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Jafari S, Ryde U, Irani M. Two local minima for structures of [4Fe-4S] clusters obtained with density functional theory methods. Sci Rep 2023; 13:10832. [PMID: 37402767 PMCID: PMC10319735 DOI: 10.1038/s41598-023-37755-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/27/2023] [Indexed: 07/06/2023] Open
Abstract
[4Fe-4S] clusters are essential cofactors in many proteins involved in biological redox-active processes. Density functional theory (DFT) methods are widely used to study these clusters. Previous investigations have indicated that there exist two local minima for these clusters in proteins. We perform a detailed study of these minima in five proteins and two oxidation states, using combined quantum mechanical and molecular mechanical (QM/MM) methods. We show that one local minimum (L state) has longer Fe-Fe distances than the other (S state), and that the L state is more stable for all cases studied. We also show that some DFT methods may only obtain the L state, while others may obtain both states. Our work provides new insights into the structural diversity and stability of [4Fe-4S] clusters in proteins, and highlights the importance of reliable DFT methods and geometry optimization. We recommend r2SCAN for optimizing [4Fe-4S] clusters in proteins, which gives the most accurate structures for the five proteins studied.
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Affiliation(s)
- Sonia Jafari
- Department of Chemistry, University of Kurdistan, P.O.Box 66175-416, Sanandaj, Iran
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, P.O.Box 124, 221 00, Lund, Sweden
| | - Mehdi Irani
- Department of Chemistry, University of Kurdistan, P.O.Box 66175-416, Sanandaj, Iran.
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2
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Classen A, Ayyer K, Chapman HN, Röhlsberger R, von Zanthier J. Incoherent Diffractive Imaging via Intensity Correlations of Hard X Rays. PHYSICAL REVIEW LETTERS 2017; 119:053401. [PMID: 28949712 DOI: 10.1103/physrevlett.119.053401] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Indexed: 06/07/2023]
Abstract
Established x-ray diffraction methods allow for high-resolution structure determination of crystals, crystallized protein structures, or even single molecules. While these techniques rely on coherent scattering, incoherent processes like fluorescence emission-often the predominant scattering mechanism-are generally considered detrimental for imaging applications. Here, we show that intensity correlations of incoherently scattered x-ray radiation can be used to image the full 3D arrangement of the scattering atoms with significantly higher resolution compared to conventional coherent diffraction imaging and crystallography, including additional three-dimensional information in Fourier space for a single sample orientation. We present a number of properties of incoherent diffractive imaging that are conceptually superior to those of coherent methods.
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Affiliation(s)
- Anton Classen
- Institut für Optik, Information und Photonik, Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
- Erlangen Graduate School in Advanced Optical Technologies (SAOT), Universität Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Kartik Ayyer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Department Physik, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Ralf Röhlsberger
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Joachim von Zanthier
- Institut für Optik, Information und Photonik, Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
- Erlangen Graduate School in Advanced Optical Technologies (SAOT), Universität Erlangen-Nürnberg, 91052 Erlangen, Germany
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3
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part V. {[Fe4S4](SCysγ)4} proteins. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Holm RH, Lo W. Structural Conversions of Synthetic and Protein-Bound Iron–Sulfur Clusters. Chem Rev 2016; 116:13685-13713. [DOI: 10.1021/acs.chemrev.6b00276] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. H. Holm
- Department
of Chemistry and
Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Wayne Lo
- Department
of Chemistry and
Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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5
