1
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Pradhan N, Hilty C. Cross-Polarization of Insensitive Nuclei from Water Protons for Detection of Protein-Ligand Binding. J Am Chem Soc 2024; 146:24754-24758. [PMID: 39225120 PMCID: PMC11403598 DOI: 10.1021/jacs.4c08241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Hyperpolarization derived from water protons enhances the NMR signal of 15N nuclei in a small molecule, enabling the sensitive detection of a protein-ligand interaction. The water hyperpolarized by dissolution dynamic nuclear polarization (D-DNP) acts as a universal signal enhancement agent. The 15N signal of benzamidine was increased by 1480-fold through continuous polarization transfer by J-coupling-mediated cross-polarization (J-CP) via the exchangeable protons. The signal enhancement factor favorably compares to factors of 110- or 17-fold using non-CP-based polarization transfer mechanisms. The hyperpolarization enabled detection of the binding of benzamidine to the target protein trypsin with a single-scan measurement of 15N R2 relaxation. J-CP provides an efficient polarization mechanism for 15N or other low-frequency nuclei near an exchangeable proton. The hyperpolarization transfer sustained within the relaxation time limit of water protons additionally can be applied for the study of macromolecular structure and biological processes.
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Affiliation(s)
- Nirmalya Pradhan
- Chemistry Department, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
| | - Christian Hilty
- Chemistry Department, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
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2
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Levien M, Yang L, van der Ham A, Reinhard M, John M, Purea A, Ganz J, Marquardsen T, Tkach I, Orlando T, Bennati M. Overhauser enhanced liquid state nuclear magnetic resonance spectroscopy in one and two dimensions. Nat Commun 2024; 15:5904. [PMID: 39003303 PMCID: PMC11246421 DOI: 10.1038/s41467-024-50265-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 07/02/2024] [Indexed: 07/15/2024] Open
Abstract
Nuclear magnetic resonance (NMR) is fundamental in the natural sciences, from chemical analysis and structural biology, to medicine and physics. Despite its enormous achievements, one of its most severe limitations is the low sensitivity, which arises from the small population difference of nuclear spin states. Methods such as dissolution dynamic nuclear polarization and parahydrogen induced hyperpolarization can enhance the NMR signal by several orders of magnitude, however, their intrinsic limitations render multidimensional hyperpolarized liquid-state NMR a challenge. Here, we report an instrumental design for 9.4 Tesla liquid-state dynamic nuclear polarization that enabled enhanced high-resolution NMR spectra in one and two-dimensions for small molecules, including drugs and metabolites. Achieved enhancements of up to two orders of magnitude translate to signal acquisition gains up to a factor of 10,000. We show that hyperpolarization can be transferred between nuclei, allowing DNP-enhanced two-dimensional 13C-13C correlation experiments at 13C natural abundance. The enhanced sensitivity opens up perspectives for structural determination of natural products or characterization of drugs, available in small quantities. The results provide a starting point for a broader implementation of DNP in liquid-state NMR.
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Affiliation(s)
- Marcel Levien
- Electron-Spin Resonance Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
- Institute of Physical Chemistry, Department of Chemistry, Georg-August-University, Tammannstr. 6, 37077, Göttingen, Germany
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Luming Yang
- Electron-Spin Resonance Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Alex van der Ham
- Electron-Spin Resonance Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Maik Reinhard
- Electron-Spin Resonance Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
- Institute of Physical Chemistry, Department of Chemistry, Georg-August-University, Tammannstr. 6, 37077, Göttingen, Germany
| | - Michael John
- Institute of Organic and Biomolecular Chemistry, Department of Chemistry, Georg-August-University, Tammannstr. 2, 37077, Göttingen, Germany
| | - Armin Purea
- Bruker Biospin GmbH, Rudolf-Plank-Str. 23, 76275, Ettlingen, Germany
| | - Jürgen Ganz
- Bruker Biospin GmbH, Rudolf-Plank-Str. 23, 76275, Ettlingen, Germany
| | | | - Igor Tkach
- Electron-Spin Resonance Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Tomas Orlando
- Electron-Spin Resonance Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
- National High Magnetic Field Laboratory, 1800 E. Paul Dirac Dr., 32310, Tallahassee, FL, USA
| | - Marina Bennati
- Electron-Spin Resonance Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany.
- Institute of Physical Chemistry, Department of Chemistry, Georg-August-University, Tammannstr. 6, 37077, Göttingen, Germany.
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3
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Zachrdla M, Turhan E, Pötzl C, Sadet A, Vasos PR, Kurzbach D. Hyperpolarized nuclear Overhauser enhancement of alanine methyl groups by doubly relayed proton exchange. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 364:107727. [PMID: 38941676 DOI: 10.1016/j.jmr.2024.107727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 06/03/2024] [Accepted: 06/20/2024] [Indexed: 06/30/2024]
Abstract
Hyperpolarized water in dissolution dynamic nuclear polarization (dDNP) experiments has emerged as a promising method for enhancing nuclear magnetic resonance (NMR) signals, particularly in studies of proteins and peptides. Herein, we focus on the application of "proton exchange-doubly relayed" nuclear Overhauser effects (NOE) from hyperpolarized water to achieve positive signal enhancement of methyl groups in the side chain of an alanine-glycine peptide. In particular, we show a cascade hyperpolarization transfer. Initial proton exchange between solvent and amide introduces hyperpolarization into the peptide. Subsequently, intermolecular NOE relays the hyperpolarization first to Ala-Hα and then in a second step to the Ala-CH3 moiety. Both NOEs have negative signs. Hence, the twice-relayed NOE pathway leads to a positive signal enhancement of the methyl group with respect to the thermal equilibrium magnetization. This effect might indicate a way towards hyperpolarized water-based signal enhancement for methyl groups, which are often used for NMR studies of large proteins in solution.
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Affiliation(s)
- Milan Zachrdla
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria.
| | - Ertan Turhan
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria; University of Vienna, Vienna Doctoral School in Chemistry (DoSChem), Währinger Str. 42, 1090 Vienna, Austria
| | - Christopher Pötzl
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria; University of Vienna, Vienna Doctoral School in Chemistry (DoSChem), Währinger Str. 42, 1090 Vienna, Austria
| | - Aude Sadet
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria; Biophysics and Biomedical Applications Laboratory and Group, LGED, Extreme Light Infrastructure-Nuclear Physics, "Horia Hulubei" National Institute for Physics and Nuclear Engineering IFIN-HH, Reactorului Street, No. 30, 077125 Bucharest-Magurele, Romania
| | - Paul R Vasos
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria; Biophysics and Biomedical Applications Laboratory and Group, LGED, Extreme Light Infrastructure-Nuclear Physics, "Horia Hulubei" National Institute for Physics and Nuclear Engineering IFIN-HH, Reactorului Street, No. 30, 077125 Bucharest-Magurele, Romania; University of Bucharest, Interdisciplinary School for Doctoral Studies (ISDS), 36-46 Bd Kogalniceanu, RO-050107 Bucharest, Romania
| | - Dennis Kurzbach
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
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4
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Stern Q, Reynard-Feytis Q, Elliott SJ, Ceillier M, Cala O, Ivanov K, Jannin S. Rapid and Simple 13C-Hyperpolarization by 1H Dissolution Dynamic Nuclear Polarization Followed by an Inline Magnetic Field Inversion. J Am Chem Soc 2023; 145:27576-27586. [PMID: 38054954 DOI: 10.1021/jacs.3c09209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Dissolution dynamic nuclear polarization (dDNP) is a method of choice for preparing hyperpolarized 13C metabolites such as 1-13C-pyruvate used for in vivo applications, including the real-time monitoring of cancer cell metabolism in human patients. The approach consists of transferring the high polarization of electron spins to nuclear spins via microwave irradiation at low temperatures (1.0-1.5 K) and moderate magnetic fields (3.3-7 T). The solid sample is then dissolved and transferred to an NMR spectrometer or MRI scanner for detection in the liquid state. Common dDNP protocols use direct hyperpolarization of 13C spins reaching polarizations of >50% in ∼1-2 h. Alternatively, 1H spins are polarized before transferring their polarization to 13C spins using cross-polarization, reaching polarization levels similar to those of direct DNP in only ∼20 min. However, it relies on more complex instrumentation, requiring highly skilled personnel. Here, we explore an alternative route using 1H dDNP followed by inline adiabatic magnetic field inversion in the liquid state during the transfer. 1H polarizations of >70% in the solid state are obtained in ∼5-10 min. As the hyperpolarized sample travels from the dDNP polarizer to the NMR spectrometer, it goes through a field inversion chamber, which causes the 1H → 13C polarization transfer. This transfer is made possible by the J-coupling between the heteronuclei, which mixes the Zeeman states at zero-field and causes an antilevel crossing. We report liquid-state 13C polarization up to ∼17% for 3-13C-pyruvate and 13C-formate. The instrumentation needed to perform this experiment in addition to a conventional dDNP polarizer is simple and readily assembled.
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Affiliation(s)
- Quentin Stern
- Université Claude Bernard Lyon 1, CRMN UMR-5082, CNRS, ENS Lyon, Villeurbanne 69100 France
| | - Quentin Reynard-Feytis
- Université Claude Bernard Lyon 1, CRMN UMR-5082, CNRS, ENS Lyon, Villeurbanne 69100 France
| | - Stuart J Elliott
- Université Claude Bernard Lyon 1, CRMN UMR-5082, CNRS, ENS Lyon, Villeurbanne 69100 France
- Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom
| | - Morgan Ceillier
- Université Claude Bernard Lyon 1, CRMN UMR-5082, CNRS, ENS Lyon, Villeurbanne 69100 France
| | - Olivier Cala
- Université Claude Bernard Lyon 1, CRMN UMR-5082, CNRS, ENS Lyon, Villeurbanne 69100 France
| | - Konstantin Ivanov
- International Tomography Center, Siberian Branch of the Russian Academy of Science, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Sami Jannin
- Université Claude Bernard Lyon 1, CRMN UMR-5082, CNRS, ENS Lyon, Villeurbanne 69100 France
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5
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Topor A, Voda MA, Vasos PR. Earth's field NMR relaxation of pre-polarised water protons for real-time detection of free-radical formation. Chem Commun (Camb) 2023; 59:11672-11675. [PMID: 37695610 DOI: 10.1039/d3cc02502k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Real-time imaging of free-radical formation is important in physical chemistry, biochemistry, and radiobiology, especially for the study of radiation dose-rate effects. Herein, we show for the first time that the formation of free radicals during the time course of a chemical reaction can be imaged through NMR relaxation measurements of water protons in the Earth's magnetic field, in an open-coil spectrometer. The relaxation rate constants of water magnetisation are enhanced as reactions leading to the formation of hydroxyl radicals and oxygen proceed on the timescale of tens of minutes. The reaction rate of iodide-catalysed H2O2 decay was followed by Earth-field 1H NMR relaxation in real time. The relaxivities of the reaction product and several other paramagnetic compounds were determined. Spin-trap molecules were then used to capture ˙OH radical species, thus altering the reaction rate in proportion to the formation of new paramagnetic compounds. Thereby, a new experimental method for magnetic resonance imaging of the formation of intermediate and stable radical species in water is proposed.
