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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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Chowdhury MH, Lakowicz JR, Ray K. Ensemble and Single Molecule Studies on the Use of Metallic Nanostructures to Enhance the Intrinsic Emission of Enzyme Cofactors. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2011; 115:7298-7308. [PMID: 21603075 PMCID: PMC3097113 DOI: 10.1021/jp112255j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We present a strategy for enhancing the intrinsic emission of the enzyme cofactors flavin adenine dinucleotide (FAD), flavin mononucleotide (FMN) and nicotinamide adenine dinucleotide (NADH). Ensemble studies show that silver island films (SIFs) are the optimal metal enhanced fluorescence (MEF) substrates for flavins and gave emission enhancements of over 10-fold for both FAD and FMN. A reduction in the lifetime of FAD and FMN on SIFs was also observed. Thermally evaporated aluminum films on quartz slides were found to be the optimal MEF substrate for NADH and gave a 5-fold increase in the emission intensity of NADH. We present finite-difference time-domain (FDTD) calculations that compute the enhancement in the radiated power emitting from an excited state dipole emitting in the wavelength range of NADH in close proximity to an aluminum nanoparticle, and a dipole emitting in the emission wavelength of flavins next to a silver nanoparticle. These calculations confirm that aluminum serves as the optimal MEF substrate for NADH and silver was the optimal MEF substrate for flavins. This is because the plasmon resonance properties of aluminum lie in the UV-blue regime and that of silver lie in the visible region. We also present the results of single molecule studies on FMN which show SIFs can both significantly enhance the intrinsic emission from single FMN molecules, significantly reduce their lifetimes and also significantly reduce FMN blinking. This is the first report of the observation of MEF from cofactors both at the ensemble and single molecule level. We hope this study will serve as a platform to encourage the future use of metallic nanostructures to study cofactors using their intrinsic fluorescence to directly monitor enzyme binding reactions without the need of extrinsic labeling of the molecules.
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Abstract
Review - Flavins as photoreceptors of blue light and their spectroscopic propertiesThis review describes 1) the development of studies on flavin photoreceptors as blue light photoreceptors in many living organisms: their kinds and functions; 2) the studies on spectroscopic properties of flavins, both their dimers and monomers; 3) nonradiative excitation energy transport in the presence of monomers and fluorescent/nonflurescent FMN dimers (excitation traps). The existence equilibrated luminescent FMN centers, energy migration and excitation sink to FMN dimers are taken into account.
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Paladini DH, Musumeci MA, Carrillo N, Ceccarelli EA. Induced fit and equilibrium dynamics for high catalytic efficiency in ferredoxin-NADP(H) reductases. Biochemistry 2009; 48:5760-8. [PMID: 19435322 DOI: 10.1021/bi9004232] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ferredoxin-NADP(H) reductase (FNR) is a FAD-containing protein that catalyzes the reversible transfer of electrons between NADP(H) and ferredoxin or flavodoxin. This enzyme participates in the redox-based metabolism of plastids, mitochondria, and bacteria. Plastidic plant-type FNRs are very efficient reductases in supporting photosynthesis. They have a strong preference for NADP(H) over NAD(H), consistent with the main physiological role of NADP(+) photoreduction. In contrast, FNRs from organisms with heterotrophic metabolisms or anoxygenic photosynthesis display turnover rates that are up to 100-fold lower than those of their plastidic and cyanobacterial counterparts. With the aim of elucidating the mechanisms by which plastidic enzymes achieve such high catalytic efficiencies and NADP(H) specificity, we investigated the manner in which the NADP(H) nicotinamide enters and properly binds to the catalytic site. Analyzing the interaction of different nucleotides, substrate analogues, and aromatic compounds with the wild type and the mutant Y308S-FNR from pea, we found that the interaction of the 2'-P-AMP moiety from NADP(+) induces a change that favors the interaction of the nicotinamide, thereby facilitating the catalytic process. Furthermore, the main role of the terminal tyrosine, Y308, is to destabilize the interaction of the nicotinamide with the enzyme, inducing product release and favoring discrimination of the nucleotide substrate. We determined that this function can be replaced by the addition of aromatic compounds that freely diffuse in solution and establish a dynamic equilibrium, reversing the effect of the mutation in the Y308S-FNR mutant.
