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Narasimhan S, Scherpe S, Lucini Paioni A, van der Zwan J, Folkers GE, Ovaa H, Baldus M. DNP-Supported Solid-State NMR Spectroscopy of Proteins Inside Mammalian Cells. Angew Chem Int Ed Engl 2019; 58:12969-12973. [PMID: 31233270 PMCID: PMC6772113 DOI: 10.1002/anie.201903246] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Indexed: 11/25/2022]
Abstract
Elucidating at atomic level how proteins interact and are chemically modified in cells represents a leading frontier in structural biology. We have developed a tailored solid‐state NMR spectroscopic approach that allows studying protein structure inside human cells at atomic level under high‐sensitivity dynamic nuclear polarization (DNP) conditions. We demonstrate the method using ubiquitin (Ub), which is critically involved in cellular functioning. Our results pave the way for structural studies of larger proteins or protein complexes inside human cells, which have remained elusive to in‐cell solution‐state NMR spectroscopy due to molecular size limitations.
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Affiliation(s)
- Siddarth Narasimhan
- NMR Spectroscopy group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Stephan Scherpe
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Alessandra Lucini Paioni
- NMR Spectroscopy group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Johan van der Zwan
- NMR Spectroscopy group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Gert E Folkers
- NMR Spectroscopy group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Marc Baldus
- NMR Spectroscopy group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
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Narasimhan S, Scherpe S, Lucini Paioni A, van der Zwan J, Folkers GE, Ovaa H, Baldus M. DNP‐Supported Solid‐State NMR Spectroscopy of Proteins Inside Mammalian Cells. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903246] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Siddarth Narasimhan
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Stephan Scherpe
- Oncode Institute and Department of Cell and Chemical Biology Leiden University Medical Center (LUMC) Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Alessandra Lucini Paioni
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Johan van der Zwan
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Gert E. Folkers
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical Biology Leiden University Medical Center (LUMC) Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Marc Baldus
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
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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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Thomas B, Rombouts J, Oostergetel GT, Gupta KBSS, Buda F, Lammertsma K, Orru R, de Groot HJM. A Hybrid Solid-State NMR and Electron Microscopy Structure-Determination Protocol for Engineering Advanced para-Crystalline Optical Materials. Chemistry 2017; 23:3280-3284. [PMID: 28117921 PMCID: PMC5347911 DOI: 10.1002/chem.201700324] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Indexed: 01/04/2023]
Abstract
Hybrid magic‐angle spinning (MAS) NMR spectroscopy and TEM were demonstrated for de novo structure determination of para‐crystalline materials with a bioinspired fused naphthalene diimide (NDI)–salphen–phenazine prototype light‐harvesting compound. Starting from chiral building blocks with C2 molecular symmetry, the asymmetric unit was determined by MAS NMR spectroscopy, index low‐resolution TEM diffraction data, and resolve reflection conditions, and for the first time the ability to determine the space group from reciprocal space data using this hybrid approach was shown. Transfer of molecular C2 symmetry into P2/c packing symmetry provided a connection across length scales to overcome both lack of long‐range order and missing diffraction‐phase information. Refinement with heteronuclear distance constraints confirmed the racemic P2/c packing that was scaffolded by molecular recognition of salphen zinc in a pseudo‐octahedral environment with bromide and with alkyl chains folding along the phenazine. The NDI light‐harvesting stacks ran orthogonal to the intermolecular electric dipole moment present in the solid. Finally, the orientation of flexible lamellae on an electrode surface was determined.
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Affiliation(s)
- Brijith Thomas
- Leiden Institute of Chemistry, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - Jeroen Rombouts
- Vrije University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Gert T Oostergetel
- Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | | | - Francesco Buda
- Leiden Institute of Chemistry, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - Koop Lammertsma
- Vrije University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands.,Department of Chemistry, University of Johannesburg, Auckland Park, Johannesburg, 2006, South Africa
| | - Romano Orru
- Vrije University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Huub J M de Groot
- Leiden Institute of Chemistry, Einsteinweg 55, 2333CC, Leiden, The Netherlands
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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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Schubeis T, Lührs T, Ritter C. Unambiguous Assignment of Short- and Long-Range Structural Restraints by Solid-State NMR Spectroscopy with Segmental Isotope Labeling. Chembiochem 2014; 16:51-4. [DOI: 10.1002/cbic.201402446] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Indexed: 11/11/2022]
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Chen Y, Zhang Z, Tang X, Li J, Glaubitz C, Yang J. Conformation and Topology of Diacylglycerol Kinase inE.coliMembranes Revealed by Solid-state NMR Spectroscopy. Angew Chem Int Ed Engl 2014; 53:5624-8. [DOI: 10.1002/anie.201311203] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Revised: 02/05/2014] [Indexed: 01/04/2023]
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Chen Y, Zhang Z, Tang X, Li J, Glaubitz C, Yang J. Conformation and Topology of Diacylglycerol Kinase inE.coliMembranes Revealed by Solid-state NMR Spectroscopy. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201311203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Fricke P, Demers JP, Becker S, Lange A. Studies on the MxiH Protein in T3SS Needles Using DNP-Enhanced ssNMR Spectroscopy. Chemphyschem 2013; 15:57-60. [DOI: 10.1002/cphc.201300994] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Indexed: 01/25/2023]
