1
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Mouli MSSV, Mishra AK. Synthesis, characterization and photophysical studies of the flavopeptide conjugates as model for the covalently linked flavoenzymes. J CHEM SCI 2022. [DOI: 10.1007/s12039-022-02050-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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2
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Taniguchi S, Chosrowjan H, Tamaoki H, Nishina Y, Nueangaudom A, Tanaka F. Ultrafast photoinduced electron transfer in o-aminobenzoate – d-Amino acid oxidase complex. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2021.113448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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3
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Effects of protein association on the rates of photoinduced electron transfer from tryptophan residues to excited flavin in medium-chain acyl-Co A dehydrogenase. Molecular dynamics simulation. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2020.113039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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4
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Nunthaboot N, Taniguchi S, Chosrowjan H, Tanaka F. Equivalence between inverted regions of the energy gap law and inverted regions of donor–acceptor distances in photoinduced electron transfer processes in flavoproteins. RSC Adv 2021; 11:8821-8832. [PMID: 35423406 PMCID: PMC8695315 DOI: 10.1039/d0ra09716k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/04/2021] [Indexed: 11/26/2022] Open
Abstract
In the present work, we discuss about the relationship between the energy gap law and extended Dutton law in flavoproteins. The extend Dutton law is defined herein as the dependence of logarithmic rates (ln Rate) of photoinduced electron transfer (ET) from aromatic amino acids to excited isoalloxazine (Iso*) on donor–acceptor distances (Rcs). Both functions of ln Rate vs. negative values of the standard free energy gap and ln Rate vs. Rc display a parabolic behavior, when the ET rates are ultrafast. The negative values of the standard free energy gap at peaks of ln Rate [Xm(ES)] were obtained for FMN-binding protein, wild-type pyranose 2-oxidase, T169S (Thr169 is replaced by Ser) pyranose 2-oxidase, and medium-chain acyl-CoA dehydrogenase. The values of Rc at peaks of ln Rate [Xm(Rc)] were also obtained for these flavoproteins. The negative values of the standard free energy gap decreased with approximate linear functions of Rc. The negative values of standard free energy gap [Xm(ESRc)] at Rc = Xm(Rc) were evaluated using the linear functions of the negative standard free energy gap with Rc. The values of Xm(ESRc) were mostly in very good agreement with the values of Xm(ES). This implies that the energy gap law and the extend Dutton law are equivalent. Xm(ES) values in ET donors displaying the linear extend Dutton law with Rc were obtained by energy gap law, and then Xm(Rc) values were evaluated with the negative standard free energy gap. Thus, the obtained Xm(Rc) values were much smaller than the Rc range obtained by the method of molecular dynamics simulation. This suggests that ET processes with linear profiles of the extend Dutton law could be parabolic when Rc becomes much shorter than the Rc range obtained by the method of molecular dynamics simulation. Relationship between EXDL and SEGL.![]()
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Affiliation(s)
- Nadtanet Nunthaboot
- Department of Chemistry and Center of Excellence for Innovation in Chemistry
- Faculty of Science
- Mahasarakham University
- Thailand
| | - Seiji Taniguchi
- Division of Laser Biochemistry
- Institute for Laser Technology
- Osaka 550-0004
- Japan
| | - Haik Chosrowjan
- Division of Laser Biochemistry
- Institute for Laser Technology
- Osaka 550-0004
- Japan
| | - Fumio Tanaka
- Division of Laser Biochemistry
- Institute for Laser Technology
- Osaka 550-0004
- Japan
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5
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Su D, Smitherman C, Gadda G. A Metastable Photoinduced Protein–Flavin Adduct in Choline Oxidase, an Enzyme Not Involved in Light-Dependent Processes. J Phys Chem B 2020; 124:3936-3943. [DOI: 10.1021/acs.jpcb.0c02633] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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6
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Taniguchi S, Chosrowjan H, Ito S, Miyasaka H, Katane M, Homma H, Tanaka F, Nueangaudom A, Lugsanangarm K, Kokpol S. Comparative studies on picosecond-resolved fluorescence of d-amino acid oxidases from human with one from porcine kidney. Photoinduced electron transfer from aromatic amino acids to the excited flavin. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2019; 198:111546. [PMID: 31351309 DOI: 10.1016/j.jphotobiol.2019.111546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 06/20/2019] [Accepted: 06/28/2019] [Indexed: 10/26/2022]
Abstract
Fluorescence dynamics of human d-amino acid oxidase (hDAAO) and its five inhibitors have been studied in the picoseconds time domain, and compared with one in d-amino acid oxidase from porcine kidney (pkDAAO) reported. The fluorescence lifetimes were identified as 47 ps in the dimer, 235 ps in the monomer, which are compared with those of pkDAAO (45 ps-185 ps). The fluorescence lifetimes of the hDAAO did not change upon the inhibitor bindings despite of modifications in the absorption spectra. This indicates that the lifetimes of the complexes are too short to detect with the picosecond lifetime instrument. Numbers of the aromatic amino acids are similar between the both DAAOs. The fluorescence lifetimes of hDAAO were analysed with an ET theory using the crystal structure. The difference in the lifetimes of the dimer and monomer was well described in terms of difference in the electron affinity of the excited isoalloxazine (Iso*) between the two forms of the protein, though it is not known whether the structure of the monomer is different from the dimer. Three fastest ET donors were Tyr314, Trp52 and Tyr224 in the dimer, while Tyr314, Tyr224 and Tyr55 in the monomer, which are compared to those in pkDAAO, Tyr314, Tyr224 and Tyr228 in the dimer, and Tyr224, Tyr314 and Tyr228 in the monomer. The ET rate from Trp55 in hDAAO dimer was much faster compared to the rate in pkDAAO dimer. A rise component with negative pre-exponential factor was not observed in hDAAO, which are found in pkDAAO.
