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Dergachev ID, Dergachev VD, Rooein M, Mirzanejad A, Varganov SA. Predicting Kinetics and Dynamics of Spin-Dependent Processes. Acc Chem Res 2023; 56:856-866. [PMID: 36926853 DOI: 10.1021/acs.accounts.2c00843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
ConspectusPredicting mechanisms and rates of nonadiabatic spin-dependent processes including photoinduced intersystem crossings, thermally activated spin-forbidden reactions, and spin crossovers in metal centers is a very active field of research. These processes play critical roles in transition-metal-based and metalloenzymatic catalysis, molecular magnets, light-harvesting materials, organic light-emitting diodes, photosensitizers for photodynamic therapy, and many other applications. Therefore, accurate modeling of spin-dependent processes in complex systems and on different time scales is important for many problems in chemistry, biochemistry, and materials sciences.Nonadiabatic statistical theory (NAST) and nonadiabatic molecular dynamics (NAMD) are two complementary approaches to modeling the kinetics and dynamics of spin-dependent processes. NAST predicts the probabilities and rate constants of nonradiative transitions between electronic states with different spin multiplicities using molecular properties at only few critical points on the potential energy surfaces (PESs), including the reactant minimum and the minimum energy crossing point (MECP) between two spin states. This makes it possible to obtain molecular properties for NAST calculations using accurate but often computationally expensive electronic structure methods, which is critical for predicting the rate constants of spin-dependent processes. Alternatively, NAST can be used to study spin-dependent processes in very large complex molecular systems using less computationally expensive electronic structure methods. The nuclear quantum effects, such as zero-point vibrational energy, tunneling, and interference between reaction paths can be easily incorporated. However, the statistical and local nature of NAST makes it more suitable for large systems and slow kinetics. In contrast, NAMD explores entire PESs of interacting electronic states, making it ideal for modeling fast barrierless spin-dependent processes. Because the knowledge of large portions of PESs is often needed, the simulations require a very large number of electronic structure calculations, which limits the NAMD applicability to relatively small molecular systems and ultrafast kinetics.In this Account, we discuss our contribution to the development of the NAST and NAMD approaches for predicting the rates and mechanism of spin-dependent processes. First, we briefly describe our NAST and NAMD implementations. The NAST implementation is an extension of the transition state theory to the processes involving two crossing potential energy surfaces of different spin multiplicities. The NAMD approach includes the trajectory surface hopping (TSH) and ab initio multiple spawning (AIMS) methods. Second, we discuss several applications of NAST and NAMD to model spin-dependent processes in different systems. The NAST applicability to large complex systems is demonstrated by the studies of the spin-forbidden isomerization of the active sites of metal-sulfur proteins. Our implementation of the MECP search algorithm within the fully ab initio fragment molecular orbital method allows applying NAST to systems with thousands of atoms, such as the solvated protein rubredoxin. Applications of NAMD to ultrafast spin-dependent processes are represented by the generalized AIMS simulations utilizing the fast GPU-based TeraChem electronic structure program to gain insight into the complex photoexcited state relaxation in 2-cyclopentenone.
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Affiliation(s)
- Ilya D Dergachev
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557-0216, United States
| | - Vsevolod D Dergachev
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557-0216, United States
| | - Mitra Rooein
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557-0216, United States
| | - Amir Mirzanejad
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557-0216, United States
| | - Sergey A Varganov
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557-0216, United States
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An alternative plant-like cyanobacterial ferredoxin with unprecedented structural and functional properties. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:148084. [DOI: 10.1016/j.bbabio.2019.148084] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/02/2019] [Accepted: 09/08/2019] [Indexed: 11/23/2022]
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3
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Kapoor K, Cashman DJ, Nientimp L, Bruce BD, Baudry J. Binding Mechanisms of Electron Transport Proteins with Cyanobacterial Photosystem I: An Integrated Computational and Experimental Model. J Phys Chem B 2018; 122:1026-1036. [PMID: 29211957 DOI: 10.1021/acs.jpcb.7b08307] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The stromal domain (PsaC, D, and E) of photosystem I (PSI) in cyanobacteria accepts electrons from PsaA and PsaB of photosystem I (PSI). These electrons are then used in the reduction of transiently bound ferredoxin (Fd) or flavodoxin. Experimental X-ray and NMR structures are known for all of these protein partners separately, yet to date, there is no known experimental structure of the PSI/Fd complexes in the published literature. Computational models of Fd docked with the stromal domain of cyanobacterial PSI were assembled here starting from X-ray and NMR structures of PSI and Fd. Predicted models of specific regions of protein-protein interactions were built on the basis of energetic frustration, residue conservation and evolutionary importance, as well as from experimental site-directed mutagenesis and cross-linking studies. Microsecond time-scale molecular dynamics simulations of the PSI/Fd complexes suggest, rather than a single complex structure, the possible existence of multiple transient complexes of Fd bound to PSI.
