1
|
Roy RR, Ullmann GM. Virtual Model Compound Approach for Calculating Redox Potentials of [Fe 2S 2]-Cys 4 Centers in Proteins - Structure Quality Matters. J Chem Theory Comput 2023; 19:8930-8941. [PMID: 37974307 DOI: 10.1021/acs.jctc.3c00779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The midpoint potential of the [Fe2S2]-Cys4-cluster in proteins is known to vary between -200 and -450 mV. This variation is caused by the different electrostatic environment of the cluster in the respective proteins. Continuum electrostatics can quantify the impact of the protein environment on the redox potential. Thus, if the redox potential of a [Fe2S2]-Cys4-cluster model compound in aqueous solution would be known, then redox potentials in various protein complexes could be calculated. However, [Fe2S2]-Cys4-cluster models are not water-soluble, and thus, their redox potential can not be measured in aqueous solution. To overcome this problem, we introduce a method that we call Virtual Model Compound Approach (VMCA) to extrapolate the model redox potential from known redox potentials of proteins. We carefully selected high-resolution structures for our analysis and divide them into a fit set, for fitting the model redox potential, and an independent test set, to check the validity of the model redox potential. However, from our analysis, we realized that the some structures can not be used as downloaded from the PDB but had to be re-refined in order to calculate reliable redox potentials. Because of the re-refinement, we were able to significantly reduce the standard deviation of our derived model redox potential for the [Fe2S2]-Cys4-cluster from 31 mV to 10 mV. As the model redox potential, we obtained -184 mV. This model redox potential can be used to analyze the redox behavior of [Fe2S2]-Cys4-clusters in larger protein complexes.
Collapse
Affiliation(s)
- Rajeev Ranjan Roy
- Computational Biochemistry, Universitätsstr. 30, NWI, University of Bayreuth, Bayreuth, 95440, Germany
| | - G Matthias Ullmann
- Computational Biochemistry, Universitätsstr. 30, NWI, University of Bayreuth, Bayreuth, 95440, Germany
| |
Collapse
|
2
|
Vos MH, Salman M, Ramodiharilafy R, Liebl U. Fluorescent iron‑sulfur centers: Photochemistry of the PetA Rieske protein from Aquifex aeolicus. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148385. [PMID: 33516769 DOI: 10.1016/j.bbabio.2021.148385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/12/2021] [Accepted: 01/22/2021] [Indexed: 11/28/2022]
Abstract
Cytochrome bc1 complexes are energy-transducing enzymes and key components of respiratory electron chains. They contain Rieske 2Fe2S proteins that absorb very weakly in the visible absorption region compared to the heme cofactors of the cytochromes, but are known to yield photoproducts. Here, the photoreactions of isolated Rieske proteins from the hyperthermophilic bacterium Aquifex aeolicus are studied in two redox states using ultrafast transient fluorescence and absorption spectroscopy. We provide evidence, for the first time in iron‑sulfur proteins, of very weak fluorescence of the excited state, in the oxidized as well as the reduced state. The excited states of the oxidized and reduced forms decay in 1.5 ps and 30 ps, respectively. In both cases they give rise to product states with lifetimes beyond 1 ns, reflecting photo-reduction of oxidized centers as well as photo-oxidation of reduced centers. Potential reaction partners are discussed and studied using site-directed mutagenesis. For the reduced state, a nearby disulfide bridge is suggested as an electron acceptor. The resulting photoproducts in either state may play a role in photoactivation processes.
