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Oney-Hawthorne SD, Barondeau DP. Fe-S cluster biosynthesis and maturation: Mass spectrometry-based methods advancing the field. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119784. [PMID: 38908802 DOI: 10.1016/j.bbamcr.2024.119784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/25/2024] [Accepted: 06/10/2024] [Indexed: 06/24/2024]
Abstract
Iron‑sulfur (FeS) clusters are inorganic protein cofactors that perform essential functions in many physiological processes. Spectroscopic techniques have historically been used to elucidate details of FeS cluster type, their assembly and transfer, and changes in redox and ligand binding properties. Structural probes of protein topology, complex formation, and conformational dynamics are also necessary to fully understand these FeS protein systems. Recent developments in mass spectrometry (MS) instrumentation and methods provide new tools to investigate FeS cluster and structural properties. With the unique advantage of sampling all species in a mixture, MS-based methods can be utilized as a powerful complementary approach to probe native dynamic heterogeneity, interrogate protein folding and unfolding equilibria, and provide extensive insight into protein binding partners within an entire proteome. Here, we highlight key advances in FeS protein studies made possible by MS methodology and contribute an outlook for its role in the field.
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Affiliation(s)
| | - David P Barondeau
- Department of Chemistry, Texas A&M University, College Station, TX 77842, USA.
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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] [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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Silva JM, Grifagni D, Cantini F, Piccioli M. 1H, 13C and 15N assignment of the human mitochondrial paramagnetic iron-sulfur protein CISD3. BIOMOLECULAR NMR ASSIGNMENTS 2023; 17:17-22. [PMID: 36520264 DOI: 10.1007/s12104-022-10113-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/25/2022] [Indexed: 06/02/2023]
Abstract
CISD3 is a mitochondrial protein that contains two [2Fe-2S] clusters. This protein is overexpressed in some types of cancer, so it has emerged as a potential drug target. A detailed characterization of this protein is crucial to understand how CISD3 is involved in these physiopathologies. In this study, isotopically labeled human CISD3 was expressed in Escherichia coli. A set of double and triple resonance experiments performed with standard parameters/datasets provided the assignment of 40% of the HN resonances, 47% of Cα, and 46% of C' resonances. Tailored paramagnetic HSQC, CON and CACO experiments extended up to 59% for HN, 70% for Cα and 69% for C'. The 1H, 13C and 15N NMR chemical shift assignment of human CISD3 is reported here.
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Affiliation(s)
- José Malanho Silva
- 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
| | - Francesca Cantini
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metalloproteine, 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.
- Consorzio Interuniversitario Risonanze Magnetiche Metalloproteine, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.
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Grifagni D, Silva JM, Cantini F, Piccioli M, Banci L. Relaxation-based NMR assignment: Spotlights on ligand binding sites in human CISD3. J Inorg Biochem 2023; 239:112089. [PMID: 36502664 DOI: 10.1016/j.jinorgbio.2022.112089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/26/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
CISD3 is a mitochondrial protein belonging to the NEET proteins family, bearing two [Fe2S2] clusters coordinated by CDGSH domains. At variance with the other proteins of the NEET family, very little is known about its structure-function relationships. NMR is the only technique to obtain information at the atomic level in solution on the residues involved in intermolecular interactions; however, in paramagnetic proteins this is limited by the broadening of signals of residues around the paramagnetic center. Tailored experiments can revive signals of the cluster surrounding; however, signals identification without specific residue assignment remains useless. Here, we show how paramagnetic relaxation can drive the signal assignment of residues in the proximity of the paramagnetic center(s). This allowed us to identify the potential key players of the biological function of the CISD3 protein.