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Affiliation(s)
- Alexandru Topor
- Biophysics and Biomedical Applications Group and Laboratory, Extreme Light Infrastructure-Nuclear Physics (ELI-NP), Laser Gamma Experiments Department (LGED), "Horia Hulubei" National Institute for Physics and Nuclear Engineering (IFIN-HH), Reactorului Str. 30, Bucharest-Magurele 077125, Romania
- University of Bucharest, Doctoral School of Chemistry, 4-12 Regina Elisabeta Bd, 030018 Bucharest, Romania
- C. D. Nenitzescu Institute of Organic and Supramolecular Chemistry, 202B Splaiul Independenţei Bucharest, Romania
| | - Mihai A Voda
- Biophysics and Biomedical Applications Group and Laboratory, Extreme Light Infrastructure-Nuclear Physics (ELI-NP), Laser Gamma Experiments Department (LGED), "Horia Hulubei" National Institute for Physics and Nuclear Engineering (IFIN-HH), Reactorului Str. 30, Bucharest-Magurele 077125, Romania
| | - Paul R Vasos
- Biophysics and Biomedical Applications Group and Laboratory, Extreme Light Infrastructure-Nuclear Physics (ELI-NP), Laser Gamma Experiments Department (LGED), "Horia Hulubei" National Institute for Physics and Nuclear Engineering (IFIN-HH), Reactorului Str. 30, Bucharest-Magurele 077125, Romania
- University of Bucharest, Interdisciplinary School of Doctoral Studies, ISDS, 4-12 Regina Elisabeta Bd, 030018 Bucharest, Romania.
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6
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Abyzov A, Mandelkow E, Zweckstetter M, Rezaei-Ghaleh N. Fast Motions Dominate Dynamics of Intrinsically Disordered Tau Protein at High Temperatures. Chemistry 2023; 29:e202203493. [PMID: 36579699 DOI: 10.1002/chem.202203493] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/17/2022] [Accepted: 12/21/2022] [Indexed: 12/30/2022]
Abstract
Reorientational dynamics of intrinsically disordered proteins (IDPs) contain multiple motions often clustered around three motional modes: ultrafast librational motions of amide groups, fast local backbone conformational fluctuations and slow chain segmental motions. This dynamic picture is mainly based on 15 N NMR relaxation studies of IDPs at relatively low temperatures where the amide-water proton exchange rates are sufficiently small. Less is known, however, about the dynamics of IDPs at more physiological temperatures. Here, we investigate protein dynamics in a 441-residue long IDP, tau protein, in the temperature range from 0-25 °C, using 15 N NMR relaxation rates and spectral density analysis. While at these temperatures relaxation rates are still better described in terms of amide group librational motions, local backbone dynamics and chain segmental motions, the temperature-dependent trend of spectral densities suggests that the timescales of fast backbone conformational fluctuations and slower chain segmental motions might become inseparable at higher temperatures. Our data demonstrate the remarkable dynamic plasticity of this prototypical IDP and highlight the need for dynamic studies of IDPs at multiple temperatures.
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Affiliation(s)
- Anton Abyzov
- Translational Structural Biology Group, German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, D-37075, Göttingen, Germany
| | - Eckhard Mandelkow
- German Center for Neurodegenerative Diseases (DZNE), Venusberg-Campus 1, D-53127, Bonn, Germany
- Research Center CAESAR, Ludwig-Erhard-Allee 2, D-53175, Bonn, Germany
| | - Markus Zweckstetter
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
- Translational Structural Biology Group, German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, D-37075, Göttingen, Germany
| | - Nasrollah Rezaei-Ghaleh
- Institute of Physical Biology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, D-40225, Düsseldorf, Germany
- Institute of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, D-52428, Jülich, Germany
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077, Göttingen, Germany
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7
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Negroni M, Kurzbach D. Missing Pieces in Structure Puzzles: How Hyperpolarized NMR Spectroscopy Can Complement Structural Biology and Biochemistry. Chembiochem 2023; 24:e202200703. [PMID: 36624049 DOI: 10.1002/cbic.202200703] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/11/2023]
Abstract
Structure determination lies at the heart of many biochemical research programs. However, the "giants": X-ray diffraction, electron microscopy, molecular dynamics simulations, and nuclear magnetic resonance, among others, leave quite a few dark spots on the structural pictures drawn of proteins, nucleic acids, membranes, and other biomacromolecules. For example, structural models under physiological conditions or of short-lived intermediates often remain out of reach of the established experimental methods. This account frames the possibility of including hyperpolarized, that is, dramatically signal-enhanced NMR in existing workflows to fill these spots with detailed depictions. We highlight how integrating methods based on dissolution dynamic nuclear polarization can provide valuable complementary information about formerly inaccessible conformational spaces for many systems. A particular focus will be on hyperpolarized buffers to facilitate the NMR structure determination of challenging systems.
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Affiliation(s)
- Mattia Negroni
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Dennis Kurzbach
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
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8
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Epasto LM, Honegger P, Che K, Kozak F, Jörg F, Schröder C, Kurzbach D. Nuclear Overhauser spectroscopy in hyperpolarized water - chemical vs. magnetic exchange. Chem Commun (Camb) 2022; 58:11661-11664. [PMID: 36169286 PMCID: PMC9578288 DOI: 10.1039/d2cc03735a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/21/2022] [Indexed: 11/29/2022]
Abstract
Dissolution dynamic nuclear polarization (dDNP) is a versatile hyperpolarization technique to boost signal intensities in nuclear magnetic resonance (NMR) spectroscopy. The possibility to dissolve biomolecules in a hyperpolarized aqueous buffer under mild conditions has recently widened the scope of NMR by dDNP. The water-to-target hyperpolarization transfer mechanisms remain yet unclear, not least due to an often-encountered dilemma of dDNP experiments: The strongly enhanced signal intensities are accompanied by limited structural information as data acquisition is restricted to short time series of only one-dimensional spectra or a single correlation spectrum. Tackling this challenge, we combine dDNP with molecular dynamics (MD) simulations and predictions of cross-relaxation rates to unravel the spin dynamics of magnetization flow in hyperpolarized solutions.
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Affiliation(s)
- Ludovica Martina Epasto
- University of Vienna, Faculty of Chemistry, Department of Biological Chemistry, Währingerstr. 38, 1090 Vienna, Austria.
- University of Vienna, Doctoral School in Chemistry (DoSChem), Währingerstr. 42, 1090 Vienna, Austria
| | - Philipp Honegger
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstr. 17, 1090 Vienna, Austria
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Kateryna Che
- University of Vienna, Faculty of Chemistry, Department of Biological Chemistry, Währingerstr. 38, 1090 Vienna, Austria.
| | - Fanny Kozak
- University of Vienna, Faculty of Chemistry, Department of Biological Chemistry, Währingerstr. 38, 1090 Vienna, Austria.
- University of Vienna, Doctoral School in Chemistry (DoSChem), Währingerstr. 42, 1090 Vienna, Austria
| | - Florian Jörg
- University of Vienna, Doctoral School in Chemistry (DoSChem), Währingerstr. 42, 1090 Vienna, Austria
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstr. 17, 1090 Vienna, Austria
| | - Christian Schröder
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstr. 17, 1090 Vienna, Austria
| | - Dennis Kurzbach
- University of Vienna, Faculty of Chemistry, Department of Biological Chemistry, Währingerstr. 38, 1090 Vienna, Austria.
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9
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Matsumoto N, Nishimura K, Kimizuka N, Nishiyama Y, Tateishi K, Uesaka T, Yanai N. Proton Hyperpolarization Relay from Nanocrystals to Liquid Water. J Am Chem Soc 2022; 144:18023-18029. [DOI: 10.1021/jacs.2c07518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Naoto Matsumoto
- Department of Applied Chemistry, Graduate School of Engineering, Center for Molecular Systems, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Koki Nishimura
- Department of Applied Chemistry, Graduate School of Engineering, Center for Molecular Systems, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Nobuo Kimizuka
- Department of Applied Chemistry, Graduate School of Engineering, Center for Molecular Systems, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yusuke Nishiyama
- NanoCrystallography Unit, RIKEN-JEOL Collaboration Center, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- JEOL RESONANCE Inc., 3-1-2 Musashino, Akishima, Tokyo 196-8558, Japan
| | - Kenichiro Tateishi
- Cluster for Pioneering Research, RIKEN, RIKEN Nishina Center for Accelerator-Based Science, Wako, Saitama 351-0198, Japan
| | - Tomohiro Uesaka
- Cluster for Pioneering Research, RIKEN, RIKEN Nishina Center for Accelerator-Based Science, Wako, Saitama 351-0198, Japan
| | - Nobuhiro Yanai
- Department of Applied Chemistry, Graduate School of Engineering, Center for Molecular Systems, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
- PRESTO and FOREST, JST, Honcho 4-1-8, Kawaguchi, Saitama 332-0012, Japan
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10
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Epasto LM, Che K, Kozak F, Selimovic A, Kadeřávek P, Kurzbach D. Toward protein NMR at physiological concentrations by hyperpolarized water-Finding and mapping uncharted conformational spaces. SCIENCE ADVANCES 2022; 8:eabq5179. [PMID: 35930648 PMCID: PMC9355353 DOI: 10.1126/sciadv.abq5179] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/23/2022] [Indexed: 05/12/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a key method for determining the structural dynamics of proteins in their native solution state. However, the low sensitivity of NMR typically necessitates nonphysiologically high sample concentrations, which often limit the relevance of the recorded data. We show how to use hyperpolarized water by dissolution dynamic nuclear polarization (DDNP) to acquire protein spectra at concentrations of 1 μM within seconds and with a high signal-to-noise ratio. The importance of approaching physiological concentrations is demonstrated for the vital MYC-associated factor X, which we show to switch conformations when diluted. While in vitro conditions lead to a population of the well-documented dimer, concentrations lowered by more than two orders of magnitude entail dimer dissociation and formation of a globularly folded monomer. We identified this structure by integrating DDNP with computational techniques to overcome the often-encountered constraint of DDNP of limited structural information provided by the typically detected one-dimensional spectra.
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Affiliation(s)
- Ludovica M. Epasto
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Währinger Str. 38, 1090 Vienna, Austria
| | - Kateryna Che
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Währinger Str. 38, 1090 Vienna, Austria
| | - Fanny Kozak
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Währinger Str. 38, 1090 Vienna, Austria
| | - Albina Selimovic
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Währinger Str. 38, 1090 Vienna, Austria
| | - Pavel Kadeřávek
- Masaryk University, CEITEC, Kamenice 5, 625 00 Brno, Czech Republic
| | - Dennis Kurzbach
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Währinger Str. 38, 1090 Vienna, Austria
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11
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Negroni M, Guarin D, Che K, Epasto LM, Turhan E, Selimović A, Kozak F, Cousin S, Abergel D, Bodenhausen G, Kurzbach D. Inversion of Hyperpolarized 13C NMR Signals through Cross-Correlated Cross-Relaxation in Dissolution DNP Experiments. J Phys Chem B 2022; 126:4599-4610. [PMID: 35675502 PMCID: PMC9234958 DOI: 10.1021/acs.jpcb.2c03375] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 05/25/2022] [Indexed: 11/29/2022]
Abstract
Dissolution dynamic nuclear polarization (DDNP) is a versatile tool to boost signal amplitudes in solution-state nuclear magnetic resonance (NMR) spectroscopy. For DDNP, nuclei are spin-hyperpolarized "ex situ" in a dedicated DNP device and then transferred to an NMR spectrometer for detection. Dramatic signal enhancements can be achieved, enabling shorter acquisition times, real-time monitoring of fast reactions, and reduced sample concentrations. Here, we show how the sample transfer in DDNP experiments can affect NMR spectra through cross-correlated cross-relaxation (CCR), especially in the case of low-field passages. Such processes can selectively invert signals of 13C spins in proton-carrying moieties. For their investigations, we use schemes for simultaneous or "parallel" detection of hyperpolarized 1H and 13C nuclei. We find that 1H → 13C CCR can invert signals of 13C spins if the proton polarization is close to 100%. We deduce that low-field passage in a DDNP experiment, a common occurrence due to the introduction of so-called "ultra-shielded" magnets, accelerates these effects due to field-dependent paramagnetic relaxation enhancements that can influence CCR. The reported effects are demonstrated for various molecules, laboratory layouts, and DDNP systems. As coupled 13C-1H spin systems are ubiquitous, we expect similar effects to be observed in various DDNP experiments. This might be exploited for selective spectroscopic labeling of hydrocarbons.
