1
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Zhu PK, Zeng MY, Lin YH, Tang Y, He TY, Zheng YS, Chen LY. Variability in Leaf Color Induced by Chlorophyll Deficiency: Transcriptional Changes in Bamboo Leaves. Curr Issues Mol Biol 2024; 46:1503-1515. [PMID: 38392215 PMCID: PMC10888276 DOI: 10.3390/cimb46020097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
The diversity of leaf characteristics, particularly leaf color, underscores a pivotal area of inquiry within plant science. The synthesis and functionality of chlorophyll, crucial for photosynthesis, largely dictate leaf coloration, with varying concentrations imparting different shades of green. Complex gene interactions regulate the synthesis and degradation of chlorophyll, and disruptions in these pathways can result in abnormal chlorophyll production, thereby affecting leaf pigmentation. This study focuses on Bambusa multiplex f. silverstripe, a natural variant distinguished by a spectrum of leaf colors, such as green, white, and green-white, attributed to genetic variations influencing gene expression. By examining the physiological and molecular mechanisms underlying chlorophyll anomalies and genetic factors in Silverstripe, this research sheds light on the intricate gene interactions and regulatory networks that contribute to leaf color diversity. The investigation includes the measurement of photosynthetic pigments and nutrient concentrations across different leaf color types, alongside transcriptomic analyses for identifying differentially expressed genes. The role of key genes in pathways such as ALA biosynthesis, chlorophyll synthesis, photosynthesis, and sugar metabolism is explored, offering critical insights for advancing research and plant breeding practices.
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Affiliation(s)
- Peng-Kai Zhu
- College of Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mei-Yin Zeng
- College of Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yu-Han Lin
- College of Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yu Tang
- College of Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tian-You He
- College of Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yu-Shan Zheng
- College of Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ling-Yan Chen
- College of Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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2
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Ha Y, Dille SA, Braun A, Colston K, Hedman B, Hodgson KO, Basu P, Solomon EI. S K-edge XAS of Cu II, Cu I, and Zn II oxidized Dithiolene complexes: Covalent contributions to structure and the Jahn-Teller effect. J Inorg Biochem 2022; 230:111752. [PMID: 35202982 PMCID: PMC9680909 DOI: 10.1016/j.jinorgbio.2022.111752] [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: 11/02/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 11/26/2022]
Abstract
Reduced dithiolene ligands are bound to high valent Mo centers in the active site of the oxotransferase family of enzymes. Related model complexes have been studied with great insight by Prof. Holm and his colleagues. This study focuses on the other limit of dithiolene chemistry: an investigation of the 2-electron oxidized dithiolene bound to low-valent late transition metal (TM) ions (ZnII, CuI, and CuII). The bonding descriptions of the oxidized dithiolene [N,N-dimethyl piperazine 2,3-dithione (Me2Dt0)] complexes are probed using S K-edge X-ray absorption spectroscopy (XAS) and the results are correlated to density functional theory (DFT) calculations. These experimentally supported calculations are then extended to explain the different geometric structures of the three complexes. The ZnII(Me2Dt0)2 complex has only ligand-ligand repulsion so it is stabilized at the D2d symmetry limit. The CuI(Me2Dt0)2 complex has additional weak backbonding thus distorts somewhat from D2d toward D2h symmetry. The CuII(Me2Dt0)2 complex has a strong σ donor bond that leads to both a large Jahn-Teller stabilization to D2h and an additional covalent contribution to the geometry. The combined strong stabilization results in the square planar, D2h structure. This study quantifies the competition between the ligand-ligand repulsion and the change in electronic structures in determining the final geometric structures of the oxidized dithiolene complexes, and provides quantitative insights into the Jahn-Teller stabilization energy and its origin.
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Affiliation(s)
- Yang Ha
- Department of Chemistry, Stanford University, Stanford, CA 94035, United States; Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, United States; Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, United States
| | - Sara A Dille
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N Blackford St, Indianapolis, IN 46202, United States
| | - Augustin Braun
- Department of Chemistry, Stanford University, Stanford, CA 94035, United States; Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, United States
| | - Kyle Colston
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N Blackford St, Indianapolis, IN 46202, United States
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, United States
| | - Keith O Hodgson
- Department of Chemistry, Stanford University, Stanford, CA 94035, United States; Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, United States
| | - Partha Basu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N Blackford St, Indianapolis, IN 46202, United States
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, CA 94035, United States; Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, United States.