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Affiliation(s)
- Karan Kapoor
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States.,UT/ORNL Center for Molecular Biophysics , Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Derek J Cashman
- Department of Chemistry, Tennessee Technological University , Box 5055, Cookeville, Tennessee 38505-0001, United States
| | - Luke Nientimp
- Department of Chemistry, Tennessee Technological University , Box 5055, Cookeville, Tennessee 38505-0001, United States
| | - Barry D Bruce
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Jerome Baudry
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States.,UT/ORNL Center for Molecular Biophysics , Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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Cashman DJ, Zhu T, Simmerman RF, Scott C, Bruce BD, Baudry J. Molecular interactions between photosystem I and ferredoxin: an integrated energy frustration and experimental model. J Mol Recognit 2015; 27:597-608. [PMID: 25178855 DOI: 10.1002/jmr.2384] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Revised: 03/21/2014] [Accepted: 04/18/2014] [Indexed: 11/10/2022]
Abstract
The stromal domain (PsaC, PsaD, and PsaE) of photosystem I (PSI) reduces transiently bound ferredoxin (Fd) or flavodoxin. Experimental structures exist for all of these protein partners individually, but no experimental structure of the PSI/Fd or PSI/flavodoxin complexes is presently available. Molecular models of Fd docked onto the stromal domain of the cyanobacterial PSI site are constructed here utilizing X-ray and NMR structures of PSI and Fd, respectively. Predictions of potential protein-protein interaction regions are based on experimental site-directed mutagenesis and cross-linking studies to guide rigid body docking calculations of Fd into PSI, complemented by energy landscape theory to bring together regions of high energetic frustration on each of the interacting proteins. The results identify two regions of high localized frustration on the surface of Fd that contain negatively charged Asp and Glu residues. This study predicts that these regions interact predominantly with regions of high localized frustration on the PsaC, PsaD, and PsaE chains of PSI, which include several residues predicted by previous experimental studies.
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Affiliation(s)
- Derek J Cashman
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA; UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, University of Tennessee, Oak Ridge, TN, 37831, USA
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5
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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: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Zhang J, Lu X, Li JJ. Conversion of fatty aldehydes into alk (a/e)nes by in vitro reconstituted cyanobacterial aldehyde-deformylating oxygenase with the cognate electron transfer system. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:86. [PMID: 23759169 PMCID: PMC3691600 DOI: 10.1186/1754-6834-6-86] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 06/03/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Biosynthesis of fatty alk(a/e)ne in cyanobacteria has been considered as a potential basis for the sunlight-driven and carbon-neutral bioprocess producing advanced solar biofuels. Aldehyde-deformylating oxygenase (ADO) is a key enzyme involved in that pathway. The heterologous or chemical reducing systems were generally used in in vitro ADO activity assay. The cognate electron transfer system from cyanobacteria to support ADO activity is still unknown. RESULTS We identified the potential endogenous reducing system including ferredoxin (Fd) and ferredoxin-NADP+ reductase (FNR) to support ADO activity in Synechococcus elongatus PCC7942. ADO (Synpcc7942_1593), FNR (SynPcc7942_0978), and Fd (SynPcc7942_1499) from PCC7942 were cloned, overexpressed, purified, and characterized. ADO activity was successfully supported with the endogenous electron transfer system, which worked more effectively than the heterologous and chemical ones. The results of the hybrid Fd/FNR reducing systems demonstrated that ADO was selective against Fd. And it was observed that the cognate reducing system produced less H2O2 than the heterologous one by 33% during ADO-catalyzed reactions. Importantly, kcat value of ADO 1593 using the homologous Fd/FNR electron transfer system is 3.7-fold higher than the chemical one. CONCLUSIONS The cognate electron transfer system from cyanobacteria to support ADO activity was identified and characterized. For the first time, ADO was functionally in vitro reconstituted with the endogenous reducing system from cyanobacteria, which supported greater activity than the surrogate and chemical ones, and produced less H2O2 than the heterologous one. The identified Fd/FNR electron transfer system will be potentially useful for improving ADO activity and further enhancing the biosynthetic efficiency of hydrocarbon biofuels in cyanobacteria.
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Affiliation(s)
- Jingjing Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuefeng Lu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
| | - Jian-Jun Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
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7
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Affiliation(s)
- LUCIA BANCI
- Dipartimento di Chimica and CERM, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
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8
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Jagannathan B, Shen G, Golbeck JH. The Evolution of Type I Reaction Centers: The Response to Oxygenic Photosynthesis. FUNCTIONAL GENOMICS AND EVOLUTION OF PHOTOSYNTHETIC SYSTEMS 2012. [DOI: 10.1007/978-94-007-1533-2_12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Lei C, Rider SD, Wang C, Zhang H, Tan X, Zhu G. The apicomplexan Cryptosporidium parvum possesses a single mitochondrial-type ferredoxin and ferredoxin:NADP+ reductase system. Protein Sci 2011; 19:2073-84. [PMID: 20737579 DOI: 10.1002/pro.487] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We have successfully expressed recombinant mitochondrial-type ferredoxin (mtFd) and ferredoxin:NADP(+) reductase (mtFNR) from Cryptosporidium parvum and characterized their biochemical features for the first time for an apicomplexan. Both C. parvum mtFd (CpmtFd) and FNR (CpmtFNR) were obtained and purified as holo-proteins, in which the correct assembly of [2Fe-2S] cluster in Fd and that of FAD in FNR were confirmed and characterized by UV/vis and electron paramagnetic resonance. These proteins were fully functional and CpmtFNR was capable of transferring electrons from NADPH to CpmtFd in a cytochrome c-coupled assay that followed a typical Michaelis-Menten kinetics. Apicomplexan mtFd and mtFNR proteins were evolutionarily divergent from their counterparts in humans and animals and could be explored as potential drug targets in Cryptosporidium and other apicomplexans.
