Flavin dynamics in oxidized Clostridium beijerinckii flavodoxin as assessed by time-resolved polarized fluorescence

Molecular insights into the role of heme in the transcriptional regulatory system AppA/PpsR

Heme has been shown to have a crucial role in the signal transduction mechanism of the facultative photoheterotrophic bacterium Rhodobacter sphaeroides. It interacts with the transcriptional regulatory complex AppA/PpsR in which AppA and PpsR function as the antirepressor and repressor, respectively of photosynthesis gene expression. The mechanism, however of this interaction remains incompletely understood. In this study, we combined EPR spectroscopy and FRET to demonstrate the ligation of heme in PpsR with a proposed cysteine residue. We show that heme binding in AppA affects the fluorescent properties of the dark-adapted state of the protein, suggesting a less constrained flavin environment compared to the absence of heme and the light-adapted state. We performed ultrafast transient absorption measurements in order to reveal potential differences in the dynamic processes in the full-length AppA and its heme-binding domain alone. Comparison of the CO-binding dynamics demonstrates a more open heme pocket in the holo-protein, qualitatively similar to what has been observed in the CO sensor RcoM-2, and suggests a communication path between the BLUF and SCHIC domains of AppA. We have also examined quantitatively, the affinity of PpsR to bind to individual DNA fragments of the puc promoter using fluorescence anisotropy assays. We conclude that oligomerization of PpsR is initially triggered by binding of one of the two DNA fragments and observe a ∼10-fold increase in the dissociation constant K_d for DNA binding upon heme binding to PpsR. Our study provides significant new insight at the molecular level on the regulatory role of heme that modulates the complex transcriptional regulation in R. sphaeroides and supports the two levels of heme signaling, via its binding to AppA and PpsR and via the sensing of gases like oxygen.

Functional dynamics of a single tryptophan residue in a BLUF protein revealed by fluorescence spectroscopy

Blue Light Using Flavin (BLUF) domains are increasingly being adopted for use in optogenetic constructs. Despite this, much remains to be resolved on the mechanism of their activation. The advent of unnatural amino acid mutagenesis opens up a new toolbox for the study of protein structural dynamics. The tryptophan analogue, 7-aza-Trp (7AW) was incorporated in the BLUF domain of the Activation of Photopigment and pucA (AppA) photoreceptor in order to investigate the functional dynamics of the crucial W104 residue during photoactivation of the protein. The 7-aza modification to Trp makes selective excitation possible using 310 nm excitation and 380 nm emission, separating the signals of interest from other Trp and Tyr residues. We used Förster energy transfer (FRET) between 7AW and the flavin to estimate the distance between Trp and flavin in both the light- and dark-adapted states in solution. Nanosecond fluorescence anisotropy decay and picosecond fluorescence lifetime measurements for the flavin revealed a rather dynamic picture for the tryptophan residue. In the dark-adapted state, the major population of W104 is pointing away from the flavin and can move freely, in contrast to previous results reported in the literature. Upon blue-light excitation, the dominant tryptophan population is reorganized, moves closer to the flavin occupying a rigidly bound state participating in the hydrogen-bond network around the flavin molecule.

Bioluminophore and Flavin Mononucleotide Fluorescence Quenching of Bacterial Bioluminescence-A Theoretical Study

Bacterial bioluminescence with continuous glow has been applied to the fields of environmental toxin monitoring, drug screening, and in vivo imaging. Nonetheless, the chemical form of the bacterial bioluminophore is still a bone of contention. Flavin mononucleotide (FMN), one of the light-emitting products, and 4a-hydroxy-5-hydro flavin mononucleotide (HFOH), an intermediate of the chemical reactions, have both been assumed candidates for the light emitter because they have similar molecular structures and fluorescence wavelengths. The latter is preferred in experiments and was assigned in our previous density functional study. HFOH displays weak fluorescence in solutions, but exhibits strong bioluminescence in the bacterial luciferase. FMN shows the opposite behavior; its fluorescence is quenched when it is bound to the luciferase. This is the first example of flavin fluorescence quenching observed in bioluminescent systems and is merely an observation, both the quenching mechanism and quencher are still unclear. Based on theoretical analysis of high-level quantum mechanics (QM), combined QM and molecular mechanics (QM/MM), and molecular dynamics (MD), this paper confirms that HFOH in its first singlet excited state is the bioluminophore of bacterial bioluminescence. More importantly, the computational results indicate that Tyr110 in the luciferase quenches the FMN fluorescence via an electron-transfer mechanism.

Sensitive fluorescence-based detection of magnetic field effects in photoreactions of flavins

Magnetic field effect studies have been conducted on a variety of flavin-based radical pair systems chosen to model the magnetosensitivity of the photoinduced radical pairs found in cryptochrome flavoproteins. Cryptochromes are blue-light photoreceptor proteins which are thought to mediate avian magnetoreception, an hypothesis supported by recent in vitro observations of magnetic field-dependent reaction kinetics for a light-induced radical pair in a cryptochrome from the plant Arabidopsis thaliana. Many cryptochromes are difficult to express in large quantities or high concentrations and are easily photodegraded. Magnetic field effects are typically measured by spectroscopic detection of the transient radical (pair) concentrations. Due to its low sensitivity, single-pass transient absorption spectroscopy can be of limited use in such experiments and much recent work has involved development of other methodologies offering improved sensitivity. Here we explore the use of flavin fluorescence as the magnetosensitive probe and demonstrate the exceptional sensitivity of this technique which allows the detection of magnetic field effects in flavin samples at sub-nanomolar concentrations and in cryptochromes.