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3
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Zhang Y, Duan W, Wang Q, Zheng L, Wang J, Chen J, Sun T. Covalency between the uranyl ion and dithiophosphinate by sulfur K-edge X-ray absorption spectroscopy and density functional theory. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:11-20. [PMID: 34985418 PMCID: PMC8733989 DOI: 10.1107/s160057752101198x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/10/2021] [Indexed: 06/14/2023]
Abstract
The dithiophosphinic acids (HS2PR2) have been used for the selective separation of trivalent actinides (AnIII) from lanthanides (LnIII) over the past decades. The substituents on the dithiophosphinic acids dramatically impact the separation performance, but the mechanism is still open for debate. In this work, two dithiophosphinic acids with significantly different AnIII/LnIII separation performance, i.e. diphenyl dithiophosphinic acid (HS2PPh2) and bis(ortho-trifluoromethylphenyl) dithiophosphinic acid [HS2P(o-CF3C6H4)2], are employed to understand the substituent effect on the bonding covalency between the S2PR2- anions (R = Ph and o-CF3C6H4) and the uranyl ion by sulfur K-edge X-ray absorption spectroscopy (XAS) in combination with density functional theory calculations. The two UO2(S2PR2)(EtOH) complexes display similar XAS spectra, in which the first pre-edge feature with an intensity of 0.16 is entirely attributed to the transitions from S 1s orbitals to the unoccupied molecular orbitals due to the mixing between U 5f and S 3p orbitals. The Mulliken population analysis indicates that the amount of \% S 3p character in these orbitals is essentially identical for the UO2(S2PPh2)2(EtOH) and UO2[S2P(o-CF3C6H4)2]2(EtOH) complexes, which is lower than that in the U 6d-based orbitals. The essentially identical covalency in U-S bonds for the two UO2(S2PR2)2(EtOH) complexes are contradictory to the significantly different AnIII/LnIII separation performance of the two dithiophosphinic acids, thus the covalency seems to be unable to account for substituent effects in the AnIII/LnIII separation by the dithiophosphinic acids. The results in this work provide valuable insight into the understanding of the mechanism in the AnIII/LnIII separation by the dithiophosphinic acids.
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Affiliation(s)
- Yusheng Zhang
- Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing 100084, People's Republic of China
| | - Wuhua Duan
- Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing 100084, People's Republic of China
| | - Qiang Wang
- Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing 100084, People's Republic of China
| | - Lei Zheng
- Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Jianchen Wang
- Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing 100084, People's Republic of China
| | - Jing Chen
- Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing 100084, People's Republic of China
| | - Taoxiang Sun
- Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing 100084, People's Republic of China
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4
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Gilep A, Kuzikov A, Sushko T, Grabovec I, Masamrekh R, Sigolaeva LV, Pergushov DV, Schacher FH, Strushkevich N, Shumyantseva VV. Electrochemical characterization of mutant forms of rubredoxin B from Mycobacterium tuberculosis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1870:140734. [PMID: 34662730 DOI: 10.1016/j.bbapap.2021.140734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/09/2021] [Accepted: 10/12/2021] [Indexed: 12/01/2022]
Abstract
Electron transfer in metalloproteins is a driving force for many biological processes and widely distributed in nature. Rubredoxin B (RubB) from Mycobacterium tuberculosis is a first example among [1Fe-0S] proteins that support catalytic activity of terminal sterol-monooxygenases enabling its application in metabolic engineering. To explore the tolerance of RubB to the specific amino acid changes we evaluated the effect of surface mutations on its electrochemical properties. Based on the RubB fold we also designed the mutant with a putative additional site for protein-protein interactions to further evaluate electron transfer and electrochemical properties. The investigation of redox properties of mutant variants of RubB was done using screen-printed graphite electrodes (SPEs) modified with stable dispersion of multi-walled carbon nanotubes (MWCNTs). The redox potentials (midpoint potentials, E0Ꞌ) of mutants did not significantly differ from the wild type protein and vary in the range of -264 to -231 mV vs. Ag/AgCl electrode. However, all mutations affect electron transfer rate between the protein and electrode. Notably, the modulation of the protein-protein interactions was observed for the insertion mutant suggesting the possibility of tailoring of rubredoxin for the selected redox-partner. Overall, RubB is tolerant to the significant modifications in its structure enabling rational engineering of novel redox proteins.