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Affiliation(s)
- Darío H Paladini
- Molecular Biology Division, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK Rosario, Argentina
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Kudryashova EV, Visser AJWG, van Berkel WJH. Monomer formation and function of p-hydroxybenzoate hydroxylase in reverse micelles and in dimethylsulfoxide/water mixtures. Chembiochem 2008; 9:413-9. [PMID: 18176933 DOI: 10.1002/cbic.200700267] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
It has previously been postulated that the dimeric form of the flavoprotein p-hydroxybenzoate hydroxylase (PHBH) is important for catalysis. Here it is demonstrated that the monomeric form of PHBH is active. In a water/AOT/isooctane reverse micellar system, the function of the monomeric and dimeric forms of PHBH could be observed separately by varying the size of the micelles. A considerable decrease in the K(M) value for p-hydroxybenzoate (POHB) was found for monomeric PHBH, accompanied by a 1.5-fold decrease in enzymatic activity. The same tendency was observed when monomers of PHBH were formed by adding DMSO to the buffer. The FAD in PHBH and PHBH labeled with the fluorescence dye Alexa488 was investigated by time-resolved fluorescence anisotropy to observe monomer formation in water/DMSO mixtures. Monomer formation of PHBH occurred gradually with increasing DMSO content in the mixture. Pure PHBH monomers were detected at DMSO concentrations of 30 % (v/v) and higher.
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Affiliation(s)
- Elena V Kudryashova
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
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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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van den Berg PA, Mulrooney SB, Gobets B, van Stokkum IH, van Hoek A, Williams CH, Visser AJ. Exploring the conformational equilibrium of E. coli thioredoxin reductase: characterization of two catalytically important states by ultrafast flavin fluorescence spectroscopy. Protein Sci 2001; 10:2037-49. [PMID: 11567095 PMCID: PMC2374229 DOI: 10.1110/ps.06701] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The conformational dynamics of wild-type Escherichia coli thioredoxin reductase (TrxR) and the mutant enzyme C138S were studied by ultrafast time-resolved fluorescence of the flavin cofactor in combination with circular dichroism (both in the flavin fingerprint and far-UV regions) and steady-state fluorescence and absorption spectroscopy. The spectroscopic data show two conformational states of the enzyme (named FO and FR), of which the physical characteristics differ considerably. Ultrafast fluorescence lifetime measurements make it possible to distinguish between the two different populations: Dominant picosecond lifetimes of approximately 1 ps (contribution 75%) and 7 ps (8%) are associated with the FO species in TrxR C138S. Long-lived fluorescence with two time constants in the range of 0.2-1 ns (total contribution 17%) originates from enzyme molecules in the FR conformation. The near absence of fast lifetime components in oxidized wild-type TrxR supports the idea of this enzyme being predominantly in the FR conformation. The emission spectrum of the FO conformation is blue-shifted with respect to that of the FR conformation. Because of the large difference in fluorescence characteristics, fluorescence measurements on time scales longer than 100 ps are fully determined by the fraction of enzyme molecules in the FR conformation. Binding of the thiol reagent phenyl mercuric acetate to wild-type enzyme and TrxR C138S stabilizes the enzymes in the FR conformation. Specific binding of the NADPH-analog, AADP(+), to the FR conformation resulted in dynamic fluorescence quenching in support of the multiple quenching sites model. Raising the temperature from 277K-323K resulted in a moderate shift to the FR conformation for TrxR C138S. High concentrations of the cosolvent glycerol triggered the domain rotation from the FO to the FR conformation.
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Affiliation(s)
- P A van den Berg
- MicroSpectroscopy Centre, Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
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