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Trindade IB, Coelho A, Cantini F, Piccioli M, Louro RO. NMR of paramagnetic metalloproteins in solution: Ubi venire, quo vadis? J Inorg Biochem 2022; 234:111871. [DOI: 10.1016/j.jinorgbio.2022.111871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/16/2022] [Accepted: 05/19/2022] [Indexed: 10/18/2022]
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2
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Le Marchand T, Schubeis T, Bonaccorsi M, Paluch P, Lalli D, Pell AJ, Andreas LB, Jaudzems K, Stanek J, Pintacuda G. 1H-Detected Biomolecular NMR under Fast Magic-Angle Spinning. Chem Rev 2022; 122:9943-10018. [PMID: 35536915 PMCID: PMC9136936 DOI: 10.1021/acs.chemrev.1c00918] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Indexed: 02/08/2023]
Abstract
Since the first pioneering studies on small deuterated peptides dating more than 20 years ago, 1H detection has evolved into the most efficient approach for investigation of biomolecular structure, dynamics, and interactions by solid-state NMR. The development of faster and faster magic-angle spinning (MAS) rates (up to 150 kHz today) at ultrahigh magnetic fields has triggered a real revolution in the field. This new spinning regime reduces the 1H-1H dipolar couplings, so that a direct detection of 1H signals, for long impossible without proton dilution, has become possible at high resolution. The switch from the traditional MAS NMR approaches with 13C and 15N detection to 1H boosts the signal by more than an order of magnitude, accelerating the site-specific analysis and opening the way to more complex immobilized biological systems of higher molecular weight and available in limited amounts. This paper reviews the concepts underlying this recent leap forward in sensitivity and resolution, presents a detailed description of the experimental aspects of acquisition of multidimensional correlation spectra with fast MAS, and summarizes the most successful strategies for the assignment of the resonances and for the elucidation of protein structure and conformational dynamics. It finally outlines the many examples where 1H-detected MAS NMR has contributed to the detailed characterization of a variety of crystalline and noncrystalline biomolecular targets involved in biological processes ranging from catalysis through drug binding, viral infectivity, amyloid fibril formation, to transport across lipid membranes.
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Affiliation(s)
- Tanguy Le Marchand
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Tobias Schubeis
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Marta Bonaccorsi
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
- Department
of Biochemistry and Biophysics, Stockholm
University, Svante Arrhenius
väg 16C SE-106 91, Stockholm, Sweden
| | - Piotr Paluch
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Daniela Lalli
- Dipartimento
di Scienze e Innovazione Tecnologica, Università
del Piemonte Orientale “A. Avogadro”, Viale Teresa Michel 11, 15121 Alessandria, Italy
| | - Andrew J. Pell
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
- Department
of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Svante Arrhenius väg 16 C, SE-106
91 Stockholm, Sweden
| | - Loren B. Andreas
- Department
for NMR-Based Structural Biology, Max-Planck-Institute
for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Kristaps Jaudzems
- Latvian
Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006 Latvia
- Faculty
of Chemistry, University of Latvia, Jelgavas 1, Riga LV-1004, Latvia
| | - Jan Stanek
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Guido Pintacuda
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
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3
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Blahut J, Lejeune AL, Ehrling S, Senkovska I, Kaskel S, Wisser FM, Pintacuda G. Untersuchung von Dynamik, Struktur und Magnetismus von schaltbaren Metall‐organischen Gerüstverbindungen mittels
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H‐detektierter MAS‐NMR‐Spektroskopie. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107032] [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)
- Jan Blahut
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs UMR 5082 CNRS ENS Lyon UCBL) Université de Lyon 69100 Villeurbanne Frankreich
- NMR Laboratory Faculty of Science Charles University Hlavova 8 12842 Prag Czech Republic
| | - Arthur L. Lejeune
