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Krafčíková MD, Beriashvili D, Bahri S, Bergmeijer M, Howes SC, Gurinov A, Förster FG, Folkers GE, Baldus M. A DNP-Supported Solid-State NMR Approach to Study Nucleic Acids In Situ Reveals Berberine-Stabilized Hoogsteen Structures in Mitochondria. Angew Chem Int Ed Engl 2025:e202424131. [PMID: 40052409 DOI: 10.1002/anie.202424131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2024] [Revised: 03/04/2025] [Accepted: 03/06/2025] [Indexed: 03/19/2025]
Abstract
Mitochondria are central to cellular bioenergetics, with the unique ability to translate and transcribe a subset of their own proteome. Given the critical importance of energy production, mitochondria seem to utilize higher-order nucleic acid structures to regulate gene expression, much like nuclei. Herein, we introduce a tailored approach to probe the formation of such structures, specifically G-quadruplexes, within intact mitochondria by using sensitivity-enhanced dynamic nuclear polarization-supported solid-state NMR (DNP-ssNMR). We acquired NMR spectra on isolated intact isotopically labeled mitochondria treated with berberine, a known high-affinity G-quadruplex stabilizer. The DNP-ssNMR data revealed spectral changes in nucleic acid sugar correlations, increased signal intensity for guanosine carbons, and enhanced Hoogsteen hydrogen bond formation, providing evidence of in vivo G-quadruplex formation in mitochondria. Together, our workflow enables the study of mitochondrial nucleic acid-ligand interactions at endogenous concentrations within biologically relevant environments by DNP-ssNMR, thus paving the way for future research into mitochondrial diseases and their potential treatments.
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Affiliation(s)
- Michaela Dzurov Krafčíková
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - David Beriashvili
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - Salima Bahri
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - Menno Bergmeijer
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, Utrecht, 3584CG, The Netherlands
| | - Stuart C Howes
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, Utrecht, 3584CG, The Netherlands
| | - Andrei Gurinov
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - Friedrich G Förster
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, Utrecht, 3584CG, The Netherlands
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
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2
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Tan X, Zhou J, Yang L, Chang Q, Li SY, Rockenbauer A, Song Y, Liu Y. Simultaneous Quantitation of Persulfides, Biothiols, and Hydrogen Sulfide through Sulfur Exchange Reaction with Trityl Spin Probes. J Am Chem Soc 2024; 146:30422-30433. [PMID: 39431326 DOI: 10.1021/jacs.4c10266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2024]
Abstract
Reactive sulfur species (RSS) including persulfides (RSSHs), biothiols, and hydrogen sulfide (H2S) are key regulators in various physiological processes. To better understand the symbiotic relationship and interconversion of these RSS, it is highly desirable but challenging to develop analytical techniques that are capable of detecting and quantifying them. Herein, we report the rational design and synthesis of novel trityl-radical-based electron paramagnetic resonance (EPR) probes dubbed CT02-TNB and OX-TNB. CT02-TNB underwent fast sulfur exchange reactions with two reactive RSSHs (PS1 and PS2) which were released from their corresponding donors PSD1 and PSD2 to afford the specific conjugates. The resulting conjugates exhibit characteristic EPR spectra, thus enabling discriminative detection and quantitation of the two RSSHs. Moreover, CT02-TNB showed good response toward other RSS including glutathione (GSH), cysteine (Cys), H2S, and sulfite as well. Importantly, based on the updated EPR spectral simulation program, simultaneous quantitation of multiple RSS (e.g., PS1/GSH/Cys or PS1/GSH/H2S) by CT02-TNB was also achieved. Finally, the levels of released PS1 from PSD1 and endogenous GSH in isolated mouse livers were measured by the hydrophilic OX-TNB. This work represents the first study achieving discriminative and quantitative detection of different persulfides and other RSS by a spectroscopic method.
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Affiliation(s)
- Xiaoli Tan
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Jiaxin Zhou
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Luhua Yang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Qi Chang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Shao-Yong Li
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Antal Rockenbauer
- Institute of Materials and Environmental Chemistry, Hungarian Academy of Sciences and, Department of Physics, Budapest University of Technology and Economics, Budafoki ut 8, Budapest 1111, Hungary
| | - Yuguang Song
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Yangping Liu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
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3
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Stepanov AV, Yarovenko VN, Nasyrova DI, Dezhenkova LG, Akchurin IO, Krayushkin MM, Ilyushenkova VV, Shchekotikhin AE, Tretyakov EV. A Spin-Labeled Derivative of Gossypol. Molecules 2024; 29:4966. [PMID: 39459334 PMCID: PMC11510377 DOI: 10.3390/molecules29204966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Revised: 10/18/2024] [Accepted: 10/18/2024] [Indexed: 10/28/2024] Open
Abstract
Gossypol and its derivatives arouse interest due to their broad spectrum of biological activities. Despite its wide potential application, there is no reported example of gossypol derivatives bearing stable radical functional groups. The first gossypol nitroxide hybrid compound was prepared here via formation of a Schiff base. By this approach, synthesis of a gossypol nitroxide conjugate was performed by condensation of gossypol with a 4-amino-TEMPO (4-amino-2,2,6,6-tetramethylpiperidin-1-oxyl) free radical, which afforded the target product in high yield. Its structure was proven by a combination of NMR and EPR spectroscopy, infrared spectroscopy, mass spectrometry, and high-resolution mass spectrometry. In addition, the structure of the gossypol nitroxide was determined by single-crystal X-ray diffraction measurements. In crystals, the paramagnetic Schiff base exists in an enamine-enamine tautomeric form. The tautomer is strongly stabilized by the intra- and intermolecular hydrogen bonds promoted by the resonance of π-electrons in the aromatic system. NMR analyses of the gossypol derivative proved that in solutions, the enamine-enamine tautomeric form prevailed. The gossypol nitroxide at micromolar concentrations suppressed the growth of tumor cells; however, compared to gossypol, the cytotoxicity of the obtained conjugate was substantially lower.
