Donor−Acceptor Distance-Dependence of Photoinduced Electron-Transfer Rate in Flavoproteins

Balance between photoreduction efficiency, cofactor affinity, and allosteric coupling of halogenase flavoenzymes

Flavin-dependent halogenases (FDHs) are promising candidates for the sustainable production of halogenated organic molecules by biocatalysis. FDHs require only oxygen, halide and a fully reduced flavin adenine dinucleotide (FADH-) cofactor to generate the reactive HOX that diffuses 10 Å to the substrate binding pocket and enables regioselective oxidative halogenation. A key challenge for the application of FDHs is the regeneration of the FADH-. In vitro, FADH- can be regenerated by photoreduction of the oxidized FAD inside the protein using blue light, turning the halogenase into an inefficient artificial photoenzyme. We aimed to improve the photochemical properties of the tryptophan 5-halogenase PyrH from Streptomyces rugosporus by structure-guided mutagenesis. W279 and W281 of the conserved WxWxIP-motif close to FAD were exchanged against phenylalanine. Time-resolved UV-vis spectroscopy showed that the W281F exchange indeed increased the quantum yield of the one- and two-electron reduction, respectively. The cofactor binding affinity decreased slightly with dissociation constants rising from 31 to 74 μM, as examined by fluorescence anisotropy. FTIR difference spectroscopy demonstrated that the allosteric coupling between the FAD and substrate binding sites was mostly preserved. In contrast, the double mutant did not improve the yield further, while negatively affecting binding affinity and structural coupling. The distal W279F exchange was less effective in all parameters. Photoreductions were additionally delayed by a reversible inactive conformation. We conclude that there is a delicate balance to be considered for screening of FDHs for biocatalysis. Variant PyrH-W281F was found to be the most promising candidate for the application as artificial photoenzyme.

Strategic engineering of alkyl spacer length for a pH-tolerant lysosome marker and dual organelle localization

Long-term visualization of lysosomal properties is extremely crucial to evaluate diseases related to their dysfunction. However, many of the reported lysotrackers are less conducive to imaging lysosomes precisely because they suffer from fluorescence quenching and other inherent drawbacks such as pH-sensitivity, polarity insensitivity, water insolubility, slow diffusibility, and poor photostability. To overcome these limitations, we have utilized an alkyl chain length engineering strategy and synthesized a series of lysosome targeting fluorescent derivatives namely NIMCs by attaching a morpholine moiety at the peri position of the 1,8-naphthalimide (NI) ring through varying alkyl spacers between morpholine and 1,8-naphthalimide. The structural and optical properties of the synthesized NIMCs were explored by 1H-NMR, single-crystal X-ray diffraction, UV-Vis, and fluorescence spectroscopy. Afterward, optical spectroscopic measurements were carefully performed to identify a pH-tolerant, polarity sensitive, and highly photostable fluoroprobes for further live-cell imaging applications. NIMC6 displayed excellent pH-tolerant and polarity-sensitive properties. Consequently, all NIMCs were employed in kidney fibroblast cells (BHK-21) to investigate their applicability for lysosome targeting and probing lysosomal micropolarity. Interestingly, a switching of localization from lysosomes to the endoplasmic reticulum (ER) was also achieved by controlling the linker length and this phenomenon was subsequently applied in determining ER micropolarity. Additionally, the selected probe NIMC6 was also employed in BHK-21 cells for 3-D spheroid imaging and in Caenorhabditis elegans (C. elegans) for in vivo imaging, to evaluate its efficacy for imaging animal models.

Ultrafast photoinduced flavin dynamics in the unusual active site of the tRNA methyltransferase TrmFO

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.

