1
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Uleanya KO, Anstöter CS, Dessent CEH. Photodissociative decay pathways of the flavin mononucleotide anion and its complexes with tryptophan and glutamic acid. Phys Chem Chem Phys 2023; 25:30697-30707. [PMID: 37934009 DOI: 10.1039/d3cp04359b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Flavin mononucleotide (FMN) is a highly versatile biological chromophore involved in a range of biochemical pathways including blue-light sensing proteins and the control of circadian rhythms. Questions exist about the effect of local amino acids on the electronic properties and photophysics of the chromophore. Using gas-phase anion laser photodissociation spectroscopy, we have measured the intrinsic electronic spectroscopy (3.1-5.7 eV) and accompanying photodissociative decay pathways of the native deprotonated form of FMN, i.e. [FMN-H]- complexed with the amino acids tryptophan (TRP) and glutamic acid (GLU), i.e. [FMN-H]-·TRP and [FMN-H]-·GLU, to investigate the extent to which these amino acids perturb the electronic properties and photodynamics of the [FMN-H]- chromophore. The overall photodepletion profiles of [FMN-H]-·TRP and [FMN-H]-·GLU are similar to that of the monomer, revealing that amino acid complexation occurs without significant spectral shifting of the [FMN-H]- electronic excitations over this region. Both [FMN-H]-·TRP and [FMN-H]-·GLU are observed to decay by non-statistical photodecay pathways, although the behaviour of [FMN-H]-·TRP is closer to statistical fragmentation. Long-lived FMN excited states (triplet) are therefore relatively quenched when TRP binds to [FMN-H]-. Importantly, we find that [FMN-H]-, [FMN-H]-·TRP and [FMN-H]-·GLU all decay predominantly via electron detachment following photoexcitation of the flavin chromophore, with amino acid complexation appearing not to inhibit this decay channel. The strong propensity for electron detachment is attributed to excited-state proton transfer within FMN, with proton transfer from a ribose alcohol to the phosphate preceding electron detachment.
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Affiliation(s)
- Kelechi O Uleanya
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
| | - Cate S Anstöter
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
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2
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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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3
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Yang J, Zhang Y, Lu Y, Wang L, Lu F, Zhong D. Ultrafast Dynamics of Nonequilibrium Short-Range Electron Transfer in Semiquinone Flavodoxin. J Phys Chem Lett 2022; 13:3202-3208. [PMID: 35377652 DOI: 10.1021/acs.jpclett.2c00057] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Short-range protein electron transfer (ET) is crucially important in light-induced biological processes such as in photoenzymes and photoreceptors and often occurs on time scales similar to those of environment fluctuations, leading to a coupled dynamic process. Herein, we use semiquinone Anabaena flavodoxin to characterize the ultrafast photoinduced redox cycle of the wild type and seven mutants by ultrafast spectroscopy. We have found that the forward and backward ET dynamics show stretched behaviors in a few picoseconds (1-5 ps), indicating a coupling with the local protein fluctuations. By comparison with the results from semiquinone D. vulgaris flavodoxin, we find that the electronic coupling is crucial to the ET rates. With our new nonergodic model, we obtain smaller values of the outer reorganization energy (λoγ) of environment fluctuations and the reaction free energy force (ΔGγ), a signature of nonequilibrium ET dynamics.
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Affiliation(s)
- Jie Yang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yifei Zhang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yangyi Lu
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lijuan Wang
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Faming Lu
- Center for Ultrafast Science and Technology, School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dongping Zhong
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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4
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Dimitriev OP. Dynamics of Excitons in Conjugated Molecules and Organic Semiconductor Systems. Chem Rev 2022; 122:8487-8593. [PMID: 35298145 DOI: 10.1021/acs.chemrev.1c00648] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The exciton, an excited electron-hole pair bound by Coulomb attraction, plays a key role in photophysics of organic molecules and drives practically important phenomena such as photoinduced mechanical motions of a molecule, photochemical conversions, energy transfer, generation of free charge carriers, etc. Its behavior in extended π-conjugated molecules and disordered organic films is very different and very rich compared with exciton behavior in inorganic semiconductor crystals. Due to the high degree of variability of organic systems themselves, the exciton not only exerts changes on molecules that carry it but undergoes its own changes during all phases of its lifetime, that is, birth, conversion and transport, and decay. The goal of this review is to give a systematic and comprehensive view on exciton behavior in π-conjugated molecules and molecular assemblies at all phases of exciton evolution with emphasis on rates typical for this dynamic picture and various consequences of the above dynamics. To uncover the rich variety of exciton behavior, details of exciton formation, exciton transport, exciton energy conversion, direct and reverse intersystem crossing, and radiative and nonradiative decay are considered in different systems, where these processes lead to or are influenced by static and dynamic disorder, charge distribution symmetry breaking, photoinduced reactions, electron and proton transfer, structural rearrangements, exciton coupling with vibrations and intermediate particles, and exciton dissociation and annihilation as well.
