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Atomic structural details of a protein grafted onto gold nanoparticles. Sci Rep 2017; 7:17934. [PMID: 29263419 PMCID: PMC5738368 DOI: 10.1038/s41598-017-18109-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/05/2017] [Indexed: 12/18/2022] Open
Abstract
The development of a methodology for the structural characterization at atomic detail of proteins conjugated to nanoparticles would be a breakthrough in nanotechnology. Solution and solid-state NMR spectroscopies are currently used to investigate molecules and peptides grafted onto nanoparticles, but the strategies used so far fall short in the application to proteins, which represent a thrilling development in theranostics. We here demonstrate the feasibility of highly-resolved multidimensional heteronuclear spectra of a large protein assembly conjugated to PEGylated gold nanoparticles. The spectra have been obtained by direct proton detection under fast MAS and allow for both a fast fingerprinting for the assessment of the preservation of the native fold and for resonance assignment. We thus demonstrate that the structural characterization and the application of the structure-based methodologies to proteins bound to gold nanoparticles is feasible and potentially extensible to other hybrid protein-nanomaterials.
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52
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Baker LA, Sinnige T, Schellenberger P, de Keyzer J, Siebert CA, Driessen AJM, Baldus M, Grünewald K. Combined 1H-Detected Solid-State NMR Spectroscopy and Electron Cryotomography to Study Membrane Proteins across Resolutions in Native Environments. Structure 2017; 26:161-170.e3. [PMID: 29249608 PMCID: PMC5758107 DOI: 10.1016/j.str.2017.11.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 10/02/2017] [Accepted: 11/15/2017] [Indexed: 11/15/2022]
Abstract
Membrane proteins remain challenging targets for structural biology, despite much effort, as their native environment is heterogeneous and complex. Most methods rely on detergents to extract membrane proteins from their native environment, but this removal can significantly alter the structure and function of these proteins. Here, we overcome these challenges with a hybrid method to study membrane proteins in their native membranes, combining high-resolution solid-state nuclear magnetic resonance spectroscopy and electron cryotomography using the same sample. Our method allows the structure and function of membrane proteins to be studied in their native environments, across different spatial and temporal resolutions, and the combination is more powerful than each technique individually. We use the method to demonstrate that the bacterial membrane protein YidC adopts a different conformation in native membranes and that substrate binding to YidC in these native membranes differs from purified and reconstituted systems. CryoET and ssNMR give complementary information about proteins in native membranes One sample can be prepared for both methods without the use of detergents Hybrid method shows differences between purified and native preparations of YidC Sample preparation reduces costs and time and suggests new strategy for assignment
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Affiliation(s)
- Lindsay A Baker
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands; Oxford Particle Imaging Centre, Division of Structural Biology, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
| | - Tessa Sinnige
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Pascale Schellenberger
- Oxford Particle Imaging Centre, Division of Structural Biology, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jeanine de Keyzer
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands; The Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 11, 9747 AG Groningen, the Netherlands
| | - C Alistair Siebert
- Oxford Particle Imaging Centre, Division of Structural Biology, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands; The Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 11, 9747 AG Groningen, the Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands.
| | - Kay Grünewald
- Oxford Particle Imaging Centre, Division of Structural Biology, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
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53
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Fraga H, Arnaud CA, Gauto DF, Audin M, Kurauskas V, Macek P, Krichel C, Guan JY, Boisbouvier J, Sprangers R, Breyton C, Schanda P. Solid-State NMR H-N-(C)-H and H-N-C-C 3D/4D Correlation Experiments for Resonance Assignment of Large Proteins. Chemphyschem 2017; 18:2697-2703. [PMID: 28792111 PMCID: PMC5632560 DOI: 10.1002/cphc.201700572] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/08/2017] [Indexed: 12/16/2022]
Abstract
Solid-state NMR spectroscopy can provide insight into protein structure and dynamics at the atomic level without inherent protein size limitations. However, a major hurdle to studying large proteins by solid-state NMR spectroscopy is related to spectral complexity and resonance overlap, which increase with molecular weight and severely hamper the assignment process. Here the use of two sets of experiments is shown to expand the tool kit of 1 H-detected assignment approaches, which correlate a given amide pair either to the two adjacent CO-CA pairs (4D hCOCANH/hCOCAcoNH), or to the amide 1 H of the neighboring residue (3D HcocaNH/HcacoNH, which can be extended to 5D). The experiments are based on efficient coherence transfers between backbone atoms using INEPT transfers between carbons and cross-polarization for heteronuclear transfers. The utility of these experiments is exemplified with application to assemblies of deuterated, fully amide-protonated proteins from approximately 20 to 60 kDa monomer, at magic-angle spinning (MAS) frequencies from approximately 40 to 55 kHz. These experiments will also be applicable to protonated proteins at higher MAS frequencies. The resonance assignment of a domain within the 50.4 kDa bacteriophage T5 tube protein pb6 is reported, and this is compared to NMR assignments of the isolated domain in solution. This comparison reveals contacts of this domain to the core of the polymeric tail tube assembly.