Tailing miniSOG: structural bases of the complex photophysics of a flavin-binding singlet oxygen photosensitizing protein

miniSOG is the first flavin-binding protein that has been developed with the specific aim of serving as a genetically-encodable light-induced source of singlet oxygen (¹O₂). We have determined its 1.17 Å resolution structure, which has allowed us to investigate its mechanism of photosensitization using an integrated approach combining spectroscopic and structural methods. Our results provide a structural framework to explain the ability of miniSOG to produce ¹O₂ as a competition between oxygen- and protein quenching of its triplet state. In addition, a third excited-state decay pathway has been identified that is pivotal for the performance of miniSOG as ¹O₂ photosensitizer, namely the photo-induced transformation of flavin mononucleotide (FMN) into lumichrome, which increases the accessibility of oxygen to the flavin FMN chromophore and makes protein quenching less favourable. The combination of the two effects explains the increase in the ¹O₂ quantum yield by one order of magnitude upon exposure to blue light. Besides, we have identified several surface electron-rich residues that are progressively photo-oxidized, further contributing to facilitate the production of ¹O₂. Our results help reconcile the apparent poor level of ¹O₂ generation by miniSOG and its excellent performance in correlative light and electron microscopy experiments.

Light-induced chromophore and protein responses and mechanical signal transduction of BLUF proteins

Photoreceptor proteins have been used to study how protein conformational changes are induced by alterations in their environments and how their signals are transmitted to downstream factors to dictate physiological responses. These proteins are attractive models because their signal transduction aspects and structural changes can be precisely regulated in vivo and in vitro based on light intensity. Among the known photoreceptors, members of the blue light–using flavin (BLUF) protein family have been well characterized with regard to how they control various light-dependent physiological responses in several microorganisms. Herein, we summarize our current understanding of their photoactivation and signal-transduction mechanisms. For signal transduction, we review recent studies concerning how the BLUF protein, PixD, transmits a light-induced signal to its downstream factor, PixE, to modulate phototaxis of the cyanobacterium Synechocystis sp. PCC6803.

Molecular Mechanism of Flavin Photoprotection by Archaeal Dodecin: Photoinduced Electron Transfer and Mg2+-Promoted Proton Transfer

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.

Synthesis and electronic properties of π-extended flavins

Flavin derivatives with an extended π-conjugation were synthesized in moderate to good yields from aryl bromides via a Buchwald-Hartwig palladium catalyzed amination protocol, followed by condensation of the corresponding aromatic amines with violuric acid. The electronic properties of the new compounds were investigated by absorption and emission spectroscopy, cyclic voltammetry, density functional theory (DFT) and time dependent density functional theory (TDDFT). The compounds absorb up to 550 nm and show strong luminescence. The photoluminescence quantum yields ϕPL measured in dichloromethane reach 80% and in PMMA (poly(methyl methacrylate)) 77%, respectively, at ambient temperature. The electrochemical redox behaviour of π-extended flavins follows the mechanism previously described for the parent flavin.

LucY: A Versatile New Fluorescent Reporter Protein

We report on the discovery, isolation, and use of a novel yellow fluorescent protein. Lucigen Yellow (LucY) binds one FAD molecule within its core, thus shielding it from water and maintaining its structure so that fluorescence is 10-fold higher than freely soluble FAD. LucY displays excitation and emission spectra characteristic of FAD, with 3 excitation peaks at 276 nm, 377 nm, and 460 nm and a single emission peak at 530 nm. These excitation and emission maxima provide the large Stokes shift beneficial to fluorescence experimentation. LucY belongs to the MurB family of UDP-N-acetylenolpyruvylglucosamine reductases. The high resolution crystal structure shows that in contrast to other structurally resolved MurB enzymes, LucY does not contain a potentially quenching aromatic residue near the FAD isoalloxazine ring, which may explain its increased fluorescence over related proteins. Using E. coli as a system in which to develop LucY as a reporter, we show that it is amenable to circular permutation and use as a reporter of protein-protein interaction. Fragmentation between its distinct domains renders LucY non-fluorescent, but fluorescence can be partially restored by fusion of the fragments to interacting protein domains. Thus, LucY may find application in Protein-fragment Complementation Assays for evaluating protein-protein interactions.

Excited state dynamics can be used to probe donor-acceptor distances for H-tunneling reactions catalyzed by flavoproteins

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.