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Affiliation(s)
- Cheng Lei
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, People's Republic of China
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10
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Nouailler M, Morelli X, Bornet O, Chetrit B, Dermoun Z, Guerlesquin F. Solution structure of HndAc: a thioredoxin-like domain involved in the NADP-reducing hydrogenase complex. Protein Sci 2006; 15:1369-78. [PMID: 16731971 PMCID: PMC2242533 DOI: 10.1110/ps.051916606] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The NADP-reducing hydrogenase complex from Desulfovibrio fructosovorans is a heterotetramer encoded by the hndABCD operon. Sequence analysis indicates that the HndC subunit (52 kDa) corresponds to the NADP-reducing unit, and the HndD subunit (63.5 kDa) is homologous to Clostridium pasteurianum hydrogenase. The role of HndA and HndB subunits (18.8 kDa and 13.8 kDa, respectively) in the complex remains unknown. The HndA subunit belongs to the [2Fe-2S] ferredoxin family typified by C. pasteurianum ferredoxin. HndA is organized into two independent structural domains, and we report in the present work the NMR structure of its C-terminal domain, HndAc. HndAc has a thioredoxin-like fold consisting in four beta-strands and two relatively long helices. The [2Fe-2S] cluster is located near the surface of the protein and bound to four cysteine residues particularly well conserved in this class of proteins. Electron exchange between the HndD N-terminal [2Fe-2S] domain (HndDN) and HndAc has been previously evidenced, and in the present studies we have mapped the binding site of the HndDN domain on HndAc. A structural analysis of HndB indicates that it is a FeS subunit with 41% similarity with HndAc and it contains a possible thioredoxin-like fold. Our data let us propose that HndAc and HndB can form a heterodimeric intermediate in the electron transfer between the hydrogenase (HndD) active site and the NADP reduction site in HndC.
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Affiliation(s)
- Matthieu Nouailler
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM-CNRS, Marseille Cedex 20, France
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11
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Iverson TM. Evolution and unique bioenergetic mechanisms in oxygenic photosynthesis. Curr Opin Chem Biol 2006; 10:91-100. [PMID: 16504567 DOI: 10.1016/j.cbpa.2006.02.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2005] [Accepted: 02/16/2006] [Indexed: 11/17/2022]
Abstract
Oxygenic photosynthesis is one example of the many bioenergetic pathways utilized by different organisms to harvest energy from the environment. These pathways revolve around a theme of coupling oxidation-reduction reactions to the formation of membrane potential and subsequent ATP synthesis. Although the basic principles underlying bioenergetics are universally conserved, the constituents of the bioenergetic pathways in different organisms have evolved unique aspects to fill an evolutionary niche. Three-dimensional structures of all of the membrane-spanning components of the electron-transfer chain of oxygenic photosynthesis have revealed those unique aspects of this fascinating process, including the unique metallocofactor for catalysis, the determinants of the uniquely high voltage cofactor, and the numerous photoprotective mechanisms that guard against radical damage.
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Affiliation(s)
- Tina M Iverson
- Department of Pharmacology, Center for Structural Biology and Vanderbilt Institute for Chemical Biology, Vanderbilt University Medical Center, Nashville, TN 37232-6600, USA.
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12
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Fish A, Danieli T, Ohad I, Nechushtai R, Livnah O. Structural Basis for the Thermostability of Ferredoxin from the Cyanobacterium Mastigocladus laminosus. J Mol Biol 2005; 350:599-608. [PMID: 15961101 DOI: 10.1016/j.jmb.2005.04.071] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2005] [Revised: 04/26/2005] [Accepted: 04/28/2005] [Indexed: 11/23/2022]
Abstract
Plant-type ferredoxins (Fds) carry a single [2Fe-2S] cluster and serve as electron acceptors of photosystem I (PSI). The ferredoxin from the thermophilic cyanobacterium Mastigocladus laminosus displays optimal activity at 65 degrees C. In order to reveal the molecular factors that confer thermostability, the crystal structure of M.laminosus Fd (mFd) was determined to 1.25 A resolution and subsequently analyzed in comparison with four similar plant-type mesophilic ferredoxins. The topologies of the plant-type ferredoxins are similar, yet two structural determinants were identified that may account for differences in thermostability, a salt bridge network in the C-terminal region, and the flexible L1,2 loop that increases hydrophobic accessible surface area. These conclusions were verified by three mutations, i.e. substitution of L1,2 into a rigid beta-turn ((Delta)L1,2) and two point mutations (E90S and E96S) that disrupt the salt bridge network at the C-terminal region. All three mutants have shown reduced electron transfer (ET) capabilities and [2Fe-2S] stability at high temperatures in comparison to the wild-type mFd. The results have also provided new insights into the involvement of the L1,2 loop in the Fd interactions with its electron donor, the PSI complex.