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Affiliation(s)
- Andrey V. Stepanov
- N.D. Zelinsky Institute of Organic Chemistry, Leninsky Ave. 47, Moscow 119991, Russia; (A.V.S.); (V.N.Y.); (D.I.N.); (V.V.I.)
| | - Vladimir N. Yarovenko
- N.D. Zelinsky Institute of Organic Chemistry, Leninsky Ave. 47, Moscow 119991, Russia; (A.V.S.); (V.N.Y.); (D.I.N.); (V.V.I.)
| | - Darina I. Nasyrova
- N.D. Zelinsky Institute of Organic Chemistry, Leninsky Ave. 47, Moscow 119991, Russia; (A.V.S.); (V.N.Y.); (D.I.N.); (V.V.I.)
| | - Lyubov G. Dezhenkova
- Gause Institute of New Antibiotics, Bolshaya Pirogovskaya St. 11, Moscow 119021, Russia; (L.G.D.); (I.O.A.); (A.E.S.)
| | - Igor O. Akchurin
- Gause Institute of New Antibiotics, Bolshaya Pirogovskaya St. 11, Moscow 119021, Russia; (L.G.D.); (I.O.A.); (A.E.S.)
- D. Mendeleev University of Chemical Technology of Russia, Miusskaya Sq. 9, Moscow 125047, Russia
| | - Mickhail M. Krayushkin
- N.D. Zelinsky Institute of Organic Chemistry, Leninsky Ave. 47, Moscow 119991, Russia; (A.V.S.); (V.N.Y.); (D.I.N.); (V.V.I.)
| | - Valentina V. Ilyushenkova
- N.D. Zelinsky Institute of Organic Chemistry, Leninsky Ave. 47, Moscow 119991, Russia; (A.V.S.); (V.N.Y.); (D.I.N.); (V.V.I.)
| | - Andrey E. Shchekotikhin
- Gause Institute of New Antibiotics, Bolshaya Pirogovskaya St. 11, Moscow 119021, Russia; (L.G.D.); (I.O.A.); (A.E.S.)
| | - Evgeny V. Tretyakov
- N.D. Zelinsky Institute of Organic Chemistry, Leninsky Ave. 47, Moscow 119991, Russia; (A.V.S.); (V.N.Y.); (D.I.N.); (V.V.I.)
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4
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Niccoli L, Casano G, Menzildjian G, Yulikov M, Robinson T, Akrial SE, Wang Z, Reiter C, Purea A, Siri D, Venkatesh A, Emsley L, Gajan D, Lelli M, Ouari O, Lesage A. Efficient DNP at high fields and fast MAS with antenna-sensitized dinitroxides. Chem Sci 2024:d4sc04473h. [PMID: 39309076 PMCID: PMC11411413 DOI: 10.1039/d4sc04473h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Accepted: 09/10/2024] [Indexed: 09/25/2024] Open
Abstract
Dynamic Nuclear Polarization (DNP) can significantly enhance the sensitivity of solid-state NMR. In DNP, microwave irradiation induces polarization transfer from unpaired electron spins to 1H nuclear spins via hyperfine couplings and spin-diffusion. The structure of the polarizing agents that host the electron spins is key for DNP efficiency. Currently, only a handful of structures perform well at very high magnetic fields (≥18.8 T), and enhancements are significantly lower than those obtained at lower fields. Here, we introduce a new series of water-soluble nitroxide biradicals with a scaffold augmented by dihydroxypropyl antenna chains that perform significantly better than previous dinitroxides at 18.8 T. The new radical M-TinyPol(OH)4 yields enhancement factors of ∼220 at 18.8 T and 60 kHz MAS, which is a nearly factor 2 larger than for the previous best performing dinitroxides. The performance is understood through 2H ESEEM measurements to probe solvent accessibility, supported by Molecular Dynamics simulations, and by experiments on deuterated samples. We find that the deuterated glycerol molecules in the matrix are located mainly in the second solvation shell of the NO bond, limiting access for protonated water molecules, and restricting spin diffusion pathways. This provides a rational understanding of why the dihydroxypropyl chains present in the best-performing structures are essential to deliver the polarization to the bulk solution.
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Affiliation(s)
- Lorenzo Niccoli
- Centre de RMN à Hauts Champs de Lyon, UMR 5082, Université de Lyon (CNRS/ENS Lyon/UCBL) 5 rue de la Doua Villeurbanne 69100 France
- Center of Magnetic Resonance (CERM), University of Florence 50019 Sesto Fiorentino Italy
- Department of Chemistry 'Ugo Schiff', University of Florence Via della Lastruccia 13 50019 Sesto Fiorentino FI Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metalloproteine Paramagnetiche (CIRMMP) Via Luigi Sacconi 6 50019 Sesto Fiorentino FI Italy
| | | | - Georges Menzildjian
- Centre de RMN à Hauts Champs de Lyon, UMR 5082, Université de Lyon (CNRS/ENS Lyon/UCBL) 5 rue de la Doua Villeurbanne 69100 France
| | - Maxim Yulikov
- Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich CH-8093 Zürich Switzerland
| | - Thomas Robinson
- Centre de RMN à Hauts Champs de Lyon, UMR 5082, Université de Lyon (CNRS/ENS Lyon/UCBL) 5 rue de la Doua Villeurbanne 69100 France
| | - Salah-Eddine Akrial
- Centre de RMN à Hauts Champs de Lyon, UMR 5082, Université de Lyon (CNRS/ENS Lyon/UCBL) 5 rue de la Doua Villeurbanne 69100 France
| | - Zhuoran Wang
- Centre de RMN à Hauts Champs de Lyon, UMR 5082, Université de Lyon (CNRS/ENS Lyon/UCBL) 5 rue de la Doua Villeurbanne 69100 France
| | | | | | - Didier Siri
- Aix Marseille Uni, CNRS, ICR 13013 Marseille France
| | - Amrit Venkatesh
- Laboratory of Magnetic Resonance, Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne Switzerland
- National High Magnetic Field Laboratory, Florida State University Tallahassee FL 32310 USA
| | - Lyndon Emsley
- Laboratory of Magnetic Resonance, Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne Switzerland
| | - David Gajan
- Centre de RMN à Hauts Champs de Lyon, UMR 5082, Université de Lyon (CNRS/ENS Lyon/UCBL) 5 rue de la Doua Villeurbanne 69100 France
| | - Moreno Lelli
- Center of Magnetic Resonance (CERM), University of Florence 50019 Sesto Fiorentino Italy
- Department of Chemistry 'Ugo Schiff', University of Florence Via della Lastruccia 13 50019 Sesto Fiorentino FI Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metalloproteine Paramagnetiche (CIRMMP) Via Luigi Sacconi 6 50019 Sesto Fiorentino FI Italy
| | | | - Anne Lesage
- Centre de RMN à Hauts Champs de Lyon, UMR 5082, Université de Lyon (CNRS/ENS Lyon/UCBL) 5 rue de la Doua Villeurbanne 69100 France
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5
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Dwivedi N, Patra B, Mentink-Vigier F, Wi S, Sinha N. Unveiling Charge-Pair Salt-Bridge Interaction Between GAGs and Collagen Protein in Cartilage: Atomic Evidence from DNP-Enhanced ssNMR at Natural Isotopic Abundance. J Am Chem Soc 2024; 146:23663-23668. [PMID: 38980938 PMCID: PMC11572119 DOI: 10.1021/jacs.4c05539] [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: 07/11/2024]
