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Querci L, Piccioli M, Ciofi-Baffoni S, Banci L. Structural aspects of iron‑sulfur protein biogenesis: An NMR view. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119786. [PMID: 38901495 DOI: 10.1016/j.bbamcr.2024.119786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/15/2024] [Accepted: 06/10/2024] [Indexed: 06/22/2024]
Abstract
Over the last decade, structural aspects involving iron‑sulfur (Fe/S) protein biogenesis have played an increasingly important role in understanding the high mechanistic complexity of mitochondrial and cytosolic machineries maturing Fe/S proteins. In this respect, solution NMR has had a significant impact because of its ability to monitor transient protein-protein interactions, which are abundant in the networks of pathways leading to Fe/S cluster biosynthesis and transfer, as well as thanks to the developments of paramagnetic NMR in both terms of new methodologies and accurate data interpretation. Here, we review the use of solution NMR in characterizing the structural aspects of human Fe/S proteins and their interactions in the framework of Fe/S protein biogenesis. We will first present a summary of the recent advances that have been achieved by paramagnetic NMR and then we will focus our attention on the role of solution NMR in the field of human Fe/S protein biogenesis.
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Affiliation(s)
- Leonardo Querci
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019 Florence, Italy
| | - Mario Piccioli
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019 Florence, Italy
| | - Simone Ciofi-Baffoni
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019 Florence, Italy.
| | - Lucia Banci
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019 Florence, Italy; Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy.
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2
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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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3
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Pinto SMA, Ferreira ARR, Teixeira DSS, Nunes SCC, Batista de Carvalho ALM, Almeida JMS, Garda Z, Pallier A, Pais AACC, Brett CMA, Tóth É, Marques MPM, Pereira MM, Geraldes CFGC. Fluorinated Mn(III)/(II)-Porphyrin with Redox-Responsive 1 H and 19 F Relaxation Properties. Chemistry 2023; 29:e202301442. [PMID: 37606898 DOI: 10.1002/chem.202301442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Indexed: 08/23/2023]
Abstract
A new fluorinated manganese porphyrin, (Mn-TPP-p-CF3 ) is reported capable of providing, based on the Mn(III)/Mn(II) equilibrium, dual 1 H relaxivity and 19 F NMR response to redox changes. The physical-chemical characterization of both redox states in DMSO-d6 /H2 O evidenced that the 1 H relaxometric and 19 F NMR properties are appropriate for differential redox MRI detection. The Mn(III)-F distance (dMn-F =9.7-10 Å), as assessed by DFT calculations, is well tailored to allow for adequate paramagnetic effect of Mn(III) on 19 F T1 and T2 relaxation times. Mn-TPP-p-CF3 has a reversible Mn(II)/Mn(III) redox potential of 0.574 V vs. NHE in deoxygenated aqueous HEPES/ THF solution. The reduction of Mn(III)-TPP-p-CF3 in the presence of ascorbic acid is slowly, but fully reversed in the presence of air oxygen, as monitored by UV-Vis spectrometry and 19 F NMR. The broad 1 H and 19 F NMR signals of Mn(III)-TPP-p-CF3 disappear in the presence of 1 equivalent ascorbate replaced by a shifted and broadened 19 F NMR signal from Mn(II)-TPP-p-CF3 . Phantom 19 F MR images in DMSO show a MRI signal intensity decrease upon reduction of Mn(III)-TPP-p-CF3 , retrieved upon complete reoxidation in air within ~24 h. 1 H NMRD curves of the Mn(III)/(II)-TPP-p-CF3 chelates in mixed DMSO/water solvent have the typical shape of Mn(II)/Mn(III) porphyrins.
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Affiliation(s)
- Sara M A Pinto
- University of Coimbra, CQC-IMS, Department of Chemistry, P-3004-535, Coimbra, Portugal
- Coimbra Chemistry Center, University of Coimbra, Rua Larga Largo D. Dinis, 3004-535, Coimbra, Portugal
| | - Ana R R Ferreira
- University of Coimbra, CQC-IMS, Department of Chemistry, P-3004-535, Coimbra, Portugal
- Coimbra Chemistry Center, University of Coimbra, Rua Larga Largo D. Dinis, 3004-535, Coimbra, Portugal
| | - Daniela S S Teixeira
- University of Coimbra, CQC-IMS, Department of Chemistry, P-3004-535, Coimbra, Portugal
- Coimbra Chemistry Center, University of Coimbra, Rua Larga Largo D. Dinis, 3004-535, Coimbra, Portugal
| | - Sandra C C Nunes
- University of Coimbra, CQC-IMS, Department of Chemistry, P-3004-535, Coimbra, Portugal
- Coimbra Chemistry Center, University of Coimbra, Rua Larga Largo D. Dinis, 3004-535, Coimbra, Portugal
| | - Ana L M Batista de Carvalho
- Molecular Physical Chemistry R&D Unit Department of Chemistry, University of Coimbra, Rua Larga, 3004-535, Coimbra, Portugal
- Department of Life Sciences, Faculty of Science and Technology, Calçada Martim de Freitas, 3000-393, Coimbra, Portugal
| | - Joseany M S Almeida
- University of Coimbra, CQC-IMS, Department of Chemistry, P-3004-535, Coimbra, Portugal
- CEMMPRE, University of Coimbra, Pinhal de Marrocos, 3030-788, Coimbra, Portugal
| | - Zoltan Garda
- Centre de Biophysique Moléculaire, CNRS, UPR 4301, Université d'Orléans, Rue Charles Sadron, 45071, Orléans Cedex 2, France
| | - Agnés Pallier
- Centre de Biophysique Moléculaire, CNRS, UPR 4301, Université d'Orléans, Rue Charles Sadron, 45071, Orléans Cedex 2, France
| | - Alberto A C C Pais
- University of Coimbra, CQC-IMS, Department of Chemistry, P-3004-535, Coimbra, Portugal
- Coimbra Chemistry Center, University of Coimbra, Rua Larga Largo D. Dinis, 3004-535, Coimbra, Portugal
| | - Christopher M A Brett
