1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Grunwald L, Abbott DF, Mougel V. Gauging Iron-Sulfur Cubane Reactivity from Covalency: Trends with Oxidation State. JACS AU 2024; 4:1315-1322. [PMID: 38665672 PMCID: PMC11040707 DOI: 10.1021/jacsau.4c00213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024]
Abstract
We investigated room-temperature metal and ligand K-edge X-ray absorption (XAS) spectra of a complete redox series of cubane-type iron-sulfur clusters. The Fe K-edge position provides a qualitative but convenient alternative to the traditional spectroscopic descriptors used to identify oxidation states in these systems, which we demonstrate by providing a calibration curve based on two analytic methods. Furthermore, high energy resolution fluorescence detected XAS (HERFD-XAS) at the S K-edge was used to measure Fe-S bond covalencies and record their variation with the average valence of the Fe atoms. While the Fe-S(thiolate) covalency evolves linearly, gaining 11 ± 0.4% per bond and hole, the Fe-S(μ3) covalency evolves asystematically, reflecting changes in the magnetic exchange mechanism. A strong discontinuity manifested for superoxidation to the all-ferric state, distinguishing its electronic structure and its potential (bio)chemical role from those of its redox congeners. We highlight the functional implications of these trends for the reactivity of iron-sulfur cubanes.
Collapse
Affiliation(s)
- Liam Grunwald
- Department
of Chemistry and Applied Biosciences (D-CHAB), Swiss Federal Institute of Technology Zürich (ETHZ), Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Daniel F. Abbott
- Department
of Chemistry and Applied Biosciences (D-CHAB), Swiss Federal Institute of Technology Zürich (ETHZ), Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Victor Mougel
- Department
of Chemistry and Applied Biosciences (D-CHAB), Swiss Federal Institute of Technology Zürich (ETHZ), Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| |
Collapse
|
3
|
Kurisu G. Fifty years of Protein Data Bank in the Journal of Biochemistry. J Biochem 2021; 171:3-11. [PMID: 34865074 PMCID: PMC8826841 DOI: 10.1093/jb/mvab133] [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: 11/05/2021] [Accepted: 11/29/2021] [Indexed: 11/21/2022] Open
Abstract
Protein Data Bank (PDB), jointly founded in 1971 by Brookhaven National Laboratory, USA, and the Cambridge Crystallographic Data Centre, UK, is the single global archive of experimentally determined biological macromolecular structures. PDB deposition is mandatory for publication in most scientific journals, which means ‘no PDB deposition, no structural publication’. The current PDB archive contains more than 180,000 entries and includes many structures from Asian institutions. The first protein structure from Japan was that of cytochrome c determined by Prof Masao Kakudo’s group at the Institute for Protein Research, Osaka University, in 1971 at a resolution of 4 Å, and a subsequent atomic structure at 2.3 Å resolution was deposited to PDB in 1976 as the 1st Asian and 21st entry of the entire PDB archive. Since then, 317 protein structures whose primary citation was the Journal of Biochemistry (J. Biochem.) have been deposited to PDB. Based on this long history between PDB and J. Biochem., a statistical analysis of all structural reports in J. Biochem. has been carried out using the relational database system at PDBj (https://pdbj.org) and reviewed the yearly distribution, resolution, quality of structure, type of target protein, number of citations and comparison against other major journals.
Collapse
Affiliation(s)
- Genji Kurisu
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| |
Collapse
|
4
|
Jamieson EMG, Modicom F, Goldup SM. Chirality in rotaxanes and catenanes. Chem Soc Rev 2018; 47:5266-5311. [PMID: 29796501 PMCID: PMC6049620 DOI: 10.1039/c8cs00097b] [Citation(s) in RCA: 187] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Indexed: 12/20/2022]
Abstract
Although chiral mechanically interlocked molecules (MIMs) have been synthesised and studied, enantiopure examples are relatively under-represented in the pantheon of reported catenanes and rotaxanes and the underlying chirality of the system is often even overlooked. This is changing with the advent of new applications of MIMs in catalysis, sensing and materials and the appearance of new methods to access unusual stereogenic units unique to the mechanical bond. Here we discuss the different stereogenic units that have been investigated in catenanes and rotaxanes, examples of their application, methods for assigning absolute stereochemistry and provide a perspective on future developments.
Collapse
Affiliation(s)
- E. M. G. Jamieson
- Chemistry
, University of Southampton
,
University Road, Highfield
, Southampton
, SO17 1BJ
, UK
.
| | - F. Modicom
- Chemistry
, University of Southampton
,
University Road, Highfield
, Southampton
, SO17 1BJ
, UK
.
| | - S. M. Goldup
- Chemistry
, University of Southampton
,
University Road, Highfield
, Southampton
, SO17 1BJ
, UK
.
