1
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Valetti F, Morra S, Barbieri L, Dezzani S, Ratto A, Catucci G, Sadeghi SJ, Gilardi G. Oxygen-resistant [FeFe]hydrogenases: new biocatalysis tools for clean energy and cascade reactions. Faraday Discuss 2024; 252:223-240. [PMID: 38836410 DOI: 10.1039/d4fd00010b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
The use of enzymes to generate hydrogen, instead of using rare metal catalysts, is an exciting area of study in modern biochemistry and biotechnology, as well as biocatalysis driven by sustainable hydrogen. Thus far, the oxygen sensitivity of the fastest hydrogen-producing/exploiting enzymes, [FeFe]hydrogenases, has hindered their practical application, thereby restricting innovations mainly to their [NiFe]-based, albeit slower, counterparts. Recent exploration of the biodiversity of clostridial hydrogen-producing enzymes has yielded the isolation of representatives from a relatively understudied group. These enzymes possess an inherent defense mechanism against oxygen-induced damage. This discovery unveils fresh opportunities for applications such as electrode interfacing, biofuel cells, immobilization, and entrapment for enhanced stability in practical uses. Furthermore, it suggests potential combinations with cascade reactions for CO2 conversion or cofactor regeneration, like NADPH, facilitating product separation in biotechnological processes. This work provides an overview of this new class of biocatalysts, incorporating unpublished protein engineering strategies to further investigate the dynamic mechanism of oxygen protection and to address crucial details remaining elusive such as still unidentified switching hot-spots and their effects. Variants with improved kcat as well as chimeric versions with promising features to attain gain-of-function variants and applications in various biotechnological processes are also presented.
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Affiliation(s)
- Francesca Valetti
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy.
| | - Simone Morra
- Faculty of Engineering, University of Nottingham, Nottingham, UK
| | - Lisa Barbieri
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy.
- University School for Advanced Studies IUSS Pavia, Italy
| | - Sabrina Dezzani
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy.
- University School for Advanced Studies IUSS Pavia, Italy
| | - Alessandro Ratto
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy.
| | - Gianluca Catucci
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy.
| | - Sheila J Sadeghi
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy.
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy.
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2
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Kisgeropoulos EC, Bharadwaj VS, Mulder DW, King PW. The Contribution of Proton-Donor pKa on Reactivity Profiles of [FeFe]-hydrogenases. Front Microbiol 2022; 13:903951. [PMID: 36246213 PMCID: PMC9563086 DOI: 10.3389/fmicb.2022.903951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/17/2022] [Indexed: 11/24/2022] Open
Abstract
The [FeFe]-hydrogenases are enzymes that catalyze the reversible activation of H2 coupled to the reduction-oxidation of electron carriers. Members of the different taxonomic groups of [FeFe]-hydrogenases display a wide range of preference, or bias, for H2 oxidation or H2 production reactions, despite sharing a common catalytic cofactor, or H-cluster. Identifying the properties that control reactivity remains an active area of investigation, and models have emerged that include diversity in the catalytic site coordination environments and compositions of electron transfer chains. The kinetics of proton-coupled electron transfer at the H-cluster might be expected to be a point of control of reactivity. To test this hypothesis, systematic changes were made to the conserved cysteine residue that functions in proton exchange with the H-cluster in the three model enzymes: CaI, CpII, and CrHydA1. CaI and CpII both employ electron transfer accessory clusters but differ in bias, whereas CrHydA1 lacks accessory clusters having only the H-cluster. Changing from cysteine to either serine (more basic) or aspartate (more acidic) modifies the sidechain pKa and thus the barrier for the proton exchange step. The reaction rates for H2 oxidation or H2 evolution were surveyed and measured for model [FeFe]-hydrogenases, and the results show that the initial proton-transfer step in [FeFe]-hydrogenase is tightly coupled to the control of reactivity; a change from cysteine to more basic serine favored H2 oxidation in all enzymes, whereas a change to more acidic aspartate caused a shift in preference toward H2 evolution. Overall, the changes in reactivity profiles were profound, spanning 105 in ratio of the H2 oxidation-to-H2 evolution rates. The fact that the change in reactivity follows a common trend implies that the effect of changing the proton-transfer residue pKa may also be framed as an effect on the scaling relationship between the H-cluster di(thiolmethyl)amine (DTMA) ligand pKa and E m values of the H-cluster. Experimental observations that support this relationship, and how it relates to catalytic function in [FeFe]-hydrogenases, are discussed.
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Affiliation(s)
| | | | | | - Paul W. King
- National Renewable Energy Lab, Biosciences Center, Golden, CO, United States
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3
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Fontenot CR, Cheng Z, Ding H. Nitric oxide reversibly binds the reduced [2Fe-2S] cluster in mitochondrial outer membrane protein mitoNEET and inhibits its electron transfer activity. Front Mol Biosci 2022; 9:995421. [PMID: 36158570 PMCID: PMC9490426 DOI: 10.3389/fmolb.2022.995421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/12/2022] [Indexed: 11/30/2022] Open
Abstract
MitoNEET is a mitochondrial outer membrane protein that regulates energy metabolism, iron homeostasis, and production of reactive oxygen species in cells. Aberrant expression of mitoNEET in tissues has been linked to type II diabetes, neurodegenerative diseases, and several types of cancer. Structurally, the N-terminal domain of mitoNEET has a single transmembrane alpha helix that anchors the protein to mitochondrial outer membrane. The C-terminal cytosolic domain of mitoNEET hosts a redox active [2Fe-2S] cluster via an unusual ligand arrangement of three cysteine and one histidine residues. Here we report that the reduced [2Fe-2S] cluster in the C-terminal cytosolic domain of mitoNEET (mitoNEET45-108) is able to bind nitric oxide (NO) without disruption of the cluster. Importantly, binding of NO at the reduced [2Fe-2S] cluster effectively inhibits the redox transition of the cluster in mitoNEET45-108. While the NO-bound [2Fe-2S] cluster in mitoNEET45-108 is stable, light excitation releases NO from the NO-bound [2Fe-2S] cluster and restores the redox transition activity of the cluster in mitoNEET45-108. The results suggest that NO may regulate the electron transfer activity of mitoNEET in mitochondrial outer membrane via reversible binding to its reduced [2Fe-2S] cluster.
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Affiliation(s)
| | | | - Huangen Ding
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States
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4
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Valer L, Rossetto D, Parkkila T, Sebastianelli L, Guella G, Hendricks AL, Cowan JA, Sang L, Mansy SS. Histidine Ligated Iron-Sulfur Peptides. Chembiochem 2022; 23:e202200202. [PMID: 35674331 PMCID: PMC9400863 DOI: 10.1002/cbic.202200202] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/08/2022] [Indexed: 11/17/2022]
Abstract
Iron-sulfur clusters are thought to be ancient cofactors that could have played a role in early protometabolic systems. Thus far, redox active, prebiotically plausible iron-sulfur clusters have always contained cysteine ligands to the cluster. However, extant iron-sulfur proteins can be found to exploit other modes of binding, including ligation by histidine residues, as seen with [2Fe-2S] Rieske and MitoNEET proteins. Here, we investigated the ability of cysteine- and histidine-containing peptides to coordinate a mononuclear Fe2+ center and a [2Fe-2S] cluster and compare their properties with purified iron-sulfur proteins. The iron-sulfur peptides were characterized by UV-vis, circular dichroism, and paramagnetic NMR spectroscopies and cyclic voltammetry. Small (≤6 amino acids) peptides can coordinate [2Fe-2S] clusters through a combination of cysteine and histidine residues with similar reduction potentials as their corresponding proteins. Such complexes may have been important for early cell-like systems.
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Affiliation(s)
- Luca Valer
- D-CIBIOUniversity of Trentovia Sommarive 938123Trento 28123Italy
- Department of ChemistryUniversity of Alberta11227 Saskatchewan DriveEdmontonT6G 2G2AlbertaCanada
| | - Daniele Rossetto
- D-CIBIOUniversity of Trentovia Sommarive 938123Trento 28123Italy
- Department of ChemistryUniversity of Alberta11227 Saskatchewan DriveEdmontonT6G 2G2AlbertaCanada
| | - Taylor Parkkila
- Department of ChemistryUniversity of Alberta11227 Saskatchewan DriveEdmontonT6G 2G2AlbertaCanada
| | - Lorenzo Sebastianelli
- Department of ChemistryUniversity of Alberta11227 Saskatchewan DriveEdmontonT6G 2G2AlbertaCanada
| | - Graziano Guella
- Department of PhysicsUniversity of TrentoVia Sommarive 14Trento38123Italy
| | - Amber L. Hendricks
- Department of Chemistry and BiochemistryThe Ohio State University100 West 18th AveColumbusOH 43210USA
| | - James A. Cowan
- Department of Chemistry and BiochemistryThe Ohio State University100 West 18th AveColumbusOH 43210USA
| | - Lingzi Sang
- Department of ChemistryUniversity of Alberta11227 Saskatchewan DriveEdmontonT6G 2G2AlbertaCanada
| | - Sheref S. Mansy
- D-CIBIOUniversity of Trentovia Sommarive 938123Trento 28123Italy
- Department of ChemistryUniversity of Alberta11227 Saskatchewan DriveEdmontonT6G 2G2AlbertaCanada
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5
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Senger M, Duan J, Pavliuk MV, Apfel UP, Haumann M, Stripp ST. Trapping an Oxidized and Protonated Intermediate of the [FeFe]-Hydrogenase Cofactor under Mildly Reducing Conditions. Inorg Chem 2022; 61:10036-10042. [PMID: 35729755 DOI: 10.1021/acs.inorgchem.2c00954] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The H-cluster is the catalytic cofactor of [FeFe]-hydrogenase, a metalloenzyme that catalyzes the formation of dihydrogen (H2). The catalytic diiron site of the H-cluster carries two cyanide and three carbon monoxide ligands, making it an excellent target for IR spectroscopy. In previous work, we identified an oxidized and protonated H-cluster species, whose IR signature differs from that of the oxidized resting state (Hox) by a small but distinct shift to higher frequencies. This "blue shift" was explained by a protonation at the [4Fe-4S] subcomplex of the H-cluster. The novel species, denoted HoxH, was preferentially accumulated at low pH and in the presence of the exogenous reductant sodium dithionite (NaDT). When HoxH was reacted with H2, the hydride state (Hhyd) was formed, a key intermediate of [FeFe]-hydrogenase turnover. A recent publication revisited our protocol for the accumulation of HoxH in wild-type [FeFe]-hydrogenase, concluding that inhibition by NaDT decay products rather than cofactor protonation causes the spectroscopic "blue shift". Here, we demonstrate that HoxH formation does not require the presence of NaDT (or its decay products), but accumulates also with the milder reductants tris(2-carboxyethyl)phosphine, dithiothreitol, or ascorbic acid, in particular at low pH. Our data consistently suggest that HoxH is accumulated when deprotonation of the H-cluster is impaired, thereby preventing the regain of the oxidized resting state Hox in the catalytic cycle.