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Affiliation(s)
- Mattia Negroni
- Faculty
of Chemistry, Institute of Biological Chemistry, University Vienna, Währinger
Str. 38, 1090 Vienna, Austria
| | - David Guarin
- Athinoula
A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts 02129, United States
- Polarize
ApS, 1808 Frederiksberg, Denmark
| | - Kateryna Che
- Faculty
of Chemistry, Institute of Biological Chemistry, University Vienna, Währinger
Str. 38, 1090 Vienna, Austria
| | - Ludovica M. Epasto
- Faculty
of Chemistry, Institute of Biological Chemistry, University Vienna, Währinger
Str. 38, 1090 Vienna, Austria
| | - Ertan Turhan
- Faculty
of Chemistry, Institute of Biological Chemistry, University Vienna, Währinger
Str. 38, 1090 Vienna, Austria
| | - Albina Selimović
- Faculty
of Chemistry, Institute of Biological Chemistry, University Vienna, Währinger
Str. 38, 1090 Vienna, Austria
| | - Fanny Kozak
- Faculty
of Chemistry, Institute of Biological Chemistry, University Vienna, Währinger
Str. 38, 1090 Vienna, Austria
| | - Samuel Cousin
- Institut
de Chimie Radicalaire—UMR 7273, Saint-Jérôme
Campus, Av. Esc. Normandie Niemen, Aix-Marseille Université/CNRS, 13397 Marseille
Cedex 20, France
| | - Daniel Abergel
- Laboratoire
des Biomolécules, LBM, Département de chimie, École
Normale Supérieure, PSL University, Sorbonne Université,
CNRS, 24 rue Lhomond, 75005 Paris, France
| | - Geoffrey Bodenhausen
- Laboratoire
des Biomolécules, LBM, Département de chimie, École
Normale Supérieure, PSL University, Sorbonne Université,
CNRS, 24 rue Lhomond, 75005 Paris, France
| | - Dennis Kurzbach
- Faculty
of Chemistry, Institute of Biological Chemistry, University Vienna, Währinger
Str. 38, 1090 Vienna, Austria
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12
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Pham P, Mandal R, Qi C, Hilty C. Interfacing Liquid State Hyperpolarization Methods with NMR Instrumentation. JOURNAL OF MAGNETIC RESONANCE OPEN 2022; 10-11:100052. [PMID: 35530721 PMCID: PMC9070690 DOI: 10.1016/j.jmro.2022.100052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Advances in liquid state hyperpolarization methods have enabled new applications of high-resolution NMR spectroscopy. Utilizing strong signal enhancements from hyperpolarization allows performing NMR spectroscopy at low concentration, or with high time resolution. Making use of the high, but rapidly decaying hyperpolarization in the liquid state requires new techniques to interface hyperpolarization equipment with liquid state NMR spectrometers. This article highlights rapid injection, high resolution NMR spectroscopy with hyperpolarization produced by the techniques of dissolution dynamic nuclear polarization (D-DNP) and para-hydrogen induced polarization (PHIP). These are popular, albeit not the only methods to produce high polarization levels for liquid samples. Gas and liquid driven sample injection techniques are compatible with both of these hyperpolarization methods. The rapid sample injection techniques are combined with adapted NMR experiments working in a single, or small number of scans. They expand the application of liquid state hyperpolarization to spins with comparably short relaxation times, provide enhanced control over sample conditions, and allow for mixing experiments to study reactions in real time.
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13
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Abstract
Thanks to recent improvements in NMR spectrometer hardware and pulse sequence design, modern 13C NMR has become a useful tool for biomolecular applications. The complete assignment of a protein can be accomplished by using 13C detected multinuclear experiments and it can provide unique information relevant for the study of a variety of different biomolecules including paramagnetic proteins and intrinsically disordered proteins. A wide range of NMR observables can be measured, concurring to the structural and dynamic characterization of a protein in isolation, as part of a larger complex, or even inside a living cell. We present the different properties of 13C with respect to 1H, which provide the rationale for the experiments developed and their application, the technical aspects that need to be faced, and the many experimental variants designed to address different cases. Application areas where these experiments successfully complement proton NMR are also described.
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Affiliation(s)
- Isabella C. Felli
- Department of Chemistry “Ugo
Schiff” and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy
| | - Roberta Pierattelli
- Department of Chemistry “Ugo
Schiff” and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy
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14
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Hilty C, Kurzbach D, Frydman L. Hyperpolarized water as universal sensitivity booster in biomolecular NMR. Nat Protoc 2022; 17:1621-1657. [PMID: 35546640 DOI: 10.1038/s41596-022-00693-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 02/25/2022] [Indexed: 11/09/2022]
Abstract
NMR spectroscopy is the only method to access the structural dynamics of biomolecules at high (atomistic) resolution in their native solution state. However, this method's low sensitivity has two important consequences: (i) typically experiments have to be performed at high concentrations that increase sensitivity but are not physiological, and (ii) signals have to be accumulated over long periods, complicating the determination of interaction kinetics on the order of seconds and impeding studies of unstable systems. Both limitations are of equal, fundamental relevance: non-native conditions are of limited pharmacological relevance, and the function of proteins, enzymes and nucleic acids often relies on their interaction kinetics. To overcome these limitations, we have developed applications that involve 'hyperpolarized water' to boost signal intensities in NMR of proteins and nucleic acids. The technique includes four stages: (i) preparation of the biomolecule in partially deuterated buffers, (ii) preparation of 'hyperpolarized' water featuring enhanced 1H NMR signals via cryogenic dynamic nuclear polarization, (iii) sudden melting of the cryogenic pellet and dissolution of the protein or nucleic acid in the hyperpolarized water (enabling spontaneous exchanges of protons between water and target) and (iv) recording signal-amplified NMR spectra targeting either labile 1H or neighboring 15N/13C nuclei in the biomolecule. Water in the ensuing experiments is used as a universal 'hyperpolarization' agent, rendering the approach versatile and applicable to any biomolecule possessing labile hydrogens. Thus, questions can be addressed, ranging from protein and RNA folding problems to resolving structure-function relationships of intrinsically disordered proteins to investigating membrane interactions.
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Affiliation(s)
- Christian Hilty
- Chemistry Department, Texas A&M University, College Station, TX, USA.
| | - Dennis Kurzbach
- Faculty of Chemistry, Institute for Biological Chemistry, University of Vienna, Vienna, Austria.
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
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15
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Hu J, Kim J, Hilty C. Detection of Protein-Ligand Interactions by 19F Nuclear Magnetic Resonance Using Hyperpolarized Water. J Phys Chem Lett 2022; 13:3819-3823. [PMID: 35465675 PMCID: PMC9088881 DOI: 10.1021/acs.jpclett.2c00448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The transfer of nuclear spin hyperpolarization from water to ligand 19F spins results in a transient signal change that is indicative of protein-ligand interaction. The 19F nucleus allows for background-free detection of these signals, which are modulated by polarization transfer via pathways similar to those in a hyperpolarized 1H water LOGSY experiment. Quantification of the apparent heteronuclear cross-relaxation rates is facilitated by a simultaneous dual-channel detection of 1H and 19F signals. Calculated cross-relaxation rates for the 1H-19F transfer step indicate that these rates are sensitive to binding to medium- and large-sized proteins. The heteronuclear observation of hyperpolarization transfer from water may be used to screen protein-ligand interactions in drug discovery and other applications.
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Affiliation(s)
- Jiandu Hu
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, TX 77843, USA
| | | | - Christian Hilty
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, TX 77843, USA
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16
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Residue-resolved monitoring of protein hyperpolarization at sub-second time resolution. Commun Chem 2021; 4:147. [PMID: 36697662 PMCID: PMC9814832 DOI: 10.1038/s42004-021-00587-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/05/2021] [Indexed: 02/07/2023] Open
Abstract
Signal-enhancement techniques for NMR spectroscopy are important to amplify the weak resonances provided by nuclear spins. Recently, 'hyperpolarization' techniques have been intensively investigated. These provide nuclear spin states far from equilibrium yielding strong signal boosts up to four orders of magnitude. Here we propose a method for real-time NMR of 'hyperpolarized' proteins at residue resolution. The approach is based on dissolution dynamic nuclear polarization (d-DNP), which enables the use of hyperpolarized buffers that selectively boost NMR signals of solvent-exposed protein residues. The resulting spectral sparseness and signal enhancements enable recording of residue-resolved spectra at a 2 Hz sampling rate. Thus, we monitor the hyperpolarization level of different protein residues simultaneously under near-physiological conditions. We aim to address two points: 1) NMR experiments are often performed under conditions that increase sensitivity but are physiologically irrelevant; 2) long signal accumulation impedes fast real-time monitoring. Both limitations are of fundamental relevance to ascertain pharmacological relevance and study protein kinetics.
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17
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Elliott SJ, Stern Q, Ceillier M, El Daraï T, Cousin SF, Cala O, Jannin S. Practical dissolution dynamic nuclear polarization. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2021; 126-127:59-100. [PMID: 34852925 DOI: 10.1016/j.pnmrs.2021.04.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 06/13/2023]
Abstract
This review article intends to provide insightful advice for dissolution-dynamic nuclear polarization in the form of a practical handbook. The goal is to aid research groups to effectively perform such experiments in their own laboratories. Previous review articles on this subject have covered a large number of useful topics including instrumentation, experimentation, theory, etc. The topics to be addressed here will include tips for sample preparation and for checking sample health; a checklist to correctly diagnose system faults and perform general maintenance; the necessary mechanical requirements regarding sample dissolution; and aids for accurate, fast and reliable polarization quantification. Herein, the challenges and limitations of each stage of a typical dissolution-dynamic nuclear polarization experiment are presented, with the focus being on how to quickly and simply overcome some of the limitations often encountered in the laboratory.
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Affiliation(s)
- Stuart J Elliott
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs - UMR 5082 Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, 5 Rue de la Doua, 69100 Villeurbanne, France
| | - Quentin Stern
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs - UMR 5082 Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, 5 Rue de la Doua, 69100 Villeurbanne, France
| | - Morgan Ceillier
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs - UMR 5082 Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, 5 Rue de la Doua, 69100 Villeurbanne, France
| | - Théo El Daraï
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs - UMR 5082 Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, 5 Rue de la Doua, 69100 Villeurbanne, France
| | - Samuel F Cousin
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs - UMR 5082 Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, 5 Rue de la Doua, 69100 Villeurbanne, France
| | - Olivier Cala
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs - UMR 5082 Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, 5 Rue de la Doua, 69100 Villeurbanne, France
| | - Sami Jannin
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs - UMR 5082 Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, 5 Rue de la Doua, 69100 Villeurbanne, France.
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18
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Korchak S, Kaltschnee L, Dervisoglu R, Andreas L, Griesinger C, Glöggler S. Spontaneous Enhancement of Magnetic Resonance Signals Using a RASER. Angew Chem Int Ed Engl 2021; 60:20984-20990. [PMID: 34289241 PMCID: PMC8518078 DOI: 10.1002/anie.202108306] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Indexed: 11/06/2022]
Abstract
Nuclear magnetic resonance is usually drastically limited by its intrinsically low sensitivity: Only a few spins contribute to the overall signal. To overcome this limitation, hyperpolarization methods were developed that increase signals several times beyond the normal/thermally polarized signals. The ideal case would be a universal approach that can signal enhance the complete sample of interest in solution to increase detection sensitivity. Here, we introduce a combination of para-hydrogen enhanced magnetic resonance with the phenomenon of the RASER: Large signals of para-hydrogen enhanced molecules interact with the magnetic resonance coil in a way that the signal is spontaneously converted into an in-phase signal. These molecules directly interact with other compounds via dipolar couplings and enhance their signal. We demonstrate that this is not only possible for solvent molecules but also for an amino acid.