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs UMR 5082 CNRS ENS Lyon UCBL) Université de Lyon 69100 Villeurbanne Frankreich
- IFP Energies Nouvelles 69360 Solaize Frankreich
| | - Sebastian Ehrling
- Professur für Anorganische Chemie I Technische Universität Dresden 01069 Dresden Deutschland
- Derzeitige Adresse: 3P Instruments GmbH & Co. KG Rudolf-Diesel-Straße 12 85235 Odelzhausen Deutschland
| | - Irena Senkovska
- Professur für Anorganische Chemie I Technische Universität Dresden 01069 Dresden Deutschland
| | - Stefan Kaskel
- Professur für Anorganische Chemie I Technische Universität Dresden 01069 Dresden Deutschland
| | - Florian M. Wisser
- IRCELYON (UMR 5256 CNRS, UCBL) Université de Lyon 69100 Villeurbanne Frankreich
- Institut für Anorganische Chemie Universität Regensburg 93040 Regensburg Deutschland
| | - Guido Pintacuda
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs UMR 5082 CNRS ENS Lyon UCBL) Université de Lyon 69100 Villeurbanne Frankreich
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4
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Blahut J, Lejeune AL, Ehrling S, Senkovska I, Kaskel S, Wisser FM, Pintacuda G. Monitoring Dynamics, Structure, and Magnetism of Switchable Metal-Organic Frameworks via 1 H-Detected MAS NMR. Angew Chem Int Ed Engl 2021; 60:21778-21783. [PMID: 34273230 PMCID: PMC8519119 DOI: 10.1002/anie.202107032] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/12/2021] [Indexed: 01/03/2023]
Abstract
We present a toolbox for the rapid characterisation of powdered samples of paramagnetic metal-organic frameworks at natural abundance by 1 H-detected solid-state NMR. Very fast MAS rates at room and cryogenic temperatures and a set of tailored radiofrequency irradiation schemes help overcome the sensitivity and resolution limits often associated with the characterisation of MOF materials. We demonstrate the approach on DUT-8(Ni), a framework containing Ni2+ paddle-wheel units which can exist in two markedly different architectures. Resolved 1 H and 13 C resonances of organic linkers are detected and assigned in few hours with only 1-2 mg of sample at natural isotopic abundance, and used to rapidly extract information on structure and local internal dynamics of the assemblies, as well as to elucidate the metal electronic properties over an extended temperature range. The experiments disclose new possibilities for describing local and global structural changes and correlating them to electronic and magnetic properties of the assemblies.
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Affiliation(s)
- Jan Blahut
- Centre de Résonance Magnétique Nucléaire à Très Hauts ChampsUMR 5082 CNRSENS LyonUCBL)Université de Lyon69100VilleurbanneFrance
- NMR LaboratoryFaculty of ScienceCharles UniversityHlavova 812842PragueCzech Republic
| | - Arthur L. Lejeune
- Centre de Résonance Magnétique Nucléaire à Très Hauts ChampsUMR 5082 CNRSENS LyonUCBL)Université de Lyon69100VilleurbanneFrance
- IFP Energies Nouvelles69360SolaizeFrance
| | - Sebastian Ehrling
- Chair of Inorganic Chemistry ITechnische Universität Dresden01069DresdenGermany
- Present address: 3P Instruments GmbH & Co. KGRudolf-Diesel-Strasse 1285235OdelzhausenGermany
| | - Irena Senkovska
- Chair of Inorganic Chemistry ITechnische Universität Dresden01069DresdenGermany
| | - Stefan Kaskel
- Chair of Inorganic Chemistry ITechnische Universität Dresden01069DresdenGermany
| | - Florian M. Wisser
- IRCELYON (UMR 5256 CNRS, UCBL)Université de Lyon69100VilleurbanneFrance
- Institute of Inorganic ChemistryUniversity of Regensburg93040RegensburgGermany
| | - Guido Pintacuda
- Centre de Résonance Magnétique Nucléaire à Très Hauts ChampsUMR 5082 CNRSENS LyonUCBL)Université de Lyon69100VilleurbanneFrance
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5
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Blahut J, Benda L, Lejeune AL, Sanders KJ, Burcher B, Jeanneau E, Proriol D, Catita L, Breuil PAR, Quoineaud AA, Pell AJ, Pintacuda G. Proton-detected fast-magic-angle spinning NMR of paramagnetic inorganic solids. RSC Adv 2021; 11:29870-29876. [PMID: 35479571 PMCID: PMC9040908 DOI: 10.1039/d1ra04110j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/17/2021] [Indexed: 02/01/2023] Open
Abstract
Fast (60 kHz) magic angle spinning solid-state NMR allows very sensitive proton detection in highly paramagnetic organometallic powders. We showcase this technique with the complete assignment of 1H and 13C resonances in a high-spin Fe(ii) polymerisation catalyst with less than 2 mg of sample at natural abundance.