Fluorescence quenching of (dimethylamino)naphthalene dyes Badan and Prodan by tryptophan in cytochromes P450 and micelles

Fluorescence of 2-(N,N-dimethylamino)-6-propionylnaphthalene dyes Badan and Prodan is quenched by tryptophan in Brij 58 micelles as well as in two cytochrome P450 proteins (CYP102, CYP119) with Badan covalently attached to a cysteine residue. Formation of nonemissive complexes between a dye molecule and tryptophan accounts for about 76% of the fluorescence intensity quenching in micelles, the rest is due to diffusive encounters. In the absence of tryptophan, fluorescence of Badan-labeled cytochromes decays with triexponential kinetics characterized by lifetimes of about 100 ps, 700–800 ps, and 3 ns. Site mutation of a histidine residue in the vicinity of the Badan label by tryptophan results in shortening of all three decay lifetimes. The relative amplitude of the fastest component increases at the expense of the two slower ones. The average quenching rate constants are 4.5 × 10⁸ s^–1 (CYP102) and 3.7 × 10⁸ s^–1 (CYP119), at 288 K. Cyclic voltammetry of Prodan in MeCN shows a reversible reduction peak at −1.85 V vs NHE that becomes chemically irreversible and shifts positively upon addition of water. A quasireversible reduction at −0.88 V was observed in an aqueous buffer (pH 7.3). The excited-state reduction potential of Prodan (and Badan) is estimated to vary from about +0.6 V (vs NHE) in polar aprotic media (MeCN) to approximately +1.6 V in water. Tryptophan quenching of Badan/Prodan fluorescence in CYPs and Brij 58 micelles is exergonic by ≤0.5 V and involves tryptophan oxidation by excited Badan/Prodan, coupled with a fast reaction between the reduced dye and water. Photoreduction is a new quenching mechanism for 2-(N,N-dimethylamino)-6-propionylnaphthalene dyes that are often used as solvatochromic polarity probes, FRET donors and acceptors, as well as reporters of solvation dynamics.

Structural heterogeneity among four subunits in pyranose 2-oxidase: A molecular dynamics simulation study

The homotetramer pyranose 2-oxidase (P2O) from Tetrametes multicolor contains flavin adenine dinucleotide (FAD) as a cofactor, and displays two conformers with different transient fluorescence spectra and lifetimes (ca. 0.1 ps and 360 ps). The ultrashort lifetimes of isoalloxazine (Iso) are ascribed to the photoinduced electron transfer (ET) from Trp168 to the excited Iso. Here, the structural heterogeneity among the four subunits in solution was studied by means of molecular dynamics simulation (MDS). The ET donor–acceptor distances in crystal and solution were compared. The distribution of the H-bond distances between Iso and the surrounding amino acids revealed appreciable differences among the four subunits. The structural fluctuations in two distant places were examined for the Iso-P and Iso-Q distances (where P and Q are Trp or Tyr) with the correlation coefficients between Iso-P and Iso-Q distances, revealing cooperative motions even though P and Q were more than 1 nm apart and located in different subunits. Moreover, distributions of the distances between Iso and its closest ionic amino acids markedly differed among the four subunits. Electrostatic (ES) energies between the Iso anion and the ionic amino acids in the entire protein were obtained using a static dielectric constant of 1. The ES energy in each subunit was strongly influenced by the other subunits, whilst the distributions of the ES energies greatly differed among the four subunits. This heterogeneous distribution of the ES energy between subunits may contribute to the large differences in the experimentally detected ET rates.

Photoinduced electron transfer modeling to simulate flavoprotein fluorescence decay

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.

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

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.

Ultrafast excited-state deactivation of flavins bound to dodecin

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.

Phototriggering electron flow through Re(I)-modified Pseudomonas aeruginosa azurins

