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Gigli L, Silva JM, Cerofolini L, Macedo AL, Geraldes CFGC, Suturina EA, Calderone V, Fragai M, Parigi G, Ravera E, Luchinat C. Machine Learning-Enhanced Quantum Chemistry-Assisted Refinement of the Active Site Structure of Metalloproteins. Inorg Chem 2024; 63:10713-10725. [PMID: 38805564 DOI: 10.1021/acs.inorgchem.4c01274] [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: 05/30/2024]
Abstract
Understanding the fine structural details of inhibitor binding at the active site of metalloenzymes can have a profound impact on the rational drug design targeted to this broad class of biomolecules. Structural techniques such as NMR, cryo-EM, and X-ray crystallography can provide bond lengths and angles, but the uncertainties in these measurements can be as large as the range of values that have been observed for these quantities in all the published structures. This uncertainty is far too large to allow for reliable calculations at the quantum chemical (QC) levels for developing precise structure-activity relationships or for improving the energetic considerations in protein-inhibitor studies. Therefore, the need arises to rely upon computational methods to refine the active site structures well beyond the resolution obtained with routine application of structural methods. In a recent paper, we have shown that it is possible to refine the active site of cobalt(II)-substituted MMP12, a metalloprotein that is a relevant drug target, by matching to the experimental pseudocontact shifts (PCS) those calculated using multireference ab initio QC methods. The computational cost of this methodology becomes a significant bottleneck when the starting structure is not sufficiently close to the final one, which is often the case with biomolecular structures. To tackle this problem, we have developed an approach based on a neural network (NN) and a support vector regression (SVR) and applied it to the refinement of the active site structure of oxalate-inhibited human carbonic anhydrase 2 (hCAII), another prototypical metalloprotein target. The refined structure gives a remarkably good agreement between the QC-calculated and the experimental PCS. This study not only contributes to the knowledge of CAII but also demonstrates the utility of combining machine learning (ML) algorithms with QC calculations, offering a promising avenue for investigating other drug targets and complex biological systems in general.
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Affiliation(s)
- Lucia Gigli
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
| | - José Malanho Silva
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
| | - Anjos L Macedo
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
- Associate Laboratory i4HB─Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Carlos F G C Geraldes
- Department of Life Sciences, Faculty of Science and Technology, 3000-393 Coimbra, Portugal
- Coimbra Chemistry Center─Institute of Molecular Sciences (CCC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal
| | | | - Vito Calderone
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
- Florence Data Science, University of Florence, Florence 50134, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
- Giotto Biotech, S.R.L., Sesto Fiorentino 50019, Italy
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Koppe J, Pell AJ. Structure Determination and Refinement of Paramagnetic Materials by Solid-State NMR. ACS PHYSICAL CHEMISTRY AU 2023; 3:419-433. [PMID: 37780542 PMCID: PMC10540298 DOI: 10.1021/acsphyschemau.3c00019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/08/2023] [Accepted: 06/08/2023] [Indexed: 10/03/2023]
Abstract
Paramagnetism in solid-state materials has long been considered an additional challenge for structural investigations by using solid-state nuclear magnetic resonance spectroscopy (ssNMR). The strong interactions between unpaired electrons and the surrounding atomic nuclei, on the one hand, are complex to describe, and on the other hand can cause fast decaying signals and extremely broad resonances. However, significant progress has been made over the recent years in developing both theoretical models to understand and calculate the frequency shifts due to paramagnetism and also more sophisticated experimental protocols for obtaining high-resolution ssNMR spectra. While the field is continuously moving forward, to date, the combination of state-of-the-art numerical and experimental techniques enables us to obtain high-quality data for a variety of systems. This involves the determination of several ssNMR parameters that represent different contributions to the frequency shift in paramagnetic solids. These contributions encode structural information on the studied material on various length scales, ranging from crystal morphologies, to the mid- and long-range order, down to the local atomic bonding environment. In this perspective, the different ssNMR parameters characteristic for paramagnetic materials are discussed with a focus on their interpretation in terms of structure. This includes a summary of studies that have explored the information content of these ssNMR parameters, mostly to complement experimental data from other methods, e.g., X-ray diffraction. The presented overview aims to demonstrate how far ssNMR has hitherto been able to determine and refine the structures of materials and to discuss where it currently falls short of its full potential. We attempt to highlight how much further ssNMR can be pushed to determine and refine structure to deliver a comprehensive structural characterization of paramagnetic materials comparable to what is to date achieved by the combined effort of electron microscopy, diffraction, and spectroscopy.
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Affiliation(s)
- Jonas Koppe
- Centre
de RMN à Très Hauts Champs de Lyon (UMR 5082 −
CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 Rue de la Doua, 69100 Villeurbanne, France
| | - Andrew J. Pell
- Centre
de RMN à Très Hauts Champs de Lyon (UMR 5082 −
CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 Rue de la Doua, 69100 Villeurbanne, France
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3
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Ince R, Doudouh A, Claiser N, Furet É, Guizouarn T, Le Pollès L, Kervern G. Determining Local Magnetic Susceptibility Tensors in Paramagnetic Lanthanide Crystalline Powders from Solid-State NMR Chemical Shift Anisotropies. J Phys Chem A 2023; 127:1547-1554. [PMID: 36744789 DOI: 10.1021/acs.jpca.2c06955] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Exploring magnetic properties at the molecular level is a challenge that has been met by developing many experimental and theoretical solutions, such as polarized neutron diffraction (PND), muon-spin rotation (μ-SR), electron paramagnetic resonance (EPR), SQUID-based magnetometry measurements, and advanced modeling on open-shell systems and relativistic calculations. These methods are powerful tools that shed light on the local magnetic response in specifically designed magnetic materials such as contrast agents, for MRI, molecular magnets, magnetic tags for biological NMR, etc. All of these methods have their advantages and disadvantages. In order to complement the possibilities offered by these methods, we propose a new tool that implements a new approach combining simulation and fitting for high-resolution solid-state NMR spectra of lanthanide-based paramagnetic species. This method relies on a rigorous acquisition thanks to short high-power adiabatic pulses (SHAP) of high-resolution solid-state NMR isotropic and anisotropic data on a powdered magnetic material. It is also based on an efficient modeling of this data thanks to a semiempirical model based on a parametrization of the local magnetism and the crystal structure provided by diffraction methods. The efficiency of the calculation relies on a thorough simplification of the electron-nucleus interactions (point-dipole interaction, no Fermi contact) which is validated by experimental analysis. By taking advantage of the efficient calculation possibilities offered by our method, we can compare a great number of simulated spectra to experimental data and find the best-matching local magnetic susceptibility tensor. This method was applied to a series of isostructural lanthanide oxalates which are used as a benchmark system for many analytical methods. We present the results of thorough solid-state NMR and extensive modeling of the hyperfine interaction (including up to 400 paramagnetic centers) that yield local magnetic susceptibility tensor measurements that are self-consistent as well as consistent with bulk susceptibility measurements.