| |
Collapse
|
5
|
Mills MJL, Sale KL, Simmons BA, Popelier PLA. Rhorix: An interface between quantum chemical topology and the 3D graphics program blender. J Comput Chem 2017; 38:2538-2552. [PMID: 28857244 PMCID: PMC5656898 DOI: 10.1002/jcc.25054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 08/14/2017] [Accepted: 08/16/2017] [Indexed: 12/24/2022]
Abstract
Chemical research is assisted by the creation of visual representations that map concepts (such as atoms and bonds) to 3D objects. These concepts are rooted in chemical theory that predates routine solution of the Schrödinger equation for systems of interesting size. The method of Quantum Chemical Topology (QCT) provides an alternative, parameter-free means to understand chemical phenomena directly from quantum mechanical principles. Representation of the topological elements of QCT has lagged behind the best tools available. Here, we describe a general abstraction (and corresponding file format) that permits the definition of mappings between topological objects and their 3D representations. Possible mappings are discussed and a canonical example is suggested, which has been implemented as a Python "Add-On" named Rhorix for the state-of-the-art 3D modeling program Blender. This allows chemists to use modern drawing tools and artists to access QCT data in a familiar context. A number of examples are discussed. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Matthew J. L. Mills
- Deconstruction DivisionJoint BioEnergy InstituteEmeryvilleCalifornia
- Biomass Science and Conversion Technology DepartmentSandia National LaboratoriesLivermoreCalifonia
| | - Kenneth L. Sale
- Deconstruction DivisionJoint BioEnergy InstituteEmeryvilleCalifornia
- Biomass Science and Conversion Technology DepartmentSandia National LaboratoriesLivermoreCalifonia
| | - Blake A. Simmons
- Deconstruction DivisionJoint BioEnergy InstituteEmeryvilleCalifornia
- Biological Systems and Engineering Division, Lawrence Berkeley National LaboratoryBerkeleyCalifonia
| | - Paul L. A. Popelier
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester and School of Chemistry, University of Manchester, Oxford RoadManchesterGreat Britain
| |
Collapse
|
6
|
Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part V. {[Fe4S4](SCysγ)4} proteins. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
7
|
Christ S, Leichert LI, Willms A, Lill R, Mühlenhoff U. Defects in Mitochondrial Iron–Sulfur Cluster Assembly Induce Cysteine S-Polythiolation on Iron–Sulfur Apoproteins. Antioxid Redox Signal 2016; 25:28-40. [DOI: 10.1089/ars.2015.6599] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Stefan Christ
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Marburg, Germany
| | - Lars I. Leichert
- Institute for Biochemistry and Pathobiochemistry—Microbial Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - Anna Willms
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Marburg, Germany
| | - Roland Lill
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Marburg, Germany
- LOEWE Zentrum für Synthetische Mikrobiologie SYNMIKRO, Marburg, Germany
| | - Ulrich Mühlenhoff
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Marburg, Germany
| |
Collapse
|
8
|
Abstract
The generalized cluster type [M4(μ3-Q)4L n ] x contains the cubane-type [M4Q4] z core unit that can approach, but typically deviates from, perfect Td symmetry. The geometric properties of this structure have been analyzed with reference to Td symmetry by a new protocol. Using coordinates of M and Q atoms, expressions have been derived for interatomic separations, bond angles, and volumes of tetrahedral core units (M4, Q4) and the total [M4Q4] core (as a tetracapped M4 tetrahedron). Values for structural parameters have been calculated from observed average values for a given cluster type. Comparison of calculated and observed values measures the extent of deviation of a given parameter from that required in an exact tetrahedral structure. The procedure has been applied to the structures of over 130 clusters containing [Fe4Q4] (Q = S2-, Se2-, Te2-, [NPR3]-, [NR]2-) units, of which synthetic and biological sulfide-bridged clusters constitute the largest subset. General structural features and trends in structural parameters are identified and summarized. An extensive database of structural properties (distances, angles, volumes) has been compiled in Supporting Information.
Collapse
Affiliation(s)
- Lay Ling Tan
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L3G1, Canada
| | | | | |
Collapse
|
9
|
|
10
|
Mehner D, Osadnik H, Lünsdorf H, Brüser T. The Tat system for membrane translocation of folded proteins recruits the membrane-stabilizing Psp machinery in Escherichia coli. J Biol Chem 2012; 287:27834-42. [PMID: 22689583 DOI: 10.1074/jbc.m112.374983] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tat systems transport folded proteins across energized membranes of bacteria, archaea, and plant plastids. In Escherichia coli, TatBC complexes recognize the transported proteins, and TatA complexes are recruited to facilitate transport. We achieved an abstraction of TatA from membranes without use of detergents and observed a co-purification of PspA, a membrane-stress response protein. The N-terminal transmembrane domain of TatA was required for the interaction. Electron microscopy displayed TatA complexes in direct contact with PspA. PspB and PspC were important for the TatA-PspA contact. The activator protein PspF was not involved in the PspA-TatA interaction, demonstrating that basal levels of PspA already interact with TatA. Elevated TatA levels caused membrane stress that induced a strictly PspBC- and PspF-dependent up-regulation of PspA. TatA complexes were found to destabilize membranes under these conditions. At native TatA levels, PspA deficiency clearly affected anaerobic TMAO respiratory growth, suggesting that energetic costs for transport of large Tat substrates such as TMAO reductase can become growth limiting in the absence of PspA. The physiological role of PspA recruitment to TatA may therefore be the control of membrane stress at active translocons.
Collapse
Affiliation(s)
- Denise Mehner
- Institute of Microbiology, Leibniz University Hannover, Schneiderberg 50, D-30167 Hannover, Germany
| | | | | | | |
Collapse
|
11
|
Brehmer T, Kerth A, Graubner W, Malesevic M, Hou B, Brüser T, Blume A. Negatively charged phospholipids trigger the interaction of a bacterial Tat substrate precursor protein with lipid monolayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:3534-3541. [PMID: 22263701 DOI: 10.1021/la204473t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Folded proteins can be translocated across biological membranes via the Tat machinery. It has been shown in vitro that these Tat substrates can interact with membranes prior to translocation. Here we report a monolayer and infrared reflection-absorption spectroscopic (IRRAS) study of the initial states of this membrane interaction, the binding to a lipid monolayer at the air/water interface serving as a model for half of a biological membrane. Using the model Tat substrate HiPIP (high potential iron-sulfur protein) from Allochromatium vinosum, we found that the precursor preferentially interacts with monolayers of negatively charged phospholipids. The signal peptide is essential for the interaction of the precursor protein with the monolayer because the mature HiPIP protein showed no interaction with the lipid monolayer. However, the individual signal peptide interacted differently with the monolayer compared to the complete precursor protein. IRRA spectroscopy indicated that the individual signal peptide forms mainly aggregated β-sheet structures. This β-sheet formation did not occur for the signal peptide when being part of the full length precursor. In this case it adopted an α-helical structure upon membrane insertion. The importance of the signal peptide and the mature domain for the membrane interaction is discussed in terms of current ideas of Tat substrate-membrane interactions.