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Affiliation(s)
- Oleg P Dimitriev
- V. Lashkaryov Institute of Semiconductor Physics NAS of Ukraine, pr. Nauki 41, Kyiv 03028, Ukraine
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5
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Dozova N, Lacombat F, Lombard M, Hamdane D, Plaza P. Ultrafast dynamics of fully reduced flavin in catalytic structures of thymidylate synthase ThyX. Phys Chem Chem Phys 2021; 23:22692-22702. [PMID: 34605505 DOI: 10.1039/d1cp03379d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thymidylate is a vital DNA precursor synthesized by thymidylate synthases. ThyX is a flavin-dependent thymidylate synthase found in several human pathogens and absent in humans, which makes it a potential target for antimicrobial drugs. This enzyme methylates the 2'-deoxyuridine 5'-monophosphate (dUMP) to 2'-deoxythymidine 5'-monophosphate (dTMP) using a reduced flavin adenine dinucleotide (FADH-) as prosthetic group and (6R)-N5,N10-methylene-5,6,7,8-tetrahydrofolate (CH2THF) as a methylene donor. Recently, it was shown that ThyX-catalyzed reaction is a complex process wherein FADH- promotes both methylene transfer and reduction of the transferred methylene into a methyl group. Here, we studied the dynamic and photophysics of FADH- bound to ThyX, in several substrate-binding states (no substrate, in the presence of dUMP or folate or both) by femtosecond transient absorption spectroscopy. This methodology provides valuable information about the ground-state configuration of the isoalloxazine moiety of FADH- and the rigidity of its local environment, through spectra shape and excited-state lifetime parameters. In the absence of substrate, the environment of FADH- in ThyX is only mildly more constrained than that of free FADH- in solution. The addition of dUMP however narrows the distribution of ground-state configurations and increases the constraints on the butterfly bending motion in the excited state. Folate binding results in the selection of new ground-state configurations, presumably located at a greater distance from the conical intersection where excited-state decay occurs. When both substrates are present, the ground-state configuration appears on the contrary rather limited to a geometry close to the conical intersection, which explains the relatively fast excited-state decay (100 ps on the average), even if the environment of the isoalloxazine is densely packed. Hence, although the environment of the flavin is dramatically constrained, FADH- retains a dynamic necessary to shuttle carbon from folate to dUMP. Our study demonstrates the high sensitivity of FADH- photophysics to the constraints exerted by its immediate surroundings.
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Affiliation(s)
- Nadia Dozova
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Fabien Lacombat
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Murielle Lombard
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège de France, Sorbonne Université, 75005 Paris, France.
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège de France, Sorbonne Université, 75005 Paris, France.
| | - Pascal Plaza
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
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6
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Duan HD, Khan SA, Miller AF. Photogeneration and reactivity of flavin anionic semiquinone in a bifurcating electron transfer flavoprotein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148415. [PMID: 33727071 DOI: 10.1016/j.bbabio.2021.148415] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 02/15/2021] [Accepted: 03/10/2021] [Indexed: 02/04/2023]
Abstract
Electron transfer bifurcation allows production of a strongly reducing carrier at the expense of a weaker one, by redistributing energy among a pair of electrons. Thus, two weakly-reducing electrons from NADH are consumed to produce a strongly reducing ferredoxin or flavodoxin, paid for by reduction of an oxidizing acceptor. The prevailing mechanism calls for participation of a strongly reducing flavin semiquinone which has been difficult to observe with site-certainly in multi-flavin systems. Using blue light (450 nm) to photoexcite the flavins of bifurcating electron transfer flavoprotein (ETF), we demonstrate accumulation of anionic flavin semiquinone in excess of what is observed in equilibrium titrations, and establish its ability to reduce the low-potential electron acceptor benzyl viologen. This must occur at the bifurcating flavin because the midpoint potentials of the electron transfer (ET) flavin are not sufficiently negative. We show that bis-tris propane buffer is an effective electron donor to the flavin photoreduction, but that if the system is prepared with the ET flavin chemically reduced, so that only the bifurcating flavin is oxidized and photochemically active, flavin anionic semiquinone is formed more rapidly. Thus, excited bifurcating flavin is able to draw on an electron stored at the ET flavin. Flavin semiquinone photogenerated at the bifurcation site must therefore be accompanied by additional semiquinone formation by oxidation of the ET flavin. Consistent with the expected instability of bifurcating flavin semiquinone, it subsides immediately upon cessation of illumination. However comparison with yields of semiquinone in equilibrium titrations suggest that during continuous illumination at pH 9 a steady state population of 0.3 equivalents of bifurcating flavin semiquinone accumulates, and then undergoes further photoreduction to the hydroquinone. Although transient, the population of bifurcating flavin semiquinone explains the system's ability to conduct light-driven electron transfer from bis-tris propane to benzyl viologen, in effect trapping energy from light.
