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Querci L, Grifagni D, Trindade IB, Silva JM, Louro RO, Cantini F, Piccioli M. Paramagnetic NMR to study iron sulfur proteins: 13C detected experiments illuminate the vicinity of the metal center. JOURNAL OF BIOMOLECULAR NMR 2023; 77:247-259. [PMID: 37853207 PMCID: PMC10687126 DOI: 10.1007/s10858-023-00425-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/25/2023] [Indexed: 10/20/2023]
Abstract
The robustness of NMR coherence transfer in proximity of a paramagnetic center depends on the relaxation properties of the nuclei involved. In the case of Iron-Sulfur Proteins, different pulse schemes or different parameter sets often provide complementary results. Tailored versions of HCACO and CACO experiments significantly increase the number of observed Cα/C' connectivities in highly paramagnetic systems, by recovering many resonances that were lost due to paramagnetic relaxation. Optimized 13C direct detected experiments can significantly extend the available assignments, improving the overall knowledge of these systems. The different relaxation properties of Cα and C' nuclei are exploited in CACO vs COCA experiments and the complementarity of the two experiments is used to obtain structural information. The two [Fe2S2]+ clusters containing NEET protein CISD3 and the one [Fe4S4]2+ cluster containing HiPIP protein PioC have been taken as model systems. We show that tailored experiments contribute to decrease the blind sphere around the cluster, to extend resonance assignment of cluster bound cysteine residues and to retrieve details on the topology of the iron-bound ligand residues.
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Affiliation(s)
- Leonardo Querci
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Deborah Grifagni
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Inês B Trindade
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Av. da República (EAN), 2780-157, Oeiras, Portugal
- Division of Biology and Biological Engineering, California Institute of Technology, CA 91125, Pasadena, USA
| | - José Malanho Silva
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Ricardo O Louro
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Av. da República (EAN), 2780-157, Oeiras, Portugal
| | - Francesca Cantini
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Mario Piccioli
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.
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Sequence-specific assignments in NMR spectra of paramagnetic systems: A non-systematic approach. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2020.119984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Paramagnetic NMR Spectroscopy Is a Tool to Address Reactivity, Structure, and Protein–Protein Interactions of Metalloproteins: The Case of Iron–Sulfur Proteins. MAGNETOCHEMISTRY 2020. [DOI: 10.3390/magnetochemistry6040046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The study of cellular machineries responsible for the iron–sulfur (Fe–S) cluster biogenesis has led to the identification of a large number of proteins, whose importance for life is documented by an increasing number of diseases linked to them. The labile nature of Fe–S clusters and the transient protein–protein interactions, occurring during the various steps of the maturation process, make their structural characterization in solution particularly difficult. Paramagnetic nuclear magnetic resonance (NMR) has been used for decades to characterize chemical composition, magnetic coupling, and the electronic structure of Fe–S clusters in proteins; it represents, therefore, a powerful tool to study the protein–protein interaction networks of proteins involving into iron–sulfur cluster biogenesis. The optimization of the various NMR experiments with respect to the hyperfine interaction will be summarized here in the form of a protocol; recently developed experiments for measuring longitudinal and transverse nuclear relaxation rates in highly paramagnetic systems will be also reviewed. Finally, we will address the use of extrinsic paramagnetic centers covalently bound to diamagnetic proteins, which contributed over the last twenty years to promote the applications of paramagnetic NMR well beyond the structural biology of metalloproteins.
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Invernici M, Trindade IB, Cantini F, Louro RO, Piccioli M. Measuring transverse relaxation in highly paramagnetic systems. JOURNAL OF BIOMOLECULAR NMR 2020; 74:431-442. [PMID: 32710399 PMCID: PMC7508935 DOI: 10.1007/s10858-020-00334-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 07/09/2020] [Indexed: 05/16/2023]
Abstract
The enhancement of nuclear relaxation rates due to the interaction with a paramagnetic center (known as Paramagnetic Relaxation Enhancement) is a powerful source of structural and dynamics information, widely used in structural biology. However, many signals affected by the hyperfine interaction relax faster than the evolution periods of common NMR experiments and therefore they are broadened beyond detection. This gives rise to a so-called blind sphere around the paramagnetic center, which is a major limitation in the use of PREs. Reducing the blind sphere is extremely important in paramagnetic metalloproteins. The identification, characterization, and proper structural restraining of the first coordination sphere of the metal ion(s) and its immediate neighboring regions is key to understand their biological function. The novel HSQC scheme we propose here, that we termed R2-weighted, HSQC-AP, achieves this aim by detecting signals that escaped detection in a conventional HSQC experiment and provides fully reliable R2 values in the range of 1H R2 rates ca. 50-400 s-1. Independently on the type of paramagnetic center and on the size of the molecule, this experiment decreases the radius of the blind sphere and increases the number of detectable PREs. Here, we report the validation of this approach for the case of PioC, a small protein containing a high potential 4Fe-4S cluster in the reduced [Fe4S4]2+ form. The blind sphere was contracted to a minimal extent, enabling the measurement of R2 rates for the cluster coordinating residues.