Collapse
Affiliation(s)
- Tina Brehmer
- Institute of Chemistry-Physical Chemistry, Martin-Luther-University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle, Germany
| | | | | | | | | | | | | |
Collapse
|
12
|
Structure at 1.0 Å resolution of a high-potential iron–sulfur protein involved in the aerobic respiratory chain of Rhodothermus marinus. J Biol Inorg Chem 2009; 15:303-13. [DOI: 10.1007/s00775-009-0603-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
13
|
CHUMAN H, MOMANY F, SCHÄFER L. Backbone conformations, bend structures, helix structures and other tests of an improved conformational energy program for peptides: ECEPP83. ACTA ACUST UNITED AC 2009. [DOI: 10.1111/j.1399-3011.1984.tb00951.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
14
|
Kim J, Park JG, Chong Y. FlexE ensemble docking approach to virtual screening for CDK2 inhibitors. MOLECULAR SIMULATION 2007. [DOI: 10.1080/08927020701297401] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
15
|
|
16
|
Alam MS, Garg SK, Agrawal P. Molecular function of WhiB4/Rv3681c of Mycobacterium tuberculosis H37Rv: a [4Fe?4S] cluster co-ordinating protein disulphide reductase. Mol Microbiol 2007; 63:1414-31. [PMID: 17302817 DOI: 10.1111/j.1365-2958.2007.05589.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The genome sequence of Mycobacterium tuberculosis H37Rv revealed the presence of seven whiB-like open reading frames. In spite of several genetic studies on whiB genes, the biochemical properties of WhiB proteins are poorly understood. All WhiB-like proteins have four conserved cysteine residues, out of which two are present in a CXXC motif. We report for the first time the detailed biochemical and biophysical properties of M. tuberculosis WhiB4/Rv3681c and demonstrate the functional relevance of four conserved cysteines and the CXXC motif. UV-visible absorption spectra of freshly purified mWhiB4 showed the presence of a [2Fe-2S] cluster, whereas the electron paramagnetic resonance (EPR) spectra of reconstituted protein showed the presence of a [4Fe-4S] cluster. The iron-sulphur cluster was redox sensitive but stably co-ordinated to the protein even in the presence of high concentration of chaotropic agents. Despite primary sequence divergence from thioredoxin family proteins, the apo mWhiB4 has properties similar to thioredoxins and functions as a protein disulphide reductase, whereas holo mWhiB4 is enzymatically inactive. Apart from the cysteine thiol of CXXC motif the distantly placed thiol pair also contributes equally to the enzymatic activity of mWhiB4. A functional model of mWhiB4 in redox signaling during oxidative stress in M. tuberculosis has been presented.
Collapse
Affiliation(s)
- Md Suhail Alam
- Institute of Microbial Technology, Sector-39A, Chandigarh, 160 036, India
| | | | | |
Collapse
|
17
|
Chou PY, Fasman GD. Prediction of the secondary structure of proteins from their amino acid sequence. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 47:45-148. [PMID: 364941 DOI: 10.1002/9780470122921.ch2] [Citation(s) in RCA: 878] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
18
|
Mortenson LE, Seefeldt LC, Morgan TV, Bolin JT. The role of metal clusters and MgATP in nitrogenase catalysis. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 67:299-374. [PMID: 8322617 DOI: 10.1002/9780470123133.ch4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- L E Mortenson
- Center for Metalloenzyme Studies, University of Georgia, Athens
| | | | | | | |
Collapse
|
19
|
Bruscella P, Cassagnaud L, Ratouchniak J, Brasseur G, Lojou E, Amils R, Bonnefoy V. The HiPIP from the acidophilic Acidithiobacillus ferrooxidans is correctly processed and translocated in Escherichia coli, in spite of the periplasm pH difference between these two micro-organisms. MICROBIOLOGY-SGM 2005; 151:1421-1431. [PMID: 15870452 DOI: 10.1099/mic.0.27476-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The gene encoding a putative high-potential iron-sulfur protein (HiPIP) from the strictly acidophilic and chemolithoautotrophic Acidithiobacillus ferrooxidans ATCC 33020 has been cloned and sequenced. This potential HiPIP was overproduced in the periplasm of the neutrophile and heterotroph Escherichia coli. As shown by optical and EPR spectra and by electrochemical studies, the recombinant protein has all the biochemical properties of a HiPIP, indicating that the iron-sulfur cluster was correctly inserted. Translocation of this protein in the periplasm of E. coli was not detected in a DeltatatC mutant, indicating that it is dependent on the Tat system. The genetic organization of the iro locus in strains ATCC 23270 and ATCC 33020 is different from that found in strains Fe-1 and BRGM. Indeed, in A. ferrooxidans ATCC 33020 and ATCC 23270 (the type strain), iro was not located downstream from purA but was instead downstream from petC2, encoding cytochrome c1 from the second A. ferrooxidans cytochrome bc1 complex. These findings underline the genotypic heterogeneity within the A. ferrooxidans species. The results suggest that Iro transfers electrons from a cytochrome bc1 complex to a terminal oxidase, as proposed for the HiPIP in photosynthetic bacteria.