Abstract
The interactions between glycosaminoglycans (GAGs) and proteins are essential in numerous biochemical processes that involve ion-pair interactions. However, there is no evidence of direct and specific interactions between GAGs and collagen proteins in native cartilage. The resolution of solid-state NMR (ssNMR) can offer such information but the detection of GAG interactions in cartilage is limited by the sensitivity of the experiments when 13C and 15N isotopes are at natural abundance. In this communication, this limitation is overcome by taking advantage of dynamic nuclear polarization (DNP)-enhanced magic-angle spinning (MAS) experiments to obtain two-dimensional (2D) 15N-13C and 13C-13C correlations on native samples at natural abundance. These experiments unveiled inter-residue correlations in the aliphatic regions of the collagen protein previously unobserved. Additionally, our findings provide direct evidence of charge-pair salt-bridge interactions between negatively charged GAGs and positively charged arginine (Arg) residues of collagen protein. We also identified potential hydrogen bonding interactions between hydroxyproline (Hyp) and GAGs, offering atomic insights into the biochemical interactions within the extracellular matrix of native cartilage. Our approach may provide a new avenue for the structural characterization of other native systems.
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Affiliation(s)
- Navneet Dwivedi
- Centre of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow – 226014, INDIA
| | - Bijaylaxmi Patra
- Centre of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow – 226014, INDIA
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad −201002, India
| | - Frederic Mentink-Vigier
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, USA
| | - Sungsool Wi
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, USA
| | - Neeraj Sinha
- Centre of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow – 226014, INDIA
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad −201002, India
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6
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Beriashvili D, Zhou J, Liu Y, Folkers GE, Baldus M. Cellular Applications of DNP Solid-State NMR - State of the Art and a Look to the Future. Chemistry 2024; 30:e202400323. [PMID: 38451060 DOI: 10.1002/chem.202400323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/08/2024]
Abstract
Sensitivity enhanced dynamic nuclear polarization solid-state NMR is emerging as a powerful technique for probing the structural properties of conformationally homogenous and heterogenous biomolecular species irrespective of size at atomic resolution within their native environments. Herein we detail advancements that have made acquiring such data, specifically within the confines of intact bacterial and eukaryotic cell a reality and further discuss the type of structural information that can presently be garnered by the technique's exploitation. Subsequently, we discuss bottlenecks that have thus far curbed cellular DNP-ssNMR's broader adoption namely due a lack of sensitivity and spectral resolution. We also explore possible solutions ranging from utilization of new pulse sequences, design of better performing polarizing agents, and application of additional biochemical/ cell biological methodologies.
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Affiliation(s)
- David Beriashvili
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padaulaan 8, 3584 CH, Utrecht, The Netherlands
| | - Jiaxin Zhou
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics, Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P. R. China
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics, Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P. R. China
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padaulaan 8, 3584 CH, Utrecht, The Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padaulaan 8, 3584 CH, Utrecht, The Netherlands
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7
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Harrabi R, Halbritter T, Alarab S, Chatterjee S, Wolska-Pietkiewicz M, Damodaran KK, van Tol J, Lee D, Paul S, Hediger S, Sigurdsson ST, Mentink-Vigier F, De Paëpe G. AsymPol-TEKs as efficient polarizing agents for MAS-DNP in glass matrices of non-aqueous solvents. Phys Chem Chem Phys 2024; 26:5669-5682. [PMID: 38288878 PMCID: PMC10849081 DOI: 10.1039/d3cp04271e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 01/22/2024] [Indexed: 02/03/2024]
Abstract
Two polarizing agents from the AsymPol family, AsymPol-TEK and cAsymPol-TEK (methyl-free version) are introduced for MAS-DNP applications in non-aqueous solvents. The performance of these new biradicals is rationalized in detail using a combination of electron paramagnetic resonance spectroscopy, density functional theory, molecular dynamics and quantitative MAS-DNP spin dynamics simulations. By slightly modifying the experimental protocol to keep the sample temperature low at insertion, we are able to obtain reproducable DNP-NMR data with 1,1,2,2-tetrachloroethane (TCE) at 100 K, which facilitates optimization and comparison of different polarizing agents. At intermediate magnetic fields, AsymPol-TEK and cAsymPol-TEK provide 1.5 to 3-fold improvement in sensitivity compared to TEKPol, one of the most widely used polarizing agents for organic solvents, with significantly shorter DNP build-up times of ∼1 s and ∼2 s at 9.4 and 14.1 T respectively. In the course of the work, we also isolated and characterized two diastereoisomers that can form during the synthesis of AsymPol-TEK; their difference in performance is described and discussed. Finally, the advantages of the AsymPol-TEKs are demonstrated by recording 2D 13C-13C correlation experiments at natural 13C-abundance of proton-dense microcrystals and by polarizing the surface of ZnO nanocrystals (NCs) coated with diphenyl phosphate ligands. For those experiments, cAsymPol-TEK yielded a three-fold increase in sensitivity compared to TEKPol, corresponding to a nine-fold time saving.