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Affiliation(s)
- Seiji Taniguchi
- Division of Laser Biochemistry, Institute for Laser Technology, Utsubo-Honmachi, 1-8-4, Nishiku, Osaka 550-0004, Japan.
| | - Haik Chosrowjan
- Division of Laser Biochemistry, Institute for Laser Technology, Utsubo-Honmachi, 1-8-4, Nishiku, Osaka 550-0004, Japan
| | - Shoji Ito
- Department of Chemistry, School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Hiroshi Miyasaka
- Department of Chemistry, School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Masumi Katane
- Laboratory of Biomolecular Science, Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Hiroshi Homma
- Laboratory of Biomolecular Science, Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Fumio Tanaka
- Division of Laser Biochemistry, Institute for Laser Technology, Utsubo-Honmachi, 1-8-4, Nishiku, Osaka 550-0004, Japan; Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10,330, Thailand.
| | - Arthit Nueangaudom
- Program of General Science, Faculty of Science and Technology, Thepsatri Rajabhat University, Lopburi 15,000, Thailand
| | - Kiattisak Lugsanangarm
- Program of Chemistry, Faculty of Science, Bansomdejchaopraya Rajabhat University, Bangkok 10,600, Thailand
| | - Sirirat Kokpol
- Department of Chemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10,330, Thailand
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7
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Bialas C, Barnard DT, Auman DB, McBride RA, Jarocha LE, Hore PJ, Dutton PL, Stanley RJ, Moser CC. Ultrafast flavin/tryptophan radical pair kinetics in a magnetically sensitive artificial protein. Phys Chem Chem Phys 2019; 21:13453-13461. [PMID: 31187821 PMCID: PMC7301759 DOI: 10.1039/c9cp01916b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Radical pair formation and decay are implicated in a wide range of biological processes including avian magnetoreception. However, studying such biological radical pairs is complicated by both the complexity and relative fragility of natural systems. To resolve open questions about how natural flavin-amino acid radical pair systems are engineered, and to create new systems with novel properties, we developed a stable and highly adaptable de novo artificial protein system. These protein maquettes are designed with intentional simplicity and transparency to tolerate aggressive manipulations that are impractical or impossible in natural proteins. Here we characterize the ultrafast dynamics of a series of maquettes with differing electron-transfer distance between a covalently ligated flavin and a tryptophan in an environment free of other potential radical centers. We resolve the spectral signatures of the cysteine-ligated flavin singlet and triplet states and reveal the picosecond formation and recombination of singlet-born radical pairs. Magnetic field-sensitive triplet-born radical pair formation and recombination occurs at longer timescales. These results suggest that both triplet- and singlet-born radical pairs could be exploited as biological magnetic sensors.
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Affiliation(s)
- Chris Bialas
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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8
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Kundu M, He TF, Lu Y, Wang L, Zhong D. Short-Range Electron Transfer in Reduced Flavodoxin: Ultrafast Nonequilibrium Dynamics Coupled with Protein Fluctuations. J Phys Chem Lett 2018; 9:2782-2790. [PMID: 29722985 PMCID: PMC7304529 DOI: 10.1021/acs.jpclett.8b00882] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Short-range electron transfer (ET) in proteins is an ultrafast process on the similar time scales as local protein-solvent fluctuation, and thus the two dynamics are coupled. Here we use semiquinone flavodoxin and systematically characterized the photoinduced redox cycle with 11 mutations of different aromatic electron donors (tryptophan and tyrosine) and local residues to change redox properties. We observed the forward and backward ET dynamics in a few picoseconds, strongly following a stretched behavior resulting from a coupling between local environment relaxations and these ET processes. We further observed the hot vibrational-state formation through charge recombination and the subsequent cooling dynamics also in a few picoseconds. Combined with the ET studies in oxidized flavodoxin, these results coherently reveal the evolution of the ET dynamics from single to stretched exponential behaviors and thus elucidate critical time scales for the coupling. The observed hot vibration-state formation is robust and should be considered in all photoinduced back ET processes in flavoproteins.
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9
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Zanetti-Polzi L, Aschi M, Amadei A, Daidone I. Alternative Electron-Transfer Channels Ensure Ultrafast Deactivation of Light-Induced Excited States in Riboflavin Binding Protein. J Phys Chem Lett 2017; 8:3321-3327. [PMID: 28665138 DOI: 10.1021/acs.jpclett.7b01575] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Flavoproteins, containing flavin chromophores, are enzymes capable of transferring electrons at very high speeds. The ultrafast photoinduced electron-transfer (ET) kinetics of riboflavin binding protein to the excited riboflavin was studied by femtosecond spectroscopy and found to occur within a few hundred femtoseconds [ Zhong and Zewail, Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 11867-11872 ]. This ultrafast kinetics was attributed to the presence of two aromatic rings that could transfer the electron to riboflavin: the side chains of tryptophan 156 and tyrosine 75. However, the underlying ET mechanism remained unclear. Here, using a hybrid quantum mechanical-molecular dynamics approach, we perform ET dynamics simulations taking into account the motion of the protein and the solvent upon ET. This approach reveals that ET occurs via a major reaction channel involving tyrosine 75 (83%) and a minor one involving tryptophan 156 (17%). We also show that the protein environment is designed to ensure the fast quenching of the riboflavin excited state.