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Affiliation(s)
- Ridvan Ince
- Université de Lorraine, UMR 7036 (UL-CNRS) CRM2, BP 70239 Boulevard des Aiguillettes, F 54506Vandœuvre-lès-Nancy, France
| | - Abdelatif Doudouh
- Université de Lorraine, UMR 7036 (UL-CNRS) CRM2, BP 70239 Boulevard des Aiguillettes, F 54506Vandœuvre-lès-Nancy, France
| | - Nicolas Claiser
- Université de Lorraine, UMR 7036 (UL-CNRS) CRM2, BP 70239 Boulevard des Aiguillettes, F 54506Vandœuvre-lès-Nancy, France
| | - Éric Furet
- ENSCR, UMR 6226 (UL-CNRS) École Nationale Supérieure de Chimie de Rennes, Campus de Beaulieu - Bâtiment 10B, F 35042Rennes Cedex, France
| | - Thierry Guizouarn
- ISCR, UMR 6226 (UL-CNRS) Université de Rennes 1, Campus de Beaulieu - Bâtiment 10B, F 35042Rennes Cedex, France
| | - Laurent Le Pollès
- ENSCR, UMR 6226 (UL-CNRS) École Nationale Supérieure de Chimie de Rennes, Campus de Beaulieu - Bâtiment 10B, F 35042Rennes Cedex, France
| | - Gwendal Kervern
- Université de Lorraine, UMR 7036 (UL-CNRS) CRM2, BP 70239 Boulevard des Aiguillettes, F 54506Vandœuvre-lès-Nancy, France
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Aguion PI, Marchanka A, Carlomagno T. Nucleic acid-protein interfaces studied by MAS solid-state NMR spectroscopy. J Struct Biol X 2022; 6:100072. [PMID: 36090770 PMCID: PMC9449856 DOI: 10.1016/j.yjsbx.2022.100072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/20/2022] Open
Abstract
Solid-state NMR (ssNMR) has become a well-established technique to study large and insoluble protein assemblies. However, its application to nucleic acid-protein complexes has remained scarce, mainly due to the challenges presented by overlapping nucleic acid signals. In the past decade, several efforts have led to the first structure determination of an RNA molecule by ssNMR. With the establishment of these tools, it has become possible to address the problem of structure determination of nucleic acid-protein complexes by ssNMR. Here we review first and more recent ssNMR methodologies that study nucleic acid-protein interfaces by means of chemical shift and peak intensity perturbations, direct distance measurements and paramagnetic effects. At the end, we review the first structure of an RNA-protein complex that has been determined from ssNMR-derived intermolecular restraints.
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Affiliation(s)
- Philipp Innig Aguion
- Institute for Organic Chemistry and Centre of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Alexander Marchanka
- Institute for Organic Chemistry and Centre of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Teresa Carlomagno
- School of Biosciences/College of Life and Enviromental Sciences, Institute of Cancer and Genomic Sciences/College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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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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6
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Zehnder J, Cadalbert R, Yulikov M, Künze G, Wiegand T. Paramagnetic spin labeling of a bacterial DnaB helicase for solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 332:107075. [PMID: 34597956 DOI: 10.1016/j.jmr.2021.107075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
Labeling of biomolecules with a paramagnetic probe for nuclear magnetic resonance (NMR) spectroscopy enables determining long-range distance restraints, which are otherwise not accessible by classically used dipolar coupling-based NMR approaches. Distance restraints derived from paramagnetic relaxation enhancements (PREs) can facilitate the structure determination of large proteins and protein complexes. We herein present the site-directed labeling of the large oligomeric bacterial DnaB helicase from Helicobacter pylori with cysteine-reactive maleimide tags carrying either a nitroxide radical or a lanthanide ion. The success of the labeling reaction was followed by quantitative continuous-wave electron paramagnetic resonance (EPR) experiments performed on the nitroxide-labeled protein. PREs were extracted site-specifically from 2D and 3D solid-state NMR spectra. A good agreement with predicted PRE values, derived by computational modeling of nitroxide and Gd3+ tags in the low-resolution DnaB crystal structure, was found. Comparison of experimental PREs and model-predicted spin label-nucleus distances indicated that the size of the "blind sphere" around the paramagnetic center, in which NMR resonances are not detected, is slightly larger for Gd3+ (∼14 Å) than for nitroxide (∼11 Å) in 13C-detected 2D spectra of DnaB. We also present Gd3+-Gd3+ dipolar electron-electron resonance EPR experiments on DnaB supporting the conclusion that DnaB was present as a hexameric assembly.
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Affiliation(s)
| | | | - Maxim Yulikov
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Georg Künze
- Institute for Drug Discovery, Medical School, Leipzig University, 04103 Leipzig, Germany.
| | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland; Max-Planck-Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany; Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany.
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Ravera E, Gigli L, Suturina EA, Calderone V, Fragai M, Parigi G, Luchinat C. A High-Resolution View of the Coordination Environment in a Paramagnetic Metalloprotein from its Magnetic Properties. Angew Chem Int Ed Engl 2021; 60:14960-14966. [PMID: 33595173 DOI: 10.1002/anie.202101149] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Indexed: 12/13/2022]
Abstract
Metalloproteins constitute a significant fraction of the proteome of all organisms and their characterization is critical for both basic sciences and biomedical applications. A large portion of metalloproteins bind paramagnetic metal ions, and paramagnetic NMR spectroscopy has been widely used in their structural characterization. However, the signals of nuclei in the immediate vicinity of the metal center are often broadened beyond detection. In this work, we show that it is possible to determine the coordination environment of the paramagnetic metal in the protein at a resolution inaccessible to other techniques. Taking the structure of a diamagnetic analogue as a starting point, a geometry optimization is carried out by fitting the pseudocontact shifts obtained from first principles quantum chemical calculations to the experimental ones.
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Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (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
| | - Lucia Gigli
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (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
| | | | - Vito Calderone
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (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
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (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
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (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), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (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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8
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Ravera E, Gigli L, Suturina EA, Calderone V, Fragai M, Parigi G, Luchinat C. A High‐Resolution View of the Coordination Environment in a Paramagnetic Metalloprotein from its Magnetic Properties. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (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
| | - Lucia Gigli
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (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
| | | | - Vito Calderone
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (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
| | - Marco Fragai
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (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
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (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) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (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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9
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Zehnder J, Cadalbert R, Terradot L, Ernst M, Böckmann A, Güntert P, Meier BH, Wiegand T. Paramagnetic Solid-State NMR to Localize the Metal-Ion Cofactor in an Oligomeric DnaB Helicase. Chemistry 2021; 27:7745-7755. [PMID: 33822417 PMCID: PMC8252064 DOI: 10.1002/chem.202100462] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Indexed: 12/17/2022]
Abstract
Paramagnetic metal ions can be inserted into ATP-fueled motor proteins by exchanging the diamagnetic Mg2+ cofactor with Mn2+ or Co2+ . Then, paramagnetic relaxation enhancement (PRE) or pseudo-contact shifts (PCSs) can be measured to report on the localization of the metal ion within the protein. We determine the metal position in the oligomeric bacterial DnaB helicase from Helicobacter pylori complexed with the transition-state ATP-analogue ADP:AlF4 - and single-stranded DNA using solid-state NMR and a structure-calculation protocol employing CYANA. We discuss and compare the use of Mn2+ and Co2+ in localizing the ATP cofactor in large oligomeric protein assemblies. 31 P PCSs induced in the Co2+ -containing sample are then used to localize the DNA phosphate groups on the Co2+ PCS tensor surface enabling structural insights into DNA binding to the DnaB helicase.
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Affiliation(s)
- Johannes Zehnder
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Riccardo Cadalbert
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | | | - Matthias Ernst
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | | | - Peter Güntert
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
- Institute of Biophysical ChemistryCenter for Biomolecular Magnetic ResonanceGoethe University Frankfurt am Main60438Frankfurt am MainGermany
- Department of ChemistryTokyo Metropolitan UniversityHachiojiTokyo1920397Japan
| | - Beat H. Meier
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Thomas Wiegand
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
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10
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Ahmed M, Marchanka A, Carlomagno T. Structure of a Protein–RNA Complex by Solid‐State NMR Spectroscopy. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915465] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Mumdooh Ahmed
- Centre for Biomolecular Drug Research and Institute of Organic ChemistryLeibniz University Hannover Schneiderberg 38 30167 Hannover Germany
| | - Alexander Marchanka
- Centre for Biomolecular Drug Research and Institute of Organic ChemistryLeibniz University Hannover Schneiderberg 38 30167 Hannover Germany
| | - Teresa Carlomagno
- Centre for Biomolecular Drug Research and Institute of Organic ChemistryLeibniz University Hannover Schneiderberg 38 30167 Hannover Germany
- Group of NMR-based Structural ChemistryHelmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany
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11
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Ahmed M, Marchanka A, Carlomagno T. Structure of a Protein-RNA Complex by Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2020; 59:6866-6873. [PMID: 32023357 PMCID: PMC7187219 DOI: 10.1002/anie.201915465] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Indexed: 12/17/2022]
Abstract
Solid‐state NMR (ssNMR) is applicable to high molecular‐weight (MW) protein assemblies in a non‐amorphous precipitate. The technique yields atomic resolution structural information on both soluble and insoluble particles without limitations of MW or requirement of crystals. Herein, we propose and demonstrate an approach that yields the structure of protein–RNA complexes (RNP) solely from ssNMR data. Instead of using low‐sensitivity magnetization transfer steps between heteronuclei of the protein and the RNA, we measure paramagnetic relaxation enhancement effects elicited on the RNA by a paramagnetic tag coupled to the protein. We demonstrate that this data, together with chemical‐shift‐perturbation data, yields an accurate structure of an RNP complex, starting from the bound structures of its components. The possibility of characterizing protein–RNA interactions by ssNMR may enable applications to large RNP complexes, whose structures are not accessible by other methods.