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Affiliation(s)
- Rania Harrabi
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, MEM, 38000 Grenoble, France.
| | - Thomas Halbritter
- University of Iceland, Department of Chemistry, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland.
| | - Shadi Alarab
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, MEM, 38000 Grenoble, France.
| | - Satyaki Chatterjee
- University of Iceland, Department of Chemistry, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland.
| | | | - Krishna K Damodaran
- University of Iceland, Department of Chemistry, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland.
| | - Johan van Tol
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32301, USA.
| | - Daniel Lee
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, MEM, 38000 Grenoble, France.
| | - Subhradip Paul
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, MEM, 38000 Grenoble, France.
| | - Sabine Hediger
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, MEM, 38000 Grenoble, France.
| | - Snorri Th Sigurdsson
- University of Iceland, Department of Chemistry, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland.
| | - Frederic Mentink-Vigier
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32301, USA.
| | - Gaël De Paëpe
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, MEM, 38000 Grenoble, France.
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8
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Beriashvili D, Yao R, D'Amico F, Krafčíková M, Gurinov A, Safeer A, Cai X, Mulder MPC, Liu Y, Folkers GE, Baldus M. A high-field cellular DNP-supported solid-state NMR approach to study proteins with sub-cellular specificity. Chem Sci 2023; 14:9892-9899. [PMID: 37736634 PMCID: PMC10510770 DOI: 10.1039/d3sc02117c] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/24/2023] [Indexed: 09/23/2023] Open
Abstract
Studying the structural aspects of proteins within sub-cellular compartments is of growing interest. Dynamic nuclear polarization supported solid-state NMR (DNP-ssNMR) is uniquely suited to provide such information, but critically lacks the desired sensitivity and resolution. Here we utilize SNAPol-1, a novel biradical, to conduct DNP-ssNMR at high-magnetic fields (800 MHz/527 GHz) inside HeLa cells and isolated cell nuclei electroporated with [13C,15N] labeled ubiquitin. We report that SNAPol-1 passively diffuses and homogenously distributes within whole cells and cell nuclei providing ubiquitin spectra of high sensitivity and remarkably improved spectral resolution. For cell nuclei, physical enrichment facilitates a further 4-fold decrease in measurement time and provides an exclusive structural view of the nuclear ubiquitin pool. Taken together, these advancements enable atomic interrogation of protein conformational plasticity at atomic resolution and with sub-cellular specificity.
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Affiliation(s)
- David Beriashvili
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Ru Yao
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Francesca D'Amico
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC) Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Michaela Krafčíková
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Andrei Gurinov
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Adil Safeer
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Xinyi Cai
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Monique P C Mulder
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC) Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
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9
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Shukla R, Peoples AJ, Ludwig KC, Maity S, Derks MGN, De Benedetti S, Krueger AM, Vermeulen BJA, Harbig T, Lavore F, Kumar R, Honorato RV, Grein F, Nieselt K, Liu Y, Bonvin AMJJ, Baldus M, Kubitscheck U, Breukink E, Achorn C, Nitti A, Schwalen CJ, Spoering AL, Ling LL, Hughes D, Lelli M, Roos WH, Lewis K, Schneider T, Weingarth M. An antibiotic from an uncultured bacterium binds to an immutable target. Cell 2023; 186:4059-4073.e27. [PMID: 37611581 DOI: 10.1016/j.cell.2023.07.038] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 06/01/2023] [Accepted: 07/28/2023] [Indexed: 08/25/2023]
Abstract
Antimicrobial resistance is a leading mortality factor worldwide. Here, we report the discovery of clovibactin, an antibiotic isolated from uncultured soil bacteria. Clovibactin efficiently kills drug-resistant Gram-positive bacterial pathogens without detectable resistance. Using biochemical assays, solid-state nuclear magnetic resonance, and atomic force microscopy, we dissect its mode of action. Clovibactin blocks cell wall synthesis by targeting pyrophosphate of multiple essential peptidoglycan precursors (C55PP, lipid II, and lipid IIIWTA). Clovibactin uses an unusual hydrophobic interface to tightly wrap around pyrophosphate but bypasses the variable structural elements of precursors, accounting for the lack of resistance. Selective and efficient target binding is achieved by the sequestration of precursors into supramolecular fibrils that only form on bacterial membranes that contain lipid-anchored pyrophosphate groups. This potent antibiotic holds the promise of enabling the design of improved therapeutics that kill bacterial pathogens without resistance development.
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Affiliation(s)
- Rhythm Shukla
- NMR Spectroscopy, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Membrane Biochemistry and Biophysics, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | | | - Kevin C Ludwig
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Sourav Maity
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Maik G N Derks
- NMR Spectroscopy, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Membrane Biochemistry and Biophysics, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Stefania De Benedetti
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Annika M Krueger
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Bram J A Vermeulen
- NMR Spectroscopy, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Theresa Harbig
- Integrative Transcriptomics, Center for Bioinformatics, University of Tübingen, 72070 Tübingen, Germany
| | - Francesca Lavore
- NMR Spectroscopy, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Raj Kumar
- NMR Spectroscopy, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Rodrigo V Honorato
- NMR Spectroscopy, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Fabian Grein
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, Germany; German Center for Infection Research (DZIF), partner site Bonn-Cologne, Bonn, Germany
| | - Kay Nieselt
- Integrative Transcriptomics, Center for Bioinformatics, University of Tübingen, 72070 Tübingen, Germany
| | - Yangping Liu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Alexandre M J J Bonvin
- NMR Spectroscopy, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Ulrich Kubitscheck
- Clausius-Institute for Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | | | - Anthony Nitti
- NovoBiotic Pharmaceuticals, Cambridge, MA 02138, USA
| | | | | | | | - Dallas Hughes
- NovoBiotic Pharmaceuticals, Cambridge, MA 02138, USA
| | - Moreno Lelli
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), via Sacconi 6, Sesto Fiorentino 50019, Italy
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Kim Lewis
- Antimicrobial Discovery Center, Northeastern University, Department of Biology, Boston, MA 02115, USA
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, Germany; German Center for Infection Research (DZIF), partner site Bonn-Cologne, Bonn, Germany.