- University of Coimbra, CQC-IMS, Department of Chemistry, P-3004-535, Coimbra, Portugal
- CEMMPRE, University of Coimbra, Pinhal de Marrocos, 3030-788, Coimbra, Portugal
| | - Éva Tóth
- Centre de Biophysique Moléculaire, CNRS, UPR 4301, Université d'Orléans, Rue Charles Sadron, 45071, Orléans Cedex 2, France
| | - Maria P M Marques
- Molecular Physical Chemistry R&D Unit Department of Chemistry, University of Coimbra, Rua Larga, 3004-535, Coimbra, Portugal
- Department of Life Sciences, Faculty of Science and Technology, Calçada Martim de Freitas, 3000-393, Coimbra, Portugal
| | - Mariette M Pereira
- University of Coimbra, CQC-IMS, Department of Chemistry, P-3004-535, Coimbra, Portugal
- Coimbra Chemistry Center, University of Coimbra, Rua Larga Largo D. Dinis, 3004-535, Coimbra, Portugal
| | - Carlos F G C Geraldes
- Coimbra Chemistry Center, University of Coimbra, Rua Larga Largo D. Dinis, 3004-535, Coimbra, Portugal
- Department of Life Sciences, Faculty of Science and Technology, Calçada Martim de Freitas, 3000-393, Coimbra, Portugal
- CIBIT/ICNAS, University of Coimbra, Azinhaga de Santa Comba, 3000-548, Coimbra, Portugal
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Camponeschi F, Piccioli M, Banci L. The Intriguing mitoNEET: Functional and Spectroscopic Properties of a Unique [2Fe-2S] Cluster Coordination Geometry. Molecules 2022; 27:8218. [PMID: 36500311 PMCID: PMC9737848 DOI: 10.3390/molecules27238218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/10/2022] [Accepted: 11/19/2022] [Indexed: 11/29/2022] Open
Abstract
Despite the number of cellular and pathological mitoNEET-related processes, very few details are known about the mechanism of action of the protein. The recently discovered existence of a link between NEET proteins and cancer pave the way to consider mitoNEET and its Fe-S clusters as suitable targets to inhibit cancer cell proliferation. Here, we will review the variety of spectroscopic techniques that have been applied to study mitoNEET in an attempt to explain the drastic difference in clusters stability and reactivity observed for the two redox states, and to elucidate the cellular function of the protein. In particular, the extensive NMR assignment and the characterization of first coordination sphere provide a molecular fingerprint helpful to assist the design of drugs able to impair cellular processes or to directly participate in redox reactions or protein-protein recognition mechanisms.
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Affiliation(s)
- Francesca Camponeschi
- Consorzio Internuniversitario Risonanze Magnetiche Metallo Proteine, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Mario Piccioli
- Consorzio Internuniversitario Risonanze Magnetiche Metallo Proteine, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Lucia Banci
- Consorzio Internuniversitario Risonanze Magnetiche Metallo Proteine, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
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5
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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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Werr M, Kaifer E, Enders M, Asyuda A, Zharnikov M, Himmel H. Synthese eines Kupfer(I)‐Komplexes mit zwei ungepaarten Elektronen durch Oxidation eines Kupfer(II)‐Komplexes mit zwei redoxaktiven Liganden. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Marco Werr
- Anorganisch-Chemisches Institut Ruprecht-Karls Universität Heidelberg Im Neuenheimer Feld 270 69120 Heidelberg Deutschland
| | - Elisabeth Kaifer
- Anorganisch-Chemisches Institut Ruprecht-Karls Universität Heidelberg Im Neuenheimer Feld 270 69120 Heidelberg Deutschland
| | - Markus Enders
- Anorganisch-Chemisches Institut Ruprecht-Karls Universität Heidelberg Im Neuenheimer Feld 270 69120 Heidelberg Deutschland
| | - Andika Asyuda
- Angewandte Physikalische Chemie Ruprecht-Karls Universität Heidelberg Im Neuenheimer Feld 253 69120 Heidelberg Deutschland
| | - Michael Zharnikov
- Angewandte Physikalische Chemie Ruprecht-Karls Universität Heidelberg Im Neuenheimer Feld 253 69120 Heidelberg Deutschland
| | - Hans‐Jörg Himmel
- Anorganisch-Chemisches Institut Ruprecht-Karls Universität Heidelberg Im Neuenheimer Feld 270 69120 Heidelberg Deutschland
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Werr M, Kaifer E, Enders M, Asyuda A, Zharnikov M, Himmel H. A Copper(I) Complex with Two Unpaired Electrons, Synthesised by Oxidation of a Copper(II) Complex with Two Redox-Active Ligands. Angew Chem Int Ed Engl 2021; 60:23451-23462. [PMID: 34423532 PMCID: PMC8596453 DOI: 10.1002/anie.202109367] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 07/30/2021] [Indexed: 01/10/2023]
Abstract
Two homoleptic copper(II) complexes [Cu(L1)2 ] and [Cu(L2)2 ] with anionic redox-active ligands were synthesised, one with urea azine (L1) and the other with thio-urea azine (L2) ligands. One-electron oxidation of the complexes initiates an unprecedented redox-induced electron transfer process, leading to monocationic copper(I) complexes [Cu(L1)2 ]+ and [Cu(L2)2 ]+ with two oxidised ligands. While [Cu(L1)2 ]+ is best described as a CuI complex with two neutral radical ligands that couple antiferromagnetically, [Cu(L2)2 ]+ is a CuI complex with two clearly different ligand units in the solid state and with a magnetic susceptibility close to a diamagnetic compound. Further one-electron oxidation of the complex with L1 ligands results in a dication [Cu(L1)2 ]2+ , best described as a CuI complex with a twofold oxidised, monocationic ligand and a neutral radical ligand. The stability in at least three redox states, the accumulation of spin density at the ligands and the facile ligand-metal electron transfer make these complexes highly attractive for a variety of applications; here the catalytic aerobic oxidation of alcohols to aldehydes is tested.