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Affiliation(s)
- Moritz Senger
- Department of Chemistry, Physical Chemistry, Uppsala University, Uppsala 75120, Sweden
| | - Jifu Duan
- Faculty of Biology and Biotechnology, Photobiotechnology, Ruhr-Universität Bochum, Bochum 44801, Germany
| | - Mariia V Pavliuk
- Department of Chemistry, Physical Chemistry, Uppsala University, Uppsala 75120, Sweden
| | - Ulf-Peter Apfel
- Faculty of Chemistry and Biochemistry, Small Molecule Activation, Ruhr-Universität Bochum, Bochum 44801, Germany.,Electrosynthesis, Fraunhofer UMSICHT, Oberhausen 46047, Germany
| | - Michael Haumann
- Department of Physics, Biophysics of Metalloenzymes, Freie Universität Berlin, Berlin 14195, Germany
| | - Sven T Stripp
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Berlin 14195, Germany
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6
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Heghmanns M, Günzel A, Brandis D, Kutin Y, Engelbrecht V, Winkler M, Happe T, Kasanmascheff M. Fine-tuning of FeS proteins monitored via pulsed EPR redox potentiometry at Q-band. BIOPHYSICAL REPORTS 2021; 1:100016. [PMID: 36425453 PMCID: PMC9680799 DOI: 10.1016/j.bpr.2021.100016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/30/2021] [Indexed: 06/16/2023]
Abstract
As essential electron translocating proteins in photosynthetic organisms, multiple plant-type ferredoxin (Fdx) isoforms are involved in a high number of reductive metabolic processes in the chloroplast. To allow quick cellular responses under changing environmental conditions, different plant-type Fdxs in Chlamydomonas reinhardtii were suggested to have adapted their midpoint potentials to a wide range of interaction partners. We performed pulsed electron paramagnetic resonance (EPR) monitored redox potentiometry at Q-band on three Fdx isoforms for a straightforward determination of their midpoint potentials. Additionally, site-directed mutagenesis was used to tune the midpoint potential of CrFdx1 in a range of approximately -338 to -511 mV, confirming the importance of single positions in the protein environment surrounding the [2Fe2S] cluster. Our results present a new target for future studies aiming to modify the catalytic activity of CrFdx1 that plays an essential role either as electron acceptor of photosystem I or as electron donor to hydrogenases under certain conditions. Additionally, the precisely determined redox potentials in this work using pulsed EPR demonstrate an alternative method that provides additional advantages compared with the well-established continuous wave EPR technique.
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Affiliation(s)
- Melanie Heghmanns
- TU Dortmund University, Department of Chemistry and Chemical Biology, Dortmund, Germany
| | - Alexander Günzel
- Ruhr University Bochum, Faculty of Biology and Biotechnology, Photobiotechnology, Bochum, Germany
| | - Dörte Brandis
- TU Dortmund University, Department of Chemistry and Chemical Biology, Dortmund, Germany
| | - Yury Kutin
- TU Dortmund University, Department of Chemistry and Chemical Biology, Dortmund, Germany
| | - Vera Engelbrecht
- Ruhr University Bochum, Faculty of Biology and Biotechnology, Photobiotechnology, Bochum, Germany
| | - Martin Winkler
- Ruhr University Bochum, Faculty of Biology and Biotechnology, Photobiotechnology, Bochum, Germany
| | - Thomas Happe
- Ruhr University Bochum, Faculty of Biology and Biotechnology, Photobiotechnology, Bochum, Germany
| | - Müge Kasanmascheff
- TU Dortmund University, Department of Chemistry and Chemical Biology, Dortmund, Germany
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7
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Liang Q, DeMuth JC, Radović A, Wolford NJ, Neidig ML, Song D. [2Fe-2S] Cluster Supported by Redox-Active o-Phenylenediamide Ligands and Its Application toward Dinitrogen Reduction. Inorg Chem 2021; 60:13811-13820. [PMID: 34043353 DOI: 10.1021/acs.inorgchem.1c00683] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
As prevalent cofactors in living organisms, iron-sulfur clusters participate in not only the electron-transfer processes but also the biosynthesis of other cofactors. Many synthetic iron-sulfur clusters have been used in model studies, aiming to mimic their biological functions and to gain mechanistic insight into the related biological systems. The smallest [2Fe-2S] clusters are typically used for one-electron processes because of their limited capacity. Our group is interested in functionalizing small iron-sulfur clusters with redox-active ligands to enhance their electron storage capacity, because such functionalized clusters can potentially mediate multielectron chemical transformations. Herein we report the synthesis, structural characterization, and catalytic activity of a diferric [2Fe-2S] cluster functionalized with two o-phenylenediamide ligands. The electrochemical and chemical reductions of such a cluster revealed rich redox chemistry. The functionalized diferric cluster can store up to four electrons reversibly, where the first two reduction events are ligand-based and the remainder metal-based. The diferric [2Fe-2S] cluster displays catalytic activity toward silylation of dinitrogen, affording up to 88 equiv of the amine product per iron center.
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Affiliation(s)
- Qiuming Liang
- Davenport Chemical Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Joshua C DeMuth
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Aleksa Radović
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Nikki J Wolford
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Michael L Neidig
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Datong Song
- Davenport Chemical Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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8
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Abstract
This work demonstrates that the outer mitochondrial-anchored [2Fe-2S] mitoNEET is able to bind within the central cavity of the voltage-dependent anion channel (VDAC) and regulate its gating in a redox-dependent manner. These findings have implications for ferroptosis, apoptosis, and iron metabolism by linking VDAC function, mitoNEET, and the redox environment of the cell. Furthermore, these findings introduce a potential player to the many mechanisms that may alter VDAC’s governance in times of homeostasis or strife. MitoNEET is an outer mitochondrial membrane protein essential for sensing and regulation of iron and reactive oxygen species (ROS) homeostasis. It is a key player in multiple human maladies including diabetes, cancer, neurodegeneration, and Parkinson’s diseases. In healthy cells, mitoNEET receives its clusters from the mitochondrion and transfers them to acceptor proteins in a process that could be altered by drugs or during illness. Here, we report that mitoNEET regulates the outer-mitochondrial membrane (OMM) protein voltage-dependent anion channel 1 (VDAC1). VDAC1 is a crucial player in the cross talk between the mitochondria and the cytosol. VDAC proteins function to regulate metabolites, ions, ROS, and fatty acid transport, as well as function as a “governator” sentry for the transport of metabolites and ions between the cytosol and the mitochondria. We find that the redox-sensitive [2Fe-2S] cluster protein mitoNEET gates VDAC1 when mitoNEET is oxidized. Addition of the VDAC inhibitor 4,4′-diisothiocyanatostilbene-2,2′-disulfonate (DIDS) prevents both mitoNEET binding in vitro and mitoNEET-dependent mitochondrial iron accumulation in situ. We find that the DIDS inhibitor does not alter the redox state of MitoNEET. Taken together, our data indicate that mitoNEET regulates VDAC in a redox-dependent manner in cells, closing the pore and likely disrupting VDAC’s flow of metabolites.