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Affiliation(s)
- H Diessel Duan
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
| | - Sharique A Khan
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
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7
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Zhuang B, Seo D, Aleksandrov A, Vos MH. Characterization of Light-Induced, Short-Lived Interacting Radicals in the Active Site of Flavoprotein Ferredoxin-NADP + Oxidoreductase. J Am Chem Soc 2021; 143:2757-2768. [PMID: 33591179 DOI: 10.1021/jacs.0c09627] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Radicals of flavin adenine dinucleotide (FAD), as well as tyrosine and tryptophan, are widely involved as key reactive intermediates during electron-transfer (ET) reactions in flavoproteins. Due to the high reactivity of these species and their corresponding short lifetime, characterization of these intermediates in functional processes of flavoproteins is usually challenging but can be achieved by ultrafast spectroscopic studies of light-activatable flavoproteins. In ferredoxin-NADP+ oxidoreductase from Bacillus subtilis (BsFNR), fluorescence of the FAD cofactor that very closely interacts with a neighboring tyrosine residue (Tyr50) is strongly quenched. Here we study short-lived photoproducts of this enzyme and its variants, with Tyr50 replaced by tryptophan or glycine. Using time-resolved fluorescence and absorption spectroscopies, we show that, upon the excitation of WT BsFNR, ultrafast ET from Tyr50 to the excited FAD cofactor occurs in ∼260 fs, an order of magnitude faster than the decay by charge recombination, facilitating the characterization of the reaction intermediates in the charge-separated state with respect to other recently studied systems. These studies are corroborated by experiments on the Y50W mutant protein, which yield photoproducts qualitatively similar to those observed in other tryptophan-bearing flavoproteins. By combining the experimental results with molecular dynamics simulations and quantum mechanics calculations, we investigate in detail the effects of protein environment and relaxations on the spectral properties of those radical intermediates and demonstrate that the spectral features of radical anionic FAD are highly sensitive to its environment, and in particular to the dynamics and nature of the counterions formed in the photoproducts. Altogether, comprehensive characterizations are provided for important radical intermediates that are generally involved in functional processes of flavoproteins.
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Affiliation(s)
- Bo Zhuang
- LOB, CNRS, INSERM, École Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Daisuke Seo
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, 920-1192 Kanazawa, Ishikawa, Japan
| | - Alexey Aleksandrov
- LOB, CNRS, INSERM, École Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Marten H Vos
- LOB, CNRS, INSERM, École Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France
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8
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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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9
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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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10
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Lu Y, Kundu M, Zhong D. Effects of nonequilibrium fluctuations on ultrafast short-range electron transfer dynamics. Nat Commun 2020; 11:2822. [PMID: 32499536 PMCID: PMC7272615 DOI: 10.1038/s41467-020-15535-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 03/16/2020] [Indexed: 01/10/2023] Open
Abstract
A variety of electron transfer (ET) reactions in biological systems occurs at short distances and is ultrafast. Many of them show behaviors that deviate from the predictions of the classic Marcus theory. Here, we show that these ultrafast ET dynamics highly depend on the coupling between environmental fluctuations and ET reactions. We introduce a dynamic factor, γ (0 ≤ γ ≤ 1), to describe such coupling, with 0 referring to the system without coupling to a “frozen” environment, and 1 referring to the system’s complete coupling with the environment. Significantly, this system’s coupling with the environment modifies the reaction free energy, ΔGγ, and the reorganization energy, λγ, both of which become smaller. This new model explains the recent ultrafast dynamics in flavodoxin and elucidates the fundamental mechanism of nonequilibrium ET dynamics, which is critical to uncovering the molecular nature of many biological functions. Ultrafast electron-transfer reactions are fundamental to protein functions. Here the authors show that these reaction dynamics are affected by the ruggedness of protein energy landscape, which even modifies the reaction free energy and reorganization energy.
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Affiliation(s)
- Yangyi Lu
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Mainak Kundu
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Dongping Zhong
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA. .,Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, School of Physics and Astronomy, Shanghai Jiao Tong University, 200240, Shanghai, China.