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Affiliation(s)
- Mumdooh Ahmed
- Centre for Biomolecular Drug Research and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Alexander Marchanka
- Centre for Biomolecular Drug Research and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Teresa Carlomagno
- Centre for Biomolecular Drug Research and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany.,Group of NMR-based Structural Chemistry, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
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12
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Kocman V, Di Mauro GM, Veglia G, Ramamoorthy A. Use of paramagnetic systems to speed-up NMR data acquisition and for structural and dynamic studies. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2019; 102:36-46. [PMID: 31325686 PMCID: PMC6698407 DOI: 10.1016/j.ssnmr.2019.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 05/05/2023]
Abstract
NMR spectroscopy is a powerful experimental technique to study biological systems at the atomic resolution. However, its intrinsic low sensitivity results in long acquisition times that in extreme cases lasts for days (or even weeks) often exceeding the lifetime of the sample under investigation. Different paramagnetic agents have been used in an effort to decrease the spin-lattice (T1) relaxation times of the studied nuclei, which are the main cause for long acquisition times necessary for signal averaging to enhance the signal-to-noise ratio of NMR spectra. Consequently, most of the experimental time is "wasted" in waiting for the magnetization to recover between successive scans. In this review, we discuss how to set up an optimal paramagnetic relaxation enhancement (PRE) system to effectively reduce the T1 relaxation times avoiding significant broadening of NMR signals. Additionally, we describe how PRE-agents can be used to provide structural and dynamic information and can even be used to follow the intermediates of chemical reactions and to speed-up data acquisition. We also describe the unique challenges and benefits associated with the application of PRE to solid-state NMR spectroscopy, explaining how the use of PREs is more complex for membrane mimetic systems as PREs can also be exploited to change the alignment of oriented membrane systems. Functionalization of membrane mimetics, such as bicelles, can provide a controlled region of paramagnetic effect that has the potential, together with the desired alignment, to provide crucial biologically relevant structural information. And finally, we discuss how paramagnetic metals can be utilized to further increase the dynamic nuclear polarization (DNP) effects and how to preserve the enhancements when dissolution DNP is implemented.
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Affiliation(s)
- Vojč Kocman
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA; Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, USA
| | | | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA; Biophysics, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, USA.
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13
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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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14
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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: 210] [Impact Index Per Article: 42.0] [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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15
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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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16
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Ravera E, Takis PG, Fragai M, Parigi G, Luchinat C. NMR Spectroscopy and Metal Ions in Life Sciences. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800875] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- 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
| | - Panteleimon G. Takis
- Giotto Biotech S.R.L.; Via Madonna del Piano 6 50019 Sesto Fiorentino (FI) Italy
| | - Marco Fragai
- 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
| | - 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
| | - 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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17
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Lou X, Shen M, Li C, Chen Q, Hu B. Reduction of the 13C cross-polarization experimental time for pharmaceutical samples with long T 1 by ball milling in solid-state NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2018; 94:20-25. [PMID: 30125796 DOI: 10.1016/j.ssnmr.2018.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 08/02/2018] [Accepted: 08/02/2018] [Indexed: 06/08/2023]
Abstract
Many pharmaceutical samples have notably long 1H T1 (proton spin-lattice relaxation time), leading to lengthy experiments lasting several days in solid-state NMR studies. In this work, we propose the use of ball milling on the pharmaceutical samples to reduce the 1H T1, which also leads to enhanced sensitivity in {1H}-13C Cross-Polarization (CP) experiments due to reduced particle sizes and increased surface areas of the samples. Experimentally, we determined that depending on the substrates and milling time, the signal-to-noise ratio (S/N) of a 1D 13C CP spectrum can be increased by a factor of 3-6, which means that the experimental time can be shortened by a factor of 9-36. Furthermore, the application of simple ball-milling within a short time avoids the amorphization of the studied samples such that no signal due to amorphous state is observed in the 13C CP spectrum. This simple ball milling method used for sensitivity enhancement can be further applied in the SS-NMR studies of pharmaceutical samples.
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Affiliation(s)
- Xiaobing Lou
- State Key Laboratory of Precision Spectroscopy & Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Materials Science, East China Normal University, Shanghai, 200062, China
| | - Ming Shen
- State Key Laboratory of Precision Spectroscopy & Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Materials Science, East China Normal University, Shanghai, 200062, China
| | - Chao Li
- State Key Laboratory of Precision Spectroscopy & Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Materials Science, East China Normal University, Shanghai, 200062, China
| | - Qun Chen
- State Key Laboratory of Precision Spectroscopy & Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Materials Science, East China Normal University, Shanghai, 200062, China
| | - Bingwen Hu
- State Key Laboratory of Precision Spectroscopy & Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Materials Science, East China Normal University, Shanghai, 200062, China.
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18
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Quinn CM, Wang M, Polenova T. NMR of Macromolecular Assemblies and Machines at 1 GHz and Beyond: New Transformative Opportunities for Molecular Structural Biology. Methods Mol Biol 2018; 1688:1-35. [PMID: 29151202 PMCID: PMC6217836 DOI: 10.1007/978-1-4939-7386-6_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
As a result of profound gains in sensitivity and resolution afforded by ultrahigh magnetic fields, transformative applications in the fields of structural biology and materials science are being realized. The development of dual low temperature superconducting (LTS)/high-temperature superconducting (HTS) magnets has enabled the achievement of magnetic fields above 1 GHz (23.5 T), which will open doors to an unprecedented new range of applications. In this contribution, we discuss the promise of ultrahigh field magnetic resonance. We highlight several methodological developments pertinent at high-magnetic fields including measurement of 1H-1H distances and 1H chemical shift anisotropy in the solid state as well as studies of quadrupolar nuclei such as 17O. Higher magnetic fields have advanced heteronuclear detection in solution NMR, valuable for applications including metabolomics and disordered proteins, as well as expanded use of proton detection in the solid state in conjunction with ultrafast magic angle spinning. We also present several recent applications to structural studies of the AP205 bacteriophage, the M2 channel from Influenza A, and biomaterials such as human bone. Gains in sensitivity and resolution from increased field strengths will enable advanced applications of NMR spectroscopy including in vivo studies of whole cells and intact virions.
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Affiliation(s)
- Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, 036 Brown Laboratories, Newark, DE, 19716, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave, Pittsburgh, PA, 15261, USA
| | - Mingzhang Wang
- Department of Chemistry and Biochemistry, University of Delaware, 036 Brown Laboratories, Newark, DE, 19716, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave, Pittsburgh, PA, 15261, USA
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, 036 Brown Laboratories, Newark, DE, 19716, USA.
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave, Pittsburgh, PA, 15261, USA.
