1
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Trindade IB, Coelho A, Cantini F, Piccioli M, Louro RO. NMR of paramagnetic metalloproteins in solution: Ubi venire, quo vadis? J Inorg Biochem 2022; 234:111871. [DOI: 10.1016/j.jinorgbio.2022.111871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/16/2022] [Accepted: 05/19/2022] [Indexed: 10/18/2022]
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2
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Rossbach LM, Brede DA, Nuyts G, Cagno S, Olsson RMS, Oughton DH, Falkenberg G, Janssens K, Lind OC. Synchrotron XRF Analysis Identifies Cerium Accumulation Colocalized with Pharyngeal Deformities in CeO 2 NP-Exposed Caenorhabditis elegans. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:5081-5089. [PMID: 35378039 PMCID: PMC9022427 DOI: 10.1021/acs.est.1c08509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
A combination of synchrotron radiation-based elemental imaging, in vivo redox status analysis, histology, and toxic responses was used to investigate the uptake, biodistribution, and adverse effects of Ce nanoparticles (CeO2 NP; 10 nm; 0.5-34.96 mg Ce L-1) or Ce(NO3)3 (2.3-26 mg Ce L-1) in Caenorhabditis elegans. Elemental mapping of the exposed nematodes revealed Ce uptake in the alimentary canal prior to depuration. Retention of CeO2 NPs was low compared to that of Ce(NO3)3 in depurated individuals. X-ray fluorescence (XRF) mapping showed that Ce translocation was confined to the pharyngeal valve and foregut. Ce(NO3)3 exposure significantly decreased growth, fertility, and reproduction, caused slightly reduced fecundity. XRF mapping and histological analysis revealed severe tissue deformities colocalized with retained Ce surrounding the pharyngeal valve. Both forms of Ce activated the sod-1 antioxidant defense, particularly in the pharynx, whereas no significant effects on the cellular redox balance were identified. The CeO2 NP-induced deformities did not appear to impair the pharyngeal function or feeding ability as growth effects were restricted to Ce(NO3)3 exposure. The results demonstrate the utility of integrated submicron-resolution SR-based XRF elemental mapping of tissue-specific distribution and adverse effect analysis to obtain robust toxicological evaluations of metal-containing contaminants.
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Affiliation(s)
- Lisa Magdalena Rossbach
- Faculty
of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, P.O. BOX 5003 NMBU, No-1432 Ås, Norway
- Centre
for Environmental Radioactivity (CERAD CoE), Faculty of Environmental
Sciences and Natural Resource Management, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432 Ås, Norway
| | - Dag Anders Brede
- Faculty
of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, P.O. BOX 5003 NMBU, No-1432 Ås, Norway
- Centre
for Environmental Radioactivity (CERAD CoE), Faculty of Environmental
Sciences and Natural Resource Management, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432 Ås, Norway
| | - Gert Nuyts
- Faculty
of Science, AXIS Research group, University
of Antwerp, Groenenborgerlaan
171, 2020 Antwerp, Belgium
| | - Simone Cagno
- Faculty
of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, P.O. BOX 5003 NMBU, No-1432 Ås, Norway
- Centre
for Environmental Radioactivity (CERAD CoE), Faculty of Environmental
Sciences and Natural Resource Management, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432 Ås, Norway
| | - Ragni Maria Skjervold Olsson
- Faculty
of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, P.O. BOX 5003 NMBU, No-1432 Ås, Norway
- Faculty
of Natural Sciences, Norwegian University
of Science and Technology, P.O. Box 8900, No-7491 Trondheim, Torgarden, Norway
| | - Deborah Helen Oughton
- Faculty
of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, P.O. BOX 5003 NMBU, No-1432 Ås, Norway
- Centre
for Environmental Radioactivity (CERAD CoE), Faculty of Environmental
Sciences and Natural Resource Management, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432 Ås, Norway
| | - Gerald Falkenberg
- Photon
Science, Deutsches Elektronen-Synchrotron
DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Koen Janssens
- Faculty
of Science, AXIS Research group, University
of Antwerp, Groenenborgerlaan
171, 2020 Antwerp, Belgium
| | - Ole Christian Lind
- Faculty
of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, P.O. BOX 5003 NMBU, No-1432 Ås, Norway
- Centre
for Environmental Radioactivity (CERAD CoE), Faculty of Environmental
Sciences and Natural Resource Management, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432 Ås, Norway
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Abstract
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Thanks to recent
improvements in NMR spectrometer hardware and
pulse sequence design, modern 13C NMR has become a useful
tool for biomolecular applications. The complete assignment of a protein
can be accomplished by using 13C detected multinuclear
experiments and it can provide unique information relevant for the
study of a variety of different biomolecules including paramagnetic
proteins and intrinsically disordered proteins. A wide range of NMR
observables can be measured, concurring to the structural and dynamic
characterization of a protein in isolation, as part of a larger complex,
or even inside a living cell. We present the different properties
of 13C with respect to 1H, which provide the
rationale for the experiments developed and their application, the
technical aspects that need to be faced, and the many experimental
variants designed to address different cases. Application areas where
these experiments successfully complement proton NMR are also described.
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Affiliation(s)
- Isabella C Felli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy
| | - Roberta Pierattelli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy
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4
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Müntener T, Joss D, Häussinger D, Hiller S. Pseudocontact Shifts in Biomolecular NMR Spectroscopy. Chem Rev 2022; 122:9422-9467. [PMID: 35005884 DOI: 10.1021/acs.chemrev.1c00796] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Paramagnetic centers in biomolecules, such as specific metal ions that are bound to a protein, affect the nuclei in their surrounding in various ways. One of these effects is the pseudocontact shift (PCS), which leads to strong chemical shift perturbations of nuclear spins, with a remarkably long range of 50 Å and beyond. The PCS in solution NMR is an effect originating from the anisotropic part of the dipole-dipole interaction between the magnetic momentum of unpaired electrons and nuclear spins. The PCS contains spatial information that can be exploited in multiple ways to characterize structure, function, and dynamics of biomacromolecules. It can be used to refine structures, magnify effects of dynamics, help resonance assignments, allows for an intermolecular positioning system, and gives structural information in sensitivity-limited situations where all other methods fail. Here, we review applications of the PCS in biomolecular solution NMR spectroscopy, starting from early works on natural metalloproteins, following the development of non-natural tags to chelate and attach lanthanoid ions to any biomolecular target to advanced applications on large biomolecular complexes and inside living cells. We thus hope to not only highlight past applications but also shed light on the tremendous potential the PCS has in structural biology.
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Affiliation(s)
- Thomas Müntener
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Daniel Joss
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Daniel Häussinger
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
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5
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Abstract
The variety of magnetic properties exhibited by paramagnetic lanthanoids provides outstanding information in NMR-based structural biology and therefore can be a very useful tool for characterizing lanthanoid-binding proteins. Because of their dependence on the relative positions of the protein nuclei and of the lanthanoid ion, the paramagnetic restraints (PCS, PRDC and PRE) provide information on structure and dynamics of proteins. In this Chapter, we cover the use of lanthanoids in structural biology including protein sample preparation, NMR experiments and data interpretation.