Collapse
Affiliation(s)
- Marten H Vos
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France.
| | - Mayla Salman
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France
| | - Rivo Ramodiharilafy
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France
| | - Ursula Liebl
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France
| |
Collapse
|
3
|
Mao Z, Liou SH, Khadka N, Jenney FE, Goodin DB, Seefeldt LC, Adams MWW, Cramer SP, Larsen DS. Cluster-Dependent Charge-Transfer Dynamics in Iron-Sulfur Proteins. Biochemistry 2018; 57:978-990. [PMID: 29303562 DOI: 10.1021/acs.biochem.7b01159] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Photoinduced charge-transfer dynamics and the influence of cluster size on the dynamics were investigated using five iron-sulfur clusters: the 1Fe-4S cluster in Pyrococcus furiosus rubredoxin, the 2Fe-2S cluster in Pseudomonas putida putidaredoxin, the 4Fe-4S cluster in nitrogenase iron protein, and the 8Fe-7S P-cluster and the 7Fe-9S-1Mo FeMo cofactor in nitrogenase MoFe protein. Laser excitation promotes the iron-sulfur clusters to excited electronic states that relax to lower states. The electronic relaxation lifetimes of the 1Fe-4S, 8Fe-7S, and 7Fe-9S-1Mo clusters are on the picosecond time scale, although the dynamics of the MoFe protein is a mixture of the dynamics of the latter two clusters. The lifetimes of the 2Fe-2S and 4Fe-4S clusters, however, extend to several nanoseconds. A competition between reorganization energies and the density of electronic states (thus electronic coupling between states) mediates the charge-transfer lifetimes, with the 2Fe-2S cluster of Pdx and the 4Fe-4S cluster of Fe protein lying at the optimum leading to them having significantly longer lifetimes. Their long lifetimes make them the optimal candidates for long-range electron transfer and as external photosensitizers for other photoactivated chemical reactions like solar hydrogen production. Potential electron-transfer and hole-transfer pathways that possibly facilitate these charge transfers are proposed.
Collapse
Affiliation(s)
- Ziliang Mao
- Department of Chemistry, University of California at Davis , One Shields Avenue, Davis, California 95616, United States
| | - Shu-Hao Liou
- Department of Chemistry, University of California at Davis , One Shields Avenue, Davis, California 95616, United States
| | - Nimesh Khadka
- Department of Chemistry and Biochemistry, Utah State University , 0300 Old Main Hill, Logan, Utah 84322, United States
| | - Francis E Jenney
- Georgia Campus, Philadelphia College of Osteopathic Medicine , Suwanee, Georgia 30024, United States
| | - David B Goodin
- Department of Chemistry, University of California at Davis , One Shields Avenue, Davis, California 95616, United States
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University , 0300 Old Main Hill, Logan, Utah 84322, United States
| | - Michael W W Adams
- Department of Biochemistry, The University of Georgia , Athens, Georgia 30602, United States
| | - Stephen P Cramer
- Department of Chemistry, University of California at Davis , One Shields Avenue, Davis, California 95616, United States
| | - Delmar S Larsen
- Department of Chemistry, University of California at Davis , One Shields Avenue, Davis, California 95616, United States
| |
Collapse
|
4
|
Mao Z, Carroll EC, Kim PW, Cramer SP, Larsen DS. Ultrafast Charge-Transfer Dynamics in the Iron-Sulfur Complex of Rhodobacter capsulatus Ferredoxin VI. J Phys Chem Lett 2017; 8:4498-4503. [PMID: 28872878 PMCID: PMC7187928 DOI: 10.1021/acs.jpclett.7b02026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Iron-sulfur proteins play essential roles in various biological processes. Their electronic structure and vibrational dynamics are key to their rich chemistry but nontrivial to unravel. Here, the first ultrafast transient absorption and impulsive coherent vibrational spectroscopic (ICVS) studies on 2Fe-2S clusters in Rhodobacter capsulatus ferreodoxin VI are characterized. Photoexcitation initiated populations on multiple excited electronic states that evolve into each other in a long-lived charge-transfer state. This suggests a potential light-induced electron-transfer pathway as well as the possibility of using iron-sulfur proteins as photosensitizers for light-dependent enzymes. A tyrosine chain near the active site suggests potential hole-transfer pathways and affirms this electron-transfer pathway. The ICVS data revealed vibrational bands at 417 and 484 cm-1, with the latter attributed to an excited-state mode. The temperature dependence of the ICVS modes suggests that the temperature effect on protein structure or conformational heterogeneities needs to be considered during cryogenic temperature studies.