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Affiliation(s)
- Marco Werr
- Anorganisch-Chemisches InstitutRuprecht-Karls Universität HeidelbergIm Neuenheimer Feld 27069120HeidelbergGermany
| | - Elisabeth Kaifer
- Anorganisch-Chemisches InstitutRuprecht-Karls Universität HeidelbergIm Neuenheimer Feld 27069120HeidelbergGermany
| | - Markus Enders
- Anorganisch-Chemisches InstitutRuprecht-Karls Universität HeidelbergIm Neuenheimer Feld 27069120HeidelbergGermany
| | - Andika Asyuda
- Angewandte Physikalische ChemieRuprecht-Karls Universität HeidelbergIm Neuenheimer Feld 25369120HeidelbergGermany
| | - Michael Zharnikov
- Angewandte Physikalische ChemieRuprecht-Karls Universität HeidelbergIm Neuenheimer Feld 25369120HeidelbergGermany
| | - Hans‐Jörg Himmel
- Anorganisch-Chemisches InstitutRuprecht-Karls Universität HeidelbergIm Neuenheimer Feld 27069120HeidelbergGermany
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Saudino G, Suraci D, Nasta V, Ciofi-Baffoni S, Banci L. Molecular Basis of Multiple Mitochondrial Dysfunctions Syndrome 2 Caused by CYS59TYR BOLA3 Mutation. Int J Mol Sci 2021; 22:4848. [PMID: 34063696 PMCID: PMC8125686 DOI: 10.3390/ijms22094848] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 11/16/2022] Open
Abstract
Multiple mitochondrial dysfunctions syndrome (MMDS) is a rare neurodegenerative disorder associated with mutations in genes with a vital role in the biogenesis of mitochondrial [4Fe-4S] proteins. Mutations in one of these genes encoding for BOLA3 protein lead to MMDS type 2 (MMDS2). Recently, a novel phenotype for MMDS2 with complete clinical recovery was observed in a patient containing a novel variant (c.176G > A, p.Cys59Tyr) in compound heterozygosity. In this work, we aimed to rationalize this unique phenotype observed in MMDS2. To do so, we first investigated the structural impact of the Cys59Tyr mutation on BOLA3 by NMR, and then we analyzed how the mutation affects both the formation of a hetero-complex between BOLA3 and its protein partner GLRX5 and the iron-sulfur cluster-binding properties of the hetero-complex by various spectroscopic techniques and by experimentally driven molecular docking. We show that (1) the mutation structurally perturbed the iron-sulfur cluster-binding region of BOLA3, but without abolishing [2Fe-2S]2+ cluster-binding on the hetero-complex; (2) tyrosine 59 did not replace cysteine 59 as iron-sulfur cluster ligand; and (3) the mutation promoted the formation of an aberrant apo C59Y BOLA3-GLRX5 complex. All these aspects allowed us to rationalize the unique phenotype observed in MMDS2 caused by Cys59Tyr mutation.
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Affiliation(s)
- Giovanni Saudino
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy; (G.S.); (D.S.); (V.N.)
| | - Dafne Suraci
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy; (G.S.); (D.S.); (V.N.)
| | - Veronica Nasta
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy; (G.S.); (D.S.); (V.N.)
| | - Simone Ciofi-Baffoni
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy; (G.S.); (D.S.); (V.N.)
- Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Lucia Banci
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy; (G.S.); (D.S.); (V.N.)
- Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), 50019 Sesto Fiorentino, Italy
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Camponeschi F, Gallo A, Piccioli M, Banci L. The long-standing relationship between paramagnetic NMR and iron-sulfur proteins: the mitoNEET example. An old method for new stories or the other way around? MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:203-221. [PMID: 37904758 PMCID: PMC10539769 DOI: 10.5194/mr-2-203-2021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/18/2021] [Indexed: 11/01/2023]
Abstract
Paramagnetic NMR spectroscopy and iron-sulfur (Fe-S) proteins have maintained a synergic relationship for decades. Indeed, the hyperfine shifts with their temperature dependencies and the relaxation rates of nuclei of cluster-bound residues have been extensively used as a fingerprint of the type and of the oxidation state of the Fe-S cluster within the protein frame. The identification of NMR signals from residues surrounding the metal cofactor is crucial for understanding the structure-function relationship in Fe-S proteins, but it is generally impaired in standard NMR experiments by paramagnetic relaxation enhancement due to the presence of the paramagnetic cluster(s). On the other hand, the availability of systems of different sizes and stabilities has, over the years, stimulated NMR spectroscopists to exploit iron-sulfur proteins as paradigmatic cases to develop experiments, models, and protocols. Here, the cluster-binding properties of human mitoNEET have been investigated by 1D and 2D 1 H diamagnetic and paramagnetic NMR, in its oxidized and reduced states. The NMR spectra of both oxidation states of mitoNEET appeared to be significantly different from those reported for previously investigated [ Fe 2 S 2 ] 2 + / + proteins. The protocol we have developed in this work conjugates spectroscopic information arising from "classical" paramagnetic NMR with an extended mapping of the signals of residues around the cluster which can be taken, even before the sequence-specific assignment is accomplished, as a fingerprint of the protein region constituting the functional site of the protein. We show how the combined use of 1D NOE experiments, 13 C direct-detected experiments, and double- and triple-resonance experiments tailored using R1 - and/or R2 -based filters significantly reduces the "blind" sphere of the protein around the paramagnetic cluster. This approach provided a detailed description of the unique electronic properties of mitoNEET, which are responsible for its biological function. Indeed, the NMR properties suggested that the specific electronic structure of the cluster possibly drives the functional properties of different [ Fe 2 S 2 ] proteins.
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Affiliation(s)
- Francesca Camponeschi
- Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine,
Sesto Fiorentino, 50019, Italy
| | - Angelo Gallo
- Department of Pharmacy, University of Patras, Patras, 26504,
Greece
| | - Mario Piccioli
- Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine,
Sesto Fiorentino, 50019, Italy
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, 50019, Italy
| | - Lucia Banci
- Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine,
Sesto Fiorentino, 50019, Italy
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, 50019, Italy
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10
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Dasgupta R, Gupta KBSS, de Groot HJM, Ubbink M. The Resting Oxidized State of Small Laccase Analyzed with Paramagnetic NMR Spectroscopy. Chemphyschem 2021; 22:733-740. [PMID: 33682979 PMCID: PMC8252789 DOI: 10.1002/cphc.202100063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/28/2021] [Indexed: 12/28/2022]
Abstract
The enzyme laccase catalyzes the reduction of dioxygen to water at the trinuclear copper center (TNC). The TNC comprises a type‐3 (T3) and a type‐2 (T2) copper site. The paramagnetic NMR spectrum of the small laccase from Streptomyces coelicolor (SLAC) without the substrate shows a mixture of two catalytic states, the resting oxidized (RO) state and the native intermediate (NI) state. An analysis of the resonances of the RO state is reported. In this state, hydrogen resonances only of the T3 copper ligands can be found, in the region of 12–22 ppm. Signals from all six histidine ligands are found and can be attributed to Hδ1, Hβ or backbone amide HN nuclei. Two sequence‐specific assignments are proposed on the basis of a second‐coordination shell variant that also lacks the copper ion at the T1 site, SLAC−T1D/Q291E. This double mutant is found to be exclusively in the RO state, revealing a subtle balance between the RO and the NI states.
