- Laboratory of Structural Biology and Radiobiology, Institute for Integrative Biology of the Cell (CEA, CNRS, University Paris South), University Paris-Saclay, Gif-sur-Yvette, France
| | - Ana-Andreea Arteni
- Department of Structural Virology, Institute for Integrative Biology of the Cell (CEA, CNRS, University Paris South), University Paris-Saclay, Gif-sur-Yvette, France
| | - François-Xavier Theillet
- Laboratory of Structural Biology and Radiobiology, Institute for Integrative Biology of the Cell (CEA, CNRS, University Paris South), University Paris-Saclay, Gif-sur-Yvette, France
| | - Béatrice Alpha-Bazin
- Laboratory 'Innovative technologies for Detection and Diagnostics', Institute of Biology and Technology Saclay, CEA, Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Laboratory 'Innovative technologies for Detection and Diagnostics', Institute of Biology and Technology Saclay, CEA, Bagnols-sur-Cèze, France
| | - Catherine Coirault
- Center for Research in Myology (INSERM, CNRS), Université Pierre et Marie Curie Paris 06, Sorbonne Universités, France
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany.,Institut für Biologie, Humboldt-Universität zu Berlin, Germany
| | - Sophie Zinn-Justin
- Laboratory of Structural Biology and Radiobiology, Institute for Integrative Biology of the Cell (CEA, CNRS, University Paris South), University Paris-Saclay, Gif-sur-Yvette, France
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11
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Hanff E, Böhmer A, Zinke M, Gambaryan S, Schwarz A, Supuran CT, Tsikas D. Carbonic anhydrases are producers of S-nitrosothiols from inorganic nitrite and modulators of soluble guanylyl cyclase in human platelets. Amino Acids 2016; 48:1695-706. [PMID: 27129464 DOI: 10.1007/s00726-016-2234-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 04/08/2016] [Indexed: 12/29/2022]
Abstract
Nitric oxide (NO), S-nitrosoglutathione (GSNO) and S-nitrosocysteine are highly potent signaling molecules, acting both by cGMP-dependent and cGMP-independent mechanisms. The NO metabolite nitrite (NO2 (-)) is a major NO reservoir. Hemoglobin, xanthine oxidoreductase and carbonic anhydrase (CA) have been reported to reduce/convert nitrite to NO. We evaluated the role and the physiological importance of CA for an extra-platelet CA/nitrite/NO/cGMP pathway in human platelets. Authentic NO was analyzed by an NO-sensitive electrode. GSNO and GS(15)NO were measured by liquid chromatography-tandem mass spectrometry (LC-MS/MS). cGMP was determined by LC-MS/MS or RIA. In reduced glutathione (GSH) containing aqueous buffer (pH 7.4), human and bovine erythrocytic CAII-mediated formation of GSNO from nitrite and GS(15)NO from (15)N-nitrite. In the presence of L-cysteine and GSH, this reaction was accompanied by NO release. Incubation of nitrite with bovine erythrocytic CAII and recombinant soluble guanylyl cyclase resulted in cGMP formation. Upon incubation of nitrite with bovine erythrocytic CAII and washed human platelets, cGMP and P-VASP(S239) were formed in the platelets. This study provides the first evidence that extra-platelet nitrite and erythrocytic CAII may modulate platelet function in a cGMP-dependent manner. The new nitrite-dependent CA activity may be a general principle and explain the cardioprotective effects of inorganic nitrite in the vasculature. We propose that nitrous acid (ONOH) is the primary CA-catalyzed reaction product of nitrite.