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Affiliation(s)
- Hugo Fraga
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, F-38044 Grenoble (France)
- Departamento de Bioquimica, Faculdade de Medicina da Universidade do Porto, Portugal
| | - Charles-Adrien Arnaud
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, F-38044 Grenoble (France)
| | - Diego F. Gauto
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, F-38044 Grenoble (France)
| | - Maxime Audin
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen (Germany)
| | - Vilius Kurauskas
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, F-38044 Grenoble (France)
| | - Pavel Macek
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, F-38044 Grenoble (France)
| | - Carsten Krichel
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, F-38044 Grenoble (France)
| | - Jia-Ying Guan
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, F-38044 Grenoble (France)
| | - Jerome Boisbouvier
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, F-38044 Grenoble (France)
| | - Remco Sprangers
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen (Germany)
- Department of Biophysics I, University of Regensburg, 93053, Regensburg (Germany)
| | - Cécile Breyton
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, F-38044 Grenoble (France)
| | - Paul Schanda
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, F-38044 Grenoble (France)
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54
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Asami S, Reif B. Comparative Study of REDOR and CPPI Derived Order Parameters by 1H-Detected MAS NMR and MD Simulations. J Phys Chem B 2017; 121:8719-8730. [DOI: 10.1021/acs.jpcb.7b06812] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Sam Asami
- Munich
Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747 Garching, Germany
| | - Bernd Reif
- Munich
Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747 Garching, Germany
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter
Landstr. 1, 85764 Neuherberg, Germany
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55
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Damron JT, Kersten KM, Pandey MK, Mroue KH, Yarava JR, Nishiyama Y, Matzger AJ, Ramamoorthy A. Electrostatic Constraints Assessed by 1H MAS NMR Illuminate Differences in Crystalline Polymorphs. J Phys Chem Lett 2017; 8:4253-4257. [PMID: 28825828 PMCID: PMC6295661 DOI: 10.1021/acs.jpclett.7b01650] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Atomically resolved crystal structures not only suffer from the inherent uncertainty in accurately locating H atoms but also are incapable of fully revealing the underlying forces enabling the formation of final structures. Therefore, the development and application of novel techniques to illuminate intermolecular forces in crystalline solids are highly relevant to understand the role of hydrogen atoms in structure adoption. Novel developments in 1H NMR MAS methodology can now achieve robust measurements of 1H chemical shift anisotropy (CSA) tensors which are highly sensitive to electrostatics. Herein, we use 1H CSA tensors, measured by MAS experiments and characterized using DFT calculations, to reveal the structure-driving factors between the two polymorphic forms of acetaminophen (aka Tylenol or paracetamol) including differences in hydrogen bonding and the role of aromatic interactions. We demonstrate how the 1H CSAs can provide additional insights into the static picture provided by diffraction to elucidate rigid molecules.
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Affiliation(s)
- Joshua T. Damron
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Kortney M. Kersten
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | - Manoj Kumar Pandey
- RIKEN CLST-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Kamal H. Mroue
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
- Biophysics Program, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | | | - Yusuke Nishiyama
- RIKEN CLST-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan
- JEOL RESONANCE, Inc., Musashino, Akishima, Tokyo 186-8558, Japan
| | - Adam J. Matzger
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
- Macromolecular Science and Engineering, University of Michigan, 2300 Hayward Avenue, Ann Arbor, Michigan 48109, United States
- Corresponding Authors: .
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
- Biophysics Program, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
- Corresponding Authors: .
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56
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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] [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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57
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Applications of solid-state NMR to membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1577-1586. [PMID: 28709996 DOI: 10.1016/j.bbapap.2017.07.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 06/30/2017] [Accepted: 07/07/2017] [Indexed: 11/23/2022]
Abstract
Membrane proteins mediate flow of molecules, signals, and energy between cells and intracellular compartments. Understanding membrane protein function requires a detailed understanding of the structural and dynamic properties involved. Lipid bilayers provide a native-like environment for structure-function investigations of membrane proteins. In this review we give a general discourse on the recent progress in the field of solid-state NMR of membrane proteins. Solid-state NMR is a variation of NMR spectroscopy that is applicable to molecular systems with restricted mobility, such as high molecular weight proteins and protein complexes, supramolecular assemblies, or membrane proteins in a phospholipid environment. We highlight recent advances in applications of solid-state NMR to membrane proteins, specifically focusing on the recent developments in the field of Dynamic Nuclear Polarization, proton detection, and solid-state NMR applications in situ (in cell membranes). This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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58
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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] [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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59
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Zhang R, Duong NT, Nishiyama Y, Ramamoorthy A. 3D Double-Quantum/Double-Quantum Exchange Spectroscopy of Protons under 100 kHz Magic Angle Spinning. J Phys Chem B 2017; 121:5944-5952. [DOI: 10.1021/acs.jpcb.7b03480] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Rongchun Zhang
- Biophysics
and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Nghia Tuan Duong
- RIKEN
CLST-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Yusuke Nishiyama
- RIKEN
CLST-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan
- JEOL Resonance Inc., Musashino, Akishima, Tokyo 196-8558, Japan
| | - Ayyalusamy Ramamoorthy
- Biophysics
and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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