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Affiliation(s)
- Sergey Korchak
- NMR Signal Enhancement GroupMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
- Center for Biostructural Imaging of Neurodegeneration of UMGVon-Siebold-Str. 3A37075GöttingenGermany
| | - Lukas Kaltschnee
- NMR Signal Enhancement GroupMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
- Center for Biostructural Imaging of Neurodegeneration of UMGVon-Siebold-Str. 3A37075GöttingenGermany
| | - Riza Dervisoglu
- Research Group for Solid State NMRMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
| | - Loren Andreas
- Research Group for Solid State NMRMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
| | - Christian Griesinger
- Department of NMR-based Structural BiologyMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
| | - Stefan Glöggler
- NMR Signal Enhancement GroupMax Planck Institute for Biophysical ChemistryAm Fassberg 1137077GöttingenGermany
- Center for Biostructural Imaging of Neurodegeneration of UMGVon-Siebold-Str. 3A37075GöttingenGermany
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19
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Korchak S, Kaltschnee L, Dervisoglu R, Andreas L, Griesinger C, Glöggler S. Spontaneous Enhancement of Magnetic Resonance Signals Using a RASER. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108306] [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)
- Sergey Korchak
- NMR Signal Enhancement Group Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
- Center for Biostructural Imaging of Neurodegeneration of UMG Von-Siebold-Str. 3A 37075 Göttingen Germany
| | - Lukas Kaltschnee
- NMR Signal Enhancement Group Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
- Center for Biostructural Imaging of Neurodegeneration of UMG Von-Siebold-Str. 3A 37075 Göttingen Germany
| | - Riza Dervisoglu
- Research Group for Solid State NMR Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
| | - Loren Andreas
- Research Group for Solid State NMR Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
| | - Christian Griesinger
- Department of NMR-based Structural Biology Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
| | - Stefan Glöggler
- NMR Signal Enhancement Group Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
- Center for Biostructural Imaging of Neurodegeneration of UMG Von-Siebold-Str. 3A 37075 Göttingen Germany
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20
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Felli IC, Bermel W, Pierattelli R. Exclusively heteronuclear NMR experiments for the investigation of intrinsically disordered proteins: focusing on proline residues. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:511-522. [PMID: 37904768 PMCID: PMC10539766 DOI: 10.5194/mr-2-511-2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/02/2021] [Indexed: 11/01/2023]
Abstract
NMR represents a key spectroscopic technique that contributes to the emerging field of highly flexible, intrinsically disordered proteins (IDPs) or protein regions (IDRs) that lack a stable three-dimensional structure. A set of exclusively heteronuclear NMR experiments tailored for proline residues, highly abundant in IDPs/IDRs, are presented here. They provide a valuable complement to the widely used approach based on amide proton detection, filling the gap introduced by the lack of amide protons in proline residues within polypeptide chains. The novel experiments have very interesting properties for the investigations of IDPs/IDRs of increasing complexity.
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Affiliation(s)
- Isabella C. Felli
- CERM and Department of Chemistry “Ugo Schiff”, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Roberta Pierattelli
- CERM and Department of Chemistry “Ugo Schiff”, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
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21
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Structural Constraint of Osteopontin Facilitates Efficient Binding to CD44. Biomolecules 2021; 11:biom11060813. [PMID: 34070790 PMCID: PMC8228714 DOI: 10.3390/biom11060813] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 11/21/2022] Open
Abstract
Since the original description in 1996, the interaction between the cytokine osteopontin (OPN) and the homing receptor CD44 has been extensively studied in cancer, inflammation, bone remodeling, and various other conditions. Alternative splicing and extensive posttranslational modifications by both binding partners, as well as the possibility for lateral recruitment of additional membrane receptors or soluble co-ligands into a complex have left the exact molecular requirements for high-affinity OPN-CD44 binding unresolved. We now report that there is a moderate engagement between the unmodified molecules, which results in curved double-reciprocal plots for OPN titration, suggesting the existence of two binding sites or two binding conformations. Structural constraint of OPN, by immobilization or by addition of heparin, is required for its strong ligation of CD44. Prior literature provides evidence that heparin binding to OPN prompts the unfolding of a core element in the protein. This conformational adjustment may be essential for efficient CD44 interaction. The integrin α9β1 seems to compete with the OPN-CD44 engagement, while the integrin αVβ3 reflects additive binding, suggesting that the CD44 contact sites on OPN are downstream of the RGD motif but overlap with the SVVYGLR domain. Hyaluronate has no effect, placing the relevant domain on CD44 downstream of the N-terminus.
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22
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Teleanu F, Sadet A, Vasos PR. Symmetry versus entropy: Long-lived states and coherences. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2021; 122:63-75. [PMID: 33632418 DOI: 10.1016/j.pnmrs.2020.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/28/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
In recent years, new molecular symmetry-based approaches for magnetic resonance have been invented. The implications of these discoveries will be significant for molecular imaging via magnetic resonance, in vitro as well as in vivo, for quantum computing and for other fields. Since the initial observation in 2004 in Southampton that effective spin symmetry can be instilled in a molecule during magnetic resonance experiments, spin states that are resilient to relaxation mechanisms have been increasingly used. Most of these states are related to the nuclear singlet in a pair of J-coupled spins. Tailored relaxation rate constants for magnetization became available in molecules of different sizes and structures, as experimental developments broadened the scope of symmetry-adapted spin states. The ensuing access to timescales longer than the classically-attained ones by circa one order of magnitude allows the study of processes such as slow diffusion or slow exchange that were previously beyond reach. Long-lived states formed by differences between populations of singlets and triplets have overcome the limitations imposed by longitudinal relaxation times (T1) by factors up to 40. Long-lived coherences formed by superpositions of singlets and triplets have overcome the limit of classical transverse coherence (T2) by a factor 9. We present here an overview of the development and applications of long-lived states (LLS) and long-lived coherences (LLC's) and considerations on future perspectives.
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Affiliation(s)
- Florin Teleanu
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, Laser Gamma Experiments Department (LGED), "Horia Hulubei" National Institute for Physics and Nuclear Engineering IFIN-HH, 30 Reactorului Street, RO-077125 Bucharest-Măgurele, Romania; College for Advanced Performance Studies, Babeș-Bolyai University, Mihail Kogălniceanu Street 1, Cluj-Napoca, Romania; Interdisciplinary School of Doctoral Studies, University of Bucharest, B-dul Regina Elisabeta, Bucharest, Romania
| | - Aude Sadet
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, Laser Gamma Experiments Department (LGED), "Horia Hulubei" National Institute for Physics and Nuclear Engineering IFIN-HH, 30 Reactorului Street, RO-077125 Bucharest-Măgurele, Romania
| | - Paul R Vasos
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, Laser Gamma Experiments Department (LGED), "Horia Hulubei" National Institute for Physics and Nuclear Engineering IFIN-HH, 30 Reactorului Street, RO-077125 Bucharest-Măgurele, Romania; Interdisciplinary School of Doctoral Studies, University of Bucharest, B-dul Regina Elisabeta, Bucharest, Romania.
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23
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Nishimura K, Kouno H, Kawashima Y, Orihashi K, Fujiwara S, Tateishi K, Uesaka T, Kimizuka N, Yanai N. Materials chemistry of triplet dynamic nuclear polarization. Chem Commun (Camb) 2020; 56:7217-7232. [PMID: 32495753 DOI: 10.1039/d0cc02258f] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Dynamic nuclear polarization with photo-excited triplet electrons (triplet-DNP) has the potential to enhance the sensitivity of nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) at a moderate temperature. While many efforts have been devoted to achieving a large nuclear polarization based on triplet-DNP, the application of triplet-DNP has been limited to nuclear physics experiments. The recent introduction of materials chemistry into the field of triplet-DNP has achieved air-stable and water-soluble polarizing agents as well as the hyperpolarization of nanomaterials with a large surface area such as nanoporous metal-organic frameworks (MOFs) and nanocrystal dispersion in water. This Feature Article overviews the recently-emerged materials chemistry of triplet-DNP that paves new paths towards unprecedented biological and medical applications.
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Affiliation(s)
- Koki Nishimura
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Hironori Kouno
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Yusuke Kawashima
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Kana Orihashi
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Saiya Fujiwara
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Kenichiro Tateishi
- Cluster for Pioneering Research, RIKEN, RIKEN Nishina Center for Accelerator-Based Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tomohiro Uesaka
- Cluster for Pioneering Research, RIKEN, RIKEN Nishina Center for Accelerator-Based Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Nobuo Kimizuka
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Nobuhiro Yanai
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan. and PRESTO, JST, Honcho 4-1-8, Kawaguchi, Saitama 332-0012, Japan
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24
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Kawasaki R, Tate SI. Impact of the Hereditary P301L Mutation on the Correlated Conformational Dynamics of Human Tau Protein Revealed by the Paramagnetic Relaxation Enhancement NMR Experiments. Int J Mol Sci 2020; 21:ijms21113920. [PMID: 32486218 PMCID: PMC7313075 DOI: 10.3390/ijms21113920] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 12/23/2022] Open
Abstract
Tau forms intracellular insoluble aggregates as a neuropathological hallmark of Alzheimer’s disease. Tau is largely unstructured, which complicates the characterization of the tau aggregation process. Recent studies have demonstrated that tau samples two distinct conformational ensembles, each of which contains the soluble and aggregation-prone states of tau. A shift to populate the aggregation-prone ensemble may promote tau fibrillization. However, the mechanism of this ensemble transition remains elusive. In this study, we explored the conformational dynamics of a tau fragment by using paramagnetic relaxation enhancement (PRE) and interference (PRI) NMR experiments. The PRE correlation map showed that tau is composed of segments consisting of residues in correlated motions. Intriguingly, residues forming the β-structures in the heparin-induced tau filament coincide with residues in these segments, suggesting that each segment behaves as a structural unit in fibrillization. PRI data demonstrated that the P301L mutation exclusively alters the transiently formed tau structures by changing the short- and long-range correlated motions among residues. The transient conformations of P301L tau expose the amyloid motif PHF6 to promote tau self-aggregation. We propose the correlated motions among residues within tau determine the population sizes of the conformational ensembles, and perturbing the correlated motions populates the aggregation-prone form.
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Affiliation(s)
- Ryosuke Kawasaki
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan;
| | - Shin-ichi Tate
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan;
- Department of Mathematical and Life Sciences, Graduate School of the Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
- Correspondence: ; Tel.: +81-82-424-7387
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25
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Szekely O, Olsen GL, Novakovic M, Rosenzweig R, Frydman L. Assessing Site-Specific Enhancements Imparted by Hyperpolarized Water in Folded and Unfolded Proteins by 2D HMQC NMR. J Am Chem Soc 2020; 142:9267-9284. [PMID: 32338002 PMCID: PMC7304870 DOI: 10.1021/jacs.0c00807] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Hyperpolarized water
can be a valuable aid in protein NMR, leading
to amide group 1H polarizations that are orders of magnitude
larger than their thermal counterparts. Suitable procedures can exploit
this to deliver 2D 1H–15N correlations
with good resolution and enhanced sensitivity. These enhancements
depend on the exchange rates between the amides and the water, thereby
yielding diagnostic information about solvent accessibility. This
study applied this “HyperW” method to four proteins
exhibiting a gamut of exchange behaviors: PhoA(350–471), an unfolded 122-residue fragment; barstar, a fully folded ribonuclease
inhibitor; R17, a 13.3 kDa system possessing folded and unfolded forms
under slow interconversion; and drkN SH3, a protein domain whose folded
and unfolded forms interchange rapidly and with temperature-dependent
population ratios. For PhoA4(350–471) HyperW sensitivity
enhancements were ≥300×, as expected for an unfolded protein
sequence. Though fully folded, barstar also exhibited substantial
enhancements; these, however, were not uniform and, according to CLEANEX
experiments, reflected the solvent-exposed residues. R17 showed the
expected superposition of ≥100-fold enhancements for its unfolded
form, coexisting with more modest enhancements for their folded counterparts.