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Affiliation(s)
- Andrei Gilep
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus; Institute of Biomedical Chemistry, Moscow, Russia
| | - Alexey Kuzikov
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Irina Grabovec
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Rami Masamrekh
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | - Larisa V Sigolaeva
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Dmitry V Pergushov
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Felix H Schacher
- Institute of Organic Chemistry and Macromolecular Chemistry (IOMC), Friedrich-Schiller-University Jena, D-07743 Jena, Germany; Jena Center for Soft Matter (JCSM), Friedrich-Schiller-University Jena, D-07743 Jena, Germany; Center for Energy and Environmental Chemistry (CEEC), Friedrich-Schiller-University Jena, D-07743 Jena, Germany
| | | | - Victoria V Shumyantseva
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia.
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5
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Henthorn J, Arias RJ, Koroidov S, Kroll T, Sokaras D, Bergmann U, Rees DC, DeBeer S. Localized Electronic Structure of Nitrogenase FeMoco Revealed by Selenium K-Edge High Resolution X-ray Absorption Spectroscopy. J Am Chem Soc 2019; 141:13676-13688. [PMID: 31356071 PMCID: PMC6716209 DOI: 10.1021/jacs.9b06988] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Indexed: 11/28/2022]
Abstract
The size and complexity of Mo-dependent nitrogenase, a multicomponent enzyme capable of reducing dinitrogen to ammonia, have made a detailed understanding of the FeMo cofactor (FeMoco) active site electronic structure an ongoing challenge. Selective substitution of sulfur by selenium in FeMoco affords a unique probe wherein local Fe-Se interactions can be directly interrogated via high-energy resolution fluorescence detected X-ray absorption spectroscopic (HERFD XAS) and extended X-ray absorption fine structure (EXAFS) studies. These studies reveal a significant asymmetry in the electronic distribution of the FeMoco, suggesting a more localized electronic structure picture than is typically assumed for iron-sulfur clusters. Supported by experimental small molecule model data in combination with time dependent density functional theory (TDDFT) calculations, the HERFD XAS data is consistent with an assignment of Fe2/Fe6 as an antiferromagnetically coupled diferric pair. HERFD XAS and EXAFS have also been applied to Se-substituted CO-inhibited MoFe protein, demonstrating the ability of these methods to reveal electronic and structural changes that occur upon substrate binding. These results emphasize the utility of Se HERFD XAS and EXAFS for selectively probing the local electronic and geometric structure of FeMoco.
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Affiliation(s)
- Justin
T. Henthorn
- Max
Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der
Ruhr, Germany
| | - Renee J. Arias
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Sergey Koroidov
- PULSE
Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Thomas Kroll
- Stanford
Synchrotron Radiation Lightsource, SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Dimosthenis Sokaras
- Stanford
Synchrotron Radiation Lightsource, SLAC
National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Uwe Bergmann
- PULSE
Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Douglas C. Rees
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
- Howard
Hughes Medical Institute, California Institute
of Technology, Pasadena, California 91125, United States
| | - Serena DeBeer
- Max
Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der
Ruhr, Germany
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6
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Xia Q, Huang B, Yuan X, Wang H, Wu Z, Jiang L, Xiong T, Zhang J, Zeng G, Wang H. Modified stannous sulfide nanoparticles with metal-organic framework: Toward efficient and enhanced photocatalytic reduction of chromium (VI) under visible light. J Colloid Interface Sci 2018; 530:481-492. [DOI: 10.1016/j.jcis.2018.05.015] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/07/2018] [Accepted: 05/08/2018] [Indexed: 01/10/2023]
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7
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Maiti BK, Almeida RM, Moura I, Moura JJ. Rubredoxins derivatives: Simple sulphur-rich coordination metal sites and its relevance for biology and chemistry. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Yen TH, He ZC, Lee GH, Tseng MC, Shen YH, Tseng TW, Liaw WF, Chiang MH. Reduced thione ligation is preferred over neutral phosphine ligation in diiron biomimics regarding electronic functionality: a spectroscopic and computational investigation. Chem Commun (Camb) 2017; 53:332-335. [DOI: 10.1039/c6cc08042a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Sulfur means superiority: effective electronic communication and buffering by sulfur ligation.
