1
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Runda ME, de Kok NAW, Schmidt S. Rieske Oxygenases and Other Ferredoxin-Dependent Enzymes: Electron Transfer Principles and Catalytic Capabilities. Chembiochem 2023; 24:e202300078. [PMID: 36964978 DOI: 10.1002/cbic.202300078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 03/27/2023]
Abstract
Enzymes that depend on sophisticated electron transfer via ferredoxins (Fds) exhibit outstanding catalytic capabilities, but despite decades of research, many of them are still not well understood or exploited for synthetic applications. This review aims to provide a general overview of the most important Fd-dependent enzymes and the electron transfer processes involved. While several examples are discussed, we focus in particular on the family of Rieske non-heme iron-dependent oxygenases (ROs). In addition to illustrating their electron transfer principles and catalytic potential, the current state of knowledge on structure-function relationships and the mode of interaction between the redox partner proteins is reviewed. Moreover, we highlight several key catalyzed transformations, but also take a deeper dive into their engineerability for biocatalytic applications. The overall findings from these case studies highlight the catalytic capabilities of these biocatalysts and could stimulate future interest in developing additional Fd-dependent enzyme classes for synthetic applications.
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Affiliation(s)
- Michael E Runda
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Niels A W de Kok
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Sandy Schmidt
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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2
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Wei RJ, Khaniya U, Mao J, Liu J, Batista VS, Gunner MR. Tools for analyzing protonation states and for tracing proton transfer pathways with examples from the Rb. sphaeroides photosynthetic reaction centers. PHOTOSYNTHESIS RESEARCH 2023; 156:101-112. [PMID: 36307598 DOI: 10.1007/s11120-022-00973-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Protons participate in many reactions. In proteins, protons need paths to move in and out of buried active sites. The vectorial movement of protons coupled to electron transfer reactions establishes the transmembrane electrochemical gradient used for many reactions, including ATP synthesis. Protons move through hydrogen bonded chains of waters and hydroxy side chains via the Grotthuss mechanism and by proton binding and release from acidic and basic residues. MCCE analysis shows that proteins exist in a large number of protonation states. Knowledge of the equilibrium ensemble can provide a rational basis for setting protonation states in simulations that fix them, such as molecular dynamics (MD). The proton path into the QB site in the bacterial reaction centers (RCs) of Rb. sphaeroides is analyzed by MD to provide an example of the benefits of using protonation states found by the MCCE program. A tangled web of side chains and waters link the cytoplasm to QB. MCCE analysis of snapshots from multiple trajectories shows that changing the input protonation state of a residue in MD biases the trajectory shifting the proton affinity of that residue. However, the proton affinity of some residues is more sensitive to the input structure. The proton transfer networks derived from different trajectories are quite robust. There are some changes in connectivity that are largely restricted to the specific residues whose protonation state is changed. Trajectories with QB•- are compared with earlier results obtained with QB [Wei et. al Photosynthesis Research volume 152, pages153-165 (2022)] showing only modest changes. While introducing new methods the study highlights the difficulty of establishing the connections between protein conformation.
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Affiliation(s)
- Rongmei Judy Wei
- Ph.D. Program in Chemistry, The Graduate Center, City University of New York, New York, NY, 10016, USA
- Department of Physics, City College of New York, New York, NY, 10031, USA
| | - Umesh Khaniya
- Department of Physics, City College of New York, New York, NY, 10031, USA
- Ph.D. Program in Physics, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Junjun Mao
- Department of Physics, City College of New York, New York, NY, 10031, USA
| | - Jinchan Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - M R Gunner
- Ph.D. Program in Chemistry, The Graduate Center, City University of New York, New York, NY, 10016, USA.
- Department of Physics, City College of New York, New York, NY, 10031, USA.
- Ph.D. Program in Physics, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
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3
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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-CIBIO, University of Trento, via Sommarive 9, 38123, Trento 28123, Italy.,Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, T6G 2G2, Alberta, Canada
| | - Daniele Rossetto
- D-CIBIO, University of Trento, via Sommarive 9, 38123, Trento 28123, Italy.,Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, T6G 2G2, Alberta, Canada
| | - Taylor Parkkila
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, T6G 2G2, Alberta, Canada
| | - Lorenzo Sebastianelli
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, T6G 2G2, Alberta, Canada
| | - Graziano Guella
- Department of Physics, University of Trento, Via Sommarive 14, Trento, 38123, Italy
| | - Amber L Hendricks
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Ave, Columbus, OH 43210, USA
| | - James A Cowan
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Ave, Columbus, OH 43210, USA
| | - Lingzi Sang
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, T6G 2G2, Alberta, Canada
| | - Sheref S Mansy
- D-CIBIO, University of Trento, via Sommarive 9, 38123, Trento 28123, Italy.,Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, T6G 2G2, Alberta, Canada
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4
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Lubner CE, Artz JH, Mulder DW, Oza A, Ward RJ, Williams SG, Jones AK, Peters JW, Smalyukh II, Bharadwaj VS, King PW. A site-differentiated [4Fe-4S] cluster controls electron transfer reactivity of Clostridium acetobutylicum [FeFe]-hydrogenase I. Chem Sci 2022; 13:4581-4588. [PMID: 35656134 PMCID: PMC9019909 DOI: 10.1039/d1sc07120c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/24/2022] [Indexed: 01/11/2023] Open
Abstract
