1
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Perras FA, Matsuki Y, Southern SA, Dubroca T, Flesariu DF, Van Tol J, Constantinides CP, Koutentis PA. Mechanistic origins of methyl-driven Overhauser DNP. J Chem Phys 2023; 158:154201. [PMID: 37093991 DOI: 10.1063/5.0149664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 03/31/2023] [Indexed: 04/26/2023] Open
Abstract
The Overhauser effect in the dynamic nuclear polarization (DNP) of non-conducting solids has drawn much attention due to the potential for efficient high-field DNP as well as a general interest in the underlying principles that enable the Overhauser effect in small molecules. We recently reported the observation of 1H and 2H Overhauser effects in H3C- or D3C-functionalized Blatter radical analogs, which we presumed to be caused by methyl rotation. In this work, we look at the mechanism for methyl-driven Overhauser DNP in greater detail, considering methyl librations and tunneling in addition to classical rotation. We predict the temperature dependence of these mechanisms using density functional theory and spin dynamics simulations. Comparisons with results from ultralow-temperature magic angle spinning-DNP experiments revealed that cross-relaxation at temperatures above 60 K originates from both libration and rotation, while librations dominate at lower temperatures. Due to the zero-point vibrational nature of these motions, they are not quenched by very low temperatures, and methyl-driven Overhauser DNP is expected to increase in efficiency down to 0 K, predominantly due to increases in nuclear relaxation times.
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Affiliation(s)
- Frédéric A Perras
- Chemical and Biological Sciences Division, Ames National Laboratory, Ames, Iowa 50011, USA
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
| | - Yoh Matsuki
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Scott A Southern
- Chemical and Biological Sciences Division, Ames National Laboratory, Ames, Iowa 50011, USA
| | - Thierry Dubroca
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, USA
| | - Dragos F Flesariu
- Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - Johan Van Tol
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, USA
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2
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Chow WY, De Paëpe G, Hediger S. Biomolecular and Biological Applications of Solid-State NMR with Dynamic Nuclear Polarization Enhancement. Chem Rev 2022; 122:9795-9847. [PMID: 35446555 DOI: 10.1021/acs.chemrev.1c01043] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Solid-state NMR spectroscopy (ssNMR) with magic-angle spinning (MAS) enables the investigation of biological systems within their native context, such as lipid membranes, viral capsid assemblies, and cells. However, such ambitious investigations often suffer from low sensitivity due to the presence of significant amounts of other molecular species, which reduces the effective concentration of the biomolecule or interaction of interest. Certain investigations requiring the detection of very low concentration species remain unfeasible even with increasing experimental time for signal averaging. By applying dynamic nuclear polarization (DNP) to overcome the sensitivity challenge, the experimental time required can be reduced by orders of magnitude, broadening the feasible scope of applications for biological solid-state NMR. In this review, we outline strategies commonly adopted for biological applications of DNP, indicate ongoing challenges, and present a comprehensive overview of biological investigations where MAS-DNP has led to unique insights.
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Affiliation(s)
- Wing Ying Chow
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France.,Univ. Grenoble Alpes, CEA, CNRS, Inst. Biol. Struct. IBS, 38044 Grenoble, France
| | - Gaël De Paëpe
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France
| | - Sabine Hediger
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France
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3
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Biedenbänder T, Aladin V, Saeidpour S, Corzilius B. Dynamic Nuclear Polarization for Sensitivity Enhancement in Biomolecular Solid-State NMR. Chem Rev 2022; 122:9738-9794. [PMID: 35099939 DOI: 10.1021/acs.chemrev.1c00776] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Solid-state NMR with magic-angle spinning (MAS) is an important method in structural biology. While NMR can provide invaluable information about local geometry on an atomic scale even for large biomolecular assemblies lacking long-range order, it is often limited by low sensitivity due to small nuclear spin polarization in thermal equilibrium. Dynamic nuclear polarization (DNP) has evolved during the last decades to become a powerful method capable of increasing this sensitivity by two to three orders of magnitude, thereby reducing the valuable experimental time from weeks or months to just hours or days; in many cases, this allows experiments that would be otherwise completely unfeasible. In this review, we give an overview of the developments that have opened the field for DNP-enhanced biomolecular solid-state NMR including state-of-the-art applications at fast MAS and high magnetic field. We present DNP mechanisms, polarizing agents, and sample constitution methods suitable for biomolecules. A wide field of biomolecular NMR applications is covered including membrane proteins, amyloid fibrils, large biomolecular assemblies, and biomaterials. Finally, we present perspectives and recent developments that may shape the field of biomolecular DNP in the future.
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Affiliation(s)
- Thomas Biedenbänder
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Victoria Aladin
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Siavash Saeidpour
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Björn Corzilius
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
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4
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Gurinov A, Sieland B, Kuzhelev A, Elgabarty H, Kühne TD, Prisner T, Paradies J, Baldus M, Ivanov KL, Pylaeva S. Gemischtvalente Verbindungen als polarisierende Mittel für die dynamische Kern‐Overhauser‐Polarisation in Festkörpern**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Andrei Gurinov
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584CH Utrecht Niederlande
| | - Benedikt Sieland
- Department of Chemistry Paderborn University Warburger Straße 100 Paderborn 33098 Deutschland
| | - Andrey Kuzhelev
- Goethe University Frankfurt am Main Institute of Physical and Theoretical Chemistry Center for Biomolecular Magnetic Resonance Max von Laue Straße 7 60438 Frankfurt am Main Deutschland
| | - Hossam Elgabarty
- Dynamics of Condensed Matter and Center for Sustainable Systems Design Chair of Theoretical Chemistry University of Paderborn Warburger Straße 100 33098 Paderborn Deutschland
| | - Thomas D. Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design Chair of Theoretical Chemistry University of Paderborn Warburger Straße 100 33098 Paderborn Deutschland
| | - Thomas Prisner
- Goethe University Frankfurt am Main Institute of Physical and Theoretical Chemistry Center for Biomolecular Magnetic Resonance Max von Laue Straße 7 60438 Frankfurt am Main Deutschland
| | - Jan Paradies
- Department of Chemistry Paderborn University Warburger Straße 100 Paderborn 33098 Deutschland
| | - Marc Baldus
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584CH Utrecht Niederlande
| | - Konstantin L. Ivanov
- International Tomography Center Siberian Branch of the Russian Academy of Sciences Novosibirsk 630090 Russland
- Novosibirsk State University Novosibirsk 630090 Russland
| | - Svetlana Pylaeva
- Dynamics of Condensed Matter and Center for Sustainable Systems Design Chair of Theoretical Chemistry University of Paderborn Warburger Straße 100 33098 Paderborn Deutschland
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5
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Gurinov A, Sieland B, Kuzhelev A, Elgabarty H, Kühne TD, Prisner T, Paradies J, Baldus M, Ivanov KL, Pylaeva S. Mixed-Valence Compounds as Polarizing Agents for Overhauser Dynamic Nuclear Polarization in Solids*. Angew Chem Int Ed Engl 2021; 60:15371-15375. [PMID: 33908694 PMCID: PMC8361920 DOI: 10.1002/anie.202103215] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Indexed: 11/25/2022]
Abstract
Herein, we investigate a novel set of polarizing agents—mixed‐valence compounds—by theoretical and experimental methods and demonstrate their performance in high‐field dynamic nuclear polarization (DNP) NMR experiments in the solid state. Mixed‐valence compounds constitute a group of molecules in which molecular mobility persists even in solids. Consequently, such polarizing agents can be used to perform Overhauser‐DNP experiments in the solid state, with favorable conditions for dynamic nuclear polarization formation at ultra‐high magnetic fields.
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Affiliation(s)
- Andrei Gurinov
- NMR Spectroscopy group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands
| | - Benedikt Sieland
- Department of Chemistry, Paderborn University, Warburger Strasse 100, Paderborn, 33098, Germany
| | - Andrey Kuzhelev
- Goethe University Frankfurt am Main, Institute of Physical and Theoretical Chemistry, Center for Biomolecular Magnetic Resonance, Max von Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Hossam Elgabarty
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, Warburger Strasse 100, 33098, Paderborn, Germany
| | - Thomas D Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, Warburger Strasse 100, 33098, Paderborn, Germany
| | - Thomas Prisner
- Goethe University Frankfurt am Main, Institute of Physical and Theoretical Chemistry, Center for Biomolecular Magnetic Resonance, Max von Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Jan Paradies
- Department of Chemistry, Paderborn University, Warburger Strasse 100, Paderborn, 33098, Germany
| | - Marc Baldus
- NMR Spectroscopy group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands
| | - Konstantin L Ivanov
- International Tomography Center, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Svetlana Pylaeva
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, Warburger Strasse 100, 33098, Paderborn, Germany
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6
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Sergeyev IV, Quinn CM, Struppe J, Gronenborn A, Polenova T. Competing Transfer Pathways in Direct and Indirect Dynamic Nuclear Polarization MAS NMR Experiments on HIV-1 Capsid Assemblies: Implications for Sensitivity and Resolution. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:239-249. [PMID: 34136885 PMCID: PMC8203495 DOI: 10.5194/mr-2-239-2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/23/2021] [Indexed: 04/25/2023]
Abstract
Dynamic nuclear polarization-enhanced (DNP) magic angle spinning (MAS) NMR of biological systems is a rapidly growing field. Large signal enhancements make the technique particularly attractive for signal-limited cases, such as studies of complex biological assemblies or at natural isotopic abundance. However, spectral resolution is considerably reduced compared to ambient-temperature non-DNP spectra. Herein, we report a systematic investigation into sensitivity and resolution of 1D and 2D 13C-detected DNP MAS NMR experiments on HIV-1 CA tubular assemblies. We show that the magnitude and sign of signal enhancement as well as the homogeneous line width are strongly dependent on the biradical concentration, the dominant polarization transfer pathway, and the enhancement buildup time. Our findings provide guidance for optimal choice of sample preparation and experimental conditions in DNP experiments.