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Affiliation(s)
- Jan Blahut
- Université de Lyon, Centre de RMN à Très Hauts Champs de Lyon (UMR 5082 - CNRS, ENS Lyon, UCB Lyon 1) 5 rue de la Doua 69100 Villeurbanne France
| | - Ladislav Benda
- Université de Lyon, Centre de RMN à Très Hauts Champs de Lyon (UMR 5082 - CNRS, ENS Lyon, UCB Lyon 1) 5 rue de la Doua 69100 Villeurbanne France
| | - Arthur L Lejeune
- Université de Lyon, Centre de RMN à Très Hauts Champs de Lyon (UMR 5082 - CNRS, ENS Lyon, UCB Lyon 1) 5 rue de la Doua 69100 Villeurbanne France
- IFP Energies Nouvelles, Rond-point de l'échangeur de Solaize 69360 Solaize France
| | - Kevin J Sanders
- Université de Lyon, Centre de RMN à Très Hauts Champs de Lyon (UMR 5082 - CNRS, ENS Lyon, UCB Lyon 1) 5 rue de la Doua 69100 Villeurbanne France
| | - Benjamin Burcher
- IFP Energies Nouvelles, Rond-point de l'échangeur de Solaize 69360 Solaize France
| | - Erwann Jeanneau
- Université de Lyon, Centre de Diffractométrie Henri Longchambon (UCB Lyon 1) 5 rue de la Doua 69100 Villeurbanne France
| | - David Proriol
- IFP Energies Nouvelles, Rond-point de l'échangeur de Solaize 69360 Solaize France
| | - Leonor Catita
- IFP Energies Nouvelles, Rond-point de l'échangeur de Solaize 69360 Solaize France
| | | | | | - Andrew J Pell
- Université de Lyon, Centre de RMN à Très Hauts Champs de Lyon (UMR 5082 - CNRS, ENS Lyon, UCB Lyon 1) 5 rue de la Doua 69100 Villeurbanne France
- Stockholm University, Department of Materials and Environmental Chemistry Svante Arrhenius väg 16C SE-106 91 Stockholm Sweden
| | - Guido Pintacuda
- Université de Lyon, Centre de RMN à Très Hauts Champs de Lyon (UMR 5082 - CNRS, ENS Lyon, UCB Lyon 1) 5 rue de la Doua 69100 Villeurbanne France
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6
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Carvalho JP, Pell AJ. Frequency-swept adiabatic pulses for broadband solid-state MAS NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 324:106911. [PMID: 33482528 DOI: 10.1016/j.jmr.2020.106911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/17/2020] [Accepted: 12/25/2020] [Indexed: 06/12/2023]
Abstract
We present a complete description of frequency-swept adiabatic pulses applied to isolated spin-1/2 nuclei with a shift anisotropy in solid materials under magic-angle spinning. Our theoretical framework unifies the existing descriptions of adiabatic pulses in the high-power regime, where the radiofrequency (RF) amplitude is greater than twice the spinning frequency, and the low-power regime, where the RF power is less than the spinning frequency, and so links the short high-powered adiabatic pulse (SHAP) and single-sideband-selective adiabatic pulses (S3AP) schemes used in paramagnetic solid-state NMR. We also identify a hitherto unidentified third regime intermediate between the low- and high-power regimes, and separated from them by rotary resonance conditions. We show that the prevailing benchmark of inversion performance based on (super) adiabatic factors is only applicable in the high- and intermediate-power regimes, but fails to account both for the poor performance at rotary resonance, and the impressive inversion seen in the low-power regime. For low-power pulses, which are non-adiabatic according to this definition of (super) adiabaticity, the effective Floquet Hamiltonian in the jolting frame reveals "hidden" (super) adiabaticity. The theory is demonstrated using a combination of simulation and experiment, and is used to refine the practical recommendations for the experimentalist who wishes to use these pulses.