One of the many functions of reduction–oxidation (redox) cofactors is to mediate electron transfer in biological enzymes catalyzing redox-based chemical transformation reactions. There are numerous examples of enzymes that utilize redox cofactors to form electron transfer relays to connect catalytic sites to external electron donors and acceptors. The compositions of relays are diverse and tune transfer thermodynamics and kinetics towards the chemical reactivity of the enzyme. Diversity in relay design is exemplified among different members of hydrogenases, enzymes which catalyze reversible H2 activation, which also couple to diverse types of donor and acceptor molecules. The [FeFe]-hydrogenase I from Clostridium acetobutylicum (CaI) is a member of a large family of structurally related enzymes where interfacial electron transfer is mediated by a terminal, non-canonical, His-coordinated, [4Fe–4S] cluster. The function of His coordination was examined by comparing the biophysical properties and reactivity to a Cys substituted variant of CaI. This demonstrated that His coordination strongly affected the distal [4Fe–4S] cluster spin state, spin pairing, and spatial orientations of molecular orbitals, with a minor effect on reduction potential. The deviations in these properties by substituting His for Cys in CaI, correlated with pronounced changes in electron transfer and reactivity with the native electron donor–acceptor ferredoxin. The results demonstrate that differential coordination of the surface localized [4Fe–4S]His cluster in CaI is utilized to control intermolecular and intramolecular electron transfer where His coordination creates a physical and electronic environment that enables facile electron exchange between electron carrier molecules and the iron–sulfur cluster relay for coupling to reversible H2 activation at the catalytic site. Histidine coordination of the distal [4Fe–4S] cluster in [FeFe]-hydrogenase was demonstrated to tune the cluster spin-states, spin-pairing and surrounding molecular orbitals to enable more facile electron transfer compared to cysteine coordination.![]()
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Affiliation(s)
| | - Jacob H Artz
- National Renewable Energy Laboratory Golden Colorado USA
| | - David W Mulder
- National Renewable Energy Laboratory Golden Colorado USA
| | - Aisha Oza
- National Renewable Energy Laboratory Golden Colorado USA
| | - Rachel J Ward
- Department of Physics, University of Colorado Boulder Boulder Colorado USA
| | - S Garrett Williams
- School of Molecular Sciences, Arizona State University Tempe Arizona USA.,Sandia National Laboratories Albuquerque New Mexico USA
| | - Anne K Jones
- School of Molecular Sciences, Arizona State University Tempe Arizona USA
| | - John W Peters
- Institute of Biological Chemistry, Washington State University Pullman Washington USA
| | - Ivan I Smalyukh
- Department of Physics, University of Colorado Boulder Boulder Colorado USA.,Renewable and Sustainable Energy Institute, National Renewable Energy Laboratory and University of Colorado Boulder Boulder Colorado USA
| | | | - Paul W King
- National Renewable Energy Laboratory Golden Colorado USA .,Renewable and Sustainable Energy Institute, National Renewable Energy Laboratory and University of Colorado Boulder Boulder Colorado USA
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5
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Francia F, Khalfaoui-Hassani B, Lanciano P, Musiani F, Noodleman L, Venturoli G, Daldal F. The cytochrome b lysine 329 residue is critical for ubihydroquinone oxidation and proton release at the Q o site of bacterial cytochrome bc 1. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1860:167-179. [PMID: 30550726 DOI: 10.1016/j.bbabio.2018.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 12/06/2018] [Accepted: 12/07/2018] [Indexed: 11/16/2022]
Abstract
The ubihydroquinone:cytochrome (cyt) c oxidoreductase (or cyt bc1) is an important enzyme for photosynthesis and respiration. In bacteria like Rhodobacter capsulatus, this membrane complex has three subunits, the iron‑sulfur protein (ISP) with its Fe2S2 cluster, cyt c1 and cyt b, forming two catalytic domains, the Qo (hydroquinone (QH2) oxidation) and Qi (quinone (Q) reduction) sites. At the Qo site, the electron transfer pathways originating from QH2 oxidation are known, but their associated proton release routes are less well defined. Earlier, we demonstrated that the His291 of cyt b is important for this latter process. In this work, using the bacterial cyt bc1 and site directed mutagenesis, we show that Lys329 of cyt b is also critical for electron and proton transfer at the Qo site. Of the mutants examined, Lys329Arg was photosynthesis proficient and had quasi-wild type cyt bc1 activity. In contrast, the Lys329Ala and Lys329Asp were photosynthesis-impaired and contained defective but assembled cyt bc1. In particular, the bifurcated electron transfer and associated proton(s) release reactions occurring during QH2 oxidation were drastically impaired in Lys329Asp mutant. Furthermore, in silico docking studies showed that in this mutant the location and the H-bonding network around the Fe2S2 cluster of ISP on cyt b surface was different than the wild type enzyme. Based on these experimental findings and theoretical considerations, we propose that the presence of a positive charge at position 329 of cyt b is critical for efficient electron transfer and proton release for QH2 oxidation at the Qo site of cyt bc1.
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Affiliation(s)
- Francesco Francia
- Dipartimento di Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy
| | | | - Pascal Lanciano
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Francesco Musiani
- Dipartimento di Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy
| | - Louis Noodleman
- The Scripps Research Institute, Department of Integrative Structural and Computational Biology, La Jolla, CA 92037, USA
| | - Giovanni Venturoli
- Dipartimento di Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy; Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy
| | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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6
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The cytochrome b6f complex: DFT modeling of the first step of plastoquinol oxidation by the iron-sulfur protein. J Organomet Chem 2018. [DOI: 10.1016/j.jorganchem.2018.01.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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7
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Birrell JA, Laurich C, Reijerse EJ, Ogata H, Lubitz W. Importance of Hydrogen Bonding in Fine Tuning the [2Fe-2S] Cluster Redox Potential of HydC from Thermotoga maritima. Biochemistry 2016; 55:4344-55. [PMID: 27396836 DOI: 10.1021/acs.biochem.6b00341] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Iron-sulfur clusters form one of the largest and most diverse classes of enzyme cofactors in nature. They may serve as structural factors, form electron transfer chains between active sites and external redox partners, or form components of enzyme active sites. Their specific role is a consequence of the cluster type and the surrounding protein environment. The relative effects of these factors are not completely understood, and it is not yet possible to predict the properties of iron-sulfur clusters based on amino acid sequences or rationally tune their properties to generate proteins with new desirable functions. Here, we generate mutations in a [2Fe-2S] cluster protein, the TmHydC subunit of the trimeric [FeFe]-hydrogenase from Thermotoga maritima, to study the factors that affect its redox potential. Saturation mutagenesis of Val131 was used to tune the redox potential over a 135 mV range and revealed that cluster redox potential and electronic properties correlate with amino acid hydrophobicity and the ability to form hydrogen bonds to the cluster. Proline scanning mutagenesis between pairs of ligating cysteines was used to remove backbone amide hydrogen bonds to the cluster and decrease the redox potential by up to 132 mV, without large structural changes in most cases. However, substitution of Gly83 with proline caused a change of HydC to a [4Fe-4S] cluster protein with a redox potential of -526 mV. Together, these results confirm the importance of hydrogen bonding in tuning cluster redox potentials and demonstrate the versatility of iron-sulfur cluster protein folds at binding different types of clusters.