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19
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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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20
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Rogawski R, McDermott AE. New NMR tools for protein structure and function: Spin tags for dynamic nuclear polarization solid state NMR. Arch Biochem Biophys 2017; 628:102-113. [PMID: 28623034 PMCID: PMC5815514 DOI: 10.1016/j.abb.2017.06.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/05/2017] [Accepted: 06/12/2017] [Indexed: 12/13/2022]
Abstract
Magic angle spinning solid state NMR studies of biological macromolecules [1-3] have enabled exciting studies of membrane proteins [4,5], amyloid fibrils [6], viruses, and large macromolecular assemblies [7]. Dynamic nuclear polarization (DNP) provides a means to enhance detection sensitivity for NMR, particularly for solid state NMR, with many recent biological applications and considerable contemporary efforts towards elaboration and optimization of the DNP experiment. This review explores precedents and innovations in biological DNP experiments, especially highlighting novel chemical biology approaches to introduce the radicals that serve as a source of polarization in DNP experiments.
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Affiliation(s)
- Rivkah Rogawski
- Department of Chemistry, Columbia University, NY, NY 10027, United States
| | - Ann E McDermott
- Department of Chemistry, Columbia University, NY, NY 10027, United States.
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21
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Bertarello A, Schubeis T, Fuccio C, Ravera E, Fragai M, Parigi G, Emsley L, Pintacuda G, Luchinat C. Paramagnetic Properties of a Crystalline Iron–Sulfur Protein by Magic-Angle Spinning NMR Spectroscopy. Inorg Chem 2017; 56:6624-6629. [DOI: 10.1021/acs.inorgchem.7b00674] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Andrea Bertarello
- Centre de RMN à
Très Hauts Champs, Institut des Sciences Analytiques (CNRS,
ENS Lyon, UCB Lyon 1), Université de Lyon, 69100 Villeurbanne, France
| | - Tobias Schubeis
- Centre de RMN à
Très Hauts Champs, Institut des Sciences Analytiques (CNRS,
ENS Lyon, UCB Lyon 1), Université de Lyon, 69100 Villeurbanne, France
- Giotto Biotech S.R.L., Via Madonna
del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Carmelo Fuccio
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 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
| | - Marco Fragai
- 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
| | - 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
| | - Lyndon Emsley
- Institut
des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Guido Pintacuda
- Centre de RMN à
Très Hauts Champs, Institut des Sciences Analytiques (CNRS,
ENS Lyon, UCB Lyon 1), Université de Lyon, 69100 Villeurbanne, France
| | - Claudio Luchinat
- Giotto Biotech S.R.L., Via Madonna
del Piano 6, 50019 Sesto Fiorentino, Italy
- 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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22
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Rovó P, Grohe K, Giller K, Becker S, Linser R. Proton Transverse Relaxation as a Sensitive Probe for Structure Determination in Solid Proteins. Chemphyschem 2015; 16:3791-6. [PMID: 26359781 DOI: 10.1002/cphc.201500799] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Indexed: 11/11/2022]
Abstract
Solid-state nuclear magnetic resonance (NMR) spectroscopy has been successfully applied to elucidate the atomic-resolution structures of insoluble proteins. The major bottleneck is the difficulty to obtain valuable long-distance structural information. Here, we propose the use of distance restraints as long as 32 Å, obtained from the quantification of transverse proton relaxation induced by a methanethiosulfonate spin label (MTSL). Combined with dipolar proton-proton distance restraints, this method allows us to obtain protein structures with excellent precision from single spin-labeled 1 mg protein samples using fast magic angle spinning.
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Affiliation(s)
- Petra Rovó
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Kristof Grohe
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Karin Giller
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stefan Becker
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Rasmus Linser
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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23
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Park SH, Wang V, Radoicic J, De Angelis AA, Berkamp S, Opella SJ. Paramagnetic relaxation enhancement of membrane proteins by incorporation of the metal-chelating unnatural amino acid 2-amino-3-(8-hydroxyquinolin-3-yl)propanoic acid (HQA). JOURNAL OF BIOMOLECULAR NMR 2015; 61:185-96. [PMID: 25430059 PMCID: PMC4398598 DOI: 10.1007/s10858-014-9884-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 11/20/2014] [Indexed: 05/16/2023]
Abstract
The use of paramagnetic constraints in protein NMR is an active area of research because of the benefits of long-range distance measurements (>10 Å). One of the main issues in successful execution is the incorporation of a paramagnetic metal ion into diamagnetic proteins. The most common metal ion tags are relatively long aliphatic chains attached to the side chain of a selected cysteine residue with a chelating group at the end where it can undergo substantial internal motions, decreasing the accuracy of the method. An attractive alternative approach is to incorporate an unnatural amino acid that binds metal ions at a specific site on the protein using the methods of molecular biology. Here we describe the successful incorporation of the unnatural amino acid 2-amino-3-(8-hydroxyquinolin-3-yl)propanoic acid (HQA) into two different membrane proteins by heterologous expression in E. coli. Fluorescence and NMR experiments demonstrate complete replacement of the natural amino acid with HQA and stable metal chelation by the mutated proteins. Evidence of site-specific intra- and inter-molecular PREs by NMR in micelle solutions sets the stage for the use of HQA incorporation in solid-state NMR structure determinations of membrane proteins in phospholipid bilayers.
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24
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Jaroniec CP. Structural studies of proteins by paramagnetic solid-state NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:50-9. [PMID: 25797004 PMCID: PMC4371136 DOI: 10.1016/j.jmr.2014.12.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 12/17/2014] [Indexed: 05/03/2023]
Abstract
Paramagnetism-based nuclear pseudocontact shifts and spin relaxation enhancements contain a wealth of information in solid-state NMR spectra about electron-nucleus distances on the ∼20 Å length scale, far beyond that normally probed through measurements of nuclear dipolar couplings. Such data are especially vital in the context of structural studies of proteins and other biological molecules that suffer from a sparse number of experimentally-accessible atomic distances constraining their three-dimensional fold or intermolecular interactions. This perspective provides a brief overview of the recent developments and applications of paramagnetic magic-angle spinning NMR to biological systems, with primary focus on the investigations of metalloproteins and natively diamagnetic proteins modified with covalent paramagnetic tags.
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Affiliation(s)
- Christopher P Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
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Ravera E, Schubeis T, Martelli T, Fragai M, Parigi G, Luchinat C. NMR of sedimented, fibrillized, silica-entrapped and microcrystalline (metallo)proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:60-70. [PMID: 25797005 DOI: 10.1016/j.jmr.2014.12.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 12/06/2014] [Accepted: 12/17/2014] [Indexed: 06/04/2023]
Abstract
Resolution and sensitivity in solid state NMR (SSNMR) can rival the results achieved by solution NMR, and even outperform them in the case of large systems. However, several factors affect the spectral quality in SSNMR samples, and not all systems turn out to be equally amenable for this methodology. In this review we attempt at analyzing the causes of this variable behavior and at providing hints to increase the chances of experimental success.
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Affiliation(s)
- Enrico Ravera
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Tobias Schubeis
- Giotto Biotech, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Tommaso Martelli
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy; Giotto Biotech, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
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Li S, Trébosc J, Lafon O, Zhou L, Shen M, Pourpoint F, Amoureux JP, Deng F. Observation of 1H-13C and 1H-1H proximities in a paramagnetic solid by NMR at high magnetic field under ultra-fast MAS. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 251:36-42. [PMID: 25557861 DOI: 10.1016/j.jmr.2014.11.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 11/28/2014] [Accepted: 11/30/2014] [Indexed: 06/04/2023]
Abstract
The assignment of NMR signals in paramagnetic solids is often challenging since: (i) the large paramagnetic shifts often mask the diamagnetic shifts specific to the local chemical environment, and (ii) the hyperfine interactions with unpaired electrons broaden the NMR spectra and decrease the coherence lifetime, thus reducing the efficiency of usual homo- and hetero-nuclear NMR correlation experiments. Here we show that the assignment of (1)H and (13)C signals in isotopically unmodified paramagnetic compounds with moderate hyperfine interactions can be facilitated by the use of two two-dimensional (2D) experiments: (i) (1)H-(13)C correlations with (1)H detection and (ii) (1)H-(1)H double-quantum↔single-quantum correlations. These methods are experimentally demonstrated on isotopically unmodified copper (II) complex of l-alanine at high magnetic field (18.8 T) and ultra-fast Magic Angle Spinning (MAS) frequency of 62.5 kHz. Compared to (13)C detection, we show that (1)H detection leads to a 3-fold enhancement in sensitivity for (1)H-(13)C 2D correlation experiments. By combining (1)H-(13)C and (1)H-(1)H 2D correlation experiments with the analysis of (13)C longitudinal relaxation times, we have been able to assign the (1)H and (13)C signals of each l-alanine ligand.