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11
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Dozova N, Lacombat F, Bou-Nader C, Hamdane D, Plaza P. Ultrafast photoinduced flavin dynamics in the unusual active site of the tRNA methyltransferase TrmFO. Phys Chem Chem Phys 2019; 21:8743-8756. [PMID: 30968076 DOI: 10.1039/c8cp06072j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Flavoproteins often stabilize their flavin coenzyme by stacking interactions involving the isoalloxazine moiety of the flavin and an aromatic residue from the apoprotein. The bacterial FAD and folate-dependent tRNA methyltransferase TrmFO has the unique property of stabilizing its FAD coenzyme by an unusual H-bond-assisted π-π stacking interaction, involving a conserved tyrosine (Y346 in Bacillus subtilis TrmFO, BsTrmFO), the isoalloxazine of FAD and the backbone of a catalytic cysteine (C53). Here, the interaction between FAD and Y346 has been investigated by measuring the photoinduced flavin dynamics of BsTrmFO in the wild-type (WT) protein, C53A and several Y346 mutants by ultrafast transient absorption spectroscopy. In C53A, the excited FAD very rapidly (0.43 ps) abstracts an electron from Y346, yielding the FAD˙-/Y346OH˙+ radical pair, while relaxation of the local environment (1.3 ps) of the excited flavin produces a slight Stokes shift of its stimulated emission band. The radical pair then decays via charge recombination, mostly in 3-4 ps, without any deprotonation of the Y346OH˙+ radical. Presumably, the H-bond between Y346 and the amide group of C53 increases the pKa of Y346OH˙+ and slows down its deprotonation. The dynamics of WT BsTrmFO shows additional slow decay components (43 and 700 ps), absent in the C53A mutant, assigned to excited FADox populations not undergoing fast photoreduction. Their presence is likely due to a more flexible structure of the WT protein, favored by the presence of C53. Interestingly, mutations of Y346 canceling its electron donating character lead to multiple slower quenching channels in the ps-ns regime. These channels are proposed to be due to electron abstraction either (i) from the adenine moiety of FAD, a distribution of the isoalloxazine-adenine distance in the absence of Y346 explaining the multiexponential decay, or (ii) from the W286 residue, possibly accounting for one of the decays. This work supports the idea that H-bond-assisted π-π stacking controls TrmFO's active site dynamics, required for competent orientation of the reactive centers during catalysis.
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Affiliation(s)
- Nadia Dozova
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
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12
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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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13
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Su D, Kabir MP, Orozco-Gonzalez Y, Gozem S, Gadda G. Fluorescence Properties of Flavin Semiquinone Radicals in Nitronate Monooxygenase. Chembiochem 2019; 20:1646-1652. [PMID: 30748074 DOI: 10.1002/cbic.201900016] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Indexed: 11/09/2022]
Abstract
Fluorescent cofactors like flavins can be exploited to probe their local environment with spatial and temporal resolution. Although the fluorescence properties of the oxidized and two-electron-reduced states of flavins have been studied extensively, this is not the case for the one-electron-reduced state. Both the neutral and anionic semiquinones have proven particularly challenging to examine, as they are unstable in solution and are transient, short-lived species in many catalytic cycles. Here, we report that the nitronate monooxygenase (NMO) from Pseudomonas aeruginosa PAO1 is capable of stabilizing both semiquinone forms anaerobically for hours, thus enabling us to study their spectroscopy in a constant protein environment. We found that in the active site of NMO, the anionic semiquinone exhibits no fluorescence, whereas the neutral semiquinone radical shows a relatively strong fluorescence, with a behavior that violates the Kasha-Vavilov rule. These fluorescence properties are discussed in the context of time-dependent density functional theory calculations, which reveal low-lying dark states in both systems.
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Affiliation(s)
- Dan Su
- Department of Chemistry, Georgia State University, 50 Decatur St. SE, Atlanta, GA, 30302, USA
| | - Mohammad Pabel Kabir
- Department of Chemistry, Georgia State University, 50 Decatur St. SE, Atlanta, GA, 30302, USA
| | - Yoelvis Orozco-Gonzalez
- Department of Chemistry, Georgia State University, 50 Decatur St. SE, Atlanta, GA, 30302, USA
| | - Samer Gozem
- Department of Chemistry, Georgia State University, 50 Decatur St. SE, Atlanta, GA, 30302, USA
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, 50 Decatur St. SE, Atlanta, GA, 30302, USA.,Department of Biology, Georgia State University, 100 Piedmond Ave., Atlanta, GA, 30303, USA.,Center for Diagnostics and Therapeutics, Georgia State University, P.O. Box 5090, Atlanta, GA, 30303, USA.,Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, 30302, USA
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14
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Villabona-Monsalve JP, Varnavski O, Palfey BA, Goodson T. Two-Photon Excitation of Flavins and Flavoproteins with Classical and Quantum Light. J Am Chem Soc 2018; 140:14562-14566. [DOI: 10.1021/jacs.8b08515] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Oleg Varnavski
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bruce A. Palfey
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606, United States
| | - Theodore Goodson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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15
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Duan HD, Lubner CE, Tokmina-Lukaszewska M, Gauss GH, Bothner B, King PW, Peters JW, Miller AF. Distinct properties underlie flavin-based electron bifurcation in a novel electron transfer flavoprotein FixAB from Rhodopseudomonas palustris. J Biol Chem 2018; 293:4688-4701. [PMID: 29462786 DOI: 10.1074/jbc.ra117.000707] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 02/08/2018] [Indexed: 11/06/2022] Open
Abstract