| | - Markus Weingarth
- NMR Spectroscopy, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
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10
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Menzildjian G, Schlagnitweit J, Casano G, Ouari O, Gajan D, Lesage A. Polarizing agents for efficient high field DNP solid-state NMR spectroscopy under magic-angle spinning: from design principles to formulation strategies. Chem Sci 2023; 14:6120-6148. [PMID: 37325158 PMCID: PMC10266460 DOI: 10.1039/d3sc01079a] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/09/2023] [Indexed: 06/17/2023] Open
Abstract
Dynamic Nuclear Polarization (DNP) has recently emerged as a cornerstone approach to enhance the sensitivity of solid-state NMR spectroscopy under Magic Angle Spinning (MAS), opening unprecedented analytical opportunities in chemistry and biology. DNP relies on a polarization transfer from unpaired electrons (present in endogenous or exogenous polarizing agents) to nearby nuclei. Developing and designing new polarizing sources for DNP solid-state NMR spectroscopy is currently an extremely active research field per se, that has recently led to significant breakthroughs and key achievements, in particular at high magnetic fields. This review describes recent developments in this area, highlighting key design principles that have been established over time and led to the introduction of increasingly more efficient polarizing sources. After a short introduction, Section 2 presents a brief history of solid-state DNP, highlighting the main polarization transfer schemes. The third section is devoted to the development of dinitroxide radicals, discussing the guidelines that were progressively established to design the fine-tuned molecular structures in use today. In Section 4, we describe recent efforts in developing hybrid radicals composed of a narrow EPR line radical covalently linked to a nitroxide, highlighting the parameters that modulate the DNP efficiency of these mixed structures. Section 5 reviews recent advances in the design of metal complexes suitable for DNP MAS NMR as exogenous electron sources. In parallel, current strategies that exploit metal ions as endogenous polarization sources are discussed. Section 6 briefly describes the recent introduction of mixed-valence radicals. In the last part, experimental aspects regarding sample formulation are reviewed to make best use of these polarizing agents in a broad panel of application fields.
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Affiliation(s)
- Georges Menzildjian
- Centre de RMN à, Très Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCB Lyon 1) 5 Rue de la doua 69100 Villeurbanne France
| | - Judith Schlagnitweit
- Centre de RMN à, Très Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCB Lyon 1) 5 Rue de la doua 69100 Villeurbanne France
| | - Gilles Casano
- Aix Marseille Univ., CNRS, Institut de Chimie Radicalaire, UMR 7273 Marseille France
| | - Olivier Ouari
- Aix Marseille Univ., CNRS, Institut de Chimie Radicalaire, UMR 7273 Marseille France
| | - David Gajan
- Centre de RMN à, Très Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCB Lyon 1) 5 Rue de la doua 69100 Villeurbanne France
| | - Anne Lesage
- Centre de RMN à, Très Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCB Lyon 1) 5 Rue de la doua 69100 Villeurbanne France
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11
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Dervişoğlu R, Antonschmidt L, Nimerovsky E, Sant V, Kim M, Ryazanov S, Leonov A, Carlos Fuentes-Monteverde J, Wegstroth M, Giller K, Mathies G, Giese A, Becker S, Griesinger C, Andreas LB. Anle138b interaction in α-synuclein aggregates by dynamic nuclear polarization NMR. Methods 2023; 214:18-27. [PMID: 37037308 DOI: 10.1016/j.ymeth.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/22/2023] [Accepted: 04/06/2023] [Indexed: 04/12/2023] Open
Abstract
Small molecules that bind to oligomeric protein species such as membrane proteins and fibrils are of clinical interest for development of therapeutics and diagnostics. Definition of the binding site at atomic resolution via NMR is often challenging due to low binding stoichiometry of the small molecule. For fibrils and aggregation intermediates grown in the presence of lipids, we report atomic-resolution contacts to the small molecule at sub nm distance via solid-state NMR using dynamic nuclear polarization (DNP) and orthogonally labelled samples of the protein and the small molecule. We apply this approach to α-synuclein (αS) aggregates in complex with the small molecule anle138b, which is a clinical drug candidate for disease modifying therapy. The small central pyrazole moiety of anle138b is detected in close proximity to the protein backbone and differences in the contacts between fibrils and early intermediates are observed. For intermediate species, the 100 K condition for DNP helps to preserve the aggregation state, while for both fibrils and oligomers, the DNP enhancement is essential to obtain sufficient sensitivity.
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Affiliation(s)
- Rıza Dervişoğlu
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Leif Antonschmidt
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Evgeny Nimerovsky
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Vrinda Sant
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Myeongkyu Kim
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Sergey Ryazanov
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Center for Neuropathology and Prion Research, Ludwig-Maximilians University, Munich, Germany
| | - Andrei Leonov
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Center for Neuropathology and Prion Research, Ludwig-Maximilians University, Munich, Germany
| | | | - Melanie Wegstroth
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Karin Giller
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | | | - Armin Giese
- Center for Neuropathology and Prion Research, Ludwig-Maximilians University, Munich, Germany
| | - Stefan Becker
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Christian Griesinger
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Loren B Andreas
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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12
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Halbritter T, Harrabi R, Paul S, van Tol J, Lee D, Hediger S, Sigurdsson ST, Mentink-Vigier F, De Paëpe G. PyrroTriPol: a semi-rigid trityl-nitroxide for high field dynamic nuclear polarization. Chem Sci 2023; 14:3852-3864. [PMID: 37035686 PMCID: PMC10074417 DOI: 10.1039/d2sc05880d] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/12/2023] [Indexed: 03/18/2023] Open
Abstract
Magic angle spinning (MAS) dynamic nuclear polarization (DNP) has significantly broadened the scope of solid-state NMR to study biomolecular systems and materials. In recent years, the advent of very high field DNP combined with fast MAS has brought new challenges in the design of polarizing agents (PA) used to enhance nuclear spin polarization. Here, we present a trityl-nitroxide PA family based on a piperazine linker, named PyrroTriPol, for both aqueous and organic solutions. These new radicals have similar properties to that of TEMTriPol-I and can be readily synthesized, and purified in large quantities thereby ensuring widespread application. The family relies on a rigid bridge connecting the trityl and the nitroxide offering a better control of the electron spin-spin interactions thus providing improved performance across a broad range of magnetic fields and MAS frequencies while requiring reduced microwave power compared to bis-nitroxides. We demonstrate the efficiency of the PyrroTriPol family under a magnetic field of 9.4, 14.1 and 18.8 T with respect to TEMTriPol-I. In particular, the superiority of PyrroTriPol was demonstrated on γ-Al2O3 nanoparticles which enabled the acquisition of a high signal-to-noise surface-selective 27Al multiple-quantum MAS experiment at 18.8 T and 40 kHz MAS frequency.