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6
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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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7
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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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8
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Rizzo G, Lo Presti M, Giannini C, Sibillano T, Milella A, Matzeu G, Musio R, Omenetto FG, Farinola GM. Silk Fibroin Processing from CeCl
3
Aqueous Solution: Fibers Regeneration and Doping with Ce(III). MACROMOL CHEM PHYS 2020. [DOI: 10.1002/macp.202000066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Giorgio Rizzo
- Dipartimento di ChimicaUniversità degli Studi di Bari “Aldo Moro” via Orabona 4 Bari 70126 Italy
| | - Marco Lo Presti
- Dipartimento di ChimicaUniversità degli Studi di Bari “Aldo Moro” via Orabona 4 Bari 70126 Italy
| | - Cinzia Giannini
- CNR IC–Institute of Crystallography via Amendola 122/O Bari 70126 Italy
| | - Teresa Sibillano
- CNR IC–Institute of Crystallography via Amendola 122/O Bari 70126 Italy
| | - Antonella Milella
- Dipartimento di ChimicaUniversità degli Studi di Bari “Aldo Moro” via Orabona 4 Bari 70126 Italy
| | - Giusy Matzeu
- Silklab, Department of Biomedical EngineeringTufts University 4 Colby Street Medford MA 02155 USA
| | - Roberta Musio
- Dipartimento di ChimicaUniversità degli Studi di Bari “Aldo Moro” via Orabona 4 Bari 70126 Italy
| | - Fiorenzo G. Omenetto
- Silklab, Department of Biomedical EngineeringTufts University 4 Colby Street Medford MA 02155 USA
| | - Gianluca M. Farinola
- Dipartimento di ChimicaUniversità degli Studi di Bari “Aldo Moro” via Orabona 4 Bari 70126 Italy
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9
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Wang Y, Lai CK, Lau JKC, Hopkinson AC, Siu KWM. Structures and Dissociation Products of Ce/Peptide Complexes: Competition between Coordination and Charge Delocalization. J Phys Chem B 2019; 123:5229-5237. [PMID: 31242740 DOI: 10.1021/acs.jpcb.9b03098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structures of [Ce(GGG)]3+ and [Ce(GGG ? H)]2+ have been investigated by DFT calculations. The two lowest-energy structures of the triply charged metal complex have the peptide in either the iminol or conventional zwitterionic form, and these ions have almost identical energies. In the doubly charged complex, the iminol and charge-solvated structures are the best structures on the potential energy surface, but the latter is favored. In both iminol structures, the metal ion coordinates to the iminol oxygen rather than to the nitrogen, unlike in previously reported iminol-containing complexes. Triply charged [Ce(peptide)]3+ complexes are fragile and not easily isolated in a mass spectrometer, whereas the doubly charged [Ce(peptide ? H)]2+ complexes are more robust. Here, we studied the fragmentations of 37 [Ce(peptide ? H)]2+ and 30 [Ce(peptide)(peptide ? H)]2+ complexes and the results are systematically summarized. Losses of CO and/or H2O are the most commonly observed fragmentation channels for [Ce(peptide ? H)]2+ complexes and these dissociation pathways are modeled by DFT calculations. For [Ce(peptide)(peptide ? H)]2+ complexes the neutral peptide plays the role of a solvent molecule but, unlike in the dissociations of [Ce(CH3CN)(peptide ? H)]2+ complexes, the loss of the solvent molecule is not observed. Instead, fragmentation occurs by cleavage of the second amide bond of the solvating peptide molecule.
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Affiliation(s)
- Yating Wang
- Department of Chemistry and Centre for Research in Mass Spectrometry , York University , 4700 Keele Street , Toronto , Ontario M3J 1P3 , Canada
| | - Cheuk-Kuen Lai
- Department of Chemistry and Centre for Research in Mass Spectrometry , York University , 4700 Keele Street , Toronto , Ontario M3J 1P3 , Canada
| | - Justin Kai-Chi Lau
- Department of Chemistry and Centre for Research in Mass Spectrometry , York University , 4700 Keele Street , Toronto , Ontario M3J 1P3 , Canada.,Department of Chemistry and Biochemistry , University of Windsor , 401 Sunset Avenue , Windsor , Ontario N9B 3P4 , Canada
| | - Alan C Hopkinson
- Department of Chemistry and Centre for Research in Mass Spectrometry , York University , 4700 Keele Street , Toronto , Ontario M3J 1P3 , Canada
| | - K W Michael Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry , York University , 4700 Keele Street , Toronto , Ontario M3J 1P3 , Canada.,Department of Chemistry and Biochemistry , University of Windsor , 401 Sunset Avenue , Windsor , Ontario N9B 3P4 , Canada
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10
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Kosak Née Röhder LA, Brandt T, Sigg L, Behra R. Uptake and effects of cerium(III) and cerium oxide nanoparticles to Chlamydomonas reinhardtii. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 197:41-46. [PMID: 29433081 DOI: 10.1016/j.aquatox.2018.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/31/2018] [Accepted: 02/06/2018] [Indexed: 06/08/2023]
Abstract
Cerium (Ce) and cerium oxide nanoparticles (CeO2 NP) are increasingly used in different applications. Upon their release into the aquatic environment, the exposure of aquatic organisms becomes likely. In this study, the uptake of CeO2 NP and Ce3+ into the wild type and cell wall free mutant of Chlamydomonas reinhardtii was examined upon short term exposure. Separation of CeO2 NP and Ce3+ not taken up or loosely bound to the cells was performed by washing algae with EDTA. Despite a concentration and time dependent increase of cellular Ce upon exposure to CeO2 NP with the maximal calculated Ce concentration corresponding to 1.1 CeO2 NP per cell, an internalization of CeO2 NP with a mean size of 140 nm in C. reinhardtii was excluded. In contrast, dissolved Ce3+ (1 and 10 μM) was taken up both in the wild type and cell wall free mutant of C. reinhardtii, with a linear increase of cellular Ce within 1-2 h and maximal cellular Ce of 6.04 × 10-4 mol Lcell-1 (wild type) and 9.0 × 10-5 mol Lcell-1 (cell wall free mutant). Based on competition with Ca2+ for Ce3+ uptake, on the comparison of the wild type and the cell wall free mutant and on inhibition of photosynthetic yield, we suggest that no efficient uptake routes for Ce3+ are available in C. reinhardtii and that a fraction of the cellular Ce in the wild type strongly sorbs to the algal cell wall.
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Affiliation(s)
- Lena A Kosak Née Röhder
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Environmental Toxicology, Dübendorf, 8600, Switzerland; ETH-Zurich, Institute of Biogeochemistry and Pollutant Dynamics, Zürich, 8092, Switzerland
| | - Tanja Brandt
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Environmental Toxicology, Dübendorf, 8600, Switzerland
| | - Laura Sigg
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Environmental Toxicology, Dübendorf, 8600, Switzerland; ETH-Zurich, Institute of Biogeochemistry and Pollutant Dynamics, Zürich, 8092, Switzerland
| | - Renata Behra
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Environmental Toxicology, Dübendorf, 8600, Switzerland.