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Affiliation(s)
- Ivan V. Sergeyev
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA 01821, United States
| | - Caitlin M. Quinn
- Department of Chemistry and Biochemistry, University of Delaware,
Newark, DE 19716, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA 01821, United States
| | - Angela M. Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of
Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth
Avenue, Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware,
Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of
Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth
Avenue, Pittsburgh, PA 15261, United States
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7
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Gauto D, Dakhlaoui O, Marin-Montesinos I, Hediger S, De Paëpe G. Targeted DNP for biomolecular solid-state NMR. Chem Sci 2021; 12:6223-6237. [PMID: 34084422 PMCID: PMC8115112 DOI: 10.1039/d0sc06959k] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/18/2021] [Indexed: 12/23/2022] Open
Abstract
High-field dynamic nuclear polarization is revolutionizing the scope of solid-state NMR with new applications in surface chemistry, materials science and structural biology. In this perspective article, we focus on a specific DNP approach, called targeted DNP, in which the paramagnets introduced to polarize are not uniformly distributed in the sample but site-specifically located on the biomolecular system. After reviewing the various targeting strategies reported to date, including a bio-orthogonal chemistry-based approach, we discuss the potential of targeted DNP to improve the overall NMR sensitivity while avoiding the use of glass-forming DNP matrix. This is especially relevant to the study of diluted biomolecular systems such as, for instance, membrane proteins within their lipidic environment. We also discuss routes towards extracting structural information from paramagnetic relaxation enhancement (PRE) induced by targeted DNP at cryogenic temperature, and the possibility to recover site-specific information in the vicinity of the paramagnetic moieties using high-resolution selective DNP spectra. Finally, we review the potential of targeted DNP for in-cell NMR studies and how it can be used to extract a given protein NMR signal from a complex cellular background.
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Affiliation(s)
- Diego Gauto
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
| | - Ons Dakhlaoui
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
- Univ. Grenoble Alpes, CNRS, CERMAV Grenoble France
| | - Ildefonso Marin-Montesinos
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
- University of Aveiro, CICECO Chem. Dept. Aveiro Portugal
| | - Sabine Hediger
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
| | - Gaël De Paëpe
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
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8
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Varner TA, Mohamed-Raseek N, Miller AF. Assignments of 19F NMR resonances and exploration of dynamics in a long-chain flavodoxin. Arch Biochem Biophys 2021; 703:108839. [PMID: 33727041 DOI: 10.1016/j.abb.2021.108839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/04/2021] [Accepted: 03/09/2021] [Indexed: 12/23/2022]
Abstract
Flavodoxin is a small protein that employs a non-covalently bound flavin to mediate single-electron transfer at low potentials. The long-chain flavodoxins possess a long surface loop that is proposed to interact with partner proteins. We have incorporated 19F-labeled tyrosine in long-chain flavodoxin from Rhodopseudomonas palustris to gain a probe of possible loop dynamics, exploiting the presence of a Tyr in the long loop in addition to Tyr residues near the flavin. We report 19F resonance assignments for all four Tyrs, and demonstration of a pair of resonances in slow exchange, both corresponding to a Tyr adjacent to the flavin. We also provide evidence for dynamics affecting the Tyr in the long loop. Thus, we show that 19F NMR of 19F-Tyr labeled flavodoxin holds promise for monitoring possible changes in conformation upon binding to partner proteins.
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Affiliation(s)
- Taylor A Varner
- Department of Chemistry, University of Kentucky, Lexington, KY, 40506, USA
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9
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Tran NT, Mentink-Vigier F, Long JR. Dynamic Nuclear Polarization of Biomembrane Assemblies. Biomolecules 2020; 10:E1246. [PMID: 32867275 PMCID: PMC7565305 DOI: 10.3390/biom10091246] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 01/02/2023] Open
Abstract
While atomic scale structural and dynamic information are hallmarks of nuclear magnetic resonance (NMR) methodologies, sensitivity is a fundamental limitation in NMR studies. Fully exploiting NMR capabilities to study membrane proteins is further hampered by their dilution within biological membranes. Recent developments in dynamic nuclear polarization (DNP), which can transfer the relatively high polarization of unpaired electrons to nuclear spins, show promise for overcoming the sensitivity bottleneck and enabling NMR characterization of membrane proteins under native-like conditions. Here we discuss fundamental aspects of DNP-enhanced solid-state NMR spectroscopy, experimental details relevant to the study of lipid assemblies and incorporated proteins, and sensitivity gains which can be realized in biomembrane-based samples. We also present unique insights which can be gained from DNP measurements and prospects for further development of the technique for elucidating structures and orientations of membrane proteins in native lipid environments.
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Affiliation(s)
- Nhi T. Tran
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA;
| | - Frédéric Mentink-Vigier
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA;
| | - Joanna R. Long
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA;
- Department of Biochemistry & Molecular Biology and McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
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10
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Abstract
Dynamic nuclear polarization (DNP) is one of the most prominent methods of sensitivity enhancement in nuclear magnetic resonance (NMR). Even though solid-state DNP under magic-angle spinning (MAS) has left the proof-of-concept phase and has become an important tool for structural investigations of biomolecules as well as materials, it is still far from mainstream applicability because of the potentially overwhelming combination of unique instrumentation, complex sample preparation, and a multitude of different mechanisms and methods available. In this review, I introduce the diverse field and history of DNP, combining aspects of NMR and electron paramagnetic resonance. I then explain the general concepts and detailed mechanisms relevant at high magnetic field, including solution-state methods based on Overhauser DNP but with a greater focus on the more established MAS DNP methods. Finally, I review practical considerations and fields of application and discuss future developments.
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Affiliation(s)
- Björn Corzilius
- Institute of Chemistry and Department of Life, Light and Matter, University of Rostock, 18059 Rostock, Germany;
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11
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Tateishi K, Negoro M, Nonaka H, Kagawa A, Sando S, Wada S, Kitagawa M, Uesaka T. Dynamic nuclear polarization with photo-excited triplet electrons using 6,13-diphenylpentacene. Phys Chem Chem Phys 2019; 21:19737-19741. [PMID: 31498341 DOI: 10.1039/c9cp00977a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Dynamic nuclear polarization with photo-excited triplet electrons (Triplet-DNP) is demonstrated using 6,13-diphenylpentacene (DPPentacene). DPPentacene is soluble in various organic solvents, while pentacene, which is used in most of the triplet-DNP experiments, has limited solubility. An enhancement factor of 81 is obtained for 1H spins in the glass of ethanol-d6 : water = 80 : 20 (w/w) doped with 0.1 mM DPPentacene at 90 K in 0.67 T.
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12
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Daube D, Vogel M, Suess B, Corzilius B. Dynamic nuclear polarization on a hybridized hammerhead ribozyme: An explorative study of RNA folding and direct DNP with a paramagnetic metal ion cofactor. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2019; 101:21-30. [PMID: 31078101 DOI: 10.1016/j.ssnmr.2019.04.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/16/2019] [Accepted: 04/16/2019] [Indexed: 06/09/2023]
Abstract
While uniform isotope labeling of ribonucleic acids (RNA) can simply and efficiently be achieved by in-vitro transcription, the specific introduction of nucleotides in larger constructs is non-trivial and often ineffective. Here, we demonstrate how a medium-sized (67-mer), biocatalytically relevant RNA (hammerhead ribozyme, HHRz) can be formed by spontaneous hybridization of two differently isotope-labeled strands, each individually synthesized by in-vitro transcription. This allows on the one hand for a significant reduction in the number of isotope-labeled nucleotides and thus spectral overlap particularly under magic-angle spinning (MAS) dynamic nuclear polarization (DNP) NMR conditions, on the other hand for orthogonal 13C/15N-labeling of complementary strands and thus for specific investigation of structurally or functionally relevant inter-strand and/or inter-stem contacts. By this method, we are able to confirm a non-canonical interaction due to single-site resolution and unique spectral assignments by two-dimensional 13C-13C (PDSD) as well as 15N-13C (TEDOR) correlation spectroscopy under "conventional" DNP enhancement. This contact is indicative of the ribozyme's functional conformation, and is present in frozen solution irrespective of the presence or absence of a Mg2+ co-factor. Finally, we use different isotope-labeling schemes in order to investigate the distance dependence of paramagnetic interactions and direct metal-ion DNP if the diamagnetic Mg2+ is substituted by paramagnetic Mn2+.
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Affiliation(s)
- Diane Daube
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt am Main, Germany
| | - Marc Vogel
- Fachbereich Biologie, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287 Darmstadt, Germany
| | - Beatrix Suess
- Fachbereich Biologie, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287 Darmstadt, Germany
| | - Björn Corzilius
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt am Main, Germany; Institut für Chemie, Universität Rostock, Albert-Einstein-Str. 3a, 18059 Rostock, Germany; Department LL&M, Universität Rostock, Albert-Einstein-Str. 25, 18059 Rostock, Germany.