Collapse
Affiliation(s)
- Patrice Bruscella
- Laboratoire de Chimie Bactérienne, IBSM, CNRS, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Laure Cassagnaud
- Laboratoire de Chimie Bactérienne, IBSM, CNRS, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Jeanine Ratouchniak
- Laboratoire de Chimie Bactérienne, IBSM, CNRS, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Gaël Brasseur
- Laboratoire de Bioénergétique et Ingénierie des Protéines, IBSM, CNRS, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Elisabeth Lojou
- Laboratoire de Bioénergétique et Ingénierie des Protéines, IBSM, CNRS, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Ricardo Amils
- Universidad Autonoma de Madrid, Centro de Biologia Molecular, Cantoblanco, Madrid, Spain
| | - Violaine Bonnefoy
- Laboratoire de Chimie Bactérienne, IBSM, CNRS, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| |
Collapse
|
20
|
Ciurli S, Musiani F. High potential iron-sulfur proteins and their role as soluble electron carriers in bacterial photosynthesis: tale of a discovery. PHOTOSYNTHESIS RESEARCH 2005; 85:115-31. [PMID: 15977063 DOI: 10.1007/s11120-004-6556-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2001] [Accepted: 11/22/2001] [Indexed: 05/03/2023]
Abstract
This review is an attempt to retrace the chronicle of the discovery of the role of high-potential iron-sulfur proteins (HiPIPs) as electron carriers in the photosynthetic chain of bacteria. Data and facts are presented through the magnifying lenses of the authors, using their best judgment to filter and elaborate on the many facets of the research carried out on this class of proteins over the years. The tale is divided into four main periods: the seeds, the blooming, the ripening, and the harvest, representing the times from the discovery of these proteins to the most recent advancements in the understanding of the relationship between their structure and their function.
Collapse
Affiliation(s)
- Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Agro-Environmental Science and Technology, University of Bologna Viale Giuseppe Fanin 40, 40127, Bologna, Italy.
| | | |
Collapse
|
21
|
Nogi T, Hirano Y, Miki K. Structural and functional studies on the tetraheme cytochrome subunit and its electron donor proteins: the possible docking mechanisms during the electron transfer reaction. PHOTOSYNTHESIS RESEARCH 2005; 85:87-99. [PMID: 15977061 DOI: 10.1007/s11120-004-2416-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2004] [Accepted: 08/30/2004] [Indexed: 05/03/2023]
Abstract
The photosynthetic reaction centers (RCs) classified as the group II possess a peripheral cytochrome (Cyt) subunit, which serves as the electron mediator to the special-pair. In the cycle of the photosynthetic electron transfer reactions, the Cyt subunit accepts electrons from soluble electron carrier proteins, and re-reduces the photo-oxidized special-pair of the bacteriochlorophyll. Physiologically, high-potential cytochromes such as the cytochrome c2 and the high-potential iron-sulfur protein (HiPIP) function as the electron donors to the Cyt subunit. Most of the Cyt subunits possess four heme c groups, and it was unclear which heme group first accepts the electron from the electron donor. The most distal heme to the special-pair, the heme-1, has a lower redox potential than the electron donors, which makes it difficult to understand the electron transfer mechanism mediated by the Cyt subunit. Extensive mutagenesis combined with kinetic studies has made a great contribution to our understanding of the molecular interaction mechanisms, and has demonstrated the importance of the region close to the heme-1 in the electron transfer. Moreover, crystallographic studies have elucidated two high-resolution three-dimensional structures for the RCs containing the Cyt subunit, the Blastochloris viridis and Thermochromatium tepidum RCs, as well as the structures of their electron donors. An examination of the structural data also suggested that the binding sites for both the cytochrome c2 and the HiPIP are located adjacent to the solvent-accessible edge of the heme-1. In addition, it is also indicated by the structural and biochemical data that the cytochrome c2 and the HiPIP dock with the Cyt subunit by c2 is recognized through electrostatic interactions while hydrophobic interactions are important in the HiPIP docking.
Collapse
Affiliation(s)
- Terukazu Nogi
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, 565-0871, Japan
| | | | | |
Collapse
|
22
|
Dey A, Glaser T, Couture MMJ, Eltis LD, Holm RH, Hedman B, Hodgson KO, Solomon EI. Ligand K-Edge X-ray Absorption Spectroscopy of [Fe4S4]1+,2+,3+ Clusters: Changes in Bonding and Electronic Relaxation upon Redox. J Am Chem Soc 2004; 126:8320-8. [PMID: 15225075 DOI: 10.1021/ja0484956] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sulfur K-edge X-ray absorption spectroscopy (XAS) is reported for [Fe(4)S(4)](1+,2+,3+) clusters. The results are quantitatively and qualitatively compared with DFT calculations. The change in covalency upon redox in both the [Fe(4)S(4)](1+/2+) (ferredoxin) and the [Fe(4)S(4)](2+/3+) (HiPIP) couple are much larger than that expected from just the change in number of 3d holes. Moreover, the change in the HiPIP couple is higher than that of the ferredoxin couple. These changes in electronic structure are analyzed using DFT calculations in terms of contributions from the nature of the redox active molecular orbital (RAMO) and electronic relaxation. The results indicate that the RAMO of HiPIP has 50% ligand character, and hence, the HiPIP redox couple involves limited electronic relaxation. Alternatively, the RAMO of the ferredoxin couple is metal-based, and the ferredoxin redox couple involves extensive electronic relaxation. The contributions of these RAMO differences to ET processes in the different proteins are discussed.
Collapse
Affiliation(s)
- Abhishek Dey
- Department of Chemistry and Stanford Synchrotron Radiation Laboratory, Stanford University, Stanford, CA 94305, USA
| | | | | | | | | | | | | | | |
Collapse
|
23
|
Kipping M, Lilie H, Lindenstrauss U, Andreesen JR, Griesinger C, Carlomagno T, Brüser T. Structural studies on a twin-arginine signal sequence. FEBS Lett 2003; 550:18-22. [PMID: 12935879 DOI: 10.1016/s0014-5793(03)00804-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Translocation of folded proteins across biological membranes can be mediated by the so-called 'twin-arginine translocation' (Tat) system. To be translocated, Tat substrates require N-terminal signal sequences which usually contain the eponymous twin-arginine motif. Here we report the first structural analysis of a twin-arginine signal sequence, the signal sequence of the high potential iron-sulfur protein from Allochromatium vinosum. Nuclear magnetic resonance (NMR) analyses of amide proton resonances did not indicate a signal sequence structure. Accordingly, data from H/D exchange matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry showed that the amide protons of the signal sequence exchange rapidly, indicating the absence of secondary structure in the signal sequence up to L29. We conclude that the conserved twin-arginine motif does not form a structure by itself or as a result of intramolecular interactions.