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Affiliation(s)
- Alexander Fish
- The Department of Plant Sciences, The Wolfson Centre for Applied Structural Biology, The Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
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Machonkin TE, Westler WM, Markley JL. Strategy for the study of paramagnetic proteins with slow electronic relaxation rates by nmr spectroscopy: application to oxidized human [2Fe-2S] ferredoxin. J Am Chem Soc 2004; 126:5413-26. [PMID: 15113213 DOI: 10.1021/ja037077i] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
NMR studies of paramagnetic proteins are hampered by the rapid relaxation of nuclei near the paramagnetic center, which prevents the application of conventional methods to investigations of the most interesting regions of such molecules. This problem is particularly acute in systems with slow electronic relaxation rates. We present a strategy that can be used with a protein with slow electronic relaxation to identify and assign resonances from nuclei near the paramagnetic center. Oxidized human [2Fe-2S] ferredoxin (adrenodoxin) was used to test the approach. The strategy involves six steps: (1) NMR signals from (1)H, (13)C, and (15)N nuclei unaffected or minimally affected by paramagnetic effects are assigned by standard multinuclear two- and three-dimensional (2D and 3D) spectroscopic methods with protein samples labeled uniformly with (13)C and (15)N. (2) The very broad, hyperfine-shifted signals from carbons in the residues that ligate the metal center are classified by amino acid and atom type by selective (13)C labeling and one-dimensional (1D) (13)C NMR spectroscopy. (3) Spin systems involving carbons near the paramagnetic center that are broadened but not hyperfine-shifted are elucidated by (13)C[(13)C] constant time correlation spectroscopy (CT-COSY). (4) Signals from amide nitrogens affected by the paramagnetic center are assigned to amino acid type by selective (15)N labeling and 1D (15)N NMR spectroscopy. (5) Sequence-specific assignments of these carbon and nitrogen signals are determined by 1D (13)C[(15)N] difference decoupling experiments. (6) Signals from (1)H nuclei in these spin systems are assigned by paramagnetic-optimized 2D and 3D (1)H[(13)C] experiments. For oxidized human ferredoxin, this strategy led to assignments (to amino acid and atom type) for 88% of the carbons in the [2Fe-2S] cluster-binding loops (residues 43-58 and 89-94). These included complete carbon spin-system assignments for eight of the 22 residues and partial assignments for each of the others. Sequence-specific assignments were determined for the backbone (15)N signals from nine of the 22 residues and ambiguous assignments for five of the others.
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Affiliation(s)
- Timothy E Machonkin
- National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Gelis I, Katsaros N, Luchinat C, Piccioli M, Poggi L. A simple protocol to study blue copper proteins by NMR. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:600-9. [PMID: 12581200 DOI: 10.1046/j.1432-1033.2003.03400.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In the case of oxidized plastocyanin from Synechocystis sp. PCC6803, an NMR approach based on classical two and three dimensional experiments for sequential assignment leaves unobserved 14 out of 98 amino acids. A protocol which simply makes use of tailored versions of 2D HSQC and 3D CBCA(CO)NH and CBCANH leads to the identification of nine of the above 14 residues. The proposed protocol differs from previous approaches in that it does not involve the use of unconventional experiments designed specifically for paramagnetic systems, and does not exploit the occurrence of a corresponding diamagnetic species in chemical exchange with the blue copper form. This protocol is expected to extend the popularity of NMR in the structural studies of copper (II) proteins, allowing researchers to increase the amount of information available via NMR on the neighborhood of a paramagnetic center without requiring a specific expertise in the field. The resulting 3D spectra are standard spectra that can be handled by any standard software for protein NMR data analysis.
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Affiliation(s)
- Ioannis Gelis
- NCSR Demokritos, Institute of Physical Chemistry, Agia Paraskevi Attikis, Greece
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Crossnoe CR, Germanas JP, LeMagueres P, Mustata G, Krause KL. The crystal structure of Trichomonas vaginalis ferredoxin provides insight into metronidazole activation. J Mol Biol 2002; 318:503-18. [PMID: 12051855 DOI: 10.1016/s0022-2836(02)00051-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Crystallographic studies revealing the three-dimensional structure of the oxidized form of the [2Fe-2S] ferredoxin from Trichomonas vaginalis (TvFd) are presented. TvFd, a member of the hydrogenosomal class of ferredoxins, possesses a unique combination of redox and spectroscopic properties, and is believed to be the biological molecule that activates the drug metronidazole reductively in the treatment of trichomoniasis. It is the first hydrogenosomal ferredoxin to have its structure determined. The structure of TvFd reveals a monomeric, 93 residue protein with a fold similar to that of other known [2Fe-2S] ferredoxins. It contains nine hydrogen bonds to the sulfur atoms of the cluster, which is more than the number predicted on the basis of the spectroscopic data. The TvFd structure contains a large dipole moment like adrenodoxin, and appears to have a similar interaction domain. Our analysis demonstrates that TvFd has a unique cavity near the iron-sulfur cluster that exposes one of the inorganic sulfur atoms of the cluster to solvent. This cavity is not seen in any other [2Fe-2S] ferredoxin with known structure, and is hypothesized to be responsible for the high rate of metronidazole reduction by TvFd.