Collapse
Affiliation(s)
- Ziliang Mao
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
| | - Elizabeth C. Carroll
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
| | - Peter W. Kim
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
| | - Stephen P. Cramer
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
- Corresponding Authors: &
| | - Delmar S. Larsen
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, United States
- Corresponding Authors: &
| |
Collapse
|
5
|
Atkinson JT, Campbell I, Bennett GN, Silberg JJ. Cellular Assays for Ferredoxins: A Strategy for Understanding Electron Flow through Protein Carriers That Link Metabolic Pathways. Biochemistry 2016; 55:7047-7064. [DOI: 10.1021/acs.biochem.6b00831] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joshua T. Atkinson
- Systems,
Synthetic, and Physical Biology Graduate Program, Rice University, MS-180, 6100 Main Street, Houston, Texas 77005, United States
| | - Ian Campbell
- Biochemistry
and Cell Biology Graduate Program, Rice University, MS-140, 6100
Main Street, Houston, Texas 77005, United States
| | - George N. Bennett
- Department
of Biosciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
- Department
of Chemical and Biomolecular Engineering, Rice University, MS-362,
6100 Main Street, Houston, Texas 77005, United States
| | - Jonathan J. Silberg
- Department
of Biosciences, Rice University, MS-140, 6100 Main Street, Houston, Texas 77005, United States
- Department
of Bioengineering, Rice University, MS-142, 6100 Main Street, Houston, Texas 77005, United States
| |
Collapse
|
6
|
von Stetten D, Giraud T, Carpentier P, Sever F, Terrien M, Dobias F, Juers DH, Flot D, Mueller-Dieckmann C, Leonard GA, de Sanctis D, Royant A. In crystallo optical spectroscopy (icOS) as a complementary tool on the macromolecular crystallography beamlines of the ESRF. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:15-26. [PMID: 25615856 PMCID: PMC4304682 DOI: 10.1107/s139900471401517x] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 06/27/2014] [Indexed: 01/04/2023]
Abstract
The analysis of structural data obtained by X-ray crystallography benefits from information obtained from complementary techniques, especially as applied to the crystals themselves. As a consequence, optical spectroscopies in structural biology have become instrumental in assessing the relevance and context of many crystallographic results. Since the year 2000, it has been possible to record such data adjacent to, or directly on, the Structural Biology Group beamlines of the ESRF. A core laboratory featuring various spectrometers, named the Cryobench, is now in its third version and houses portable devices that can be directly mounted on beamlines. This paper reports the current status of the Cryobench, which is now located on the MAD beamline ID29 and is thus called the ID29S-Cryobench (where S stands for `spectroscopy'). It also reviews the diverse experiments that can be performed at the Cryobench, highlighting the various scientific questions that can be addressed.
Collapse
Affiliation(s)
| | - Thierry Giraud
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | | | - Franc Sever
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | - Maxime Terrien
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Fabien Dobias
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | - Douglas H. Juers
- Department of Physics, Whitman College, Walla Walla, WA 99362, USA
| | - David Flot
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | | | | | | | - Antoine Royant
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| |
Collapse
|
7
|
Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part II. {[Fe2S2](SγCys)4} proteins. Coord Chem Rev 2014. [DOI: 10.1016/j.ccr.2014.08.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
8
|
Yan R, Adinolfi S, Iannuzzi C, Kelly G, Oregioni A, Martin S, Pastore A. Cluster and fold stability of E. coli ISC-type ferredoxin. PLoS One 2013; 8:e78948. [PMID: 24265733 PMCID: PMC3827102 DOI: 10.1371/journal.pone.0078948] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 09/22/2013] [Indexed: 11/25/2022] Open
Abstract
Iron-sulfur clusters are essential protein prosthetic groups that provide their redox potential to several different metabolic pathways. Formation of iron-sulfur clusters is assisted by a specialised machine that comprises, among other proteins, a ferredoxin. As a first step to elucidate the precise role of this protein in cluster assembly, we have studied the factors governing the stability and the dynamic properties of E. coli ferredoxin using different spectroscopic techniques. The cluster-loaded protein is monomeric and well structured with a flexible C-terminus but is highly oxygen sensitive so that it readily loses the cluster leading to an irreversible unfolding under aerobic conditions. This process is slowed down by reducing conditions and high ionic strengths. NMR relaxation experiments on the cluster-loaded protein also show that, once the cluster is in place, the protein forms a globular and relatively rigid domain. These data indicate that the presence of the iron-sulfur cluster is the switch between a functional and a non-functional state.