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Affiliation(s)
- Rubin Dasgupta
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratory, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Karthick B S S Gupta
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratory, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Huub J M de Groot
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratory, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Marcellus Ubbink
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratory, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
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11
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Suraci D, Saudino G, Nasta V, Ciofi-Baffoni S, Banci L. ISCA1 Orchestrates ISCA2 and NFU1 in the Maturation of Human Mitochondrial [4Fe-4S] Proteins. J Mol Biol 2021; 433:166924. [PMID: 33711344 DOI: 10.1016/j.jmb.2021.166924] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/12/2021] [Accepted: 03/01/2021] [Indexed: 10/21/2022]
Abstract
The late-acting steps of the pathway responsible for the maturation of mitochondrial [4Fe-4S] proteins are still elusive. Three proteins ISCA1, ISCA2 and NFU1 were shown to be implicated in the assembly of [4Fe-4S] clusters and their transfer into mitochondrial apo proteins. We present here a NMR-based study showing a detailed molecular model of the succession of events performed in a coordinated manner by ISCA1, ISCA2 and NFU1 to make [4Fe-4S] clusters available to mitochondrial apo proteins. We show that ISCA1 is the key player of the [4Fe-4S] protein maturation process because of its ability to interact with both NFU1 and ISCA2, which, instead do not interact each other. ISCA1 works as the promoter of the interaction between ISCA2 and NFU1 being able to determine the formation of a transient ISCA1-ISCA2-NFU1 ternary complex. We also show that ISCA1, thanks to its specific interaction with the C-terminal cluster-binding domain of NFU1, drives [4Fe-4S] cluster transfer from the site where the cluster is assembled on the ISCA1-ISCA2 complex to a cluster binding site formed by ISCA1 and NFU1 in the ternary ISCA1-ISCA2-NFU1 complex. Such mechanism guarantees that the [4Fe-4S] cluster can be safely moved from where it is assembled on the ISCA1-ISCA2 complex to NFU1, thereby resulting the [4Fe-4S] cluster available for the mitochondrial apo proteins specifically requiring NFU1 for their maturation.
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Affiliation(s)
- Dafne Suraci
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Giovanni Saudino
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Veronica Nasta
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Simone Ciofi-Baffoni
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy.
| | - Lucia Banci
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy.
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12
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Dasgupta R, Gupta K, de Groot H, Ubbink M. Towards resolving the complex paramagnetic nuclear magnetic resonance (NMR) spectrum of small laccase: assignments of resonances to residue-specific nuclei. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:15-23. [PMID: 37904765 PMCID: PMC10539750 DOI: 10.5194/mr-2-15-2021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/19/2021] [Indexed: 11/01/2023]
Abstract
Laccases efficiently reduce dioxygen to water in an active site containing a tri-nuclear copper centre (TNC). The dynamics of the protein matrix is a determining factor in the efficiency in catalysis. To probe mobility, nuclear magnetic resonance (NMR) spectroscopy is highly suitable. However, several factors complicate the assignment of resonances to active site nuclei in laccases. The paramagnetic nature causes large shifts and line broadening. Furthermore, the presence of slow chemical exchange processes of the imidazole rings of copper ligand results in peak doubling. A third complicating factor is that the enzyme occurs in two states, the native intermediate (NI) and resting oxidized (RO) states, with different paramagnetic properties. The present study aims at resolving the complex paramagnetic NMR spectra of the TNC of Streptomyces coelicolor small laccase (SLAC). With a combination of paramagnetically tailored NMR experiments, all eight His Nδ 1 and Hδ 1 resonances for the NI state are identified, as well as His Hβ protons for the RO state. With the help of second-shell mutagenesis, selective resonances are tentatively assigned to the histidine ligands of the copper in the type-2 site. This study demonstrates the utility of the approaches used for the sequence-specific assignment of the paramagnetic NMR spectra of ligands in the TNC that ultimately may lead to a description of the underlying motion.
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Affiliation(s)
- Rubin Dasgupta
- Leiden Institute of Chemistry, University of Leiden, Gorlaeus Laboratory, Einsteinweg 55, 2333 CC, Leiden, the Netherlands
| | - Karthick B. S. S. Gupta
- Leiden Institute of Chemistry, University of Leiden, Gorlaeus Laboratory, Einsteinweg 55, 2333 CC, Leiden, the Netherlands
| | - Huub J. M. de Groot
- Leiden Institute of Chemistry, University of Leiden, Gorlaeus Laboratory, Einsteinweg 55, 2333 CC, Leiden, the Netherlands
| | - Marcellus Ubbink
- Leiden Institute of Chemistry, University of Leiden, Gorlaeus Laboratory, Einsteinweg 55, 2333 CC, Leiden, the Netherlands
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13
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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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14
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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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15
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Camponeschi F, Prusty NR, Heider SAE, Ciofi-Baffoni S, Banci L. GLRX3 Acts as a [2Fe-2S] Cluster Chaperone in the Cytosolic Iron-Sulfur Assembly Machinery Transferring [2Fe-2S] Clusters to NUBP1. J Am Chem Soc 2020; 142:10794-10805. [PMID: 32429669 PMCID: PMC8007109 DOI: 10.1021/jacs.0c02266] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Human
cytosolic monothiol glutaredoxin-3 (GLRX3) is a protein essential
for the maturation of cytosolic [4Fe–4S] proteins. We show
here that dimeric cluster-bridged GLRX3 transfers its [2Fe–2S]2+ clusters to the human P-loop NTPase NUBP1, an essential
early component of the cytosolic iron–sulfur assembly (CIA)
machinery. Specifically, we observed that [2Fe–2S]2+ clusters are transferred from GLRX3 to monomeric apo NUBP1 and reductively
coupled to form [4Fe–4S]2+ clusters on both N-terminal
CX13CX2CX5C and C-terminal CPXC motifs
of NUBP1 in the presence of glutathione that acts as a reductant.
In this process, cluster binding to the C-terminal motif of NUBP1
promotes protein dimerization, while cluster binding to the N-terminal
motif does not affect the quaternary structure of NUBP1. The cluster
transfer/assembly process is not complete on both N- and C-terminal
motifs and indeed requires a reductant stronger than GSH to increase
its efficiency. We also showed that the [4Fe–4S]2+ cluster formed at the N-terminal motif of NUBP1 is tightly bound,
while the [4Fe–4S]2+ cluster bound at the C-terminal
motif is labile. Our findings provide the first evidence for GLRX3
acting as a [2Fe–2S] cluster chaperone in the early stage of
the CIA machinery.