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Affiliation(s)
- Tao-Hung Yen
- Institute of Chemistry
- Academia Sinica
- Taipei 115
- Taiwan
- Molecular Science Technology Program
| | - Zong-Cheng He
- Department of Chemical Engineering and Biotechnology
- National Taipei University of Technology
- Taipei 106
- Taiwan
| | - Gene-Hsiang Lee
- Instrumentation Center
- National Taiwan University
- Taipei 106
- Taiwan
| | | | - Yu-Hsuan Shen
- Department of Chemistry
- National Taiwan University
- Taipei 106
- Taiwan
| | - Tien-Wen Tseng
- Department of Chemical Engineering and Biotechnology
- National Taipei University of Technology
- Taipei 106
- Taiwan
| | - Wen-Feng Liaw
- Department of Chemistry
- National Tsing Hua University
- Hsinchu 300
- Taiwan
| | - Ming-Hsi Chiang
- Institute of Chemistry
- Academia Sinica
- Taipei 115
- Taiwan
- Molecular Science Technology Program
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9
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Mono- and binuclear non-heme iron chemistry from a theoretical perspective. J Biol Inorg Chem 2016; 21:619-44. [DOI: 10.1007/s00775-016-1357-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/29/2016] [Indexed: 10/21/2022]
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10
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Olson AC, Keith JM, Batista ER, Boland KS, Daly SR, Kozimor SA, MacInnes MM, Martin RL, Scott BL. Using solution- and solid-state S K-edge X-ray absorption spectroscopy with density functional theory to evaluate M-S bonding for MS4(2-) (M = Cr, Mo, W) dianions. Dalton Trans 2015; 43:17283-95. [PMID: 25311904 DOI: 10.1039/c4dt02302a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we have evaluated relative changes in M-S electronic structure and orbital mixing in Group 6 MS4(2-) dianions using solid- and solution-phase S K-edge X-ray absorption spectroscopy (XAS; M = Mo, W), as well as density functional theory (DFT; M = Cr, Mo, W) and time-dependent density functional theory (TDDFT) calculations. To facilitate comparison with solution measurements (conducted in acetonitrile), theoretical models included gas-phase calculations as well as those that incorporated an acetonitrile dielectric, the latter of which provided better agreement with experiment. Two pre-edge features arising from S 1s → e* and t electron excitations were observed in the S K-edge XAS spectra and were reasonably assigned as (1)A1 → (1)T2 transitions. For MoS4(2-), both solution-phase pre-edge peak intensities were consistent with results from the solid-state spectra. For WS4(2-), solution- and solid-state pre-edge peak intensities for transitions involving e* were equivalent, while transitions involving the t orbitals were less intense in solution. Experimental and computational results have been presented in comparison to recent analyses of MO4(2-) dianions, which allowed M-S and M-O orbital mixing to be evaluated as the principle quantum number (n) for the metal valence d orbitals increased (3d, 4d, 5d). Overall, the M-E (E = O, S) analyses revealed distinct trends in orbital mixing. For example, as the Group 6 triad was descended, e* (π*) orbital mixing remained constant in the M-S bonds, but increased appreciably for M-O interactions. For the t orbitals (σ* + π*), mixing decreased slightly for M-S bonding and increased only slightly for the M-O interactions. These results suggested that the metal and ligand valence orbital energies and radial extensions delicately influenced the orbital compositions for isoelectronic ME4(2-) (E = O, S) dianions.
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Affiliation(s)
- Angela C Olson
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.
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11
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Maiti BK, Maia LB, Silveira CM, Todorovic S, Carreira C, Carepo MSP, Grazina R, Moura I, Pauleta SR, Moura JJG. Incorporation of molybdenum in rubredoxin: models for mononuclear molybdenum enzymes. J Biol Inorg Chem 2015; 20:821-9. [PMID: 25948393 DOI: 10.1007/s00775-015-1268-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 04/29/2015] [Indexed: 12/21/2022]
Abstract
Molybdenum is found in the active site of enzymes usually coordinated by one or two pyranopterin molecules. Here, we mimic an enzyme with a mononuclear molybdenum-bis pyranopterin center by incorporating molybdenum in rubredoxin. In the molybdenum-substituted rubredoxin, the metal ion is coordinated by four sulfurs from conserved cysteine residues of the apo-rubredoxin and two other exogenous ligands, oxygen and thiol, forming a Mo((VI))-(S-Cys)4(O)(X) complex, where X represents -OH or -SR. The rubredoxin molybdenum center is stabilized in a Mo(VI) oxidation state, but can be reduced to Mo(IV) via Mo(V) by dithionite, being a suitable model for the spectroscopic properties of resting and reduced forms of molybdenum-bis pyranopterin-containing enzymes. Preliminary experiments indicate that the molybdenum site built in rubredoxin can promote oxo transfer reactions, as exemplified with the oxidation of arsenite to arsenate.