Collapse
Affiliation(s)
- Robert Yan
- Division of Molecular Structure, National Institute for Medical Research of the Medical Research Council, London, United Kingdom
| | - Salvatore Adinolfi
- Division of Molecular Structure, National Institute for Medical Research of the Medical Research Council, London, United Kingdom
| | - Clara Iannuzzi
- Division of Molecular Structure, National Institute for Medical Research of the Medical Research Council, London, United Kingdom
| | - Geoff Kelly
- Division of Molecular Structure, National Institute for Medical Research of the Medical Research Council, London, United Kingdom
| | - Alain Oregioni
- Division of Molecular Structure, National Institute for Medical Research of the Medical Research Council, London, United Kingdom
| | - Stephen Martin
- Division of Molecular Structure, National Institute for Medical Research of the Medical Research Council, London, United Kingdom
| | - Annalisa Pastore
- Division of Molecular Structure, National Institute for Medical Research of the Medical Research Council, London, United Kingdom
| |
Collapse
|
9
|
Bell SG, McMillan JHC, Yorke JA, Kavanagh E, Johnson EOD, Wong LL. Tailoring an alien ferredoxin to support native-like P450 monooxygenase activity. Chem Commun (Camb) 2012; 48:11692-4. [DOI: 10.1039/c2cc35968e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
10
|
Ewen KM, Hannemann F, Iametti S, Morleo A, Bernhardt R. Functional characterization of Fdx1: evidence for an evolutionary relationship between P450-type and ISC-type ferredoxins. J Mol Biol 2011; 413:940-51. [PMID: 21945528 DOI: 10.1016/j.jmb.2011.09.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 08/26/2011] [Accepted: 09/06/2011] [Indexed: 10/17/2022]
Abstract
Ferredoxins are ubiquitous proteins with electron transfer activity involved in a variety of biological processes. In this work, we investigated the characteristics and function of Fdx1 from Sorangium cellulosum So ce56 by using a combination of bioinformatics and of biochemical/biophysical approaches. We were able to experimentally confirm a role of Fdx1 in the iron-sulfur cluster biosynthesis by in vitro reduction studies with cluster-loaded So ce56 IscU and by transfer studies of the cluster from the latter protein to apo-aconitase A. Moreover, we found that Fdx1 can replace mammalian adrenodoxin in supporting the activity of bovine CYP11A1. This makes S. cellulosum Fdx1 the first prokaryotic ferredoxin reported to functionally interact with this mammalian enzyme. Although the interaction with CYP11A1 is non-physiological, this is-to the best of our knowledge-the first study to experimentally prove the activity of a postulated ISC-type ferredoxin in both the ISC assembly and a cytochrome P450 system. This proves that a single ferredoxin can be structurally able to provide electrons to both cytochromes P450 and IscU and thus support different biochemical processes. Combining this finding with phylogenetic and evolutionary trace analyses led us to propose the evolution of eukaryotic mitochondrial P450-type ferredoxins and ISC-type ferredoxins from a common prokaryotic ISC-type ancestor.