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Affiliation(s)
- James A Birrell
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Christoph Laurich
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Edward J Reijerse
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion , Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
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8
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Li J, Farrokhnia M, Rulíšek L, Ryde U. Catalytic Cycle of Multicopper Oxidases Studied by Combined Quantum- and Molecular-Mechanical Free-Energy Perturbation Methods. J Phys Chem B 2015; 119:8268-84. [DOI: 10.1021/acs.jpcb.5b02864] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Jilai Li
- Department
of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
- Institute
of Theoretical Chemistry, Jilin University, Changchun 130023, People’s Republic of China
| | - Maryam Farrokhnia
- Department
of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
- The
Persian Gulf Marine Biotechnology Research Center, The Persian Gulf
Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Lubomír Rulíšek
- Institute
of Organic Chemistry and Biochemistry, Gilead Sciences and IOCB Research
Center, Academy of Sciences of the Czech Republic, Flemingovo
náměstí 2, 166
10 Prague 6, Czech Republic
| | - Ulf Ryde
- Department
of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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9
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Karagas NE, Jones CN, Osborn DJ, Dzierlenga AL, Oyala P, Konkle ME, Whitney EM, David Britt R, Hunsicker-Wang LM. The reduction rates of DEPC-modified mutant Thermus thermophilus Rieske proteins differ when there is a negative charge proximal to the cluster. J Biol Inorg Chem 2014; 19:1121-35. [PMID: 24916128 DOI: 10.1007/s00775-014-1167-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 05/31/2014] [Indexed: 10/25/2022]
Abstract
Rieske and Rieske-type proteins are electron transport proteins involved in key biological processes such as respiration, photosynthesis, and detoxification. They have a [2Fe-2S] cluster ligated by two cysteines and two histidines. A series of mutations, L135E, L135R, L135A, and Y158F, of the Rieske protein from Thermus thermophilus has been produced which probe the effects of the neighboring residues, in the second sphere, on the dynamics of cluster reduction and the reactivity of the ligating histidines. These properties were probed using titrations and modifications with diethyl pyrocarbonate (DEPC) at various pH values monitored using UV-Visible and circular dichroism spectrophotometry. These results, along with results from EPR studies, provide information on ligating histidine modification and rate of reduction of each of the mutant proteins. L135R, L135A, and Y158F react with DEPC similarly to wild type, resulting in modified protein with a reduced [2Fe-2S] cluster in <90 min, whereas L135E requires >15 h under the same conditions. Thus, the negative charge slows down the rate of reduction and provides an explanation as to why negatively charged residues are rarely, if ever, found in the equivalent position of other Rieske and Rieske-type proteins.
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Affiliation(s)
- Nicholas E Karagas
- Department of Chemistry, Trinity University, One Trinity Place, San Antonio, TX, 78212, USA
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10
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 549] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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11
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Albers A, Demeshko S, Dechert S, Saouma CT, Mayer JM, Meyer F. Fast proton-coupled electron transfer observed for a high-fidelity structural and functional [2Fe-2S] Rieske model. J Am Chem Soc 2014; 136:3946-54. [PMID: 24506804 PMCID: PMC3985845 DOI: 10.1021/ja412449v] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Rieske cofactors
have a [2Fe–2S] cluster with unique {His2Cys2} ligation and distinct Fe subsites. The histidine
ligands are functionally relevant, since they allow for coupling of
electron and proton transfer (PCET) during quinol oxidation in respiratory
and photosynthetic ET chains. Here we present the highest fidelity
synthetic analogue for the Rieske [2Fe–2S] cluster reported
so far. This synthetic analogue 5x– emulates the heteroleptic {His2Cys2} ligation of the [2Fe–2S] core, and it also serves
as a functional model that undergoes fast concerted proton and electron
transfer (CPET) upon reaction of the mixed-valent (ferrous/ferric)
protonated 5H2– with TEMPO. The thermodynamics
of the PCET square scheme for 5x– have been determined, and three species (diferric 52–, protonated diferric 5H–, and mixed-valent 53–) have been characterized by X-ray diffraction. pKa values for 5H– and 5H2– differ by about 4 units, and the reduction
potential of 5H– is shifted anodically
by about +230 mV compared to that of 52–. While the N–H bond dissociation free energy of 5H2– (60.2 ± 0.5 kcal mol–1) and the free energy, ΔG°CPET, of its reaction with TEMPO (−6.3 kcal mol–1) are similar to values recently reported for a homoleptic {N2/N2}-coordinated [2Fe–2S] cluster, CPET
is significantly faster for 5H2– with
biomimetic {N2/S2} ligation (k = (9.5 ± 1.2) × 104 M–1 s–1, ΔH‡ = 8.7
± 1.0 kJ mol–1, ΔS‡ = −120 ± 40 J mol–1 K–1, and ΔG‡ = 43.8 ± 0.3 kJ mol–1 at 293 K). These parameters,
and the comparison with homoleptic analogues, provide important information
and new perspectives for the mechanistic understanding of the biological
Rieske cofactor.
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Affiliation(s)
- Antonia Albers
- Institute of Inorganic Chemistry, Georg-August-University Göttingen , Tammannstrasse 4, D-37077 Göttingen, Germany
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12
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Ohki Y. Synthetic Analogues of the Active Sites of Nitrogenase and [NiFe] Hydrogenase. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2014. [DOI: 10.1246/bcsj.20130207] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yasuhiro Ohki
- Department of Chemistry, Graduate School of Science, Nagoya University
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13
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Faiella M, Roy A, Sommer D, Ghirlanda G. De novo design of functional proteins: Toward artificial hydrogenases. Biopolymers 2013; 100:558-71. [DOI: 10.1002/bip.22420] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 07/08/2013] [Accepted: 09/18/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Marina Faiella
- Department of Chemistry and Biochemistry; Arizona State University; Tempe AZ
| | - Anindya Roy
- Department of Chemistry and Biochemistry; Arizona State University; Tempe AZ
| | - Dayn Sommer
- Department of Chemistry and Biochemistry; Arizona State University; Tempe AZ
| | - Giovanna Ghirlanda
- Department of Chemistry and Biochemistry; Arizona State University; Tempe AZ
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14
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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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15
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Abstract
Induction of cytokines by small interfering RNA (siRNA) polyplexes has been a significant concern of researchers attempting to minimize the toxicity of this promising therapy. Although cationic carriers of siRNA are known to increase cytokine levels, few systematic studies have been done to determine what properties of the carrier are important to modulate cytokines. Because branched histidine-lysine (HK) peptides are effective carriers of siRNA and their sequence can be readily modified, we selected this class of carrier to determine which sequences of the peptide were important for cytokine induction. With the use of peripheral blood mononuclear cells (PBMCs), the HK peptide with a higher number of histidines (H3K(+H)4b) in complex with siRNA induced lower levels of cytokines compared with other HK (e.g., H2K4b, H3K4b, H3K(+N)4b) siRNA nanoplexes. Notably, these peptides' siRNA polyplexes showed a similar pattern of cytokine induction when injected intravenously in a mouse model, i.e., the HK with higher content of histidines induced cytokines the least. As indicated by the pH-sensitive dye within acidic endosomes, the greater pH-buffering capacity of H3K(+H)4b compared with other HK peptides may explain why cytokine levels were reduced. In addition to buffering capacity, the size of HK polyplexes markedly influenced cytokine production.