A newly recognized third fundamental mechanism of energy conservation in biology, electron bifurcation, uses free energy from exergonic redox reactions to drive endergonic redox reactions. Flavin-based electron bifurcation furnishes low-potential electrons to demanding chemical reactions, such as reduction of dinitrogen to ammonia. We employed the heterodimeric flavoenzyme FixAB from the diazotrophic bacterium Rhodopseudomonas palustris to elucidate unique properties that underpin flavin-based electron bifurcation. FixAB is distinguished from canonical electron transfer flavoproteins (ETFs) by a second FAD that replaces the AMP of canonical ETF. We exploited near-UV-visible CD spectroscopy to resolve signals from the different flavin sites in FixAB and to interrogate the putative bifurcating FAD. CD aided in assigning the measured reduction midpoint potentials (E° values) to individual flavins, and the E° values tested the accepted model regarding the redox properties required for bifurcation. We found that the higher-E° flavin displays sequential one-electron (1-e-) reductions to anionic semiquinone and then to hydroquinone, consistent with the reactivity seen in canonical ETFs. In contrast, the lower-E° flavin displayed a single two-electron (2-e-) reduction without detectable accumulation of semiquinone, consistent with unstable semiquinone states, as required for bifurcation. This is the first demonstration that a FixAB protein possesses the thermodynamic prerequisites for bifurcating activity, and the separation of distinct optical signatures for the two flavins lays a foundation for mechanistic studies to learn how electron flow can be directed in a protein environment. We propose that a novel optical signal observed at long wavelength may reflect electron delocalization between the two flavins.
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Affiliation(s)
- H Diessel Duan
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506
| | | | | | - George H Gauss
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - Paul W King
- National Renewable Energy Laboratory, Golden, Colorado 80401
| | - John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99163
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16
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Scheurer M, Brisker-Klaiman D, Dreuw A. Molecular Mechanism of Flavin Photoprotection by Archaeal Dodecin: Photoinduced Electron Transfer and Mg 2+-Promoted Proton Transfer. J Phys Chem B 2017; 121:10457-10466. [PMID: 29069901 DOI: 10.1021/acs.jpcb.7b08597] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Photoinduced biochemical reactions are ubiquitously governed by derivatives of flavin, which is a key player in a manifold of cellular redox reactions. The photoreactivity of flavins is also one of their greatest disadvantages as the molecules are sensitive to photodegradation. To prevent this unfavorable reaction, UV-light-exposed archaea bacteria, such as Halobacterium salinarum, manage the task of protecting flavin derivatives by dodecin, a protein which stores flavins and efficiently photoprotects them. In this study, we shed light on the photoprotection mechanism, i.e., the excited state quenching mechanism by dodecin using computational methodology. Molecular dynamics (MD) simulations unraveled the hydrogen bond network in the flavin binding pocket as a starting point for proton transfer upon preceding electron transfer. Using high-level ab initio quantum chemical methods, different proton transfer channels have been investigated and an energetically feasible Mg2+-promoted channel has been identified fully explaining previous experimental observations. This is the first extensive theoretical study of archaeal dodecin, furthering the understanding of its photocycle and manipulation.
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Affiliation(s)
- Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing , Im Neuenheimer Feld 205A, 69120 Heidelberg, Germany
| | - Daria Brisker-Klaiman
- Interdisciplinary Center for Scientific Computing , Im Neuenheimer Feld 205A, 69120 Heidelberg, Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing , Im Neuenheimer Feld 205A, 69120 Heidelberg, Germany
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17
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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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18
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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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19
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Hoben JP, Lubner CE, Ratzloff MW, Schut GJ, Nguyen DMN, Hempel KW, Adams MWW, King PW, Miller AF. Equilibrium and ultrafast kinetic studies manipulating electron transfer: A short-lived flavin semiquinone is not sufficient for electron bifurcation. J Biol Chem 2017; 292:14039-14049. [PMID: 28615449 DOI: 10.1074/jbc.m117.794214] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 06/11/2017] [Indexed: 11/06/2022] Open
Abstract
Flavin-based electron transfer bifurcation is emerging as a fundamental and powerful mechanism for conservation and deployment of electrochemical energy in enzymatic systems. In this process, a pair of electrons is acquired at intermediate reduction potential (i.e. intermediate reducing power), and each electron is passed to a different acceptor, one with lower and the other with higher reducing power, leading to "bifurcation." It is believed that a strongly reducing semiquinone species is essential for this process, and it is expected that this species should be kinetically short-lived. We now demonstrate that the presence of a short-lived anionic flavin semiquinone (ASQ) is not sufficient to infer the existence of bifurcating activity, although such a species may be necessary for the process. We have used transient absorption spectroscopy to compare the rates and mechanisms of decay of ASQ generated photochemically in bifurcating NADH-dependent ferredoxin-NADP+ oxidoreductase and the non-bifurcating flavoproteins nitroreductase, NADH oxidase, and flavodoxin. We found that different mechanisms dominate ASQ decay in the different protein environments, producing lifetimes ranging over 2 orders of magnitude. Capacity for electron transfer among redox cofactors versus charge recombination with nearby donors can explain the range of ASQ lifetimes that we observe. Our results support a model wherein efficient electron propagation can explain the short lifetime of the ASQ of bifurcating NADH-dependent ferredoxin-NADP+ oxidoreductase I and can be an indication of capacity for electron bifurcation.