Collapse
Affiliation(s)
- Marc Kipping
- Max Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, D-06120 Halle, Germany
| | | | | | | | | | | | | |
Collapse
|
24
|
Lieutaud C, Nitschke W, Verméglio A, Parot P, Schoepp-Cothenet B. HiPIP in Rubrivivax gelatinosus is firmly associated to the membrane in a conformation efficient for electron transfer towards the photosynthetic reaction centre. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1557:83-90. [PMID: 12615351 DOI: 10.1016/s0005-2728(02)00397-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
High potential iron-sulfur protein (HiPIP), a small soluble redox protein, has been shown to serve in vivo as electron donor to the photosynthetic reaction centre (RC) in Rubrivivax gelatinosus [Biochemistry 34 (1995) 11736]. The results of time-resolved optical spectroscopy on membrane-fragments from this organism indicates that the photooxidized RC is re-reduced by HiPIP even in the absence of the soluble fraction. This implies that a significant fraction of HiPIP can firmly bind to the membrane in a conformation able to interact with the RCs. Salt treatment of the membrane-fragments abolishes these re-reduction kinetics, demonstrating the presence of HiPIP on the membrane due to association with the RC rather than due to simple trapping in hypothetical chromatophores. The existence of such a functional complex in membranes is confirmed and its structure further examined by electron paramagnetic resonance (EPR) performed on membrane-fragments. Orientation-dependent EPR spectra of HiPIP were recorded on partially ordered membranes, oxidized either chemically or photochemically. Whereas hardly any preferential orientation of the HiPIP was seen in the chemically oxidised sample, a subpopulation of HiPIP showing specific orientations could be photooxidised. This fraction arises from the electron transfer complex between HiPIP and the RC.
Collapse
Affiliation(s)
- Clément Lieutaud
- Laboratoire de Biophysique des Transporteurs d'Electrons, Faculté des Sciences de Luminy, 136 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | | | | | | | | |
Collapse
|
25
|
Brüser T, Yano T, Brune DC, Daldal F. Membrane targeting of a folded and cofactor-containing protein. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:1211-21. [PMID: 12631279 DOI: 10.1046/j.1432-1033.2003.03481.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Targeting of proteins to and translocation across the membranes is a fundamental biological process in all organisms. In bacteria, the twin arginine translocation (Tat) system can transport folded proteins. Here, we demonstrate in vivo that the high potential iron-sulfur protein (HiPIP) from Allochromatium vinosum is translocated into the periplasmic space by the Tat system of Escherichia coli. In vitro, reconstituted HiPIP precursor (preHoloHiPIP) was targeted to inverted membrane vesicles from E. coli by a process requiring ATP when the Tat substrate was properly folded. During membrane targeting, the protein retained its cofactor, indicating that it was targeted in a folded state. Membrane targeting did not require a twin arginine motif and known Tat system components. On the basis of these findings, we propose that a pathway exists for the insertion of folded cofactor-containing proteins such as HiPIP into the bacterial cytoplasmic membrane.
Collapse
Affiliation(s)
- Thomas Brüser
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104-6018, USA.
| | | | | | | |
Collapse
|
26
|
Torrens F. Calculation of organic solvent–water partition coefficients of iron–sulfur protein models. Polyhedron 2002. [DOI: 10.1016/s0277-5387(02)00956-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
27
|
Beinert H. Spectroscopy of succinate dehydrogenases, a historical perspective. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1553:7-22. [PMID: 11803014 DOI: 10.1016/s0005-2728(01)00235-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
An attempt is made to retrace, from personal experience, the discovery of redox-reactive non-heme iron in living matter, which turned out to occur in the form of iron-sulfur (Fe-S) clusters, and then to recount the immediate application of this knowledge in exploring the composition of the mitochondrial respiratory chain, and in the rather detailed description of the workings of its components and, for the purposes of the present volume, of succinate dehydrogenase. The relationship of these events to the general status of technology and the available methodology and instrumentation is considered in some detail, with the conclusion that there scarcely was a way that these discoveries could have been made earlier. It is then shown how methods, techniques and interpretations of results were developed and evolved during the applications that were made to a complex problem such as that of the composition, structure and functioning of succinate dehydrogenase. A tabulation of the most significant events--concerning specifically spectroscopy and its interpretations--in this development is given up to the year 2000.
Collapse
Affiliation(s)
- Helmut Beinert
- Institute for Enzyme Research and Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison, 1710 University Avenue, Madison, WI 53705-4098, USA.
| |
Collapse
|
28
|
Johnson KA, Amster IJ. First observation by mass spectrometry of a 3+ oxidation state for a [4Fe-4S] metalloprotein: an ESI-FTICR mass spectrometry study of the high potential iron-sulfur protein from Chromatium vinosum. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2001; 12:819-825. [PMID: 11444604 DOI: 10.1016/s1044-0305(01)00263-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FTICR) is used to measure the molecular weight of the high potential iron-sulfur protein (HiPIP) from Chromatium vinosum (C. vinosum) and its corresponding apoprotein. By accurate mass measurement of the metalloprotein, the oxidation state of the [4Fe-4S] metal center is assigned as 3+. This is the highest oxidation state yet observed by mass spectrometry for a [4Fe-4S] cluster, which usually appears in the 2+ oxidation state. In order to make this assignment correctly, the mass spectrum of the apoprotein was acquired, and a 1 Da difference was found between the molecular mass of the apoprotein and its published amino acid sequence. The mass spectra of the trypsin and cyanogen bromide digests of the alkylated apoprotein were obtained, and the data suggests that the C-terminal glycine residue is amidated.