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Affiliation(s)
- Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences, University of L'Aquila , via Vetoio (Coppito 1), 67010 L'Aquila, Italy
| | - Massimiliano Aschi
- Department of Physical and Chemical Sciences, University of L'Aquila , via Vetoio (Coppito 1), 67010 L'Aquila, Italy
| | - Andrea Amadei
- Department of Chemical and Technological Sciences, University of Rome "Tor Vergata" , Via della Ricerca Scientifica, 00185 Rome, Italy
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila , via Vetoio (Coppito 1), 67010 L'Aquila, Italy
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10
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Lugsanangarm K, Nueangaudom A, Pianwanit S, Kokpol S, Nunthaboot N, Tanaka F, Taniguchi S, Chosrowjan H. Dynamics of the protein structure of T169S pyranose 2-oxidase in solution: Molecular dynamics simulation. Proteins 2017; 85:1913-1924. [DOI: 10.1002/prot.25345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 06/20/2017] [Accepted: 06/26/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Kiattisak Lugsanangarm
- Program of Chemistry, Faculty of Science and Technology; Bansomdejchaopraya Rajabhat University; Bangkok 10600 Thailand
| | - Arthit Nueangaudom
- Program of General Science, Faculty of Science and Technology; Thepsatri Rajabhat University; Lopburi 15000 Thailand
| | - Somsak Pianwanit
- Department of Chemistry, Faculty of Science; Chulalongkorn University; Bangkok 10330 Thailand
| | - Sirirat Kokpol
- Department of Chemistry, Faculty of Science; Chulalongkorn University; Bangkok 10330 Thailand
| | - Nadtanet Nunthaboot
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science; Mahasarakham University; Mahasarakham 44150 Thailand
| | - Fumio Tanaka
- Department of Chemistry, Faculty of Science; Chulalongkorn University; Bangkok 10330 Thailand
- Division of Laser Biochemistry; Institute for Laser Technology; Osaka 550-0004 Japan
| | - Seiji Taniguchi
- Division of Laser Biochemistry; Institute for Laser Technology; Osaka 550-0004 Japan
| | - Haik Chosrowjan
- Division of Laser Biochemistry; Institute for Laser Technology; Osaka 550-0004 Japan
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11
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Nunthaboot N, Lugsanangarm K, Nueangaudom A, Pianwanit S, Kokpol S, Tanaka F, Taniguchi S, Chosrowjan H, Nakanishi T, Kitamura M. Photoinduced electron transfer from aromatic amino acids to the excited isoalloxazine in single mutated flavin mononucleotide binding proteins: Effect of the dimer formation on the rate and the electrostatic energy inside the proteins. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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12
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Valle L, Abatedaga I, Vieyra FEM, Bortolotti A, Cortez N, Borsarelli CD. Enhancement of photophysical and photosensitizing properties of flavin adenine dinucleotide by mutagenesis of the C-terminal extension of a bacterial flavodoxin reductase. Chemphyschem 2015; 16:872-83. [PMID: 25641205 DOI: 10.1002/cphc.201402774] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Indexed: 12/26/2022]
Abstract
The role of the mobile C-terminal extension present in Rhodobacter capsulatus ferredoxin-NADP(H) reductase (RcFPR) was evaluated using steady-state and dynamic spectroscopies for both intrinsic Trp and FAD in a series of mutants in the absence of NADP(H). Deletion of the six C-terminal amino acids beyond Ala266 was combined with the replacement A266Y to emulate the structure of plastidic reductases. Our results show that these modifications of the wild-type RcFPR produce subtle global conformational changes, but strongly reduce the local rigidity of the FAD-binding pocket, exposing the isoalloxazine ring to the solvent. Thus, the ultrafast charge-transfer quenching of (1) FAD* by the conserved Tyr66 residue was absent in the mutant series, producing enhancement of the excited singlet- and triplet-state properties of FAD. This work highlights the delicate balance of the specific interactions between FAD and the surrounding amino acids, and how the functionality and/or photostability of redox flavoproteins can be modified.
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Affiliation(s)
- Lorena Valle
- Centro de Investigaciones y Transferencia de Santiago del Estero (CITSE-CONICET), Universidad Nacional de Santiago del Estero, RN9 Km 1125. 4206, Santiago del Estero (Argentina)
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13
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Tanaka F, Lugsanangarm K, Nunthaboot N, Nueangaudom A, Pianwanit S, Kokpol S, Taniguchi S, Chosrowjan H. Classification of the mechanisms of photoinduced electron transfer from aromatic amino acids to the excited flavins in flavoproteins. Phys Chem Chem Phys 2015; 17:16813-25. [DOI: 10.1039/c5cp01432h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Emission wavelength-dependence of the relationship between logarithmic ET rate vs. donor–acceptor distance in pyranose 2-oxidase.