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13
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Alaniva N, Saliba EP, Sesti EL, Judge PT, Barnes AB. Electron Decoupling with Chirped Microwave Pulses for Rapid Signal Acquisition and Electron Saturation Recovery. Angew Chem Int Ed Engl 2019; 58:7259-7262. [DOI: 10.1002/anie.201900139] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/01/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Nicholas Alaniva
- Department of Chemistry Washington University in St. Louis One Brookings Drive St. Louis MO 63130 USA
| | - Edward P. Saliba
- Department of Chemistry Washington University in St. Louis One Brookings Drive St. Louis MO 63130 USA
| | - Erika L. Sesti
- Department of Chemistry Washington University in St. Louis One Brookings Drive St. Louis MO 63130 USA
| | - Patrick T. Judge
- Department of Chemistry Washington University in St. Louis One Brookings Drive St. Louis MO 63130 USA
- Department of Biochemistry, Biophysics, and Biology Washington University in St. Louis School of Medicine 660 S. Euclid Ave St Louis MO 63110 USA
| | - Alexander B. Barnes
- Department of Chemistry Washington University in St. Louis One Brookings Drive St. Louis MO 63130 USA
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14
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Alaniva N, Saliba EP, Sesti EL, Judge PT, Barnes AB. Electron Decoupling with Chirped Microwave Pulses for Rapid Signal Acquisition and Electron Saturation Recovery. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201900139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Nicholas Alaniva
- Department of Chemistry Washington University in St. Louis One Brookings Drive St. Louis MO 63130 USA
| | - Edward P. Saliba
- Department of Chemistry Washington University in St. Louis One Brookings Drive St. Louis MO 63130 USA
| | - Erika L. Sesti
- Department of Chemistry Washington University in St. Louis One Brookings Drive St. Louis MO 63130 USA
| | - Patrick T. Judge
- Department of Chemistry Washington University in St. Louis One Brookings Drive St. Louis MO 63130 USA
- Department of Biochemistry, Biophysics, and Biology Washington University in St. Louis School of Medicine 660 S. Euclid Ave St Louis MO 63110 USA
| | - Alexander B. Barnes
- Department of Chemistry Washington University in St. Louis One Brookings Drive St. Louis MO 63130 USA
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15
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Lu M, Wang M, Sergeyev IV, Quinn CM, Struppe J, Rosay M, Maas W, Gronenborn AM, Polenova T. 19F Dynamic Nuclear Polarization at Fast Magic Angle Spinning for NMR of HIV-1 Capsid Protein Assemblies. J Am Chem Soc 2019; 141:5681-5691. [PMID: 30871317 PMCID: PMC6521953 DOI: 10.1021/jacs.8b09216] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We report remarkably high, up to 100-fold, signal enhancements in 19F dynamic nuclear polarization (DNP) magic angle spinning (MAS) spectra at 14.1 T on HIV-1 capsid protein (CA) assemblies. These enhancements correspond to absolute sensitivity ratios of 12-29 and are of similar magnitude to those seen for 1H signals in the same samples. At MAS frequencies above 20 kHz, it was possible to record 2D 19F-13C HETCOR spectra, which contain long-range intra- and intermolecular correlations. Such correlations provide unique distance restraints, inaccessible in conventional experiments without DNP, for protein structure determination. Furthermore, systematic quantification of the DNP enhancements as a function of biradical concentration, MAS frequency, temperature, and microwave power is reported. Our work establishes the power of DNP-enhanced 19F MAS NMR spectroscopy for structural characterization of HIV-1 CA assemblies, and this approach is anticipated to be applicable to a wide range of large biomolecular systems.
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Affiliation(s)
- Manman Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Mingzhang Wang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Ivan V. Sergeyev
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, United States
| | - Caitlin M. Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, United States
| | - Melanie Rosay
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, United States
| | - Werner Maas
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, United States
| | - Angela M. Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
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16
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König A, Schölzel D, Uluca B, Viennet T, Akbey Ü, Heise H. Hyperpolarized MAS NMR of unfolded and misfolded proteins. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2019; 98:1-11. [PMID: 30641444 DOI: 10.1016/j.ssnmr.2018.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/28/2018] [Accepted: 12/30/2018] [Indexed: 05/09/2023]
Abstract
In this article we give an overview over the use of DNP-enhanced solid-state NMR spectroscopy for the investigation of unfolded, disordered and misfolded proteins. We first provide an overview over studies in which DNP spectroscopy has successfully been applied for the structural investigation of well-folded amyloid fibrils formed by short peptides as well as full-length proteins. Sample cooling to cryogenic temperatures often leads to severe line broadening of resonance signals and thus a loss in resolution. However, inhomogeneous line broadening at low temperatures provides valuable information about residual dynamics and flexibility in proteins, and, in combination with appropriate selective isotope labeling techniques, inhomogeneous linewidths in disordered proteins or protein regions may be exploited for evaluation of conformational ensembles. In the last paragraph we highlight some recent studies where DNP-enhanced MAS-NMR-spectroscopy was applied to the study of disordered proteins/protein regions and inhomogeneous sample preparations.
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Affiliation(s)
- Anna König
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Center Jülich, 52425, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Daniel Schölzel
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Center Jülich, 52425, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Boran Uluca
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Center Jülich, 52425, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Thibault Viennet
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Center Jülich, 52425, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Ümit Akbey
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Center Jülich, 52425, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Henrike Heise
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Center Jülich, 52425, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
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17
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Flori A, Giovannetti G, Santarelli MF, Aquaro GD, De Marchi D, Burchielli S, Frijia F, Positano V, Landini L, Menichetti L. Biomolecular imaging of 13C-butyrate with dissolution-DNP: Polarization enhancement and formulation for in vivo studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 199:153-160. [PMID: 29597071 DOI: 10.1016/j.saa.2018.03.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 01/19/2018] [Accepted: 03/08/2018] [Indexed: 06/08/2023]
Abstract
Magnetic Resonance Spectroscopy of hyperpolarized isotopically enriched molecules facilitates the non-invasive real-time investigation of in vivo tissue metabolism in the time-frame of a few minutes; this opens up a new avenue in the development of biomolecular probes. Dissolution Dynamic Nuclear Polarization is a hyperpolarization technique yielding a more than four orders of magnitude increase in the 13C polarization for in vivo Magnetic Resonance Spectroscopy studies. As reported in several studies, the dissolution Dynamic Nuclear Polarization polarization performance relies on the chemico-physical properties of the sample. In this study, we describe and quantify the effects of the different sample components on the dissolution Dynamic Nuclear Polarization performance of [1-13C]butyrate. In particular, we focus on the polarization enhancement provided by the incremental addition of the glassy agent dimethyl sulfoxide and gadolinium chelate to the formulation. Finally, preliminary results obtained after injection in healthy rats are also reported, showing the feasibility of an in vivo Magnetic Resonance Spectroscopy study with hyperpolarized [1-13C]butyrate using a 3T clinical set-up.
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Affiliation(s)
- Alessandra Flori
- Fondazione CNR/Regione Toscana G. Monasterio, Pisa, Italy; Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.
| | - Giulio Giovannetti
- Institute of Clinical Physiology, National Research Council (CNR), Pisa, Italy
| | | | | | | | | | | | | | - Luigi Landini
- Fondazione CNR/Regione Toscana G. Monasterio, Pisa, Italy; Department of Electronic Engineering, University of Pisa, Italy
| | - Luca Menichetti
- Institute of Clinical Physiology, National Research Council (CNR), Pisa, Italy; Fondazione CNR/Regione Toscana G. Monasterio, Pisa, Italy
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18
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Ji X, Can TV, Mentink-Vigier F, Bornet A, Milani J, Vuichoud B, Caporini MA, Griffin RG, Jannin S, Goldman M, Bodenhausen G. Overhauser effects in non-conducting solids at 1.2 K. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 286:138-142. [PMID: 29241045 PMCID: PMC5767554 DOI: 10.1016/j.jmr.2017.11.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/23/2017] [Accepted: 11/26/2017] [Indexed: 05/05/2023]
Abstract
Recently, it was observed that protons in non-conducting solids doped with 1,3-bisdiphenylene-2-phenylallyl (BDPA) or its sulfonated derivative (SA-BDPA) can be polarized through Overhauser effects via resonant microwave irradiation. These effects were present under magic angle spinning conditions in magnetic fields between 5 and 18.8 T and at temperatures near 100 K. This communication reports similar effects in static samples at 6.7 T and, more importantly, at temperatures as low as 1.2 K, in a different dynamic regime than in the previous study. Our results provide new information towards understanding the mechanism of the Overhauser effect in non-conducting solids. We discuss possible origins of the fluctuations that can give rise to an Overhauser effect at such low temperatures.
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Affiliation(s)
- X Ji
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Departement de Chimie, Ecole Normale Superieure, PSL Research University, UPMC Univ Paris 06, CNRS, Laboratoire des Biomolecules (LBM), 24 rue Lhomond, 75005 Paris, France; Sorbonne Universites, UPMC Univ Paris 06, Ecole Normale Superieure, CNRS, Laboratoire des Biomolecules (LBM), Paris, France
| | - T V Can
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - F Mentink-Vigier
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - A Bornet
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Univ Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, 69100 Villeurbanne, France
| | - J Milani
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Univ Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, 69100 Villeurbanne, France
| | - B Vuichoud
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Univ Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, 69100 Villeurbanne, France
| | - M A Caporini
- Amgen Inc., 360 Binney Street Cambridge, MA 02142, USA
| | - R G Griffin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - S Jannin
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Univ Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, 69100 Villeurbanne, France
| | - M Goldman
- 2 Allée Geneviève Anthonioz de Gaulle, 93260 Les Lilas, France
| | - G Bodenhausen
- Departement de Chimie, Ecole Normale Superieure, PSL Research University, UPMC Univ Paris 06, CNRS, Laboratoire des Biomolecules (LBM), 24 rue Lhomond, 75005 Paris, France; Sorbonne Universites, UPMC Univ Paris 06, Ecole Normale Superieure, CNRS, Laboratoire des Biomolecules (LBM), Paris, France.