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Affiliation(s)
- Thomas Halbritter
- Department of Chemistry, University of Iceland, Science Institute Dunhaga 3 107 Reykjavik Iceland
| | - Rania Harrabi
- IRIG, MEM, Univ. Grenoble Alpes, CEA, CNRS 38000 Grenoble France
| | - Subhradip Paul
- IRIG, MEM, Univ. Grenoble Alpes, CEA, CNRS 38000 Grenoble France
| | - Johan van Tol
- National High Magnetic Field Laboratory, Florida State University Tallahassee FL 32310 USA
| | - Daniel Lee
- IRIG, MEM, Univ. Grenoble Alpes, CEA, CNRS 38000 Grenoble France
- Department of Chemical Engineering, University of Manchester Manchester M13 9PL UK
| | - Sabine Hediger
- IRIG, MEM, Univ. Grenoble Alpes, CEA, CNRS 38000 Grenoble France
| | - Snorri Th Sigurdsson
- Department of Chemistry, University of Iceland, Science Institute Dunhaga 3 107 Reykjavik Iceland
| | | | - Gaël De Paëpe
- IRIG, MEM, Univ. Grenoble Alpes, CEA, CNRS 38000 Grenoble France
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13
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Kumar A, Watbled B, Baussanne I, Hediger S, Demeunynck M, De Paëpe G. Optimizing chemistry at the surface of prodrug-loaded cellulose nanofibrils with MAS-DNP. Commun Chem 2023; 6:58. [PMID: 36977767 PMCID: PMC10049993 DOI: 10.1038/s42004-023-00852-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 03/09/2023] [Indexed: 03/30/2023] Open
Abstract
Studying the surface chemistry of functionalized cellulose nanofibrils at atomic scale is an ongoing challenge, mainly because FT-IR, NMR, XPS and RAMAN spectroscopy are limited in sensitivity or resolution. Herein, we show that dynamic nuclear polarization (DNP) enhanced 13C and 15N solid-state NMR is a uniquely suited technique to optimize the drug loading on nanocellulose using aqueous heterogenous chemistry. We compare the efficiency of two conventional coupling agents (DMTMM vs EDC/NHS) to bind a complex prodrug of ciprofloxacin designed for controlled drug release. Besides quantifying the drug grafting, we also evidence the challenge to control the concurrent prodrug adsorption and to optimize washing procedures. We notably highlight the presence of an unexpected prodrug cleavage mechanism triggered by carboxylates at the surface of the cellulose nanofibrils.
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Affiliation(s)
- Akshay Kumar
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM, Grenoble, France
| | | | | | - Sabine Hediger
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM, Grenoble, France
| | | | - Gaël De Paëpe
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM, Grenoble, France.
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14
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An EPR Study on Highly Stable Nitroxyl-Nitroxyl Biradicals for Dynamic Nuclear Polarization Applications at High Magnetic Fields. Molecules 2023; 28:molecules28041926. [PMID: 36838912 PMCID: PMC9958542 DOI: 10.3390/molecules28041926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Nitroxide biradicals are efficient polarizing agents in dynamic nuclear polarization (DNP) solid-state nuclear magnetic resonance. Many recently reported radicals possess substantial DNP efficiency in organic solvents but have poor solubility in water media which is unfavorable for biological applications. In this paper, we report DNP efficiency at a high magnetic field for two water-soluble biradicals resistant to reducing media. Water solubility was achieved by obtaining the radicals in the form of quaternary ammonium salts. Parameters of hyperfine interaction and exchange interaction were quantified by EPR spectroscopy, and their influence on the DNP effect was determined. The resistance of the biradicals to strongly reducing media was characterized. High stability was achieved using tetraethyl substituents and pyrrolidine moieties.
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15
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Yao R, Beriashvili D, Zhang W, Li S, Safeer A, Gurinov A, Rockenbauer A, Yang Y, Song Y, Baldus M, Liu Y. Highly bioresistant, hydrophilic and rigidly linked trityl-nitroxide biradicals for cellular high-field dynamic nuclear polarization. Chem Sci 2022; 13:14157-14164. [PMID: 36540821 PMCID: PMC9728575 DOI: 10.1039/d2sc04668g] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 11/16/2022] [Indexed: 09/23/2023] Open
Abstract
Cellular dynamic nuclear polarization (DNP) has been an effective means of overcoming the intrinsic sensitivity limitations of solid-state nuclear magnetic resonance (ssNMR) spectroscopy, thus enabling atomic-level biomolecular characterization in native environments. Achieving DNP signal enhancement relies on doping biological preparations with biradical polarizing agents (PAs). Unfortunately, PA performance within cells is often limited by their sensitivity to the reductive nature of the cellular lumen. Herein, we report the synthesis and characterization of a highly bioresistant and hydrophilic PA (StaPol-1) comprising the trityl radical OX063 ligated to a gem-diethyl pyrroline nitroxide via a rigid piperazine linker. EPR experiments in the presence of reducing agents such as ascorbate and in HeLa cell lysates demonstrate the reduction resistance of StaPol-1. High DNP enhancements seen in small molecules, proteins and cell lysates at 18.8 T confirm that StaPol-1 is an excellent PA for DNP ssNMR investigations of biomolecular systems at high magnetic fields in reductive environments.