Collapse
Affiliation(s)
- Kerstin Maria Ewen
- Department of Biochemistry, Saarland University, D-66041 Saarbrücken, Germany
| | | | | | | | | |
Collapse
|
11
|
Müller JJ, Hannemann F, Schiffler B, Ewen KM, Kappl R, Heinemann U, Bernhardt R. Structural and thermodynamic characterization of the adrenodoxin-like domain of the electron-transfer protein Etp1 from Schizosaccharomyces pombe. J Inorg Biochem 2011; 105:957-65. [DOI: 10.1016/j.jinorgbio.2011.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 03/16/2011] [Accepted: 04/02/2011] [Indexed: 10/18/2022]
|
12
|
Iwasaki T, Kappl R, Bracic G, Shimizu N, Ohmori D, Kumasaka T. ISC-like [2Fe-2S] ferredoxin (FdxB) dimer from Pseudomonas putida JCM 20004: structural and electron-nuclear double resonance characterization. J Biol Inorg Chem 2011; 16:923-35. [PMID: 21647778 DOI: 10.1007/s00775-011-0793-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Accepted: 05/16/2011] [Indexed: 12/11/2022]
Abstract
The crystal structure of the ISC-like [2Fe-2S] ferredoxin (FdxB), probably involved in the de novo iron-sulfur cluster biosynthesis (ISC) system of Pseudomonas putida JCM 20004, was determined at 1.90-Å resolution and displayed a novel tail-to-tail dimeric form. P. putida FdxB lacks the consensus free cysteine usually present near the cluster of ISC-like ferredoxins, indicating its primarily electron transfer role in the iron-sulfur cluster. Orientation-selective electron-nuclear double resonance spectroscopic analysis of reduced FdxB in conjunction with the crystal structure has identified the innermost Fe2 site with a high positive spin population as the nonreducible iron retaining the Fe(3+) valence and the outermost Fe1 site as the reduced iron with a low negative spin density. The average g (max) direction is skewed, forming an angle of about 27.3° (±4°) with the normal of the [2Fe-2S] plane, whereas the g (int) and g (min) directions are distributed in the cluster plane, presumably tilted by the same angle with respect to this plane. These results are related to those for other [2Fe-2S] proteins in different electron transport chains (e.g. adrenodoxin) and suggest a significant distortion of the electronic structure of the reduced [2Fe-2S] cluster under the influence of the protein environment around each iron site in general.
Collapse
Affiliation(s)
- Toshio Iwasaki
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Sendagi, Bunkyo-ku, Tokyo, 113-8602, Japan.
| | | | | | | | | | | |
Collapse
|
13
|
Yang W, Bell SG, Wang H, Zhou W, Hoskins N, Dale A, Bartlam M, Wong LL, Rao Z. Molecular characterization of a class I P450 electron transfer system from Novosphingobium aromaticivorans DSM12444. J Biol Chem 2010; 285:27372-27384. [PMID: 20576606 DOI: 10.1074/jbc.m110.118349] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytochrome P450 (CYP) enzymes of the CYP101 and CYP111 families from the oligotrophic bacterium Novosphingobium aromaticivorans DSM12444 are heme monooxygenases that receive electrons from NADH via Arx, a [2Fe-2S] ferredoxin, and ArR, a ferredoxin reductase. These systems show fast NADH turnovers (k(cat) = 39-91 s(-1)) that are efficiently coupled to product formation. The three-dimensional structures of ArR, Arx, and CYP101D1, which form a physiological class I P450 electron transfer chain, have been resolved by x-ray crystallography. The general structural features of these proteins are similar to their counterparts in other class I systems such as putidaredoxin reductase (PdR), putidaredoxin (Pdx), and CYP101A1 of the camphor hydroxylase system from Pseudomonas putida, and adrenodoxin (Adx) of the mitochondrial steroidogenic CYP11 and CYP24A1 systems. However, significant differences in the proposed protein-protein interaction surfaces of the ferredoxin reductase, ferredoxin, and P450 enzyme are found. There are regions of positive charge on the likely interaction face of ArR and CYP101D1 and a corresponding negatively charged area on the surface of Arx. The [2Fe-2S] cluster binding loop in Arx also has a neutral, hydrophobic patch on the surface. These surface characteristics are more in common with those of Adx than Pdx. The observed structural features are consistent with the ionic strength dependence of the activity.