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Affiliation(s)
- José P Carvalho
- Materials and Environmental Chemistry, Stockholm University, Svänte Arrhenius väg 16 C 106 91, Stockholm, Sweden
| | - Andrew J Pell
- Materials and Environmental Chemistry, Stockholm University, Svänte Arrhenius väg 16 C 106 91, Stockholm, Sweden; Centre de RMN Trés Hauts Champs de Lyon (FRE 2034 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France.
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7
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Bertarello A, Benda L, Sanders KJ, Pell AJ, Knight MJ, Pelmenschikov V, Gonnelli L, Felli IC, Kaupp M, Emsley L, Pierattelli R, Pintacuda G. Picometer Resolution Structure of the Coordination Sphere in the Metal-Binding Site in a Metalloprotein by NMR. J Am Chem Soc 2020; 142:16757-16765. [PMID: 32871082 DOI: 10.1021/jacs.0c07339] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Most of our understanding of chemistry derives from atomic-level structures obtained with single-crystal X-ray diffraction. Metal centers in X-ray structures of small organometallic or coordination complexes are often extremely well-defined, with errors in the positions on the order of 10-4-10-5 Å. Determining the metal coordination geometry to high accuracy is essential for understanding metal center reactivity, as even small structural changes can dramatically alter the metal activity. In contrast, the resolution of X-ray structures in proteins is limited typically to the order of 10-1 Å. This resolution is often not sufficient to develop precise structure-activity relations for the metal sites in proteins, because the uncertainty in positions can cover all of the known ranges of bond lengths and bond angles for a given type of metal complex. Here we introduce a new approach that enables the determination of a high-definition structure of the active site of a metalloprotein from a powder sample, by combining magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy, tailored radio frequency (RF) irradiation schemes, and computational approaches. This allows us to overcome the "blind sphere" in paramagnetic proteins, and to observe and assign 1H, 13C, and 15N resonances for the ligands directly coordinating the metal center. We illustrate the method by determining the bond lengths in the structure of the CoII coordination sphere at the core of human superoxide dismutase 1 (SOD) with 0.7 pm precision. The coordination geometry of the resulting structure explains the nonreactive nature of the CoII/ZnII centers in these proteins, which allows them to play a purely structural role.