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19
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Rogawski R, Sergeyev IV, Zhang Y, Tran TH, Li Y, Tong L, McDermott AE. NMR Signal Quenching from Bound Biradical Affinity Reagents in DNP Samples. J Phys Chem B 2017; 121:10770-10781. [PMID: 29116793 PMCID: PMC5842680 DOI: 10.1021/acs.jpcb.7b08274] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We characterize the effect of specifically bound biradicals on the NMR spectra of dihydrofolate reductase from E. coli. Dynamic nuclear polarization methods enhance the signal-to-noise of solid state NMR experiments by transferring polarization from unpaired electrons of biradicals to nuclei. There has been recent interest in colocalizing the paramagnetic polarizing agents with the analyte of interest through covalent or noncovalent specific interactions. This experimental approach broadens the scope of dynamic nuclear polarization methods by offering the possibility of selective signal enhancements and the potential to work in a broad range of environments. Paramagnetic compounds can have other effects on the NMR spectroscopy of nearby nuclei, including broadening of nuclear resonances due to the proximity of the paramagnetic agent. Understanding the distance dependence of these interactions is important for the success of the technique. Here we explore paramagnetic signal quenching due to a bound biradical, specifically a biradical-derivatized trimethoprim ligand of E. coli dihydrofolate reductase. Biradical-derivatized trimethoprim has nanomolar affinity for its target, and affords strong and selective signal enhancements in dynamic nuclear polarization experiments. In this work, we show that, although the trimethoprim fragment is well ordered, the biradical (TOTAPOL) moiety is disordered when bound to the protein. The distance dependence in bleaching of NMR signal intensity allows us to detect numerous NMR signals in the protein. We present the possibility that static disorder and electron spin diffusion play roles in this observation, among other contributions. The fact that the majority of signals are observed strengthens the case for the use of high affinity or covalent radicals in dynamic nuclear polarization solid state NMR enhancement.
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Affiliation(s)
- Rivkah Rogawski
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Ivan V Sergeyev
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Yinglu Zhang
- Department of Biological Sciences, Columbia University , New York, New York 10027, United States
| | - Timothy H Tran
- Department of Biological Sciences, Columbia University , New York, New York 10027, United States
| | - Yongjun Li
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Liang Tong
- Department of Biological Sciences, Columbia University , New York, New York 10027, United States
| | - Ann E McDermott
- Department of Chemistry, Columbia University , New York, New York 10027, United States
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20
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Lilly Thankamony AS, Wittmann JJ, Kaushik M, Corzilius B. Dynamic nuclear polarization for sensitivity enhancement in modern solid-state NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 102-103:120-195. [PMID: 29157490 DOI: 10.1016/j.pnmrs.2017.06.002] [Citation(s) in RCA: 268] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/03/2017] [Accepted: 06/08/2017] [Indexed: 05/03/2023]
Abstract
The field of dynamic nuclear polarization has undergone tremendous developments and diversification since its inception more than 6 decades ago. In this review we provide an in-depth overview of the relevant topics involved in DNP-enhanced MAS NMR spectroscopy. This includes the theoretical description of DNP mechanisms as well as of the polarization transfer pathways that can lead to a uniform or selective spreading of polarization between nuclear spins. Furthermore, we cover historical and state-of-the art aspects of dedicated instrumentation, polarizing agents, and optimization techniques for efficient MAS DNP. Finally, we present an extensive overview on applications in the fields of structural biology and materials science, which underlines that MAS DNP has moved far beyond the proof-of-concept stage and has become an important tool for research in these fields.
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Affiliation(s)
- Aany Sofia Lilly Thankamony
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Johannes J Wittmann
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Monu Kaushik
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Björn Corzilius
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany.
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21
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Rogawski R, McDermott AE. New NMR tools for protein structure and function: Spin tags for dynamic nuclear polarization solid state NMR. Arch Biochem Biophys 2017; 628:102-113. [PMID: 28623034 PMCID: PMC5815514 DOI: 10.1016/j.abb.2017.06.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/05/2017] [Accepted: 06/12/2017] [Indexed: 12/13/2022]
Abstract
Magic angle spinning solid state NMR studies of biological macromolecules [1-3] have enabled exciting studies of membrane proteins [4,5], amyloid fibrils [6], viruses, and large macromolecular assemblies [7]. Dynamic nuclear polarization (DNP) provides a means to enhance detection sensitivity for NMR, particularly for solid state NMR, with many recent biological applications and considerable contemporary efforts towards elaboration and optimization of the DNP experiment. This review explores precedents and innovations in biological DNP experiments, especially highlighting novel chemical biology approaches to introduce the radicals that serve as a source of polarization in DNP experiments.
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Affiliation(s)
- Rivkah Rogawski
- Department of Chemistry, Columbia University, NY, NY 10027, United States
| | - Ann E McDermott
- Department of Chemistry, Columbia University, NY, NY 10027, United States.
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22
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DeHaven BA, Tokarski JT, Korous AA, Mentink-Vigier F, Makris TM, Brugh AM, Forbes MDE, van Tol J, Bowers CR, Shimizu LS. Persistent Radicals of Self-assembled Benzophenone bis-Urea Macrocycles: Characterization and Application as a Polarizing Agent for Solid-state DNP MAS Spectroscopy. Chemistry 2017; 23:8315-8319. [PMID: 28423212 PMCID: PMC5724385 DOI: 10.1002/chem.201701705] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Indexed: 12/22/2022]
Abstract
UV-irradiation of a self-assembled benzophenone bis-urea macrocycle generates μm amounts of radicals that persist for weeks under ambient conditions. High-field EPR and variable-temperature X-band EPR studies suggest a resonance stabilized radical pair through H-abstraction. These endogenous radicals were applied as a polarizing agent for magic angle spinning (MAS) dynamic nuclear polarization (DNP) NMR enhancement. The field-stepped DNP enhancement profile exhibits a sharp peak with a maximum enhancement of ϵon/off =4 superimposed on a nearly constant DNP enhancement of ϵon/off =2 over a broad field range. This maximum coincides with the high field EPR absorption spectrum, consistent with an Overhauser effect mechanism. DNP enhancement was observed for both the host and guests, suggesting that even low levels of endogenous radicals can facilitate the study of host-guest relationships in the solid-state.
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Affiliation(s)
- Baillie A DeHaven
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, 29208, USA
| | - John T Tokarski
- Department of Chemistry, University of Florida, Gainesville, Florida, 32611, USA
| | - Arthur A Korous
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, 29208, USA
| | - Frederic Mentink-Vigier
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida, 32310, USA
| | - Thomas M Makris
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, 29208, USA
| | - Alexander M Brugh
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio, 43403, USA
| | - Malcolm D E Forbes
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio, 43403, USA
| | - Johan van Tol
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, Florida, 32310, USA
| | - Clifford R Bowers
- Department of Chemistry, University of Florida, Gainesville, Florida, 32611, USA
| | - Linda S Shimizu
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, 29208, USA
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23
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Kaushik M, Qi M, Godt A, Corzilius B. Bis-Gadolinium Complexes for Solid Effect and Cross Effect Dynamic Nuclear Polarization. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Monu Kaushik
- Goethe-Universität Frankfurt am Main; Institut für Physikalische und Theoretische Chemie; Institut für Biophysikalische Chemie und Biomolekulares Magnetresonanzzentrum (BMRZ); Max-von-Laue-Strasse 7-9 60438 Frankfurt am Main Germany
| | - Mian Qi
- Fakultät für Chemie und Centrum für Molekulare Materialien (CM 2 ); Universität Bielefeld; Universitätsstrasse 25 33615 Bielefeld Germany
| | - Adelheid Godt
- Fakultät für Chemie und Centrum für Molekulare Materialien (CM 2 ); Universität Bielefeld; Universitätsstrasse 25 33615 Bielefeld Germany
| | - Björn Corzilius
- Goethe-Universität Frankfurt am Main; Institut für Physikalische und Theoretische Chemie; Institut für Biophysikalische Chemie und Biomolekulares Magnetresonanzzentrum (BMRZ); Max-von-Laue-Strasse 7-9 60438 Frankfurt am Main Germany
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24
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Kaushik M, Qi M, Godt A, Corzilius B. Bis-Gadolinium Complexes for Solid Effect and Cross Effect Dynamic Nuclear Polarization. Angew Chem Int Ed Engl 2017; 56:4295-4299. [DOI: 10.1002/anie.201612388] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Monu Kaushik
- Goethe-Universität Frankfurt am Main; Institut für Physikalische und Theoretische Chemie; Institut für Biophysikalische Chemie und Biomolekulares Magnetresonanzzentrum (BMRZ); Max-von-Laue-Strasse 7-9 60438 Frankfurt am Main Germany
| | - Mian Qi
- Fakultät für Chemie und Centrum für Molekulare Materialien (CM 2 ); Universität Bielefeld; Universitätsstrasse 25 33615 Bielefeld Germany
| | - Adelheid Godt
- Fakultät für Chemie und Centrum für Molekulare Materialien (CM 2 ); Universität Bielefeld; Universitätsstrasse 25 33615 Bielefeld Germany
| | - Björn Corzilius
- Goethe-Universität Frankfurt am Main; Institut für Physikalische und Theoretische Chemie; Institut für Biophysikalische Chemie und Biomolekulares Magnetresonanzzentrum (BMRZ); Max-von-Laue-Strasse 7-9 60438 Frankfurt am Main Germany
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25
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Rogawski R, Sergeyev IV, Li Y, Ottaviani MF, Cornish V, McDermott AE. Dynamic Nuclear Polarization Signal Enhancement with High-Affinity Biradical Tags. J Phys Chem B 2017; 121:1169-1175. [PMID: 28099013 DOI: 10.1021/acs.jpcb.6b09021] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Dynamic nuclear polarization is an emerging technique for sensitizing solid-state NMR experiments by transferring polarization from electrons to nuclei. Stable biradicals, the polarization source for the cross effect mechanism, are typically codissolved at millimolar concentrations with proteins of interest. Here we describe the high-affinity biradical tag TMP-T, created by covalently linking trimethoprim, a nanomolar affinity ligand of dihydrofolate reductase (DHFR), to the biradical polarizing agent TOTAPOL. With TMP-T bound to DHFR, large enhancements of the protein spectrum are observed, comparable to when TOTAPOL is codissolved with the protein. In contrast to TOTAPOL, the tight binding TMP-T can be added stoichiometrically at radical concentrations orders of magnitude lower than in previously described preparations. Benefits of the reduced radical concentration include reduced spectral bleaching, reduced chemical perturbation of the sample, and the ability to selectively enhance signals for the protein of interest.