Unexpected, however, was the behavior of drkN SH3, for which HyperW
enhanced the unfolded but, surprisingly, enhanced even more certain folded protein sites. These preferential enhancements were
repeatedly and reproducibly observed. A number of explanations—including
three-site exchange magnetization transfers between water and the
unfolded and folded states; cross-correlated relaxation processes
from hyperpolarized “structural” waters and labile side-chain
protons; and the possibility that faster solvent exchange rates characterize
certain folded sites over their unfolded counterparts—are considered
to account for them.
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26
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Pinon AC, Capozzi A, Ardenkjær-Larsen JH. Hyperpolarized water through dissolution dynamic nuclear polarization with UV-generated radicals. Commun Chem 2020; 3:57. [PMID: 36703471 PMCID: PMC9814647 DOI: 10.1038/s42004-020-0301-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/09/2020] [Indexed: 01/29/2023] Open
Abstract
In recent years, hyperpolarization of water protons via dissolution Dynamic Nuclear Polarization (dDNP) has attracted increasing interest in the magnetic resonance community. Hyperpolarized water may provide an alternative to Gd-based contrast agents for angiographic and perfusion Magnetic Resonance Imaging (MRI) examinations, and it may report on chemical and biochemical reactions and proton exchange while perfoming Nuclear Magnetic Resonance (NMR) investigations. However, hyperpolarizing water protons is challenging. The main reason is the presence of radicals, required to create the hyperpolarized nuclear spin state. Indeed, the radicals will also be the main source of relaxation during the dissolution and transfer to the NMR or MRI system. In this work, we report water magnetizations otherwise requiring a field of 10,000 T at room temperature on a sample of pure water, by employing dDNP via UV-generated, labile radicals. We demonstrate the potential of our methodology by acquiring a 15N spectrum from natural abundance urea with a single scan, after spontaneous magnetization transfer from water protons to nitrogen nuclei.
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Affiliation(s)
- Arthur C. Pinon
- grid.5170.30000 0001 2181 8870Center for Hyperpolarization in Magnetic Resonance, Department of Health Technology, Technical University of Denmark, Building 349, 2800 Kgs Lyngby, Denmark
| | - Andrea Capozzi
- grid.5170.30000 0001 2181 8870Center for Hyperpolarization in Magnetic Resonance, Department of Health Technology, Technical University of Denmark, Building 349, 2800 Kgs Lyngby, Denmark
| | - Jan Henrik Ardenkjær-Larsen
- grid.5170.30000 0001 2181 8870Center for Hyperpolarization in Magnetic Resonance, Department of Health Technology, Technical University of Denmark, Building 349, 2800 Kgs Lyngby, Denmark
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27
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Olsen GL, Szekely O, Mateos B, Kadeřávek P, Ferrage F, Konrat R, Pierattelli R, Felli IC, Bodenhausen G, Kurzbach D, Frydman L. Sensitivity-enhanced three-dimensional and carbon-detected two-dimensional NMR of proteins using hyperpolarized water. JOURNAL OF BIOMOLECULAR NMR 2020; 74:161-171. [PMID: 32040802 PMCID: PMC7080779 DOI: 10.1007/s10858-020-00301-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/27/2020] [Indexed: 05/11/2023]
Abstract
Signal enhancements of up to two orders of magnitude in protein NMR can be achieved by employing HDO as a vector to introduce hyperpolarization into folded or intrinsically disordered proteins. In this approach, hyperpolarized HDO produced by dissolution-dynamic nuclear polarization (D-DNP) is mixed with a protein solution waiting in a high-field NMR spectrometer, whereupon amide proton exchange and nuclear Overhauser effects (NOE) transfer hyperpolarization to the protein and enable acquisition of a signal-enhanced high-resolution spectrum. To date, the use of this strategy has been limited to 1D and 1H-15N 2D correlation experiments. Here we introduce 2D 13C-detected D-DNP, to reduce exchange-induced broadening and other relaxation penalties that can adversely affect proton-detected D-DNP experiments. We also introduce hyperpolarized 3D spectroscopy, opening the possibility of D-DNP studies of larger proteins and IDPs, where assignment and residue-specific investigation may be impeded by spectral crowding. The signal enhancements obtained depend in particular on the rates of chemical and magnetic exchange of the observed residues, thus resulting in non-uniform 'hyperpolarization-selective' signal enhancements. The resulting spectral sparsity, however, makes it possible to resolve and monitor individual amino acids in IDPs of over 200 residues at acquisition times of just over a minute. We apply the proposed experiments to two model systems: the compactly folded protein ubiquitin, and the intrinsically disordered protein (IDP) osteopontin (OPN).
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Affiliation(s)
- Gregory L Olsen
- Faculty of Chemistry, Institute for Biological Chemistry, University of Vienna, Währinger Straße 38, 1090, Vienna, Austria.
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
| | - Or Szekely
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Borja Mateos
- Department of Structural and Computational Biology, University of Vienna, Vienna BioCenter 5, 1030, Vienna, Austria
| | - Pavel Kadeřávek
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Fabien Ferrage
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Robert Konrat
- Department of Structural and Computational Biology, University of Vienna, Vienna BioCenter 5, 1030, Vienna, Austria
| | - Roberta Pierattelli
- Magnetic Resonance Center and Department of Chemistry Ugo Schiff, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
| | - Isabella C Felli
- Magnetic Resonance Center and Department of Chemistry Ugo Schiff, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
| | - Geoffrey Bodenhausen
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Dennis Kurzbach
- Faculty of Chemistry, Institute for Biological Chemistry, University of Vienna, Währinger Straße 38, 1090, Vienna, Austria.
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France.
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
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28
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A 300-fold enhancement of imino nucleic acid resonances by hyperpolarized water provides a new window for probing RNA refolding by 1D and 2D NMR. Proc Natl Acad Sci U S A 2020; 117:2449-2455. [PMID: 31949004 DOI: 10.1073/pnas.1916956117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
NMR sensitivity-enhancement methods involving hyperpolarized water could be of importance for solution-state biophysical investigations. Hyperpolarized water (HyperW) can enhance the 1H NMR signals of exchangeable sites by orders of magnitude over their thermal counterparts, while providing insight into chemical exchange and solvent accessibility at a site-resolved level. As HyperW's enhancements are achieved by exploiting fast solvent exchanges associated with minimal interscan delays, possibilities for the rapid monitoring of chemical reactions and biomolecular (re)folding are opened. HyperW NMR can also accommodate heteronuclear transfers, facilitating the rapid acquisition of 2-dimensional (2D) 15N-1H NMR correlations, and thereby combining an enhanced spectral resolution with speed and sensitivity. This work demonstrates how these qualities can come together for the study of nucleic acids. HyperW injections were used to target the guanine-sensing riboswitch aptamer domain (GSRapt) of the xpt-pbuX operon in Bacillus subtilis Unlike what had been observed in proteins, where residues benefited of HyperW NMR only if/when sufficiently exposed to water, these enhancements applied to every imino resonance throughout the RNA. The >300-fold enhancements observed in the resulting 1H NMR spectra allowed us to monitor in real time the changes that GSRapt undergoes upon binding hypoxanthine, a high-affinity interaction leading to conformational refolding on a ∼1-s timescale at 36 °C. Structural responses could be identified for several nucleotides by 1-dimensional (1D) imino 1H NMR as well as by 2D HyperW NMR spectra acquired upon simultaneous injection of hyperpolarized water and hypoxanthine. The folding landscape revealed by this HyperW strategy for GSRapt, is briefly discussed.
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29
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Kouno H, Orihashi K, Nishimura K, Kawashima Y, Tateishi K, Uesaka T, Kimizuka N, Yanai N. Triplet dynamic nuclear polarization of crystalline ice using water-soluble polarizing agents. Chem Commun (Camb) 2020; 56:3717-3720. [DOI: 10.1039/d0cc00836b] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The first example of triplet dynamic nuclear polarization of crystalline ice is demonstrated by developing a water-soluble triplet polarizing agent.
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Affiliation(s)
- Hironori Kouno
- Department of Chemistry and Biochemistry
- Graduate School of Engineering
- Center for Molecular Systems (CMS)
- Kyushu University
- Fukuoka 819-0395
| | - Kana Orihashi
- Department of Chemistry and Biochemistry
- Graduate School of Engineering
- Center for Molecular Systems (CMS)
- Kyushu University
- Fukuoka 819-0395
| | - Koki Nishimura
- Department of Chemistry and Biochemistry
- Graduate School of Engineering
- Center for Molecular Systems (CMS)
- Kyushu University
- Fukuoka 819-0395
| | - Yusuke Kawashima
- Department of Chemistry and Biochemistry
- Graduate School of Engineering
- Center for Molecular Systems (CMS)
- Kyushu University
- Fukuoka 819-0395
| | - Kenichiro Tateishi
- Cluster for Pioneering Research
- RIKEN
- RIKEN Nishina Center for Accelerator-Based Science
- Saitama 351-0198
- Japan
| | - Tomohiro Uesaka
- Cluster for Pioneering Research
- RIKEN
- RIKEN Nishina Center for Accelerator-Based Science
- Saitama 351-0198
- Japan
| | - Nobuo Kimizuka
- Department of Chemistry and Biochemistry
- Graduate School of Engineering
- Center for Molecular Systems (CMS)
- Kyushu University
- Fukuoka 819-0395
| | - Nobuhiro Yanai
- Department of Chemistry and Biochemistry
- Graduate School of Engineering
- Center for Molecular Systems (CMS)
- Kyushu University
- Fukuoka 819-0395
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30
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Asavei T, Bobeica M, Nastasa V, Manda G, Naftanaila F, Bratu O, Mischianu D, Cernaianu MO, Ghenuche P, Savu D, Stutman D, Tanaka KA, Radu M, Doria D, Vasos PR. Laser-driven radiation: Biomarkers for molecular imaging of high dose-rate effects. Med Phys 2019; 46:e726-e734. [PMID: 31357243 PMCID: PMC6899889 DOI: 10.1002/mp.13741] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 04/11/2019] [Accepted: 07/03/2019] [Indexed: 12/15/2022] Open
Abstract
Recently developed short‐pulsed laser sources garner high dose‐rate beams such as energetic ions and electrons, x rays, and gamma rays. The biological effects of laser‐generated ion beams observed in recent studies are different from those triggered by radiation generated using classical accelerators or sources, and this difference can be used to develop new strategies for cancer radiotherapy. High‐power lasers can now deliver particles in doses of up to several Gy within nanoseconds. The fast interaction of laser‐generated particles with cells alters cell viability via distinct molecular pathways compared to traditional, prolonged radiation exposure. The emerging consensus of recent literature is that the differences are due to the timescales on which reactive molecules are generated and persist, in various forms. Suitable molecular markers have to be adopted to monitor radiation effects, addressing relevant endogenous molecules that are accessible for investigation by noninvasive procedures and enable translation to clinical imaging. High sensitivity has to be attained for imaging molecular biomarkers in cells and in vivo to follow radiation‐induced functional changes. Signal‐enhanced MRI biomarkers enriched with stable magnetic nuclear isotopes can be used to monitor radiation effects, as demonstrated recently by the use of dynamic nuclear polarization (DNP) for biomolecular observations in vivo. In this context, nanoparticles can also be used as radiation enhancers or biomarker carriers. The radiobiology‐relevant features of high dose‐rate secondary radiation generated using high‐power lasers and the importance of noninvasive biomarkers for real‐time monitoring the biological effects of radiation early on during radiation pulse sequences are discussed.