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11
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Modification of Nonionic Vesicles by Adding Decanol and Functional Lanthanide Ions. J SURFACTANTS DETERG 2016. [DOI: 10.1007/s11743-016-1911-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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12
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Razzaghi S, Brooks EK, Bordignon E, Hubbell WL, Yulikov M, Jeschke G. EPR relaxation-enhancement-based distance measurements on orthogonally spin-labeled T4-lysozyme. Chembiochem 2013; 14:1883-90. [PMID: 23775845 PMCID: PMC3804414 DOI: 10.1002/cbic.201300165] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Indexed: 12/20/2022]
Abstract
Lanthanide-induced enhancement of the longitudinal relaxation of nitroxide radicals in combination with orthogonal site-directed spin labeling is presented as a systematic distance measurement method intended for studies of bio-macromolecules and bio-macromolecular complexes. The approach is tested on a water-soluble protein (T4-lysozyme) for two different commercially available lanthanide labels, and complemented by previously reported data on a membrane-inserted polypeptide. Single temperature measurements are shown to be sufficient for reliable distance determination, with an upper measurable distance limit of about 5-6 nm. The extracted averaged distances represent the closest approach in Ln(III) -nitroxide distance distributions. Studies of conformational changes and of bio-macromolecule association-dissociation are proposed as possible application area of the relaxation-enhancement-based distance measurements.
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Affiliation(s)
| | - Evan K. Brooks
- Jules Stein Eye Institute and the Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | | | - Wayne L. Hubbell
- Jules Stein Eye Institute and the Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich, Switzerland
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13
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Karimi Feiz Abadi H, Yusof R, Maryam Eshrati S, Naghib SD, Rahmani M, Ghadiri M, Akbari E, Ahmadi MT. Current–voltage modeling of graphene-based DNA sensor. Neural Comput Appl 2013. [DOI: 10.1007/s00521-013-1464-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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14
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Molecular view of an electron transfer process essential for iron-sulfur protein biogenesis. Proc Natl Acad Sci U S A 2013; 110:7136-41. [PMID: 23596212 DOI: 10.1073/pnas.1302378110] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Biogenesis of iron-sulfur cluster proteins is a highly regulated process that requires complex protein machineries. In the cytosolic iron-sulfur protein assembly machinery, two human key proteins--NADPH-dependent diflavin oxidoreductase 1 (Ndor1) and anamorsin--form a stable complex in vivo that was proposed to provide electrons for assembling cytosolic iron-sulfur cluster proteins. The Ndor1-anamorsin interaction was also suggested to be implicated in the regulation of cell survival/death mechanisms. In the present work we unravel the molecular basis of recognition between Ndor1 and anamorsin and of the electron transfer process. This is based on the structural characterization of the two partner proteins, the investigation of the electron transfer process, and the identification of those protein regions involved in complex formation and those involved in electron transfer. We found that an unstructured region of anamorsin is essential for the formation of a specific and stable protein complex with Ndor1, whereas the C-terminal region of anamorsin, containing the [2Fe-2S] redox center, transiently interacts through complementary charged residues with the FMN-binding site region of Ndor1 to perform electron transfer. Our results propose a molecular model of the electron transfer process that is crucial for understanding the functional role of this interaction in human cells.
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15
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Triple Click to Tripodal Triazole-Based Ligands - Synthesis and Characterization of Blue-Emitting Ce3+Complexes. Eur J Inorg Chem 2013. [DOI: 10.1002/ejic.201201361] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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16
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Iwaya N, Takasu H, Goda N, Shirakawa M, Tanaka T, Hamada D, Hiroaki H. MIT domain of Vps4 is a Ca2+-dependent phosphoinositide-binding domain. J Biochem 2013; 153:473-81. [PMID: 23423459 DOI: 10.1093/jb/mvt012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The microtubule interacting and trafficking (MIT) domain is a small protein module that is conserved in proteins of diverged function, such as Vps4, spastin and sorting nexin 15 (SNX15). The molecular function of the MIT domain is protein-protein interaction, in which the domain recognizes peptides containing MIT-interacting motifs. Recently, we identified an evolutionarily related domain, 'variant' MIT domain at the N-terminal region of the microtubule severing enzyme katanin p60. We found that the domain was responsible for binding to microtubules and Ca(2+). Here, we have examined whether the authentic MIT domains also bind Ca(2+). We found that the loop between the first and second α-helices of the MIT domain binds a Ca(2+) ion. Furthermore, the MIT domains derived from Vps4b and SNX15a showed phosphoinositide-binding activities in a Ca(2+)-dependent manner. We propose that the MIT domain is a novel membrane-associating domain involved in endosomal trafficking.
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Affiliation(s)
- Naoko Iwaya
- Laboratory of Structural and Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
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17
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Iwaya N, Akiyama K, Goda N, Tenno T, Fujiwara Y, Hamada D, Ikura T, Shirakawa M, Hiroaki H. Effect of Ca2+ on the microtubule-severing enzyme p60-katanin. Insight into the substrate-dependent activation mechanism. FEBS J 2012; 279:1339-52. [PMID: 22325007 DOI: 10.1111/j.1742-4658.2012.08528.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Katanin p60 (p60-katanin) is a microtubule (MT)-severing enzyme and its activity is regulated by the p80 subunit (adaptor-p80). p60-katanin consists of an N-terminal domain, followed by a single ATPase associated with various cellular activities (AAA) domain. We have previously shown that the N-terminal domain serves as the binding site for MT, the substrate of p60-katanin. In this study, we show that the same domain shares another interface with the C-terminal domain of adaptor-p80. We further show that Ca(2+) ions inhibit the MT-severing activity of p60-katanin, whereas the MT-binding activity is preserved in the presence of Ca(2+). In detail, the basal ATPase activity of p60-katanin is stimulated twofold by both MTs and the C-terminal domain of adaptor-p80, whereas Ca(2+) reduces elevated ATPase activity to the basal level. We identify the Ca(2+) -binding site at the end of helix 2 of the N-terminal domain, which is different from the MT-binding interface. On the basis of these observations, we propose a speculative model in which spatial rearrangement of the N-terminal domain relative to the C-terminal AAA domain may be important for productive ATP hydrolysis towards MT-severing. Our model can explain how Ca(2+) regulates both severing and ATP hydrolysis activity, because the Ca(2+) -binding site on the N-terminal domain moves close to the AAA domain during MT severing.