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Affiliation(s)
- Rivkah Rogawski
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Ivan V Sergeyev
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Yongjun Li
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - M Francesca Ottaviani
- Department of Pure and Applied Sciences, University of Urbino , Loc. Crocicchia, 61029 Urbino, Italy
| | - Virginia Cornish
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Ann E McDermott
- Department of Chemistry, Columbia University , New York, New York 10027, United States
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26
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Kaushik M, Bahrenberg T, Can TV, Caporini MA, Silvers R, Heiliger J, Smith AA, Schwalbe H, Griffin RG, Corzilius B. Gd(iii) and Mn(ii) complexes for dynamic nuclear polarization: small molecular chelate polarizing agents and applications with site-directed spin labeling of proteins. Phys Chem Chem Phys 2016; 18:27205-27218. [PMID: 27545112 PMCID: PMC5053914 DOI: 10.1039/c6cp04623a] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigate complexes of two paramagnetic metal ions Gd3+ and Mn2+ to serve as polarizing agents for solid-state dynamic nuclear polarization (DNP) of 1H, 13C, and 15N at magnetic fields of 5, 9.4, and 14.1 T. Both ions are half-integer high-spin systems with a zero-field splitting and therefore exhibit a broadening of the mS = -1/2 ↔ +1/2 central transition which scales inversely with the external field strength. We investigate experimentally the influence of the chelator molecule, strong hyperfine coupling to the metal nucleus, and deuteration of the bulk matrix on DNP properties. At small Gd-DOTA concentrations the narrow central transition allows us to polarize nuclei with small gyromagnetic ratio such as 13C and even 15N via the solid effect. We demonstrate that enhancements observed are limited by the available microwave power and that large enhancement factors of >100 (for 1H) and on the order of 1000 (for 13C) can be achieved in the saturation limit even at 80 K. At larger Gd(iii) concentrations (≥10 mM) where dipolar couplings between two neighboring Gd3+ complexes become substantial a transition towards cross effect as dominating DNP mechanism is observed. Furthermore, the slow spin-diffusion between 13C and 15N, respectively, allows for temporally resolved observation of enhanced polarization spreading from nuclei close to the paramagnetic ion towards nuclei further removed. Subsequently, we present preliminary DNP experiments on ubiquitin by site-directed spin-labeling with Gd3+ chelator tags. The results hold promise towards applications of such paramagnetically labeled proteins for DNP applications in biophysical chemistry and/or structural biology.
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Affiliation(s)
- Monu Kaushik
- Institute of Physical and Theoretical Chemistry and Institute of Biophysical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt am Main, Germany.
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27
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Akbey Ü, Oschkinat H. Structural biology applications of solid state MAS DNP NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 269:213-224. [PMID: 27095695 DOI: 10.1016/j.jmr.2016.04.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 04/05/2016] [Accepted: 04/05/2016] [Indexed: 06/05/2023]
Abstract
Dynamic Nuclear Polarization (DNP) has long been an aim for increasing sensitivity of nuclear magnetic resonance (NMR) spectroscopy, delivering spectra in shorter experiment times or of smaller sample amounts. In recent years, it has been applied in magic angle spinning (MAS) solid-state NMR to a large range of samples, including biological macromolecules and functional materials. New research directions in structural biology can be envisaged by DNP, facilitating investigations on very large complexes or very heterogeneous samples. Here we present a summary of state of the art DNP MAS NMR spectroscopy and its applications to structural biology, discussing the technical challenges and factors affecting DNP performance.
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Affiliation(s)
- Ümit Akbey
- Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Høegh-Guldbergs Gade 6B, 8000 Aarhus C, Denmark; Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
| | - Hartmut Oschkinat
- Leibniz Institute für Molekulare Pharmakologie (FMP), NMR Supported Structural Biology, Robert Roessle Str. 10, 13125 Berlin, Germany.
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Viennet T, Viegas A, Kuepper A, Arens S, Gelev V, Petrov O, Grossmann TN, Heise H, Etzkorn M. Selective Protein Hyperpolarization in Cell Lysates Using Targeted Dynamic Nuclear Polarization. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603205] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Thibault Viennet
- Institute of Physical Biology; Heinrich Heine University; Universitätsstr. 1 40225 Düsseldorf Germany
- Institute of Complex Systems (ICS-6); Forschungszentrum Jülich; Wilhelm Jonen Strasse Jülich Germany
| | - Aldino Viegas
- Institute of Physical Biology; Heinrich Heine University; Universitätsstr. 1 40225 Düsseldorf Germany
- Institute of Complex Systems (ICS-6); Forschungszentrum Jülich; Wilhelm Jonen Strasse Jülich Germany
| | - Arne Kuepper
- Chemical Genomics Centre of the Max Planck Society; Otto-Hahn-Str. 15 44227 Dortmund Germany
| | - Sabine Arens
- Institute of Physical Biology; Heinrich Heine University; Universitätsstr. 1 40225 Düsseldorf Germany
- Institute of Complex Systems (ICS-6); Forschungszentrum Jülich; Wilhelm Jonen Strasse Jülich Germany
| | - Vladimir Gelev
- Faculty of Chemistry and Pharmacy; Sofia University; 1 James Bourchier Blvd. 1164 Sofia Bulgaria
| | - Ognyan Petrov
- Faculty of Chemistry and Pharmacy; Sofia University; 1 James Bourchier Blvd. 1164 Sofia Bulgaria
| | - Tom N. Grossmann
- Chemical Genomics Centre of the Max Planck Society; Otto-Hahn-Str. 15 44227 Dortmund Germany
- VU University Amsterdam; Department of Chemistry and Pharmaceutical Sciences; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Henrike Heise
- Institute of Physical Biology; Heinrich Heine University; Universitätsstr. 1 40225 Düsseldorf Germany
- Institute of Complex Systems (ICS-6); Forschungszentrum Jülich; Wilhelm Jonen Strasse Jülich Germany
| | - Manuel Etzkorn
- Institute of Physical Biology; Heinrich Heine University; Universitätsstr. 1 40225 Düsseldorf Germany
- Institute of Complex Systems (ICS-6); Forschungszentrum Jülich; Wilhelm Jonen Strasse Jülich Germany
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Viennet T, Viegas A, Kuepper A, Arens S, Gelev V, Petrov O, Grossmann TN, Heise H, Etzkorn M. Selective Protein Hyperpolarization in Cell Lysates Using Targeted Dynamic Nuclear Polarization. Angew Chem Int Ed Engl 2016; 55:10746-50. [DOI: 10.1002/anie.201603205] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Thibault Viennet
- Institute of Physical Biology; Heinrich Heine University; Universitätsstr. 1 40225 Düsseldorf Germany
- Institute of Complex Systems (ICS-6); Forschungszentrum Jülich; Wilhelm Jonen Strasse Jülich Germany
| | - Aldino Viegas
- Institute of Physical Biology; Heinrich Heine University; Universitätsstr. 1 40225 Düsseldorf Germany
- Institute of Complex Systems (ICS-6); Forschungszentrum Jülich; Wilhelm Jonen Strasse Jülich Germany
| | - Arne Kuepper
- Chemical Genomics Centre of the Max Planck Society; Otto-Hahn-Str. 15 44227 Dortmund Germany
| | - Sabine Arens
- Institute of Physical Biology; Heinrich Heine University; Universitätsstr. 1 40225 Düsseldorf Germany
- Institute of Complex Systems (ICS-6); Forschungszentrum Jülich; Wilhelm Jonen Strasse Jülich Germany
| | - Vladimir Gelev
- Faculty of Chemistry and Pharmacy; Sofia University; 1 James Bourchier Blvd. 1164 Sofia Bulgaria
| | - Ognyan Petrov
- Faculty of Chemistry and Pharmacy; Sofia University; 1 James Bourchier Blvd. 1164 Sofia Bulgaria
| | - Tom N. Grossmann
- Chemical Genomics Centre of the Max Planck Society; Otto-Hahn-Str. 15 44227 Dortmund Germany
- VU University Amsterdam; Department of Chemistry and Pharmaceutical Sciences; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Henrike Heise
- Institute of Physical Biology; Heinrich Heine University; Universitätsstr. 1 40225 Düsseldorf Germany
- Institute of Complex Systems (ICS-6); Forschungszentrum Jülich; Wilhelm Jonen Strasse Jülich Germany
| | - Manuel Etzkorn
- Institute of Physical Biology; Heinrich Heine University; Universitätsstr. 1 40225 Düsseldorf Germany
- Institute of Complex Systems (ICS-6); Forschungszentrum Jülich; Wilhelm Jonen Strasse Jülich Germany
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Smith AN, Long JR. Dynamic Nuclear Polarization as an Enabling Technology for Solid State Nuclear Magnetic Resonance Spectroscopy. Anal Chem 2016; 88:122-32. [PMID: 26594903 PMCID: PMC5704910 DOI: 10.1021/acs.analchem.5b04376] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Adam N Smith
- Department of Chemistry, University of Florida , 214 Leigh Hall, Gainesville, Florida 32611-7200, United States
| | - Joanna R Long
- Department of Biochemistry and Molecular Biology, University of Florida , P. O. Box 100245, Gainesville, Florida 32610-0245, United States
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Wenk P, Kaushik M, Richter D, Vogel M, Suess B, Corzilius B. Dynamic nuclear polarization of nucleic acid with endogenously bound manganese. JOURNAL OF BIOMOLECULAR NMR 2015. [PMID: 26219517 DOI: 10.1007/s10858-015-9972-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
We report the direct dynamic nuclear polarization (DNP) of (13)C nuclei of a uniformly [(13)C,(15)N]-labeled, paramagnetic full-length hammerhead ribozyme (HHRz) complex with Mn(2+) where the enhanced polarization is fully provided by the endogenously bound metal ion and no exogenous polarizing agent is added. A (13)C enhancement factor of ε = 8 was observed by intra-complex DNP at 9.4 T. In contrast, "conventional" indirect and direct DNP experiments were performed using AMUPol as polarizing agent where we obtained a (1)H enhancement factor of ε ≈ 250. Comparison with the diamagnetic (Mg(2+)) HHRz complex shows that the presence of Mn(2+) only marginally influences the (DNP-enhanced) NMR properties of the RNA. Furthermore two-dimensional correlation spectra ((15)N-(13)C and (13)C-(13)C) reveal structural inhomogeneity in the frozen, amorphous state indicating the coexistence of several conformational states. These demonstrations of intra-complex DNP using an endogenous metal ion as well as DNP-enhanced MAS NMR of RNA in general yield important information for the development of new methods in structural biology.