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Affiliation(s)
- Biplab K Maiti
- UCIBIO, REQUIMTE, Departamento Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
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12
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 549] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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13
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Harris TV, Szilagyi RK. Iron-sulfur bond covalency from electronic structure calculations for classical iron-sulfur clusters. J Comput Chem 2014; 35:540-52. [PMID: 24458434 DOI: 10.1002/jcc.23518] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 11/11/2013] [Accepted: 12/04/2013] [Indexed: 11/06/2022]
Abstract
The covalent character of iron-sulfur bonds is a fundamental electronic structural feature for understanding the electronic and magnetic properties and the reactivity of biological and biomimetic iron-sulfur clusters. Conceptually, bond covalency obtained from X-ray absorption spectroscopy (XAS) can be directly related to orbital compositions from electronic structure calculations, providing a standard for evaluation of density functional theoretical methods. Typically, a combination of functional and basis set that optimally reproduces experimental bond covalency is chosen, but its dependence on the population analysis method is often neglected, despite its important role in deriving theoretical bond covalency. In this study of iron tetrathiolates, and classical [2Fe-2S] and [4Fe-4S] clusters with only thiolate ligands, we find that orbital compositions can vary significantly depending on whether they are derived from frontier orbitals, spin densities, or electron sharing indexes from "Átoms in Molecules" (ÁIM) theory. The benefits and limitations of Mulliken, Minimum Basis Set Mulliken, Natural, Coefficients-Squared, Hirshfeld, and AIM population analyses are described using ab initio wave function-based (QCISD) and experimental (S K-edge XAS) bond covalency. We find that the AIM theory coupled with a triple-ζ basis set and the hybrid functional B(5%HF)P86 gives the most reasonable electronic structure for the studied Fe-S clusters.
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Affiliation(s)
- Travis V Harris
- Department of Chemistry and Biochemistry, NAI Astrobiology Biogeocatalysis Research Center, Montana State University, Bozeman, Montana, 59717
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14
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Zheng P, Chou CC, Guo Y, Wang Y, Li H. Single Molecule Force Spectroscopy Reveals the Molecular Mechanical Anisotropy of the FeS4 Metal Center in Rubredoxin. J Am Chem Soc 2013; 135:17783-92. [DOI: 10.1021/ja406695g] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Peng Zheng
- Department
of Chemistry, University of British Columbia Vancouver, British Columbia V6T 1Z1, Canada
| | - Chih-Chung Chou
- Department
of Chemistry, University of British Columbia Vancouver, British Columbia V6T 1Z1, Canada
| | - Ying Guo
- Department
of Chemistry, University of British Columbia Vancouver, British Columbia V6T 1Z1, Canada
| | - Yanyan Wang
- Department
of Chemistry, University of British Columbia Vancouver, British Columbia V6T 1Z1, Canada
- State
Key Laboratory of Precision Measurements Technology and Instruments,
School of Precision Instrument and Opto-Electronics Engineering, Tianjin University, Tianjin, 30072 P. R. China
| | - Hongbin Li
- Department
of Chemistry, University of British Columbia Vancouver, British Columbia V6T 1Z1, Canada
- State
Key Laboratory of Precision Measurements Technology and Instruments,
School of Precision Instrument and Opto-Electronics Engineering, Tianjin University, Tianjin, 30072 P. R. China
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15
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Hadt RG, Sun N, Marshall NM, Hodgson KO, Hedman B, Lu Y, Solomon EI. Spectroscopic and DFT studies of second-sphere variants of the type 1 copper site in azurin: covalent and nonlocal electrostatic contributions to reduction potentials. J Am Chem Soc 2012; 134:16701-16. [PMID: 22985400 PMCID: PMC3506006 DOI: 10.1021/ja306438n] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The reduction potentials (E(0)) of type 1 (T1) or blue copper (BC) sites in proteins and enzymes with identical first coordination spheres around the redox active copper ion can vary by ~400 mV. Here, we use a combination of low-temperature electronic absorption and magnetic circular dichroism, electron paramagnetic resonance, resonance Raman, and S K-edge X-ray absorption spectroscopies to investigate a series of second-sphere variants--F114P, N47S, and F114N in Pseudomonas aeruginosa azurin--which modulate hydrogen bonding to and protein-derived dipoles nearby the Cu-S(Cys) bond. Density functional theory calculations correlated to the experimental data allow for the fractionation of the contributions to tuning E(0) into covalent and nonlocal electrostatic components. These are found to be significant, comparable in magnitude, and additive for active H-bonds, while passive H-bonds are mostly nonlocal electrostatic in nature. For dipoles, these terms can be additive to or oppose one another. This study provides a methodology for uncoupling covalency from nonlocal electrostatics, which, when coupled to X-ray crystallographic data, distinguishes specific local interactions from more long-range protein/active interactions, while affording further insight into the second-sphere mechanisms available to the protein to tune the E(0) of electron-transfer sites in biology.