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Affiliation(s)
- Francesca Camponeschi
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, Florence 50019, Italy
| | - Nihar Ranjan Prusty
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, Florence 50019, Italy
| | - Sabine Annemarie Elisabeth Heider
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, Florence 50019, Italy.,Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
| | - Simone Ciofi-Baffoni
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, Florence 50019, Italy.,Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
| | - Lucia Banci
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, Florence 50019, Italy.,Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, Florence 50019, Italy
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16
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Camponeschi F, Muzzioli R, Ciofi-Baffoni S, Piccioli M, Banci L. Paramagnetic 1H NMR Spectroscopy to Investigate the Catalytic Mechanism of Radical S-Adenosylmethionine Enzymes. J Mol Biol 2019; 431:4514-4522. [PMID: 31493409 DOI: 10.1016/j.jmb.2019.08.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/30/2019] [Accepted: 08/30/2019] [Indexed: 10/26/2022]
Abstract
Iron-sulfur clusters in radical S-adenosylmethionine (SAM) enzymes catalyze an astonishing array of complex and chemically challenging reactions across all domains of life. Here we showed that 1H NMR spectroscopy experiments tailored to reveal hyperfine-shifted signals of metal-ligands is a powerful tool to monitor the binding of SAM and of the octanoyl-peptide substrate to the two [4Fe-4S] clusters of human lipoyl synthase. The paramagnetically shifted signals of the iron-ligands were specifically assigned to each of the two bound [4Fe-4S] clusters, and then used to examine the interaction of SAM and substrate molecules with each of the two [4Fe-4S] clusters of human lipoyl synthase. 1H NMR spectroscopy can therefore contribute to the description of the catalityc mechanism of radical SAM enzymes.
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Affiliation(s)
- Francesca Camponeschi
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Riccardo Muzzioli
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Simone Ciofi-Baffoni
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Mario Piccioli
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Lucia Banci
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy.
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17
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Ravera E, Takis PG, Fragai M, Parigi G, Luchinat C. NMR Spectroscopy and Metal Ions in Life Sciences. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800875] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Panteleimon G. Takis
- Giotto Biotech S.R.L.; Via Madonna del Piano 6 50019 Sesto Fiorentino (FI) Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
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18
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Gourdoupis S, Nasta V, Calderone V, Ciofi-Baffoni S, Banci L. IBA57 Recruits ISCA2 to Form a [2Fe-2S] Cluster-Mediated Complex. J Am Chem Soc 2018; 140:14401-14412. [DOI: 10.1021/jacs.8b09061] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Spyridon Gourdoupis
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Veronica Nasta
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Vito Calderone
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Simone Ciofi-Baffoni
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Lucia Banci
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
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19
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Banci L, Camponeschi F, Ciofi-Baffoni S, Piccioli M. The NMR contribution to protein-protein networking in Fe-S protein maturation. J Biol Inorg Chem 2018; 23:665-685. [PMID: 29569085 PMCID: PMC6006191 DOI: 10.1007/s00775-018-1552-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 03/12/2018] [Indexed: 12/12/2022]
Abstract
Iron–sulfur proteins were among the first class of metalloproteins that were actively studied using NMR spectroscopy tailored to paramagnetic systems. The hyperfine shifts, their temperature dependencies and the relaxation rates of nuclei of cluster-bound residues are an efficient fingerprint of the nature and the oxidation state of the Fe–S cluster. NMR significantly contributed to the analysis of the magnetic coupling patterns and to the understanding of the electronic structure occurring in [2Fe–2S], [3Fe–4S] and [4Fe–4S] clusters bound to proteins. After the first NMR structure of a paramagnetic protein was obtained for the reduced E. halophila HiPIP I, many NMR structures were determined for several Fe–S proteins in different oxidation states. It was found that differences in chemical shifts, in patterns of unobserved residues, in internal mobility and in thermodynamic stability are suitable data to map subtle changes between the two different oxidation states of the protein. Recently, the interaction networks responsible for maturing human mitochondrial and cytosolic Fe–S proteins have been largely characterized by combining solution NMR standard experiments with those tailored to paramagnetic systems. We show here the contribution of solution NMR in providing a detailed molecular view of “Fe–S interactomics”. This contribution was particularly effective when protein–protein interactions are weak and transient, and thus difficult to be characterized at high resolution with other methodologies.
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Affiliation(s)
- Lucia Banci
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy. .,Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019, Florence, Italy.
| | - Francesca Camponeschi
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy.,Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019, Florence, Italy
| | - Simone Ciofi-Baffoni
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy.,Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019, Florence, Italy
| | - Mario Piccioli
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy. .,Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019, Florence, Italy.
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20
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Nasta V, Giachetti A, Ciofi-Baffoni S, Banci L. Structural insights into the molecular function of human [2Fe-2S] BOLA1-GRX5 and [2Fe-2S] BOLA3-GRX5 complexes. Biochim Biophys Acta Gen Subj 2017; 1861:2119-2131. [PMID: 28483642 DOI: 10.1016/j.bbagen.2017.05.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 04/03/2017] [Accepted: 05/04/2017] [Indexed: 01/12/2023]
Abstract
Members of the monothiol glutaredoxin family and members of the BolA-like protein family have recently emerged as specific interacting partners involved in iron-sulfur protein maturation and redox regulation pathways. It is known that human mitochondrial BOLA1 and BOLA3 form [2Fe-2S] cluster-bridged dimeric heterocomplexes with the monothiol glutaredoxin GRX5. The structure and cluster coordination of the two [2Fe-2S] heterocomplexes as well as their molecular function are, however, not defined yet. Experimentally-driven structural models of the two [2Fe-2S] cluster-bridged dimeric heterocomplexes, the relative stability of the two complexes and the redox properties of the [2Fe-2S] cluster bound to these complexes are here presented on the basis of UV/vis, CD, EPR and NMR spectroscopies and computational protein-protein docking. While the BOLA1-GRX5 complex coordinates a reduced, Rieske-type [2Fe-2S]1+ cluster, an oxidized, ferredoxin-like [2Fe-2S]2+ cluster is present in the BOLA3-GRX5 complex. The [2Fe-2S] BOLA1-GRX5 complex is preferentially formed over the [2Fe-2S] BOLA3-GRX5 complex, as a result of a higher cluster binding affinity. All these observed differences provide the first indications discriminating the molecular function of the two [2Fe-2S] heterocomplexes.
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Affiliation(s)
- Veronica Nasta
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Andrea Giachetti
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Simone Ciofi-Baffoni
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Lucia Banci
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy.
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21
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Bansal D, Gupta R. Hydroxide-bridged dicopper complexes: the influence of secondary coordination sphere on structure and catecholase activity. Dalton Trans 2017; 46:4617-4627. [DOI: 10.1039/c6dt04858g] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work illustrates the syntheses, structures and catecholase activities of dicopper(ii) complexes having a Cu(μ-OH)Cu core encased within a secondary coordination sphere intricately created by appended heterocyclic rings.
