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David G, Fogeron ML, Schledorn M, Montserret R, Haselmann U, Penzel S, Badillo A, Lecoq L, André P, Nassal M, Bartenschlager R, Meier BH, Böckmann A. Structural Studies of Self-Assembled Subviral Particles: Combining Cell-Free Expression with 110 kHz MAS NMR Spectroscopy. Angew Chem Int Ed Engl 2018; 57:4787-4791. [PMID: 29457857 DOI: 10.1002/anie.201712091] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/25/2018] [Indexed: 01/08/2023]
Abstract
Viral membrane proteins are prime targets in combatting infection. Still, the determination of their structure remains a challenge, both with respect to sample preparation and the need for structural methods allowing for analysis in a native-like lipid environment. Cell-free protein synthesis and solid-state NMR spectroscopy are promising approaches in this context, the former with respect to its great potential in the native expression of complex proteins, and the latter for the analysis of membrane proteins in lipids. Herein, we show that milligram amounts of the small envelope protein of the duck hepatitis B virus (DHBV) can be produced by cell-free expression, and that the protein self-assembles into subviral particles. Proton-detected 2D NMR spectra recorded at a magic-angle-spinning frequency of 110 kHz on <500 μg protein show a number of isolated peaks with line widths comparable to those of model membrane proteins, paving the way for structural studies of this protein that is homologous to a potential drug target in HBV infection.
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Affiliation(s)
- Guillaume David
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Marie-Laure Fogeron
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
| | | | - Roland Montserret
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Uta Haselmann
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany.,Division of Virus-Associated Carcinogenesis Germany, Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120, Heidelberg, Germany
| | - Susanne Penzel
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Aurélie Badillo
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France.,RD-Biotech, Recombinant Protein Unit, 3 rue Henri Baigue, 25000, Besançon, France
| | - Lauriane Lecoq
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Patrice André
- Centre International de Recherche en Infectiologie, Institut National de la Santé et de la Recherche Médicale Unité 1111, Centre National de la Recherche Scientifique Unités Mixte de Recherche, 5308, Lyon, France.,Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France.,Université de Lyon, Laboratoire de Virologie, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - Michael Nassal
- University Hospital Freiburg, Internal Medicine II/Molecular Biology, Hugstetter Str. 55, 79106, Freiburg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany.,Division of Virus-Associated Carcinogenesis Germany, Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120, Heidelberg, Germany
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
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David G, Fogeron M, Schledorn M, Montserret R, Haselmann U, Penzel S, Badillo A, Lecoq L, André P, Nassal M, Bartenschlager R, Meier BH, Böckmann A. Strukturelle Untersuchung subviraler Partikel durch die Kombination von zellfreier Proteinherstellung mit 110 kHz MAS‐NMR‐Spektroskopie. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Guillaume David
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS Université de Lyon 7 passage du Vercors 69367 Lyon Frankreich
| | - Marie‐Laure Fogeron
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS Université de Lyon 7 passage du Vercors 69367 Lyon Frankreich
| | | | - Roland Montserret
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS Université de Lyon 7 passage du Vercors 69367 Lyon Frankreich
| | - Uta Haselmann
- Department für Infektiologie Molekulare Virologie Universitätsklinikum Heidelberg Im Neuenheimer Feld 345 69120 Heidelberg Deutschland
- Abteilung Virus-assoziierte Karzinogenese Deutsches Krebsforschungszentrum (DKFZ) Im Neuenheimer Feld 242 69120 Heidelberg Deutschland
| | - Susanne Penzel
- Lab. für Physikalische Chemie ETH Zürich 8093 Zürich Schweiz
| | - Aurélie Badillo
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS Université de Lyon 7 passage du Vercors 69367 Lyon Frankreich
- RD-Biotech Recombinant Protein Unit 3 rue Henri Baigue 25000 Besançon Frankreich
| | - Lauriane Lecoq
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS Université de Lyon 7 passage du Vercors 69367 Lyon Frankreich
| | - Patrice André
- Centre International de Recherche en Infectiologie Institut National de la Santé et de la Recherche Médicale Unité 1111 Centre National de la Recherche Scientifique Unités Mixte de Recherche 5308 Lyon Frankreich
- Ecole Normale Supérieure de Lyon, Lyon, France Université Claude Bernard Lyon 1 Villeurbanne Frankreich
- Université de Lyon, Lyon, France Laboratoire de Virologie Hôpital de la Croix-Rousse Hospices Civils de Lyon Lyon Frankreich
| | - Michael Nassal
- Universitätsklinikum Freiburg Klinik für Innere Medizin II/ Molekulare Biologie Hugstetter Straße 55 79106 Freiburg Deutschland
| | - Ralf Bartenschlager
- Department für Infektiologie Molekulare Virologie Universitätsklinikum Heidelberg Im Neuenheimer Feld 345 69120 Heidelberg Deutschland
- Abteilung Virus-assoziierte Karzinogenese Deutsches Krebsforschungszentrum (DKFZ) Im Neuenheimer Feld 242 69120 Heidelberg Deutschland
| | - Beat H. Meier
- Lab. für Physikalische Chemie ETH Zürich 8093 Zürich Schweiz
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS Université de Lyon 7 passage du Vercors 69367 Lyon Frankreich
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Lamley JM, Öster C, Stevens RA, Lewandowski JR. Intermolecular Interactions and Protein Dynamics by Solid-State NMR Spectroscopy. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 127:15594-15598. [PMID: 27478273 PMCID: PMC4954056 DOI: 10.1002/ange.201509168] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Indexed: 11/21/2022]
Abstract
Understanding the dynamics of interacting proteins is a crucial step toward describing many biophysical processes. Here we investigate the backbone dynamics for protein GB1 in two different assemblies: crystalline GB1 and the precipitated GB1-antibody complex with a molecular weight of more than 300 kDa. We perform these measurements on samples containing as little as eight nanomoles of GB1. From measurements of site-specific 15N relaxation rates including relaxation dispersion we obtain snapshots of dynamics spanning nine orders of magnitude in terms of the time scale. A comparison of measurements for GB1 in either environment reveals that while many of the dynamic features of the protein are conserved between them (in particular for the fast picosecond-nanosecond motions), much greater differences occur for slow motions with motions in the >500 ns range being more prevalent in the complex. The data suggest that GB1 can potentially undergo a small-amplitude overall anisotropic motion sampling the interaction interface in the complex.