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Affiliation(s)
- Fumio Tanaka
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330
- Thailand
| | - Kiattisak Lugsanangarm
- Program of Science
- Faculty of Education
- Bansomdejchaopraya Rajabhat University
- Bangkok 10600
- Thailand
| | - Nadtanet Nunthaboot
- Department of Chemistry
- Faculty of Science
- Mahasarakham University
- Mahasarakham 44150
- Thailand
| | - Arthit Nueangaudom
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330
- Thailand
| | - Somsak Pianwanit
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330
- Thailand
| | - Sirirat Kokpol
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330
- Thailand
| | - Seiji Taniguchi
- Division of Laser Biochemistry
- Institute for Laser Technology
- Osaka 550-0004
- Japan
| | - Haik Chosrowjan
- Division of Laser Biochemistry
- Institute for Laser Technology
- Osaka 550-0004
- Japan
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14
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Photoinduced electron transfer modeling to simulate flavoprotein fluorescence decay. Methods Mol Biol 2014; 1076:337-55. [PMID: 24108633 DOI: 10.1007/978-1-62703-649-8_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A method of analysis is described on the photoinduced electron transfer (PET) from aromatic amino acids as tryptophans (Trp) and tyrosines (Tyr) to the excited isoalloxazine (Iso*) in FMN-binding proteins (FBP) from Desulfovibrio vulgaris (strain, Miyazaki F). Time-dependent geometrical factors as the donor-acceptor distances are determined by means of a molecular dynamics simulation (MDS) of the proteins. Fluorescence decays of the single mutated isoforms of FBP are used as experimental data. The electrostatic (ES) energy between the photoproducts and ionic groups in the proteins is introduced into the Kakitani and Mataga (KM) model, which is modeled for an electron transfer process in solution. The PET parameters contained in the KM rate are determined by means of a nonlinear least square method, according to the Marquardt algorithm. The agreement between the observed and calculated decays is quite good, but not optimal. Characteristics on PET in flavoproteins, obtained by the present method, are described. Possible improvements of the method are discussed.
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15
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Nunthaboot N, Lugsanangarm K, Nueangaudom A, Pianwanit S, Kokpol S, Tanaka F. Role of the electrostatic energy between the photo-products and ionic groups on the photoinduced electron transfer rates from aromatic amino acids to the excited flavin in five single-point substitution isoforms of the charged amino acid residue-13 in the FMN-binding protein. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.902534] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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16
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Nunthaboot N, Lugsanangarm K, Pianwanit S, Kokpol S, Tanaka F, Taniguchi S, Chosrowjan H, Nakanishi T, Kitamura M. Bell-shaped dependence of the rate of ultrafast photoinduced electron transfer from aromatic amino acids to the excited flavin on the donor–acceptor distance in FMN binding proteins. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2013.12.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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17
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Nueangaudom A, Lugsanangarm K, Pianwanit S, Kokpol S, Nunthaboot N, Tanaka F, Taniguchi S, Chosrowjan H. Theoretical analyses of the fluorescence lifetimes of the d-amino acid oxidase–benzoate complex dimer from porcine kidney: molecular dynamics simulation and photoinduced electron transfer. RSC Adv 2014. [DOI: 10.1039/c4ra05211k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The mechanism of photoinduced electron transfer from benzoate and aromatic amino acids to the excited isoalloxazine in the d-amino acid oxidase–benzoate complex dimer was studied using molecular dynamics simulation and an electron transfer theory.
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Affiliation(s)
- Arthit Nueangaudom
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330, Thailand
| | - Kiattisak Lugsanangarm
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330, Thailand
| | - Somsak Pianwanit
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330, Thailand
| | - Sirirat Kokpol
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330, Thailand
| | | | - Fumio Tanaka
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330, Thailand
- Division of Laser Biochemistry
| | - Seiji Taniguchi
- Division of Laser Biochemistry
- Institute for Laser Technology
- Osaka 550-0004, Japan
| | - Haik Chosrowjan
- Division of Laser Biochemistry
- Institute for Laser Technology
- Osaka 550-0004, Japan
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18
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Nueangaudom A, Lugsanangarm K, Pianwanit S, Kokpol S, Nunthaboot N, Tanaka F. Non-equivalent conformations ofd-amino acid oxidase dimer from porcine kidney between the two subunits. Molecular dynamics simulation and photoinduced electron transfer. Phys Chem Chem Phys 2014; 16:1930-44. [DOI: 10.1039/c3cp53826e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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He TF, Guo L, Guo X, Chang CW, Wang L, Zhong D. Femtosecond dynamics of short-range protein electron transfer in flavodoxin. Biochemistry 2013; 52:9120-8. [PMID: 24289221 PMCID: PMC3909472 DOI: 10.1021/bi401137u] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Intraprotein electron transfer (ET) in flavoproteins is important for understanding the correlation of their redox, configuration, and reactivity at the active site. Here, we used oxidized flavodoxin as a model system and report our complete characterization of a photoinduced redox cycle from the initial charge separation in 135-340 fs to subsequent charge recombination in 0.95-1.6 ps and to the final cooling relaxation of the product(s) in 2.5-4.3 ps. With 11 mutations at the active site, we observed that these ultrafast ET dynamics, much faster than active-site relaxation, mainly depend on the reduction potentials of the electron donors with minor changes caused by mutations, reflecting a highly localized ET reaction between the stacked donor and acceptor at a van der Waals distance and leading to a gas-phase type of bimolecular ET reaction confined in the active-site nanospace. Significantly, these ultrafast ET reactions ensure our direct observation of vibrationally excited reaction product(s), suggesting that the back ET barrier is effectively reduced because of the decrease in the total free energy in the Marcus inverted region, leading to the accelerated charge recombination. Such vibrationally coupled charge recombination should be a general feature of flavoproteins with similar configurations and interactions between the cofactor flavin and neighboring aromatic residues.