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Affiliation(s)
- Deborah Grifagni
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| | - José M Silva
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| | - Francesca Cantini
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine, 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; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| | - Lucia Banci
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
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The Intriguing mitoNEET: Functional and Spectroscopic Properties of a Unique [2Fe-2S] Cluster Coordination Geometry. Molecules 2022; 27:molecules27238218. [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] [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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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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Invernici M, Selvolini G, Silva JM, Marrazza G, Ciofi-Baffoni S, Piccioli M. Interconversion between [2Fe-2S] and [4Fe-4S] cluster glutathione complexes. Chem Commun (Camb) 2022; 58:3533-3536. [PMID: 35195626 DOI: 10.1039/d1cc03566e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present here how different iron-sulfide-glutathione ratios, applied in in vitro conditions comparable to those present in the mitochondrial matrix, affect the speciation of iron-sulfur cluster glutathione complexes. An excess of sulfide with respect to iron ions promotes the formation of a tetranuclear [FeII2FeIII2S4(GS)4]2- complex, while an excess of iron ions favors the formation of a dinuclear [FeIIFeIIIS2(GS)4]3- complex. These two complexes establish an interconversion equilibrium. The latter might play a role in the composition of the mitochondrial labile iron pool potentially contributing to the regulation of cellular iron homeostasis.
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Affiliation(s)
- Michele Invernici
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, Sesto Fiorentino 50019, Italy. .,Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, Sesto Fiorentino 50019, Italy
| | - Giulia Selvolini
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - José Malanho Silva
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, Sesto Fiorentino 50019, Italy. .,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Giovanna Marrazza
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Simone Ciofi-Baffoni
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, Sesto Fiorentino 50019, Italy. .,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Mario Piccioli
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, Sesto Fiorentino 50019, Italy. .,Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, Sesto Fiorentino 50019, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, Sesto Fiorentino 50019, Italy
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Phillips AH, Hernandez JA, Payá-Tormo L, Burén S, Cuevas-Zuviría B, Pacios LF, Pelton JG, Wemmer DE, Rubio LM. Environment and coordination of FeMo-co in the nitrogenase metallochaperone NafY. RSC Chem Biol 2021; 2:1462-1465. [PMID: 34704049 PMCID: PMC8496260 DOI: 10.1039/d1cb00086a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/27/2021] [Indexed: 11/30/2022] Open
Abstract
In nitrogenase biosynthesis, the iron-molybdenum cofactor (FeMo–co) is externally assembled at scaffold proteins and delivered to the NifDK nitrogenase component by the NafY metallochaperone. Here we have used nuclear magnetic resonance, molecular dynamics, and functional analysis to elucidate the environment and coordination of FeMo–co in NafY. H121 stands as the key FeMo–co ligand. Regions near FeMo–co diverge from H121 and include the η1, α1, α2 helical lobe and a narrow path between H121 and C196. Broadening of NMR resonance spins used to map binding of paramagnetic FeMo–co to the nitrogenase metallocluster escort protein NafY.![]()
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Affiliation(s)
| | - Jose A Hernandez
- Department of Biochemistry and Molecular Genetics, College of Graduate Studies, Midwestern University Glendale AZ 85308 USA.,Arizona College of Osteopathic Medicine, Midwestern University Glendale AZ 85308 USA
| | - Lucía Payá-Tormo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón Madrid 28223 Spain
| | - Stefan Burén
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón Madrid 28223 Spain
| | - Bruno Cuevas-Zuviría
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón Madrid 28223 Spain
| | - Luis F Pacios
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón Madrid 28223 Spain
| | - Jeffrey G Pelton
- QB3 Institute, University of California Berkeley CA 94720 USA .,Division of Physical Biosciences of Lawrence Berkeley National Laboratory, University of California Berkeley CA 94720 USA
| | - David E Wemmer
- QB3 Institute, University of California Berkeley CA 94720 USA .,Division of Physical Biosciences of Lawrence Berkeley National Laboratory, University of California Berkeley CA 94720 USA.,Department of Chemistry, University of California Berkeley CA 94720 USA
| | - Luis M Rubio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón Madrid 28223 Spain
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