The [Re(I)(CO)(3)(4,7-dimethyl-1,10-phenanthroline)(histidine-124)(tryptophan-122)] complex, denoted [Re(I)(dmp)(W122)], of Pseudomonas aeruginosa azurin behaves as a single photoactive unit that triggers very fast electron transfer (ET) from a distant (2 nm) Cu(I) center in the protein. Analysis of time-resolved (ps-μs) IR spectroscopic and kinetics data collected on [Re(I)(dmp)(W122)AzM] (in which M=Zn(II), Cu(II), Cu(I); Az=azurin) and position-122 tyrosine (Y), phenylalanine (F), and lysine (K) mutants, together with excited-state DFT/time-dependent (TD)DFT calculations and X-ray structural characterization, reveal the character, energetics, and dynamics of the relevant electronic states of the [Re(I)(dmp)(W122)] unit and a cascade of photoinduced ET and relaxation steps in the corresponding Re-azurins. Optical population of [Re(I)(imidazole-H124)(CO)(3)]→dmp (1)CT states (CT=charge transfer) is followed by around 110 fs intersystem crossing and about 600 ps structural relaxation to a (3)CT state. The IR spectrum indicates a mixed Re(I)(CO)(3),A→dmp/π→π(*)(dmp) character for aromatic amino acids A122 (A=W, Y, F) and Re(I)(CO)(3)→dmp metal-ligand charge transfer (MLCT) for [Re(I)(dmp)(K122)AzCu(II)]. In a few ns, the (3)CT state of [Re(I)(dmp)(W122)AzM] establishes an equilibrium with the [Re(I)(dmp(.-))(W122(.+))AzM] charge-separated state, (3)CS, whereas the (3)CT state of the other Y, F, and K122 proteins decays to the ground state. In addition to this main pathway, (3)CS is populated by fs- and ps-W(indole)→Re(II) ET from (1)CT and the initially "hot" (3)CT states, respectively. The (3)CS state undergoes a tens-of-ns dmp(.-)→W122(.+) ET recombination leading to the ground state or, in the case of the Cu(I) azurin, a competitively fast (≈30 ns over 1.12 nm) Cu(I)→W(.+) ET, to give [Re(I)(dmp(.-))(W122)AzCu(II)]. The overall photoinduced Cu(I)→Re(dmp) ET through [Re(I)(dmp)(W122)AzCu(I)] occurs over a 2 nm distance in <50 ns after excitation, with the intervening fast (3)CT-(3)CS equilibrium being the principal accelerating factor. No reaction was observed for the three Y, F, and K122 analogues. Although the presence of [Re(dmp)(W122)AzCu(II)] oligomers in solution was documented by mass spectrometry and phosphorescence anisotropy, the kinetics data do not indicate any significant interference from the intermolecular ET steps. The ground-state dmp-indole π-π interaction together with well-matched W/W(.+) and excited-state [Re(II)(CO)(3)(dmp(.-))]/[Re(I)(CO)(3)(dmp(.-))] potentials that result in very rapid electron interchange and (3)CT-(3)CS energetic proximity, are the main factors responsible for the unique ET behavior of [Re(I)(dmp)(W122)]-containing azurins.

Inhibiting intramolecular electron transfer in flavin adenine dinucleotide by host-guest interaction: a fluorescence study

Modulation in the photophysical properties and intramolecular electron transfer behavior of the flavin adenine dinucleotide (FAD) molecule has been investigated in the presence of the macrocyclic hosts, alpha-, beta- and gamma-cyclodextrins (CDs), using absorption and steady-state and time-resolved fluorescence measurements. The results demonstrate that only the beta-CD host has a suitable cavity dimension to form a weak inclusion complex with FAD by encapsulating the adenine moiety, which is the preferred binding site in the large FAD molecule. Interestingly, in spite of the weak binding interaction, a significant enhancement in the fluorescence intensity of FAD is observed on complexation with beta-CD, and this has been attributed mainly to the modulation in the conformational dynamics of FAD in the presence of beta-CD. In aqueous solutions, a good fraction of FAD molecules exist in a "closed" conformation with the adenine and isoalloxazine rings stacked on each other, thus leading to very efficient fluorescence quenching due to the ultrafast intramolecular electron transfer from adenine to the isoalloxazine moiety. Complex formation with beta-CD inhibits this intramolecular electron transfer by changing the "closed" conformation of FAD to the "open" form, wherein the adenine and isoalloxazine moieties are widely separated, thus prohibiting the fluorescence quenching process. Further evidence for the conformational changes has been obtained by the observation of a long lifetime component in the fluorescence decay of FAD in the presence of beta-CD, which corresponds to the decay of the unquenched "open" form of FAD. Fluorescence up-conversion studies also indicate the absence of any ultrafast component in the fluorescence decay arising from the complexed FAD, thus supporting the formation of the "open" form in the presence of beta-CD, with no intramolecular electron transfer.