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Srebro M, Autschbach J. Computational Analysis of47/49Ti NMR Shifts and Electric Field Gradient Tensors of Half-Titanocene Complexes: Structure-Bonding-Property Relationships. Chemistry 2013; 19:12018-33. [DOI: 10.1002/chem.201301301] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Indexed: 11/08/2022]
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Li F, Shi P, Li J, Yang F, Wang T, Zhang W, Gao F, Ding W, Li D, Li J, Xiong Y, Sun J, Gong W, Tian C, Wang J. A Genetically Encoded19F NMR Probe for Tyrosine Phosphorylation. Angew Chem Int Ed Engl 2013; 52:3958-62. [DOI: 10.1002/anie.201300463] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Indexed: 11/09/2022]
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Li F, Shi P, Li J, Yang F, Wang T, Zhang W, Gao F, Ding W, Li D, Li J, Xiong Y, Sun J, Gong W, Tian C, Wang J. A Genetically Encoded19F NMR Probe for Tyrosine Phosphorylation. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201300463] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Ren J, Eckert H. Eine homonukleare Rotationsecho-Doppelresonanzmethode zur Messung aufgelöster Abstandsverteilungen inI=1/2-Spinpaaren, -Spinclustern und -Vielspinsystemen. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201207094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Ren J, Eckert H. A Homonuclear Rotational Echo Double-Resonance Method for Measuring Site-Resolved Distance Distributions in I=1/2 Spin Pairs, Clusters, and Multispin Systems. Angew Chem Int Ed Engl 2012; 51:12888-91. [DOI: 10.1002/anie.201207094] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Indexed: 11/05/2022]
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Hu B, Trébosc J, Lafon O, Chen Q, Masuda Y, Takegoshi K, Amoureux JP. Very-Long-Distance Correlations in Proteins Revealed by Solid-State NMR Spectroscopy. Chemphyschem 2012; 13:3585-8. [DOI: 10.1002/cphc.201200548] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Indexed: 11/11/2022]
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Webber AL, Pell AJ, Barbet-Massin E, Knight MJ, Bertini I, Felli IC, Pierattelli R, Emsley L, Lesage A, Pintacuda G. Combination of DQ and ZQ coherences for sensitive through-bond NMR correlation experiments in biosolids under ultra-fast MAS. Chemphyschem 2012; 13:2405-11. [PMID: 22528552 DOI: 10.1002/cphc.201200099] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 04/02/2012] [Indexed: 11/08/2022]
Abstract
A double-zero quantum (DZQ)-refocused INADEQUATE experiment is introduced for J-based NMR correlations under ultra-fast (60 kHz) magic angle spinning (MAS). The experiment records two spectra in the same dataset, a double quantum-single quantum (DQ-SQ) and zero quantum-single quantum (ZQ-SQ) spectrum, whereby the corresponding signals appear at different chemical shifts in ω(1). Furthermore, the spin-state selective excitation (S(3)E) J-decoupling block is incorporated in place of the second refocusing echo of the INADEQUATE scheme, providing an additional gain in sensitivity and resolution. The two sub-spectra acquired in this way can be treated separately by a shearing transformation, producing two diagonal-free single quantum (SQ-SQ)-type spectra, which are subsequently recombined to give an additional sensitivity enhancement, thus offering an improvement greater than a factor of two as compared to the original refocused INADEQUATE experiment. The combined DZQ scheme retains transverse magnetization on the initially polarized (I) spin, which typically exhibits a longer transverse dephasing time (T(2)') than its through-bond neighbour (S). By doing so, less magnetization is lost during the refocusing periods in the sequence to give even further gains in sensitivity for the J correlations. The experiment is demonstrated for the correlation between the carbonyl (CO) and alpha (CA) carbons in a microcrystalline sample of fully protonated, [(15)N,(13)C]-labelled Cu(II),Zn(II) superoxide dismutase, and its efficiency is discussed with respect to other J-based schemes.
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Affiliation(s)
- Amy L Webber
- Centre de RMN à Très Hauts Champs, UMR 5280 CNRS/Ecole Normale Supérieure de Lyon, University of Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
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Gopinath T, Veglia G. Dual acquisition magic-angle spinning solid-state NMR-spectroscopy: simultaneous acquisition of multidimensional spectra of biomacromolecules. Angew Chem Int Ed Engl 2012; 51:2731-5. [PMID: 22311700 PMCID: PMC3513283 DOI: 10.1002/anie.201108132] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Indexed: 11/05/2022]
Abstract
Fast data collection: a general method for dual data acquisition of multidimensional magic-angle spinning solid-state NMR experiments is presented. The method uses a simultaneous Hartmann-Hahn cross-polarization from (1)H to (13)C and (15)N nuclei and exploits the long-living (15)N polarization for parallel acquisition of two multidimensional experiments.
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Affiliation(s)
- T. Gopinath
- Department of Chemistry and Department of Biochemistry, Molecular Biology and Biophysics, 321 Church St. SE, Minneapolis, MN 55455 USA
| | - Gianluigi Veglia
- Department of Chemistry and Department of Biochemistry, Molecular Biology and Biophysics, 321 Church St. SE, Minneapolis, MN 55455 USA
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Gopinath T, Veglia G. Dual Acquisition Magic-Angle Spinning Solid-State NMR-Spectroscopy: Simultaneous Acquisition of Multidimensional Spectra of Biomacromolecules. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Renault M, Pawsey S, Bos MP, Koers EJ, Nand D, Tommassen-van Boxtel R, Rosay M, Tommassen J, Maas WE, Baldus M. Solid-State NMR Spectroscopy on Cellular Preparations Enhanced by Dynamic Nuclear Polarization. Angew Chem Int Ed Engl 2012; 51:2998-3001. [DOI: 10.1002/anie.201105984] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 11/02/2011] [Indexed: 11/05/2022]
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Renault M, Pawsey S, Bos MP, Koers EJ, Nand D, Tommassen-van Boxtel R, Rosay M, Tommassen J, Maas WE, Baldus M. Festkörper-NMR-Spektroskopie an zellulären Proben: verbesserte Empfindlichkeit durch dynamische Kernpolarisation. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201105984] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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