Collapse
Affiliation(s)
- Wen Yang
- Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Stephen G Bell
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom.
| | - Hui Wang
- Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
| | - Weihong Zhou
- Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Nicola Hoskins
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Alison Dale
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Mark Bartlam
- Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin 300071, China; Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China.
| | - Luet-Lok Wong
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Zihe Rao
- Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin 300071, China; Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
| |
Collapse
|
14
|
Ewen KM, Kleser M, Bernhardt R. Adrenodoxin: the archetype of vertebrate-type [2Fe-2S] cluster ferredoxins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:111-25. [PMID: 20538075 DOI: 10.1016/j.bbapap.2010.06.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 05/28/2010] [Accepted: 06/01/2010] [Indexed: 11/15/2022]
Abstract
Adrenodoxin is probably the best characterized member of the vertebrate-type [2Fe-2S]-cluster ferredoxins. It has been in the spotlight of scientific interest for many years due to its essential role in mammalian steroid hormone biosynthesis, where it acts as electron mediator between the NADPH-dependent adrenodoxin reductase and several mitochondrial cytochromes P450. In this review we will focus on the present knowledge about protein-protein recognition in the mitochondrial cytochrome P450 system and the modulation of the electron transfer between Adx and its redox partners, AdR and CYP(s). We also intend to point out the potential biotechnological applications of Adx as a versatile electron donor to different cytochromes P450, both in vitro and in vivo. Finally we will address the comparison between the mammalian cytochrome P450-associated adrenodoxin and ferredoxins involved in iron-sulfur-cluster biosynthesis. Despite their different functions, these proteins display an amazing similarity regarding their primary sequence, tertiary structure and biophysical features.
Collapse
Affiliation(s)
- Kerstin Maria Ewen
- Department of Biochemistry, Saarland University, D-66041 Saarbrücken, Germany
| | | | | |
Collapse
|
15
|
Xiao Y, Tan ML, Ichiye T, Wang H, Guo Y, Smith MC, Meyer J, Sturhahn W, Alp EE, Zhao J, Yoda Y, Cramer SP. Dynamics of Rhodobacter capsulatus [2FE-2S] ferredoxin VI and Aquifex aeolicus ferredoxin 5 via nuclear resonance vibrational spectroscopy (NRVS) and resonance Raman spectroscopy. Biochemistry 2010; 47:6612-27. [PMID: 18512953 DOI: 10.1021/bi701433m] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study the Fe(2)S(2)(Cys)(4) sites in oxidized and reduced [2Fe-2S] ferredoxins from Rhodobacter capsulatus (Rc FdVI) and Aquifex aeolicus (Aa Fd5). In the oxidized forms, nearly identical NRVS patterns are observed, with strong bands from Fe-S stretching modes peaking around 335 cm(-1), and additional features observed as high as the B(2u) mode at approximately 421 cm(-1). Both forms of Rc FdVI have also been investigated by resonance Raman (RR) spectroscopy. There is good correspondence between NRVS and Raman frequencies, but because of different selection rules, intensities vary dramatically between the two kinds of spectra. For example, the B(3u) mode at approximately 288 cm(-1), attributed to an asymmetric combination of the two FeS(4) breathing modes, is often the strongest resonance Raman feature. In contrast, it is nearly invisible in the NRVS, as there is almost no Fe motion in such FeS(4) breathing. NRVS and RR analysis of isotope shifts with (36)S-substituted into bridging S(2-) ions in Rc FdVI allowed quantitation of S(2-) motion in different normal modes. We observed the symmetric Fe-Fe stretching mode at approximately 190 cm(-1) in both NRVS and RR spectra. At still lower energies, the NRVS presents a complex envelope of bending, torsion, and protein modes, with a maximum at 78 cm(-1). The (57)Fe partial vibrational densities of states (PVDOS) were interpreted by normal-mode analysis with optimization of Urey-Bradley force fields. Progressively more complex D(2h) Fe(2)S(2)S'(4), C(2h) Fe(2)S(2)(SCC)(4), and C(1) Fe(2)S(2)(Cys)(4) models were optimized by comparison with the experimental spectra. After modification of the CHARMM22 all-atom force field by the addition of refined Fe-S force constants, a simulation employing the complete protein structure was used to reproduce the PVDOS, with better results in the low frequency protein mode region. This process was then repeated for analysis of data on the reduced FdVI. Finally, the degree of collectivity was used to quantitate the delocalization of the dynamic properties of the redox-active Fe site. The NRVS technique demonstrates great promise for the observation and quantitative interpretation of the dynamical properties of Fe-S proteins.