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Affiliation(s)
- Deepak Bansal
- Department of Chemistry
- University of Delhi
- Delhi 110 007
- India
| | - Rajeev Gupta
- Department of Chemistry
- University of Delhi
- Delhi 110 007
- India
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22
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Eberle B, Damjanović M, Enders M, Leingang S, Pfisterer J, Krämer C, Hübner O, Kaifer E, Himmel HJ. Radical Monocationic Guanidino-Functionalized Aromatic Compounds (GFAs) as Bridging Ligands in Dinuclear Metal Acetate Complexes: Synthesis, Electronic Structure, and Magnetic Coupling. Inorg Chem 2016; 55:1683-96. [DOI: 10.1021/acs.inorgchem.5b02614] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Benjamin Eberle
- Ruprecht-Karls-Universität Heidelberg, Anorganisch-Chemisches Institut, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Marko Damjanović
- Ruprecht-Karls-Universität Heidelberg, Anorganisch-Chemisches Institut, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Markus Enders
- Ruprecht-Karls-Universität Heidelberg, Anorganisch-Chemisches Institut, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Simone Leingang
- Ruprecht-Karls-Universität Heidelberg, Anorganisch-Chemisches Institut, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Jessica Pfisterer
- Ruprecht-Karls-Universität Heidelberg, Anorganisch-Chemisches Institut, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Christoph Krämer
- Ruprecht-Karls-Universität Heidelberg, Anorganisch-Chemisches Institut, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Olaf Hübner
- Ruprecht-Karls-Universität Heidelberg, Anorganisch-Chemisches Institut, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Elisabeth Kaifer
- Ruprecht-Karls-Universität Heidelberg, Anorganisch-Chemisches Institut, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Hans-Jörg Himmel
- Ruprecht-Karls-Universität Heidelberg, Anorganisch-Chemisches Institut, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
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Piccioli M, Turano P. Transient iron coordination sites in proteins: Exploiting the dual nature of paramagnetic NMR. Coord Chem Rev 2015. [DOI: 10.1016/j.ccr.2014.05.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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24
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Human anamorsin binds [2Fe–2S] clusters with unique electronic properties. J Biol Inorg Chem 2013; 18:883-93. [DOI: 10.1007/s00775-013-1033-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 08/05/2013] [Indexed: 11/27/2022]
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25
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Anamorsin Is a [2Fe-2S] Cluster-Containing Substrate of the Mia40-Dependent Mitochondrial Protein Trapping Machinery. ACTA ACUST UNITED AC 2011; 18:794-804. [DOI: 10.1016/j.chembiol.2011.03.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 02/24/2011] [Accepted: 03/08/2011] [Indexed: 11/24/2022]
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26
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Abriata LA, Ledesma GN, Pierattelli R, Vila AJ. Electronic structure of the ground and excited states of the Cu(A) site by NMR spectroscopy. J Am Chem Soc 2009; 131:1939-46. [PMID: 19146411 DOI: 10.1021/ja8079669] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The electronic properties of Thermus thermophilus Cu(A) in the oxidized form were studied by (1)H and (13)C NMR spectroscopy. All of the (1)H and (13)C resonances from cysteine and imidazole ligands were observed and assigned in a sequence-specific fashion. The detection of net electron spin density on a peptide moiety is attributed to the presence of a H-bond to a coordinating sulfur atom. This hydrogen bond is conserved in all natural Cu(A) variants and plays an important role for maintaining the electronic structure of the metal site, rendering the two Cys ligands nonequivalent. The anomalous temperature dependence of the chemical shifts is explained by the presence of a low-lying excited state located about 600 cm(-1) above the ground state. The room-temperature shifts can be described as the thermal average of a sigma(u)* ground state and a pi(u) excited state. These results provide a detailed description of the electronic structure of the Cu(A) site at atomic resolution in solution at physiologically relevant temperature.
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Affiliation(s)
- Luciano A Abriata
- IBR (Instituto de Biologia Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Facultad de Ciencias Bioquimicas y Farmaceuticas, Universidad Nacional de Rosario, Suipacha 531, Argentina
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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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29
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1H NMRD PROFILES OF PARAMAGNETIC COMPLEXES AND METALLOPROTEINS. ADVANCES IN INORGANIC CHEMISTRY 2005. [DOI: 10.1016/s0898-8838(05)57003-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Ziessel R, Stroh C, Heise H, Köhler FH, Turek P, Claiser N, Souhassou M, Lecomte C. Strong Exchange Interactions between Two Radicals Attached to Nonaromatic Spacers Deduced from Magnetic, EPR, NMR, and Electron Density Measurements. J Am Chem Soc 2004; 126:12604-13. [PMID: 15453793 DOI: 10.1021/ja0305959] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A nitronyl-nitroxide (NIT) biradical D-NIT2 linked by a single double bond has been engineered and investigated in the solid state by a combination of X-ray diffraction, magnetic susceptibility measurement, EPR, as well as solid-state (1)H and (13)C NMR spectroscopies, and experimental electron density distribution. All techniques reveal that a double bond is a very efficient coupling unit for exchange interactions between two radical moieties. Using a Bleaney-Bowers model dimer (H = -JS(1)S(2)), a singlet-triplet energy gap of J = -460 K was found with the singlet state being the ground state. This very strong intramolecular interaction was confirmed by EPR measurements in CH(2)Cl(2) solution (6 10(-4) M) or dispersed in a polymer matrix at low concentration. In keeping with these unusual interactions, solid-state NMR signals of the biradical were found to be considerably less shifted than those found for related monoradicals. Temperature-dependent solid-state (13)C NMR spectra of D-NIT2 confirmed the very strong intramolecular coupling constant (J = -504 K). The electron density distribution of D-NIT2 was measured by high resolution X-ray diffraction, which also revealed that this biradical is an ideally conjugated system. The in-depth characterization includes the deformation maps and the observed electron density ellipticities, which exhibit a pronounced sigma-pi character of the O-N-C=C-N-O cores in keeping with an efficient electronic delocalization along the alkene spacer.
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Affiliation(s)
- Raymond Ziessel
- Laboratoire de Chimie Moléculaire, Ecole de Chimie, Polymères et Matériaux (ECPM), UMR 7008, Université Louis Pasteur (ULP), 25, rue Becquerel, F-67087 Strasbourg Cedex 2, France.