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Affiliation(s)
- Ru Yao
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - David Beriashvili
- NMR Spectroscopy Group, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Wenxiao Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Shuai Li
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Adil Safeer
- NMR Spectroscopy Group, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Andrei Gurinov
- NMR Spectroscopy Group, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Antal Rockenbauer
- Institute of Materials and Environmental Chemistry, Hungarian Academy of Sciences And, Department of Physics, Budapest University of Technology and Economics Budafoki Ut 8 1111 Budapest Hungary
| | - Yin Yang
- State Key Laboratory of Elemento-organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University Tianjin 300071 China
| | - Yuguang Song
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Marc Baldus
- NMR Spectroscopy Group, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Yangping Liu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
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16
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Michaelis VK, Keeler EG, Bahri S, Ong TC, Daviso E, Colvin MT, Griffin RG. Biradical Polarizing Agents at High Fields. J Phys Chem B 2022; 126:7847-7856. [PMID: 36194539 PMCID: PMC9886493 DOI: 10.1021/acs.jpcb.2c03985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The sensitivity enhancements available from dynamic nuclear polarization (DNP) are rapidly reshaping the research landscape and expanding the field of nuclear magnetic resonance (NMR) spectroscopy as a tool for solving complex chemical and structural problems. The past decade has seen considerable advances in this burgeoning method, while efforts to further improve its capabilities continue along many avenues. In this report, we examine the influence of static magnetic field strength and temperature on the reported 1H DNP enhancements from three conventional organic biradicals: TOTAPOL, AMUPol, and SPIROPOL. In contrast to the conventional wisdom, our findings show that at liquid nitrogen temperatures and 700 MHz/460.5 GHz, these three bisnitroxides all provide similar 1H DNP enhancements, ε ≈ 60. Furthermore, we investigate the influence of temperature, microwave power, magnetic field strength, and protein sample deuteration on the NMR experimental results.
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Affiliation(s)
- Vladimir K. Michaelis
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge 02139 Massachusetts, United States; Department of Chemistry, University of Alberta, Edmonton T6G 2G2 Alberta, Canada
| | - Eric G. Keeler
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge 02139 Massachusetts, United States; New York Structural Biology Center, New York 10027, New York, United States
| | - Salima Bahri
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge 02139 Massachusetts, United States; Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht 3584CH, The Netherlands
| | - Ta-Chung Ong
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge 02139 Massachusetts, United States; Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles 90095 California, United States
| | - Eugenio Daviso
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge 02139 Massachusetts, United States; Department of Scientific Support and Applications Development, Covaris LLC, Woburn 01801 Massachusetts, United States
| | - Michael T. Colvin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge 02139 Massachusetts, United States; Ortho Clinical Diagnostics, Rochester 14626 New York, United States
| | - Robert G. Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge 02139 Massachusetts, United States
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17
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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18
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Yau WM, Blake Wilson C, Jeon J, Tycko R. Nitroxide-based triradical dopants for efficient low-temperature dynamic nuclear polarization in aqueous solutions over a broad pH range. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 342:107284. [PMID: 35986970 PMCID: PMC9463097 DOI: 10.1016/j.jmr.2022.107284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 05/31/2023]
Abstract
Dynamic nuclear polarization (DNP) can provide substantial sensitivity enhancements in solid state nuclear magnetic resonance (ssNMR) measurements on frozen solutions, thereby enabling experiments that would otherwise be impractical. Previous work has shown that nitroxide-based triradical compounds are particularly effective as dopants in DNP-enhanced measurements at moderate magic-angle spinning frequencies and moderate magnetic field strengths, generally leading to a more rapid build-up of nuclear spin polarizations under microwave irradiation than the more common biradical dopants at the same electron spin concentrations. Here we report the synthesis and DNP performance at 25 K and 9.41 T for two new triradical compounds, sulfoacetyl-DOTOPA and PEG12-DOTOPA. Under our experimental conditions, these compounds exhibit ssNMR signal enhancements and DNP build-up times that are nearly identical to those of previously described triradical dopants. Moreover, these compounds have high solubility in aqueous buffers and water/glycerol mixtures at both acidic and basic pH values, making them useful in a wide variety of experiments on biomolecular systems.
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Affiliation(s)
- Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States
| | - C Blake Wilson
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States
| | - Jaekyun Jeon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, United States.
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19
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Chow WY, De Paëpe G, Hediger S. Biomolecular and Biological Applications of Solid-State NMR with Dynamic Nuclear Polarization Enhancement. Chem Rev 2022; 122:9795-9847. [PMID: 35446555 DOI: 10.1021/acs.chemrev.1c01043] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Solid-state NMR spectroscopy (ssNMR) with magic-angle spinning (MAS) enables the investigation of biological systems within their native context, such as lipid membranes, viral capsid assemblies, and cells. However, such ambitious investigations often suffer from low sensitivity due to the presence of significant amounts of other molecular species, which reduces the effective concentration of the biomolecule or interaction of interest. Certain investigations requiring the detection of very low concentration species remain unfeasible even with increasing experimental time for signal averaging. By applying dynamic nuclear polarization (DNP) to overcome the sensitivity challenge, the experimental time required can be reduced by orders of magnitude, broadening the feasible scope of applications for biological solid-state NMR. In this review, we outline strategies commonly adopted for biological applications of DNP, indicate ongoing challenges, and present a comprehensive overview of biological investigations where MAS-DNP has led to unique insights.