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16
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Heimdal J, Kaukonen M, Srnec M, Rulíšek L, Ryde U. Reduction potentials and acidity constants of Mn superoxide dismutase calculated by QM/MM free-energy methods. Chemphyschem 2011; 12:3337-47. [PMID: 21960467 DOI: 10.1002/cphc.201100339] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Indexed: 11/10/2022]
Abstract
We used two theoretical methods to estimate reduction potentials and acidity constants in Mn superoxide dismutase (MnSOD), namely combined quantum mechanical and molecular mechanics (QM/MM) thermodynamic cycle perturbation (QTCP) and the QM/MM-PBSA approach. In the latter, QM/MM energies are combined with continuum solvation energies calculated by solving the Poisson-Boltzmann equation (PB) or by the generalised Born approach (GB) and non-polar solvation energies calculated from the solvent-exposed surface area. We show that using the QTCP method, we can obtain accurate and precise estimates of the proton-coupled reduction potential for MnSOD, 0.30±0.01 V, which compares favourably with experimental estimates of 0.26-0.40 V. However, the calculated potentials depend strongly on the DFT functional used: The B3LYP functional gives 0.6 V more positive potentials than the PBE functional. The QM/MM-PBSA approach leads to somewhat too high reduction potentials for the coupled reaction and the results depend on the solvation model used. For reactions involving a change in the net charge of the metal site, the corresponding results differ by up to 1.3 V or 24 pK(a) units, rendering the QM/MM-PBSA method useless to determine absolute potentials. However, it may still be useful to estimate relative shifts, although the QTCP method is expected to be more accurate.
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Affiliation(s)
- Jimmy Heimdal
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, 221 00 Lund, Sweden
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17
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El Khoury Y, Hellwig P. A combined far-infrared spectroscopic and electrochemical approach for the study of iron-sulfur proteins. Chemphyschem 2011; 12:2669-74. [PMID: 21887734 DOI: 10.1002/cphc.201100165] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 06/15/2011] [Indexed: 11/11/2022]
Abstract
Herein, we present the development of a far-infrared spectroscopic approach for studying metalloenzyme active sites in a redox-dependent manner. An electrochemical cell with 5 mm path and based on silicon windows was found to be appropriate for the measurement of aqueous solutions down to 200 cm(-1) . The cell was probed with the infrared redox signature of the metal-ligand vibrations of different iron-sulfur proteins. Each Fe-S cluster type was found to show a specific spectral signature. As a common feature, a downshift of the frequency of the Fe-S vibrations was seen upon reduction, in line with the increase of the Fe-S bond. This downshift was found to be fully reversible. Electrochemically induced FTIR difference spectroscopy in the far infrared is now possible, opening new perspectives on the understanding of metalloproteins in function of the redox state.
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Affiliation(s)
- Youssef El Khoury
- Institut de Chimie, UMR, Laboratoire de spectroscopie vibrationnelle et électrochimie des biomolécules Université de Strasbourg, France
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18
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Zuris JA, Halim DA, Conlan AR, Abresch EC, Nechushtai R, Paddock ML, Jennings PA. Engineering the redox potential over a wide range within a new class of FeS proteins. J Am Chem Soc 2010; 132:13120-2. [PMID: 20812736 PMCID: PMC2944382 DOI: 10.1021/ja103920k] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Indexed: 11/30/2022]
Abstract
MitoNEET is a newly discovered mitochondrial protein and a target of the TZD class of antidiabetes drugs. MitoNEET is homodimeric with each protomer binding a [2Fe-2S] center through a rare 3-Cys and 1-His coordination geometry. Both the fold and the coordination of the [2Fe-2S] centers suggest that it could have novel properties compared to other known [2Fe-2S] proteins. We tested the robustness of mitoNEET to mutation and the range over which the redox potential (E(M)) could be tuned. We found that the protein could tolerate an array of mutations that modified the E(M) of the [2Fe-2S] center over a range of ∼700 mV, which is the largest E(M) range engineered in an FeS protein and, importantly, spans the cellular redox range (+200 to -300 mV). These properties make mitoNEET potentially useful for both physiological studies and industrial applications as a stable, water-soluble, redox agent.
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19
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El Khoury Y, Trivella A, Gross J, Hellwig P. Probing the Hydrogen Bonding Structure in the Rieske Protein. Chemphyschem 2010; 11:3313-9. [DOI: 10.1002/cphc.201000331] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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20
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Kuznetsov AM, Zueva EM, Masliy AN, Krishtalik LI. Redox potential of the Rieske iron-sulfur protein quantum-chemical and electrostatic study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1797:347-59. [PMID: 20026009 DOI: 10.1016/j.bbabio.2009.12.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Revised: 12/04/2009] [Accepted: 12/08/2009] [Indexed: 11/15/2022]
Abstract
Quantum-chemical study of structures, energies, and effective partial charge distribution for several models of the Rieske protein redox center is performed in terms of the B3LYP density functional method in combination with the broken symmetry approach using three different atomic basis sets. The structure of the redox complex optimized in vacuum differs markedly from that inside the protein. This means that the protein matrix imposes some stress on the active site resulting in distortion of its structure. The redox potentials calculated for the real active site structure are in a substantially better agreement with the experiment than those calculated for the idealized structure. This shows an important role of the active site distortion in tuning its redox potential. The reference absolute electrode potential of the standard hydrogen electrode is used that accounts for the correction caused by the water surface potential. Electrostatic calculations are performed in the framework of the polarizable solute model. Two dielectric permittivities of the protein are employed: the optical permittivity for calculation of the intraprotein electric field, and the static permittivity for calculation of the dielectric response energy. Only this approach results in a reasonable agreement of the calculated and experimental redox potentials.