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Affiliation(s)
- Michele Invernici
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Inês B Trindade
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Av. da República (EAN), 2780-157, Oeiras, Portugal
| | - Francesca Cantini
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Ricardo O Louro
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Av. da República (EAN), 2780-157, Oeiras, Portugal.
| | - Mario Piccioli
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.
- Consorzio Interuniversitario Risonanze Magnetiche Di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.
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Mori M, Kateb F, Bodenhausen G, Piccioli M, Abergel D. Toward Structural Dynamics: Protein Motions Viewed by Chemical Shift Modulations and Direct Detection of C′N Multiple-Quantum Relaxation. J Am Chem Soc 2010; 132:3594-600. [DOI: 10.1021/ja9103556] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mirko Mori
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Via L. Sacconi 3, 50019 Sesto Fiorentino, Italy, Laboratoire des Biomolécules, associé au CNRS, Département de Chimie, Ecole Normale Supérieure, 24, rue Lhomond, 75231 Paris cedex 05, France, and Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, Batochime, 1015 Lausanne, Switzerland
| | - Fatiha Kateb
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Via L. Sacconi 3, 50019 Sesto Fiorentino, Italy, Laboratoire des Biomolécules, associé au CNRS, Département de Chimie, Ecole Normale Supérieure, 24, rue Lhomond, 75231 Paris cedex 05, France, and Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, Batochime, 1015 Lausanne, Switzerland
| | - Geoffrey Bodenhausen
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Via L. Sacconi 3, 50019 Sesto Fiorentino, Italy, Laboratoire des Biomolécules, associé au CNRS, Département de Chimie, Ecole Normale Supérieure, 24, rue Lhomond, 75231 Paris cedex 05, France, and Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, Batochime, 1015 Lausanne, Switzerland
| | - Mario Piccioli
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Via L. Sacconi 3, 50019 Sesto Fiorentino, Italy, Laboratoire des Biomolécules, associé au CNRS, Département de Chimie, Ecole Normale Supérieure, 24, rue Lhomond, 75231 Paris cedex 05, France, and Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, Batochime, 1015 Lausanne, Switzerland
| | - Daniel Abergel
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Via L. Sacconi 3, 50019 Sesto Fiorentino, Italy, Laboratoire des Biomolécules, associé au CNRS, Département de Chimie, Ecole Normale Supérieure, 24, rue Lhomond, 75231 Paris cedex 05, France, and Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, Batochime, 1015 Lausanne, Switzerland
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Zhang J, Spring A, Germann MW. Facilitated assignment of adenine H2 resonances in oligonucleotides using homonuclear long-range couplings. J Am Chem Soc 2009; 131:5380-1. [PMID: 19323530 PMCID: PMC2889177 DOI: 10.1021/ja900771b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The small homonuclear coupling constant between H2 and H8 protons of adenine (0.5 +/- 0.2 Hz) was determined and exploited to assign the H2 proton of adenine residues in DNA oligonucleotides. The utility of this approach is demonstrated for two different DNA sequences in D(2)O, for which we show a rapid and unambiguous assignment of the A H2 resonances.
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Affiliation(s)
- Jin Zhang
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
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Mori M, Jiménez B, Piccioli M, Battistoni A, Sette M. The Solution Structure of the Monomeric Copper, Zinc Superoxide Dismutase from Salmonella enterica: Structural Insights To Understand the Evolution toward the Dimeric Structure. Biochemistry 2008; 47:12954-63. [DOI: 10.1021/bi801252e] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mirko Mori
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino (FI), Italy, Department of Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy, National Institute of Biostructures and Biosystems (INBB), Viale delle Medaglie d’Oro 305, 00136 Rome, Italy, and Department of Chemical Science and Technology, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Beatriz Jiménez
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino (FI), Italy, Department of Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy, National Institute of Biostructures and Biosystems (INBB), Viale delle Medaglie d’Oro 305, 00136 Rome, Italy, and Department of Chemical Science and Technology, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Mario Piccioli
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino (FI), Italy, Department of Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy, National Institute of Biostructures and Biosystems (INBB), Viale delle Medaglie d’Oro 305, 00136 Rome, Italy, and Department of Chemical Science and Technology, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Andrea Battistoni
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino (FI), Italy, Department of Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy, National Institute of Biostructures and Biosystems (INBB), Viale delle Medaglie d’Oro 305, 00136 Rome, Italy, and Department of Chemical Science and Technology, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Marco Sette
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino (FI), Italy, Department of Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy, National Institute of Biostructures and Biosystems (INBB), Viale delle Medaglie d’Oro 305, 00136 Rome, Italy, and Department of Chemical Science and Technology, University of Rome “Tor Vergata”, 00133 Rome, Italy
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Bertini I, Jiménez B, Pierattelli R, Wedd AG, Xiao Z. Protonless 13C direct detection NMR: characterization of the 37 kDa trimeric protein CutA1. Proteins 2008; 70:1196-205. [PMID: 17847095 DOI: 10.1002/prot.21577] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The major limitation of nuclear magnetic resonance spectroscopy arises from the increase of nuclear transverse relaxation rates with increasing molecular mass. This causes reduction in spectral resolution and coherence transfer efficiency. The use of 2H-labeling to eliminate 1H-mediated relaxation pathways and the constructive use of cross correlation effects (TROSY, CRINEPT) alleviate the phenomenon. An alternative approach is to use direct detection of heteronuclei. Specifically designed 13C direct detection experiments can complement the set of 1H-based NMR experiments commonly used for structure determination providing an additional source of information less affected by the detrimental transverse relaxation effect. We applied this novel methodology to the study of the CutA1 protein (12.3 kDa) from E. coli that forms a homotrimer in solution with a total molecular mass of 37 kDa. In this work we demonstrate that the information available from 13C direct detection experiments makes it possible to completely assign the NMR resonances of the backbone of this 37 kDa trimeric protein without the need of deuteration. The structural and dynamical knowledge obtained for this system may contribute to understand its biological role.