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Affiliation(s)
- John P Hoben
- From the Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506
| | | | | | - Gerrit J Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Diep M N Nguyen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Karl W Hempel
- From the Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Paul W King
- National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Anne-Frances Miller
- From the Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506.
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20
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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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21
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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 flavin mononucleotide binding protein. Is the rate in the inverted region of donor–acceptor distance not real? J Photochem Photobiol A Chem 2016. [DOI: 10.1016/j.jphotochem.2016.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Farrán MÁ, Listorti A, Roiati V, Accorsi G, Gigli G, Clarkson GJ, Claramunt RM. Photoinduced processes in macrocyclic isoalloxazine–anthracene systems. J Photochem Photobiol A Chem 2016. [DOI: 10.1016/j.jphotochem.2015.08.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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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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24
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Chosrowjan H, Taniguchi S, Tanaka F. Ultrafast fluorescence upconversion technique and its applications to proteins. FEBS J 2015; 282:3003-15. [DOI: 10.1111/febs.13180] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 12/15/2014] [Accepted: 12/17/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Haik Chosrowjan
- Division of Laser Biochemistry; Institute for Laser Technology; Utsubo-Honmachi; Nishiku Osaka Japan
| | - Seiji Taniguchi
- Division of Laser Biochemistry; Institute for Laser Technology; Utsubo-Honmachi; Nishiku Osaka Japan
| | - Fumio Tanaka
- Division of Laser Biochemistry; Institute for Laser Technology; Utsubo-Honmachi; Nishiku Osaka Japan
- Department of Chemistry; Faculty of Science; Chulalongkorn University; Bangkok Thailand
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25
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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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26
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Absorption and emission spectroscopic characterization of photo-dynamics of photoactivated adenylyl cyclase mutant bPAC-Y7F of Beggiatoa sp. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 140:182-93. [DOI: 10.1016/j.jphotobiol.2014.06.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/26/2014] [Accepted: 06/30/2014] [Indexed: 11/19/2022]
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27
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Hardman SJO, Pudney CR, Hay S, Scrutton NS. Excited state dynamics can be used to probe donor-acceptor distances for H-tunneling reactions catalyzed by flavoproteins. Biophys J 2014; 105:2549-58. [PMID: 24314085 DOI: 10.1016/j.bpj.2013.10.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 10/09/2013] [Accepted: 10/21/2013] [Indexed: 10/26/2022] Open
Abstract
In enzyme systems where fast motions are thought to contribute to H-transfer efficiency, the distance between hydrogen donor and acceptor is a very important factor. Sub-ångstrom changes in donor-acceptor distance can have a large effect on the rate of reaction, so a sensitive probe of these changes is a vital tool in our understanding of enzyme function. In this study we use ultrafast transient absorption spectroscopy to investigate the photoinduced electron transfer rates, which are also very sensitive to small changes in distance, between coenzyme analog, NAD(P)H4, and the isoalloxazine center in the model flavoenzymes morphinone reductase (wild-type and selected variants) and pentaerythritol tetranitrate reductase (wild-type). It is shown that upon addition of coenzyme to the protein the rate of photoinduced electron transfer is increased. By comparing the magnitude of this increase with existing values for NAD(P)H4-FMN distances, based on charge-transfer complex absorbance and experimental kinetic isotope effect reaction data, we show that this method can be used as a sensitive probe of donor-acceptor distance in a range of enzyme systems.