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Affiliation(s)
- Andrey M Kuznetsov
- Kazan State Technological University, ul. K. Marksa 68, 420015, Kazan, Russia.
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21
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Lhee S, Kolling DRJ, Nair SK, Dikanov SA, Crofts AR. Modifications of protein environment of the [2Fe-2S] cluster of the bc1 complex: effects on the biophysical properties of the rieske iron-sulfur protein and on the kinetics of the complex. J Biol Chem 2009; 285:9233-48. [PMID: 20023300 DOI: 10.1074/jbc.m109.043505] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The rate-determining step in the overall turnover of the bc(1) complex is electron transfer from ubiquinol to the Rieske iron-sulfur protein (ISP) at the Q(o)-site. Structures of the ISP from Rhodobacter sphaeroides show that serine 154 and tyrosine 156 form H-bonds to S-1 of the [2Fe-2S] cluster and to the sulfur atom of the cysteine liganding Fe-1 of the cluster, respectively. These are responsible in part for the high potential (E(m)(,7) approximately 300 mV) and low pK(a) (7.6) of the ISP, which determine the overall reaction rate of the bc(1) complex. We have made site-directed mutations at these residues, measured thermodynamic properties using protein film voltammetry to evaluate the E(m) and pK(a) values of ISPs, explored the local proton environment through two-dimensional electron spin echo envelope modulation, and characterized function in strains S154T, S154C, S154A, Y156F, and Y156W. Alterations in reaction rate were investigated under conditions in which concentration of one substrate (ubiquinol or ISP(ox)) was saturating and the other was varied, allowing calculation of kinetic terms and relative affinities. These studies confirm that H-bonds to the cluster or its ligands are important determinants of the electrochemical characteristics of the ISP, likely through electron affinity of the interacting atom and the geometry of the H-bonding neighborhood. The calculated parameters were used in a detailed Marcus-Brønsted analysis of the dependence of rate on driving force and pH. The proton-first-then-electron model proposed accounts naturally for the effects of mutation on the overall reaction.
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Affiliation(s)
- Sangmoon Lhee
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801, USA
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22
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Iwasaki T, Samoilova RI, Kounosu A, Dikanov SA. Two-dimensional pulsed electron spin resonance characterization of 15N-labeled archaeal Rieske-type ferredoxin. FEBS Lett 2009; 583:3467-72. [PMID: 19804777 DOI: 10.1016/j.febslet.2009.09.050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 09/24/2009] [Accepted: 09/29/2009] [Indexed: 11/25/2022]
Abstract
Two-dimensional electron spin-echo envelope modulation (ESEEM) analysis of the uniformly (15)N-labeled archaeal Rieske-type [2Fe-2S] ferredoxin (ARF) from Sulfolobus solfataricus P1 has been conducted in comparison with the previously characterized high-potential protein homologs. Major differences among these proteins were found in the hyperfine sublevel correlation (HYSCORE) lineshapes and intensities of the signals in the (++) quadrant, which are contributed from weakly coupled (non-coordinated) peptide nitrogens near the reduced clusters. They are less pronounced in the HYSCORE spectra of ARF than those of the high-potential protein homologs, and may account for the tuning of Rieske-type clusters in various redox systems.
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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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23
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Cheap H, Bernad S, Derrien V, Gerencsér L, Tandori J, de Oliveira P, Hanson DK, Maróti P, Sebban P. M234Glu is a component of the proton sponge in the reaction center from photosynthetic bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:1505-15. [PMID: 19632193 DOI: 10.1016/j.bbabio.2009.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Revised: 07/13/2009] [Accepted: 07/15/2009] [Indexed: 10/20/2022]
Abstract
Bacterial reaction centers use light energy to couple the uptake of protons to the successive semi-reduction of two quinones, namely Q(A) and Q(B). These molecules are situated symmetrically in regard to a non-heme iron atom. Four histidines and one glutamic acid, M234Glu, constitute the five ligands of this atom. By flash-induced absorption spectroscopy and delayed fluorescence we have studied in the M234EH and M234EL variants the role played by this acidic residue on the energetic balance between the two quinones as well as in proton uptake. Delayed fluorescence from the P(+)Q(A)(-) state (P is the primary electron donor) and temperature dependence of the rate of P(+)Q(A)(-) charge recombination that are in good agreement show that in the two RC variants, both Q(A)(-) and Q(B)(-) are destabilized by about the same free energy amount: respectively approximately 100 +/- 5 meV and 90 +/- 5 meV for the M234EH and M234EL variants, as compared to the WT. Importantly, in the M234EH and M234EL variants we observe a collapse of the high pH band (present in the wild-type reaction center) of the proton uptake amplitudes associated with formation of Q(A)(-) and Q(B)(-). This band has recently been shown to be a signature of a collective behaviour of an extended, multi-entry, proton uptake network. M234Glu seems to play a central role in the proton sponge-like system formed by the RC protein.