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Affiliation(s)
- Shenhui Li
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Julien Trébosc
- Univ. Lille North of France, Unit of Catalysis and Chemistry of Solids (UCCS), CNRS UMR 8181, ENSCL, Univ. Lille 1, Villeneuve d'Ascq 59652, France
| | - Olivier Lafon
- Univ. Lille North of France, Unit of Catalysis and Chemistry of Solids (UCCS), CNRS UMR 8181, ENSCL, Univ. Lille 1, Villeneuve d'Ascq 59652, France.
| | - Lei Zhou
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Ming Shen
- Univ. Lille North of France, Unit of Catalysis and Chemistry of Solids (UCCS), CNRS UMR 8181, ENSCL, Univ. Lille 1, Villeneuve d'Ascq 59652, France; Physics Department & Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai 200062, China
| | - Frédérique Pourpoint
- Univ. Lille North of France, Unit of Catalysis and Chemistry of Solids (UCCS), CNRS UMR 8181, ENSCL, Univ. Lille 1, Villeneuve d'Ascq 59652, France
| | - Jean-Paul Amoureux
- Univ. Lille North of France, Unit of Catalysis and Chemistry of Solids (UCCS), CNRS UMR 8181, ENSCL, Univ. Lille 1, Villeneuve d'Ascq 59652, France; Physics Department & Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai 200062, China.
| | - Feng Deng
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
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Parthasarathy S, Yoo B, McElheny D, Tay W, Ishii Y. Capturing a reactive state of amyloid aggregates: NMR-based characterization of copper-bound Alzheimer disease amyloid β-fibrils in a redox cycle. J Biol Chem 2014; 289:9998-10010. [PMID: 24523414 DOI: 10.1074/jbc.m113.511345] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The interaction of redox-active copper ions with misfolded amyloid β (Aβ) is linked to production of reactive oxygen species (ROS), which has been associated with oxidative stress and neuronal damages in Alzheimer disease. Despite intensive studies, it is still not conclusive how the interaction of Cu(+)/Cu(2+) with Aβ aggregates leads to ROS production even at the in vitro level. In this study, we examined the interaction between Cu(+)/Cu(2+) and Aβ fibrils by solid-state NMR (SSNMR) and other spectroscopic methods. Our photometric studies confirmed the production of ~60 μM hydrogen peroxide (H2O2) from a solution of 20 μM Cu(2+) ions in complex with Aβ(1-40) in fibrils ([Cu(2+)]/[Aβ] = 0.4) within 2 h of incubation after addition of biological reducing agent ascorbate at the physiological concentration (~1 mM). Furthermore, SSNMR (1)H T1 measurements demonstrated that during ROS production the conversion of paramagnetic Cu(2+) into diamagnetic Cu(+) occurs while the reactive Cu(+) ions remain bound to the amyloid fibrils. The results also suggest that O2 is required for rapid recycling of Cu(+) bound to Aβ back to Cu(2+), which allows for continuous production of H2O2. Both (13)C and (15)N SSNMR results show that Cu(+) coordinates to Aβ(1-40) fibrils primarily through the side chain Nδ of both His-13 and His-14, suggesting major rearrangements from the Cu(2+) coordination via Nε in the redox cycle. (13)C SSNMR chemical shift analysis suggests that the overall Aβ conformations are largely unaffected by Cu(+) binding. These results present crucial site-specific evidence of how the full-length Aβ in amyloid fibrils offers catalytic Cu(+) centers.
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Shumilina E, Dobrovolska O, Del Conte R, Holen HW, Dikiy A. Competitive cobalt for zinc substitution in mammalian methionine sulfoxide reductase B1 overexpressed in E. coli: structural and functional insight. J Biol Inorg Chem 2013; 19:85-95. [PMID: 24271273 PMCID: PMC3889830 DOI: 10.1007/s00775-013-1064-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 10/31/2013] [Indexed: 11/26/2022]
Abstract
Expression of the mammalian enzyme methionine sulfoxide reductase B1 (MsrB1) in Escherichia coli growing in cobalt-containing media resulted in the reproducible appearance
of the stable cobalt-containing protein MsrB1-Co. NMR studies and biocomputing using the programs AnisoFit and Amber allowed us to generate a structure of MsrB1-Co sharing the overall fold with the native zinc-containing protein MsrB1-Zn. Our data suggest that the N-terminus containing resolving cysteine tends to be closer to the protein’s catalytic center than was previously reported. It is argued that this proximity supports the proposed catalytic mechanism and ensures high catalytic efficiency of MsrB1. Functional studies showed that both MsrB1-Zn and MsrB1-Co exhibit similar levels of activity, in agreement with the structural studies performed. The proposed metal ion substitution approach may have a methodological significance in determining whether methionine sulfoxide reductase B proteins contain a metal ion.
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Affiliation(s)
- Elena Shumilina
- Department of Biotechnology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
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Varghese S, Yang F, Pacheco V, Wrede K, Medvedev A, Ogata H, Knipp M, Heise H. Expression, purification, and solid-state NMR characterization of the membrane binding heme protein nitrophorin 7 in two electronic spin states. Biochemistry 2013; 52:7031-40. [PMID: 24033104 DOI: 10.1021/bi401020t] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The nitrophorins (NPs) comprise a group of NO transporting ferriheme b proteins found in the saliva of the blood sucking insect Rhodnius prolixus . In contrast to other nitrophorins (NP1-4), the recently identified membrane binding isoform NP7 tends to form oligomers and precipitates at higher concentrations in solution. Hence, solid-state NMR (ssNMR) was employed as an alternative method to gain structural insights on the precipitated protein. We report the expression and purification of (13)C,(15)N isotopically labeled protein together with the first ssNMR characterization of NP7. Because the size of NP7 (21 kDa) still provides a challenge for ssNMR, the samples were reverse labeled with Lys and Val to reduce the number of crosspeaks in two-dimensional spectra. The two electronic spin states with S = 1/2 and S = 0 at the ferriheme iron were generated by the complexation with imidazole and NO, respectively. ssNMR spectra of both forms are well resolved, which allows for sequential resonance assignments of 22 residues. Importantly, the ssNMR spectra demonstrate that aggregation does not affect the protein fold. Comparison of the spectra of the two electronic spin states allows the determination of paramagnetically shifted cross peaks due to pseudocontact shifts, which assists the assignment of residues close to the heme center.