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Affiliation(s)
- Samantha J O Hardman
- Manchester Institute of Biotechnology and Photon Science Institute, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
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28
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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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29
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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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30
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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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31
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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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32
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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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33
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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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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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35
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Staudt H, Hoesl MG, Dreuw A, Serdjukow S, Oesterhelt D, Budisa N, Wachtveitl J, Grininger M. Directed manipulation of a flavoprotein photocycle. Angew Chem Int Ed Engl 2013; 52:8463-6. [PMID: 23818044 DOI: 10.1002/anie.201302334] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Heike Staudt
- Institut für Physikalische and Theoretische Chemie, Exzellenzcluster Makromolekulare Komplexe, Goethe Universität Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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36
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Staudt H, Hoesl MG, Dreuw A, Serdjukow S, Oesterhelt D, Budisa N, Wachtveitl J, Grininger M. Gerichtete Manipulation des Photozyklus eines Flavoproteins. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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37
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Ruiz-González R, Cortajarena AL, Mejias SH, Agut M, Nonell S, Flors C. Singlet oxygen generation by the genetically encoded tag miniSOG. J Am Chem Soc 2013; 135:9564-7. [PMID: 23781844 DOI: 10.1021/ja4020524] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The genetically encodable fluorescent tag miniSOG is expected to revolutionize correlative light- and electron microscopy due to its ability to produce singlet oxygen upon light irradiation. The quantum yield of this process was reported as ΦΔ = 0.47 ± 0.05, as derived from miniSOG's ability to photooxidize the fluorescent probe anthracene dipropionic acid (ADPA). In this report, a significantly smaller value of ΦΔ = 0.03 ± 0.01 is obtained by two methods: direct measurement of its phosphorescence at 1275 nm and chemical trapping using uric acid as an alternative probe. We present insight into the photochemistry of miniSOG and ascertain the reasons for the discrepancy in ΦΔ values. We find that miniSOG oxidizes ADPA by both singlet oxygen-dependent and -independent processes. We also find that cumulative irradiation of miniSOG increases its ΦΔ value ~10-fold due to a photoinduced transformation of the protein. This may be the reason why miniSOG outperforms other fluorescent proteins reported to date as singlet oxygen generators.
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Affiliation(s)
- Rubén Ruiz-González
- Institut Quimic de Sarrià, Universitat Ramon Llull, Via Augusta 390, E-08017, Barcelona, Spain
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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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39
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Saha R, Rakshit S, Verma PK, Mitra RK, Pal SK. Protein-cofactor binding and ultrafast electron transfer in riboflavin binding protein under the spatial confinement of nanoscopic reverse micelles. J Mol Recognit 2013; 26:59-66. [DOI: 10.1002/jmr.2246] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 10/09/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Ranajay Saha
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences; Block JD, Sector III Salt Lake; Kolkata 700098; India
| | - Surajit Rakshit
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences; Block JD, Sector III Salt Lake; Kolkata 700098; India
| | - Pramod Kumar Verma
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences; Block JD, Sector III Salt Lake; Kolkata 700098; India
| | - Rajib Kumar Mitra
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences; Block JD, Sector III Salt Lake; Kolkata 700098; India
| | - Samir Kumar Pal
- Department of Chemical, Biological and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences; Block JD, Sector III Salt Lake; Kolkata 700098; India
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40
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Relationship between rate of photoinduced electron transfer and hydrogen bonding chain of tyrosine-glutamine-flavin in flavin photoreceptors: Global analyses among four TePixDs and three AppAs. J Photochem Photobiol A Chem 2013. [DOI: 10.1016/j.jphotochem.2012.11.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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41
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Farrán A, Mohanraj J, Clarkson GJ, Claramunt RM, Herranz F, Accorsi G. Tuning photoinduced processes of covalently bound isoalloxazine and anthraquinone bichromophores. Photochem Photobiol Sci 2013; 12:813-22. [DOI: 10.1039/c3pp25321j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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42
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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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43
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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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44
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Lukacs A, Zhao RK, Haigney A, Brust R, Greetham GM, Towrie M, Tonge PJ, Meech SR. Excited State Structure and Dynamics of the Neutral and Anionic Flavin Radical Revealed by Ultrafast Transient Mid-IR to Visible Spectroscopy. J Phys Chem B 2012; 116:5810-8. [DOI: 10.1021/jp2116559] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andras Lukacs
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich
NR4 7TJ, United Kingdom
- Department of Biophysics, Medical
School, University of Pecs, Hungary
| | - Rui-Kun Zhao
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich
NR4 7TJ, United Kingdom
| | - Allison Haigney
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400,
United States
| | - Richard Brust
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400,
United States
| | - Gregory M. Greetham
- Central Laser
Facility, Research
Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, United Kingdom
| | - Michael Towrie
- Central Laser
Facility, Research
Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, United Kingdom
| | - Peter J. Tonge
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400,
United States
| | - Stephen R. Meech
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich
NR4 7TJ, United Kingdom
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45
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Liu Z, Guo X, Tan C, Li J, Kao YT, Wang L, Sancar A, Zhong D. Electron tunneling pathways and role of adenine in repair of cyclobutane pyrimidine dimer by DNA photolyase. J Am Chem Soc 2012; 134:8104-14. [PMID: 22533849 DOI: 10.1021/ja2105009] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electron tunneling pathways in enzymes are critical to their catalytic efficiency. Through electron tunneling, photolyase, a photoenzyme, splits UV-induced cyclobutane pyrimidine dimer into two normal bases. Here, we report our systematic characterization and analyses of photoinitiated three electron transfer processes and cyclobutane ring splitting by following the entire dynamical evolution during enzymatic repair with femtosecond resolution. We observed the complete dynamics of the reactants, all intermediates and final products, and determined their reaction time scales. Using (deoxy)uracil and thymine as dimer substrates, we unambiguously determined the electron tunneling pathways for the forward electron transfer to initiate repair and for the final electron return to restore the active cofactor and complete the catalytic photocycle. Significantly, we found that the adenine moiety of the unusual bent flavin cofactor is essential to mediating all electron-transfer dynamics through a superexchange mechanism, leading to a delicate balance of time scales. The cyclobutane ring splitting takes tens of picoseconds, while electron-transfer dynamics all occur on a longer time scale. The active-site structural integrity, unique electron tunneling pathways, and the critical role of adenine ensure the synergy of these elementary steps in this complex photorepair machinery to achieve maximum repair efficiency which is close to unity. Finally, we used the Marcus electron-transfer theory to evaluate all three electron-transfer processes and thus obtained their reaction driving forces (free energies), reorganization energies, and electronic coupling constants, concluding that the forward and futile back-electron transfer is in the normal region and that the final electron return of the catalytic cycle is in the inverted region.