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Affiliation(s)
| | | | - Xunmin Guo
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Chih-Wei Chang
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Lijuan Wang
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Dongping Zhong
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210
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20
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Lugsanangarm K, Pianwanit S, Nueangaudom A, Kokpol S, Tanaka F, Nunthaboot N, Ogino K, Takagi R, Nakanishi T, Kitamura M, Taniguchi S, Chosrowjan H. Mechanism of photoinduced electron transfer from tyrosine to the excited flavin in the flavodoxin from Helicobacter pylori. A comparative study with the flavodoxin and flavin mononucleotide binding protein from Desulfovibrio vulgaris (Miyazaki F). J Photochem Photobiol A Chem 2013. [DOI: 10.1016/j.jphotochem.2013.06.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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21
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Taniguchi S, Chosrowjan H, Tanaka F, Nakanishi T, Sato S, Haruyama Y, Kitamura M. A Key Factor for Ultrafast Rates of Photoinduced Electron Transfer among Five Flavin Mononucleotide Binding Proteins: Effect of Negative, Positive, and Neutral Charges at Residue 13 on the Rate. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2013. [DOI: 10.1246/bcsj.20120231] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Seiji Taniguchi
- Division of Laser Biochemistry, Institute for Laser Technology
| | - Haik Chosrowjan
- Division of Laser Biochemistry, Institute for Laser Technology
| | - Fumio Tanaka
- Division of Laser Biochemistry, Institute for Laser Technology
- Department of Chemistry, Faculty of Science, Chulalongkorn University
| | - Takeshi Nakanishi
- Department of Applied Chemistry and Bioengineering, Graduate School of Engineering, Osaka City University
| | - Shuta Sato
- Department of Applied Chemistry and Bioengineering, Graduate School of Engineering, Osaka City University
| | - Yoshihiro Haruyama
- Department of Applied Chemistry and Bioengineering, Graduate School of Engineering, Osaka City University
| | - Masaya Kitamura
- Department of Applied Chemistry and Bioengineering, Graduate School of Engineering, Osaka City University
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22
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Nueangaudom A, Lugsanangarm K, Pianwanit S, Kokpol S, Nunthaboot N, Tanaka F. The mechanism of photoinduced electron transfer in the d-amino acid oxidase–benzoate complex from pig kidney: Electron transfer in the inverted region. J Photochem Photobiol A Chem 2012. [DOI: 10.1016/j.jphotochem.2012.09.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Taniguchi S, Chosrowjan H, Wongnate T, Sucharitakul J, Chaiyen P, Tanaka F. Ultrafast fluorescence dynamics of flavin adenine dinucleotide in pyranose 2-oxidases variants and their complexes with acetate: Conformational heterogeneity with different dielectric constants. J Photochem Photobiol A Chem 2012. [DOI: 10.1016/j.jphotochem.2012.06.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Chosrowjan H, Taniguchi S, Wongnate T, Sucharitakul J, Chaiyen P, Tanaka F. Conformational heterogeneity in pyranose 2-oxidase from Trametes multicolor revealed by ultrafast fluorescence dynamics. J Photochem Photobiol A Chem 2012. [DOI: 10.1016/j.jphotochem.2011.11.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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25
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Nueangaudom A, Lugsanangarm K, Pianwanit S, Kokpol S, Nunthaboot N, Tanaka F. Structural basis for the temperature-induced transition of d-amino acid oxidase from pig kidney revealed by molecular dynamic simulation and photo-induced electron transfer. Phys Chem Chem Phys 2012; 14:2567-78. [DOI: 10.1039/c2cp23001a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Lugsanangarm K, Pianwanit S, Kokpol S, Tanaka F. Homology modelling and molecular dynamics simulations of wild type and mutated flavodoxins fromDesulfovibrio vulgaris(Miyazaki F): insight into FMN–apoprotein interactions. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2011.586348] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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27
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Theoretical analyses of photoinduced electron transfer in medium chain acyl-CoA dehydrogenase: Electron transfer in the normal region. J Photochem Photobiol A Chem 2011. [DOI: 10.1016/j.jphotochem.2011.09.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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28
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Lugsanangarm K, Pianwanit S, Kokpol S, Tanaka F, Chosrowjan H, Taniguchi S, Mataga N. Photoinduced electron transfer in wild type and mutated flavodoxin from Desulfovibrio vulgaris, strain Miyazaki F.: Energy gap law. J Photochem Photobiol A Chem 2011. [DOI: 10.1016/j.jphotochem.2011.01.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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29
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Lugsanangarm K, Pianwanit S, Kokpol S, Tanaka F, Chosrowjan H, Taniguchi S, Mataga N. Analysis of photoinduced electron transfer in flavodoxin. J Photochem Photobiol A Chem 2011. [DOI: 10.1016/j.jphotochem.2010.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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30
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Nunthaboot N, Pianwanit S, Kokpol S, Tanaka F. Simultaneous analyses of photoinduced electron transfer in the wild type and four single substitution isomers of the FMN binding protein from Desulfovibrio vulgaris, Miyazaki F. Phys Chem Chem Phys 2011; 13:6085-97. [DOI: 10.1039/c0cp02634d] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Simultaneous analysis of photoinduced electron transfer in wild type and mutated AppAs. J Photochem Photobiol A Chem 2010. [DOI: 10.1016/j.jphotochem.2009.10.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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32