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Synthesis, Characterization, and Crystal Structure of Tertiary Phosphine-Substituted Diiron Propanedithiolate Complexes. J CLUST SCI 2014. [DOI: 10.1007/s10876-014-0711-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Zhao PH, Liu YF, Xiong KK, Liu YQ. Synthetic and Structural Studies on Some New Butterfly Fe/S Cluster Complexes Containing 2,6-(CH2)2C5H3N or (CH2)2 Groups. J CLUST SCI 2014. [DOI: 10.1007/s10876-014-0689-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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Don MJ, Yang K, Bott SG, Richmond MG. Ph2PPy REPLACEMENT OF THE 1,5-COD LIGAND IN THE SULFIDO-CAPPED CLUSTER Fe2(CO)6(μ3-S)2Pt(1,5-COD). X-RAY DIFFRACTION STRUCTURE AND REDOX BEHAVIOR OF Fe2(CO)6(μ3-S)2Pt(Ph2PPy)2. J COORD CHEM 2006. [DOI: 10.1080/00958979608024532] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Ming-Jaw Don
- a Center for Organometallic Research and Education, Department of Chemistry , University of North Texas , Denton , TX , 76203
| | - Kaiyuan Yang
- a Center for Organometallic Research and Education, Department of Chemistry , University of North Texas , Denton , TX , 76203
| | - Simon G. Bott
- a Center for Organometallic Research and Education, Department of Chemistry , University of North Texas , Denton , TX , 76203
| | - Michael G. Richmond
- a Center for Organometallic Research and Education, Department of Chemistry , University of North Texas , Denton , TX , 76203
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8
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Couture MMJ, Martin VJJ, Mohn WW, Eltis LD. Characterization of DitA3, the [Fe3S4] ferredoxin of an aromatic ring-hydroxylating dioxygenase from a diterpenoid-degrading microorganism. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:1462-9. [PMID: 16952485 DOI: 10.1016/j.bbapap.2006.06.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2006] [Revised: 06/23/2006] [Accepted: 06/26/2006] [Indexed: 10/24/2022]
Abstract
DitA3, a small soluble ferredoxin, is a component of a ring-hydroxylating dioxygenase involved in the microbial degradation of the diterpenoid, dehydroabietic acid. The anaerobic purification of a heterologously expressed his-tagged DitA3 yielded 20 mg of apparently homogeneous recombinant protein, rcDitA3, per liter of cell culture. Each mole of purified rcDitA3 contained 2.9 equivalents of iron and 4.2 equivalents of sulfur, indicating the presence of a single [Fe(3)S(4)] cluster. This conclusion was corroborated by UV-Visible absorption (epsilon(412)=13.4 mM(-1) cm(-1)) and EPR (g(x,y)=2.00 and g(z)=2.02) spectroscopies. The reduction potential of rcDitA3, determined using a highly oriented parallel graphite (HOPG) electrode, was -177.0+/-0.5 mV vs. the standard hydrogen electrode (SHE) (20 mM MOPS, 80 mM KCl, pH 7.0, 22 degrees C). This potential is similar to those of small, soluble Rieske-type ferredoxin components of aromatic-ring dihydroxylating dioxygenases. In contrast to these Rieske-type ferredoxins, DitA3 appears to exist as a dimer in solution. The dimeric ferredoxin may be more stable or may increase the catalytic efficiency of the dioxygenase by delivering the two reducing equivalents required for turnover of the oxygenase.
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Affiliation(s)
- Manon M-J Couture
- Department of Biochemistry, Université Laval, Ste-Foy, Québec, Canada G1K 7P4.
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9
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Adams RD, Miao S. Metal Carbonyl Derivatives of Sulfur-Containing Quinones and Hydroquinones: Synthesis, Structures, and Electrochemical Properties. Inorg Chem 2004; 43:8414-26. [PMID: 15606190 DOI: 10.1021/ic048880w] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reaction of CpMoMn(mu-S(2))(CO)(5), 1, with 1,4-benzoquinone in the presence of irradiation with visible light yielded the quinonedithiolato complex CpMoMn(CO)(5)(mu-S(2)C(6)H(2)O(2)), 2. The new complex CpMoMn(CO)(5)(mu-S(2)C(6)Cl(2)O(2)) (4) was synthesized similarly from 1 and 2,3-dichloro-1,4-benzoquinone. Compounds 2 and 4 were reduced with hydrogen to yield the hydroquinone complexes CpMoMn(CO)(5)[mu-S(2)C(6)H(2)(OH)(2)], 3, and CpMoMn(CO)(5)[mu-S(2)C(6)Cl(2)(OH)(2)], 5. UV-vis irradiation of solutions of Fe(2)(CO)(6)(mu-S(2)) and 1,4-benzoquinone yielded the hydroquinone complex Fe(2)(CO)(6)[mu-S(2)C(6)H(2)(OH)(2)], 6. Compound 6 was oxidized to the quinone complex Fe(2)(CO)(6)(mu-S(2)C(6)H(2)O(2)), 7, by using 2,3-dichloro-5,6-dicyano-1,4-benzoquinone. Substitution of the CO ligands on 6 by PPh(3) yielded the derivatives Fe(2)(CO)(5)(PPh(3))[mu-S(2)C(6)H(2)(OH)(2)], 8, and Fe(2)(CO)(4)(PPh(3))(2)[mu-S(2)C(6)H(2)(OH)(2)], 9. The electrochemical properties of 3, 5, 6, 8, and 9 were measured by cyclic voltammetry. The molecular structure of each of the new compounds 2-9 was established by single-crystal X-ray diffraction analyses.
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Affiliation(s)
- Richard D Adams
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA.