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Affiliation(s)
- Naoko Iwaya
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
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18
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Wang X, Zhao K, Kirberger M, Wong H, Chen G, Yang JJ. Analysis and prediction of calcium-binding pockets from apo-protein structures exhibiting calcium-induced localized conformational changes. Protein Sci 2010; 19:1180-90. [PMID: 20512971 DOI: 10.1002/pro.394] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Calcium binding in proteins exhibits a wide range of polygonal geometries that relate directly to an equally diverse set of biological functions. The binding process stabilizes protein structures and typically results in local conformational change and/or global restructuring of the backbone. Previously, we established the MUG program, which utilized multiple geometries in the Ca(2+)-binding pockets of holoproteins to identify such pockets, ignoring possible Ca(2+)-induced conformational change. In this article, we first report our progress in the analysis of Ca(2+)-induced conformational changes followed by improved prediction of Ca(2+)-binding sites in the large group of Ca(2+)-binding proteins that exhibit only localized conformational changes. The MUG(SR) algorithm was devised to incorporate side chain torsional rotation as a predictor. The output from MUG(SR) presents groups of residues where each group, typically containing two to five residues, is a potential binding pocket. MUG(SR) was applied to both X-ray apo structures and NMR holo structures, which did not use calcium distance constraints in structure calculations. Predicted pockets were validated by comparison with homologous holo structures. Defining a "correct hit" as a group of residues containing at least two true ligand residues, the sensitivity was at least 90%; whereas for a "correct hit" defined as a group of residues containing at least three true ligand residues, the sensitivity was at least 78%. These data suggest that Ca(2+)-binding pockets are at least partially prepositioned to chelate the ion in the apo form of the protein.
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Affiliation(s)
- Xue Wang
- Department of Computer Science, Georgia State University, Atlanta, Georgia 30303, USA
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19
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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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Bermel W, Bertini I, Felli IC, Peruzzini R, Pierattelli R. Exclusively Heteronuclear NMR Experiments to Obtain Structural and Dynamic Information on Proteins. Chemphyschem 2010; 11:689-95. [DOI: 10.1002/cphc.200900772] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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21
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Prell JS, Flick TG, Oomens J, Berden G, Williams ER. Coordination of Trivalent Metal Cations to Peptides: Results from IRMPD Spectroscopy and Theory. J Phys Chem A 2009; 114:854-60. [DOI: 10.1021/jp909366a] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- James S. Prell
- Department of Chemistry, University of California, Berkeley, California 94720-1460, FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Tawnya G. Flick
- Department of Chemistry, University of California, Berkeley, California 94720-1460, FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Jos Oomens
- Department of Chemistry, University of California, Berkeley, California 94720-1460, FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Giel Berden
- Department of Chemistry, University of California, Berkeley, California 94720-1460, FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, FOM Institute for Plasma Physics “Rijnhuizen,” Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands
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22
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Felli IC, Pierattelli R, Glaser SJ, Luy B. Relaxation-optimised Hartmann-Hahn transfer using a specifically Tailored MOCCA-XY16 mixing sequence for carbonyl-carbonyl correlation spectroscopy in 13C direct detection NMR experiments. JOURNAL OF BIOMOLECULAR NMR 2009; 43:187-96. [PMID: 19224374 DOI: 10.1007/s10858-009-9302-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Accepted: 01/06/2009] [Indexed: 05/04/2023]
Abstract
Isotropic mixing sequences are one of the key methods to achieve efficient coherence transfer. Among them, the MOCCA-XY16, which keeps the magnetization longitudinal for a significant amount of time, is characterised by favourable relaxation properties. We show here that its adapted version is particularly suited for carbonyl-carbonyl correlations in (13)C direct detection NMR experiments.
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Affiliation(s)
- Isabella C Felli
- Department of Chemistry and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
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23
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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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24
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Bertini I, Luchinat C, Parigi G, Pierattelli R. Perspectives in paramagnetic NMR of metalloproteins. Dalton Trans 2008:3782-90. [PMID: 18629397 DOI: 10.1039/b719526e] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
NMR experiments and tools for the characterization of the structure and dynamics of paramagnetic proteins are presented here. The focus is on the importance of (13)C direct-detection NMR for the assignment of paramagnetic systems in solution, on the information contained in paramagnetic effects observed both in solution and in the solid state, and on novel paramagnetism-based tools for the investigation of conformational heterogeneity in protein-protein complexes or in multi-domain proteins.
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Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, (FI), Italy.
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25
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Bermel W, Bertini I, Felli IC, Matzapetakis M, Pierattelli R, Theil EC, Turano P. A method for C(alpha) direct-detection in protonless NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 188:301-10. [PMID: 17719814 DOI: 10.1016/j.jmr.2007.07.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Revised: 07/05/2007] [Accepted: 07/18/2007] [Indexed: 05/16/2023]
Abstract
Attempts are made to efficiently decouple (13)C nuclei without significant loss of coherence during the application of the decoupling package. Such attempts are based on the S(3)E spin-state selection method. A newly developed double S(3)E (DS(3)E) is particularly efficient for C(alpha) detection for proteins as large as 480 kDa.
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26
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Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center (CERM) and Department of Chemistry – University of Florence, via L. Sacconi 6, 50019 Sesto Fiorentino, Italy, Fax: +39‐055‐457‐4271
| | - Antonio Rosato
- Magnetic Resonance Center (CERM) and Department of Chemistry – University of Florence, via L. Sacconi 6, 50019 Sesto Fiorentino, Italy, Fax: +39‐055‐457‐4271
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27
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Löhr F, Hänsel R, Rogov VV, Dötsch V. Improved pulse sequences for sequence specific assignment of aromatic proton resonances in proteins. JOURNAL OF BIOMOLECULAR NMR 2007; 37:205-24. [PMID: 17237975 DOI: 10.1007/s10858-006-9128-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2006] [Accepted: 11/23/2006] [Indexed: 05/13/2023]
Abstract
Aromatic proton resonances of proteins are notoriously difficult to assign. Through-bond correlation experiments are preferable over experiments that rely on through-space interactions because they permit aromatic chemical shift assignments to be established independently of the structure determination process. Known experimental schemes involving a magnetization transfer across the Cbeta-Cgamma bond in aromatic side chains either suffer from low efficiency for the relay beyond the Cdelta position, use sophisticated 13C mixing schemes, require probe heads suitable for application of high 13C radio-frequency fields or rely on specialized isotopic labelling patterns. Novel methods are proposed that result in sequential assignment of all aromatic protons in uniformly 13C/15N labelled proteins using standard spectrometer hardware. Pulse sequences consist of routinely used building blocks and are therefore reasonably simple to implement. Ring protons may be correlated with beta-carbons and, alternatively, with amide protons (and nitrogens) or carbonyls in order to take advantage of the superior dispersion of backbone resonances. It is possible to record spectra in a non-selective manner, yielding signals of all aromatic residues, or as amino-acid type selective versions to further reduce ambiguities. The new experiments are demonstrated with four different proteins with molecular weights ranging from 11 kDa to 23 kDa. Their performance is compared with that of (Hbeta)Cbeta(CgammaCdelta)Hdelta and (Hbeta)Cbeta(CgammaCdeltaCepsilon)Hepsilon pulse sequences.
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Affiliation(s)
- Frank Löhr
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Frankfurt, Germany.