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Affiliation(s)
- Theodor Asavei
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania
| | - Mariana Bobeica
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania
| | - Viorel Nastasa
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania.,National Institute for Laser, Plasma and Radiation Physics, 409 Atomistilor Street, RO-077125, Bucharest-Magurele, Romania
| | - Gina Manda
- Cellular and Molecular Medicine Department, "Victor Babes" National Institute of Pathology, 99-101 Splaiul Independentei, Bucharest, 050096, Romania
| | - Florin Naftanaila
- Carol Davila University of Medicine and Pharmacy Bucharest, Dr Carol Davila Central Mil University Emergency Hospital, 88th Mircea Vulcanescu Str, Bucharest, Romania.,Amethyst Radiotherapy Clinic, Dr Odaii 42, Otopeni, Romania
| | - Ovidiu Bratu
- Carol Davila University of Medicine and Pharmacy Bucharest, Dr Carol Davila Central Mil University Emergency Hospital, 88th Mircea Vulcanescu Str, Bucharest, Romania
| | - Dan Mischianu
- Carol Davila University of Medicine and Pharmacy Bucharest, Dr Carol Davila Central Mil University Emergency Hospital, 88th Mircea Vulcanescu Str, Bucharest, Romania
| | - Mihail O Cernaianu
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania
| | - Petru Ghenuche
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania
| | - Diana Savu
- Department of Life and Environmental Physics, Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania
| | - Dan Stutman
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania.,National Institute for Laser, Plasma and Radiation Physics, 409 Atomistilor Street, RO-077125, Bucharest-Magurele, Romania.,Johns Hopkins University, 3400 N Charles St, Baltimore, Maryland, 21218, USA
| | - Kazuo A Tanaka
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania
| | - Mihai Radu
- Department of Life and Environmental Physics, Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania
| | - Domenico Doria
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania.,Centre for Plasma Physics, School of Mathematics and Physics, Queen's University Belfast, Belfast, BT7 1NN, United Kingdom
| | - Paul R Vasos
- Extreme Light Infrastructure - Nuclear Physics ELI-NP, "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125, Bucharest-Magurele, Romania.,Research Institute of the University of Bucharest (ICUB), 36-46 B-dul M. Kogalniceanu, RO-050107, Bucharest, Romania
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31
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Nishimura K, Kouno H, Tateishi K, Uesaka T, Ideta K, Kimizuka N, Yanai N. Triplet dynamic nuclear polarization of nanocrystals dispersed in water at room temperature. Phys Chem Chem Phys 2019; 21:16408-16412. [PMID: 31282507 DOI: 10.1039/c9cp03330k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
While dynamic nuclear polarization using photo-excited triplet electrons (triplet-DNP) can improve the sensitivity of nuclear magnetic resonance at room temperature, it has not been carried out in water. Here, we report the first example of triplet-DNP in water by downsizing the conventional bulk crystals to nanocrystals.
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Affiliation(s)
- Koki Nishimura
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Hironori Kouno
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Kenichiro Tateishi
- Cluster for Pioneering Research, Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Tomohiro Uesaka
- Cluster for Pioneering Research, Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Keiko Ideta
- Institute for Materials Chemistry and Engineering, Kyushu University, 6-1 Kasuga-koen, Kasuga, Fukuoka 816-8580, Japan
| | - Nobuo Kimizuka
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Nobuhiro Yanai
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan. and PRESTO, JST, Honcho 4-1-8, Kawaguchi, Saitama 332-0012, Japan
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32
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Sadet A, Stavarache C, Bacalum M, Radu M, Bodenhausen G, Kurzbach D, Vasos PR. Hyperpolarized Water Enhances Two-Dimensional Proton NMR Correlations: A New Approach for Molecular Interactions. J Am Chem Soc 2019; 141:12448-12452. [PMID: 31368708 DOI: 10.1021/jacs.9b03651] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein and peptide interactions are characterized in the liquid state by multidimensional NMR spectroscopy experiments, which can take hours to record. We show that starting from hyperpolarized HDO, two-dimensional (2D) proton correlation maps of a peptide, either free in solution or interacting with liposomes, can be acquired in less than 60 s. In standard 2D NMR spectroscopy without hyperpolarization, the acquisition time required for similar spectral correlations is on the order of hours. This hyperpolarized experiment enables the identification of amino acids featuring solvent-interacting hydrogens and provides fast spectroscopic analysis of peptide conformers. Sensitivity-enhanced 2D proton correlation spectroscopy is a useful and straightforward tool for biochemistry and structural biology, as it does not recur to nitrogen-15 or carbon-13 isotope enrichment.
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Affiliation(s)
- Aude Sadet
- Research Institute of the University of Bucharest (ICUB) , 36-46 B-dul M. Kogalniceanu , RO-050107 Bucharest , Romania.,ELI-NP, Extreme Light Infrastructure - Nuclear Physics , IFIN-HH , 30 Reactorului Street , RO-077125 Bucharest-Magurele , Romania
| | - Cristina Stavarache
- Research Institute of the University of Bucharest (ICUB) , 36-46 B-dul M. Kogalniceanu , RO-050107 Bucharest , Romania.,"C.D. Nenitescu" Centre of Organic Chemistry , 202-B Spl. Independentei , RO-060023 Bucharest , Romania
| | - Mihaela Bacalum
- Department of Life and Environmental Physics , "Horia Hulubei" National Institute for Physics and Nuclear Engineering (IFIN-HH) , 30 Reactorului Street , RO-077125 Bucharest-Magurele , Romania
| | - Mihai Radu
- Department of Life and Environmental Physics , "Horia Hulubei" National Institute for Physics and Nuclear Engineering (IFIN-HH) , 30 Reactorului Street , RO-077125 Bucharest-Magurele , Romania
| | - Geoffrey Bodenhausen
- Laboratoire des Biomolécules, LBM, Département de Chimie , École Normale Supérieure, PSL University, Sorbonne Université, CNRS , 75005 Paris , France
| | - Dennis Kurzbach
- Laboratoire des Biomolécules, LBM, Département de Chimie , École Normale Supérieure, PSL University, Sorbonne Université, CNRS , 75005 Paris , France.,Institute of Biological Chemistry, Faculty of Chemistry , University of Vienna , Währinger Str. 38 , 1090 Vienna , Austria
| | - Paul R Vasos
- Research Institute of the University of Bucharest (ICUB) , 36-46 B-dul M. Kogalniceanu , RO-050107 Bucharest , Romania.,ELI-NP, Extreme Light Infrastructure - Nuclear Physics , IFIN-HH , 30 Reactorului Street , RO-077125 Bucharest-Magurele , Romania
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33
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Nastasa V, Stavarache C, Hanganu A, Coroaba A, Nicolescu A, Deleanu C, Sadet A, Vasos PR. Hyperpolarised NMR to follow water proton transport through membrane channels via exchange with biomolecules. Faraday Discuss 2019; 209:67-82. [PMID: 29989626 DOI: 10.1039/c8fd00021b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Water uptake in vesicles and the subsequent exchange between water protons and amide -NH protons in amino acids can be followed by a new, highly sensitive, type of magnetic resonance spectroscopy: dynamic nuclear polarisation (DNP)-enhanced NMR in the liquid state. Water hydrogen atoms are detected prior to and after their transfer to molecular sites in peptides and proteins featuring highly-accessible proton-exchangeable groups, as is the case for the -NH groups of intrinsically disordered proteins. The detected rates for amide proton-water proton exchange can be modulated by membrane-crossing rates, when a membrane channel is interposed. We hyperpolarised water proton spins via dynamic nuclear polarisation followed by sample dissolution (d-DNP) and transferred the created polarisation to -NH groups with high solvent accessibility in an intrinsically disordered protein domain. This domain is the membrane anchor of c-Src kinase, whose activity controls cell proliferation. The hindrance of effective water proton transfer rate constants observed in free solvent when a membrane-crossing step is involved is discussed. This study aims to assess the feasibility of recently-introduced hyperpolarised (DNP-enhanced) NMR to assess water membrane crossing dynamics.
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Affiliation(s)
- Viorel Nastasa
- Extreme Light Infrastructure - Nuclear Physics (ELI-NP), Horia Hulubei Institute for Nuclear Physics (IFIN-HH), Reactorului Str., 30, Magurele Campus, Bucharest, Romania.
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34
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Jannin S, Dumez JN, Giraudeau P, Kurzbach D. Application and methodology of dissolution dynamic nuclear polarization in physical, chemical and biological contexts. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 305:41-50. [PMID: 31203098 PMCID: PMC6616036 DOI: 10.1016/j.jmr.2019.06.001] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/28/2019] [Accepted: 06/02/2019] [Indexed: 05/06/2023]
Abstract
Dissolution dynamic nuclear polarization (d-DNP) is a versatile method to enhance nuclear magnetic resonance (NMR) spectroscopy. It boosts signal intensities by four to five orders of magnitude thereby providing the potential to improve and enable a plethora of applications ranging from the real-time monitoring of chemical or biological processes to metabolomics and in-cell investigations. This perspectives article highlights possible avenues for developments and applications of d-DNP in biochemical and physicochemical studies. It outlines how chemists, biologists and physicists with various fields of interest can transform and employ d-DNP as a powerful characterization method for their research.
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Affiliation(s)
- Sami Jannin
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, Centre de RMN à Très Hauts Champs (CRMN), FRE 2034, 69100 Villeurbanne, France
| | | | - Patrick Giraudeau
- Université de Nantes, CNRS, CEISAM (UMR 6230), 44000 Nantes, France; Institut Universitaire de France, 1 rue Descartes, 75005 Paris, France
| | - Dennis Kurzbach
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Währinger Str. 38, 1090 Vienna, Austria.
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35
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Jähnig F, Himmler A, Kwiatkowski G, Däpp A, Hunkeler A, Kozerke S, Ernst M. A spin-thermodynamic approach to characterize spin dynamics in TEMPO-based samples for dissolution DNP at 7 T field. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 303:91-104. [PMID: 31030064 DOI: 10.1016/j.jmr.2019.04.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/12/2019] [Accepted: 04/19/2019] [Indexed: 06/09/2023]
Abstract
The spin dynamics of dissolution DNP samples consisting of 4.5 M [13C]urea in a mixture of (1/1)Vol glycerol/water using 4-Oxo-TEMPO as a radical was investigated. We analyzed the DNP dynamics as function of radical concentration at 7 T and 3.4 T static magnetic field as well as function of deuteration of the solvent matrix at the high field. The spin dynamics could be reproduced in all cases, at least qualitatively, by a thermodynamic model based on spin temperatures of the nuclear Zeeman baths and an electron non-Zeeman (dipolar) bath. We find, however, that at high field (7 T) and low radical concentrations (25 mM) the nuclear spins do not reach the same spin temperature indicating a weak coupling of the two baths. At higher radical concentrations, as well as for all radical concentrations at low field (3.4 T), the two nuclear Zeeman baths reach the same spin temperature within experimental errors. Additionally, the spin system was prepared with different initial conditions. For these cases, the thermodynamic model was able to predict the time evolution of the system well. While the DNP profiles do not give clear indications to a specific polarization transfer mechanism, at high field (7 T) increased coupling is seen. The EPR line shapes cannot clarify this in absence of ELDOR type experiments, nevertheless DNP profiles and dynamics under frequency-modulated microwave irradiation illustrate the expected increase in coupling between electrons with increasing radical concentration.