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Affiliation(s)
- Andrea Bertarello
- Université de Lyon, Centre de RMN à Très Hauts Champs, FRE 2034 CNRS/Université Claude Bernard Lyon 1/ENS Lyon, 5 rue de la Doua, Villeurbanne 69100, France.,École Polytechnique Fédérale de Lausanne (EPFL), Institut des Sciences et Ingénierie Chimiques, Lausanne CH-1015, Switzerland
| | - Ladislav Benda
- Université de Lyon, Centre de RMN à Très Hauts Champs, FRE 2034 CNRS/Université Claude Bernard Lyon 1/ENS Lyon, 5 rue de la Doua, Villeurbanne 69100, France
| | - Kevin J Sanders
- Université de Lyon, Centre de RMN à Très Hauts Champs, FRE 2034 CNRS/Université Claude Bernard Lyon 1/ENS Lyon, 5 rue de la Doua, Villeurbanne 69100, France
| | - Andrew J Pell
- Université de Lyon, Centre de RMN à Très Hauts Champs, FRE 2034 CNRS/Université Claude Bernard Lyon 1/ENS Lyon, 5 rue de la Doua, Villeurbanne 69100, France
| | - Michael J Knight
- Université de Lyon, Centre de RMN à Très Hauts Champs, FRE 2034 CNRS/Université Claude Bernard Lyon 1/ENS Lyon, 5 rue de la Doua, Villeurbanne 69100, France
| | - Vladimir Pelmenschikov
- Technische Universität Berlin, Institut für Chemie, Straße des 17 Juni 135, Berlin 10623, Germany
| | - Leonardo Gonnelli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, Sesto Fiorentino 50019, Italy
| | - Isabella C Felli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, Sesto Fiorentino 50019, Italy
| | - Martin Kaupp
- Technische Universität Berlin, Institut für Chemie, Straße des 17 Juni 135, Berlin 10623, Germany
| | - Lyndon Emsley
- École Polytechnique Fédérale de Lausanne (EPFL), Institut des Sciences et Ingénierie Chimiques, Lausanne CH-1015, Switzerland
| | - Roberta Pierattelli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, Sesto Fiorentino 50019, Italy
| | - Guido Pintacuda
- Université de Lyon, Centre de RMN à Très Hauts Champs, FRE 2034 CNRS/Université Claude Bernard Lyon 1/ENS Lyon, 5 rue de la Doua, Villeurbanne 69100, France
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8
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Tang M, Lam D. Paramagnetic solid-state NMR of proteins. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2019; 103:9-16. [PMID: 31585788 DOI: 10.1016/j.ssnmr.2019.101621] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/24/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
The paramagnetic properties of metal ions and stable radicals can affect NMR spectra, which can lead to changes in peak intensities, relaxation times and chemical shifts. The changes from paramagnetic effects provide intriguing opportunities for solid-state NMR studies of proteins. In this review, we summarized the trends and progress of paramagnetic solid-state NMR of proteins in the past decade, and showed that paramagnetic effects have great potential applications for sensitivity enhancement, structure determination and topological analysis for microcrystalline proteins, protein complexes, protein aggregates and membrane proteins.
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Affiliation(s)
- Ming Tang
- Department of Chemistry, College of Staten Island - Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
| | - Dennis Lam
- Department of Chemistry, College of Staten Island - Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
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9
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Parigi G, Ravera E, Luchinat C. Magnetic susceptibility and paramagnetism-based NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 114-115:211-236. [PMID: 31779881 DOI: 10.1016/j.pnmrs.2019.06.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/17/2019] [Accepted: 06/17/2019] [Indexed: 05/18/2023]
Abstract
The magnetic interactions between the nuclear magnetic moment and the magnetic moment of unpaired electron(s) depend on the structure and dynamics of the molecules where the paramagnetic center is located and of their partners. The long-range nature of the magnetic interactions is thus a reporter of invaluable information for structural biology studies, when other techniques often do not provide enough data for the atomic-level characterization of the system. This precious information explains the flourishing of paramagnetism-assisted NMR studies in recent years. Many paramagnetic effects are related to the magnetic susceptibility of the paramagnetic metal. Although these effects have been known for more than half a century, different theoretical models and new approaches have been proposed in the last decade. In this review, we have summarized the consequences for NMR spectroscopy of magnetic interactions between nuclear and electron magnetic moments, and thus of the presence of a magnetic susceptibility due to metals, and we do so using a unified notation.