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9
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Zeamari K, Gerbaud G, Grosse S, Fourmond V, Chaspoul F, Biaso F, Arnoux P, Sabaty M, Pignol D, Guigliarelli B, Burlat B. Tuning the redox properties of a [4Fe-4S] center to modulate the activity of Mo-bisPGD periplasmic nitrate reductase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:402-413. [DOI: 10.1016/j.bbabio.2019.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 11/30/2018] [Accepted: 01/25/2019] [Indexed: 11/15/2022]
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10
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Stegmaier K, Blinn CM, Bechtel DF, Greth C, Auerbach H, Müller CS, Jakob V, Reijerse EJ, Netz DJA, Schünemann V, Pierik AJ. Apd1 and Aim32 Are Prototypes of Bishistidinyl-Coordinated Non-Rieske [2Fe–2S] Proteins. J Am Chem Soc 2019; 141:5753-5765. [DOI: 10.1021/jacs.8b13274] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Edward J. Reijerse
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D45470 Mülheim an der Ruhr, Germany
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11
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Hemschemeier A, Happe T. The plasticity of redox cofactors: from metalloenzymes to redox-active DNA. Nat Rev Chem 2018. [DOI: 10.1038/s41570-018-0029-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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12
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The unique fold and lability of the [2Fe-2S] clusters of NEET proteins mediate their key functions in health and disease. J Biol Inorg Chem 2018; 23:599-612. [PMID: 29435647 PMCID: PMC6006223 DOI: 10.1007/s00775-018-1538-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/26/2018] [Indexed: 02/08/2023]
Abstract
NEET proteins comprise a new class of [2Fe-2S] cluster proteins. In human, three genes encode for NEET proteins: cisd1 encodes mitoNEET (mNT), cisd2 encodes the Nutrient-deprivation autophagy factor-1 (NAF-1) and cisd3 encodes MiNT (Miner2). These recently discovered proteins play key roles in many processes related to normal metabolism and disease. Indeed, NEET proteins are involved in iron, Fe-S, and reactive oxygen homeostasis in cells and play an important role in regulating apoptosis and autophagy. mNT and NAF-1 are homodimeric and reside on the outer mitochondrial membrane. NAF-1 also resides in the membranes of the ER associated mitochondrial membranes (MAM) and the ER. MiNT is a monomer with distinct asymmetry in the molecular surfaces surrounding the clusters. Unlike its paralogs mNT and NAF-1, it resides within the mitochondria. NAF-1 and mNT share similar backbone folds to the plant homodimeric NEET protein (At-NEET), while MiNT's backbone fold resembles a bacterial MiNT protein. Despite the variation of amino acid composition among these proteins, all NEET proteins retained their unique CDGSH domain harboring their unique 3Cys:1His [2Fe-2S] cluster coordination through evolution. The coordinating exposed His was shown to convey the lability to the NEET proteins' [2Fe-2S] clusters. In this minireview, we discuss the NEET fold and its structural elements. Special attention is given to the unique lability of the NEETs' [2Fe-2S] cluster and the implication of the latter to the NEET proteins' cellular and systemic function in health and disease.
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13
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Yin S, Bernstein ER. Photoelectron spectroscopy and density functional theory studies of (FeS) mH - (m = 2-4) cluster anions: effects of the single hydrogen. Phys Chem Chem Phys 2017; 20:367-382. [PMID: 29210391 DOI: 10.1039/c7cp07012h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single hydrogen containing iron hydrosulfide cluster anions (FeS)mH- (m = 2-4) are studied by photoelectron spectroscopy (PES) at 3.492 eV (355 nm) and 4.661 eV (266 nm) photon energies, and by Density Functional Theory (DFT) calculations. The structural properties, relative energies of different spin states and isomers, and the first calculated vertical detachment energies (VDEs) of different spin states for these (FeS)mH- (m = 2-4) cluster anions are investigated at various reasonable theory levels. Two types of structural isomers are found for these (FeS)mH- (m = 2-4) clusters: (1) the single hydrogen atom bonds to a sulfur site (SH-type); and (2) the single hydrogen atom bonds to an iron site (FeH-type). Experimental and theoretical results suggest such available different SH- and FeH-type structural isomers should be considered when evaluating the properties and behavior of these single hydrogen containing iron sulfide clusters in real chemical and biological systems. Compared to their related, respective pure iron sulfur (FeS)m- clusters, the first VDE trend of the diverse type (FeS)mH0,1- (m = 1-4) clusters can be understood through (1) the different electron distribution properties of their highest singly occupied molecular orbital employing natural bond orbital analysis (NBO/HSOMO), and (2) the partial charge distribution on the NBO/HSOMO localized sites of each cluster anion. Generally, the properties of the NBO/HSOMOs play the principal role with regard to the physical and chemical properties of all the anions. The change of cluster VDE from low to high is associated with the change in nature of their NBO/HSOMO from a dipole bound and valence electron mixed character, to a valence p orbital on S, to a valence d orbital on Fe, and to a valence p orbital on Fe or an Fe-Fe delocalized valence bonding orbital. For clusters having the same properties for NBO/HSOMOs, the partial charge distributions at the NBO/HSOMO localized sites additionally affect their VDEs: a more negative or less positive localized charge distribution is correlated with a lower first VDE. The single hydrogen in these (FeS)mH- (m = 2-4) cluster anions is suggested to affect their first VDEs through the different structure types (SH- or FeH-), the nature of the NBO/HSOMOs at the local site, and the value of partial charge number at the local site of the NBO/HSOMO.
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Affiliation(s)
- Shi Yin
- Department of Chemistry, NSF ERC for Extreme Ultraviolet Science and Technology, Colorado State University, Fort Collins, CO 80523, USA.
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14
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Albetel AN, Outten CE. Characterization of Glutaredoxin Fe-S Cluster-Binding Interactions Using Circular Dichroism Spectroscopy. Methods Enzymol 2017; 599:327-353. [PMID: 29746245 DOI: 10.1016/bs.mie.2017.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Monothiol glutaredoxins (Grxs) with a conserved Cys-Gly-Phe-Ser (CGFS) active site are iron-sulfur (Fe-S) cluster-binding proteins that interact with a variety of partner proteins and perform crucial roles in iron metabolism including Fe-S cluster transfer, Fe-S cluster repair, and iron signaling. Various analytical and spectroscopic methods are currently being used to monitor and characterize glutaredoxin Fe-S cluster-dependent interactions at the molecular level. The electronic, magnetic, and vibrational properties of the protein-bound Fe-S cluster provide a convenient handle to probe the structure, function, and coordination chemistry of Grx complexes. However, some limitations arise from sample preparation requirements, complexity of individual techniques, or the necessity for combining multiple methods in order to achieve a complete investigation. In this chapter, we focus on the use of UV-visible circular dichroism spectroscopy as a fast and simple initial approach for investigating glutaredoxin Fe-S cluster-dependent interactions.
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Affiliation(s)
| | - Caryn E Outten
- University of South Carolina, Columbia, SC, United States.
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15
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Pesce L, Calandrini V, Marjault HB, Lipper CH, Rossetti G, Mittler R, Jennings PA, Bauer A, Nechushtai R, Carloni P. Molecular Dynamics Simulations of the [2Fe-2S] Cluster-Binding Domain of NEET Proteins Reveal Key Molecular Determinants That Induce Their Cluster Transfer/Release. J Phys Chem B 2017; 121:10648-10656. [PMID: 29086562 PMCID: PMC5713697 DOI: 10.1021/acs.jpcb.7b10584] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The NEET proteins are a novel family of iron-sulfur proteins characterized by an unusual three cysteine and one histidine coordinated [2Fe-2S] cluster. Aberrant cluster release, facilitated by the breakage of the Fe-N bond, is implicated in a variety of human diseases, including cancer. Here, the molecular dynamics in the multi-microsecond timescale, along with quantum chemical calculations, on two representative members of the family (the human NAF-1 and mitoNEET proteins), show that the loss of the cluster is associated with a dramatic decrease in secondary and tertiary structure. In addition, the calculations provide a mechanism for cluster release and clarify, for the first time, crucial differences existing between the two proteins, which are reflected in the experimentally observed difference in the pH-dependent cluster reactivity. The reliability of our conclusions is established by an extensive comparison with the NMR data of the solution proteins, in part measured in this work.
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Affiliation(s)
- Luca Pesce
- Computational Biomedicine Section, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH , 52425 Jülich, Germany
| | - Vania Calandrini
- Computational Biomedicine Section, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH , 52425 Jülich, Germany
| | - Henri-Baptiste Marjault
- The Alexander Silberman Life Science Institute and the Wolfson Center for Applied Structural Biology, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram , 91904 Jerusalem, Israel
| | - Colin H Lipper
- Departments of Chemistry and Biochemistry, University of California San Diego , La Jolla, 92093 San Diego, California, United States of America
| | - Gulia Rossetti
- Computational Biomedicine Section, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH , 52425 Jülich, Germany.,Division Computational Science - Simulation Laboratory Biology, Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH , 52428 Jülich, Germany.,Department of Oncology, Hematology and Stem Cell Transplantation, University Hospital Aachen, RWTH Aachen University , 52074 Aachen, Germany
| | - Ron Mittler
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas , 76203 Denton, Texas, United States of America
| | - Patricia A Jennings
- Departments of Chemistry and Biochemistry, University of California San Diego , La Jolla, 92093 San Diego, California, United States of America
| | - Andreas Bauer
- Molecular Organisation of the Brain Molecular Neuroimaging, Institute of Neuroscience and Medicine INM-2, Forschungszentrum Jülich GmbH , 52428 Jülich, Germany
| | - Rachel Nechushtai
- The Alexander Silberman Life Science Institute and the Wolfson Center for Applied Structural Biology, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram , 91904 Jerusalem, Israel
| | - Paolo Carloni
- Computational Biomedicine Section, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH , 52425 Jülich, Germany.,JARA-HPC , 52428 Jülich, Germany
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16
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Inupakutika MA, Sengupta S, Nechushtai R, Jennings PA, Onuchic JN, Azad RK, Padilla P, Mittler R. Phylogenetic analysis of eukaryotic NEET proteins uncovers a link between a key gene duplication event and the evolution of vertebrates. Sci Rep 2017; 7:42571. [PMID: 28205535 PMCID: PMC5311916 DOI: 10.1038/srep42571] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 01/12/2017] [Indexed: 12/17/2022] Open
Abstract
NEET proteins belong to a unique family of iron-sulfur proteins in which the 2Fe-2S cluster is coordinated by a CDGSH domain that is followed by the “NEET” motif. They are involved in the regulation of iron and reactive oxygen metabolism, and have been associated with the progression of diabetes, cancer, aging and neurodegenerative diseases. Despite their important biological functions, the evolution and diversification of eukaryotic NEET proteins are largely unknown. Here we used the three members of the human NEET protein family (CISD1, mitoNEET; CISD2, NAF-1 or Miner 1; and CISD3, Miner2) as our guides to conduct a phylogenetic analysis of eukaryotic NEET proteins and their evolution. Our findings identified the slime mold Dictyostelium discoideum’s CISD proteins as the closest to the ancient archetype of eukaryotic NEET proteins. We further identified CISD3 homologs in fungi that were previously reported not to contain any NEET proteins, and revealed that plants lack homolog(s) of CISD3. Furthermore, our study suggests that the mammalian NEET proteins, mitoNEET (CISD1) and NAF-1 (CISD2), emerged via gene duplication around the origin of vertebrates. Our findings provide new insights into the classification and expansion of the NEET protein family, as well as offer clues to the diverged functions of the human mitoNEET and NAF-1 proteins.