Sampling the conformation space of FAD in water-methanol mixtures through molecular dynamics and fluorescence measurements

The excited state of flavin adenine dinucleotide (FAD), dissolved in water, is subjected to intensive quenching due to electron transfer from the adenine moiety to the excited isoalloxazine ring. Increasing the methanol concentration in the solution enhances the quantum yield of the fluorescence. In the present study, we carried out molecular dynamics simulations of FAD in explicit water and water-methanol mixtures over time frames of hundreds of nanoseconds. The simulations record rapid structural fluctuations of the molecule, where the distance between the centers of mass (COMs) of the two nucleotides varied from contact distance (folded) up to fully extended (open) structure. The methanol affected the dynamics of the FAD by enhancing the frequency of unfolding events without any effect on the lifetime of the open state. The correlation of the molecular dynamics simulations with fluorescence titration of the FAD in water/methanol mixtures indicates that the internal quenching takes place when the distance between COMs is <5.5 +/- 0.5 A.

Ultrafast solvation dynamics of flavin mononucleotide in the reductase component of p-hydroxyphenylacetate hydroxylase

The reductase unit of p-hydroxyphenylacetate hydroxylase contains flavin mononucleotide (FMN) as a cofactor. Fluorescence decay curves measured by fluorescence up-conversion method were remarkably dependent on monitored emission wavelength. The fluorescence lifetime was shorter at the shorter emission wavelengths and longer at the longer wavelengths. Spectral shift correlation function of p-coumaric acid in water and FMN in C1 protein in buffer solution were expressed by two-exponential functions. Correlation times, phi1 and phi2, of p-coumaric acid were 0.053 and 0.650 ps, respectively, which was similar to previous works. phi1 and phi2 of C1 were 0.455 and 250 ps, respectively. The Stokes shift from t=0 to t=infinity was 2200 cm(-1), while it is 500 cm(-1) in the static Stokes shift obtained by the solvent effect of the fluorescence spectrum under static excitation. This suggests that the isoalloxazine ring of FMN in C1 is exposed in hydrophilic environment. Such large Stokes shift was unusual among flavoproteins. The biphasic decay of the spectral correlation function in C1 was discussed and compared to the biphasic decay of tryptophan in proteins.

Acceleration of electron-transfer-induced fluorescence quenching upon conversion to the signaling state in the blue-light receptor, TePixD, from Thermosynechococcus elongatus

TePixD is a blue light using flavin (BLUF) protein of a thermophilic cyanobacterium, Thermosynechococcus elongatus. The fluorescence dynamics of TePixD was observed for the first time in both its dark-adapted and signaling (red-shifted) forms with a 200-fs time resolution. The fluorescence up-conversion setup was used in the time region up to 60 ps, and the streak-camera setup was used in the time region up to 1 ns. To avoid the accumulation of the red-shifted form by the exciting laser irradiation, the sample solution was circulated using a diaphragm pump. A handmade flow cuvette with a small cross section was used to achieve a fast flow of the solution in the excited region. The fluorescence decay times were unequivocally determined to be 13.6 and 114 ps for the dark-adapted form and 1.37 ps for the red-shifted form. The double-exponential fluorescence decay in the dark-adapted form suggested the coexistence of two conformations that have the 13.6- and 114-ps decay components, respectively. The single-exponential fluorescence decay in the red-shifted form suggested the elimination of heterogeneity in the conformation upon the light-induced conversion. The fast fluorescence-quenching components were almost eliminated in the mutant in which the conserved tyrosine Tyr8 is replaced by phenylalanine. Thus, the fluorescence quench was concluded to arise from the electron transfer from Tyr8, to the excited flavin chromophore. The 10-fold-faster quenching in the red-shifted form suggested the acceleration of the electron transfer. The faster decay time of 13.6 ps for the dark-adapted form was found to be almost temperature independent in the region from 10 to 40 degrees C. This suggested that the energy gap, DeltaG, in Marcus's electron-transfer theory is optimized to give the fastest rate. The acceleration of the electron transfer in the red-shifted form is interpreted to be due to the enhancement of the electronic-coupling factor between the donor and acceptor. A shortening of the Tyr8-flavin distance by 1.0-1.5 A was suggested if we adopt the empirical formula for the donor-acceptor distance dependence of the electron transfer rate.