Collapse
Affiliation(s)
- Yuming Xiao
- Department of Applied Science, University of California, Davis, California 95616, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Protein recognition in ferredoxin–P450 electron transfer in the class I CYP199A2 system from Rhodopseudomonas palustris. J Biol Inorg Chem 2009; 15:315-28. [DOI: 10.1007/s00775-009-0604-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Accepted: 10/15/2009] [Indexed: 10/20/2022]
|
17
|
Dikanov SA, Samoilova RI, Kappl R, Crofts AR, Hüttermann J. The reduced [2Fe-2S] clusters in adrenodoxin and Arthrospira platensis ferredoxin share spin density with protein nitrogens, probed using 2D ESEEM. Phys Chem Chem Phys 2009; 11:6807-19. [PMID: 19639155 PMCID: PMC2773023 DOI: 10.1039/b904597j] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have used X-band ESEEM to study the reduced [2Fe-2S] cluster in adrenodoxin and Arthrospira platensis ferredoxin. By use of a 2D approach (HYSCORE), we have shown that the cluster is involved in weak magnetic interactions with several nitrogens in each protein. Despite substantial differences in the shape and orientational dependence of individual cross-peaks, the major spectral features in both proteins are attributable to two peptide nitrogens (N1 and N2) with similar hyperfine couplings approximately 1.1 and approximately 0.70 MHz. The couplings determined represent a small fraction (0.0003-0.0005) of the unpaired spin density of the reduced cluster transferred to these nitrogens over H-bond bridges or the covalent bonds of cysteine ligands. Simulation of the HYSCORE spectra has allowed us to estimate the orientation of the nuclear quadrupole tensors of N1 and N2 in the g-tensor coordinate system. The most likely candidates for the role of N1 and N2 have been identified in the protein environment by comparing magnetic-resonance data with crystallographic structures of the oxidized proteins. A possible influence of redox-linked structural changes on ESEEM data is analyzed using available structures for related proteins in two redox states.
Collapse
Affiliation(s)
- Sergei A Dikanov
- Department of Veterinary Clinical Medicine, University of Illinois, Urbana, IL 61801, USA.
| | | | | | | | | |
Collapse
|
18
|
George SJ, Igarashi RY, Xiao Y, Hernandez JA, Demuez M, Zhao D, Yoda Y, Ludden PW, Rubio LM, Cramer SP. Extended X-ray absorption fine structure and nuclear resonance vibrational spectroscopy reveal that NifB-co, a FeMo-co precursor, comprises a 6Fe core with an interstitial light atom. J Am Chem Soc 2008; 130:5673-80. [PMID: 18386899 DOI: 10.1021/ja0755358] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
NifB-co, an Fe-S cluster produced by the enzyme NifB, is an intermediate on the biosynthetic pathway to the iron molybdenum cofactor (FeMo-co) of nitrogenase. We have used Fe K-edge extended X-ray absorption fine structure (EXAFS) spectroscopy together with (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to probe the structure of NifB-co while bound to the NifX protein from Azotobacter vinelandii. The spectra have been interpreted in part by comparison with data for the completed FeMo-co attached to the NafY carrier protein: the NafY:FeMo-co complex. EXAFS analysis of the NifX:NifB-co complex yields an average Fe-S distance of 2.26 A and average Fe-Fe distances of 2.66 and 3.74 A. Search profile analyses reveal the presence of a single Fe-X (X = C, N, or O) interaction at 2.04 A, compared to a 2.00 A Fe-X interaction found in the NafY:FeMo-co EXAFS. This suggests that the interstitial light atom (X) proposed to be present in FeMo-co has already inserted at the NifB-co stage of biosynthesis. The NRVS exhibits strong bands from Fe-S stretching modes peaking around 270, 315, 385, and 408 cm(-1). Additional intensity at approximately 185-200 cm(-1) is interpreted as a set of cluster "breathing" modes similar to those seen for the FeMo-cofactor. The strength and location of these modes also suggest that the FeMo-co interstitial light atom seen in the crystal structure is already in place in NifB-co. Both the EXAFS and NRVS data for NifX:NifB-co are best simulated using a Fe 6S 9X trigonal prism structure analogous to the 6Fe core of FeMo-co, although a 7Fe structure made by capping one trigonal 3S terminus with Fe cannot be ruled out. The results are consistent with the conclusion that the interstitial light atom is already present at an early stage in FeMo-co biosynthesis prior to the incorporation of Mo and R-homocitrate.