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Affiliation(s)
- Chetlen R Crossnoe
- Structural and Computational Biology and Molecular Biophysics Program, Baylor College of Medicine, Houston, TX 77030, USA
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Hurley JK, Morales R, Martínez-Júlvez M, Brodie TB, Medina M, Gómez-Moreno C, Tollin G. Structure-function relationships in Anabaena ferredoxin/ferredoxin:NADP(+) reductase electron transfer: insights from site-directed mutagenesis, transient absorption spectroscopy and X-ray crystallography. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1554:5-21. [PMID: 12034466 DOI: 10.1016/s0005-2728(02)00188-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The interaction between reduced Anabaena ferredoxin and oxidized ferredoxin:NADP(+) reductase (FNR), which occurs during photosynthetic electron transfer (ET), has been investigated extensively in the authors' laboratories using transient and steady-state kinetic measurements and X-ray crystallography. The effect of a large number of site-specific mutations in both proteins has been assessed. Many of the mutations had little or no effect on ET kinetics. However, non-conservative mutations at three highly conserved surface sites in ferredoxin (F65, E94 and S47) caused ET rate constants to decrease by four orders of magnitude, and non-conservative mutations at three highly conserved surface sites in FNR (L76, K75 and E301) caused ET rate constants to decrease by factors of 25-150. These residues were deemed to be critical for ET. Similar mutations at several other conserved sites in the two proteins (D67 in Fd; E139, L78, K72, and R16 in FNR) caused smaller but still appreciable effects on ET rate constants. A strong correlation exists between these results and the X-ray crystal structure of an Anabaena ferredoxin/FNR complex. Thus, mutations at sites that are within the protein-protein interface or are directly involved in interprotein contacts generally show the largest kinetic effects. The implications of these results for the ET mechanism are discussed.
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Affiliation(s)
- John K Hurley
- Department of Biochemistry and Molecular Biophysics, University of Arizona, 1041 E. Lowell Street, Tucson, AZ 85721-0088, USA
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17
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Affiliation(s)
- I Bertini
- Magnetic Resonance Center (CERM), University of Florence, Florence 50019, Italy
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18
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Grinberg AV, Hannemann F, Schiffler B, Müller J, Heinemann U, Bernhardt R. Adrenodoxin: structure, stability, and electron transfer properties. Proteins 2000; 40:590-612. [PMID: 10899784 DOI: 10.1002/1097-0134(20000901)40:4<590::aid-prot50>3.0.co;2-p] [Citation(s) in RCA: 129] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Adrenodoxin is an iron-sulfur protein that belongs to the broad family of the [2Fe-2S]-type ferredoxins found in plants, animals and bacteria. Its primary function as a soluble electron carrier between the NADPH-dependent adrenodoxin reductase and several cytochromes P450 makes it an irreplaceable component of the steroid hormones biosynthesis in the adrenal mitochondria of vertebrates. This review intends to summarize current knowledge about structure, function, and biochemical behavior of this electron transferring protein. We discuss the recently solved first crystal structure of the vertebrate-type ferredoxin, the truncated adrenodoxin Adx(4-108), that offers the unique opportunity for better understanding of the structure-function relationships and stabilization of this protein, as well as of the molecular architecture of [2Fe-2S] ferredoxins in general. The aim of this review is also to discuss molecular requirements for the formation of the electron transfer complex. Essential comparison between bacterial putidaredoxin and mammalian adrenodoxin will be provided. These proteins have similar tertiary structure, but show remarkable specificity for interactions only with their own cognate cytochrome P450. The discussion will be largely centered on the protein-protein recognition and kinetics of adrenodoxin dependent reactions.
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Affiliation(s)
- A V Grinberg
- Naturwissenschaftlich-Technische Fakultät III, Fachrichtung 8.8 - Biochemie, Universität des Saarlandes, Saarbrücken, Germany
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Sekerina E, Rahfeld JU, Müller J, Fanghänel J, Rascher C, Fischer G, Bayer P. NMR solution structure of hPar14 reveals similarity to the peptidyl prolyl cis/trans isomerase domain of the mitotic regulator hPin1 but indicates a different functionality of the protein. J Mol Biol 2000; 301:1003-17. [PMID: 10966801 DOI: 10.1006/jmbi.2000.4013] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The 131-amino acid residue parvulin-like human peptidyl-prolyl cis/trans isomerase (PPIase) hPar14 was shown to exhibit sequence similarity to the regulator enzyme for cell cycle transitions human hPin1, but specificity for catalyzing pSer(Thr)-Pro cis/trans isomerizations was lacking. To determine the solution structure of hPar14 the (1)H, (13)C, and (15)N chemical shifts of this protein have been assigned using heteronuclear two and three-dimensional NMR experiments on unlabeled and uniformly (15)N/(13)C-labeled recombinant protein isolated from Escherichia coli cells that overexpress the protein. The chemical shift assignments were used to interpret the NOE data, which resulted in a total of 1042 NOE restraints. The NOE restraints were used along with 71 dihedral angle restraints and 38 hydrogen bonding restraints to produce 50 low-energy structures. The hPar14 folds into a betaalpha(3)betaalphabeta(2) structure, and contains an unstructured 35-amino acid basic tail N-terminal to the catalytic core that replaces the WW domain of hPin1 homologs. The three-dimensional structures of hPar14 and the PPIase domain of human hPin1 reveal a high degree of conservation. The root-mean-square deviations of the mean atomic coordinates of the heavy atoms of the backbone between residues 38 to 45, 50 to 58, 64 to 70, 81 to 86, 115 to 119 and 122 to 128 of hPar14 were 0.81(+/-0.07) A. The hPar14 model structure provides insight into how this class of PPIases may select preferential secondary catalytic sites, and also allows identification of a putative DNA-binding motif in parvulin-like PPIases.