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Affiliation(s)
| | - Soham Sengupta
- Department of Biological Sciences, University of North Texas, Denton TX 76203, USA
| | - Rachel Nechushtai
- The Alexander Silberman Institute of Life Science, Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 91904, Israel
| | - Patricia A Jennings
- Department of Chemistry &Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Jose' N Onuchic
- Center for Theoretical Biological Physics and Department of Physics and Astronomy, Chemistry and Biosciences, 239 Brockman Hall, 6100 Main Street- MS-61, Rice University, Houston, TX 77005, USA
| | - Rajeev K Azad
- Department of Biological Sciences, University of North Texas, Denton TX 76203, USA.,Department of Mathematics, University of North Texas, Denton, TX 76203, USA
| | - Pamela Padilla
- Department of Biological Sciences, University of North Texas, Denton TX 76203, USA
| | - Ron Mittler
- Department of Biological Sciences, University of North Texas, Denton TX 76203, USA
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17
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Bergner M, Dechert S, Demeshko S, Kupper C, Mayer JM, Meyer F. Model of the MitoNEET [2Fe-2S] Cluster Shows Proton Coupled Electron Transfer. J Am Chem Soc 2017; 139:701-707. [PMID: 28055193 PMCID: PMC5812485 DOI: 10.1021/jacs.6b09180] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
MitoNEET is an outer membrane protein whose exact function remains unclear, though a role of this protein in redox and iron sensing as well as in controlling maximum mitochondrial respiratory rates has been discussed. It was shown to contain a redox active and acid labile [2Fe-2S] cluster which is ligated by one histidine and three cysteine residues. Herein we present the first synthetic analogue with biomimetic {SN/S2} ligation which could be structurally characterized in its diferric form, 52-. In addition to being a high fidelity structural model for the biological cofactor, the complex is shown to mediate proton coupled electron transfer (PCET) at the {SN} ligated site, pointing at a potential functional role of the enzyme's unique His ligand. Full PCET thermodynamic square schemes for the mitoNEET model 52- and a related homoleptic {SN/SN} capped [2Fe-2S] cluster 42- are established, and kinetics of PCET reactivity are investigated by double-mixing stopped-flow experiments for both complexes. While the N-H bond dissociation free energy (BDFE) of 5H2- (230 ± 4 kJ mol-1) and the free energy ΔG°PCET for the reaction with TEMPO (-48.4 kJ mol-1) are very similar to values for the homoleptic cluster 4H2- (232 ± 4 kJ mol-1, -46.3 kJ mol-1) the latter is found to react significantly faster than the mitoNEET model (data for 5H2-: k = 135 ± 27 M-1 s-1, ΔH‡ = 17.6 ± 3.0 kJ mol-1, ΔS‡ = -143 ± 11 J mol-1 K-1, and ΔG‡ = 59.8 kJ mol-1 at 293 K). Comparison of the PCET efficiency of these clusters emphasizes the relevance of reorganization energy in this process.
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Affiliation(s)
- Marie Bergner
- Institute of Inorganic Chemistry, Georg-August-University Göttingen, Tammannstr. 4, D-37077 Göttingen, Germany
| | - Sebastian Dechert
- Institute of Inorganic Chemistry, Georg-August-University Göttingen, Tammannstr. 4, D-37077 Göttingen, Germany
| | - Serhiy Demeshko
- Institute of Inorganic Chemistry, Georg-August-University Göttingen, Tammannstr. 4, D-37077 Göttingen, Germany
| | - Claudia Kupper
- Institute of Inorganic Chemistry, Georg-August-University Göttingen, Tammannstr. 4, D-37077 Göttingen, Germany
| | - James M. Mayer
- Yale University, 225 Prospect Street, New Haven, Connecticut 06511, USA
| | - Franc Meyer
- Institute of Inorganic Chemistry, Georg-August-University Göttingen, Tammannstr. 4, D-37077 Göttingen, Germany
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18
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Koval AM, Jagger BR, Wheeler RA. Distinguishing the Protonation State of the Histidine Ligand to the Oxidized Iron-Sulfur Cluster from the MitoNEET Family of Proteins. Chemphyschem 2016; 18:39-41. [PMID: 27870532 DOI: 10.1002/cphc.201600957] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Indexed: 11/10/2022]
Abstract
The iron-sulfur cluster located in the recently discovered human mitoNEET protein (and related proteins) is structurally similar to the more well-known ferredoxin and Rieske clusters. Although its biological function is uncertain, the iron-sulfur cluster in mitoNEET has been proposed to undergo proton-coupled electron transfer involving the histidine ligand to the cluster. The cluster is also released from the protein at low pH. This contribution reports density functional calculations to model the structures, vibrations, and Heisenberg coupling constants (J) for high-spin (HS), broken symmetry (BS) singlet, and extended broken symmetry (EBS) singlet states of the oxidized iron-sulfur cluster from mitoNEET. This work suggests that J values or 15 N isotopic frequency shifts may provide methods for determining experimentally whether the histidine ligand to the oxidized iron-sulfur cluster in human mitoNEET and mitoNEET-related proteins is protonated or deprotonated.
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Affiliation(s)
- Ashlyn M Koval
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA, 15282, USA
| | - Benjamin R Jagger
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA, 15282, USA
| | - Ralph A Wheeler
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy., DeKalb, IL, 60115, USA
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19
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Yin S, Bernstein ER. Properties of iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide cluster anions through photoelectron spectroscopy and density functional theory calculations. J Chem Phys 2016; 145:154302. [DOI: 10.1063/1.4964651] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Shi Yin
- Department of Chemistry, NSF ERC for Extreme Ultraviolet Science and Technology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Elliot R. Bernstein
- Department of Chemistry, NSF ERC for Extreme Ultraviolet Science and Technology, Colorado State University, Fort Collins, Colorado 80523, USA
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20
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Rizvi MA, Mane M, Khuroo MA, Peerzada GM. Computational survey of ligand properties on iron(III)–iron(II) redox potential: exploring natural attenuation of nitroaromatic compounds. MONATSHEFTE FUR CHEMIE 2016. [DOI: 10.1007/s00706-016-1813-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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21
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Zanetti-Polzi L, Corni S, Daidone I, Amadei A. Extending the essential dynamics analysis to investigate molecular properties: application to the redox potential of proteins. Phys Chem Chem Phys 2016; 18:18450-9. [PMID: 27339768 DOI: 10.1039/c6cp03394f] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Here, a methodology is proposed to investigate the collective fluctuation modes of an arbitrary set of observables, maximally contributing to the fluctuation of another functionally relevant observable. The methodology, based on the analysis of fully classical molecular dynamics (MD) simulations, exploits the essential dynamics (ED) method, originally developed to analyse the collective motions in proteins. We apply this methodology to identify the residues that are more relevant for determining the reduction potential (E(0)) of a redox-active protein. To this aim, the fluctuation modes of the single-residue electrostatic potentials mostly contributing to the fluctuations of the total electrostatic potential (the main determinant of E(0)) are investigated for wild-type azurin and two of its mutants with a higher E(0). By comparing the results here obtained with a previous study on the same systems [Zanetti-Polzi et al., Org. Biomol. Chem., 2015, 13, 11003] we show that the proposed methodology is able to identify the key sites that determine E(0). This information can be used for a general deeper understanding of the molecular mechanisms on the basis of the redox properties of the proteins under investigation, as well as for the rational design of mutants with a higher or lower E(0). From the results of the present analysis we propose a new azurin mutant that, according to our calculations, shows a further increase of E(0).
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Affiliation(s)
- Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), 67010, L'Aquila, Italy.