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10
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Adams RD, Miao S, Smith MD, Farach H, Webster CE, Manson J, Hall MB. Nickel−Manganese Sulfido Carbonyl Cluster Complexes. Synthesis, Structure, and Properties of the Unusual Paramagnetic Complexes Cp2Ni2Mn(CO)3(μ3-E)2, E = S, Se. Inorg Chem 2004; 43:2515-25. [PMID: 15074969 DOI: 10.1021/ic0354419] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reaction of Mn(2)(CO)(7)(mu-S(2)) with [CpNi(CO)](2) yielded the paramagnetic new compound Cp(2)Ni(2)Mn(CO)(3)(mu(3)-S)(2) (1) and a new hexanuclear metal product Cp(2)Ni(2)Mn(4)(CO)(14)(mu(6)-S(2))(mu(3)-S)(2) (2). Structurally, compound 1 contains two triply bridging sulfido ligands on opposite sides of an open Ni(2)Mn triangular cluster. EPR and temperature-dependent magnetic susceptibility measurements of 1 show that it contains one unpaired electron. The electronic structure of 1 was determined by Fenske-Hall molecular orbital calculations which show that the unpaired electron occupies a low lying antibonding orbital delocalized unequally across the three metal atoms. The selenium homologue Cp(2)Ni(2)Mn(CO)(3)(mu(3)-Se)(2) (3) was obtained from the reaction of a mixture of Mn(2)(CO)(10) and [CpNi(CO)](2) with elemental selenium and Me(3)NO.2H(2)O. It also has one unpaired electron. Compound 1 reacted with elemental sulfur to yield the dinickeldimanganese compound, Cp(2)Ni(2)Mn(2)(CO)(6)(mu(4)-S(2))(mu(4)-S(5)), 4, which can also be made from the reaction of Mn(2)(CO)(7)(mu-S(2)) with [CpNi(CO)](2) and sulfur. Compound 4 was converted back to 1 by sulfur abstraction using PPh(3). The reaction of Mn(2)(CO)(10) with [CpNi(CO)](2) in the presence of thiirane yielded the ethanedithiolato compound CpNiMn(CO)(3)(mu-SCH(2)CH(2)S) (5), which was also obtained from the reaction of Mn(4)(CO)(15)(mu(3)-S(2))(mu(4)-S(2)) with [CpNi(CO)](2) in the presence of thiirane. Compound 5 reacted with additional quantities of thiirane to yield the new compound CpNiMn(CO)(3)[mu-S(CH(2)CH(2)S)(2)], 6, which contains a 3-thiapentanedithiolato ligand that bridges the two metal atoms. Compound 6 was also obtained from the reaction of Mn(2)(CO)(10) with [CpNi(CO)](2) and thiirane. The molecular structures of the new compounds 1-6 were established by single-crystal X-ray diffraction analyses.
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Affiliation(s)
- Richard D Adams
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA.
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11
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Adams RD, Kwon OS. Syntheses and Reactivity of the Diselenido Molybdenum−Manganese Complex CpMoMn(CO)5(μ-Se2). Inorg Chem 2003; 42:6175-82. [PMID: 14514293 DOI: 10.1021/ic030077z] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reaction of CpMoMn(CO)(8) with elemental selenium and Me(3)NO in the absence of light yielded the diselenido complex CpMoMn(CO)(5)(mu-Se(2)), 2. Compound 2 contains a bridging diselenido ligand lying perpendicular to the Mo-Mn bond, Mo-Mn = 2.8421(10) A. In the presence of room light, the reaction yielded the tetranuclear metal complex Cp(2)Mo(2)Mn(2)(CO)(7)(mu(3)-Se)(4), 3 (36% yield), and 2 (7% yield). Compound 2 reacted with ethylene to yield the ethanediselenato complex CpMoMn(CO)(5)(mu-SeCH(2)CH(2)Se), 4, by insertion of ethylene into the Se-Se bond. Compound 2 also reacted with (PPh(3))(2)Pt(PhC(2)Ph) and CpCo(CO)(2) to yield the complexes CpMoMnPt(PPh(3))(2)(CO)(5)(mu(3)-Se)(2), 5, and Cp(2)CoMoMn(CO)(5)(mu(3)-Se)(2), 6, respectively, by insertion of the metal groupings CpCo and Pt(PPh(3))(2) into the Se-Se bond of 2. The oxo compound Cp(2)CoMo(O)Mn(CO)(5)(mu(3)-Se)(2), 7, was obtained from 6 by decarbonylation at molybdenum by using Me(3)NO. The molecular structures of the complexes 2-7 were established by single-crystal X-ray diffraction analyses.
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Affiliation(s)
- Richard D Adams
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA.