Collapse
Affiliation(s)
- Simon J George
- Advanced Biological and Environmental X-ray Facility, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Ballmann J, Dechert S, Bill E, Ryde U, Meyer F. Secondary Bonding Interactions in Biomimetic [2Fe−2S] Clusters. Inorg Chem 2008; 47:1586-96. [DOI: 10.1021/ic702095a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joachim Ballmann
- Institut für Anorganische Chemie, Georg-August-Universität, Tammannstrasse 4, D-37077 Göttingen, Germany, Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany, and Department of Theoretical Chemistry, Lund University, Chemical Centre, S-22100 Lund, Sweden
| | - Sebastian Dechert
- Institut für Anorganische Chemie, Georg-August-Universität, Tammannstrasse 4, D-37077 Göttingen, Germany, Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany, and Department of Theoretical Chemistry, Lund University, Chemical Centre, S-22100 Lund, Sweden
| | - Eckhard Bill
- Institut für Anorganische Chemie, Georg-August-Universität, Tammannstrasse 4, D-37077 Göttingen, Germany, Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany, and Department of Theoretical Chemistry, Lund University, Chemical Centre, S-22100 Lund, Sweden
| | - Ulf Ryde
- Institut für Anorganische Chemie, Georg-August-Universität, Tammannstrasse 4, D-37077 Göttingen, Germany, Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany, and Department of Theoretical Chemistry, Lund University, Chemical Centre, S-22100 Lund, Sweden
| | - Franc Meyer
- Institut für Anorganische Chemie, Georg-August-Universität, Tammannstrasse 4, D-37077 Göttingen, Germany, Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany, and Department of Theoretical Chemistry, Lund University, Chemical Centre, S-22100 Lund, Sweden
| |
Collapse
|
20
|
Iwasaki T, Ohmori D, Shimizu N, Kumasaka T. Crystallization and preliminary X-ray diffraction studies of the ISC-like [2Fe-2S] ferredoxin (FdxB) from Pseudomonas putida JCM 20004. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:1014-6. [PMID: 18084081 DOI: 10.1107/s1744309107045757] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Accepted: 09/18/2007] [Indexed: 11/10/2022]
Abstract
The iron-sulfur (Fe-S) cluster-biosynthesis (ISC) system of the gamma-proteobacterium Pseudomonas putida JCM 20004 contains a constitutively expressed vertebrate-type [2Fe-2S] ferredoxin, FdxB, which lacks the conserved free cysteine residue near the Fe-S cluster site that has been proposed to function in the catalysis of biological Fe-S cluster assembly in other bacterial homologues. Recombinant FdxB was heterologously overproduced in Escherichia coli, purified and crystallized in its oxidized form by the hanging-drop vapour-diffusion and streak-seeding methods using 1.6 M trisodium citrate dihydrate pH 6.5. The thin needle-shaped crystals diffract to 1.90 A resolution and belong to the hexagonal space group P6(1)22, with unit-cell parameters a = 87.58, c = 73.14 A. The asymmetric unit contains one protein molecule.
Collapse
Affiliation(s)
- Toshio Iwasaki
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Sendagi, Bunkyo-ku, Tokyo 113-8602, Japan.
| | | | | | | |
Collapse
|
21
|
|