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Affiliation(s)
- E Sekerina
- Max-Planck-Stelle for Enzymology of Protein Folding, 06120 Halle/Saale, Weinberg 22, Germany
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20
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Im SC, Worrall JA, Liu G, Aliverti A, Zanetti G, Luchinat C, Bertini I, Sykes AG. The CrIIL reduction of [2Fe-2S] ferredoxins and site of attachment of CrIII using 1H NMR and site-directed mutagenesis. Inorg Chem 2000; 39:1755-64. [PMID: 12526565 DOI: 10.1021/ic991127w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The recently reported NMR solution structure of FeIIIFeIII parsley FdI has made possible 2D NOESY NMR studies to determine the point of attachment of CrIIIL in FeIIIFeIII...CrIIIL. The latter Cr-modified product was obtained by reduction of FeIIIFeIII parsley and spinach FdI forms with [Cr(15-aneN4) (H2O)2]2+ (15-aneN4 = 1,4,8,12-tetraazacyclopentadecane), referred to here as CrIIL, followed by air oxidation and chromatographic purification. From a comparison of NMR cross-peak intensities of native and Cr-modified proteins, two surface sites designated A and B, giving large paramagnetic CrIIIL broadening of a number of amino acid peaks, have been identified. The effects at site A (residues 19-22, 27, and 30) are greater than those at site B (residues 92-94 and 96), which is on the opposite side of the protein. From metal (ICP-AES) and electrospray ionization mass spectrometry (EIMS) analyses on the Cr-modified protein, attachment of a single CrIIIL only is confirmed for both parsley and spinach FdI and FdII proteins. Electrostatic interaction of the 3+ CrIIIL center covalently attached to one protein molecule (charge approximately -18) with a second (like) molecule provides an explanation for the involvement of two regions. Thus for 3-4 mM FeIIIFeIII...CrIIIL solutions used in NMR studies (CrIIIL attached at A), broadening effects due to electrostatic interactions at B on a second molecule are observed. Experiments with the Cys18Ala spinach FdI variant have confirmed that the previously suggested Cys-18 at site A is not the site of CrIIIL attachment. Line broadening at Val-22 of A gives the largest effect, and CrIIIL attachment at one or more adjacent (conserved) acidic residues in this region is indicated. The ability of CrIIL to bind in some (parsley and spinach) but not all cases (Anabaena variabilis) suggests that intramolecular H-bonding of acidic residues at A is relevant. The parsley and spinach FeIIFeIII...CrIIIL products undergo a second stage of reduction with the formation of FeIIFeII...CrIIIL. However, the spinach Glu92Ala (site B) variant undergoes only the first stage of reduction, and it appears that Glu-92 is required for the second stage of reduction to occur. A sample of CrIIIL-modified parsley FeIIIFeIII Fd is fully active as an electron carrier in the NADPH-cytochrome c reductase reaction catalyzed by ferredoxin-NADP+ reductase.
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Affiliation(s)
- S C Im
- Department of Chemistry, University of Newcastle, Newcastle upon Tyne, NE1 7RU, U.K
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21
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Ullmann GM, Hauswald M, Jensen A, Knapp EW. Structural alignment of ferredoxin and flavodoxin based on electrostatic potentials: Implications for their interactions with photosystem I and ferredoxin-NADP reductase. Proteins 2000. [DOI: 10.1002/(sici)1097-0134(20000215)38:3<301::aid-prot6>3.0.co;2-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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22
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Novakova AA, Davletshina LN, Khval'kovskaya EA, Semin BK, Belevich NP, Ivanov II, Rubin AB. Inorganic Fe2+ formation upon Fe-S protein thermodestruction in the membranes of thermophilic cyanobacteria: Mössbauer spectroscopy study. FEBS Lett 1999; 450:135-8. [PMID: 10350072 DOI: 10.1016/s0014-5793(99)00485-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A model description of the Mössbauer spectrum (80 K) of native membranes of the thermophilic cyanobacterium Synechococcus elongatus is suggested on the basis of the known values of quadrupole splitting (deltaE(Q)) and isomer shift (deltaFe) for the iron-containing components of the photosynthetic apparatus. Using this approach, we found that heating the membranes at 70-80 K results in a decrease of doublet amplitudes belonging to F(X), F(A), F(B) and ferredoxin and simultaneous formation of a new doublet with deltaE(Q) = 3.10 mm/s and delta-Fe = 1.28 mm/s, typical of inorganic hydrated forms of Fe2+. The inhibition of electron transfer via photosystem I to oxygen, catalyzed by ferredoxin, occurs within the same range of temperatures. The data demonstrate that the processes of thermoinduced Fe2+ formation and distortions in the photosystem I electron transport in the membranes are interrelated and caused mainly by the degradation of ferredoxin. The possible role of Fe2+ formation in the damage of the photosynthetic apparatus resulting from heating and the action of other extreme factors is discussed.