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12
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Seino H, Kaneko T, Fujii S, Hidai M, Mizobe Y. Cubane-type heterometallic sulfido clusters: incorporation of two metal fragments into a dinuclear ReS(mu-S)2ReS core affording bimetallic M2Re2(mu 3-S)4 clusters (M = Ru, Pt, Cu) or trimetallic MM'Re2(mu 3-S)4 clusters via incomplete cubane-type MRe2(mu 3-S)(mu 2-S)3 intermediates (M = Ru, Rh, Ir; M' = Mo, W, Pd, Ru, Rh). Inorg Chem 2003; 42:4585-96. [PMID: 12870948 DOI: 10.1021/ic030129k] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reactions of a dirhenium tetra(sulfido) complex [PPh(4)](2)[ReS(L)(mu-S)(2)ReS(L)] (L = S(2)C(2)(SiMe(3))(2)) with a series of group 8-11 metal complexes in MeCN at room temperature afforded either the cubane-type clusters [M(2)(ReL)(2)(mu(3)-S)(4)] (M = CpRu (2), PtMe(3), Cu(PPh(3)) (4); Cp = eta(5)-C(5)Me(5)) or the incomplete cubane-type clusters [M(ReL)(2)(mu(3)-S)(mu(2)-S)(3)] (M = (eta(6)-C(6)HMe(5))Ru (5), CpRh (6), CpIr (7)), depending on the nature of the metal complexes added. It has also been disclosed that the latter incomplete cubane-type clusters can serve as the good precursors to the trimetallic cubane-type clusters still poorly precedented. Thus, treatment of 5-7 with a range of metal complexes in THF at room temperature resulted in the formation of novel trimetallic cubane-type clusters, including the neutral clusters [[(eta(6)-C(6)HMe(5))Ru][W(CO)(3)](ReL)(2)(mu(3)-S)(4)], [(CpM)[W(CO)(3)](ReL)(2)(mu(3)-S)(4)] (M = Rh, Ir), [(Cp*Ir)[Mo(CO)(3)](ReL)(2)(mu(3)-S)(4)], [[(eta(6)-C(6)HMe(5))Ru][Pd(PPh(3))](ReL)(2)(mu(3)-S)(4)], and [(Cp*Ir)[Pd(PPh(3))](ReL)(2)(mu(3)-S)(4)] (13) along with the cationic clusters [(Cp*Ir)(CpRu)(ReL)(2)(mu(3)-S)(4)][PF(6)] (14) and [(Cp*Ir)[Rh(cod)](ReL)(2)(mu(3)-S)(4)][PF(6)] (cod = 1,5-cyclooctadiene). The X-ray analyses have been carried out for 2, 4, 7, 13, and the SbF(6) analogue of 14 (14') to confirm their bimetallic cubane-type, bimetallic incomplete cubane-type, or trimetallic cubane-type structures. Fluxional behavior of the incomplete cubane-type and trimetallic cubane-type clusters in solutions has been demonstrated by the variable-temperature (1)H NMR studies, which is ascribable to both the metal-metal bond migration in the cluster cores and the pseudorotation of the dithiolene ligand bonded to the square pyramidal Re centers, where the temperatures at which these processes proceed have been found to depend upon the nature of the metal centers included in the cluster cores.
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Affiliation(s)
- Hidetake Seino
- Institute of Industrial Science, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8505, Japan, and Department of Materials Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
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13
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Torres RA, Lovell T, Noodleman L, Case DA. Density functional and reduction potential calculations of Fe4S4 clusters. J Am Chem Soc 2003; 125:1923-36. [PMID: 12580620 DOI: 10.1021/ja0211104] [Citation(s) in RCA: 193] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Density functional theory geometry optimizations and reduction potential calculations are reported for all five known oxidation states of [Fe(4)S(4)(SCH(3))(4)](n)()(-) (n = 0, 1, 2, 3, 4) clusters that form the active sites of iron-sulfur proteins. The geometry-optimized structures tend to be slightly expanded relative to experiment, with the best comparison found in the [Fe(4)S(4)(SCH(3))(4)](2)(-) model cluster, having bond lengths 0.03 A longer on average than experimentally observed. Environmental effects are modeled with a continuum dielectric, allowing the solvent contribution to the reduction potential to be calculated. The calculated protein plus solvent effects on the reduction potentials of seven proteins (including high potential iron proteins, ferredoxins, the iron protein of nitrogenase, and the "X", "A", and "B" centers of photosystem I) are also examined. A good correlation between predicted and measured absolute reduction potentials for each oxidation state of the cluster is found, both for relative potentials within a given oxidation state and for the absolute potentials for all known couples. These calculations suggest that the number of amide dipole and hydrogen bonding interactions with the Fe(4)S(4) clusters play a key role in modulating the accessible redox couple. For the [Fe(4)S(4)](0) (all-ferrous) system, the experimentally observed S = 4 state is calculated to lie lowest in energy, and the predicted geometry and electronic properties for this state correlate well with the EXAFS and Mössbauer data. Cluster geometries are also predicted for the [Fe(4)S(4)](4+) (all-ferric) system, and the calculated reduction potential for the [Fe(4)S(4)(SCH(3))(4)](1)(-)(/0) redox couple is in good agreement with that estimated for experimental model clusters containing alkylthiolate ligands.