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Affiliation(s)
- Fabian Jähnig
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Aaron Himmler
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Grzegorz Kwiatkowski
- Institute for Biomedical Engineering, University and ETH Zürich, Gloriastrasse 35, 8092 Zürich, Switzerland
| | - Alexander Däpp
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Andreas Hunkeler
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Sebastian Kozerke
- Institute for Biomedical Engineering, University and ETH Zürich, Gloriastrasse 35, 8092 Zürich, Switzerland
| | - Matthias Ernst
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.
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36
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Laser- and cryogenic probe-assisted NMR enables hypersensitive analysis of biomolecules at submicromolar concentration. Proc Natl Acad Sci U S A 2019; 116:11602-11611. [PMID: 31142651 DOI: 10.1073/pnas.1820573116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Solution-state NMR typically requires 100 μM to 1 mM samples. This limitation prevents applications to mass-limited and aggregation-prone target molecules. Photochemically induced dynamic nuclear polarization was adapted to data collection on low-concentration samples by radiofrequency gating, enabling rapid 1D NMR spectral acquisition on aromatic amino acids and proteins bearing aromatic residues at nanomolar concentration, i.e., a full order of magnitude below other hyperpolarization techniques in liquids. Both backbone H1-C13 and side-chain resonances were enhanced, enabling secondary and tertiary structure analysis of proteins with remarkable spectral editing, via the 13C PREPRINT pulse sequence. Laser-enhanced 2D NMR spectra of 5 μM proteins at 600 MHz display 30-fold better S/N than conventional 2D data collected at 900 MHz. Sensitivity enhancements achieved with this technology, denoted as low-concentration photo-CIDNP (LC-photo-CIDNP), depend only weakly on laser intensity, highlighting the opportunity of safer and more cost-effective hypersensitive NMR applications employing low-power laser sources.
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37
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Kiryutin AS, Rodin BA, Yurkovskaya AV, Ivanov KL, Kurzbach D, Jannin S, Guarin D, Abergel D, Bodenhausen G. Transport of hyperpolarized samples in dissolution-DNP experiments. Phys Chem Chem Phys 2019; 21:13696-13705. [DOI: 10.1039/c9cp02600b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The magnetic field strength during sample transfer in dissolution dynamic nuclear polarization influences the resulting spectra.
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Affiliation(s)
- Alexey S. Kiryutin
- International Tomography Center SB RAS
- Institutskaya 3A
- Novosibirsk
- Russia
- Novosibirsk State University
| | - Bogdan A. Rodin
- International Tomography Center SB RAS
- Institutskaya 3A
- Novosibirsk
- Russia
- Novosibirsk State University
| | - Alexandra V. Yurkovskaya
- International Tomography Center SB RAS
- Institutskaya 3A
- Novosibirsk
- Russia
- Novosibirsk State University
| | - Konstantin L. Ivanov
- International Tomography Center SB RAS
- Institutskaya 3A
- Novosibirsk
- Russia
- Novosibirsk State University
| | - Dennis Kurzbach
- University Vienna
- Faculty of Chemistry
- Institute of Biological Chemistry
- Währinger Straße 38
- 1090 Vienna
| | - Sami Jannin
- Université de Lyon
- Centre de RMN à Très Hauts Champs (FRE2034 CNRS/UCBL/ENS Lyon)
- 5 rue de la Doua
- 69100 Villeurbanne
- France
| | - David Guarin
- Laboratoire des biomolécules
- LBM, Département de chimie, École normale supérieure
- PSL University
- Sorbonne Université
- CNRS
| | - Daniel Abergel
- Laboratoire des biomolécules
- LBM, Département de chimie, École normale supérieure
- PSL University
- Sorbonne Université
- CNRS
| | - Geoffrey Bodenhausen
- Laboratoire des biomolécules
- LBM, Département de chimie, École normale supérieure
- PSL University
- Sorbonne Université
- CNRS
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38
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Blaffert J, Haeri HH, Blech M, Hinderberger D, Garidel P. Spectroscopic methods for assessing the molecular origins of macroscopic solution properties of highly concentrated liquid protein solutions. Anal Biochem 2018; 561-562:70-88. [PMID: 30243977 DOI: 10.1016/j.ab.2018.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 09/08/2018] [Accepted: 09/17/2018] [Indexed: 01/14/2023]
Abstract
In cases of subcutaneous injection of therapeutic monoclonal antibodies, high protein concentrations (>50 mg/ml) are often required. During the development of these high concentration liquid formulations (HCLF), challenges such as aggregation, gelation, opalescence, phase separation, and high solution viscosities are more prone compared to low concentrated protein formulations. These properties can impair manufacturing processes, as well as protein stability and shelf life. To avoid such unfavourable solution properties, a detailed understanding about the nature of these properties and their driving forces are required. However, the fundamental mechanisms that lead to macroscopic solution properties, as above mentioned, are complex and not fully understood, yet. Established analytical methods for assessing the colloidal stability, i.e. the ability of a native protein to remain dispersed in solution, are restricted to dilute conditions and provide parameters such as the second osmotic virial coefficient, B22, and the diffusion interaction coefficient, kD. These parameters are routinely applied for qualitative estimations and identifications of proteins with challenging solution behaviours, such as high viscosities and aggregation, although the assays are prepared for low protein concentration conditions, typically between 0.1 and 20 mg/ml ("ideal" solution conditions). Quantitative analysis of samples of high protein concentration is difficult and it is hard to obtain information about the driving forces of such solution properties and corresponding protein-protein self-interactions. An advantage of using specific spectroscopic methods is the potential of directly analysing highly concentrated protein solutions at different solution conditions. This allows for collecting/gaining valuable information about the fundamental mechanisms of solution properties of the high protein concentration regime. In addition, the derived parameters might be more predictive as compared to the parameters originating from assays which are optimized for the low protein concentration range. The provided information includes structural data, molecular dynamics at various timescales and protein-solvent interactions, which can be obtained at molecular resolution. Herein, we provide an overview about spectroscopic techniques for analysing the origins of macroscopic solution behaviours in general, with a specific focus on pharmaceutically relevant high protein concentration and formulation conditions.
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Affiliation(s)
- Jacob Blaffert
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Haleh Hashemi Haeri
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Michaela Blech
- Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany
| | - Dariush Hinderberger
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Patrick Garidel
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany; Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany.
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39
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Kadeřávek P, Ferrage F, Bodenhausen G, Kurzbach D. High-Resolution NMR of Folded Proteins in Hyperpolarized Physiological Solvents. Chemistry 2018; 24:13418-13423. [PMID: 29969165 DOI: 10.1002/chem.201802885] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 06/28/2018] [Indexed: 11/10/2022]
Abstract
Hyperpolarized 2D exchange spectroscopy (HYPEX) to obtain high-resolution nuclear magnetic resonance (NMR) spectra of folded proteins under near-physiological conditions is reported. The technique is based on hyperpolarized water, which is prepared by dissolution dynamic nuclear polarization and mixed in situ in an NMR spectrometer with a protein in a physiological saline buffer at body temperature. Rapid exchange of labile protons with the hyperpolarized solvent, combined with cross-relaxation effects (NOEs), leads to boosted signal intensities for many amide 1 H-15 N correlations in the protein ubiquitin. As the introduction of hyperpolarization to the target protein is mediated via the solvent, the method is applicable to a broad spectrum of target molecules.
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Affiliation(s)
- Pavel Kadeřávek
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Fabien Ferrage
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Geoffrey Bodenhausen
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Dennis Kurzbach
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
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40
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Zhang G, Hilty C. Applications of dissolution dynamic nuclear polarization in chemistry and biochemistry. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:566-582. [PMID: 29602263 DOI: 10.1002/mrc.4735] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 03/12/2018] [Accepted: 03/19/2018] [Indexed: 05/15/2023]
Abstract
Sensitivity of detection is one of the most limiting aspects when applying NMR spectroscopy to current problems in the molecular sciences. A number of hyperpolarization methods exist for increasing the population difference between nuclear spin Zeeman states and enhance the signal-to-noise ratio by orders of magnitude. Among these methods, dissolution dynamic nuclear polarization (D-DNP) is unique in its capability of providing high spin polarization for many types of molecules in the liquid state. Originally proposed for biomedical applications including in vivo imaging, applications in high resolution NMR spectroscopy are now emerging. These applications are the focus of the present review. Using D-DNP, a small sample aliquot is first hyperpolarized as a frozen solid at low temperature, followed by dissolution into the liquid state. D-DNP extends the capabilities of liquid state NMR spectroscopy towards shorter timescales and enables the study of nonequilibrium processes, such as the kinetics and mechanisms of reactions. It allows the determination of intermolecular interactions, in particular based on spin relaxation parameters. At the same time, a challenge in the application of this hyperpolarization method is that spin polarization is nonrenewable. Substantial effort has been devoted to develop methods for enabling rapid correlation spectroscopy, the measurement of time-dependent signals, and the extension of the observable time window. With these methods, D-DNP has the potential to open new application areas in the chemical and biochemical sciences.
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Affiliation(s)
- Guannan Zhang
- Chemistry Department, Texas A&M University, College Station, TX, 77843, USA
| | - Christian Hilty
- Chemistry Department, Texas A&M University, College Station, TX, 77843, USA
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41
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Beier A, Schwarz TC, Kurzbach D, Platzer G, Tribuzio F, Konrat R. Modulation of Correlated Segment Fluctuations in IDPs upon Complex Formation as an Allosteric Regulatory Mechanism. J Mol Biol 2018; 430:2439-2452. [PMID: 29733855 DOI: 10.1016/j.jmb.2018.04.035] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/13/2018] [Accepted: 04/26/2018] [Indexed: 12/29/2022]
Abstract
Molecular recognition of and by intrinsically disordered proteins (IDPs) is an intriguing and still largely elusive phenomenon. Typically, protein recognition involving IDPs requires either folding upon binding or, alternatively, the formation of "fuzzy complexes." Here we show via correlation analyses of paramagnetic relaxation enhancement data unprecedented and striking alterations of the concerted fluctuations within the conformational ensemble of IDPs upon ligand binding. We study the binding of α-synuclein to calmodulin, a ubiquitous calcium-binding protein, and the binding of the extracellular matrix IDP osteopontin to heparin, a mimic of the extracellular matrix ligand hyaluronic acid. In both cases, binding leads to reduction of correlated long-range motions in these two IDPs and thus indicates a loosening of structural compaction upon binding. Most importantly, however, the simultaneous presence of correlated and anti-correlated fluctuations in IDPs suggests the prevalence of "energetic frustration" and provides an explanation for the puzzling observation of disordered allostery in IDPs.
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Affiliation(s)
- Andreas Beier
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Dr-Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Thomas C Schwarz
- Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Dennis Kurzbach
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Gerald Platzer
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Dr-Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Francesca Tribuzio
- Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Robert Konrat
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Dr-Bohr-Gasse 9, A-1030 Vienna, Austria; Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria.
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42
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Chen CH, Wang Y, Hilty C. Intermolecular interactions determined by NOE build-up in macromolecules from hyperpolarized small molecules. Methods 2018; 138-139:69-75. [PMID: 29471063 DOI: 10.1016/j.ymeth.2018.02.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 02/14/2018] [Accepted: 02/15/2018] [Indexed: 11/18/2022] Open
Abstract
The nuclear Overhauser effect (NOE) is a primary means to characterize intermolecular interactions using modern NMR spectroscopy. Multiple experiments measured using different mixing time can be used for quantifying NOE buildup and measuring cross-relaxation rates. However, this approach using conventional multi-dimensional NMR is time consuming. Hyperpolarization by dissolution dynamic nuclear polarization (D-DNP) can generate deviations from equilibrium spin polarization by orders of magnitude, thereby enhancing signals and allowing to characterize NOE build up in real-time. Since most small molecules can be hyperpolarized using D-DNP, this method is applicable to the study of intermolecular interactions between small molecules and macromolecules. This application is demonstrated using a model system for host-guest interactions including the third generation polyamidoamine dendrimer (G3 PAMAM) and the pharmaceutical phenylbutazone (PBZ). After mixing 1H hyperpolarized PBZ with PAMAM, the NOE build up is directly observed at different sites of the dendrimer in series of one-dimensional NMR spectra. Cross-relaxation rates specific to individual source and target spins are determined from the build up curves. Further, the polarization enhancement is shown to be sufficiently large to allow identification of cross-peaks not observed in a conventional 2D-NOESY spectrum. The improved signal-to-noise ratio provided by hyperpolarization allows for characterizing the intermolecular interaction in an almost instantaneous measurement, opening an application to macromolecular and biomacromolecular NMR.