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22
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Hosseinzadeh P, Lu Y. Design and fine-tuning redox potentials of metalloproteins involved in electron transfer in bioenergetics. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1857:557-581. [PMID: 26301482 PMCID: PMC4761536 DOI: 10.1016/j.bbabio.2015.08.006] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 08/20/2015] [Indexed: 12/25/2022]
Abstract
Redox potentials are a major contributor in controlling the electron transfer (ET) rates and thus regulating the ET processes in the bioenergetics. To maximize the efficiency of the ET process, one needs to master the art of tuning the redox potential, especially in metalloproteins, as they represent major classes of ET proteins. In this review, we first describe the importance of tuning the redox potential of ET centers and its role in regulating the ET in bioenergetic processes including photosynthesis and respiration. The main focus of this review is to summarize recent work in designing the ET centers, namely cupredoxins, cytochromes, and iron-sulfur proteins, and examples in design of protein networks involved these ET centers. We then discuss the factors that affect redox potentials of these ET centers including metal ion, the ligands to metal center and interactions beyond the primary ligand, especially non-covalent secondary coordination sphere interactions. We provide examples of strategies to fine-tune the redox potential using both natural and unnatural amino acids and native and nonnative cofactors. Several case studies are used to illustrate recent successes in this area. Outlooks for future endeavors are also provided. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
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Affiliation(s)
- Parisa Hosseinzadeh
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews St., Urbana, IL, 61801, USA
| | - Yi Lu
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews St., Urbana, IL, 61801, USA.
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23
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Hosseinzadeh P, Mirts EN, Pfister TD, Gao YG, Mayne C, Robinson H, Tajkhorshid E, Lu Y. Enhancing Mn(II)-Binding and Manganese Peroxidase Activity in a Designed Cytochrome c Peroxidase through Fine-Tuning Secondary-Sphere Interactions. Biochemistry 2016; 55:1494-502. [PMID: 26885726 DOI: 10.1021/acs.biochem.5b01299] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Noncovalent second-shell interactions are important in controlling metal-binding affinity and activity in metalloenzymes, but fine-tuning these interactions in designed metalloenzymes has not been fully explored. As a result, most designed metalloenzymes have low metal-binding affinity and activity. Here we identified three mutations in the second coordination shell of an engineered Mn(II)-binding site in cytochrome c peroxidase (called MnCcP.1, containing Glu45, Glu37, and Glu181 ligands) that mimics the native manganese peroxidase (MnP), and explored their effects on both Mn(II)-binding affinity and MnP activity. First, removing a hydrogen bond to Glu45 through Tyr36Phe mutation enhanced Mn(II)-binding affinity, as evidenced by a 2.8-fold decrease in the KM of Mn(II) oxidation. Second, introducing a salt bridge through Lys179Arg mutation improved Glu35 and Glu181 coordination to Mn(II), decreasing KM 2.6-fold. Third, eliminating a steric clash that prevented Glu37 from orienting toward Mn(II) resulted in an 8.6-fold increase in kcat/KM, arising primarily from a 3.6-fold decrease in KM, with a KM value comparable to that of the native enzyme (0.28 mM vs 0.19 mM for Pleurotus eryngii MnP PS3). We further demonstrated that while the effects of Tyr36Phe and Lys179Arg mutations are additive, because involved in secondary-shell interactions to different ligands, other combinations of mutations were antagonistic because they act on different aspects of the Mn(II) coordination at the same residues. Finally, we showed that these MnCcP variants are functional models of MnP that mimic its activity in both Mn(II) oxidation and degradation of a phenolic lignin model compound and kraft lignin. In addition to achieving KM in a designed protein that is similar to the that of native enzyme, our results offer molecular insight into the role of noncovalent interactions around metal-binding sites for improving metal binding and overall activity; such insight can be applied to rationally enhance these properties in other metalloenzymes and their models.
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Affiliation(s)
| | | | | | | | | | - Howard Robinson
- Department of Biology, Brookhaven National Laboratory , Upton, New York 11973, United States
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24
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His-87 ligand in mitoNEET is crucial for the transfer of iron sulfur clusters from mitochondria to cytosolic aconitase. Biochem Biophys Res Commun 2016; 470:226-232. [PMID: 26778000 DOI: 10.1016/j.bbrc.2016.01.040] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 01/07/2016] [Indexed: 01/25/2023]
Abstract
MitoNEET is the first identified iron sulfur protein that located in the mitochondrial outer membrane. We showed that knockdown of mitoNEET did not affect the iron sulfur protein expression in mitochondria and cytoplasm, but significantly reduced the cytosolic aconitase activity. The reduction of aconitase activity was rescued by transfection of wild type mitoNEET, but not by mitoNEET mutants H87C and H87S. Our results confirm the observation that mitoNEET is important in transferring the iron sulfur clusters to the cytosolic aconitase in living cells and the His-87 ligand in mitoNEET plays important role in this process.
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25
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The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part III. {[Fe2S2](Cys)3(X)} (X=Asp, Arg, His) and {[Fe2S2](Cys)2(His)2} proteins. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2015.07.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Multinuclear NMR and UV–Vis spectroscopy of site directed mutants of the diabetes drug target protein mitoNEET suggest that folding is intimately coupled to iron–sulfur cluster formation. INORG CHEM COMMUN 2016. [DOI: 10.1016/j.inoche.2015.11.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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27
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Design of a single protein that spans the entire 2-V range of physiological redox potentials. Proc Natl Acad Sci U S A 2015; 113:262-7. [PMID: 26631748 DOI: 10.1073/pnas.1515897112] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The reduction potential (E°') is a critical parameter in determining the efficiency of most biological and chemical reactions. Biology employs three classes of metalloproteins to cover the majority of the 2-V range of physiological E°'s. An ultimate test of our understanding of E°' is to find out the minimal number of proteins and their variants that can cover this entire range and the structural features responsible for the extreme E°'. We report herein the design of the protein azurin to cover a range from +970 mV to -954 mV vs. standard hydrogen electrode (SHE) by mutating only five residues and using two metal ions. Spectroscopic methods have revealed geometric parameters important for the high E°'. The knowledge gained and the resulting water-soluble redox agents with predictable E°'s, in the same scaffold with the same surface properties, will find wide applications in chemical, biochemical, biophysical, and biotechnological fields.
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28
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Reesbeck ME, Rodriguez MM, Brennessel WW, Mercado BQ, Vinyard D, Holland PL. Oxidized and reduced [2Fe-2S] clusters from an iron(I) synthon. J Biol Inorg Chem 2015; 20:875-83. [PMID: 26044124 DOI: 10.1007/s00775-015-1272-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 05/20/2015] [Indexed: 02/06/2023]
Abstract
Synthetic [2Fe-2S] clusters are often used to elucidate ligand effects on the reduction potentials and spectroscopy of natural electron-transfer sites, which can have anionic Cys ligands or neutral His ligands. Current synthetic routes to [2Fe-2S] clusters are limited in their feasibility with a range of supporting ligands. Here, we report a new synthetic route to synthetic [2Fe-2S] clusters, through oxidation of an iron(I) source with elemental sulfur. This method yields a neutral diketiminate-supported [2Fe-2S] cluster in the diiron(III)-oxidized form. The oxidized [2Fe-2S] cluster can be reduced to a mixed valent iron(II)-iron(III) compound. Both the diferric and reduced mixed valent clusters are characterized using X-ray crystallography, Mössbauer spectroscopy, EPR spectroscopy and cyclic voltammetry. The reduced compound is particularly interesting because its X-ray crystal structure shows a difference in Fe-S bond lengths to one of the iron atoms, consistent with valence localization. The valence localization is also evident from Mössbauer spectroscopy.
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Affiliation(s)
- Megan E Reesbeck
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT, 06520, USA
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29
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30
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Brown KA, Song Q, Mulder DW, King PW. Diameter dependent electron transfer kinetics in semiconductor-enzyme complexes. ACS NANO 2014; 8:10790-8. [PMID: 25244026 DOI: 10.1021/nn504561v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Excited state electron transfer (ET) is a fundamental step for the catalytic conversion of solar energy into chemical energy. To understand the properties controlling ET between photoexcited nanoparticles and catalysts, the ET kinetics were measured for solution-phase complexes of CdTe quantum dots and Clostridium acetobutylicum [FeFe]-hydrogenase I (CaI) using time-resolved photoluminescence spectroscopy. Over a 2.0-3.5 nm diameter range of CdTe nanoparticles, the observed ET rate (kET) was sensitive to CaI concentration. To account for diameter effects on CaI binding, a Langmuir isotherm and two geometric binding models were created to estimate maximal CaI affinities and coverages at saturating concentrations. Normalizing the ET kinetics to CaI surface coverage for each CdTe diameter led to k(ET) values that were insensitive to diameter, despite a decrease in the free energy for photoexcited ET (ΔGET) with increasing diameter. The turnover frequency (TOF) of CaI in CdTe-CaI complexes was measured at several molar ratios. Normalization for diameter-dependent changes in CaI coverage showed an increase in TOF with diameter. These results suggest that k(ET) and H2 production for CdTe-CaI complexes are not strictly controlled by ΔG(ET) and that other factors must be considered.