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31
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Szterenberg L, Latos-Grazyński L, Wojaczyński J. Metallobiliverdin radicals--DFT studies. Chemphyschem 2003; 4:691-8. [PMID: 12901300 DOI: 10.1002/cphc.200200611] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Several aspects of the molecular and electronic structure of biliverdin derivatives have been studied using density functional theory (DFT). The calculations have been performed for complexes of trianion (BvO2)3- and dianion [BvO(OH)]2-, derived from two tautomeric forms of biliverdin, BvO2H3 and [BvO(OH)]H2, with redox innocent metal ions: lithium(I), zinc(II), and gallium(III). One-electron-oxidized and reduced forms of each complex (cation and anion radicals) have been also considered. The molecular structures of all species investigated are characterized by a helical arrangement of tetrapyrrolic ligands with the metal ion lying in the plane formed by the two central pyrrole rings. The spin density distribution in four types of metallobiliverdin radicals--[(BvO2.)Mn+]n-2,[[BvO(OH).]Mn+]n-1 (cation radicals),[(BvO2.)Mn+]n-4,[[BvO(OH).]Mn+]n-3 (anion radicals)--has been investigated. In general, the absolute values of spin density on meso carbon atoms were larger than for the beta-carbon atoms. Sign alteration of spin density has been found for meso positions, and also for the beta-carbon atoms of at least two pyrrole rings. The calculated spin density maps accounted for the essential NMR spectroscopic features of iron biliverdin derivatives, including the considerable isotropic shifts detected for the meso resonances and shift alteration at the meso and beta-positions.
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Affiliation(s)
- Ludmiła Szterenberg
- Department of Chemistry, University of Wrocław, 14 F. Joliot-Curie St., 50-383 Wrocław, Poland
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32
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Kaizaki S. Spectroscopic Implications for Magnetic Interactions in Metal Complexes with Nitroxide Radicals. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2003. [DOI: 10.1246/bcsj.76.673] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Abstract
A flexible oxophlorin macrocycle, which allows the location of labile hydrogen atoms alternatively at the pyrrole nitrogen, oxygen, or meso-carbon atoms, has been studied by density functional theory (DFT). DFT calculations were carried out on oxophlorin 1, 5-hydroxyporphyrin 2, and two isomers of oxophlorin 3 and 4 (the proton added at the tetrahedral C(15) or the C(10) meso-carbon, respectively). The oxophlorin-hydroxyporphyrin structural changes are appropriately reflected by the significant changes of the meso carbon-oxygen bond lengths, which are in the limits of typical C=O and C-O distances. The rearrangement that creates the iso-oxophlorin macrocycle 3 (4) results in near tetrahedral geometry around the C(15) (C(10)) carbon atom, with the C(14)-C(15) and C(15)-C(16) (C(9)-C(10) and C(10)-C(11)) bond lengths corresponding to a single C-C bond. 5-Hydroxyporphyrin 2 is aromatic and has a bond pattern resembling that of regular porphyrin. In 1, 3, and 4, a localization of single and double bonds was seen, which agrees with the nonaromatic nature of oxophlorin, or isooxophlorin. The relative stability decreases in the order: 2 (0) > 3 (4.85) > 1 (5.11) > 4 (10.04) > 3-cis (12.89) (the number in parentheses is the relative energy, in kcal mol-1). The energy difference between the NH-cis and NH-trans tautomers, which is 8.04 kcal mol-1 for 3, results from a destabilizing NH-NH cis-interaction. DFT calculations were performed on the oxophlorin dianion radical (OP.)2- and a series of metallooxophlorin radicals ([(OP.)LiI]-, [(OP.)ZnII], [(OP.)GaIII]+, and (OP.)GaIIIF, in order to assess their electronic structures. Typically, the largest atomic spin density was found at the C(10) (C(20)) and C(15) meso positions, with the spin density at C(15) being twice as large as that at C(10). The spin density at the C(5) atom is negligible. A large spin density was found at the O(5) oxygen atom. The amount of spin density at the meso positions decreased as the cationic charge increased. When considering the absolute values of the spin densities, the opposite trend was observed at the pyrrolic carbon atoms. The spin density at the nucleus (Fermi contact terms) has also been analyzed. The spin distributions of iron oxophlorins determined by NMR were attributed to an oxophlorin radical electronic structure. The calculated spin density maps accounted for the essential NMR spectroscopic features of important intermediates in the heme degradation process--iron oxophlorin complexes. The DFT calculations reproduced the following spectroscopic patterns: a) |delta H(15)|>|delta H(10)|>>|delta (beta-H)|, b) a sign alteration of the contact shifts for identical substituents located on the same pyrrole ring.
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Affiliation(s)
- Ludmiła Szterenberg
- Department of Chemistry, University of Wrocław, 14F. Joliot-Curie St. 50-383 Wrocław, Poland
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Park J, Kim JY, So H, Liu J. 1H NMR study of pyridine-type ligands coordinated to the paramagnetic polyoxometalates, [CoIIW11MO39]n− (M=CoII, NiII, CuII, or FeIII). Inorganica Chim Acta 2001. [DOI: 10.1016/s0020-1693(01)00442-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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35
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The 3Fe containing ferredoxin from Desulfovibrio gigas: an NMR characterization of the oxidised and intermediate states. Coord Chem Rev 1999. [DOI: 10.1016/s0010-8545(99)00126-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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36
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Studies of hyperfine interactions in [2Fe2S] proteins by EPR and double resonance spectroscopy. Coord Chem Rev 1999. [DOI: 10.1016/s0010-8545(99)00155-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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37
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Yoshida T, Kaizaki S. NMR Spectra and Magnetic Exchange Interactions in Nickel(II) Complexes with a Chelated Nitronyl Nitroxide Radical. Inorg Chem 1999; 38:1054-1058. [PMID: 11670885 DOI: 10.1021/ic9805426] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
1H or (2)H NMR contact shifts of the beta-diketonate methine in the radical complexes [Ni(beta-diketonato)(2)(NIT2-py)] and [Ni(beta-diketonato)(tmen)(NIT2-py)](+) (NIT2-py = 2-(2'-pyridyl)-4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazolyl-3-oxide-1-oxyl and tmen = N,N,N',N'-tetramethylethylenediamine) were found to correlate to a product of the respective (1)H or (2)H NMR contact shifts of the methine in the nonradical complexes [Ni(beta-diketonato)(2)(tmen)] and the fractional contribution to the Ni(II) moiety arising from the magnetic interaction between nickel(II) ion and NIT2-py radical, proposing a new method to estimate the exchange coupling constant J value from the NMR contact shifts. Variable temperature (2)H NMR measurements of the C-D signals in [Ni(acac-d)(2)(NIT2-py)], [Ni(acac-d)(tmen)(NIT2-py)](+), and [Ni(acac-d)(2)(tmen)] suggested the topological discrimination of the acetylacetonates.