Collapse
Affiliation(s)
- K A Johnson
- Department of Chemistry, The University of Georgia, Athens 30602-2556, USA
| | | |
Collapse
|
29
|
Metzler DE, Metzler CM, Sauke DJ. Transition Metals in Catalysis and Electron Transport. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50019-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
30
|
Ambler RP, Daniel M, Meyer TE, Cusanovich MA. Amino acid sequences of two high-potential iron-sulfur proteins (HiPIPs) from the moderately halophilic purple phototrophic bacterium, Rhodospirillum salinarum. Arch Biochem Biophys 1999; 369:143-8. [PMID: 10462450 DOI: 10.1006/abbi.1999.1323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The amino acid sequences of two very different high-potential iron-sulfur protein (HiPIP) isozymes have been determined from the moderately halophilic purple phototrophic bacterium, Rhodospirillum salinarum. Iso-1 HiPIP, which is monomeric and contains 57 amino acid residues, is most similar to the Thiobacillus ferrooxidans iron-oxidizing enzyme (45% identity and a 6-residue deletion). On the other hand, iso-2 HiPIP, which is isolated as an oligomer, contains a peptide chain with 54 amino acid residues. It is the smallest reported to date and is only 31% identical to iso-1 HiPIP. A massive deletion of 17 residues is found at the N-terminus, such that only 2 residues remain prior to the first cysteine. Iso-2 HiPIP also has a 12-residue insertion and a 5-residue deletion. Prior to this study, there were only 2 absolutely conserved residues (Tyr 19 and Gly 75, Chromatium numbering) in addition to the 4 iron-sulfur cluster binding cysteine residues among the 13 HiPIPs sequenced to date. We found that Tyr 19 is absent in iso-2 HiPIP along with the entire N-terminal loop. Moreover, Gly 75 is substituted in both R. salinarum HiPIPs. These characteristics make the R. salinarum HiPIPs, and especially iso-2, the most divergent yet characterized.
Collapse
Affiliation(s)
- R P Ambler
- Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh, EH9 3JR, Scotland.
| | | | | | | |
Collapse
|
31
|
|
32
|
O'Connell TM, Wang L, Tropsha A, Hermans J. The ?random-coil? state of proteins: Comparison of database statistics and molecular simulations. Proteins 1999. [DOI: 10.1002/(sici)1097-0134(19990901)36:4<407::aid-prot4>3.0.co;2-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
33
|
Schoepp B, Brugna M, Lebrun E, Nitschke W. Iron-Sulfur Centers Involved in Photosynthetic Light Reactions. ADVANCES IN INORGANIC CHEMISTRY 1999. [DOI: 10.1016/s0898-8838(08)60082-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
34
|
Sticht H, Rösch P. The structure of iron-sulfur proteins. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1998; 70:95-136. [PMID: 9785959 DOI: 10.1016/s0079-6107(98)00027-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Ferredoxins are a group of iron-sulfur proteins for which a wealth of structural and mutational data have recently become available. Previously unknown structures of ferredoxins which are adapted to halophilic, acidophilic or hyperthermophilic environments and new cysteine patterns for cluster ligation and non-cysteine cluster ligation have been described. Site-directed mutagenesis experiments have given insight into factors that influence the geometry, stability, redox potential, electronic properties and electron-transfer reactivity of iron-sulfur clusters.
Collapse
Affiliation(s)
- H Sticht
- Lehrstuhl für Struktur und Chemie der Biopolymere, Universität Bayreuth, Germany.
| | | |
Collapse
|
35
|
Brüser T, Deutzmann R, Dahl C. Evidence against the double-arginine motif as the only determinant for protein translocation by a novel Sec-independent pathway in Escherichia coli. FEMS Microbiol Lett 1998; 164:329-36. [PMID: 9682482 DOI: 10.1111/j.1574-6968.1998.tb13106.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Proteins which are synthesized with a signal peptide containing a 'double-arginine' motif may be translocated across the bacterial cytoplasmic membrane by a mechanism that is different from the known Sec and signal recognition particle pathways. The function of the double-arginine motif as a determinant for this novel pathway was studied by expressions of gene constructs coding for the high potential iron-sulfur protein (HiPIP) from Chromatium vinosum D in Escherichia coli. When the protein was produced with its original double-arginine motif-containing signal peptide, it was in part translocated into the periplasm and thereby processed, as shown by immunoblots after cell fractionation and N-terminal sequencing of purified HiPIP. Processing was not inhibited significantly by 3 mM sodium azide, indicating that translocation of HiPIP occurs by a SecA-independent pathway. Translocation of HiPIP could be altered to the SecA-dependent mode when its signal peptide was substituted by that of PelB from Erwinia carotovora. When the HiPIP double-arginine motif (SRRDAVK) was introduced into the corresponding position of the PelB signal peptide, the transport pathway remained SecA-dependent. This indicates that additional determinants are required for translocation by the Sec-independent pathway.
Collapse
Affiliation(s)
- T Brüser
- Institut für Mikrobiologie and Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Germany.
| | | | | |
Collapse
|
36
|
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]
|
37
|
Cowan J, Lui SM. Structure-Function Correlations in High-Potential IRON Proteins. ADVANCES IN INORGANIC CHEMISTRY 1998. [DOI: 10.1016/s0898-8838(08)60028-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
38
|
Abstract
An examination of x-ray structures of single-cluster [4Fe-4S] proteins in the Protein Data Bank has revealed that all redox proteins and the glutamine 5-phosphoribosyl-l-pyrophosphate amidotransferase from Bacillus subtilis have a topological configuration arbitrarily designated as D, whereas the DNA repair enzyme endonuclease III from Escherichia coli has the opposite topological configuration L. This is the first example in which both senses of topological chirality have been observed in a class of proteins.