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Affiliation(s)
- Rhonda A Torres
- Department of Molecular Biology TPC-15, The Scripps Research Institute, La Jolla, California 92037, USA
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14
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Jung YS, Bonagura CA, Tilley GJ, Gao-Sheridan HS, Armstrong FA, Stout CD, Burgess BK. Structure of C42D Azotobacter vinelandii FdI. A Cys-X-X-Asp-X-X-Cys motif ligates an air-stable [4Fe-4S]2+/+ cluster. J Biol Chem 2000; 275:36974-83. [PMID: 10961993 DOI: 10.1074/jbc.m004947200] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
All naturally occurring ferredoxins that have Cys-X-X-Asp-X-X-Cys motifs contain [4Fe-4S](2+/+) clusters that can be easily and reversibly converted to [3Fe-4S](+/0) clusters. In contrast, ferredoxins with unmodified Cys-X-X-Cys-X-X-Cys motifs assemble [4Fe-4S](2+/+) clusters that cannot be easily interconverted with [3Fe-4S](+/0) clusters. In this study we changed the central cysteine of the Cys(39)-X-X-Cys(42)-X-X-Cys(45) of Azotobacter vinelandii FdI, which coordinates its [4Fe-4S](2+/+) cluster, into an aspartate. UV-visible, EPR, and CD spectroscopies, metal analysis, and x-ray crystallography show that, like native FdI, aerobically purified C42D FdI is a seven-iron protein retaining its [4Fe-4S](2+/+) cluster with monodentate aspartate ligation to one iron. Unlike known clusters of this type the reduced [4Fe-4S](+) cluster of C42D FdI exhibits only an S = 1/2 EPR with no higher spin signals detected. The cluster shows only a minor change in reduction potential relative to the native protein. All attempts to convert the cluster to a 3Fe cluster using conventional methods of oxygen or ferricyanide oxidation or thiol exchange were not successful. The cluster conversion was ultimately accomplished using a new electrochemical method. Hydrophobic and electrostatic interaction and the lack of Gly residues adjacent to the Asp ligand explain the remarkable stability of this cluster.
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Affiliation(s)
- Y S Jung
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA
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15
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Chen K, Tilley GJ, Sridhar V, Prasad GS, Stout CD, Armstrong FA, Burgess BK. Alteration of the reduction potential of the [4Fe-4S](2+/+) cluster of Azotobacter vinelandii ferredoxin I. J Biol Chem 1999; 274:36479-87. [PMID: 10593945 DOI: 10.1074/jbc.274.51.36479] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The [4Fe-4S](2+/+) cluster of Azotobacter vinelandii ferredoxin I (FdI) has an unusually low reduction potential (E(0')) relative to other structurally similar ferredoxins. Previous attempts to raise that E(0') by modification of surface charged residues were unsuccessful. In this study mutants were designed to alter the E(0') by substitution of polar residues for nonpolar residues near the cluster and by modification of backbone amides. Three FdI variants, P21G, I40N, and I40Q, were purified and characterized, and electrochemical E(0') measurements show that all had altered E(0') relative to native FdI. For P21G FdI and I40Q FdI, the E(0') increased by +42 and +53 mV, respectively validating the importance of dipole orientation in control of E(0'). Protein Dipole Langevin Dipole calculations based on models for those variants accurately predicted the direction of the change in E(0') while overestimating the magnitude. For I40N FdI, initial calculations based on the model predicted a +168 mV change in E(0') while a -33 mV change was observed. The x-ray structure of that variant, which was determined to 2.8 A, revealed a number of changes in backbone and side chain dipole orientation and in solvent accessibility, that were not predicted by the model and that were likely to influence E(0'). Subsequent Protein Dipole Langevin Dipole calculations (using the actual I40N x-ray structures) did quite accurately predict the observed change in E(0').
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Affiliation(s)
- K Chen
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA
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16
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Jung YS, Gao-Sheridan HS, Christiansen J, Dean DR, Burgess BK. Purification and biophysical characterization of a new [2Fe-2S] ferredoxin from Azotobacter vinelandii, a putative [Fe-S] cluster assembly/repair protein. J Biol Chem 1999; 274:32402-10. [PMID: 10542283 DOI: 10.1074/jbc.274.45.32402] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During the purification of site-directed mutant variants of Azotobacter vinelandii ferredoxin I (FdI), a pink protein, which was not observed in native FdI preparations, appeared to associate specifically with variants that had mutations in ligands to FdI [Fe-S] clusters. That protein, which we designate FdIV, has now been purified. NH(2)-terminal sequence analysis revealed that the protein is the product of a previously described gene, herein designated fdxD, that is in the A. vinelandii iscSUA operon that encodes proteins involved in iron-sulfur cluster assembly or repair. An apoprotein molecular mass of 12,434.03 +/- 0.21 Da was determined by mass spectrometry consistent with the known gene sequence. The monomeric protein was shown to contain a single [2Fe-2S](2+/+) cluster by UV/visible, CD, and EPR spectroscopies with a reduction potential of -344 mV versus the standard hydrogen electrode. When overexpressed in Escherichia coli, recombinant FdIV holoprotein was successfully assembled. However, the polypeptide of the recombinant protein was modified in some way such that the apoprotein molecular mass increased by 52 Da. Antibodies raised against FdIV and EPR spectroscopy were used to examine the relative levels of FdIV and FdI in various A. vinelandii strains leading to the conclusion that FdIV levels appear to be specifically increased under conditions where another protein, NADPH:ferredoxin reductase is also up-regulated. In that case, the fpr gene is known to be activated in response to oxidative stress. This suggests that the fdxD gene and other genes in the iron-sulfur cluster assembly or repair operon might be similarly up-regulated in response to oxidative stress.