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28
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Balayssac S, Bertini I, Luchinat C, Parigi G, Piccioli M. 13C direct detected NMR increases the detectability of residual dipolar couplings. J Am Chem Soc 2007; 128:15042-3. [PMID: 17117827 DOI: 10.1021/ja0645436] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
13C direct detection is becoming an increasingly efficient approach to identify signals of residues that escape detection in 1H detected experiments. Pulse sequences have been developed to obtain 1H partially recoupled experiments for the measurement of the 1JHalphaCalpha and 1JHN couplings with the same resolution available in conventional 1H detected experiments. A consistent set of backbone rdc obtained without any 1H-based experiment has been obtained and shown to be effective for protein solution structure determination.
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Affiliation(s)
- Stéphane Balayssac
- Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
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29
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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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Bermel W, Bertini I, Duma L, Felli IC, Emsley L, Pierattelli R, Vasos PR. Complete assignment of heteronuclear protein resonances by protonless NMR spectroscopy. Angew Chem Int Ed Engl 2006; 44:3089-92. [PMID: 15832397 DOI: 10.1002/anie.200461794] [Citation(s) in RCA: 142] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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31
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Capozzi F, Casadei F, Luchinat C. EF-hand protein dynamics and evolution of calcium signal transduction: an NMR view. J Biol Inorg Chem 2006; 11:949-62. [PMID: 16957918 DOI: 10.1007/s00775-006-0163-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Accepted: 08/09/2006] [Indexed: 10/24/2022]
Abstract
Calcium signaling, one of the most widespread signaling mechanisms in cells, is generally carried out by EF-hand proteins, characterized by a helix-loop-helix motif paired in functional domains. EF-hand proteins may be viewed as molecular switches activated by calcium concentration transients. The EF-hand structural database has grown to a point where meaningful inferences on the functional conformational rearrangements upon calcium binding can be made by comparing a fair number of pairs of end points, i.e., the structures of the apo and calcium-bound forms. More compact descriptors of the movement associated with calcium binding, in terms of principal component analysis of the six interhelical angles, have also become available. Dynamic information obtained by NMR, also with the aid of calcium substitution with paramagnetic lanthanides, is shedding light on the intrinsic amplitude of the conformational degrees of freedom sampled by the various members of the EF-hand superfamily, as well as on the time scales of the motions. Particularly, NMR of lanthanide derivatives helps in capturing long time scale motions. Both static and dynamic pictures reveal a large variety of behaviors. It is increasingly recognized that the EF-hand machinery has differentiated its behavior during evolution in several ways, e.g., by modifying one of the loops, by undergoing a further duplication after the initial motif duplication that originated the functional domain, or by acquiring the ability to dimerize.
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Affiliation(s)
- Francesco Capozzi
- Department of Food Science, University of Bologna, Piazza G. Goidanich 60, 47023, Cesena, Italy
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32
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Arnesano F, Banci L, Bertini I, Capozzi F, Ciofi-Baffoni S, Ciurli S, Luchinat C, Mangani S, Rosato A, Turano P, Viezzoli MS. An Italian contribution to structural genomics: Understanding metalloproteins. Coord Chem Rev 2006. [DOI: 10.1016/j.ccr.2006.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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33
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Caillet-Saguy C, Delepierre M, Lecroisey A, Bertini I, Piccioli M, Turano P. Direct-detected 13C NMR to investigate the iron(III) hemophore HasA. J Am Chem Soc 2006; 128:150-8. [PMID: 16390142 DOI: 10.1021/ja054902h] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hemophore HasA is a 19 kDa iron(III) hemoprotein that participates in the shuttling of heme to a specific membrane receptor. In HasA, heme iron has an original coordination environment with a His/Tyr pair as axial ligands. Recently developed two-dimensional protonless (13)C-detected experiments provide the sequence-specific assignment of all but three protein residues in the close proximity of the paramagnetic center, thus overcoming limitations due to the short relaxation times induced by the presence of the iron(III) center. Mono-dimensional (13)C and (15)N experiments tailored for the detection of paramagnetic signals allow the identification of resonances of the axial ligands. These experiments are used to characterize the conformational features and the electronic structure of the heme iron(III) environment. The good complementarity among (1)H-, (13)C-, and (15)N-detected experiments is highlighted. A thermal high-spin/low-spin equilibrium is observed and is related to a modulation of the strength of the coordination bond between the iron and the Tyr74 axial ligand. The key role of a neighboring residue, His82, for the stability of the axial coordination and its involvement in the heme delivery to the receptor is discussed.
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Affiliation(s)
- Célia Caillet-Saguy
- Unité de RMN des Biomolécules (CNRS URA 2185), Institut Pasteur, 28 rue du Docteur Roux, 75015 Paris cedex 05, France
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34
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Balayssac S, Jiménez B, Piccioli M. Assignment strategy for fast relaxing signals: complete aminoacid identification in thulium substituted calbindin D 9K. JOURNAL OF BIOMOLECULAR NMR 2006; 34:63-73. [PMID: 16518694 DOI: 10.1007/s10858-005-5359-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2005] [Accepted: 11/14/2005] [Indexed: 05/07/2023]
Abstract
Paramagnetic proteins generally contain regions with diverse relaxation properties. Nuclei in regions far from the metal center may behave like those in diamagnetic proteins, but those closer to the metal experience rapid relaxation with accompanying line broadening. We have used a set of NMR experiments optimized to capture data from these various concentric regions in assigning the signals from a paramagnetic Calbindin D 9K derivative in which one of the two calcium ions has been replaced by thulium(III). Normal double- and triple-resonance experiments with 1H detection were used in collecting data from nuclei in the diamagnetic-like region; these approaches identified signals from fewer than 50% of the amino acid residues (those with d > 17.5 A from thulium(III)). Paramagnetism-optimized two-dimensional NMR experiments with 1H detection were used in collecting data from nuclei in the next nearer region (d > 15 A). Standard (d > 14 A) and optimized (d > 9 A) 13C direct-detection experiments were used to capture data from nuclei in the next layer. Finally nuclei closest to the metal were detected by one-dimensional 13C (d > 5 A) and one-dimensional 15N data collection (d > 4.2 A). NMR signals were assigned on the basis of through-bond correlations and, for signals closest to the metal, pseudocontact shifts. The latter were determined from chemical shift differences between assigned signals in thulium(III) and lanthanum(III) derivatives of Calbindin D 9K and they were interpreted on the basis of a structural model for the lanthanide-substituted protein. This approach yielded assignments of at least one resonance per amino acid residue, including those in the thulium(III) coordination sphere.
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Affiliation(s)
- Stéphane Balayssac
- Department of Chemistry, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
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35
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Bermel W, Bertini I, Felli IC, Kümmerle R, Pierattelli R. Novel 13C direct detection experiments, including extension to the third dimension, to perform the complete assignment of proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2006; 178:56-64. [PMID: 16199190 DOI: 10.1016/j.jmr.2005.08.011] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2005] [Revised: 08/22/2005] [Accepted: 08/26/2005] [Indexed: 05/04/2023]
Abstract
Carbon-13 direct detection NMR methods are feasible thanks to the improvements in probehead technology and to the development of new NMR experiments. We present here a complete set of experiments, based on C' direct detection, developed to perform protein complete assignment of backbone and side-chains (except for aromatic rings). This strategy offers alternative solutions for demanding situations (paramagnetic and/or large molecules) and can be useful in general in conjunction with conventional experiments.