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Affiliation(s)
- Hélène Cheap
- Laboratoire de Chimie Physique, UMR 8000, University of Paris-Sud 11/CNRS, 91405 cedex, France
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24
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Tirrell TF, Paddock ML, Conlan AR, Smoll EJ, Nechushtai R, Jennings PA, Kim JE. Resonance Raman studies of the (His)(Cys)3 2Fe-2S cluster of MitoNEET: comparison to the (Cys)4 mutant and implications of the effects of pH on the labile metal center. Biochemistry 2009; 48:4747-52. [PMID: 19388667 DOI: 10.1021/bi900028r] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
MitoNEET is a 2Fe-2S outer mitochondrial membrane protein that was initially identified as a target for anti-diabetic drugs. It exhibits a novel protein fold, and in contrast to other 2Fe-2S proteins such as Rieske proteins and ferredoxins, the metal clusters in the mitoNEET homodimer are each coordinated by one histidine residue and three cysteine residues. The interaction of the ligating His87 residue with the 2Fe-2S moiety is especially significant because previous studies have shown that replacement with Cys in the H87C mutant stabilizes the cluster against release. Here, we report the resonance Raman spectra of this naturally occurring Fe(2)S(2)(His)(Cys)(3) protein to assess local structural changes associated with cluster lability. Comparison of mitoNEET to its ferredoxin-like H87C mutant indicates that Raman peaks in the approximately 250-300 cm(-1) region of mitoNEET are influenced by the Fe-His87 moiety. Systematic pH-dependent resonance Raman spectral changes were observed in this spectral region for native mitoNEET but not the H87C mutant. The approximately 250-300 cm(-1) region of native mitoNEET is also sensitive to phosphate buffer. Thus, conditions that influence cluster release are shown here to concomitantly affect the resonance Raman spectrum in the region with Fe-His contribution. These results support the hypothesis that the Fe-N(His87) interaction is modulated within the physiological pH range, and this modulation may be critical to the function of mitoNEET.
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Affiliation(s)
- Timothy F Tirrell
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, USA
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25
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Ballmann J, Albers A, Demeshko S, Dechert S, Bill E, Bothe E, Ryde U, Meyer F. A synthetic analogue of Rieske-type [2Fe-2S] clusters. Angew Chem Int Ed Engl 2008; 47:9537-41. [PMID: 18972470 DOI: 10.1002/anie.200803418] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Joachim Ballmann
- Institut für Anorganische Chemie, Georg-August-Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany
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26
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Ballmann J, Albers A, Demeshko S, Dechert S, Bill E, Bothe E, Ryde U, Meyer F. Ein synthetisches Analogon für [2Fe-2S]-Cluster des Rieske-Typs. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200803418] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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Ullmann GM, Kloppmann E, Essigke T, Krammer EM, Klingen AR, Becker T, Bombarda E. Investigating the mechanisms of photosynthetic proteins using continuum electrostatics. PHOTOSYNTHESIS RESEARCH 2008; 97:33-53. [PMID: 18478354 DOI: 10.1007/s11120-008-9306-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2007] [Accepted: 04/10/2008] [Indexed: 05/26/2023]
Abstract
Computational methods based on continuum electrostatics are widely used in theoretical biochemistry to analyze the function of proteins. Continuum electrostatic methods in combination with quantum chemical and molecular mechanical methods can help to analyze even very complex biochemical systems. In this article, applications of these methods to proteins involved in photosynthesis are reviewed. After giving a short introduction to the basic concepts of the continuum electrostatic model based on the Poisson-Boltzmann equation, we describe the application of this approach to the docking of electron transfer proteins, to the comparison of isofunctional proteins, to the tuning of absorption spectra, to the analysis of the coupling of electron and proton transfer, to the analysis of the effect of membrane potentials on the energetics of membrane proteins, and to the kinetics of charge transfer reactions. Simulations as those reviewed in this article help to analyze molecular mechanisms on the basis of the structure of the protein, guide new experiments, and provide a better and deeper understanding of protein functions.
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Affiliation(s)
- G Matthias Ullmann
- Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstr. 30, BGI, Bayreuth 95447, Germany.
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28
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Anders Borg O, Durbeej B. Which factors determine the acidity of the phytochromobilin chromophore of plant phytochrome? Phys Chem Chem Phys 2008; 10:2528-37. [PMID: 18446253 DOI: 10.1039/b719190a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quantum chemical calculations aimed at identifying the factors controlling the acidity of phytochromobilin, the tetrapyrrole chromophore of the plant photoreceptor phytochrome, are reported. Phytochrome is converted from an inactive (Pr) to an active form (Pfr) through a series of events initiated by a Z --> E photoisomerization of phytochromobilin, forming the Lumi-R intermediate, and much controversy exists as to whether the protonation state of the chromophore (cationic in Pr with all nitrogens protonated) changes during the photoactivation. Here, relative ground (S0) and excited-state (S1) pKa s of all four pyrrole moieties of phytochromobilin in all 64 possible configurations with respect to the three methine bridges are calculated in a protein-like environment, using a recently benchmarked level of theory. Accordingly, the relationships between acidity and chromophore geometry and charge distribution, hydrogen bonding, and light absorption are investigated in some detail, and discussed in terms of possible mechanisms making a proton transfer reaction more probable along the Pr --> Pfr reaction than in the parent cationic Pr state. It is found that charge distribution in the cationic species, intra-molecular hydrogen bonding in the neutral, and hydrogen bonding with two highly conserved aspartate and histidine residues have a significant effect on the acidity, while overall chromophore geometry and electronic state are less important factors. Furthermore, based on the calculations, two processes that may facilitate a proton transfer by substantially lowering the pKa s relative to their Pr values are identified: (i) a thermal Z,anti --> Z,syn isomerization at C5, occurring after formation of Lumi-R; (ii) a perturbation of the hydrogen bonding network which in Pr comprises the nitrogens of pyrroles A, B and C and the two aspartate and histidine residues.
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Affiliation(s)
- O Anders Borg
- Department of Quantum Chemistry, Uppsala University, Box 518, S-75120, Uppsala, Sweden
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29
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2D hydrogen bond networks in the crystals of [(NH4·H2O)2][(RO)(Fc)P(S)2]2 (R=3-(BzO)-Bz, 4-(n-Bu)-Bz, Bz=benzyl). J Organomet Chem 2007. [DOI: 10.1016/j.jorganchem.2007.08.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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30
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Borg OA, Durbeej B. Relative Ground and Excited-State pKa Values of Phytochromobilin in the Photoactivation of Phytochrome: A Computational Study. J Phys Chem B 2007; 111:11554-65. [PMID: 17845025 DOI: 10.1021/jp0727953] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The conversion of the plant photoreceptor phytochrome from an inactive (Pr) to an active form (Pfr) is accomplished by a red-light induced Z --> E photoisomerization of its phytochromobilin chromophore. In recent years, the question whether the photoactivation involves a change in chromophore protonation state has been the subject of many experimental studies. Here, we have used quantum chemical methods to calculate relative ground and excited-state pKa values of the different pyrrole moieties of phytochromobilin in a protein-like environment. Assuming (based on experimental data) a Pr ZaZsZa chromophore and considering isomerizations at C15 and C5, it is found that moieties B and C are the strongest acids both in the ground state and in the bright first singlet excited state, which is rationalized in simple geometric and electronic terms. It is also shown that neither light absorption nor isomerization increases the acidity of phytochromobilin relative to the reference Pr state with all pyrrolenic nitrogens protonated. Hence, provided that the subset of chromophore geometries under investigation is biologically relevant, there appears to be no intrinsic driving force for a proton-transfer event. In a series of benchmark calculations, the performance of ab initio and time-dependent density functional theory methods for excited-state studies of phytochromobilin is evaluated in light of available experimental data.