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Affiliation(s)
- Patricia Wenk
- Institute of Physical und Theoretical Chemistry, Institute of Biophysical Chemistry und Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Max-von-Laue-Str. 7-9, 60438, Frankfurt am Main, Germany
- Werner Siemens Imaging Center and Department of Preclinical Imaging and Radiopharmacy, University of Tübingen, Röntgenweg 13, 72076, Tübingen, Germany
| | - Monu Kaushik
- Institute of Physical und Theoretical Chemistry, Institute of Biophysical Chemistry und Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Max-von-Laue-Str. 7-9, 60438, Frankfurt am Main, Germany
| | - Diane Richter
- Institute of Physical und Theoretical Chemistry, Institute of Biophysical Chemistry und Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Max-von-Laue-Str. 7-9, 60438, Frankfurt am Main, Germany
| | - Marc Vogel
- Department of Biology, Technical University Darmstadt, Schnittspahnstraße 10, 64287, Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, Schnittspahnstraße 10, 64287, Darmstadt, Germany
| | - Björn Corzilius
- Institute of Physical und Theoretical Chemistry, Institute of Biophysical Chemistry und Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Max-von-Laue-Str. 7-9, 60438, Frankfurt am Main, Germany.
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Voinov MA, Good DB, Ward ME, Milikisiyants S, Marek A, Caporini MA, Rosay M, Munro RA, Ljumovic M, Brown LS, Ladizhansky V, Smirnov AI. Cysteine-Specific Labeling of Proteins with a Nitroxide Biradical for Dynamic Nuclear Polarization NMR. J Phys Chem B 2015; 119:10180-90. [DOI: 10.1021/acs.jpcb.5b05230] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Maxim A. Voinov
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | | | | | - Sergey Milikisiyants
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Antonin Marek
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Marc A. Caporini
- Bruker Biospin Ltd., Billerica, Massachusetts 01821, United States
| | - Melanie Rosay
- Bruker Biospin Ltd., Billerica, Massachusetts 01821, United States
| | | | | | | | | | - Alex I. Smirnov
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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van der Cruijsen EAW, Koers EJ, Sauvée C, Hulse RE, Weingarth M, Ouari O, Perozo E, Tordo P, Baldus M. Biomolecular DNP-Supported NMR Spectroscopy using Site-Directed Spin Labeling. Chemistry 2015; 21:12971-7. [DOI: 10.1002/chem.201501376] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Indexed: 12/24/2022]
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Georgelis N, Nikolaidis N, Cosgrove DJ. Bacterial expansins and related proteins from the world of microbes. Appl Microbiol Biotechnol 2015; 99:3807-23. [PMID: 25833181 PMCID: PMC4427351 DOI: 10.1007/s00253-015-6534-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 03/05/2015] [Accepted: 03/09/2015] [Indexed: 12/31/2022]
Abstract
The discovery of microbial expansins emerged from studies of the mechanism of plant cell growth and the molecular basis of plant cell wall extensibility. Expansins are wall-loosening proteins that are universal in the plant kingdom and are also found in a small set of phylogenetically diverse bacteria, fungi, and other organisms, most of which colonize plant surfaces. They loosen plant cell walls without detectable lytic activity. Bacterial expansins have attracted considerable attention recently for their potential use in cellulosic biomass conversion for biofuel production, as a means to disaggregate cellulosic structures by nonlytic means ("amorphogenesis"). Evolutionary analysis indicates that microbial expansins originated by multiple horizontal gene transfers from plants. Crystallographic analysis of BsEXLX1, the expansin from Bacillus subtilis, shows that microbial expansins consist of two tightly packed domains: the N-terminal domain D1 has a double-ψ β-barrel fold similar to glycosyl hydrolase family-45 enzymes but lacks catalytic residues usually required for hydrolysis; the C-terminal domain D2 has a unique β-sandwich fold with three co-linear aromatic residues that bind β-1,4-glucans by hydrophobic interactions. Genetic deletion of expansin in Bacillus and Clavibacter cripples their ability to colonize plant tissues. We assess reports that expansin addition enhances cellulose breakdown by cellulase and compare expansins with distantly related proteins named swollenin, cerato-platanin, and loosenin. We end in a speculative vein about the biological roles of microbial expansins and their potential applications. Advances in this field will be aided by a deeper understanding of how these proteins modify cellulosic structures.
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Affiliation(s)
| | - Nikolas Nikolaidis
- Department of Biological Science, California State University, Fullerton, CA 92831, USA
| | - Daniel J. Cosgrove
- Department of Biology, Penn State University, University Park, PA 16802, USA
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Shi F, Coffey A, Waddell KW, Chekmenev EY, Goodson BM. Nanoscale Catalysts for NMR Signal Enhancement by Reversible Exchange. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2015; 119:7525-7533. [PMID: 26185545 PMCID: PMC4501382 DOI: 10.1021/acs.jpcc.5b02036] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 03/11/2015] [Indexed: 05/24/2023]
Abstract
Two types of nanoscale catalysts were created to explore NMR signal enhancement via reversible exchange (SABRE) at the interface between heterogeneous and homogeneous conditions. Nanoparticle and polymer comb variants were synthesized by covalently tethering Ir-based organometallic catalysts to support materials comprised of TiO2/PMAA (poly methacrylic acid) and PVP (polyvinyl pyridine), respectively, and characterized by AAS, NMR, and DLS. Following parahydrogen (pH2) gas delivery to mixtures containing one type of "nano-SABRE" catalyst particles, a target substrate, and ethanol, up to ~(-)40-fold and ~(-)7-fold 1H NMR signal enhancements were observed for pyridine substrates using the nanoparticle and polymer comb catalysts, respectively, following transfer to high field (9.4 T). These enhancements appear to result from intact particles and not from any catalyst molecules leaching from their supports; unlike the case with homogeneous SABRE catalysts, high-field (in situ) SABRE effects were generally not observed with the nanoscale catalysts. The potential for separation and reuse of such catalyst particles is also demonstrated. Taken together, these results support the potential utility of rational design at molecular, mesoscopic, and macroscopic/engineering levels for improving SABRE and HET-SABRE (heterogeneous-SABRE) for applications varying from fundamental studies of catalysis to biomedical imaging.
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Affiliation(s)
- Fan Shi
- Department
of Chemistry and Biochemistry, Southern
Illinois University, Carbondale, Illinois 62901, United States
| | - Aaron
M. Coffey
- Institute of Imaging
Science, Department of Radiology, Department of Physics, Department of Biomedical
Engineering, Vanderbilt-Ingram Cancer Center (VICC), and Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232-2310, United States
| | - Kevin W. Waddell
- Institute of Imaging
Science, Department of Radiology, Department of Physics, Department of Biomedical
Engineering, Vanderbilt-Ingram Cancer Center (VICC), and Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232-2310, United States
| | - Eduard Y. Chekmenev
- Institute of Imaging
Science, Department of Radiology, Department of Physics, Department of Biomedical
Engineering, Vanderbilt-Ingram Cancer Center (VICC), and Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232-2310, United States
| | - Boyd M. Goodson
- Department
of Chemistry and Biochemistry, Southern
Illinois University, Carbondale, Illinois 62901, United States
- Materials
Technology Center, Southern Illinois University, Carbondale, Illinois 62901, United States
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36
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Lee D, Hediger S, De Paëpe G. Is solid-state NMR enhanced by dynamic nuclear polarization? SOLID STATE NUCLEAR MAGNETIC RESONANCE 2015; 66-67:6-20. [PMID: 25779337 DOI: 10.1016/j.ssnmr.2015.01.003] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 01/27/2015] [Accepted: 01/28/2015] [Indexed: 05/03/2023]
Abstract
The recent trend of high-field (~5-20 T), low-temperature (~100 K) ssNMR combined with dynamic nuclear polarization (DNP) under magic angle spinning (MAS) conditions is analyzed. A brief overview of the current theory of hyperpolarization for so-called MAS-DNP experiments is given, along with various reasons why the DNP-enhancement, the ratio of the NMR signal intensities obtained in the presence and absence of microwave irradiation suitable for hyperpolarization, should not be used alone to gauge the value of performing MAS-DNP experiments relative to conventional ssNMR. This is demonstrated through a dissection of the current conditions required for MAS-DNP with particular attention to resulting absolute sensitivities and spectral resolution. Consequently, sample preparation methods specifically avoiding the surplus of glass-forming solvents so as to improve the absolute sensitivity and resolution are discussed, as are samples that are intrinsically pertinent for MAS-DNP studies (high surface area, amorphous, and porous). Owing to their pertinence, examples of recent applications on these types of samples where chemically-relevant information has been obtained that would have been impossible without the sensitivity increases bestowed by MAS-DNP are also detailed. Additionally, a promising further implementation for MAS-DNP is exampled, whereby the sensitivity improvements shown for (correlation) spectroscopy of nuclei at low natural isotopic abundance, facilitate internuclear distance measurements, especially for long distances (absence of dipolar truncation). Finally, we give some speculative perspectives for MAS-DNP.