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Affiliation(s)
- Y S Jung
- Department of Molecular Biology, University of California, Irvine, California 92697, USA
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Gao-Sheridan HS, Kemper MA, Khayat R, Tilley GJ, Armstrong FA, Sridhar V, Prasad GS, Stout CD, Burgess BK. A T14C variant of Azotobacter vinelandii ferredoxin I undergoes facile [3Fe-4S]0 to [4Fe-4S]2+ conversion in vitro but not in vivo. J Biol Chem 1998; 273:33692-701. [PMID: 9837955 DOI: 10.1074/jbc.273.50.33692] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
[4Fe-4S]2+/+ clusters that are ligated by Cys-X-X-Cys-X-X-Cys sequence motifs share the general feature of being hard to convert to [3Fe-4S]+/0 clusters, whereas those that contain a Cys-X-X-Asp-X-X-Cys motif undergo facile and reversible cluster interconversion. Little is known about the factors that control the in vivo assembly and conversion of these clusters. In this study we have designed and constructed a 3Fe to 4Fe cluster conversion variant of Azotobacter vinelandii ferredoxin I (FdI) in which the sequence that ligates the [3Fe-4S] cluster in native FdI was altered by converting a nearby residue, Thr-14, to Cys. Spectroscopic and electrochemical characterization shows that when purified in the presence of dithionite, T14C FdI is an O2-sensitive 8Fe protein. Both the new and the indigenous clusters have reduction potentials that are significantly shifted compared with those in native FdI, strongly suggesting a significantly altered environment around the clusters. Interestingly, whole cell EPR have revealed that T14C FdI exists as a 7Fe protein in vivo. This 7Fe form of T14C FdI is extremely similar to native FdI in its spectroscopic, electrochemical, and structural features. However, unlike native FdI which does not undergo facile cluster conversion, the 7Fe form T14C FdI quickly converts to the 8Fe form with a high efficiency under reducing conditions.
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Affiliation(s)
- H S Gao-Sheridan
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, USA
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Kemper MA, Gao-Sheridan HS, Shen B, Duff JL, Tilley GJ, Armstrong FA, Burgess BK. Delta T 14/Delta D 15 Azotobacter vinelandii ferredoxin I: creation of a new CysXXCysXXCys motif that ligates a [4Fe-4S] cluster. Biochemistry 1998; 37:12829-37. [PMID: 9737860 DOI: 10.1021/bi9810499] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In clostridial-type ferredoxins, each of the two [4Fe-4S]2+/+ clusters receives three of its four ligands from a CysXXCysXXCys motif. Azotobacter vinelandii ferredoxin I (AvFdI) is a seven-iron ferredoxin that contains one [4Fe-4S]2+/+ cluster and one [3Fe-4S]+/0 cluster. During the evolution of the 7Fe azotobacter-type ferredoxins from the 8Fe clostridial-type ferredoxins, one of the two motifs present changed to a CysXXCysXXXXCys motif, resulting in the inability to form a 4Fe cluster and the appearance of a 3Fe cluster in that position. In a previous study, we were unsuccessful in using structure as a guide in designing a 4Fe cluster in the 3Fe cluster position of AvFdI. In this study, we have reversed part of the evolutionary process by deleting two residues between the second and third cysteines. UV/Vis, CD, and EPR spectroscopies and direct electrochemical studies of the purified protein reveal that this DeltaT14/DeltaD15 FdI variant is an 8Fe protein containing two [4Fe-4S]2+/+ clusters with reduction potentials of -466 and -612 mV versus SHE. Whole-cell EPR shows that the protein is present as an 8Fe protein in vivo. These data strongly suggest that it is the sequence motif rather than the exact sequence or the structure that is critical for the assembly of a 4Fe cluster in that region of the protein. The new oxygen-sensitive 4Fe cluster was converted in partial yield to a 3Fe cluster. In known ferredoxins and enzymes that contain reversibly interconvertible [4Fe-4S]2+/+ and [3Fe-4S]+/0 clusters, the 3Fe form always has a reduction potential ca. 200 mV more positive than the 4Fe cluster in the same position. In contrast, for DeltaT14/DeltaD15 FdI, the 3Fe and 4Fe clusters in the same location have extremely similar reduction potentials.