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Affiliation(s)
- O Anders Borg
- Department of Quantum Chemistry, Uppsala University, Box 518, S-75120 Uppsala, Sweden
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31
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Lin IJ, Chen Y, Fee JA, Song J, Westler WM, Markley JL. Rieske protein from Thermus thermophilus: 15N NMR titration study demonstrates the role of iron-ligated histidines in the pH dependence of the reduction potential. J Am Chem Soc 2007; 128:10672-3. [PMID: 16910649 DOI: 10.1021/ja0627388] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A unique feature of Rieske proteins is the pH dependence of their reduction potentials. It has been proposed that protonation of the Nepsilon2 atoms of the two histidine rings ligated to the iron-sulfur cluster is coupled with cluster reduction (electron transfer). We have incorporated [15Ndelta1, 15Nepsilon2]-histidine into the Rieske protein from Thermus thermophilis and have used 15N NMR spectroscopy to determine the pKa values of the histidine residues in the oxidized state of the protein. As expected from studies of a Rieske-type ferredoxin, the signals from the 15Ndelta1 atoms directly bound to iron were too broad to be detected, but broad signals could be detected from the 15Nepsilon2 atom of each of the ligated histidine rings. We measured the chemical shifts of these signals as a function of pH between pH 6 and pH 12 and fitted them to theoretical titration curves. The results yielded well-separated pKa values for the two histidines (7.46 and 9.24), with Hill coefficients close to unity. The pKa values are in excellent agreement with values predicted from the pH dependence of the reduction potentials (7.85 and 9.65).
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Affiliation(s)
- I-Jin Lin
- Graduate Program in Biophysics, Center for Eukaryotic Structural Genomics, National Magnetic Resonance Facility at Madison, 433 Babcock Drive, University of Wisconsin, Madison, Wisconsin 53706, USA
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32
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Klingen AR, Palsdottir H, Hunte C, Ullmann GM. Redox-linked protonation state changes in cytochrome bc1 identified by Poisson–Boltzmann electrostatics calculations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1767:204-21. [PMID: 17349966 DOI: 10.1016/j.bbabio.2007.01.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2006] [Revised: 01/15/2007] [Accepted: 01/17/2007] [Indexed: 11/16/2022]
Abstract
Cytochrome bc(1) is a major component of biological energy conversion that exploits an energetically favourable redox reaction to generate a transmembrane proton gradient. Since the mechanistic details of the coupling of redox and protonation reactions in the active sites are largely unresolved, we have identified residues that undergo redox-linked protonation state changes. Structure-based Poisson-Boltzmann/Monte Carlo titration calculations have been performed for completely reduced and completely oxidised cytochrome bc(1). Different crystallographically observed conformations of Glu272 and surrounding residues of the cytochrome b subunit in cytochrome bc(1) from Saccharomyces cerevisiae have been considered in the calculations. Coenzyme Q (CoQ) has been modelled into the CoQ oxidation site (Q(o)-site). Our results indicate that both conformational and protonation state changes of Glu272 of cytochrome b may contribute to the postulated gating of CoQ oxidation. The Rieske iron-sulphur cluster could be shown to undergo redox-linked protonation state changes of its histidine ligands in the structural context of the CoQ-bound Q(o)-site. The proton acceptor role of the CoQ ligands in the CoQ reduction site (Q(i)-site) is supported by our results. A modified path for proton uptake towards the Q(i)-site features a cluster of conserved lysine residues in the cytochrome b (Lys228) and cytochrome c(1) subunits (Lys288, Lys289, Lys296). The cardiolipin molecule bound close to the Q(i)-site stabilises protons in this cluster of lysine residues.
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Affiliation(s)
- Astrid R Klingen
- Structural Biology/Bioinformatics Group, University of Bayreuth, Germany
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Czodrowski P, Dramburg I, Sotriffer CA, Klebe G. Development, validation, and application of adapted PEOE charges to estimate pKa values of functional groups in protein-ligand complexes. Proteins 2006; 65:424-37. [PMID: 16927370 DOI: 10.1002/prot.21110] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
For routine pK(a) calculations of protein-ligand complexes in drug design, the PEOE method to compute partial charges was modified. The new method is applicable to a large scope of proteins and ligands. The adapted charges were parameterized using experimental free energies of solvation of amino acids and small organic ligands. For a data set of 80 small organic molecules, a correlation coefficient of r(2) = 0.78 between calculated and experimental solvation free energies was obtained. Continuum electrostatics pK(a) calculations based on the Poisson-Boltzmann equation were carried out on a validation set of nine proteins for which 132 experimental pK(a) values are known. In total, an overall RMSD of 0.88 log units between calculated and experimentally determined data is achieved. In particular, the predictions of significantly shifted pK(a) values are satisfactory, and reasonable estimates of protonation states in the active sites of lysozyme and xylanase could be obtained. Application of the charge-assignment and pK(a)-calculation procedure to protein-ligand complexes provides clear structural interpretations of experimentally observed changes of protonation states of functional groups upon complex formation. This information is essential for the interpretation of thermodynamic data of protein-ligand complex formation and provides the basis for the reliable factorization of the free energy of binding in enthalpic and entropic contributions. The modified charge-assignment procedure forms the basis for future automated pK(a) calculations of protein-ligand complexes.