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Affiliation(s)
- Daniel Lee
- Univ. Grenoble Alpes, INAC, SCIB, F-38000 Grenoble, France; CEA, INAC, SCIB, F-38000 Grenoble, France.
| | - Sabine Hediger
- Univ. Grenoble Alpes, INAC, SCIB, F-38000 Grenoble, France; CEA, INAC, SCIB, F-38000 Grenoble, France; CNRS, SCIB, F-38000 Grenoble, France
| | - Gaël De Paëpe
- Univ. Grenoble Alpes, INAC, SCIB, F-38000 Grenoble, France; CEA, INAC, SCIB, F-38000 Grenoble, France
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37
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Quinn CM, Lu M, Suiter CL, Hou G, Zhang H, Polenova T. Magic angle spinning NMR of viruses. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 86-87:21-40. [PMID: 25919197 PMCID: PMC4413014 DOI: 10.1016/j.pnmrs.2015.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 01/27/2015] [Accepted: 02/08/2015] [Indexed: 05/02/2023]
Abstract
Viruses, relatively simple pathogens, are able to replicate in many living organisms and to adapt to various environments. Conventional atomic-resolution structural biology techniques, X-ray crystallography and solution NMR spectroscopy provided abundant information on the structures of individual proteins and nucleic acids comprising viruses; however, viral assemblies are not amenable to analysis by these techniques because of their large size, insolubility, and inherent lack of long-range order. In this article, we review the recent advances in magic angle spinning NMR spectroscopy that enabled atomic-resolution analysis of structure and dynamics of large viral systems and give examples of several exciting case studies.
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Affiliation(s)
- Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
| | - Manman Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
| | - Christopher L Suiter
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
| | - Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
| | - Huilan Zhang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States.
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
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Li S, Trébosc J, Lafon O, Zhou L, Shen M, Pourpoint F, Amoureux JP, Deng F. Observation of 1H-13C and 1H-1H proximities in a paramagnetic solid by NMR at high magnetic field under ultra-fast MAS. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 251:36-42. [PMID: 25557861 DOI: 10.1016/j.jmr.2014.11.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 11/28/2014] [Accepted: 11/30/2014] [Indexed: 06/04/2023]
Abstract
The assignment of NMR signals in paramagnetic solids is often challenging since: (i) the large paramagnetic shifts often mask the diamagnetic shifts specific to the local chemical environment, and (ii) the hyperfine interactions with unpaired electrons broaden the NMR spectra and decrease the coherence lifetime, thus reducing the efficiency of usual homo- and hetero-nuclear NMR correlation experiments. Here we show that the assignment of (1)H and (13)C signals in isotopically unmodified paramagnetic compounds with moderate hyperfine interactions can be facilitated by the use of two two-dimensional (2D) experiments: (i) (1)H-(13)C correlations with (1)H detection and (ii) (1)H-(1)H double-quantum↔single-quantum correlations. These methods are experimentally demonstrated on isotopically unmodified copper (II) complex of l-alanine at high magnetic field (18.8 T) and ultra-fast Magic Angle Spinning (MAS) frequency of 62.5 kHz. Compared to (13)C detection, we show that (1)H detection leads to a 3-fold enhancement in sensitivity for (1)H-(13)C 2D correlation experiments. By combining (1)H-(13)C and (1)H-(1)H 2D correlation experiments with the analysis of (13)C longitudinal relaxation times, we have been able to assign the (1)H and (13)C signals of each l-alanine ligand.
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Affiliation(s)
- Shenhui Li
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Julien Trébosc
- Univ. Lille North of France, Unit of Catalysis and Chemistry of Solids (UCCS), CNRS UMR 8181, ENSCL, Univ. Lille 1, Villeneuve d'Ascq 59652, France
| | - Olivier Lafon
- Univ. Lille North of France, Unit of Catalysis and Chemistry of Solids (UCCS), CNRS UMR 8181, ENSCL, Univ. Lille 1, Villeneuve d'Ascq 59652, France.
| | - Lei Zhou
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Ming Shen
- Univ. Lille North of France, Unit of Catalysis and Chemistry of Solids (UCCS), CNRS UMR 8181, ENSCL, Univ. Lille 1, Villeneuve d'Ascq 59652, France; Physics Department & Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai 200062, China
| | - Frédérique Pourpoint
- Univ. Lille North of France, Unit of Catalysis and Chemistry of Solids (UCCS), CNRS UMR 8181, ENSCL, Univ. Lille 1, Villeneuve d'Ascq 59652, France
| | - Jean-Paul Amoureux
- Univ. Lille North of France, Unit of Catalysis and Chemistry of Solids (UCCS), CNRS UMR 8181, ENSCL, Univ. Lille 1, Villeneuve d'Ascq 59652, France; Physics Department & Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai 200062, China.
| | - Feng Deng
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
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Koers EJ, van der Cruijsen EAW, Rosay M, Weingarth M, Prokofyev A, Sauvée C, Ouari O, van der Zwan J, Pongs O, Tordo P, Maas WE, Baldus M. NMR-based structural biology enhanced by dynamic nuclear polarization at high magnetic field. JOURNAL OF BIOMOLECULAR NMR 2014; 60:157-68. [PMID: 25284462 DOI: 10.1007/s10858-014-9865-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 09/23/2014] [Indexed: 05/04/2023]
Abstract
Dynamic nuclear polarization (DNP) has become a powerful method to enhance spectroscopic sensitivity in the context of magnetic resonance imaging and nuclear magnetic resonance spectroscopy. We show that, compared to DNP at lower field (400 MHz/263 GHz), high field DNP (800 MHz/527 GHz) can significantly enhance spectral resolution and allows exploitation of the paramagnetic relaxation properties of DNP polarizing agents as direct structural probes under magic angle spinning conditions. Applied to a membrane-embedded K(+) channel, this approach allowed us to refine the membrane-embedded channel structure and revealed conformational substates that are present during two different stages of the channel gating cycle. High-field DNP thus offers atomic insight into the role of molecular plasticity during the course of biomolecular function in a complex cellular environment.
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Affiliation(s)
- Eline J Koers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
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40
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Miller AF. Solid-state NMR of flavins and flavoproteins. Methods Mol Biol 2014; 1146:307-40. [PMID: 24764096 DOI: 10.1007/978-1-4939-0452-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Why apply solid-state NMR (SSNMR) to flavins and flavoproteins? NMR provides information on an atom-specific basis about chemical functionality, structure, proximity to other groups, and dynamics of the system. Thus, it has become indispensable to the study of chemicals, materials, catalysts, and biomolecules. It is no surprise then that NMR has a great deal to offer in the study of flavins and flavoenzymes. In general, their catalytic or electron-transfer activity resides essentially in the flavin, a molecule eminently accessible by NMR. However, the specific reactivity displayed depends on a host of subtle interactions whereby the protein biases and reshapes the flavin's propensities to activate it for one reaction while suppressing other aspects of this cofactor's prodigious repertoire (Massey et al., J Biol Chem 244:3999-4006, 1969; Müller, Z Naturforsch 27B:1023-1026, 1972; Joosten and van Berkel, Curr Opin Struct Biol 11:195-202, 2007). Thus, we are fascinated to learn about how the flavin cofactor of one enzyme is, and is not, like the flavin cofactor of another. In what follows, we describe how the capabilities of SSNMR can help and are beginning to bear fruit in this exciting endeavor.
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Affiliation(s)
- Anne-Frances Miller
- Department of Chemistry, University of Kentucky, 505 Rose St, Lexington, KY, 40506-0055, USA,
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Corzilius B, Andreas LB, Smith AA, Ni QZ, Griffin RG. Paramagnet induced signal quenching in MAS-DNP experiments in frozen homogeneous solutions. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 240:113-23. [PMID: 24394190 PMCID: PMC3951579 DOI: 10.1016/j.jmr.2013.11.013] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 11/21/2013] [Accepted: 11/22/2013] [Indexed: 05/06/2023]
Abstract
The effects of nuclear signal quenching induced by the presence of a paramagnetic polarizing agent are documented for conditions used in magic angle spinning (MAS)-dynamic nuclear polarization (DNP) experiments on homogeneous solutions. In particular, we present a detailed analysis of three time constants: (1) the longitudinal build-up time constant TB for (1)H; (2) the rotating frame relaxation time constant T1ρ for (1)H and (13)C and (3) T2 of (13)C, the transverse relaxation time constant in the laboratory frame. These relaxation times were measured during microwave irradiation at a magnetic field of 5 T (140 GHz) as a function of the concentration of four polarizing agents: TOTAPOL, 4-amino-TEMPO, trityl (OX063), and Gd-DOTA and are compared to those obtained for a sample lacking paramagnetic doping. We also report the EPR relaxation time constants T1S and T2S, the DNP enhancements, ε, and the parameter E, defined below, which measures the sensitivity enhancement for the four polarizing agents as a function of the electron concentration. We observe substantial intensity losses (paramagnetic quenching) with all of the polarizing agents due to broadening mechanisms and cross relaxation during MAS. In particular, the monoradical trityl and biradical TOTAPOL induce ∼40% and 50% loss of signal intensity. In contrast there is little suppression of signal intensity in static samples containing these paramagnetic species. Despite the losses due to quenching, we find that all of the polarizing agents provide substantial gains in signal intensity with DNP, and in particular that the net enhancement is optimal for biradicals that operate with the cross effect. We discuss the possibility that much of this polarization loss can be regained with the development of instrumentation and methods to perform electron decoupling.