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Nunthaboot N, Tanaka F, Kokpol S, Chosrowjan H, Taniguchi S, Mataga N. Simulation of ultrafast non-exponential fluorescence decay induced by electron transfer in FMN binding protein. J Photochem Photobiol A Chem 2009. [DOI: 10.1016/j.jphotochem.2008.10.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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34
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Nunthaboot N, Tanaka F, Kokpol S, Chosrowjan H, Taniguchi S, Mataga N. Quantum Mechanical Study of Photoinduced Charge Transfer in FMN Binding Protein. J Phys Chem B 2008; 112:15837-43. [DOI: 10.1021/jp806272v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nadtanet Nunthaboot
- Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham 44150, Thailand, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand, and Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004,
| | - Fumio Tanaka
- Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham 44150, Thailand, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand, and Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004,
| | - Sirirat Kokpol
- Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham 44150, Thailand, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand, and Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004,
| | - Haik Chosrowjan
- Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham 44150, Thailand, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand, and Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004,
| | - Seiji Taniguchi
- Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham 44150, Thailand, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand, and Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004,
| | - Noboru Mataga
- Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham 44150, Thailand, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand, and Institute for Laser Technology, Utsubo-Hommachi 1-8-4, Nishiku, Osaka 550-0004,
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35
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Nunthaboot N, Tanaka F, Kokpol S, Chosrowjan H, Taniguchi S, Mataga N. Simultaneous analysis of ultrafast fluorescence decays of FMN binding protein and its mutated proteins by molecular dynamic simulation and electron transfer theory. J Phys Chem B 2008; 112:13121-7. [PMID: 18800855 DOI: 10.1021/jp804130j] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultrafast fluorescence decays of FMN binding proteins (FBP) from Desulfovibrio vulgaris (Miyazaki F) were analyzed with an electron transfer (ET) theory by Kakitani and Mataga (KM theory). Time-dependent distances among isoalloxazine (Iso) and Trp-32, Tyr-35, and Trp-106 in wild-type FBP (WT), among Iso and Tyr-32, Tyr-35, and Trp-106 in W32Y (Trp-32 was replaced by Tyr-32), and among Iso and Tyr-35 and Trp-106 in W32A (Trp-32 was replaced by Ala-32) were determined by molecular dynamic simulation (MD). Electrostatic energies between Iso anion and all other ionic groups, between Trp-32 cation and all other ionic groups, and between Tyr-32 cation and all other ionic groups were calculated in WT, W32Y, and W32A, from the MD coordinates. ET parameters contained in KM theory, such as frequency (nu 0), a coefficient of the ET process (beta), a critical distance of the ET process ( R 0), standard free energy related to the electron affinity of the excited Iso ( G Iso (0)), and the static dielectric constant in FBP species (epsilon 0), were determined with and without inclusion of the electrostatic energy, so as to fit the calculated fluorescence decays with the observed decays of all FBP species, by a nonlinear least-squares method according to the Marquardt algorithm. In the analyses the parameters, nu 0, beta, and R 0 were determined separately between Trp residues and Tyr residues among all FBP species. Calculated fluorescence intensities with the inclusion of the electrostatic energy fit quite well with the observed ones of all WT, W32Y, and W32A.
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Affiliation(s)
- Nadtanet Nunthaboot
- Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham 44150, Thailand
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36
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Ultrafast fluorescence dynamics of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) and its site-directed mutated proteins. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.07.089] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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37
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Tanaka F, Rujkorakarn R, Chosrowjan H, Taniguchi S, Mataga N. Analyses of donor–acceptor distance-dependent rates of photo-induced electron transfer in flavoproteins with three kinds of electron transfer theories. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2008.03.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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38
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Chosrowjan H, Taniguchi S, Mataga N, Tanaka F, Todoroki D, Kitamura M. Comparison between Ultrafast Fluorescence Dynamics of FMN Binding Protein from Desulfovibrio vulgaris, Strain Miyazaki, in Solution vs Crystal Phases. J Phys Chem B 2007; 111:8695-7. [PMID: 17608527 DOI: 10.1021/jp073702k] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultrafast fluorescence dynamics of FMN binding protein (FBP) from Desulfobivrio vulgaris, strain Miyaxaki F, were compared in solution and crystal phases. Fluorescence lifetimes of FBP were 167 fs (96%) and 1.5 ps (4%) in solution (tau(av) = 220 fs), and 730 fs (60%) and longer than 10 ps (40%) in crystals (tau(av) = 4.44 ps). The quenching of the fluorescence of flavin in the protein was considered to be due to photoinduced electron transfer (ET) from Trp or Tyr to the excited isoalloxazine (Iso) nearby. The average lifetime was 20 times longer in crystal vs in solution. Averaged distances between Iso and nearby Trp-32, Tyr-35, and Trp-106 were 8.42, 7.36, and 8.15 A in solution, respectively (obtained by NMR spectroscopy), and 7.05, 7.72, and 8.49 A in crystal, respectively (obtained by X-ray crystallography). The prolonged lifetime in crystal cannot be elucidated by the change in the distances between the states. It was suggested that the longer lifetime in crystal was ascribed to the absence of water molecules around FBP with rapid motional freedom, which may be the driving force for the ET in flavoproteins.