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Affiliation(s)
- Sabu Varghese
- ICS-6 Institute of Complex Systems-Structural Biochemistry, Forschungszentrum Jülich , D-2425 Jülich, Germany
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Sengupta I, Nadaud PS, Jaroniec CP. Protein structure determination with paramagnetic solid-state NMR spectroscopy. Acc Chem Res 2013; 46:2117-26. [PMID: 23464364 DOI: 10.1021/ar300360q] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Many structures of the proteins and protein assemblies that play central roles in fundamental biological processes and disease pathogenesis are not readily accessible via the conventional techniques of single-crystal X-ray diffraction and solution-state nuclear magnetic resonance (NMR). On the other hand, many of these challenging biological systems are suitable targets for atomic-level structural and dynamic analysis by magic-angle spinning (MAS) solid-state NMR spectroscopy, a technique that has far less stringent limitations on the molecular size and crystalline state. Over the past decade, major advances in instrumentation and methodology have prompted rapid growth in the field of biological solid-state NMR. However, despite this progress, one challenge for the elucidation of three-dimensional (3D) protein structures via conventional MAS NMR methods is the relative lack of long-distance data. Specifically, extracting unambiguous interatomic distance restraints larger than ∼5 Å from through-space magnetic dipole-dipole couplings among the protein (1)H, (13)C, and (15)N nuclei has proven to be a considerable challenge for researchers. It is possible to circumvent this problem by extending the structural studies to include several analogs of the protein of interest, intentionally modified to contain covalently attached paramagnetic tags at selected sites. In these paramagnetic proteins, the hyperfine couplings between the nuclei and unpaired electrons can manifest themselves in NMR spectra in the form of relaxation enhancements of the nuclear spins that depend on the electron-nucleus distance. These effects can be significant for nuclei located up to ∼20 Å away from the paramagnetic center. In this Account, we discuss MAS NMR structural studies of nitroxide and EDTA-Cu(2+) labeled variants of a model 56 amino acid globular protein, B1 immunoglobulin-binding domain of protein G (GB1), in the microcrystalline solid phase. We used a set of six EDTA-Cu(2+)-tagged GB1 mutants to rapidly determine the global protein fold in a de novo fashion. Remarkably, these studies required quantitative measurements of only approximately four or five backbone amide (15)N longitudinal paramagnetic relaxation enhancements per residue, in the complete absence of the usual internuclear distance restraints. Importantly, this paramagnetic solid-state NMR methodology is general and can be directly applied to larger proteins and protein complexes for which a significant fraction of the signals can be assigned in standard 2D and 3D MAS NMR chemical shift correlation spectra.
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Affiliation(s)
- Ishita Sengupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Philippe S. Nadaud
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Christopher P. Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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Knight MJ, Felli IC, Pierattelli R, Emsley L, Pintacuda G. Magic angle spinning NMR of paramagnetic proteins. Acc Chem Res 2013; 46:2108-16. [PMID: 23506094 DOI: 10.1021/ar300349y] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Metal ions are ubiquitous in biochemical and cellular processes. Since many metal ions are paramagnetic due to the presence of unpaired electrons, paramagnetic molecules are an important class of targets for research in structural biology and related fields. Today, NMR spectroscopy plays a central role in the investigation of the structure and chemical properties of paramagnetic metalloproteins, linking the observed paramagnetic phenomena directly to electronic and molecular structure. A major step forward in the study of proteins by solid-state NMR came with the advent of ultrafast magic angle spinning (MAS) and the ability to use (1)H detection. Combined, these techniques have allowed investigators to observe nuclei that previously were invisible in highly paramagnetic metalloproteins. In addition, these techniques have enabled quantitative site-specific measurement of a variety of long-range paramagnetic effects. Instead of limiting solid-state NMR studies of biological systems, paramagnetism provides an information-rich phenomenon that can be exploited in these studies. This Account emphasizes state-of-the-art methods and applications of solid-state NMR in paramagnetic systems in biological chemistry. In particular, we discuss the use of ultrafast MAS and (1)H-detection in perdeuterated paramagnetic metalloproteins. Current methodology allows us to determine the structure and dynamics of metalloenzymes, and, as an example, we describe solid-state NMR studies of microcrystalline superoxide dismutase, a 32 kDa dimer. Data were acquired with remarkably short times, and these experiments required only a few milligrams of sample.
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Affiliation(s)
- Michael J. Knight
- Université de Lyon, Institut de Sciences Analytiques (CNRS / ENS-Lyon / UCB Lyon 1), Centre de RMN à Très Hauts Champs, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Isabella C. Felli
- Department of Chemistry “Ugo Schiff“ and Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6 − 50019 Sesto Fiorentino, FI, Italy
| | - Roberta Pierattelli
- Department of Chemistry “Ugo Schiff“ and Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6 − 50019 Sesto Fiorentino, FI, Italy
| | - Lyndon Emsley
- Université de Lyon, Institut de Sciences Analytiques (CNRS / ENS-Lyon / UCB Lyon 1), Centre de RMN à Très Hauts Champs, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Guido Pintacuda
- Université de Lyon, Institut de Sciences Analytiques (CNRS / ENS-Lyon / UCB Lyon 1), Centre de RMN à Très Hauts Champs, 5 rue de la Doua, 69100 Villeurbanne, France
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Carnevale D, Perez Linde A, Bauer G, Bodenhausen G. Solid-state proton NMR of paramagnetic metal complexes: DANTE spin echoes for selective excitation in inhomogeneously broadened lines. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.06.052] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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34
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Li J, Pilla KB, Li Q, Zhang Z, Su X, Huber T, Yang J. Magic Angle Spinning NMR Structure Determination of Proteins from Pseudocontact Shifts. J Am Chem Soc 2013; 135:8294-303. [DOI: 10.1021/ja4021149] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jianping Li
- Key Laboratory of Magnetic Resonance
in Biological Systems, State Key Laboratory of Magnetic Resonance
and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance,
Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, PR China
| | - Kala Bharath Pilla
- Research School
of Chemistry, Australian National University, Canberra, ACT 0200,
Australia
| | - Qingfeng Li
- State Key Laboratory of Elemento-Organic
Chemistry, Nankai University, Tianjin300071,
PR China
| | - Zhengfeng Zhang
- Key Laboratory of Magnetic Resonance
in Biological Systems, State Key Laboratory of Magnetic Resonance
and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance,
Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, PR China
| | - Xuncheng Su
- State Key Laboratory of Elemento-Organic
Chemistry, Nankai University, Tianjin300071,
PR China
| | - Thomas Huber
- Research School
of Chemistry, Australian National University, Canberra, ACT 0200,
Australia
| | - Jun Yang
- Key Laboratory of Magnetic Resonance
in Biological Systems, State Key Laboratory of Magnetic Resonance
and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance,
Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, PR China
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35
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Emwas AHM, Al-Talla ZA, Guo X, Al-Ghamdi S, Al-Masri HT. Utilizing NMR and EPR spectroscopy to probe the role of copper in prion diseases. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:255-268. [PMID: 23436479 DOI: 10.1002/mrc.3936] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 12/19/2012] [Accepted: 01/11/2013] [Indexed: 06/01/2023]
Abstract
Copper is an essential nutrient for the normal development of the brain and nervous system, although the hallmark of several neurological diseases is a change in copper concentrations in the brain and central nervous system. Prion protein (PrP) is a copper-binding, cell-surface glycoprotein that exists in two alternatively folded conformations: a normal isoform (PrP(C)) and a disease-associated isoform (PrP(Sc)). Prion diseases are a group of lethal neurodegenerative disorders that develop as a result of conformational conversion of PrP(C) into PrP(Sc). The pathogenic mechanism that triggers this conformational transformation with the subsequent development of prion diseases remains unclear. It has, however, been shown repeatedly that copper plays a significant functional role in the conformational conversion of prion proteins. In this review, we focus on current research that seeks to clarify the conformational changes associated with prion diseases and the role of copper in this mechanism, with emphasis on the latest applications of NMR and EPR spectroscopy to probe the interactions of copper with prion proteins.
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Affiliation(s)
- Abdul-Hamid M Emwas
- NMR Core Lab, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.