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Affiliation(s)
- Paul Czodrowski
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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Dikanov SA, Kolling DRJ, Endeward B, Samoilova RI, Prisner TF, Nair SK, Crofts AR. Identification of Hydrogen Bonds to the Rieske Cluster through the Weakly Coupled Nitrogens Detected by Electron Spin Echo Envelope Modulation Spectroscopy. J Biol Chem 2006; 281:27416-25. [PMID: 16854984 DOI: 10.1074/jbc.m604103200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The interaction of the reduced[2Fe-2S] cluster of isolated Rieske fragment from the bc1 complex of Rhodobacter sphaeroides with nitrogens (14N and 15N) from the local protein environment has been studied by X- and S-band pulsed EPR spectroscopy. The two-dimensional electron spin echo envelope modulation spectra of uniformly 15N-labeled protein show two well resolved cross-peaks with weak couplings of approximately 0.3-0.4 and 1.1 MHz in addition to couplings in the range of 6-8 MHz from two coordinating Ndelta of histidine ligands. The quadrupole coupling constants for weakly coupled nitrogens determined from S-band electron spin echo envelope modulation spectra identify them as Nepsilon of histidine ligands and peptide nitrogen (Np), respectively. Analysis of the line intensities in orientation-selected S-band spectra indicated that Np is the backbone N-atom of Leu-132 residue. The hyperfine couplings from Nepsilon and Np demonstrate the predominantly isotropic character resulting from the transfer of unpaired spin density onto the 2s orbitals of the nitrogens. Spectra also show that other peptide nitrogens in the protein environment must carry a 5-10 times smaller amount of spin density than the Np of Leu-132 residue. The appearance of the excess unpaired spin density on the Np of Leu-132 residue indicates its involvement in hydrogen bond formation with the bridging sulfur of the Rieske cluster. The configuration of the hydrogen bond therefore provides a preferred path for spin density transfer. Observation of similar splittings in the 15N spectra of other Rieske-type proteins and [2Fe-2S] ferredoxins suggests that a hydrogen bond between the bridging sulfur and peptide nitrogen is a common structural feature of [2Fe-2S] clusters.
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Affiliation(s)
- Sergei A Dikanov
- Department of Veterinary Clinical Medicine, University of Illinois, Urbana, Illinois 61801, USA
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Niu S, Ichiye T. Probing the structural effects on the intrinsic electronic and redox properties of [2Fe–2S]+ clusters, a broken-symmetry density functional theory study. Theor Chem Acc 2006. [DOI: 10.1007/s00214-006-0136-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Klingen AR, Bombarda E, Ullmann GM. Theoretical investigation of the behavior of titratable groups in proteins. Photochem Photobiol Sci 2006; 5:588-96. [PMID: 16761087 DOI: 10.1039/b515479k] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper presents a theoretical analysis of the titration behavior of strongly interacting titratable residues in proteins. Strongly interacting titratable residues exist in many proteins such as for instance bacteriorhodopsin, cytochrome c oxidase, cytochrome bc(1), or the photosynthetic reaction center. Strong interaction between titratable groups can lead to irregular titration behavior. We analyze under which circumstances titration curves can become irregular. We demonstrate that conformational flexibility alone can not lead to irregular titration behavior. Strong interaction between titratable groups is a necessary, but not sufficient condition for irregular titration curves. In addition, the two interacting groups also need to titrate in the same pH-range. These two conditions together lead to irregular titration curves. The mutation of a single residue within a cluster of interacting titratable residues can influence the titration behavior of the other titratable residues in the cluster. We demonstrate this effect on a cluster of four interacting residues. This example underlines that mutational studies directed at identifying the role of a certain titratable residue in a cluster of interacting residues should always be accompanied by an analysis of the effect of the mutation on the titration behavior of the other residues.
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Affiliation(s)
- Astrid R Klingen
- Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstrasse 30, BGI, D-95447 Bayreuth, Germany
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Martins BM, Svetlitchnaia T, Dobbek H. 2-Oxoquinoline 8-monooxygenase oxygenase component: active site modulation by Rieske-[2Fe-2S] center oxidation/reduction. Structure 2005; 13:817-24. [PMID: 15893671 DOI: 10.1016/j.str.2005.03.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2004] [Revised: 03/01/2005] [Accepted: 03/06/2005] [Indexed: 11/20/2022]
Abstract
2-Oxoquinoline 8-monooxygenase is a Rieske non-heme iron oxygenase that catalyzes the NADH-dependent oxidation of the N-heterocyclic aromatic compound 2-oxoquinoline to 8-hydroxy-2-oxoquinoline in the soil bacterium Pseudomonas putida 86. The crystal structure of the oxygenase component of 2-oxoquinoline 8-monooxygenase shows a ring-shaped, C3-symmetric arrangement in which the mononuclear Fe(II) ion active site of one monomer is at a distance of 13 A from the Rieske-[2Fe-2S] center of a second monomer. Structural analyses of oxidized, reduced, and substrate bound states reveal the molecular bases for a new function of Fe-S clusters. Reduction of the Rieske center modulates the mononuclear Fe through a chain of conformational changes across the subunit interface, resulting in the displacement of Fe and its histidine ligand away from the substrate binding site. This creates an additional coordination site at the mononuclear Fe(II) ion and can open a pathway for dioxygen to bind in the substrate-containing active site.
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Kletzin A, Ferreira AS, Hechler T, Bandeiras TM, Teixeira M, Gomes CM. A Rieske ferredoxin typifying a subtype within Rieske proteins: spectroscopic, biochemical and stability studies. FEBS Lett 2005; 579:1020-6. [PMID: 15710385 DOI: 10.1016/j.febslet.2004.12.075] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2004] [Revised: 12/21/2004] [Accepted: 12/30/2004] [Indexed: 10/25/2022]
Abstract
A new subtype of archaeal Rieske ferredoxin (RFd) has been identified in the genome of the thermoacidophilic archaeon Acidianus ambivalens. The gene is inserted in an atypical genomic context in a gene cluster encoding a NiFe hydrogenase. Sequence and phyletic analysis showed that the protein is related to bacterial RFd but not to any of the known archaeal Rieske proteins. The recombinant 14 kDa protein isolated from Escherichia coli behaved as a dimer in solution. It contained approximately 2 Fe/mol and all visible and EPR spectroscopic features typical of Rieske centre-containing proteins. However, its redox potential (+170 mV) was significantly higher than those of canonical RFd. This difference is rationalized in terms of the protein structure environment, as discrete amino acid substitutions in key positions around the metal centre account for the higher potential.
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Affiliation(s)
- Arnulf Kletzin
- Institute of Microbiology and Genetics, Darmstadt University of Technology, Schnittspahnstrasse 10, 64287 Darmstadt, Germany.
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