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Affiliation(s)
- Chia-Hsiu Chen
- Chemistry Department, Texas A&M University, 3255 TAMU, College Station, TX 77843, United States
| | - Yunyi Wang
- Chemistry Department, Texas A&M University, 3255 TAMU, College Station, TX 77843, United States
| | - Christian Hilty
- Chemistry Department, Texas A&M University, 3255 TAMU, College Station, TX 77843, United States.
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43
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Szekely O, Olsen GL, Felli IC, Frydman L. High-Resolution 2D NMR of Disordered Proteins Enhanced by Hyperpolarized Water. Anal Chem 2018. [PMID: 29528228 DOI: 10.1021/acs.analchem.8b00585] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This study demonstrates the usefulness derived from relying on hyperpolarized water obtained by dissolution DNP, for site-resolved biophysical NMR studies of intrinsically disordered proteins. Thanks to the facile amide-solvent exchange experienced by protons in these proteins, 2D NMR experiments that like HMQC rely on the polarization of the amide protons, can be enhanced using hyperpolarized water by several orders of magnitude over their conventional counterparts. Optimizations of the DNP procedure and of the subsequent injection into the protein sample are necessary to achieve these gains while preserving state-of-the-art resolution; procedures enabling this transfer of the hyperpolarized water and the achievement of foamless hyperpolarized protein solutions are demonstrated. These protocols are employed to collect 2D 15N-1H HMQC NMR spectra of α-synuclein, showing residue-specific enhancements ≥100× over their thermal counterparts. These enhancements, however, vary considerably throughout the residues. The biophysics underlying this residue-specific behavior upon injection of hyperpolarized water is theoretically examined, the information that it carries is compared with results arising from alternative methods, and its overall potential is discussed.
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Affiliation(s)
- Or Szekely
- Department of Chemical and Biological Physics , The Weizmann Institute of Science , 234 Herzl Street , Rehovot 760001 , Israel
| | - Gregory Lars Olsen
- Department of Chemical and Biological Physics , The Weizmann Institute of Science , 234 Herzl Street , Rehovot 760001 , Israel
| | - Isabella C Felli
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff" , University of Florence , via Luigi Sacconi 6 , Sesto Fiorentino 50019 , Italy
| | - Lucio Frydman
- Department of Chemical and Biological Physics , The Weizmann Institute of Science , 234 Herzl Street , Rehovot 760001 , Israel
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44
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Weber EMM, Vezin H, Kempf JG, Bodenhausen G, Abergél D, Kurzbach D. Anisotropic longitudinal electronic relaxation affects DNP at cryogenic temperatures. Phys Chem Chem Phys 2018; 19:16087-16094. [PMID: 28598474 DOI: 10.1039/c7cp03242k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We report the observation of anisotropic longitudinal electronic relaxation in nitroxide radicals under typical dynamic nuclear polarization conditions. This anisotropy affects the efficiency of dynamic nuclear polarization at cryogenic temperatures of 4 K and high magnetic fields of 6.7 T. Under our experimental conditions, the electron paramagnetic resonance spectrum of nitroxides such as TEMPOL (4-hydroxy-2,2,6,6-tetramethylpiperidin-1-oxyl) is only partly averaged by electronic spectral diffusion, so that the relaxation times T1e(ω) vary across the spectrum. We demonstrate how the anisotropy of T1e(ω) can be taken into account in simple DNP models.
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Affiliation(s)
- E M M Weber
- Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 24 rue Lhomond, 75005 Paris, France.
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45
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La Penna G, Chelli R. Structural Insights into the Osteopontin-Aptamer Complex by Molecular Dynamics Simulations. Front Chem 2018; 6:2. [PMID: 29441346 PMCID: PMC5797602 DOI: 10.3389/fchem.2018.00002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/08/2018] [Indexed: 12/17/2022] Open
Abstract
Osteopontin is an intrinsically disordered protein involved in tissue remodeling. As a biomarker for pathological hypertrophy and fibrosis, the protein is targeted by an RNA aptamer. In this work, we model the interactions between osteopontin and its aptamer, including mono- (Na+) and divalent (Mg2+) cations. The molecular dynamics simulations suggest that the presence of divalent cations forces the N-terminus of osteopontin to bind the shell of divalent cations adsorbed over the surface of its RNA aptamer, the latter exposing a high negative charge density. The osteopontin plasticity as a function of the local concentration of Mg is discussed in the frame of the proposed strategies for osteopontin targeting as biomarker and in theranostic.
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Affiliation(s)
- Giovanni La Penna
- Istituto di Chimica dei Composti Organometallici, Consiglio Nazionale delle Ricerche (CNR), Florence, Italy
| | - Riccardo Chelli
- Dipartimento di Chimica, Università di Firenze, Florence, Italy
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46
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Guarin D, Marhabaie S, Rosso A, Abergel D, Bodenhausen G, Ivanov KL, Kurzbach D. Characterizing Thermal Mixing Dynamic Nuclear Polarization via Cross-Talk between Spin Reservoirs. J Phys Chem Lett 2017; 8:5531-5536. [PMID: 29076730 DOI: 10.1021/acs.jpclett.7b02233] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Dynamic nuclear polarization (DNP) embraces a family of methods to increase signal intensities in nuclear magnetic resonance (NMR) spectroscopy. Despite extensive theoretical work that allows one to distinguish at least five distinct mechanisms, it remains challenging to determine the relative weights of the processes that are responsible for DNP in state-of-the-art experiments operating with stable organic radicals like nitroxides at high magnetic fields and low temperatures. Specifically, determining experimental conditions where DNP involves thermal mixing, which denotes a spontaneous heat exchange between different spin reservoirs, remains challenging. We propose an experimental approach to ascertain the prevalence of the thermal mixing regime by monitoring characteristic signature properties of the time evolution of the hyperpolarization. We find that thermal mixing is the dominant DNP mechanism at high nitroxide radical concentrations, while a mixture of different mechanisms prevails at lower concentrations.
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Affiliation(s)
- David Guarin
- Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules (LBM), 75005 Paris, France
| | - Sina Marhabaie
- Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules (LBM), 75005 Paris, France
| | - Alberto Rosso
- Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 24 rue Lhomond, 75005 Paris, France
- Laboratoire Physique Théorique et Modèles Statistiques (LPTMS), Université Paris-Sud, Université Paris-Saclay, CNRS, 91405 Orsay, France
| | - Daniel Abergel
- Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules (LBM), 75005 Paris, France
| | - Geoffrey Bodenhausen
- Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules (LBM), 75005 Paris, France
| | - Konstantin L Ivanov
- International Tomography Center SB RAS , Institutskaya 3a, Novosibirsk 630090, Russia
- Novosibirsk State University , Pirogova 2, Novosibirsk 630090, Russia
| | - Dennis Kurzbach
- Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules (LBM), 75005 Paris, France
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47
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Kim J, Liu M, Hilty C. Modeling of Polarization Transfer Kinetics in Protein Hydration Using Hyperpolarized Water. J Phys Chem B 2017; 121:6492-6498. [PMID: 28613875 DOI: 10.1021/acs.jpcb.7b03052] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Water-protein interactions play a central role in protein structure, dynamics, and function. These interactions, traditionally, have been studied using nuclear magnetic resonance (NMR) by measuring chemical exchange and nuclear Overhauser effect (NOE). Polarization transferred from hyperpolarized water can result in substantial transient signal enhancements of protein resonances due to these processes. Here, we use dissolution dynamic nuclear polarization and flow-NMR for measuring the pH dependence of transferred signals to the protein trypsin. A maximum enhancement of 20 is visible in the amide proton region of the spectrum at pH 6.0, and of 47 at pH 7.5. The aliphatic region is enhanced up to 2.3 times at pH 6.0 and up to 2.5 times at pH 7.5. The time dependence of these observed signals can be modeled quantitatively using rate equations incorporating chemical exchange to amide sites and, optionally, intramolecular NOE to aliphatic protons. On the basis of these two- and three-site models, average exchange (kex) and cross-relaxation rates (σ) obtained were kex = 12 s-1, σ = -0.33 s-1 for pH 7.5 and kex = 1.8 s-1, σ = -0.72 s-1 for pH 6.0 at a temperature of 304 K. These values were validated using conventional EXSY and NOESY measurements. In general, a rapid measurement of exchange and cross-relaxation rates may be of interest for the study of structural changes of the protein occurring on the same time scale. Besides protein-water interactions, interactions with cosolvent or solutes can further be investigated using the same methods.
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Affiliation(s)
- Jihyun Kim
- Chemistry Department, Texas A&M University , 3255 TAMU, College Station, Texas 77843, United States
| | - Mengxiao Liu
- Chemistry Department, Texas A&M University , 3255 TAMU, College Station, Texas 77843, United States
| | - Christian Hilty
- Chemistry Department, Texas A&M University , 3255 TAMU, College Station, Texas 77843, United States
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48
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Ragavan M, Iconaru LI, Park C, Kriwacki RW, Hilty C. Real‐Time Analysis of Folding upon Binding of a Disordered Protein by Using Dissolution DNP NMR Spectroscopy. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700464] [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)
- Mukundan Ragavan
- Department of Biochemistry & Biophysics Texas A&M University College Station TX 77843 USA
- Department of Biochemistry and Molecular Biology University of Florida College of Medicine Gainesville FL 32611 USA
| | - Luigi I. Iconaru
- Department of Structural Biology St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Cheon‐Gil Park
- Department of Structural Biology St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Richard W. Kriwacki
- Department of Structural Biology St. Jude Children's Research Hospital Memphis TN 38105 USA
- Department of Microbiology, Immunology and Biochemistry The University of Tennessee Health Science Center Memphis TN 38163 USA
| | - Christian Hilty
- Department of Chemistry Texas A&M University College Station TX 77843 USA
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49
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Ragavan M, Iconaru LI, Park CG, Kriwacki RW, Hilty C. Real-Time Analysis of Folding upon Binding of a Disordered Protein by Using Dissolution DNP NMR Spectroscopy. Angew Chem Int Ed Engl 2017; 56:7070-7073. [PMID: 28508552 DOI: 10.1002/anie.201700464] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 03/17/2017] [Indexed: 01/05/2023]
Abstract
The kinase inhibitory domain of the cell cycle regulatory protein p27Kip1 (p27) was nuclear spin hyperpolarized using dissolution dynamic nuclear polarization (D-DNP). While intrinsically disordered in isolation, p27 adopts secondary structural motifs, including an α-helical structure, upon binding to cyclin-dependent kinase 2 (Cdk2)/cyclin A. The sensitivity gains obtained with hyperpolarization enable the real-time observation of 13 C NMR signals during p27 folding upon binding to Cdk2/cyclin A on a time scale of several seconds. Time-dependent intensity changes are dependent on the extent of folding and binding, as manifested in differential spin relaxation. The analysis of signal decay rates suggests the existence of a partially folded p27 intermediate during the timescale of the D-DNP NMR experiment.
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Affiliation(s)
- Mukundan Ragavan
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843, USA.,Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, FL, 32611, USA
| | - Luigi I Iconaru
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Cheon-Gil Park
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.,Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Christian Hilty
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
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