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Affiliation(s)
- Ryan G. Hadt
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Ning Sun
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Nicholas M. Marshall
- Department of Chemistry, University of Illinois, Urbana-Champaign, Illinois 61801
| | - Keith O. Hodgson
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Yi Lu
- Department of Chemistry, University of Illinois, Urbana-Champaign, Illinois 61801
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
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16
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Daly SR, Keith JM, Batista ER, Boland KS, Clark DL, Kozimor SA, Martin RL. Sulfur K-edge X-ray Absorption Spectroscopy and Time-Dependent Density Functional Theory of Dithiophosphinate Extractants: Minor Actinide Selectivity and Electronic Structure Correlations. J Am Chem Soc 2012; 134:14408-22. [DOI: 10.1021/ja303999q] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Scott R. Daly
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
| | - Jason M. Keith
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
| | - Enrique R. Batista
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
| | - Kevin S. Boland
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
| | - David L. Clark
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
| | - Stosh A. Kozimor
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
| | - Richard L. Martin
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
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17
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Zheng P, Takayama SIJ, Mauk AG, Li H. Hydrogen Bond Strength Modulates the Mechanical Strength of Ferric-Thiolate Bonds in Rubredoxin. J Am Chem Soc 2012; 134:4124-31. [DOI: 10.1021/ja2078812] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peng Zheng
- Department of Chemistry, University of British Columbia, Vancouver,
BC V6T 1Z1 Canada
| | - Shin-ichi J. Takayama
- Department of Biochemistry
and Molecular Biology and the Center for Blood Research, University of British Columbia, Vancouver,
BC V6T 1Z3 Canada
| | - A. Grant Mauk
- Department of Biochemistry
and Molecular Biology and the Center for Blood Research, University of British Columbia, Vancouver,
BC V6T 1Z3 Canada
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver,
BC V6T 1Z1 Canada
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18
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Dey A, Peng Y, Broderick WE, Hedman B, Hodgson KO, Broderick JB, Solomon EI. S K-edge XAS and DFT calculations on SAM dependent pyruvate formate-lyase activating enzyme: nature of interaction between the Fe4S4 cluster and SAM and its role in reactivity. J Am Chem Soc 2011; 133:18656-62. [PMID: 21992686 DOI: 10.1021/ja203780t] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
S K-edge X-ray absorption spectroscopy on the resting oxidized and the S-adenosyl-l-methionine (SAM) bound forms of pyruvate formate-lyase activating enzyme are reported. The data show an increase in pre-edge intensity, which is due to additional contributions from sulfide and thiolate of the Fe(4)S(4) cluster into the C-S σ* orbital. This experimentally demonstrates that there is a backbonding interaction between the Fe(4)S(4) cluster and C-S σ* orbitals of SAM in this inner sphere complex. DFT calculations that reproduce the data indicate that this backbonding is enhanced in the reduced form and that this configurational interaction between the donor and acceptor orbitals facilitates the electron transfer from the cluster to the SAM, which otherwise has a large outer sphere electron transfer barrier. The energy of the reductive cleavage of the C-S bond is sensitive to the dielectric of the protein in the immediate vicinity of the site as a high dielectric stabilizes the more charge separated reactant increasing the reaction barrier. This may provide a mechanism for generation of the 5'-deoxyadenosyl radical upon substrate binding.
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Affiliation(s)
- Abhishek Dey
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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