Collapse
Affiliation(s)
- C Liang
- Department of Chemistry, Princeton University, NJ 08544, USA
| | | |
Collapse
|
39
|
Bian S, Hemann CF, Hille R, Cowan JA. Characterization of an autoreduction pathway for the [Fe4S4]3+ cluster of mutant Chromatium vinosum high-potential iron proteins. Site-directed mutagenesis studies to probe the role of phenylalanine 66 in defining the stability of the [Fe4S4] center provide evidence for oxidative degradation via a [Fe3S4] cluster. Biochemistry 1996; 35:14544-52. [PMID: 8931551 DOI: 10.1021/bi961658l] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A number of point mutations of the conserved aromatic residue phenylalanine 66 (Phe66Tyr, -Asn, -Cys, -Ser) in Chromatium vinosum high-potential iron sulfur protein have been examined with the aim of understanding the functional role of this residue. Nonconservative replacements with polar residues have a minimal effect on the midpoint potential of the [Fe4S4]3+/2+ cluster, typically < +25 mV, with a maximum change of +40 mV for Phe66Asn. With the exception of the Phe66Tyr mutant, the oxidized state was found to be unstable relative to the recombinant native, with regeneration of the reduced state. The pathway for this transformation involves degradation of the cluster in a fraction of the sample, which provides the reducing equivalents required to bring about reduction of the remainder of the sample. This degradative reaction proceeds through a transient [Fe3S4]+ intermediate that is characterized by typical g values and power saturation behavior and is prompted by the increased solvent accessibility of the cluster core in the nonconservative Phe66 mutants as evidenced by 1H-15N HMQC NMR experiments. These results are consistent with a model where the critical role of the aromatic residues in the high-potential iron proteins is to protect the cluster from hydrolytic degradation in the oxidized state.
Collapse
Affiliation(s)
- S Bian
- Evans Laboratory of Chemistry, Ohio State University, Columbus 43210, USA
| | | | | | | |
Collapse
|
40
|
Holm RH, Kennepohl P, Solomon EI. Structural and Functional Aspects of Metal Sites in Biology. Chem Rev 1996; 96:2239-2314. [PMID: 11848828 DOI: 10.1021/cr9500390] [Citation(s) in RCA: 1850] [Impact Index Per Article: 66.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Richard H. Holm
- Departments of Chemistry, Harvard University, Cambridge, Massachusetts 02138, and Stanford University, Stanford, California 94305
| | | | | |
Collapse
|
41
|
Stephens PJ, Jollie DR, Warshel A. Protein Control of Redox Potentials of Ironminus signSulfur Proteins. Chem Rev 1996; 96:2491-2514. [PMID: 11848834 DOI: 10.1021/cr950045w] [Citation(s) in RCA: 312] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- P. J. Stephens
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482
| | | | | |
Collapse
|
42
|
Li D, Soriano A, Cowan JA. 19F NMR Studies of Fluorine-Labeled Chromatium vinosum High-Potential Iron Protein. Inorg Chem 1996. [DOI: 10.1021/ic951159t] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dawei Li
- Evans Laboratory of Chemistry, The Ohio State University, 120 West 18th Avenue, Columbus, Ohio 43210
| | - Aileen Soriano
- Evans Laboratory of Chemistry, The Ohio State University, 120 West 18th Avenue, Columbus, Ohio 43210
| | - J. A. Cowan
- Evans Laboratory of Chemistry, The Ohio State University, 120 West 18th Avenue, Columbus, Ohio 43210
| |
Collapse
|
43
|
Ciurli S, Cremonini MA, Kofod P, Luchinat C. 1H NMR of high-potential iron-sulfur protein from the purple non-sulfurbacterium Rhodoferax fermentans. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 236:405-11. [PMID: 8612609 DOI: 10.1111/j.1432-1033.1996.00405.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Oxidized and reduced forms of high-potential iron-sulfur protein (HiPIP) from the purple non-sulfur photosynthetic bacterium Rhodoferax fermentans have been characterized using 1H-NMR spectroscopy. Pairwise and sequence-specific assignments of hyperfine-shifted 1H-NMR signals to protons of cysteine residues bound to the [4Fe-4S]3+/2+ cluster have been performed using one-dimensional NOE and exchange spectroscopy experiments. 1H-NMR hyperfine shifts and relaxation rates of cluster-bound Cys beta-CH2 protons indicate that in the [4Fe-4S]3+ cluster one iron ion can be formally described as Fe(III), while electron density corresponding to one electron is unevenly delocalized onto the remaining three iron ions. This delocalization is effected by means of two different electronic distributions interconverting rapidly on the NMR time scale. The mechanism of paramagnetic proton relaxation, studied by analyzing longitudinal relaxation rates of Cys beta-CH2 protons in HiPIPs from six different sources as a function of the Fe-S-C beta-C alpha dihedral angle, indicate that the major contribution is due to a dipolar metal-centered mechanism, with a non-negligible contribution from a ligand-centered dipolar mechanism which involves the 3p orbital of the Cys sulfur atom. A semi-quantitative tool for extracting structural information from relaxation time measurements is proposed.
Collapse
Affiliation(s)
- S Ciurli
- Institute of Agricultural Chemistry, University of Bologna, Italy
| | | | | | | |
Collapse
|
44
|
Li D, Agarwal A, Cowan JA. Evaluation of Solvent Accessibility to the [Fe(4)S(4)] Binding Pocket in Native and Tyr19 Mutant High Potential Iron Proteins by (1)H-(15)N HMQC and (19)F NMR Experiments. Inorg Chem 1996; 35:1121-1125. [PMID: 11666298 DOI: 10.1021/ic951160s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The solvent accessibility of Chromatium vinosumhigh potential iron protein (HiPIP) has been investigated by use of (1)H-(15)N HMQC, and (19)F NMR spectroscopy. These NMR experiments indicate that solvent accessibility to the cluster core is similar, and minimal, for the reduced and oxidized states of native HiPIP, but increases significantly for mutant proteins (Tyr19Leu and Tyr19His). These results support a proposed role [Agarwal, A.; Li, D.; Cowan, J. A. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 9440-9444] for Tyr19 in maintaining hydrolytic stability of the [Fe(4)S(4)] cluster, and demonstrate a general strategy for mapping out the solvent accessibility of protein-bound metalloredox prosthetic centers.