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Affiliation(s)
- Takafumi Yoshida
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560 Japan
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38
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Bertini I, Luchinat C, Rosato A. NMR Spectra of Iron-Sulfur Proteins. ADVANCES IN INORGANIC CHEMISTRY 1999. [DOI: 10.1016/s0898-8838(08)60080-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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39
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Sari N, Holden MJ, Mayhew MP, Vilker VL, Coxon B. Exploration of the structural environment of the iron-sulfur cluster in putidaredoxin by nitrogen-15 NMR spectroscopy of selectively labeled cysteine residues. Biochem Biophys Res Commun 1998; 249:773-80. [PMID: 9731212 DOI: 10.1006/bbrc.1998.9227] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Putidaredoxin is a di-iron protein whose paramagnetic region is not well characterized by 1H detected NMR. We have studied the structure of this region in greater detail by directly observed 15N NMR of oxidized and reduced putidaredoxin preparations in which the six cysteine residues are selectively labeled with 15N. A new method for preparation of a stable form of reduced putidaredoxin has been developed for use in NMR. The 15N NMR spectra of the oxidized and reduced forms are characteristically different, and we have measured and compared 15N chemical shifts, spin-lattice relaxation times (T1), and chemical shift/temperature dependences for both forms. Evidence for localized valencies of the iron atoms in the reduced form is presented. From the 15N T1 values of the oxidized form, reduced distances of the cysteine backbone 15N nuclei from the center of the Fe2S2 cluster have been calculated. These distances are consistent with those calculated from X-ray crystal structure data for five ferredoxins, and confirm the structural similarity of the Fe2S2 clusters in putidaredoxin and in these ferredoxins in the oxidized state.
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Affiliation(s)
- N Sari
- Biotechnology Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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40
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Coordination sphere versus protein environment as determinants of electronic and functional properties of iron-sulfur proteins. STRUCTURE AND BONDING 1998. [DOI: 10.1007/3-540-62888-6_5] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Bertini I, Luchinat C, Rosato A. The solution structure of paramagnetic metalloproteins. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1996; 66:43-80. [PMID: 9107132 DOI: 10.1016/s0079-6107(96)00016-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- I Bertini
- Department of Chemistry, University of Florence, Italy
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43
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Bertini I, Felli IC, Kastrau DH, Luchinat C, Piccioli M, Viezzoli MS. Sequence-specific assignment of the 1H and 15N nuclear magnetic resonance spectra of the reduced recombinant high-potential iron-sulfur protein I from Ectothiorhodospira halophila. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 225:703-14. [PMID: 7957186 DOI: 10.1111/j.1432-1033.1994.00703.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A 1H and 15N NMR investigation through two-dimensional and three-dimensional spectroscopy has been performed on the reduced form ([Fe4S4]2+) of the recombinant high-potential iron-sulfur protein (HiPIP) I from Ectothiorhodospira halophila expressed in Escherichia coli. [Fe4S4]2+ clusters in proteins are paramagnetic with a relatively low mu eff of about 0.8 mu B/iron ion, but the paramagnetic effects on nuclear relaxation are so strong as to yield T1 values of a few milliseconds and linewidths of hundreds of hertz for the nuclei closet to the paramagnetic center. Despite these features, 71 out of 73 residues were identified, most of which were assigned completely as far as proton resonances are concerned; as many as 68 residues could be assigned without any reference to the existing X-ray structure. A total of 88% of all protein protons and 58 out of 69 peptide HN nitrogen signals were assigned. To the best of our knowledge, this is the most extensive 1H assignment of a paramagnetic protein to date. Protons sensitive to the proximity of the cluster were assigned through suitable NOE spectroscopy experiments. Three out of the four coordinated cysteines were assigned, and two residues have been identified whose peptide HN protons give rise to H bonds with coordinated sulfur atoms. The inter-residue NOE cross peaks are in qualitative agreement with the secondary and tertiary structure as obtained from the available X-ray crystallographic analysis of the wild-type protein at 250-pm resolution. It is therefore shown that the expressed protein is properly folded and that it is a reliable model for the wild-type protein. These data are meaningful for the detection of structural differences among mutants in future studies.
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Affiliation(s)
- I Bertini
- Department of Chemistry, University of Florence, Italy
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46
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Belinskii M. Heisenberg model for tetrameric iron clusters in high-potential iron-sulfur proteins. I. Exchange states, g-factors, hyperfine interactions. Chem Phys 1993. [DOI: 10.1016/0301-0104(93)85004-r] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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47
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Belinskii M. Heisenberg model for tetrameric iron clusters in high-potential iron-sulfur proteins. II. Double exchange in distorted cluster. Chem Phys 1993. [DOI: 10.1016/0301-0104(93)85005-s] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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48
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Belinskii M. Spin coupling model for tetrameric iron clusters in ferredoxins. I. Theory, exchange levels, g-factors. Chem Phys 1993. [DOI: 10.1016/0301-0104(93)80116-q] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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49
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Banci L, Bertini I, Ferretti S, Luchinat C, Piccioli M. The structure of iron-sulfur clusters in proteins as monitored by NMR, mössbauer, EPR and molecular dynamics. J Mol Struct 1993. [DOI: 10.1016/0022-2860(93)80101-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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50
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Bertini I, Capozzi F, Luchinat C, Piccioli M. 1H-NMR investigation of oxidized and reduced high-potential iron-sulfur protein from Rhodopseudomonas globiformis. EUROPEAN JOURNAL OF BIOCHEMISTRY 1993; 212:69-78. [PMID: 8444166 DOI: 10.1111/j.1432-1033.1993.tb17634.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
1H one-dimensional and two-dimensional NMR spectra have been recorded for the oxidized and reduced forms of the high-potential iron-sulfur protein (HiPIP) from Rhodopseudomonas globiformis which has the highest known reduction potential. The spectrum of the oxidized protein is similar to that of Chromatium vinosum and Rhodocyclus gelatinosus HiPIP but different from that of the HiPIP II from Ectothiorhodospira halophila. Surprisingly, site-specific assignment has shown that in the oxidized protein the distribution of oxidation numbers within the cluster is very similar to that found for E. halophila HiPIP II and different from that of the other two proteins. The spectrum of the reduced species is very similar to that of all other HiPIPs known to date, indicating very similar electronic and geometric structures for the reduced forms. These findings are discussed in terms of cluster structure in HiPIPs and of redox potentials.
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Affiliation(s)
- I Bertini
- Department of Chemistry, University of Florence, Italy
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