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23
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Bertini I, Luchinat C, Rosato A. NMR Spectra of Iron-Sulfur Proteins. ADVANCES IN INORGANIC CHEMISTRY 1999. [DOI: 10.1016/s0898-8838(08)60080-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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24
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Sticht H, Rösch P. The structure of iron-sulfur proteins. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1998; 70:95-136. [PMID: 9785959 DOI: 10.1016/s0079-6107(98)00027-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Ferredoxins are a group of iron-sulfur proteins for which a wealth of structural and mutational data have recently become available. Previously unknown structures of ferredoxins which are adapted to halophilic, acidophilic or hyperthermophilic environments and new cysteine patterns for cluster ligation and non-cysteine cluster ligation have been described. Site-directed mutagenesis experiments have given insight into factors that influence the geometry, stability, redox potential, electronic properties and electron-transfer reactivity of iron-sulfur clusters.
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Affiliation(s)
- H Sticht
- Lehrstuhl für Struktur und Chemie der Biopolymere, Universität Bayreuth, Germany.
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25
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Bayer P, Arndt A, Metzger S, Mahajan R, Melchior F, Jaenicke R, Becker J. Structure determination of the small ubiquitin-related modifier SUMO-1. J Mol Biol 1998; 280:275-86. [PMID: 9654451 DOI: 10.1006/jmbi.1998.1839] [Citation(s) in RCA: 303] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The recently discovered small ubiquitin-related modifier SUMO-1 belongs to the growing family of ubiquitin-related proteins involved in postranslational protein modification. Unlike ubiquitin, SUMO-1 does not appear to target proteins for degradation but seems to be involved in the modulation of protein-protein interactions. Independent studies demonstrate an essential function of SUMO-1 in the regulation of nucleo-cytoplasmic transport, and suggest a role in cell-cycle regulation and apoptosis. Here, we present the first three-dimensional structure of SUMO-1 solved by NMR. Although having only 18% amino acid sequence identity with ubiquitin, the overall structure closely resembles that of ubiquitin, featuring the betabetaalphabetabetaalphabeta fold of the ubiquitin protein family. In addition, the position of the two C-terminal Gly residues required for isopeptide bond formation is conserved between ubiquitin and SUMO-1. The most prominent feature of SUMO-1 is a long and highly flexible N terminus, which protrudes from the core of the protein and which is absent in ubiquitin. Furthermore, ubiquitin Lys48, required to generate ubiquitin polymers, is substituted in SUMO-1 by Gln69 at the same position, which provides an explanation of why SUMO-1 has not been observed to form polymers. Moreover, the hydrophobic core of SUMO-1 and ubiquitin is maintained by conserved hydrophobic residues, whereas the overall charge topology of SUMO-1 and ubiquitin differs significantly, suggesting specific modifying enzymes and target proteins for both proteins.
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Affiliation(s)
- P Bayer
- Abteilung Physikalische Biochemie, Max-Planck-Institut für molekulare Physiologie, Dortmund, Germany
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26
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Davy SL, Osborne MJ, Moore GR. Determination of the structure of oxidised Desulfovibrio africanus ferredoxin I by 1H NMR spectroscopy and comparison of its solution structure with its crystal structure. J Mol Biol 1998; 277:683-706. [PMID: 9533888 DOI: 10.1006/jmbi.1998.1631] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The solution structure of the 64 amino acid Fe4S4 ferredoxin I from Desulfovibrio africanus has been determined using two-dimensional 1H NMR spectroscopy. Sequence-specific assignments were obtained for 59 amino acid residues and the structure determined with the program DIANA on the basis of 549 nuclear Overhauser enhancement (NOE) upper distance limits, and four dihedral angle and 52 distance constraints for the Fe4S4 cluster. The NMR structure was refined using the simulated annealing and energy minimisation protocols of the program X-PLOR to yield a final family of 19 structures selected on the basis of good covalent geometry and minimal restraint violations. The r.m.s.d. values to the average structure for this family are 0.49(+/-0.07) A and 0.94(+/-0.09) A for the backbone and heavy-atoms of residues 3 to 62, respectively. The NMR structure has been compared to the previously reported X-ray structures for the two molecules within the asymmetric unit of the crystal, which have a network of seven hydrogen bonds between them. This intermolecular interface, involving residues 38, 40 to 43 and 46, has the same conformation in the solution structures showing that the crystal packing does not perturb the structure. There are three regions in which the NMR and X-ray structures differ: around the cluster, a turn involving residues 8 to 10, and a loop involving residues 29 to 32. In the family of solution structures the backbone of the loop region incorporating residues 29 to 32 is well-defined whilst in both of the X-ray molecules it is ill-defined. The small differences between the X-ray and NMR structures for the cluster environment and the turn between residues 8 to 10 probably reflects a lack of NMR constraints. The observation of relatively rapid amide NH hydrogen exchange of NH groups close to the cluster, together with rapid flipping for Phe25, which is also close to the cluster, indicates that the cluster environment is more dynamic than the corresponding regions of related Fe/S proteins.