Collapse
Affiliation(s)
- Dawei Li
- Evans Laboratory of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | | | | |
Collapse
|
45
|
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
| | | | | |
Collapse
|
46
|
Banci L, Bertini I, Ciurli S, Luchinat C, Pierattelli R. Rationalization of the reduction potentials within the series of the high potential iron-sulfur proteins. Inorganica Chim Acta 1995. [DOI: 10.1016/0020-1693(95)04540-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
47
|
Bertini I, Eltis LD, Felli IC, Kastrau DHW, Luchinat C, Piccioli M. The Solution Structure of Oxidized HiPIP I fromEctothiorhodospira halophila; Can NMR Spectroscopy Be Used to Probe Rearrangements Associated with Electron Transfer Processes? Chemistry 1995. [DOI: 10.1002/chem.19950010906] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
48
|
Iwagami SG, Creagh AL, Haynes CA, Borsari M, Felli IC, Piccioli M, Eltis LD. The role of a conserved tyrosine residue in high-potential iron sulfur proteins. Protein Sci 1995; 4:2562-72. [PMID: 8580847 PMCID: PMC2143049 DOI: 10.1002/pro.5560041213] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Conserved tyrosine-12 of Ectothiorhodospira halophila high-potential iron sulphur protein (HiPIP) iso-I was substituted with phenylalanine (Y12F), histidine (Y12H), tryptophan (Y12W), isoleucine (Y12I), and alanine (Y12A). Variants Y12A and Y12I were expressed to reasonable levels in cells grown at lower temperatures, but decomposed during purification. Variants Y12F, Y12H, and Y12W were substantially destabilized with respect to the recombinant wild-type HiPIP (rcWT) as determined by differential scanning calorimetry over a pH range of 7.0-11.0. Characterization of the Y12F variant by NMR indicates that the principal structural differences between this variant and the rcWT HiPIP result from the loss of the two hydrogen bonds of the Tyr-12 hydroxyl group with Asn-14 O delta 1 and Lys-59 NH, respectively. The effect of the loss of the latter interaction is propagated through the Lys-59/Val-58 peptide bond, thereby perturbing Gly-46. The delta delta GDapp of Y12F of 2.3 kcal/mol with respect to rcWT HiPIP (25 degrees C, pH 7.0) is entirely consistent with the contribution of these two hydrogen bonds to the stability of the latter. CD measurements show that Tyr-12 influences several electronic transitions within the cluster. The midpoint reduction potentials of variants Y12F, Y12H, and Y12W were 17, 19, and 22 mV (20 mM MOPS, 0.2 M sodium chloride, pH 6.98, 25 degrees C), respectively, higher than that of rcWT HiPIP. The current results indicate that, although conserved Tyr-12 modulates the properties of the cluster, its principle function is to stabilize the HiPIP through hydrogen bonds involving its hydroxyl group and electrostatic interactions involving its aromatic ring.
Collapse
Affiliation(s)
- S G Iwagami
- Biotechnology Laboratory, University of British Columbia, Vancouver, Canada
| | | | | | | | | | | | | |
Collapse
|
49
|
Heering HA, Bulsink YB, Hagen WR, Meyer TE. Reversible super-reduction of the cubane [4Fe-4S](3+;2+;1+) in the high-potential iron-sulfur protein under non-denaturing conditions. EPR spectroscopic and electrochemical studies. EUROPEAN JOURNAL OF BIOCHEMISTRY 1995; 232:811-817. [PMID: 7588720 DOI: 10.1111/j.1432-1033.1995.0811a.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The reversible 2 x 1 e- reduction of the cubane cluster from oxidized to reduced to super-reduced states ([4Fe-4S]3+<-->[4Fe-4S]2+<-->[4Fe-4S]1+) was studied in high-potential iron-sulfur proteins (HiPIPs). Super-reduction to the 1+ state was not observed in any of the seven HiPIPs tested during cyclic voltammetry (down to -0.95 V). However, equilibration at low potential (pH 7.5) of Rhodopila globiformis HiPIP yields a transient peak around -0.47 V due to the oxidation of super-reduced HiPIP adsorbed at the electrode. The peak area depends on the equilibration potential according to a one-electron Nernst curve with a half-wave potential at -0.91 V. Reduction of R. globiformis HiPIP with titanium (III)citrate at pH 9.5 is very slow [pseudo-first-order half-life of 23 min with a 100-fold excess Ti(III)] but is reversible, and the EPR spectrum with g values of 2.04 and 1.92 is similar to that of reduced [4Fe-4S]1+ ferredoxins. Chemical or electrochemical reoxidation of the super-reduced form resulted in an EPR spectrum with g parallel = 2.12 and g perpendicular = 2.03, i.e. identical to that of oxidized HiPIP. From the equilibrium concentration of super-reduced HiPIP at a low concentration of Ti(III), a reduction potential of -0.64 V can be estimated. Super-reduction of the large HiPIP (iso-2) from Rhodospirillum salinarum is also possible with Ti(III)(gz = 2.05) but the super-reduced state is unstable. No super-reduction with Ti(III) was observed for the other HiPIPs. The difference between the electrochemically observed reduction potential and oxidation potential is explained by a fast and reversible conformational change upon super-reduction. The rate of super-reduction with Ti(III) is limited by the small amount (0.1%) of HiPIP in the 2+ state with the super-reduced conformation.
Collapse
Affiliation(s)
- H A Heering
- Department of Biochemistry, Wageningen Agricultural University, The Netherlands
| | | | | | | |
Collapse
|
50
|
Heering HA, Bulsink YBM, Hagen WR, Meyer TE. Reversible Super-Reduction of the Cubane [4Fe-4S](3+;2+;1+) in the High-Potential Iron-Sulfur Protein Under Non-Denaturing Conditions. EPR Spectroscopic and Electrochemical Studies. ACTA ACUST UNITED AC 1995. [DOI: 10.1111/j.1432-1033.1995.tb20877.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|