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Affiliation(s)
- Erik Hanff
- Centre of Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Anke Böhmer
- Centre of Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Maximilian Zinke
- Centre of Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Stepan Gambaryan
- Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg, Russia.,Department of Cytology and Histology, S. Petersburg State University, Universitetskaya Nab 7/9, 199034, S. Petersburg, Russia
| | - Alexandra Schwarz
- Centre of Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Claudiu T Supuran
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Dimitrios Tsikas
- Centre of Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
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12
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Geiger MA, Orwick-Rydmark M, Märker K, Franks WT, Akhmetzyanov D, Stöppler D, Zinke M, Specker E, Nazaré M, Diehl A, van Rossum BJ, Aussenac F, Prisner T, Akbey Ü, Oschkinat H. Temperature dependence of cross-effect dynamic nuclear polarization in rotating solids: advantages of elevated temperatures. Phys Chem Chem Phys 2016; 18:30696-30704. [DOI: 10.1039/c6cp06154k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNP on proteins at 200 K.
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13
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Zinke M, Hanff E, Böhmer A, Supuran CT, Tsikas D. Discovery and microassay of a nitrite-dependent carbonic anhydrase activity by stable-isotope dilution gas chromatography-mass spectrometry. Amino Acids 2015; 48:245-55. [PMID: 26334347 DOI: 10.1007/s00726-015-2081-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 08/20/2015] [Indexed: 12/21/2022]
Abstract
The intrinsic activity of carbonic anhydrase (CA) is the hydration of CO2 to carbonic acid and its dehydration to CO2. CA may also function as esterase and phosphatase. Recently, we demonstrated that renal CA is mainly responsible for the reabsorption of nitrite (NO2(-)) which is the most abundant reservoir of the biologically highly potent nitric oxide (NO). By means of a stable-isotope dilution GC-MS method, we discovered a novel CA activity which strictly depends upon nitrite. We found that bovine erythrocytic CAII (beCAII) catalyses the incorporation of (18)O from H2 (18)O into nitrite at pH 7.4. After derivatization with pentafluorobenzyl bromide, gas chromatographic separation and mass spectrometric analysis, we detected ions at m/z 48 for singly (18)O-labelled nitrite ((16)O=N-(18)O(-)/(18)O=N-(16)O(-)) and at m/z 50 for doubly (18)O-labelled nitrite ((18)O=N-(18)O(-)) in addition to m/z 46 for unlabelled nitrite. Using (15)N-labelled nitrite ((15)NO2 (-), m/z 47) as an internal standard and selected-ion monitoring of m/z 46, m/z 48, m/z 50 and m/z 47, we developed a GC-MS microassay for the quantitative determination of the nitrite-dependent beCAII activity. The CA inhibitors acetazolamide and FC5 207A did not alter beCAII-catalysed formation of singly and doubly (18)O-labelled nitrite. Cysteine and the experimental CA inhibitor DIDS (a diisothiocyanate) increased several fold the beCAII-catalysed formation of the (18)O-labelled nitrite species. Cysteine, acetazolamide, FC5 207A, and DIDS by themselves had no effect on the incorporation of (18)O from H2 (18)O into nitrite. We conclude that erythrocytic CA possesses a nitrite-dependent activity which can only be detected when nitrite is used as the substrate and the reaction is performed in buffers of neutral pH values prepared in H2 (18)O. This novel CA activity, i.e., the nitrous acid anhydrase activity, represents a bioactivation of nitrite and may have both beneficial (via S-nitrosylation and subsequent NO release) and possibly adverse (via C- and N-nitrosylation) effects in living organisms.
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Affiliation(s)
- Maximilian Zinke
- Bioanalytical Research Laboratory for NO, Oxidative Stress and Eicosanoids (BIOFORNOX20), Centre of Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Erik Hanff
- Bioanalytical Research Laboratory for NO, Oxidative Stress and Eicosanoids (BIOFORNOX20), Centre of Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Anke Böhmer
- Bioanalytical Research Laboratory for NO, Oxidative Stress and Eicosanoids (BIOFORNOX20), Centre of Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Claudiu T Supuran
- Dipartmento di Chimica Ugo Schiff, Università degli Studi di Firenze, Sesto Fiorentino, Florence, Italy
| | - Dimitrios Tsikas
- Bioanalytical Research Laboratory for NO, Oxidative Stress and Eicosanoids (BIOFORNOX20), Centre of Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany.