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Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center, University of Florence, Sesto Fiorentino, Italy.
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Caillet-Saguy C, Turano P, Piccioli M, Lukat-Rodgers GS, Czjzek M, Guigliarelli B, Izadi-Pruneyre N, Rodgers KR, Delepierre M, Lecroisey A. Deciphering the Structural Role of Histidine 83 for Heme Binding in Hemophore HasA. J Biol Chem 2008; 283:5960-70. [DOI: 10.1074/jbc.m703795200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Farès C, Amata I, Carlomagno T. 13C-detection in RNA bases: revealing structure-chemical shift relationships. J Am Chem Soc 2007; 129:15814-23. [PMID: 18052161 DOI: 10.1021/ja0727417] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The chemical shifts of the unprotonated carbons in the proton-deficient nucleobases of RNA are rarely reported, despite the valuable information that they contain about base-pairing and base-stacking. We have developed 13C-detected 2D-experiments to identify the unprotonated 13C in the RNA bases and have assigned all the base nuclei of uniformly 13C,15N-labeled HIV-2 TAR-RNA. The 13C chemical shift distributions revealed perturbations correlated with the base-pairing and base-stacking properties of all four base-types. From this work, we conclude that the information contained in the chemical shift perturbations within the base rings can provide valuable restraint information for solving RNA structures, especially in conformational averaged regions, where NOE-based information is not available.
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Affiliation(s)
- Christophe Farès
- Max-Planck-Institute for Biophysical Chemistry, Department of NMR-based Structural Biology, Am Fassberg 11, D-37077 Göttingen, Germany
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Jiménez B, Mori M, Battistoni A, Sette M, Piccioli M. NMR assignment of reduced form of copper, zinc superoxide dismutase from Salmonella enterica. BIOMOLECULAR NMR ASSIGNMENTS 2007; 1:65-67. [PMID: 19636828 DOI: 10.1007/s12104-007-9017-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Accepted: 04/06/2007] [Indexed: 05/28/2023]
Abstract
Almost complete assignment (97%) of NMR resonances was obtained for the reduced, Cu(I), form of prokaryotic CuZnSOD from Salmonella enterica. 13C direct detection was used to complement the standard bouquet of 1H detected triple resonance experiments and contributed to the identification of proline backbone resonances and to side chains assignments of Asx, Glx and aromatic rings. This is the only complete assignment available for monomer SOD from prokaryotic organisms.
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Affiliation(s)
- Beatriz Jiménez
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, Via L Sacconi 6, Sesto Fiorentino, Florence 50019, Italy
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Balayssac S, Jiménez B, Piccioli M. 13C direct detected COCO-TOCSY: a tool for sequence specific assignment and structure determination in protonless NMR experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2006; 182:325-9. [PMID: 16844393 DOI: 10.1016/j.jmr.2006.06.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2006] [Revised: 06/07/2006] [Accepted: 06/13/2006] [Indexed: 05/10/2023]
Abstract
A novel experiment is proposed to provide inter-residue sequential correlations among carbonyl spins in (13)C detected, protonless NMR experiments. The COCO-TOCSY experiment connects, in proteins, two carbonyls separated from each other by three, four or even five bonds. The quantitative analysis provides structural information on backbone dihedral angles phi as well as on the side chain dihedral angles of Asx and Glx residues. This is the first dihedral angle constraint that can be obtained via a protonless approach. About 75% of backbone carbonyls in Calbindin D(9K), a 75 amino acid dicalcium protein, could be sequentially connected via a COCO-TOCSY spectrum. 49(3)J(C')(C') values were measured and related to backbone phi angles. Structural information can be extended to the side chain orientation of aminoacids containing carbonyl groups. Additionally, long range homonuclear coupling constants, (4)J(CC) and (5)J(CC), could be measured. This constitutes an unprecedented case for proteins of medium and small size.
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Affiliation(s)
- Stéphane Balayssac
- Magnetic Resonance Center (CERM), Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
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