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Affiliation(s)
- Wing Ying Chow
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France.,Univ. Grenoble Alpes, CEA, CNRS, Inst. Biol. Struct. IBS, 38044 Grenoble, France
| | - Gaël De Paëpe
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France
| | - Sabine Hediger
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France
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20
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Biedenbänder T, Aladin V, Saeidpour S, Corzilius B. Dynamic Nuclear Polarization for Sensitivity Enhancement in Biomolecular Solid-State NMR. Chem Rev 2022; 122:9738-9794. [PMID: 35099939 DOI: 10.1021/acs.chemrev.1c00776] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Solid-state NMR with magic-angle spinning (MAS) is an important method in structural biology. While NMR can provide invaluable information about local geometry on an atomic scale even for large biomolecular assemblies lacking long-range order, it is often limited by low sensitivity due to small nuclear spin polarization in thermal equilibrium. Dynamic nuclear polarization (DNP) has evolved during the last decades to become a powerful method capable of increasing this sensitivity by two to three orders of magnitude, thereby reducing the valuable experimental time from weeks or months to just hours or days; in many cases, this allows experiments that would be otherwise completely unfeasible. In this review, we give an overview of the developments that have opened the field for DNP-enhanced biomolecular solid-state NMR including state-of-the-art applications at fast MAS and high magnetic field. We present DNP mechanisms, polarizing agents, and sample constitution methods suitable for biomolecules. A wide field of biomolecular NMR applications is covered including membrane proteins, amyloid fibrils, large biomolecular assemblies, and biomaterials. Finally, we present perspectives and recent developments that may shape the field of biomolecular DNP in the future.
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Affiliation(s)
- Thomas Biedenbänder
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Victoria Aladin
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Siavash Saeidpour
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Björn Corzilius
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
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21
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Menzildjian G, Lund A, Yulikov M, Gajan D, Niccoli L, Karthikeyan G, Casano G, Jeschke G, Ouari O, Lelli M, Lesage A. Efficient Dynamic Nuclear Polarization up to 230 K with Hybrid BDPA-Nitroxide Radicals at a High Magnetic Field. J Phys Chem B 2021; 125:13329-13338. [PMID: 34818009 DOI: 10.1021/acs.jpcb.1c07307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pairing the spectral resolution provided by high magnetic fields at ambient temperature with the enhanced sensitivity offered by dynamic nuclear polarization (DNP) is a major goal of modern solid-state NMR spectroscopy, which will allow one to unlock ever-challenging applications. This study demonstrates that, by combining HyTEK2, a hybrid BDPA-nitroxide biradical polarizing agent, with ortho-terphenyl (OTP), a rigid DNP matrix, enhancement factors as high as 65 can be obtained at 230 K, 40 kHz magic angle spinning (MAS), and 18.8 T. The temperature dependence of the DNP enhancement and its behavior around the glass transition temperature (Tg) of the matrix is investigated by variable-temperature EPR measurements of the electron relaxation properties and numerical simulations. A correlation is suggested between the decrease in enhancement at the passage of the Tg and the concomitant drop of both transverse electron relaxation times in the biradical.
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Affiliation(s)
- Georges Menzildjian
- Centre de RMN à Très Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCBL), 69100 Villeurbanne, France
| | - Alicia Lund
- Centre de RMN à Très Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCBL), 69100 Villeurbanne, France
| | - Maxim Yulikov
- Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
| | - David Gajan
- Centre de RMN à Très Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCBL), 69100 Villeurbanne, France
| | - Lorenzo Niccoli
- Center of Magnetic Resonance (CERM), University of Florence, 50019 Sesto Fiorentino, Italy
| | - Ganesan Karthikeyan
- Aix Marseille Univ, CNRS, Institut de Chimie Radicalaire, 13013 Marseille, France
| | - Gilles Casano
- Aix Marseille Univ, CNRS, Institut de Chimie Radicalaire, 13013 Marseille, France
| | - Gunnar Jeschke
- Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
| | - Olivier Ouari
- Aix Marseille Univ, CNRS, Institut de Chimie Radicalaire, 13013 Marseille, France
| | - Moreno Lelli
- Center of Magnetic Resonance (CERM), University of Florence, 50019 Sesto Fiorentino, Italy
| | - Anne Lesage
- Centre de RMN à Très Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCBL), 69100 Villeurbanne, France
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22
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Moore W, Yao R, Liu Y, Eaton SS, Eaton GR. Spin-spin interaction and relaxation in two trityl-nitroxide diradicals. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 332:107078. [PMID: 34649176 PMCID: PMC8592039 DOI: 10.1016/j.jmr.2021.107078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/24/2021] [Accepted: 08/30/2021] [Indexed: 05/11/2023]
Abstract
Trityl-nitroxides show substantial promise as polarizing agents in solid state dynamic nuclear polarization. To optimize performance it is important to understand the impact of spin-spin interactions on relaxation times of the diradicals. CW spectra and electron spin relaxation were measured for two trityl-nitroxides that differ in the substituents on the amide linker and have different strengths of the exchange interaction J. Analysis of the EPR spectra in terms of overlapping AB spin-spin splitting patterns explains the impact of J on various regions of the spectra. Even modest values of J are large relative to the separation between trityl and nitroxide resonances for some nitrogen nuclear spin state. Two conformations for each diradical were observed in CW spectra in fluid solution at X-band and Q-band. For one diradical J = 15 G (83%) and 5 G (17%) at 293 K, and J = 27 G (67%) and 3 G (33%) with interspin distances of 16 Å and 12 Å, respectively, at 80 K. For the second diradical the exchange interaction is stronger: the two conformations in fluid solution at 293 K had J = 113 G (67%) and 59 G (33%) and at 80 K the value of J was 43 G and there were two conformations with interspin distances of 13 and 11.5 Å. The observation of two conformations for each diradical, with different values of J, demonstrates the dependence of their exchange interactions on through-bond orbital interactions. X-band values of spin relaxation rates 1/T1 and 1/Tm at 80 to 120 K for the trityl-nitroxides are similar to values for nitroxide mono-radicals, and faster than for trityl radicals. These observations show that even for a relatively small value of J, the nitroxide is very effective in enhancing the relaxation of the more slowly relaxing trityl.
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Affiliation(s)
- Whylder Moore
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, United States
| | - Ru Yao
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, PR China
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, PR China.
| | - Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, United States
| | - Gareth R Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, United States.
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