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Affiliation(s)
- Giacomo Parigi
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
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10
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Pell AJ, Pintacuda G, Grey CP. Paramagnetic NMR in solution and the solid state. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 111:1-271. [PMID: 31146806 DOI: 10.1016/j.pnmrs.2018.05.001] [Citation(s) in RCA: 216] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 05/11/2018] [Accepted: 05/12/2018] [Indexed: 05/22/2023]
Abstract
The field of paramagnetic NMR has expanded considerably in recent years. This review addresses both the theoretical description of paramagnetic NMR, and the way in which it is currently practised. We provide a review of the theory of the NMR parameters of systems in both solution and the solid state. Here we unify the different languages used by the NMR, EPR, quantum chemistry/DFT, and magnetism communities to provide a comprehensive and coherent theoretical description. We cover the theory of the paramagnetic shift and shift anisotropy in solution both in the traditional formalism in terms of the magnetic susceptibility tensor, and using a more modern formalism employing the relevant EPR parameters, such as are used in first-principles calculations. In addition we examine the theory first in the simple non-relativistic picture, and then in the presence of spin-orbit coupling. These ideas are then extended to a description of the paramagnetic shift in periodic solids, where it is necessary to include the bulk magnetic properties, such as magnetic ordering at low temperatures. The description of the paramagnetic shift is completed by describing the current understanding of such shifts due to lanthanide and actinide ions. We then examine the paramagnetic relaxation enhancement, using a simple model employing a phenomenological picture of the electronic relaxation, and again using a more complex state-of-the-art theory which incorporates electronic relaxation explicitly. An additional important consideration in the solid state is the impact of bulk magnetic susceptibility effects on the form of the spectrum, where we include some ideas from the field of classical electrodynamics. We then continue by describing in detail the solution and solid-state NMR methods that have been deployed in the study of paramagnetic systems in chemistry, biology, and the materials sciences. Finally we describe a number of case studies in paramagnetic NMR that have been specifically chosen to highlight how the theory in part one, and the methods in part two, can be used in practice. The systems chosen include small organometallic complexes in solution, solid battery electrode materials, metalloproteins in both solution and the solid state, systems containing lanthanide ions, and multi-component materials used in pharmaceutical controlled-release formulations that have been doped with paramagnetic species to measure the component domain sizes.
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Affiliation(s)
- Andrew J Pell
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Svante Arrhenius väg 16 C, SE-106 91 Stockholm, Sweden.
| | - Guido Pintacuda
- Institut des Sciences Analytiques (CNRS UMR 5280, ENS de Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Clare P Grey
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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11
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Metal centers in biomolecular solid-state NMR. J Struct Biol 2018; 206:99-109. [PMID: 30502494 DOI: 10.1016/j.jsb.2018.11.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/25/2018] [Accepted: 11/27/2018] [Indexed: 01/03/2023]
Abstract
Solid state NMR (SSNMR) has earned a substantial success in the characterization of paramagnetic systems over the last decades. Nowadays, the resolution and sensitivity of solid state NMR in biological molecules has improved significantly and these advancements can be translated into the study of paramagnetic biomolecules. However, the electronic properties of different metal centers affect the quality of their SSNMR spectra differently, and not all systems turn out to be equally easy to approach by this technique. In this review we will try to give an overview of the properties of different paramagnetic centers and how they can be used to increase the chances of experimental success.
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12
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Silva JM, Giuntini S, Cerofolini L, Geraldes CFGC, Macedo AL, Ravera E, Fragai M, Luchinat C, Calderone V. Non-crystallographic symmetry in proteins: Jahn-Teller-like and Butterfly-like effects? J Biol Inorg Chem 2018; 24:91-101. [PMID: 30470900 DOI: 10.1007/s00775-018-1630-0] [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: 10/09/2018] [Accepted: 11/14/2018] [Indexed: 11/29/2022]
Abstract
Partial symmetry, i.e., the presence of more than one molecule in the asymmetric unit of a crystal, is a relatively rare phenomenon in small-molecule crystallography, but is quite common in protein crystallography, where it is typically known as non-crystallographic symmetry (NCS). Several papers in literature propose molecular determinants such as crystal contacts, thermal factors, or TLS parameters as an explanation for the phenomenon of intrinsic asymmetry among molecules that are in principle equivalent. Nevertheless, are all of the above determinants the cause or are they rather the effect? In the general frame of the NCS often observed in crystals of biomolecules, this paper deals with nickel(II)-substituted human carbonic anhydrase(II) (hCAII) and its SAD structure determination at the nickel edge. The structure revealed two non-equivalent molecules in the asymmetric unit, the presence of a secondary nickel-binding site at the N-terminus of both molecules (which had never been found before in the nickel-substituted enzyme) and two different coordination geometries of the active site nickel (hexa-coordinated in one molecule and mainly penta-coordinated in the other). The above-mentioned standard molecular crystallographic determinants of this asymmetry are analyzed and presented in detail for this particular case. From these considerations, we speculate on the existence of a fundamental, although yet unknown, common cause for the partial symmetry that is so often encountered in X-ray structures of biomolecules.