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36
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Bertini I, Jiménez B, Piccioli M, Poggi L. Asymmetry in 13C-13C COSY spectra provides information on ligand geometry in paramagnetic proteins. J Am Chem Soc 2005; 127:12216-7. [PMID: 16131187 DOI: 10.1021/ja051058m] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The relative intensity of Calpha-C' cross-peaks in homonuclear 13C COSY spectra depends on the relaxation properties of Calpha and C' spins, which, in the proximity of a paramagnetic center, are related to the metal-to-carbon distance. Their quantitative analysis has lead, for the cerium-substituted dicalcium protein, calbindin D9k, to the straightforward identification of peaks arising from metal-coordinating groups. The monodentate or bidentate metal binding mode of carboxylates was identified directly via NMR.
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Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy.
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37
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Yazyev OV, Helm L, Malkin VG, Malkina OL. Quantum Chemical Investigation of Hyperfine Coupling Constants on First Coordination Sphere Water Molecule of Gadolinium(III) Aqua Complexes. J Phys Chem A 2005; 109:10997-1005. [PMID: 16331943 DOI: 10.1021/jp053825+] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hyperfine interactions (HFI) on the nuclei of the first coordination sphere water molecules in a model [Gd(H(2)O)(8)](3+) aqua complex and in the magnetic resonance imaging contrast agent [Gd(DOTA)(H(2)O)](-) were studied theoretically. Density functional theory (DFT) calculations combined with classical molecular dynamics (MD) simulations have been used in order to take into account dynamic effects in aqueous solution. DFT relativistic calculations show a strong spin-polarization of the first coordination sphere water molecules. This spin-polarization leads to a positive (17)O isotropic hyperfine coupling constant (A(iso)((17)O) = 0.58 +/- 0.11 MHz) and to a significant increase of the effective distance (r(eff)(Gd-O) = 2.72 +/- 0.06 A) of dipolar interaction compared to the mean internuclear distance (r(Gd-O) = 2.56 +/- 0.06 A) obtained from the MD trajectory of [Gd(DOTA)(H(2)O)](-) in aqueous solution. The point-dipole model for anisotropic hyperfine interaction overestimates therefore the longitudinal relaxation rate of the (17)O nucleus by approximately 45%. The (1)H isotropic hyperfine coupling constant of the bound water molecule is predicted to be very small (A(iso)((1)H) = 0.03 +/- 0.02 MHz), and the point-dipole approximation for first coordination sphere water protons holds. The calculated hyperfine parameters are in good agreement with available experimental data.
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Affiliation(s)
- Oleg V Yazyev
- Laboratoire de Chimie Inorganique et Bioinorganique, Ecole Polytechnique Fédérale de Lausanne, EPFL-BCH, CH-1015 Lausanne, Switzerland
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Abstract
This article deals with the solution structure determination of paramagnetic metalloproteins by NMR spectroscopy. These proteins were believed not to be suitable for NMR investigations for structure determination until a decade ago, but eventually novel experiments and software protocols were developed, with the aim of making the approach suitable for the goal and as user-friendly and safe as possible. In the article, we also give hints for the optimization of experiments with respect to each particular metal ion, with the aim of also providing a handy tool for nonspecialists. Finally, a section is dedicated to the significant progress made on 13C direct detection, which reduces the negative effects of paramagnetism and may constitute a new chapter in the whole field of NMR spectroscopy.
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Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy.
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39
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Machonkin TE, Westler WM, Markley JL. Paramagnetic NMR spectroscopy and density functional calculations in the analysis of the geometric and electronic structures of iron-sulfur proteins. Inorg Chem 2005; 44:779-97. [PMID: 15859246 DOI: 10.1021/ic048624j] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Paramagnetic NMR spectroscopy has been underutilized in the study of metalloproteins. One difficulty of the technique is that paramagnetic relaxation broadens signals from nuclei near paramagnetic centers. In systems with low electronic relaxation rates, this makes such signals difficult to observe or impossible to assign by traditional methods. We show how the challenges of detecting and assigning signals from nuclei near the metal center can be overcome through the combination of uniform and selective 2H, 13C, and 15N isotopic labeling with NMR experiments that utilize direct one-dimensional (2H, 13C, and 15N) and two-dimensional (13C-X) detection. We have developed methods for calculating NMR chemical shifts and relaxation rates by density functional theory (DFT) approaches. We use the correspondence between experimental NMR parameters and those calculated from structural models of iron-sulfur clusters derived from X-ray crystallography to validate the computational approach and to investigate how structural differences are manifested in these values. We have applied this strategy to three iron-sulfur proteins: Clostridium pasteurianum rubredoxin, Anabaena [2Fe-2S] ferredoxin, and human [2Fe-2S] ferredoxin. Provided that an accurate structural model of the iron-sulfur cluster and surrounding residues is available from diffraction data, our results show that DFT calculations can return NMR observables with excellent accuracy. This suggests that it might be possible to use calculations to refine structures or to generate structural models of active sites when crystal structures are unavailable. The approach has yielded insights into the electronic structures of these iron-sulfur proteins. In rubredoxin, the results show that substantial unpaired electron spin is delocalized across NH...S hydrogen bonds and that the reduction potential can be changed by 77 mV simply by altering the strength of one of these hydrogen bonds. In reduced [2Fe-2S] ferredoxins, hyperfine shift data have provided quantitative information on the degree of valence trapping. The approach described here for iron-sulfur proteins offers new avenues for detailed studies of these and other metalloprotein systems.
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Affiliation(s)
- Timothy E Machonkin
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642, USA
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Bermel W, Bertini I, Duma L, Felli IC, Emsley L, Pierattelli R, Vasos PR. Complete Assignment of Heteronuclear Protein Resonances by Protonless NMR Spectroscopy. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200461794] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Bertini I, Jiménez B, Piccioli M. 13C direct detected experiments: optimization for paramagnetic signals. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2005; 174:125-132. [PMID: 15809180 DOI: 10.1016/j.jmr.2005.01.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2004] [Revised: 01/12/2005] [Indexed: 05/24/2023]
Abstract
To optimize 13C direct detected experiments for the observation of signals close to a paramagnetic center, we have assessed the sensitivity of different sequences based on CO-Cali coherence transfer. Features of CACO experiments were tested for Calbindin D9k, in which one of the two native Ca2+ ions is replaced by the paramagnetic Ce3+ ion. We have studied the comparison of single vs multiple quantum coherence transfer evolution as well as the influence of in-phase vs anti-phase detection of 13CO signals and finally the comparison of a coherence transfer step based on a CyO in plane with respect to a Cy ali in plane. The acquisition of the anti-phase component of the signal, accomplished by the removal of the last refocusing steps, allowed the identification of some signals unobserved with other pathways. The structural dependency of paramagnetism-induced nuclear relaxation is such that the identification of the most suitable coherence transfer pathway is not known "a priori" but it is driven by the relative proximity of Cali and CO to the paramagnetic center.