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36
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Bhaumik A, Luchinat C, Parigi G, Ravera E, Rinaldelli M. NMR crystallography on paramagnetic systems: solved and open issues. CrystEngComm 2013. [DOI: 10.1039/c3ce41485j] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Wang S, Munro RA, Kim SY, Jung KH, Brown LS, Ladizhansky V. Paramagnetic Relaxation Enhancement Reveals Oligomerization Interface of a Membrane Protein. J Am Chem Soc 2012; 134:16995-8. [DOI: 10.1021/ja308310z] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | | | - So Young Kim
- Department of Life Science and
Institute of Biological Interfaces, Sogang University, Seoul, Korea
| | - Kwang-Hwan Jung
- Department of Life Science and
Institute of Biological Interfaces, Sogang University, Seoul, Korea
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38
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Knight MJ, Felli IC, Pierattelli R, Bertini I, Emsley L, Herrmann T, Pintacuda G. Rapid Measurement of Pseudocontact Shifts in Metalloproteins by Proton-Detected Solid-State NMR Spectroscopy. J Am Chem Soc 2012; 134:14730-3. [DOI: 10.1021/ja306813j] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael J. Knight
- Centre de RMN à Très
Hauts Champs, UMR 5280 CNRS/ENS Lyon/UCB Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Isabella C. Felli
- Department of Chemistry “Ugo
Schiff“ and Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, 50019
Sesto Fiorentino, Italy
| | - Roberta Pierattelli
- Department of Chemistry “Ugo
Schiff“ and Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, 50019
Sesto Fiorentino, Italy
| | - Ivano Bertini
- Department of Chemistry “Ugo
Schiff“ and Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, 50019
Sesto Fiorentino, Italy
| | - Lyndon Emsley
- Centre de RMN à Très
Hauts Champs, UMR 5280 CNRS/ENS Lyon/UCB Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Torsten Herrmann
- Centre de RMN à Très
Hauts Champs, UMR 5280 CNRS/ENS Lyon/UCB Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Guido Pintacuda
- Centre de RMN à Très
Hauts Champs, UMR 5280 CNRS/ENS Lyon/UCB Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
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39
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Structure and backbone dynamics of a microcrystalline metalloprotein by solid-state NMR. Proc Natl Acad Sci U S A 2012; 109:11095-100. [PMID: 22723345 DOI: 10.1073/pnas.1204515109] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We introduce a new approach to improve structural and dynamical determination of large metalloproteins using solid-state nuclear magnetic resonance (NMR) with (1)H detection under ultrafast magic angle spinning (MAS). The approach is based on the rapid and sensitive acquisition of an extensive set of (15)N and (13)C nuclear relaxation rates. The system on which we demonstrate these methods is the enzyme Cu, Zn superoxide dismutase (SOD), which coordinates a Cu ion available either in Cu(+) (diamagnetic) or Cu(2+) (paramagnetic) form. Paramagnetic relaxation enhancements are obtained from the difference in rates measured in the two forms and are employed as structural constraints for the determination of the protein structure. When added to (1)H-(1)H distance restraints, they are shown to yield a twofold improvement of the precision of the structure. Site-specific order parameters and timescales of motion are obtained by a gaussian axial fluctuation (GAF) analysis of the relaxation rates of the diamagnetic molecule, and interpreted in relation to backbone structure and metal binding. Timescales for motion are found to be in the range of the overall correlation time in solution, where internal motions characterized here would not be observable.
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40
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Jaroniec CP. Solid-state nuclear magnetic resonance structural studies of proteins using paramagnetic probes. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2012; 43-44:1-13. [PMID: 22464402 DOI: 10.1016/j.ssnmr.2012.02.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 02/27/2012] [Accepted: 02/28/2012] [Indexed: 05/31/2023]
Abstract
Determination of three-dimensional structures of biological macromolecules by magic-angle spinning (MAS) solid-state NMR spectroscopy is hindered by the paucity of nuclear dipolar coupling-based restraints corresponding to distances exceeding 5 Å. Recent MAS NMR studies of uniformly (13)C,(15)N-enriched proteins containing paramagnetic centers have demonstrated the measurements of site-specific nuclear pseudocontact shifts and spin relaxation enhancements, which report on electron-nucleus distances up to ~20 Å. These studies pave the way for the application of such long-distance paramagnetic restraints to protein structure elucidation and analysis of protein-protein and protein-ligand interactions in the solid phase. Paramagnetic species also facilitate the rapid acquisition of high resolution and sensitivity multidimensional solid-state NMR spectra of biomacromolecules using condensed data collection schemes, and characterization of solvent-accessible surfaces of peptides and proteins. In this review we discuss some of the latest applications of magic-angle spinning NMR spectroscopy in conjunction with paramagnetic probes to the structural studies of proteins in the solid state.
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Affiliation(s)
- Christopher P Jaroniec
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
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Sengupta I, Nadaud PS, Helmus JJ, Schwieters CD, Jaroniec CP. Protein fold determined by paramagnetic magic-angle spinning solid-state NMR spectroscopy. Nat Chem 2012; 4:410-7. [PMID: 22522262 PMCID: PMC3335742 DOI: 10.1038/nchem.1299] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 02/08/2012] [Indexed: 11/16/2022]
Abstract
Biomacromolecules that are challenging for the usual structural techniques can be studied with atomic resolution by solid-state nuclear magnetic resonance. However, the paucity of >5 Å distance restraints, traditionally derived from measurements of magnetic dipole-dipole couplings between protein nuclei, is a major bottleneck that hampers such structure elucidation efforts. Here we describe a general approach that enables the rapid determination of global protein fold in the solid phase via measurements of nuclear paramagnetic relaxation enhancements (PREs) in several analogs of the protein of interest containing covalently-attached paramagnetic tags, without the use of conventional internuclear distance restraints. The method is demonstrated using six cysteine-EDTA-Cu2+ mutants of the 56-residue B1 immunoglobulin-binding domain of protein G, for which ~230 longitudinal backbone 15N PREs corresponding to ~10-20 Å distances were obtained. The mean protein fold determined in this manner agrees with the X-ray structure with a backbone atom root-mean-square deviation of 1.8 Å.
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Affiliation(s)
- Ishita Sengupta
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
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Luchinat C, Parigi G, Ravera E, Rinaldelli M. Solid-state NMR crystallography through paramagnetic restraints. J Am Chem Soc 2012; 134:5006-9. [PMID: 22393876 DOI: 10.1021/ja210079n] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pseudocontact shifts (PCSs) measured by solid-state NMR spectroscopy (SS-NMR) on microcrystalline powders of a paramagnetic metalloprotein permit NMR crystallography. Along with other restraints for SS-NMR experiments, the protein molecular structure as well as the correct crystal packing are obtained.
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Affiliation(s)
- Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, via Sacconi 6, Sesto Fiorentino, Italy.
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Sun S, Han Y, Paramasivam S, Yan S, Siglin AE, Williams JC, Byeon IJL, Ahn J, Gronenborn AM, Polenova T. Solid-state NMR spectroscopy of protein complexes. Methods Mol Biol 2012; 831:303-31. [PMID: 22167681 PMCID: PMC4890720 DOI: 10.1007/978-1-61779-480-3_17] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Protein-protein interactions are vital for many biological processes. These interactions often result in the formation of protein assemblies that are large in size, insoluble, and difficult to crystallize, and therefore are challenging to study by structure biology techniques, such as single crystal X-ray diffraction and solution NMR spectroscopy. Solid-state NMR (SSNMR) spectroscopy is emerging as a promising technique for studies of such protein assemblies because it is not limited by molecular size, solubility, or lack of long-range order. In the past several years, we have applied magic angle spinning SSNMR-based methods to study several protein complexes. In this chapter, we discuss the general SSNMR methodologies employed for structural and dynamics analyses of protein complexes with specific examples from our work on thioredoxin reassemblies, HIV-1 capsid protein assemblies, and microtubule-associated protein assemblies. We present protocols for sample preparation and characterization, pulse sequences, SSNMR spectra collection, and data analysis.