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Affiliation(s)
- José Malanho Silva
- Magnetic Resonance Center (CERM), University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy.,UCIBIO-Requimte, Faculty of Sciences and Technology, Universidade NOVA de Lisboa, Caparica, 2829-516, Portugal
| | - Stefano Giuntini
- Magnetic Resonance Center (CERM), University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, FI, Italy
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
| | - Carlos F G C Geraldes
- Department of Life Sciences and Coimbra Chemistry Center, University of Coimbra, Coimbra, Portugal
| | - Anjos L Macedo
- UCIBIO-Requimte, Faculty of Sciences and Technology, Universidade NOVA de Lisboa, Caparica, 2829-516, Portugal
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, FI, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, FI, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy. .,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, FI, Italy.
| | - Vito Calderone
- Magnetic Resonance Center (CERM), University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy. .,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, FI, Italy.
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Sanders KJ, Pell AJ, Wegner S, Grey CP, Pintacuda G. Broadband MAS NMR spectroscopy in the low-power limit. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.01.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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14
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Paramagnetic NMR as a new tool in structural biology. Emerg Top Life Sci 2018; 2:19-28. [DOI: 10.1042/etls20170084] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 12/25/2022]
Abstract
NMR (nuclear magnetic resonance) investigation through the exploitation of paramagnetic effects is passing from an approach limited to few specialists in the field to a generally applicable method that must be considered, especially for the characterization of systems hardly affordable with other techniques. This is mostly due to the fact that paramagnetic data are long range in nature, thus providing information for the structural and dynamic characterization of complex biomolecular architectures in their native environment. On the other hand, this information usually needs to be complemented by data from other sources. Integration of paramagnetic NMR with other techniques, and the development of protocols for a joint analysis of all available data, is fundamental for achieving a comprehensive characterization of complex biological systems. We describe here a few examples of the new possibilities offered by paramagnetic data used in integrated structural approaches.
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Ravera E, Parigi G, Luchinat C. Perspectives on paramagnetic NMR from a life sciences infrastructure. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 282:154-169. [PMID: 28844254 DOI: 10.1016/j.jmr.2017.07.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/28/2017] [Accepted: 07/31/2017] [Indexed: 05/17/2023]
Abstract
The effects arising in NMR spectroscopy because of the presence of unpaired electrons, collectively referred to as "paramagnetic NMR" have attracted increasing attention over the last decades. From the standpoint of the structural and mechanistic biology, paramagnetic NMR provides long range restraints that can be used to assess the accuracy of crystal structures in solution and to improve them by simultaneous refinements through NMR and X-ray data. These restraints also provide information on structure rearrangements and conformational variability in biomolecular systems. Theoretical improvements in quantum chemistry calculations can nowadays allow for accurate calculations of the paramagnetic data from a molecular structural model, thus providing a tool to refine the metal coordination environment by matching the paramagnetic effects observed far away from the metal. Furthermore, the availability of an improved technology (higher fields and faster magic angle spinning) has promoted paramagnetic NMR applications in the fast-growing area of biomolecular solid-state NMR. Major improvements in dynamic nuclear polarization have been recently achieved, especially through the exploitation of the Overhauser effect occurring through the contact-driven relaxation mechanism: the very large enhancement of the 13C signal observed in a variety of liquid organic compounds at high fields is expected to open up new perspectives for applications of solution NMR.
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Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, via Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, via Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, via Sacconi 6, 50019 Sesto Fiorentino, Italy.
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