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Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy.
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Banci L, Bertini I, Felli IC, Sarrou J. Backbone-only restraints for fast determination of the protein fold: the role of paramagnetism-based restraints. Cytochrome b562 as an example. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2005; 172:191-200. [PMID: 15649745 DOI: 10.1016/j.jmr.2004.07.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2004] [Revised: 07/08/2004] [Indexed: 05/24/2023]
Abstract
CH(alpha) residual dipolar couplings (Deltardc's) were measured for the oxidized cytochrome b562 from Escherichia coli as a result of its partial self-orientation in high magnetic fields due to the anisotropy of the overall magnetic susceptibility tensor. Both the low spin iron (III) heme and the four-helix bundle fold contribute to the magnetic anisotropy tensor. CH(alpha) Deltardc's, which span a larger range than the analogous NH values (already available in the literature) sample large space variations at variance with NH Deltardc's, which are largely isooriented within alpha helices. The whole structure is now significantly refined with the chemical shift index and CH(alpha) Deltardc's. The latter are particularly useful also in defining the molecular magnetic anisotropy parameters. It is shown here that the backbone folding can be conveniently and accurately determined using backbone restraints only, which include NOEs, hydrogen bonds, residual dipolar couplings, pseudocontact shifts, and chemical shift index. All these restraints are easily and quickly determined from the backbone assignment. The calculated backbone structure is comparable to that obtained by using also side chain restraint. Furthermore, the structure obtained with backbone only restraints is, in its whole, very similar to that obtained with the complete set of restraints. The paramagnetism based restraints are shown to be absolutely relevant, especially for Deltardc's.
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Affiliation(s)
- Lucia Banci
- CERM and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
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Pintacuda G, Kaikkonen A, Otting G. Modulation of the distance dependence of paramagnetic relaxation enhancements by CSA x DSA cross-correlation. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2004; 171:233-43. [PMID: 15546749 DOI: 10.1016/j.jmr.2004.08.019] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2004] [Revised: 08/25/2004] [Indexed: 05/22/2023]
Abstract
Paramagnetic metal ions with fast-relaxing electronic spin and anisotropic susceptibility tensor provide a rich source of structural information that can be derived from pseudo-contact shifts, residual dipolar couplings, dipole-dipole Curie spin cross-correlation, and paramagnetic relaxation enhancements. The present study draws attention to a cross-correlation effect between nuclear relaxation due to anisotropic chemical shielding (CSA) and due to the anisotropic dipolar shielding (DSA) caused by the electronic Curie spin. This CSA x DSA cross-correlation contribution seems to have been overlooked in previous interpretations of paramagnetic relaxation enhancements. It is shown to be sufficiently large to compromise the 1/r6 distance dependence usually assumed. The effect cannot experimentally be separated from auto-correlated DSA relaxation. It can increase or decrease the observed paramagnetic relaxation enhancement. Under certain conditions, the effect can dominate the entire paramagnetic relaxation, resulting in nuclear resonances narrower than in the absence of the paramagnetic center. CSAxDSA cross-correlation becomes important when paramagnetic relaxation is predominantly due to the Curie rather than the Solomon mechanism. Therefore the effect is most pronounced for relaxation by metal ions with large magnetic susceptibility and fast-relaxing electron spin. It most strongly affects paramagnetic enhancements of transverse relaxation in macromolecules and of longitudinal relaxation in small molecules.
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Affiliation(s)
- Guido Pintacuda
- Research School of Chemistry, Australian National University, Canberra, ACT 2605, Australia
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Bertini I, Felli IC, Kümmerle R, Luchinat C, Pierattelli R. (13)C-(13)C NOESY: a constructive use of (13)C-(13)C spin-diffusion. JOURNAL OF BIOMOLECULAR NMR 2004; 30:245-51. [PMID: 15756458 DOI: 10.1007/s10858-005-1679-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2004] [Accepted: 07/14/2004] [Indexed: 05/13/2023]
Abstract
(13)C-(13)C NOESY experiments were performed under long mixing time conditions on reduced human superoxide dismutase (32 kDa, (15)N, (13C) and 70% (2)H labeled). (13)C-(13)C couplings were successfully eliminated through post-processing of in-phase-anti-phase (IPAP) data. It appears that at mixing time tau(m) of 3.0 s the spin diffusion mechanism allows the detection of 96% of the two-bond correlations involving C' and C(beta). The interpretation was confirmed by simulations. This approach broadens the range of applicability of (13)C-(13)C NOESY spectroscopy.
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Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Italy.
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Machonkin TE, Westler WM, Markley JL. Strategy for the study of paramagnetic proteins with slow electronic relaxation rates by nmr spectroscopy: application to oxidized human [2Fe-2S] ferredoxin. J Am Chem Soc 2004; 126:5413-26. [PMID: 15113213 DOI: 10.1021/ja037077i] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
NMR studies of paramagnetic proteins are hampered by the rapid relaxation of nuclei near the paramagnetic center, which prevents the application of conventional methods to investigations of the most interesting regions of such molecules. This problem is particularly acute in systems with slow electronic relaxation rates. We present a strategy that can be used with a protein with slow electronic relaxation to identify and assign resonances from nuclei near the paramagnetic center. Oxidized human [2Fe-2S] ferredoxin (adrenodoxin) was used to test the approach. The strategy involves six steps: (1) NMR signals from (1)H, (13)C, and (15)N nuclei unaffected or minimally affected by paramagnetic effects are assigned by standard multinuclear two- and three-dimensional (2D and 3D) spectroscopic methods with protein samples labeled uniformly with (13)C and (15)N. (2) The very broad, hyperfine-shifted signals from carbons in the residues that ligate the metal center are classified by amino acid and atom type by selective (13)C labeling and one-dimensional (1D) (13)C NMR spectroscopy. (3) Spin systems involving carbons near the paramagnetic center that are broadened but not hyperfine-shifted are elucidated by (13)C[(13)C] constant time correlation spectroscopy (CT-COSY). (4) Signals from amide nitrogens affected by the paramagnetic center are assigned to amino acid type by selective (15)N labeling and 1D (15)N NMR spectroscopy. (5) Sequence-specific assignments of these carbon and nitrogen signals are determined by 1D (13)C[(15)N] difference decoupling experiments. (6) Signals from (1)H nuclei in these spin systems are assigned by paramagnetic-optimized 2D and 3D (1)H[(13)C] experiments. For oxidized human ferredoxin, this strategy led to assignments (to amino acid and atom type) for 88% of the carbons in the [2Fe-2S] cluster-binding loops (residues 43-58 and 89-94). These included complete carbon spin-system assignments for eight of the 22 residues and partial assignments for each of the others. Sequence-specific assignments were determined for the backbone (15)N signals from nine of the 22 residues and ambiguous assignments for five of the others.