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Affiliation(s)
- Katherine A Brown
- Biosciences Center, National Renewable Energy Laboratory , Golden, Colorado 80401, United States
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31
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Tamir S, Paddock ML, Darash-Yahana-Baram M, Holt SH, Sohn YS, Agranat L, Michaeli D, Stofleth JT, Lipper CH, Morcos F, Cabantchik IZ, Onuchic JN, Jennings PA, Mittler R, Nechushtai R. Structure-function analysis of NEET proteins uncovers their role as key regulators of iron and ROS homeostasis in health and disease. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1294-315. [PMID: 25448035 DOI: 10.1016/j.bbamcr.2014.10.014] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 10/01/2014] [Accepted: 10/16/2014] [Indexed: 12/31/2022]
Abstract
A novel family of 2Fe-2S proteins, the NEET family, was discovered during the last decade in numerous organisms, including archea, bacteria, algae, plant and human; suggesting an evolutionary-conserved function, potentially mediated by their CDGSH Iron-Sulfur Domain. In human, three NEET members encoded by the CISD1-3 genes were identified. The structures of CISD1 (mitoNEET, mNT), CISD2 (NAF-1), and the plant At-NEET uncovered a homodimer with a unique "NEET fold", as well as two distinct domains: a beta-cap and a 2Fe-2S cluster-binding domain. The 2Fe-2S clusters of NEET proteins were found to be coordinated by a novel 3Cys:1His structure that is relatively labile compared to other 2Fe-2S proteins and is the reason of the NEETs' clusters could be transferred to apo-acceptor protein(s) or mitochondria. Positioned at the protein surface, the NEET's 2Fe-2S's coordinating His is exposed to protonation upon changes in its environment, potentially suggesting a sensing function for this residue. Studies in different model systems demonstrated a role for NAF-1 and mNT in the regulation of cellular iron, calcium and ROS homeostasis, and uncovered a key role for NEET proteins in critical processes, such as cancer cell proliferation and tumor growth, lipid and glucose homeostasis in obesity and diabetes, control of autophagy, longevity in mice, and senescence in plants. Abnormal regulation of NEET proteins was consequently found to result in multiple health conditions, and aberrant splicing of NAF-1 was found to be a causative of the neurological genetic disorder Wolfram Syndrome 2. Here we review the discovery of NEET proteins, their structural, biochemical and biophysical characterization, and their most recent structure-function analyses. We additionally highlight future avenues of research focused on NEET proteins and propose an essential role for NEETs in health and disease. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- Sagi Tamir
- The Alexander Silberman Life Science Institute and the Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 91904, Israel
| | - Mark L Paddock
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Merav Darash-Yahana-Baram
- The Alexander Silberman Life Science Institute and the Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 91904, Israel
| | - Sarah H Holt
- Department of Biology, University of North Texas, Denton, TX 76203, USA
| | - Yang Sung Sohn
- The Alexander Silberman Life Science Institute and the Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 91904, Israel
| | - Lily Agranat
- The Alexander Silberman Life Science Institute and the Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 91904, Israel
| | - Dorit Michaeli
- The Alexander Silberman Life Science Institute and the Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 91904, Israel
| | - Jason T Stofleth
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Colin H Lipper
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Faruck Morcos
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77050, USA; Department of Physics and Astronomy, Rice University, Houston, TX 77050, USA; Department of Chemistry, Rice University, Houston, TX 77050, USA; Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77050, USA
| | - Ioav Z Cabantchik
- The Alexander Silberman Life Science Institute and the Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 91904, Israel
| | - Jose' N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77050, USA; Department of Physics and Astronomy, Rice University, Houston, TX 77050, USA; Department of Chemistry, Rice University, Houston, TX 77050, USA; Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77050, USA
| | - Patricia A Jennings
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Ron Mittler
- Department of Biology, University of North Texas, Denton, TX 76203, USA
| | - Rachel Nechushtai
- The Alexander Silberman Life Science Institute and the Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 91904, Israel.
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Tamir S, Eisenberg-Domovich Y, Conlan AR, Stofleth JT, Lipper CH, Paddock ML, Mittler R, Jennings PA, Livnah O, Nechushtai R. A point mutation in the [2Fe-2S] cluster binding region of the NAF-1 protein (H114C) dramatically hinders the cluster donor properties. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1572-8. [PMID: 24914968 PMCID: PMC4051502 DOI: 10.1107/s1399004714005458] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 03/10/2014] [Indexed: 11/10/2022]
Abstract
NAF-1 is an important [2Fe-2S] NEET protein associated with human health and disease. A mis-splicing mutation in NAF-1 results in Wolfram Syndrome type 2, a lethal childhood disease. Upregulation of NAF-1 is found in epithelial breast cancer cells, and suppression of NAF-1 expression by knockdown significantly suppresses tumor growth. Key to NAF-1 function is the NEET fold with its [2Fe-2S] cluster. In this work, the high-resolution structure of native NAF-1 was determined to 1.65 Å resolution (R factor = 13.5%) together with that of a mutant in which the single His ligand of its [2Fe-2S] cluster, His114, was replaced by Cys. The NAF-1 H114C mutant structure was determined to 1.58 Å resolution (R factor = 16.0%). All structural differences were localized to the cluster binding site. Compared with native NAF-1, the [2Fe-2S] clusters of the H114C mutant were found to (i) be 25-fold more stable, (ii) have a redox potential that is 300 mV more negative and (iii) have their cluster donation/transfer function abolished. Because no global structural differences were found between the mutant and the native (wild-type) NAF-1 proteins, yet significant functional differences exist between them, the NAF-1 H114C mutant is an excellent tool to decipher the underlying biological importance of the [2Fe-2S] cluster of NAF-1 in vivo.
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Affiliation(s)
- Sagi Tamir
- The Alexander Silberman Life Science Institute and the Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 91904, Israel
| | - Yael Eisenberg-Domovich
- The Alexander Silberman Life Science Institute and the Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 91904, Israel
| | - Andrea R. Conlan
- Departments of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Jason T. Stofleth
- Departments of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Colin H. Lipper
- Departments of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Mark L. Paddock
- Departments of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Ron Mittler
- Department of Biology, University of North Texas, Denton, TX 76203, USA
| | - Patricia A. Jennings
- Departments of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Oded Livnah
- The Alexander Silberman Life Science Institute and the Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 91904, Israel
| | - Rachel Nechushtai
- The Alexander Silberman Life Science Institute and the Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 91904, Israel
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33
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Saouma CT, Pinney MM, Mayer JM. Electron transfer and proton-coupled electron transfer reactivity and self-exchange of synthetic [2Fe-2S] complexes: models for Rieske and mitoNEET clusters. Inorg Chem 2014; 53:3153-61. [PMID: 24592857 PMCID: PMC3993882 DOI: 10.1021/ic403131p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
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This report describes the thermochemistry,
proton-coupled electron transfer (PCET) reactions and self-exchange
rate constants for a set of bis-benzimidazolate-ligated [2Fe–2S]
clusters. These clusters serve as a model for the chemistry of biological
Rieske and mitoNEET clusters. PCET from [Fe2S2(Prbbim)(PrbbimH)]2– (4) and [Fe2S2(Prbbim)(PrbbimH2)]1– (5)
to TEMPO occurs via concerted proton–electron transfer (CPET)
mechanisms (PrbbimH2 = 4,4-bis-(benzimidazol-2-yl)heptane).
Intermolecular electron transfer (ET) self-exchange between [Fe2S2(Prbbim)2]2– (1) and [Fe2S2(Prbbim)2]3– (2) occurs with a rate
constant of (1.20 ± 0.06) × 105 M–1 s–1 at 26 °C. A similar self-exchange rate
constant is found for the related [2Fe–2S] cluster [Fe2S2(SArO)2]2–/3–, SArO2– = thiosalicylate. These are roughly an
order of magnitude slower than that reported for larger [4Fe–4S]
clusters and 1 order of magnitude faster than that reported for N-ligated
high-spin iron complexes. These results suggest that the rate of intermolecular
ET to/from [Fe–S] clusters is modulated by cluster size. The
measured PCET self-exchange rate constant for 1 and 4 at −30 °C is (3.8 ± 0.7) × 104 M–1 s–1. Analysis of
rate constants using the Marcus cross-relation suggests that this
process likely occurs via a concerted proton–electron transfer
(CPET) mechanism. The implications of these findings to biological
systems are also discussed, including the conclusion that histidine-ligated
[2Fe–2S] clusters should not have a strong bias to undergo
concerted e–/H+ transfers. [Fe2S2(Prbbim)(PrbbimHx)]y- clusters have been
generated in multiple redox and protonation states. Their PCET and
ET thermochemistry and reactivity are described. The PCET self-exchange
reaction occurs by concerted e−/H+ exchange, and the ET self-exchange barriers for different
clusters are shown to scale with [Fe−S] cluster size. The implications
of these results for the reactivity of biochemical imidazole-ligated
clusters is discussed.