Dodecin is the key player in flavin homeostasis of archaea

Flavins are employed to transform physical input into biological output signals. In this function, flavins catalyze a variety of light-induced reactions and redox processes. However, nature also provides flavoproteins with the ability to uncouple the mediation of signals. Such proteins are the riboflavin-binding proteins (RfBPs) with their function to store riboflavin for fast delivery of FMN and FAD. Here we present in vitro and in vivo data showing that the recently discovered archaeal dodecin is an RfBP, and we reveal that riboflavin storage is not restricted to eukaryotes. However, the function of the prokaryotic RfBP dodecin seems to be adapted to the requirement of a monocellular organism. While in eukaryotes RfBPs are involved in trafficking riboflavin, and dodecin is responsible for the flavin homeostasis of the cell. Although only 68 amino acids in length, dodecin is of high functional versatility in neutralizing riboflavin to protect the cellular environment from uncontrolled flavin reactivity. Besides the predominant ultrafast quenching of excited states, dodecin prevents light-induced riboflavin reactivity by the selective degradation of riboflavin to lumichrome. Coordinated with the high affinity for lumichrome, the directed degradation reaction is neutral to the cellular environment and provides an alternative pathway for suppressing uncontrolled riboflavin reactivity. Intriguingly, the different structural and functional properties of a homologous bacterial dodecin suggest that dodecin has different roles in different kingdoms of life.

Simultaneous analysis of ultrafast fluorescence decays of FMN binding protein and its mutated proteins by molecular dynamic simulation and electron transfer theory

Ultrafast fluorescence decays of FMN binding proteins (FBP) from Desulfovibrio vulgaris (Miyazaki F) were analyzed with an electron transfer (ET) theory by Kakitani and Mataga (KM theory). Time-dependent distances among isoalloxazine (Iso) and Trp-32, Tyr-35, and Trp-106 in wild-type FBP (WT), among Iso and Tyr-32, Tyr-35, and Trp-106 in W32Y (Trp-32 was replaced by Tyr-32), and among Iso and Tyr-35 and Trp-106 in W32A (Trp-32 was replaced by Ala-32) were determined by molecular dynamic simulation (MD). Electrostatic energies between Iso anion and all other ionic groups, between Trp-32 cation and all other ionic groups, and between Tyr-32 cation and all other ionic groups were calculated in WT, W32Y, and W32A, from the MD coordinates. ET parameters contained in KM theory, such as frequency (nu 0), a coefficient of the ET process (beta), a critical distance of the ET process ( R 0), standard free energy related to the electron affinity of the excited Iso ( G Iso (0)), and the static dielectric constant in FBP species (epsilon 0), were determined with and without inclusion of the electrostatic energy, so as to fit the calculated fluorescence decays with the observed decays of all FBP species, by a nonlinear least-squares method according to the Marquardt algorithm. In the analyses the parameters, nu 0, beta, and R 0 were determined separately between Trp residues and Tyr residues among all FBP species. Calculated fluorescence intensities with the inclusion of the electrostatic energy fit quite well with the observed ones of all WT, W32Y, and W32A.

Comparison between Ultrafast Fluorescence Dynamics of FMN Binding Protein from Desulfovibrio vulgaris, Strain Miyazaki, in Solution vs Crystal Phases

Ultrafast fluorescence dynamics of FMN binding protein (FBP) from Desulfobivrio vulgaris, strain Miyaxaki F, were compared in solution and crystal phases. Fluorescence lifetimes of FBP were 167 fs (96%) and 1.5 ps (4%) in solution (tau(av) = 220 fs), and 730 fs (60%) and longer than 10 ps (40%) in crystals (tau(av) = 4.44 ps). The quenching of the fluorescence of flavin in the protein was considered to be due to photoinduced electron transfer (ET) from Trp or Tyr to the excited isoalloxazine (Iso) nearby. The average lifetime was 20 times longer in crystal vs in solution. Averaged distances between Iso and nearby Trp-32, Tyr-35, and Trp-106 were 8.42, 7.36, and 8.15 A in solution, respectively (obtained by NMR spectroscopy), and 7.05, 7.72, and 8.49 A in crystal, respectively (obtained by X-ray crystallography). The prolonged lifetime in crystal cannot be elucidated by the change in the distances between the states. It was suggested that the longer lifetime in crystal was ascribed to the absence of water molecules around FBP with rapid motional freedom, which may be the driving force for the ET in flavoproteins.