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Affiliation(s)
- Jonathan M. Lamley
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL (UK)
| | - Carl Öster
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL (UK)
| | - Rebecca A. Stevens
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL (UK)
| | - Józef R. Lewandowski
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL (UK)
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Lamley JM, Öster C, Stevens RA, Lewandowski JR. Intermolecular Interactions and Protein Dynamics by Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2015; 54:15374-8. [PMID: 26537742 PMCID: PMC4736466 DOI: 10.1002/anie.201509168] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Indexed: 11/23/2022]
Abstract
Understanding the dynamics of interacting proteins is a crucial step toward describing many biophysical processes. Here we investigate the backbone dynamics for protein GB1 in two different assemblies: crystalline GB1 and the precipitated GB1-antibody complex with a molecular weight of more than 300 kDa. We perform these measurements on samples containing as little as eight nanomoles of GB1. From measurements of site-specific (15) N relaxation rates including relaxation dispersion we obtain snapshots of dynamics spanning nine orders of magnitude in terms of the time scale. A comparison of measurements for GB1 in either environment reveals that while many of the dynamic features of the protein are conserved between them (in particular for the fast picosecond-nanosecond motions), much greater differences occur for slow motions with motions in the >500 ns range being more prevalent in the complex. The data suggest that GB1 can potentially undergo a small-amplitude overall anisotropic motion sampling the interaction interface in the complex.
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Affiliation(s)
- Jonathan M Lamley
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL (UK)
| | - Carl Öster
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL (UK)
| | - Rebecca A Stevens
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL (UK)
| | - Józef R Lewandowski
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL (UK).
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Ravera E, Fragai M, Parigi G, Luchinat C. Differences in Dynamics between Crosslinked and Non-Crosslinked Hyaluronates Measured by using Fast Field-Cycling Relaxometry. Chemphyschem 2015; 16:2803-2809. [PMID: 26263906 DOI: 10.1002/cphc.201500446] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Indexed: 11/11/2022]
Abstract
The dynamic properties of water molecules in gels containing linear and crosslinked hyaluronic acid polymers are investigated by using an integrated approach that includes relaxometry, solid-state NMR spectroscopy, and scanning electron microscopy. A model-free analysis of field-dependent nuclear relaxation is applied to obtain information on mobility and the population of different pools of water molecules in the gels. Differences between linear and crosslinked hyaluronic acid polymers are observed, indicating that crosslinking increases both the fraction and the correlation time of water molecules with slow dynamics.
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Affiliation(s)
- Enrico Ravera
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Italy)
| | - Marco Fragai
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Italy)
| | - Giacomo Parigi
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Italy)
| | - Claudio Luchinat
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Italy)
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Beld J, Cang H, Burkart MD. Visualizing the chain-flipping mechanism in fatty-acid biosynthesis. Angew Chem Int Ed Engl 2014; 53:14456-61. [PMID: 25354391 PMCID: PMC4425425 DOI: 10.1002/anie.201408576] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Indexed: 11/08/2022]
Abstract
The acyl carrier protein (ACP) from fatty acid synthases sequesters elongating products within its hydrophobic core, but this dynamic mechanism remains poorly understood. We exploited solvatochromic pantetheine probes attached to ACP that fluoresce when sequestered. The addition of a catalytic partner lures the cargo out of the ACP and into the active site of the enzyme, thus enhancing fluorescence to reveal the elusive chain-flipping mechanism. This activity was confirmed by the use of a dual solvatochromic cross-linking probe and solution-phase NMR spectroscopy. The chain-flipping mechanism was visualized by single-molecule fluorescence techniques, thus demonstrating specificity between the Escherichia coli ACP and its ketoacyl synthase catalytic partner KASII.
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Affiliation(s)
- Joris Beld
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Hu Cang
- Waitt Advanced Biophotonics Center, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
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