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Affiliation(s)
- Timothy E Machonkin
- National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Babini E, Bertini I, Capozzi F, Felli IC, Lelli M, Luchinat C. Direct Carbon Detection in Paramagnetic Metalloproteins To Further Exploit Pseudocontact Shift Restraints. J Am Chem Soc 2004; 126:10496-7. [PMID: 15327280 DOI: 10.1021/ja047573m] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Direct detection heteronuclear NMR allows us to drastically reduce paramagnetic contributions to the line width as compared to 1H detection. As an example, a calcium binding protein (human oncomodulin), in which one of the calcium ions was selectively substituted with Tb3+, is used. Through a variety of 13C direct detection NMR experiments, resonances were detected as close as 5.5 A from the metal ion. Pseudocontact shifts measured through 13C direct detection experiments provide structural constraints in regions of the protein where 1H resonances are broadened beyond detection through Curie relaxation (up to 16 A from the paramagnetic center).
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Affiliation(s)
- Elena Babini
- Food Science Laboratory, University of Bologna, Via Ravennate 1020, 47023 Cesena, Forlì, Italy
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Bermel W, Bertini I, Felli IC, Kümmerle R, Pierattelli R. 13C direct detection experiments on the paramagnetic oxidized monomeric copper, zinc superoxide dismutase. J Am Chem Soc 2004; 125:16423-9. [PMID: 14692785 DOI: 10.1021/ja037676p] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this report, the use of 13C direct detection has been pursued in 2D experiments (13C-13C COSY, 13C-13C COCAMQ, 13C-13C NOESY) to detect broad lines in nuclear magnetic resonance spectra of paramagnetic metalloproteins. The sample is a monomeric oxidized copper, zinc superoxide dismutase. Thanks to direct detection probeheads, cryogenic technology, and implementation of 13C band-selective homodecoupling, many broadened signals were detected. Proton signals for the same residues escaped detection in 1H and 1H-15N HSQC experiments because of the broadening. Only the 13C signals which experience large contact coupling escaped detection, i.e., the 13C nuclei of the metal coordinated histidines. Otherwise, nuclei as close to copper(II) as 4 A can be detected. Paramagnetic-based restraints can in principle be used for solution structure determination of paramagnetic metalloproteins and in copper(II) proteins in particular. The present study is significant also for the study of large diamagnetic proteins for which proton relaxation makes proton-based spectroscopy not adequate.
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Bertini I, Felli IC, Kümmerle R, Moskau D, Pierattelli R. 13C−13C NOESY: An Attractive Alternative for Studying Large Macromolecules. J Am Chem Soc 2003; 126:464-5. [PMID: 14719933 DOI: 10.1021/ja0357036] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
13C direct detection provides a valuable alternative to 1H detection to overcome fast relaxation because of its smaller magnetic moment. 13C-13C NOESY spectra were acquired for a dimeric protein of molecular mass 32 000 and for a monomeric analogue. With increasing molecular mass, the quality of 13C-13C NOESY spectra improves while the scalar-based experiments become less sensitive, as predicted by the increase in the molecular mass. 13C-13C NOESY spectra of the dimer were acquired with different mixing times. The mixing time can be tuned to detect mainly one-bond correlations, or it can be increased to also detect correlations between nuclei at longer distances. It is proposed that 13C-13C dipolar-based experiments provide a promising tool for signal detection and assignment in large macromolecules, such as multimeric species and macromolecular complexes, for which scalar-based experiments become less effective.
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Affiliation(s)
- Ivano Bertini
- CERM and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy.
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Kateb F, Piccioli M. New Routes to the Detection of Relaxation Allowed Coherence Transfer in Paramagnetic Molecules. J Am Chem Soc 2003; 125:14978-9. [PMID: 14653719 DOI: 10.1021/ja038101v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A new pulse sequence is proposed to measure cross correlation rates between 1H Curie spin relaxation and 1H-15N or 1H-13C dipole-dipole coupling (%@mt;sys@%Gamma%@sx@%H,HX%@be@%CS,DD%@sxx@%%@mx@% ) in paramagnetic systems. The new sequence has been conceived to obtain quantitative measurements of cross correlation rates in the close proximity to the paramagnetic center, preventing the loss of information due to fast transverse relaxation. The approach was tested on the dicalcium protein calbindin D9k in which Ca2+ has been substituted at site II with Ce3+. At variance with previously reported experiments, all peaks observed in HSQC experiments tailored to paramagnetic signals give quantitative estimates of %@mt;sys@%Gamma%@sx@%H%@ital@%,%@rsf@%HX%@be@%CS%@ital@%,%@rsf@%DD%@sxx@%%@mx@% . This is crucial to refine the immediate proximity of the metal ion.
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Affiliation(s)
- Fathia Kateb
- Magnetic Resonance Center, University of Florence, Via L. Sacconi 4, 50019 Sesto Fiorentino, Italy
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Arnesano F, Banci L, Bertini I, Felli IC, Luchinat C, Thompsett AR. A strategy for the NMR characterization of type II copper(II) proteins: the case of the copper trafficking protein CopC from Pseudomonas Syringae. J Am Chem Soc 2003; 125:7200-8. [PMID: 12797793 DOI: 10.1021/ja034112c] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
CopC from Pseudomonas syringae was found to be a protein capable of binding both Cu(I) and Cu(II) at two different sites. The solution structure of the apo protein is available, and structural information has been obtained on the Cu(I) bound form. We attempt here to set the limits for the determination of the solution structure of a Cu(II) protein, such as the Cu(II) bound form of CopC, in which the Cu(II) ion takes a type II coordination. The electron relaxation time is estimated from NMRD measurements to be 3 ns which leads to a correlation time for the nuclear spin-electron spin dipolar interaction of 2 ns. This information allowed us to tailor the NMR experiments and to fully exploit purely heteronuclear spectroscopy to assign as many signals as possible. In this way, 37 (13)C and 11 (15)N signals that completely escape detection with conventional approaches were assigned. Paramagnetic based structural constraints were obtained by measuring paramagnetic longitudinal relaxation enhancements (rho(para)) which allowed us to precisely locate the copper ion within the protein frame. Pseudocontact shifts (pcs's) were also used as constraints for 83 (1)H and 18 (13)C nuclei. With them, together with other standard structural constraints, a structure is obtained (and submitted to PDB) where information is only missing in a sphere with a 6 A radius from the copper ion. If we borrow information from EXAFS data, which show evidence of two copper coordinated histidines, then His 1 and His 91 are unambiguously identified as copper ligands. EXAFS data indicate two more light donor atoms (O/N) which could be from Asp 27 and Glu 89, whereas the NMRD data indicate the presence of a semicoordinated water molecule at 2.8 A (Cu-O distance) roughly orthogonal to the plane identified by the other four ligands. This represents the most extensively characterized structure of a type II Cu(II) protein obtained employing the most advanced NMR methods and with the aid of EXAFS data. The knowledge of the location of the Cu(II) in the protein is important for the copper transfer mechanism.
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Affiliation(s)
- Fabio Arnesano
- CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
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