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Affiliation(s)
- M A Kemper
- Department of Molecular Biology and Biochemistry, University of California, Irvine 92697-3900, USA
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Telser J, Huang H, Lee HI, Adams MWW, Hoffman BM. Site Valencies and Spin Coupling in the 3Fe and 4Fe (S = 1/2) Clusters of Pyrococcus furiosus Ferredoxin by 57Fe ENDOR. J Am Chem Soc 1998. [DOI: 10.1021/ja971546x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joshua Telser
- Contribution from the Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and the Department of Biochemistry & Molecular Biology and the Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602-2556
| | - Heshu Huang
- Contribution from the Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and the Department of Biochemistry & Molecular Biology and the Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602-2556
| | - Hong-In Lee
- Contribution from the Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and the Department of Biochemistry & Molecular Biology and the Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602-2556
| | - Michael W. W. Adams
- Contribution from the Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and the Department of Biochemistry & Molecular Biology and the Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602-2556
| | - Brian M. Hoffman
- Contribution from the Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and the Department of Biochemistry & Molecular Biology and the Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602-2556
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Kemper MA, Stout CD, Lloyd SJ, Prasad GS, Fawcett SE, Armstrong FA, Shen B, Burgess BK, Lloyd SE, Fawcett S. Y13C Azotobacter vinelandii ferredoxin I. A designed [Fe-S] ligand motif contains a cysteine persulfide. J Biol Chem 1997; 272:15620-7. [PMID: 9188450 DOI: 10.1074/jbc.272.25.15620] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Ferredoxins that contain [4Fe-4S]2+/+ clusters often obtain three of their four cysteine ligands from a highly conserved CysXXCysXXCys sequence motif. Little is known about the in vivo assembly of these clusters and the role that this sequence motif plays in that process. In this study, we have used structure as a guide in attempts to direct the formation of a [4Fe-4S]2+/+ in the [3Fe-4S]+/0 location of native (7Fe) Azotobacter vinelandii ferredoxin I (AvFdI) by providing the correct three-dimensional orientation of cysteine ligands without introducing a CysXXCysXXCys motif. Tyr13 of AvFdI occupies the position of the fourth ligating cysteine in the homologous and structurally characterized 8Fe ferredoxin from Peptococcus aerogenes and a Y13C variant of AvFdI could be easily modeled as an 8Fe protein. However, characterization of purified Y13C FdI by UV-visible spectra, circular dichroism, electron paramagnetic resonance spectroscopies, and by x-ray crystallography revealed that the protein failed to use the introduced cysteine as a ligand and retained its [3Fe-4S]+/0 cluster. Further, electrochemical characterization showed that the redox potential and pH behavior of the cluster were unaffected by the substitution of Tyr by Cys. Although Y13C FdI is functional in vivo it does differ significantly from native FdI in that it is extremely unstable in the reduced state possibly due to increased solvent exposure of the [3Fe-4S]0 cluster. Surprisingly, the x-ray structure showed that the introduced cysteine was modified to become a persulfide. This modification may have occurred in vivo via the action of NifS, which is known to be expressed under the growth conditions used. It is interesting to note that neither of the two free cysteines present in FdI was modified. Thus, if NifS is involved in modifying the introduced cysteine there must be specificity to the reaction.
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Affiliation(s)
- M A Kemper
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, USA
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Calderoni F, Demartin F, Iapalucci MC, Laschi F, Longoni G, Zanello P. Synthesis and Chemical and Electrochemical Characterization of Fe-S Carbonyl Clusters. X-ray Crystal Structures of [N(PPh(3))(2)](2)[Fe(5)S(2)(CO)(14)] and [N(PPh(3))(2)](2)[Fe(6)S(6)(CO)(12)]. Inorg Chem 1996; 35:898-905. [PMID: 11666263 DOI: 10.1021/ic950482t] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A reinvestigation of the redox behavior of the [Fe(3)(&mgr;(3)-S)(CO)(9)](2)(-) dianion led to the isolation and characterization of the new [Fe(5)S(2)(CO)(14)](2)(-), as well as the known [Fe(6)S(6)(CO)(12)](2)(-) dianion. As a corollary, new syntheses of the [Fe(3)S(CO)(9)](2)(-) dianion are also reported. The [Fe(5)S(2)(CO)(14)](2)(-) dianion has