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Affiliation(s)
- Björn Corzilius
- Francis Bitter Magnet Laboratory, Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Loren B Andreas
- Francis Bitter Magnet Laboratory, Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Albert A Smith
- Francis Bitter Magnet Laboratory, Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Qing Zhe Ni
- Francis Bitter Magnet Laboratory, Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Robert G Griffin
- Francis Bitter Magnet Laboratory, Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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Cheng CY, Han S. Dynamic Nuclear Polarization Methods in Solids and Solutions to Explore Membrane Proteins and Membrane Systems. Annu Rev Phys Chem 2013; 64:507-32. [DOI: 10.1146/annurev-physchem-040412-110028] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Membrane proteins regulate vital cellular processes, including signaling, ion transport, and vesicular trafficking. Obtaining experimental access to their structures, conformational fluctuations, orientations, locations, and hydration in membrane environments, as well as the lipid membrane properties, is critical to understanding their functions. Dynamic nuclear polarization (DNP) of frozen solids can dramatically boost the sensitivity of current solid-state nuclear magnetic resonance tools to enhance access to membrane protein structures in native membrane environments. Overhauser DNP in the solution state can map out the local and site-specific hydration dynamics landscape of membrane proteins and lipid membranes, critically complementing the structural and dynamics information obtained by electron paramagnetic resonance spectroscopy. Here, we provide an overview of how DNP methods in solids and solutions can significantly increase our understanding of membrane protein structures, dynamics, functions, and hydration in complex biological membrane environments.
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Affiliation(s)
- Chi-Yuan Cheng
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
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Ong TC, Mak-Jurkauskas ML, Walish JJ, Michaelis VK, Corzilius B, Smith AA, Clausen AM, Cheetham JC, Swager TM, Griffin RG. Solvent-free dynamic nuclear polarization of amorphous and crystalline ortho-terphenyl. J Phys Chem B 2013; 117:3040-6. [PMID: 23421391 DOI: 10.1021/jp311237d] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dynamic nuclear polarization (DNP) of amorphous and crystalline ortho-terphenyl (OTP) in the absence of glass forming agents is presented in order to gauge the feasibility of applying DNP to pharmaceutical solid-state nuclear magnetic resonance experiments and to study the effect of intermolecular structure, or lack thereof, on the DNP enhancement. By way of (1)H-(13)C cross-polarization, we obtained a DNP enhancement (ε) of 58 for 95% deuterated OTP in the amorphous state using the biradical bis-TEMPO terephthalate (bTtereph) and ε of 36 in the crystalline state. Measurements of the (1)H T1 and electron paramagnetic resonance experiments showed the crystallization process led to phase separation of the polarization agent, creating an inhomogeneous distribution of radicals within the sample. Consequently, the effective radical concentration was decreased in the bulk OTP phase, and long-range (1)H-(1)H spin diffusion was the main polarization propagation mechanism. Preliminary DNP experiments with the glass-forming anti-inflammation drug, indomethacin, showed promising results, and further studies are underway to prepare DNP samples using pharmaceutical techniques.
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Affiliation(s)
- Ta-Chung Ong
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Improved Dynamic Nuclear Polarization Surface-Enhanced NMR Spectroscopy through Controlled Incorporation of Deuterated Functional Groups. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208699] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Zagdoun A, Rossini AJ, Conley MP, Grüning WR, Schwarzwälder M, Lelli M, Franks WT, Oschkinat H, Copéret C, Emsley L, Lesage A. Improved dynamic nuclear polarization surface-enhanced NMR spectroscopy through controlled incorporation of deuterated functional groups. Angew Chem Int Ed Engl 2013; 52:1222-5. [PMID: 23293096 DOI: 10.1002/anie.201208699] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Alexandre Zagdoun
- Centre de RMN à Très Hauts Champs, Université de Lyon (CNRS/ENS/UCB Lyon 1), 5 rue de la Doua, 69100 Villeurbanne, France
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Abstract
Nuclear magnetic resonance (NMR) spectroscopy is one of the most commonly used spectroscopic techniques to obtain information on the structure and dynamics of biological and chemical materials. A variety of samples can be studied including solutions, crystalline solids, powders and hydrated protein extracts. However, biological NMR spectroscopy is limited to concentrated samples, typically in the millimolar range, due to its intrinsic low sensitivity compared to other techniques such as fluorescence or electron paramagnetic resonance (EPR) spectroscopy.Dynamic nuclear polarization (DNP) is a method that increases the sensitivity of NMR by several orders of magnitude. It exploits a polarization transfer from unpaired electrons to neighboring nuclei which leads to an absolute increase of the signal-to-noise ratio (S/N). Consequently, biological samples with much lower concentrations can now be studied in hours or days compared to several weeks.This chapter will explain the different types of DNP enhanced NMR experiments, focusing primarily on solid-state magic angle spinning (MAS) DNP, its applications, and possible means of improvement.
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Thurber KR, Potapov A, Yau WM, Tycko R. Solid state nuclear magnetic resonance with magic-angle spinning and dynamic nuclear polarization below 25 K. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 226:100-6. [PMID: 23238592 PMCID: PMC3529848 DOI: 10.1016/j.jmr.2012.11.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 11/10/2012] [Accepted: 11/13/2012] [Indexed: 05/05/2023]
Abstract
We describe an apparatus for solid state nuclear magnetic resonance (NMR) with dynamic nuclear polarization (DNP) and magic-angle spinning (MAS) at 20-25 K and 9.4 Tesla. The MAS NMR probe uses helium to cool the sample space and nitrogen gas for MAS drive and bearings, as described earlier, but also includes a corrugated waveguide for transmission of microwaves from below the probe to the sample. With a 30 mW circularly polarized microwave source at 264 GHz, MAS at 6.8 kHz, and 21 K sample temperature, greater than 25-fold enhancements of cross-polarized (13)C NMR signals are observed in spectra of frozen glycerol/water solutions containing the triradical dopant DOTOPA-TEMPO when microwaves are applied. As demonstrations, we present DNP-enhanced one-dimensional and two-dimensional (13)C MAS NMR spectra of frozen solutions of uniformly (13)C-labeled l-alanine and melittin, a 26-residue helical peptide that we have synthesized with four uniformly (13)C-labeled amino acids.
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Affiliation(s)
- Kent R Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States.
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Abstract
Solid-state NMR spectroscopy proved to be a versatile tool for characterization of structure and dynamics of complex biochemical systems. In particular, magic angle spinning (MAS) solid-state NMR came to maturity for application towards structural elucidation of biological macromolecules. Current challenges in applying solid-state NMR as well as progress achieved recently will be discussed in the following chapter focusing on conceptual aspects important for structural elucidation of proteins.
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Affiliation(s)
- Henrik Müller
- Institute of Physical Biology, Heinrich-Heine-University of Düsseldorf, 40225, Düsseldorf, Germany
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Mentink-Vigier F, Akbey U, Hovav Y, Vega S, Oschkinat H, Feintuch A. Fast passage dynamic nuclear polarization on rotating solids. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 224:13-21. [PMID: 23000976 DOI: 10.1016/j.jmr.2012.08.013] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 08/12/2012] [Accepted: 08/15/2012] [Indexed: 05/06/2023]
Abstract
Magic Angle Spinning (MAS) Dynamic Nuclear Polarization (DNP) has proven to be a very powerful way to improve the signal to noise ratio of NMR experiments on solids. The experiments have in general been interpreted considering the Solid-Effect (SE) and Cross-Effect (CE) DNP mechanisms while ignoring the influence of sample spinning. In this paper, we show experimental data of MAS-DNP enhancements of (1)H and (13)C in proline and SH3 protein in glass forming water/glycerol solvent containing TOTAPOL. We also introduce a theoretical model that aims at explaining how the nuclear polarization is built in MAS-DNP experiments. By using Liouville space based simulations to include relaxation on two simple spin models, {electron-nucleus} and {electron-electron-nucleus}, we explain how the basic MAS-SE-DNP and MAS-CE-DNP processes work. The importance of fast energy passages and short level anti-crossing is emphasized and the differences between static DNP and MAS-DNP is explained. During a single rotor cycle the enhancement in the {electron-electron-nucleus} system arises from MAS-CE-DNP involving at least three kinds of two-level fast passages: an electron-electron dipolar anti-crossing, a single quantum electron MW encounter and an anti-crossing at the CE condition inducing nuclear polarization in- or decrements. Numerical, powder-averaged, simulations were performed in order to check the influence of the experimental parameters on the enhancement efficiencies. In particular we show that the spinning frequency dependence of the theoretical MAS-CE-DNP enhancement compares favorably with the experimental (1)H and (13)C MAS-DNP enhancements of proline and SH3.
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Rossini AJ, Zagdoun A, Hegner F, Schwarzwälder M, Gajan D, Copéret C, Lesage A, Emsley L. Dynamic nuclear polarization NMR spectroscopy of microcrystalline solids. J Am Chem Soc 2012; 134:16899-908. [PMID: 22967206 DOI: 10.1021/ja308135r] [Citation(s) in RCA: 192] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dynamic nuclear polarization (DNP) solid-state NMR has been applied to powdered microcrystalline solids to obtain sensitivity enhancements on the order of 100. Glucose, sulfathiazole, and paracetamol were impregnated with bis-nitroxide biradical (bis-cyclohexyl-TEMPO-bisketal, bCTbK) solutions of organic solvents. The organic solvents were carefully chosen to be nonsolvents for the compounds, so that DNP-enhanced solid-state NMR spectra of the unaltered solids could be acquired. A theoretical model is presented that illustrates that for externally doped organic solids characterized by long spin-lattice relaxation times (T(1)((1)H) > 200 s), (1)H-(1)H spin diffusion can relay enhanced polarization over micrometer length scales yielding substantial DNP enhancements (ε). ε on the order of 60 are obtained for microcrystalline glucose and sulfathiazole at 9.4 T and with temperatures of ca. 105 K. The large gain in sensitivity enables the rapid acquisition of (13)C-(13)C correlation spectra at natural isotopic abundance. It is anticipated that this will be a general method for enhancing the sensitivity of solid-state NMR experiments of organic solids.
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Affiliation(s)
- Aaron J Rossini
- Centre de RMN a Tres Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCB Lyon 1), 69100 Villeurbanne, France
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