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39
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Tanaka F, Chosrowjan H, Taniguchi S, Mataga N, Sato K, Nishina Y, Shiga K. Donor−Acceptor Distance-Dependence of Photoinduced Electron-Transfer Rate in Flavoproteins. J Phys Chem B 2007; 111:5694-9. [PMID: 17474766 DOI: 10.1021/jp066450g] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ultrafast fluorescence quenching of flavin in flavodoxin from Megasphaera elsdenii was investigated by means of a fluorescence up-conversion method. Fluorescence lifetimes of flavodoxin from M. elsdenii were estimated to be tau(1) approximately 165 fs (0.97%) and tau(2) approximately 10 ps (0.03%). Correlation of photoinduced electron-transfer rates (k(ET)) with averaged distances (D(av)) between isoalloxazine and nearby tryptophan or tyrosine was examined and obtained an empirical equation of ln k(ET) vs D(av) by means of a nonlinear least-squares method using reported data together with flavodoxin from M. elsdenii. The values of D(av) were calculated from X-ray structures of the flavoproteins. The ln k(ET) was approximately linear at D(av) shorter than 7 A. The model free empirical equation was expressed as ln k(ET) = 29.7 + (-0.327 D(av) + 2.84 x 10(-5))/(0.698 - D(av)(2)). We also analyzed the observed values of ln k(ET) with Marcus theory, but could not obtain reasonable results. Our analysis suggests that the average distance, rather than the shortest (edge to edge) distance or interplanar angles between the aromatics rings, is the key factor in the process of the photoinduced electron transfer in these flavoproteins.
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Affiliation(s)
- Fumio Tanaka
- SC1-414 Department of Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham 44150, Thailand.
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40
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Islam SD, Susdorf T, Penzkofer A, Hegemann P. Fluorescence quenching of flavin adenine dinucleotide in aqueous solution by pH dependent isomerisation and photo-induced electron transfer. Chem Phys 2003. [DOI: 10.1016/j.chemphys.2003.08.013] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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41
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Sato K, Nishina Y, Shiga K, Tanaka F. Hydrogen-bonding dynamics of free flavins in benzene and FAD in electron-transferring flavoprotein upon excitation. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2003; 70:67-73. [PMID: 12849696 DOI: 10.1016/s1011-1344(03)00056-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The dynamic natures of two hydrogen-bonding model systems, riboflavin tetrabutylate (RFTB)-trichloroacetic acid (TCA) and RFTB-phenol in benzene, and of electron-transferring flavoprotein (ETF) from pig kidney upon excitation of flavins was investigated by means of steady state and time-resolved fluorescence spectroscopy. In both model systems fluorescence intensities of RFTB decreased as TCA or phenol was added. The spectral characteristics of ETF under steady state excitation were quite similar to those of the RFTB-TCA system, but not to those of the RFTB-phenol system. The observed fluorescence decay curves of ETF fit well with the calculated decay curves with two lifetime components, as in the model systems. Averaged lifetime was 0.9 ns. The time-resolved fluorescence spectrum of ETF shifted toward longer wavelength with time after pulsed excitation, which was also observed in the RFTB-TCA system. In the RFTB-phenol system the emission spectrum did not shift at all with time. These results reveal that the dynamic nature of ETF can be ascribed to aliphatic hydrogen-bonding(s) of the isoalloxazine ring with surrounding amino acid(s). From the fluorescence characteristics of ETF in comparison with the model systems, human ETF and other flavoproteins, it was suggested that ETF from pig kidney does not contain Tyr-16 in the beta subunit, unlike human ETF.
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Affiliation(s)
- Kyousuke Sato
- Department of Physiology, Kumamoto University Medical School, Honjo, Kumamoto 860-0816, Japan
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42
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Mataga N, Chosrowjan H, Taniguchi S, Tanaka F, Kido N, Kitamura M. Femtosecond Fluorescence Dynamics of Flavoproteins: Comparative Studies on Flavodoxin, Its Site-Directed Mutants, and Riboflavin Binding Protein Regarding Ultrafast Electron Transfer in Protein Nanospaces. J Phys Chem B 2002. [DOI: 10.1021/jp020574l] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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43
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van den Berg PAW, Feenstra KA, Mark AE, Berendsen HJC, Visser AJWG. Dynamic Conformations of Flavin Adenine Dinucleotide: Simulated Molecular Dynamics of the Flavin Cofactor Related to the Time-Resolved Fluorescence Characteristics. J Phys Chem B 2002. [DOI: 10.1021/jp020356s] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Petra A. W. van den Berg
- MicroSpectroscopy Centre, Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands, Bioson Research Institute & Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, and Department of Structural Biology, Institute of Molecular Biological Sciences, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - K. Anton Feenstra
- MicroSpectroscopy Centre, Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands, Bioson Research Institute & Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, and Department of Structural Biology, Institute of Molecular Biological Sciences, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Alan E. Mark
- MicroSpectroscopy Centre, Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands, Bioson Research Institute & Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, and Department of Structural Biology, Institute of Molecular Biological Sciences, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Herman J. C. Berendsen
- MicroSpectroscopy Centre, Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands, Bioson Research Institute & Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, and Department of Structural Biology, Institute of Molecular Biological Sciences, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Antonie J. W. G. Visser
- MicroSpectroscopy Centre, Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands, Bioson Research Institute & Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, and Department of Structural Biology, Institute of Molecular Biological Sciences, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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44
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MacFarlane AW, Stanley RJ. Evidence of powerful substrate electric fields in DNA photolyase: implications for thymidine dimer repair. Biochemistry 2001; 40:15203-14. [PMID: 11735403 DOI: 10.1021/bi0114224] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA photolyase is a flavoprotein that repairs cyclobutylpyrimidine dimers by ultrafast photoinduced electron transfer. One unusual feature of this enzyme is the configuration of the FAD cofactor, where the isoalloxazine and adenine rings are nearly in vdW contact. We have measured the steady-state and transient absorption spectra and excited-state decay kinetics of oxidized (FAD-containing, folate-depleted) Escherichia coli DNA photolyase with and without dinucleotide and polynucleotide single-stranded thymidine dimer substrates. The steady-state absorption spectrum for the enzyme-polynucleotide substrate complex showed a blue shift, as seen previously by Jorns et al. (1). No shift was observed for the dinucleotide substrate, suggesting that there are significant differences in the binding geometry of dinucleotide versus polynucleotide dimer lesions. Evidence was obtained from transient absorption experiments for a long-lived charge-transfer complex involving the isoalloxazine of the FAD cofactor. No evidence of excited-state quenching was measurable upon binding either substrate. To explain these data, we hypothesize the existence of a large substrate electric field in the cavity containing the FAD cofactor. A calculation of the magnitude and direction of this dipolar electric field is consistent with electrochromic band shifts for both S(0) --> S(1) and S(0) --> S(2) transitions. These observations suggest that the substrate dipolar electric field may be a critical component in its electron-transfer-mediated repair by photolyase and that the unique relative orientation of the isoalloxazine and adenine rings may have resulted from the consequences of the dipolar substrate field.