been obtained by oxidative condensation of [Fe(3)S(CO)(9)](2)(-) induced by tropylium and Ag(I) salts or SCl(2), or more straightforwardly through the reaction of [Fe(4)(CO)(13)](2)(-) with SCl(2). The [Fe(6)S(6)(CO)(12)](2)(-) dianion has been isolated as a byproduct of the synthesis of [Fe(3)S(CO)(9)](2)(-) and [Fe(5)S(2)(CO)(14)](2)(-) or by reaction of [Fe(4)(CO)(13)](2)(-) with elemental sulfur. The structures of [N(PPh(3))(2)](2)[Fe(5)S(2)(CO)(14)] and [N(PPh(3))(2)](2)[Fe(6)S(6)(CO)(12)] were determined by single-crystal X-ray diffraction analyses. Crystal data: for [N(PPh(3))(2)](2)[Fe(5)S(2)(CO)(14)], monoclinic, space group P2(1)/c (No. 14), a = 24.060(5), b = 14.355(6), c = 23.898(13) Å, beta = 90.42(3) degrees, Z = 4; for [N(PPh(3))(2)](2)[Fe(6)S(6)(CO)(12)], monoclinic, space group C2/c (No. 15), a = 34.424(4), b = 14.081(2), c = 19.674(2) Å, beta = 115.72(1) degrees, Z = 4. The new [Fe(5)S(2)(CO)(14)](2)(-) dianion shows a "bow tie" arrangement of the five metal atoms. The two Fe(3) triangles sharing the central Fe atom are not coplanar and show a dihedral angle of 55.08(3) degrees. Each Fe(3) moiety is capped by a triply bridging sulfide ligand. The 14 carbonyl groups are all terminal; two are bonded to the unique central atom and three to each peripheral iron atom. Protonation of the [Fe(5)S(2)(CO)(14)](2)(-) dianion gives reversibly rise to the corresponding [HFe(5)S(2)(CO)(14)](-) monohydride derivative, which shows an (1)H-NMR signal at delta -21.7 ppm. Its further protonation results in decomposition to mixtures of Fe(2)S(2)(CO)(6) and Fe(3)S(2)(CO)(9), rather than formation of the expected H(2)Fe(5)S(2)(CO)(14) dihydride. Exhaustive reduction of [Fe(5)S(2)(CO)(14)](2)(-) with sodium diphenyl ketyl progressively leads to fragmentation into [Fe(3)S(CO)(9)](2)(-) and [Fe(CO)(4)](2)(-), whereas electrochemical, as well as chemical oxidation with silver or tropylium tetrafluoroborate, in dichloromethane, generates the corresponding [Fe(5)S(2)(CO)(14)](-) radical anion which exhibits an ESR signal at g = 2.067 at 200 K. The electrochemical studies also indicated the existence of a subsequent one-electron anodic oxidation which possesses features of chemical reversibility in dichloromethane but not in acetonitrile solution. A reexamination of the electrochemical behavior of the [Fe(3)S(CO)(9)](2)(-) dianion coupled with ESR monitoring enabled the spectroscopic characterization of the [Fe(3)S(CO)(9)](-) radical monoanion and demonstrated its direct involvement in the generation of the [Fe(5)S(2)(CO)(14)](n)()(-) (n = 0, 1, 2) system.
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Affiliation(s)
- Francesca Calderoni
- Dipartimento di Chimica Fisica ed Inorganica, viale Risorgimento 4, 40136 Bologna, Italy, Dipartimento di Chimica Strutturale e Stereochimica Inorganica, via G. Venezian 21, 20133 Milano, Italy, and Dipartimento di Chimica, Pian dei Mantellini 44, 53100 Siena, Italy
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Affiliation(s)
- J A Kovacs
- Department of Chemistry, University of Washington, Seattle 98195, USA
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Sun WH, Wang HQ, Yang SY, Zhou QF, Yu KB. Syntheses and structures of (η5-C5H4CH3)MoFeCo(CO)8(μ3-S) and (η5-C5H4CH3)2Mo2Fe(CO)7(μ3-S): metal exchange with electrophilic addition—elimination via substitution. Polyhedron 1994. [DOI: 10.1016/s0277-5387(00)81651-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
Metalloenzymes effect a variety of important chemical transformations, often involving small molecule substrates or products such as molecular oxygen, hydrogen, nitrogen, and water. A diverse array of ions or metal clusters is observed at the active-site cores, but living systems use basic recurring structures that have been modified or tuned for specific purposes. Inorganic chemists are actively involved in the elucidation of the structure, spectroscopy, and mechanism of action of these biological catalysts, in part through a synthetic modeling approach involving biomimetic studies.
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Affiliation(s)
- K D Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218
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Bencini A, Midollini S. Some synthetic and theoretical aspects of the chemistry of polynuclear transition-metal complexes. Coord Chem Rev 1992. [DOI: 10.1016/0010-8545(92)80048-v] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Holm R. Trinuclear Cuboidal and Heterometallic Cubane-Type Iron–Sulfur Clusters: New Structural and Reactivity Themes in Chemistry and Biology. ADVANCES IN INORGANIC CHEMISTRY 1992. [DOI: 10.1016/s0898-8838(08)60061-6] [Citation(s) in RCA: 201] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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