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14
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Abstract
A complete classification of types of the protein secondary structure is developed on the basis of computer analysis of the crystallographic structural data deposited in the protein Data Bank. The majority of amino acid residues fall into five conformation types. A conclusion is drawn that the number of sequence variants of torsion angles phi, psi in globular proteins is limited and is essentially less than the number of possible amino acid sequences for this chain length. Along with alpha-helix and beta-structure, the distribution analysis assigning every maximum of distribution of amino acid conformations on Ramachandran map to a certain type of the secondary structure exposed a third type of the secondary structure that was previously neglected. This type of the structure is extended left-handed helical conformation, designated as mobile (M-) conformation. A full set of M-conformation fragments that seems to play a major role in protein globule dynamics has been obtained, a small radius of correlation for the polypeptide chain in M-conformation is demonstrated. It explains a prevalence of short segments of mobile conformation revealed in globular proteins. For secondary structure types, the frequency of occurrence of amino acid residues has been computed.
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Affiliation(s)
- A A Adzhubei
- Institute of Molecular Biology, USSR Academy of Sciences, Moscow
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15
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Adzhubei AA, Eisenmenger F, Tumanyan VG, Zinke M, Brodzinski S, Esipova NG. Third type of secondary structure: noncooperative mobile conformation. Protein Data Bank analysis. Biochem Biophys Res Commun 1987; 146:934-8. [PMID: 3619942 DOI: 10.1016/0006-291x(87)90736-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Analysis of 68 proteins from Protein Data Bank disclosed a new widely spread type of the secondary structure that is designated as mobile (M-) conformation. Helical parameters of M-conformation are close to the poly-L-proline II type helix. Its occurrence in globular proteins approximates that of the beta-sheet. The angles corresponding to the position of the M-conformation maximum in distribution of amino acid residues on a conformational map are phi: -65 degrees, psi: 140 degrees. Unique features and high occurrence in proteins make it possible to distinguish the M-conformation as an independent third type of the secondary structure in globular proteins, that should be included in the present classification.
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16
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Adzhubeĭ AA, Eisenmenger F, Tumanian VG, Zinke M, Brodsinski Z. [A new type of secondary structure: mobile conformation of polypeptide chain. Data bank for protein structures]. Biofizika 1987; 32:159-61. [PMID: 3814636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
As a result of statistical analysis of Protein Data Bank a new type of secondary structure was found in globular proteins. It is mobile (M) conformation, characterised by noncooperative hydration and the increased dynamical properties of the chain. Percentage distribution of amino acid residues between the main secondary structure types is 42.7% for alpha-helix, 19.6% for beta-structure and 19.1% for M-conformation. The most frequently occurring amino acids for M-conformation are proline, cysteine and serine. Fragments of mobile conformation seem to play a major part in local and domain dynamics of protein globule.
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17
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Schulmeister T, Tschapek A, Zinke M. Visualization of the entire surface of a protein by cartographic projection. Comput Appl Biosci 1986; 2:265-8. [PMID: 3450370 DOI: 10.1093/bioinformatics/2.4.265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A minicomputer based system for the determination and schematic representation of protein surfaces is described. The algorithms are based on the atomic coordinates of globular protein molecules of the Brookhaven Protein Data Bank. Using a cartographic projection a normalized graphic representation is obtained of the amino acid residues located on the surface of the considered protein. The programs are written in FORTRAN IV (surface determination) and BASIC (graphic representation).
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Affiliation(s)
- T Schulmeister
- Department of Biomathematics, Central Institute of Molecular Biology, Academy of Sciences, Berlin-Buch, GDR
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18
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Zinke M, Zinke R. [The value of rational documentation of findings in the early diagnosis of severe diseases]. Z Arztl Fortbild (Jena) 1978; 72:891-5. [PMID: 706457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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