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Affiliation(s)
- S L Davy
- School of Chemical Sciences, University of East Anglia, Norwich, NR4 7TJ, U.K
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27
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Müller A, Müller JJ, Muller YA, Uhlmann H, Bernhardt R, Heinemann U. New aspects of electron transfer revealed by the crystal structure of a truncated bovine adrenodoxin, Adx(4-108). Structure 1998; 6:269-80. [PMID: 9551550 DOI: 10.1016/s0969-2126(98)00031-8] [Citation(s) in RCA: 122] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Adrenodoxin (Adx) is a [2Fe-2S] ferredoxin involved in steroid hormone biosynthesis in the adrenal gland mitochondrial matrix of mammals. Adx is a small soluble protein that transfers electrons from adrenodoxin reductase (AR) to different cytochrome P450 isoforms where they are consumed in hydroxylation reactions. A crystallographic study of Adx is expected to reveal the structural basis for an important electron transfer reaction mediated by a vertebrate [2Fe-2S] ferredoxin. RESULTS The crystal structure of a truncated bovine adrenodoxin, Adx(4-108), was determined at 1.85 A resolution and refined to a crystallographic R value of 0.195. The structure was determined using multiple wavelength anomalous dispersion phasing techniques, making use of the iron atoms in the [2Fe-2S] cluster of the protein. The protein displays the compact (alpha + beta) fold typical for [2Fe-2S] ferredoxins. The polypeptide chain is organized into a large core domain and a smaller interaction domain which comprises 35 residues, including all those previously determined to be involved in binding to AR and cytochrome P450. A small interdomain motion is observed as a structural difference between the two independent molecules in the asymmetric unit of the crystal. Charged residues of Adx(4-108) are clustered to yield a strikingly asymmetric electric potential of the protein molecule. CONCLUSIONS The crystal structure of Adx(4-108) provides the first detailed description of a vertebrate [2Fe-2S] ferredoxin and serves to explain a large body of biochemical studies in terms of a three-dimensional structure. The structure suggests how a change in the redox state of the [2Fe-2S] cluster may be coupled to a domain motion of the protein. It seems likely that the clearly asymmetric charge distribution on the surface of Adx(4-108) and the resulting strong molecular dipole are involved in electrostatic steering of the interactions with AR and cytochrome P450.
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Affiliation(s)
- A Müller
- Forschungsgruppe Kristallographie, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
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28
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Beissinger M, Sticht H, Sutter M, Ejchart A, Haehnel W, Rösch P. Solution structure of cytochrome c6 from the thermophilic cyanobacterium Synechococcus elongatus. EMBO J 1998; 17:27-36. [PMID: 9427738 PMCID: PMC1170355 DOI: 10.1093/emboj/17.1.27] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Cytochrome c6 is a small, soluble electron carrier between the two membrane-bound complexes cytochrome b6f and photosystem I (PSI) in oxygenic photosynthesis. We determined the solution structure of cytochrome c6 from the thermophilic cyanobacterium Synechococcus elongatus by NMR spectroscopy and molecular dynamics calculations based on 1586 interresidual distance and 28 dihedral angle restraints. The overall fold exhibits four alpha-helices and a small antiparallel beta-sheet in the vicinity of Met58, one of the axial heme ligands. The flat hydrophobic area in this cytochrome c6 is conserved in other c6 cytochromes and even in plastocyanin of higher plants. This docking region includes the site of electron transfer to PSI and possibly to the cytochrome b6f complex. The binding of cytochrome c6 to PSI in green algae involves interaction of a negative patch with a positive domain of PSI. This positive domain has not been inserted at the evolutionary level of cyanobacteria, but the negatively charged surface region is already present in S. elongatus cytochrome c6 and may thus have been optimized during evolution to improve the interaction with the positively charged cytochrome f. As the structure of PSI is known in S.elongatus, the reported cytochrome c6 structure can provide a basis for mutagenesis studies to delineate the mechanism of electron transfer between both.
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Affiliation(s)
- M Beissinger
- Lehrstuhl für Biopolymere, Universität Bayreuth, D-95440 Bayreuth
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Hatanaka H, Tanimura R, Katoh S, Inagaki F. Solution structure of ferredoxin from the thermophilic cyanobacterium Synechococcus elongatus and its thermostability. J Mol Biol 1997; 268:922-33. [PMID: 9180381 DOI: 10.1006/jmbi.1997.1001] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The three-dimensional structure of ferredoxin, purified from the thermophilic cyanobacterium Synechococcus elongatus, was determined in aqueous solution by two-dimensional proton nuclear magnetic resonance. In addition to the 946 distance constraints from nuclear Overhauser effect connectivities, we added 241 distance constraints derived from the crystal structure of Spirulina platensis ferredoxin to the 19 residues close to the [2Fe-2S] iron-sulfur center, where crosspeaks disappeared due to paramagnetic effects. The atomic root-mean-square difference of the ten converged structures from the mean structure was 0.61(+/-0.12) A for backbone atoms (N, C(alpha), C'). The main-chain structure was almost the same as the crystal structures of other mesophile ferredoxins, but comparison of the side-chain structures revealed an extension of the hydrophobic core, a unique hydrophobic patch on the surface of the large beta-sheet, and two unique charge networks in this thermostable ferredoxin structure, some of which might contribute to thermostability.
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Affiliation(s)
- H Hatanaka
- Department of Molecular Physiology, The Tokyo Metropolitan Institute of Medical Science, Bunkyo-ku, Japan
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