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Affiliation(s)
- Caroline T Saouma
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
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34
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Zheng P, Chou CC, Guo Y, Wang Y, Li H. Single Molecule Force Spectroscopy Reveals the Molecular Mechanical Anisotropy of the FeS4 Metal Center in Rubredoxin. J Am Chem Soc 2013; 135:17783-92. [DOI: 10.1021/ja406695g] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Peng Zheng
- Department
of Chemistry, University of British Columbia Vancouver, British Columbia V6T 1Z1, Canada
| | - Chih-Chung Chou
- Department
of Chemistry, University of British Columbia Vancouver, British Columbia V6T 1Z1, Canada
| | - Ying Guo
- Department
of Chemistry, University of British Columbia Vancouver, British Columbia V6T 1Z1, Canada
| | - Yanyan Wang
- Department
of Chemistry, University of British Columbia Vancouver, British Columbia V6T 1Z1, Canada
- State
Key Laboratory of Precision Measurements Technology and Instruments,
School of Precision Instrument and Opto-Electronics Engineering, Tianjin University, Tianjin, 30072 P. R. China
| | - Hongbin Li
- Department
of Chemistry, University of British Columbia Vancouver, British Columbia V6T 1Z1, Canada
- State
Key Laboratory of Precision Measurements Technology and Instruments,
School of Precision Instrument and Opto-Electronics Engineering, Tianjin University, Tianjin, 30072 P. R. China
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35
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Bak DW, Elliott SJ. Conserved hydrogen bonding networks of MitoNEET tune Fe-S cluster binding and structural stability. Biochemistry 2013; 52:4687-96. [PMID: 23758282 DOI: 10.1021/bi400540m] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
While its biological function remains unclear, the three-cysteine, one-histidine ligated human [2Fe-2S] cluster containing protein mitoNEET is of interest because of its interaction with the anti-diabetes drug pioglitazone. The mitoNEET [2Fe-2S] cluster demonstrates proton-coupled electron transfer (PCET) and marked cluster instability, which have both been linked to the single His ligand. Highly conserved hydrogen bonding networks, which include the His-87 ligand, exist around the [2Fe-2S] cluster. Through a series of site-directed mutations, PCET of the cluster has been examined, demonstrating that multiple sites of protonation exist in addition to the His ligand, which can influence redox potential. The mutations also demonstrate that while replacement of the His ligand with cysteine results in a stable cluster, the removal of Lys-55 also greatly stabilizes the cluster. We have also noted for the first time that the oxidation state of the cluster controls stability: the reduced cluster is stable, while the oxidized one is much more labile. Finally, it is shown that upon cluster loss the mitoNEET protein structure becomes less stable, while upon in vitro reconstitution, both the cluster and the secondary structure are recovered. Recently, two other proteins have been identified with a three-Cys(sulfur), one-His motif, IscR and Grx3/4-Fra2, both of which are sensors of iron and redox homeostatsis. These results lead to a model in which mitoNEET could sense the cellular oxidation state and proton concentration and respond through cluster loss and unfolding.
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Affiliation(s)
- Daniel W Bak
- Program in Molecular and Cellular Biology and Biochemistry and ‡Department of Chemistry, Boston University , Boston, Massachusetts 02215, United States
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36
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Allosteric control in a metalloprotein dramatically alters function. Proc Natl Acad Sci U S A 2012; 110:948-53. [PMID: 23271805 DOI: 10.1073/pnas.1208286110] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Metalloproteins (MPs) comprise one-third of all known protein structures. This diverse set of proteins contain a plethora of unique inorganic moieties capable of performing chemistry that would otherwise be impossible using only the amino acids found in nature. Most of the well-studied MPs are generally viewed as being very rigid in structure, and it is widely thought that the properties of the metal centers are primarily determined by the small fraction of amino acids that make up the local environment. Here we examine both theoretically and experimentally whether distal regions can influence the metal center in the diabetes drug target mitoNEET. We demonstrate that a loop (L2) 20 Å away from the metal center exerts allosteric control over the cluster binding domain and regulates multiple properties of the metal center. Mutagenesis of L2 results in significant shifts in the redox potential of the [2Fe-2S] cluster and orders of magnitude effects on the rate of [2Fe-2S] cluster transfer to an apo-acceptor protein. These surprising effects occur in the absence of any structural changes. An examination of the native basin dynamics of the protein using all-atom simulations shows that twisting in L2 controls scissoring in the cluster binding domain and results in perturbations to one of the cluster-coordinating histidines. These allosteric effects are in agreement with previous folding simulations that predicted L2 could communicate with residues surrounding the metal center. Our findings suggest that long-range dynamical changes in the protein backbone can have a significant effect on the functional properties of MPs.
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Iwasaki T, Fukazawa R, Miyajima-Nakano Y, Baldansuren A, Matsushita S, Lin MT, Gennis RB, Hasegawa K, Kumasaka T, Dikanov SA. Dissection of hydrogen bond interaction network around an iron-sulfur cluster by site-specific isotope labeling of hyperthermophilic archaeal Rieske-type ferredoxin. J Am Chem Soc 2012; 134:19731-8. [PMID: 23145461 DOI: 10.1021/ja308049u] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The electronic structure and geometry of redox-active metal cofactors in proteins are tuned by the pattern of hydrogen bonding with the backbone peptide matrix. In this study we developed a method for selective amino acid labeling of a hyperthermophilic archaeal metalloprotein with engineered Escherichia coli auxotroph strains, and we applied this to resolve the hydrogen bond interactions with the reduced Rieske-type [2Fe-2S] cluster by two-dimensional pulsed electron spin resonance technique. Because deep electron spin-echo envelope modulation of two histidine (14)N(δ) ligands of the cluster decreased non-coordinating (15)N signal intensities via the cross-suppression effect, an inverse labeling strategy was employed in which (14)N amino acid-labeled archaeal Rieske-type ferredoxin samples were examined in an (15)N-protein background. This has directly identified Lys45 N(α) as providing the major pathway for the transfer of unpaired electron spin density from the reduced cluster by a "through-bond" mechanism. All other backbone peptide nitrogens interact more weakly with the reduced cluster. The extension of this approach will allow visualizing the three-dimensional landscape of preferred pathways for the transfer of unpaired spin density from a paramagnetic metal center onto the protein frame, and will discriminate specific interactions by a "through-bond" mechanism from interactions which are "through-space" in various metalloproteins.
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Affiliation(s)
- Toshio Iwasaki
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Sendagi, Tokyo 113-8602, Japan.
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38
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Nechushtai R, Conlan AR, Harir Y, Song L, Yogev O, Eisenberg-Domovich Y, Livnah O, Michaeli D, Rosen R, Ma V, Luo Y, Zuris JA, Paddock ML, Cabantchik ZI, Jennings PA, Mittler R. Characterization of Arabidopsis NEET reveals an ancient role for NEET proteins in iron metabolism. THE PLANT CELL 2012; 24:2139-54. [PMID: 22562611 PMCID: PMC3442592 DOI: 10.1105/tpc.112.097634] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The NEET family is a newly discovered group of proteins involved in a diverse array of biological processes, including autophagy, apoptosis, aging, diabetes, and reactive oxygen homeostasis. They form a novel structure, the NEET fold, in which two protomers intertwine to form a two-domain motif, a cap, and a unique redox-active labile 2Fe-2S cluster binding domain. To accelerate the functional study of NEET proteins, as well as to examine whether they have an evolutionarily conserved role, we identified and characterized a plant NEET protein. Here, we show that the Arabidopsis thaliana At5g51720 protein (At-NEET) displays biochemical, structural, and biophysical characteristics of a NEET protein. Phenotypic characterization of At-NEET revealed a key role for this protein in plant development, senescence, reactive oxygen homeostasis, and Fe metabolism. A role in Fe metabolism was further supported by biochemical and cell biology studies of At-NEET in plant and mammalian cells, as well as mutational analysis of its cluster binding domain. Our findings support the hypothesis that NEET proteins have an ancient role in cells associated with Fe metabolism.
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Affiliation(s)
- Rachel Nechushtai
- The Alexander Silberman Institute of Life Science and the Wolfson Center for Applied Structural Biology, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Andrea R. Conlan
- Departments of Chemistry, Biochemistry, and Physics, University of California at San Diego, La Jolla, California 92093
| | - Yael Harir
- The Alexander Silberman Institute of Life Science and the Wolfson Center for Applied Structural Biology, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Luhua Song
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, Denton, Texas 76203-5017
| | - Ohad Yogev
- The Alexander Silberman Institute of Life Science and the Wolfson Center for Applied Structural Biology, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yael Eisenberg-Domovich
- The Alexander Silberman Institute of Life Science and the Wolfson Center for Applied Structural Biology, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Oded Livnah
- The Alexander Silberman Institute of Life Science and the Wolfson Center for Applied Structural Biology, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Dorit Michaeli
- The Alexander Silberman Institute of Life Science and the Wolfson Center for Applied Structural Biology, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Rachel Rosen
- The Alexander Silberman Institute of Life Science and the Wolfson Center for Applied Structural Biology, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Vincent Ma
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, Denton, Texas 76203-5017
| | - Yuting Luo
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, Denton, Texas 76203-5017
| | - John A. Zuris
- Departments of Chemistry, Biochemistry, and Physics, University of California at San Diego, La Jolla, California 92093
| | - Mark L. Paddock
- Departments of Chemistry, Biochemistry, and Physics, University of California at San Diego, La Jolla, California 92093
| | - Zvi Ioav Cabantchik
- The Alexander Silberman Institute of Life Science and the Wolfson Center for Applied Structural Biology, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Patricia A. Jennings
- Departments of Chemistry, Biochemistry, and Physics, University of California at San Diego, La Jolla, California 92093
| | - Ron Mittler
- The Alexander Silberman Institute of Life Science and the Wolfson Center for Applied Structural Biology, Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, Denton, Texas 76203-5017
- Address correspondence to
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Zuris JA, Ali SS, Yeh H, Nguyen TA, Nechushtai R, Paddock ML, Jennings PA. NADPH inhibits [2Fe-2S] cluster protein transfer from diabetes drug target MitoNEET to an apo-acceptor protein. J Biol Chem 2012; 287:11649-55. [PMID: 22351774 DOI: 10.1074/jbc.m111.319731] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
MitoNEET (mNT) is the founding member of the recently discovered CDGSH family of [2Fe-2S] proteins capable of [2Fe-2S] cluster transfer to apo-acceptor proteins. It is a target of the thiazolidinedione (TZD) class of anti-diabetes drugs whose binding modulate both electron transfer and cluster transfer properties. The [2Fe-2S] cluster in mNT is destabilized upon binding of NADPH, which leads to loss of the [2Fe-2S] cluster to the solution environment. Because mNT is capable of transferring [2Fe-2S] clusters to apo-acceptor proteins, we sought to determine whether NADPH binding also affects cluster transfer. We show that NADPH inhibits transfer of the [2Fe-2S] cluster to an apo-acceptor protein with an inhibition constant (K(i)) of 200 μm, which reflects that of NADPH concentrations expected under physiological conditions. In addition, we determined that the strictly conserved cluster interacting residue Asp-84 in the CDGSH domain is necessary for the NADPH-dependent inhibition of [2Fe-2S] cluster transfer. The most critical cellular function of NADPH is in the maintenance of a pool of reducing equivalents, which is essential to counteract oxidative damage. Taken together, our findings suggest that NADPH can regulate both mNT [2Fe-2S] cluster levels in the cell as well as the ability of the protein to transfer [2Fe-2S] clusters to cytosolic or mitochondrial acceptors.