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Affiliation(s)
- Zheyun Liu
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, United States
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46
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Sengupta A, Sasikala WD, Mukherjee A, Hazra P. Comparative study of flavins binding with human serum albumin: a fluorometric, thermodynamic, and molecular dynamics approach. Chemphyschem 2012; 13:2142-53. [PMID: 22532419 DOI: 10.1002/cphc.201200044] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 03/12/2012] [Indexed: 01/20/2023]
Abstract
Flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) are derivatives of riboflavin (RF), a water-soluble vitamin, more commonly known as vitamin B(2). Flavins have attracted special attention in the last few years because of the recent discovery of a large number of flavoproteins. In this work, these flavins are used as extrinsic fluorescence markers for probing the microheterogeneous environment of a well-known transport protein, human serum albumin (HSA). Steady-state and time-resolved fluorescence experiments confirm that both FMN and FAD bind to the Sudlow's site-1 (SS1) binding pocket of HSA, where Trp214 resides. In the case of RF, a fraction of RF molecules binds at the SS1, whereas the major fraction of RF molecules remains unbound or surface bound to the protein. Moreover, flavin(s)-HSA interactions are monitored with the help of isothermal titration calorimetry, which provides free energy, enthalpy, and entropy changes of binding along with the binding constants. The molecular picture of binding interaction between flavins and HSA is well explored by docking and molecular dynamics studies.
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Affiliation(s)
- Abhigyan Sengupta
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Pune 411021, Maharashtra, India
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47
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Staudt H, Oesterhelt D, Grininger M, Wachtveitl J. Ultrafast excited-state deactivation of flavins bound to dodecin. J Biol Chem 2012; 287:17637-17644. [PMID: 22451648 DOI: 10.1074/jbc.m111.331652] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dodecins, a group of flavin-binding proteins with a dodecameric quaternary structure, are able to incorporate two flavins within each of their six identical binding pockets building an aromatic tetrade with two tryptophan residues. Dodecin from the archaeal Halobacterium salinarum is a riboflavin storage device. We demonstrate that unwanted side reactions induced by reactive riboflavin species and degradation of riboflavin are avoided by ultrafast depopulation of the reactive excited state of riboflavin. Intriguingly, in this process, the staggered riboflavin dimers do not interact in ground and photoexcited states. Rather, within the tetrade assembly, each riboflavin is kept under the control of the respective adjacent tryptophan, which suggests that the stacked arrangement is a matter of optimizing the flavin load. We further identify an electron transfer in combination with a proton transfer as a central element of the effective excited state depopulation mechanism. Structural and functional comparisons of the archaeal dodecin with bacterial homologs reveal diverging evolution. Bacterial dodecins bind the flavin FMN instead of riboflavin and exhibit a clearly different binding pocket design with inverse incorporations of flavin dimers. The different adoption of flavin changes photochemical properties, making bacterial dodecin a comparably less efficient quencher of flavins. This supports a functional role different for bacterial and archaeal dodecins.
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Affiliation(s)
- Heike Staudt
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Dieter Oesterhelt
- Department of Membrane Biochemistry, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Martin Grininger
- Department of Membrane Biochemistry, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany.
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48
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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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49
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Sun Q, Lu R, Yu A. Structural Heterogeneity in the Collision Complex between Organic Dyes and Tryptophan in Aqueous Solution. J Phys Chem B 2011; 116:660-6. [DOI: 10.1021/jp2100304] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Qinfang Sun
- Department of Chemistry, Renmin University of China, Beijing 100872, People’s Republic of China
| | - Rong Lu
- Department of Chemistry, Renmin University of China, Beijing 100872, People’s Republic of China
| | - Anchi Yu
- Department of Chemistry, Renmin University of China, Beijing 100872, People’s Republic of China
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50
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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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