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Affiliation(s)
- Shangjin Sun
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
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Nadaud PS, Sengupta I, Helmus JJ, Jaroniec CP. Evaluation of the influence of intermolecular electron-nucleus couplings and intrinsic metal binding sites on the measurement of 15N longitudinal paramagnetic relaxation enhancements in proteins by solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2011; 51:293-302. [PMID: 21826518 DOI: 10.1007/s10858-011-9536-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 07/25/2011] [Indexed: 05/31/2023]
Abstract
Magic-angle spinning solid-state NMR measurements of (15)N longitudinal paramagnetic relaxation enhancements (PREs) in (13)C,(15)N-labeled proteins modified with Cu(2+)-chelating tags can yield multiple long-range electron-nucleus distance restraints up to ~20 Å (Nadaud et al. in J Am Chem Soc 131:8108-8120, 2009). Using the EDTA-Cu(2+) K28C mutant of B1 immunoglobulin binding domain of protein G (GB1) as a model, we investigate the effects on such measurements of intermolecular electron-nucleus couplings and intrinsic metal binding sites, both of which may potentially complicate the interpretation of PRE data in terms of the intramolecular protein fold. To quantitatively assess the influence of intermolecular (15)N-Cu(2+) interactions we have determined a nearly complete set of longitudinal (15)N PREs for a series of microcrystalline samples containing ~10, 15 and 25 mol percent of the (13)C,(15)N-labeled EDTA-Cu(2+)-tagged protein diluted in a matrix of diamagnetic natural abundance GB1. The residual intermolecular interactions were found to be minor on the whole and account for only a fraction of the relatively small but systematic deviations observed between the experimental (15)N PREs and corresponding values calculated using protein structural models for residues furthest removed from the EDTA-Cu(2+) tag. This suggests that these deviations are also caused in part by other factors not related to the protein structure, such as the presence in the protein of intrinsic secondary sites capable of binding Cu(2+) ions. To probe this issue we performed a Cu(2+) titration study for K28C-EDTA GB1 monitored by 2D (15)N-(1)H solution-state NMR, which revealed that while for Cu(2+):protein molar ratios of ≤ 1.0 Cu(2+) binds primarily to the high-affinity EDTA tag, as anticipated, at even slightly super-stoichiometric ratios the Cu(2+) ions can also associate with side-chains of aspartate and glutamate residues. This in turn is expected to lead to enhanced PREs for residues located in the vicinity of the secondary Cu(2+) binding sites, and indeed many of these residues were ones found to display the elevated longitudinal (15)N PREs in the solid phase.
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Affiliation(s)
- Philippe S Nadaud
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
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Flambard A, Köhler FH, Lescouëzec R, Revel B. Probing Spin Density and Local Structure in the Prussian Blue Analogues CsCd[Fe/Co(CN)6]⋅0.5 H2O and Cd3[Fe/Co(CN)6]2⋅15 H2O with Solid-State MAS NMR Spectroscopy. Chemistry 2011; 17:11567-75. [DOI: 10.1002/chem.201100778] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Indexed: 11/11/2022]
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Wheat-germ cell-free production of prion proteins for solid-state NMR structural studies. N Biotechnol 2011; 28:232-8. [DOI: 10.1016/j.nbt.2010.06.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Accepted: 06/28/2010] [Indexed: 12/14/2022]
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Parthasarathy S, Long F, Miller Y, Xiao Y, McElheny D, Thurber K, Ma B, Nussinov R, Ishii Y. Molecular-level examination of Cu2+ binding structure for amyloid fibrils of 40-residue Alzheimer's β by solid-state NMR spectroscopy. J Am Chem Soc 2011; 133:3390-400. [PMID: 21341665 PMCID: PMC3074258 DOI: 10.1021/ja1072178] [Citation(s) in RCA: 162] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cu(2+) binding to Alzheimer's β (Aβ) peptides in amyloid fibrils has attracted broad attention, as it was shown that Cu ion concentration elevates in Alzheimer's senile plaque and such association of Aβ with Cu(2+) triggers the production of neurotoxic reactive oxygen species (ROS) such as H(2)O(2). However, detailed binding sites and binding structures of Cu(2+) to Aβ are still largely unknown for Aβ fibrils or other aggregates of Aβ. In this work, we examined molecular details of Cu(2+) binding to amyloid fibrils by detecting paramagnetic signal quenching in 1D and 2D high-resolution (13)C solid-state NMR (SSNMR) for full-length 40-residue Aβ(1-40). Selective quenching observed in (13)C SSNMR of Cu(2+)-bound Aβ(1-40) suggested that primary Cu(2+) binding sites in Aβ(1-40) fibrils include N(ε) in His-13 and His-14 and carboxyl groups in Val-40 as well as in Glu sidechains (Glu-3, Glu-11, and/or Glu-22). (13)C chemical shift analysis demonstrated no major structural changes upon Cu(2+) binding in the hydrophobic core regions (residues 18-25 and 30-36). Although the ROS production via oxidization of Met-35 in the presence of Cu(2+) has been long suspected, our SSNMR analysis of (13)C(ε)H(3)-S- in M35 showed little changes after Cu(2+) binding, excluding the possibility of Met-35 oxidization by Cu(2+) alone. Preliminary molecular dynamics (MD) simulations on Cu(2+)-Aβ complex in amyloid fibrils confirmed binding sites suggested by the SSNMR results and the stabilities of such bindings. The MD simulations also indicate the coexistence of a variety of Cu(2+)-binding modes unique in Aβ fibril, which are realized by both intra- and intermolecular contacts and highly concentrated coordination sites due to the in-register parallel β-sheet arrangements.
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Affiliation(s)
| | - Fei Long
- Department of Chemistry, University of Illinois at Chicago, Chicago IL 60607
| | - Yifat Miller
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702
| | - Yiling Xiao
- Department of Chemistry, University of Illinois at Chicago, Chicago IL 60607
| | - Dan McElheny
- Department of Chemistry, University of Illinois at Chicago, Chicago IL 60607
| | - Kent Thurber
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda MD 20892
| | - Buyong Ma
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702
- Basic Science Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702
| | - Ruth Nussinov
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702
- Sackler Inst. of Molecular Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yoshitaka Ishii
- Department of Chemistry, University of Illinois at Chicago, Chicago IL 60607
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Nadaud PS, Helmus JJ, Sengupta I, Jaroniec CP. Rapid acquisition of multidimensional solid-state NMR spectra of proteins facilitated by covalently bound paramagnetic tags. J Am Chem Soc 2010; 132:9561-3. [PMID: 20583834 DOI: 10.1021/ja103545e] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe a condensed data collection approach that facilitates rapid acquisition of multidimensional magic-angle spinning solid-state nuclear magnetic resonance (SSNMR) spectra of proteins by combining rapid sample spinning, optimized low-power radio frequency pulse schemes and covalently attached paramagnetic tags to enhance protein (1)H spin-lattice relaxation. Using EDTA-Cu(2+)-modified K28C and N8C mutants of the B1 immunoglobulin binding domain of protein G as models, we demonstrate that high resolution and sensitivity 2D and 3D SSNMR chemical shift correlation spectra can be recorded in as little as several minutes and several hours, respectively, for samples containing approximately 0.1-0.2 micromol of (13)C,(15)N- or (2)H,(13)C,(15)N-labeled protein. This mode of data acquisition is naturally suited toward the structural SSNMR studies of paramagnetic proteins, for which the typical (1)H longitudinal relaxation time constants are inherently a factor of at least approximately 3-4 lower relative to their diamagnetic counterparts. To illustrate this, we demonstrate the rapid site-specific determination of backbone amide (15)N longitudinal paramagnetic relaxation enhancements using a pseudo-3D SSNMR experiment based on (15)N-(13)C correlation spectroscopy, and we show that such measurements yield valuable long-range (15)N-Cu(2+) distance restraints which report on the three-dimensional protein fold.
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Affiliation(s)
- Philippe S Nadaud
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
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Affiliation(s)
- Gottfried Otting
- Australian National University, Research School of Chemistry, Canberra, ACT 0200, Australia;
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