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Affiliation(s)
- John A Zuris
- Department of Chemistry, University of California at San Diego, La Jolla, California 92093, USA
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40
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New SY, Marshall NM, Hor TSA, Xue F, Lu Y. Redox tuning of two biological copper centers through non-covalent interactions: same trend but different magnitude. Chem Commun (Camb) 2012; 48:4217-9. [DOI: 10.1039/c2cc30901g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Structure and molecular evolution of CDGSH iron-sulfur domains. PLoS One 2011; 6:e24790. [PMID: 21949752 PMCID: PMC3174974 DOI: 10.1371/journal.pone.0024790] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 08/18/2011] [Indexed: 12/26/2022] Open
Abstract
The recently discovered CDGSH iron-sulfur domains (CISDs) are classified into seven major types with a wide distribution throughout the three domains of life. The type 1 protein mitoNEET has been shown to fold into a dimer with the signature CDGSH motif binding to a [2Fe-2S] cluster. However, the structures of all other types of CISDs were unknown. Here we report the crystal structures of type 3, 4, and 6 CISDs determined at 1.5 Å, 1.8 Å and 1.15 Å resolution, respectively. The type 3 and 4 CISD each contain one CDGSH motif and adopt a dimeric structure. Although similar to each other, the two structures have permutated topologies, and both are distinct from the type 1 structure. The type 6 CISD contains tandem CDGSH motifs and adopts a monomeric structure with an internal pseudo dyad symmetry. All currently known CISD structures share dual iron-sulfur binding modules and a β-sandwich for either intermolecular or intramolecular dimerization. The iron-sulfur binding module, the β-strand N-terminal to the module and a proline motif are conserved among different type structures, but the dimerization module and the interface and orientation between the two iron-sulfur binding modules are divergent. Sequence analysis further shows resemblance between CISD types 4 and 7 and between 1 and 2. Our findings suggest that all CISDs share common ancestry and diverged into three primary folds with a characteristic phylogenetic distribution: a eukaryote-specific fold adopted by types 1 and 2 proteins, a prokaryote-specific fold adopted by types 3, 4 and 7 proteins, and a tandem-motif fold adopted by types 5 and 6 proteins. Our comprehensive structural, sequential and phylogenetic analysis provides significant insight into the assembly principles and evolutionary relationship of CISDs.
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42
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A novel binding assay identifies high affinity ligands to the rosiglitazone binding site of mitoNEET. Bioorg Med Chem Lett 2011; 21:5498-501. [DOI: 10.1016/j.bmcl.2011.06.111] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 06/24/2011] [Indexed: 11/24/2022]
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43
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Facile transfer of [2Fe-2S] clusters from the diabetes drug target mitoNEET to an apo-acceptor protein. Proc Natl Acad Sci U S A 2011; 108:13047-52. [PMID: 21788481 DOI: 10.1073/pnas.1109986108] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
MitoNEET (mNT) is an outer mitochondrial membrane target of the thiazolidinedione diabetes drugs with a unique fold and a labile [2Fe-2S] cluster. The rare 1-His and 3-Cys coordination of mNT's [2Fe-2S] leads to cluster lability that is strongly dependent on the presence of the single histidine ligand (His87). These properties of mNT are similar to known [2Fe-2S] shuttle proteins. Here we investigated whether mNT is capable of cluster transfer to acceptor protein(s). Facile [2Fe-2S] cluster transfer is observed between oxidized mNT and apo-ferredoxin (a-Fd) using UV-VIS spectroscopy and native-PAGE, as well as with a mitochondrial iron detection assay in cells. The transfer is unidirectional, proceeds to completion, and occurs with a second-order-reaction rate that is comparable to known iron-sulfur transfer proteins. Mutagenesis of His87 with Cys (H87C) inhibits transfer of the [2Fe-2S] clusters to a-Fd. This inhibition is beyond that expected from increased cluster kinetic stability, as the equivalently stable Lys55 to Glu (K55E) mutation did not inhibit transfer. The H87C mutant also failed to transfer its iron to mitochondria in HEK293 cells. The diabetes drug pioglitazone inhibits iron transfer from WT mNT to mitochondria, indicating that pioglitazone affects a specific property, [2Fe-2S] cluster transfer, in the cellular environment. This finding is interesting in light of the role of iron overload in diabetes. Our findings suggest a likely role for mNT in [2Fe-2S] and/or iron transfer to acceptor proteins and support the idea that pioglitazone's antidiabetic mode of action may, in part, be to inhibit transfer of mNT's [2Fe-2S] cluster.
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44
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Conlan AR, Paddock ML, Homer C, Axelrod HL, Cohen AE, Abresch EC, Zuris JA, Nechushtai R, Jennings PA. Mutation of the His ligand in mitoNEET stabilizes the 2Fe-2S cluster despite conformational heterogeneity in the ligand environment. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:516-23. [PMID: 21636891 PMCID: PMC3107049 DOI: 10.1107/s0907444911011577] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 03/28/2011] [Indexed: 01/04/2023]
Abstract
MitoNEET is the only identified Fe-S protein localized to the outer mitochondrial membrane and a 1.5 Å resolution X-ray analysis has revealed a unique structure [Paddock et al. (2007), Proc. Natl Acad. Sci. USA, 104, 14342-14347]. The 2Fe-2S cluster is bound with a 3Cys-1His coordination which defines a new class of 2Fe-2S proteins. The hallmark feature of this class is the single noncysteine ligand His87, which when replaced by Cys decreases the redox potential (E(m)) by ∼300 mV and increases the stability of the cluster by around sixfold. Unexpectedly, the pH dependence of the lifetime of the 2Fe-2S cluster remains the same as in the wild-type protein. Here, the crystal structure of H87C mitoNEET was determined to 1.7 Å resolution (R factor = 18%) to investigate the structural basis of the changes in the properties of the 2Fe-2S cluster. In comparison to the wild type, structural changes are localized to the immediate vicinity of the cluster-binding region. Despite the increased stability, Cys87 displays two distinct conformations, with distances of 2.3 and 3.2 Å between the S(γ) and the outer Fe of the 2Fe-2S cluster. In addition, Lys55 exhibits multiple conformations in the H87C mutant protein. The structure and distinct characteristics of the H87C mutant provide a framework for further studies investigating the effects of mutation on the properties of the 2Fe-2S cluster in this new class of proteins.
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Affiliation(s)
- Andrea R. Conlan
- Departments of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Mark L. Paddock
- Department of Physics, University of California at San Diego, La Jolla, CA 92093, USA
| | - Christina Homer
- Department of Physics, University of California at San Diego, La Jolla, CA 92093, USA
| | - Herbert L. Axelrod
- Stanford Synchrotron Radiation Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Edward C. Abresch
- Department of Physics, University of California at San Diego, La Jolla, CA 92093, USA
| | - John A. Zuris
- Departments of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Rachel Nechushtai
- Department of Plant and Environmental Sciences, The Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Patricia A. Jennings
- Departments of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
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Interdomain communication revealed in the diabetes drug target mitoNEET. Proc Natl Acad Sci U S A 2011; 108:5266-71. [PMID: 21402934 DOI: 10.1073/pnas.1017604108] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
MitoNEET is a recently identified drug target for a commonly prescribed diabetes drug, Pioglitazone. It belongs to a previously uncharacterized ancient family of proteins for which the hallmark is the presence of a unique 39 amino acid CDGSH domain. In order to characterize the folding landscape of this novel fold, we performed thermodynamic simulations on MitoNEET using a structure-based model. Additionally, we implement a method of contact map clustering to partition out alternate pathways in folding. This cluster analysis reveals a detour late in folding and enables us to carefully examine the folding mechanism of each pathway rather than the macroscopic average. We observe that tightness in a region distal to the iron-sulfur cluster creates a constraint in folding and additionally appears to mediate communication in folding between the two domains of the protein. We demonstrate that by making changes at this site we are able to tweak the order of folding events in the cluster binding domain as well as decrease the barrier to folding.
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