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Affiliation(s)
- A W MacFarlane
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
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45
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Visser AJ, van Hoek A, Kulinski T, Le Gall J. Time-resolved fluorescence studies of flavodoxin Demonstration of picosecond fluorescence lifetimes of FMN inDesulfovibrioflavodoxins. FEBS Lett 2001. [DOI: 10.1016/0014-5793(87)80493-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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46
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Zhong D, Zewail AH. Femtosecond dynamics of flavoproteins: charge separation and recombination in riboflavine (vitamin B2)-binding protein and in glucose oxidase enzyme. Proc Natl Acad Sci U S A 2001; 98:11867-72. [PMID: 11592997 PMCID: PMC59734 DOI: 10.1073/pnas.211440398] [Citation(s) in RCA: 197] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2001] [Indexed: 11/18/2022] Open
Abstract
Flavoproteins can function as hydrophobic sites for vitamin B(2) (riboflavin) or, in other structures, with cofactors for catalytic reactions such as glucose oxidation. In this contribution, we report direct observation of charge separation and recombination in two flavoproteins: riboflavin-binding protein and glucose oxidase. With femtosecond resolution, we observed the ultrafast electron transfer from tryptophan(s) to riboflavin in the riboflavin-binding protein, with two reaction times: approximately 100 fs (86% component) and 700 fs (14%). The charge recombination was observed to take place in 8 ps, as probed by the decay of the charge-separated state and the recovery of the ground state. The time scale for charge separation and recombination indicates the local structural tightness for the dynamics to occur that fast and with efficiency of more than 99%. In contrast, in glucose oxidase, electron transfer between flavin-adenine-dinucleotide and tryptophan(s)/tyrosine(s) takes much longer times, 1.8 ps (75%) and 10 ps (25%); the corresponding charge recombination occurs on two time scales, 30 ps and nanoseconds, and the efficiency is still more than 97%. The contrast in time scales for the two structurally different proteins (of the same family) correlates with the distinction in function: hydrophobic recognition of the vitamin in the former requires a tightly bound structure (ultrafast dynamics), and oxidation-reduction reactions in the latter prefer the formation of a charge-separated state that lives long enough for chemistry to occur efficiently. Finally, we also studied the influence on the dynamics of protein conformations at different ionic strengths and denaturant concentrations and observed the sharp collapse of the hydrophobic cleft and, in contrast, the gradual change of glucose oxidase.
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Affiliation(s)
- D Zhong
- Laboratory for Molecular Sciences, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125, USA
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47
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Abstract
Flavins and flavoproteins are versatile redox cofactors that can perform both one- and two-electron transfer. Because they are highly colored in all three oxidation states, optical spectroscopy has been exploited for decades to study these redox changes. This review summarizes the application of optical spectroscopies to flavins and flavoproteins since 1990. Special emphasis is placed on new techniques, such as Stark spectroscopy, as well as significant refinements in more well known techniques, such as resonance Raman spectroscopy and ultrafast spectroscopy.
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Affiliation(s)
- R J Stanley
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA.
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48
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Tracking Molecular Dynamics of Flavoproteins with Time-Resolved Fluorescence Spectroscopy. ACTA ACUST UNITED AC 2001. [DOI: 10.1007/978-3-642-56853-4_22] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
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49
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Mataga N, Chosrowjan H, Shibata Y, Tanaka F, Nishina Y, Shiga K. Dynamics and Mechanisms of Ultrafast Fluorescence Quenching Reactions of Flavin Chromophores in Protein Nanospace. J Phys Chem B 2000. [DOI: 10.1021/jp002145y] [Citation(s) in RCA: 117] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | - Fumio Tanaka
- Mie Prefectural College of Nursing, Yumegaoka, 1-1-1, Tsu 514-0116, Japan
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50
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Stanley RJ, MacFarlane. Ultrafast Excited State Dynamics of Oxidized Flavins: Direct Observations of Quenching by Purines. J Phys Chem A 2000. [DOI: 10.1021/jp000003y] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Robert J. Stanley
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - MacFarlane
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
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