Ultrafast real-time visualization of active site flexibility of flavoenzyme thymidylate synthase ThyX

In many bacteria the flavoenzyme thymidylate synthase ThyX produces the DNA nucleotide deoxythymidine monophosphate from dUMP, using methylenetetrahydrofolate as carbon donor and NADPH as hydride donor. Because all three substrates bind in close proximity to the catalytic flavin adenine dinucleotide group, substantial flexibility of the ThyX active site has been hypothesized. Using femtosecond time-resolved fluorescence spectroscopy, we have studied the conformational heterogeneity and the conformational interconversion dynamics in real time in ThyX from the hyperthermophilic bacterium Thermotoga maritima. The dynamics of electron transfer to excited flavin adenine dinucleotide from a neighboring tyrosine residue are used as a sensitive probe of the functional dynamics of the active site. The fluorescence decay spanned a full three orders of magnitude, demonstrating a very wide range of conformations. In particular, at physiological temperatures, multiple angstrom cofactor-residue displacements occur on the picoseconds timescale. These experimental findings are supported by molecular dynamics simulations. Binding of the dUMP substrate abolishes this flexibility and stabilizes the active site in a configuration where dUMP closely interacts with the flavin cofactor and very efficiently quenches fluorescence itself. Our results indicate a dynamic selected-fit mechanism where binding of the first substrate dUMP at high temperature stabilizes the enzyme in a configuration favorable for interaction with the second substrate NADPH, and more generally have important implications for the role of active site flexibility in enzymes interacting with multiple poly-atom substrates and products. Moreover, our data provide the basis for exploring the effect of inhibitor molecules on the active site dynamics of ThyX and other multisubstrate flavoenzymes.

Rotational diffusion of the α(2a) adrenergic receptor revealed by FlAsH labeling in living cells

The fluorescein arsenical hairpin binder (FlAsH) shows much promise to determine the relative orientations of protein regions and structures even in living cells and in the plasma membrane. In this study, we characterized FlAsH's photophysical properties by steady-state anisotropy and time-resolved single photon counting for further applications with G-protein coupled receptors. We find that FlAsH has a relatively high initial anisotropy of 0.31 ± 0.01 and a three-component fluorescence lifetime with an average of 4.1 ± 0.1 ns. We characterized the FlAsH fluorophore orientation in the α(2A) adrenergic receptor revealing rigid orientations of FlAsH in the membrane plane for rotational correlation times of ∼50 ns in living cells. To elucidate the fluorophore-membrane orientation and rotational correlation time, an anisotropy treatment similar to that of another researcher (Axelrod, D. 1979. Biophys. J. 26:557-573) was developed. The rotational correlation times were observed to increase by up to 16 ns after agonist addition. The rotational correlation time also allowed for a comparison to the theoretical relationship between translational and rotational diffusion (originally proposed by Saffman, P. G., and M. Delbrück. 1975. Proc. Natl. Acad. Sci. USA. 72:3111-3113) and revealed a discrepancy of a factor between 10 and 100.

Self-quenching of uranin: Instrument response function for color sensitive photo-detectors

Concentration is a key determining factor in the fluorescence properties of organic fluorophores. We studied self-quenching of disodium fluorescein (uranin) fluorescence in polyvinyl alcohol (PVA) thin films. The concentration dependent changes in brightness and anisotropy were followed by a lifetime decrease. We found that at a concentration of 0.54 M, the lifetime decreases to 7 ps. At a concentration of 0.18 M the lifetime was 10 ps with the relatively high quantum yield of 0.002. In these conditions the fluorescence intensity decay was homogeneous (well approximated by a single lifetime). We realized that such a sample was an ideal fluorescence lifetime standard for spectroscopy and microscopy, and therefore characterized instrument response functions for a time-domain technique. We show that self-quenched uranin enables measurements free of the color effect, making it a superior choice for a lifetime reference over scattered light.

Fluorescence instrument response standards in two-photon time-resolved spectroscopy

We studied the fluorescence properties of several potential picosecond lifetime standards suitable for two-photon excitation from a Ti:sapphire femtosecond laser. The fluorescence emission of the selected fluorophores (rose bengal, pyridine 1, and LDS 798) covered the visible to near-infrared wavelength range from 550 to 850 nm. We suggest that these compounds can be used to measure the appropriate instrument response functions needed for accurate deconvolution of fluorescence lifetime data. Lifetime measurements with multiphoton excitation that use scatterers as a reference may fail to properly resolve fluorescence intensity decays. This is because of the different sensitivities of photodetectors in different spectral regions. Also, detectors often lose sensitivity in the near-infrared region. We demonstrate that the proposed references allow a proper reconvolution of measured lifetimes. We believe that picosecond lifetime standards for two-photon excitation will find broad applications in multiphoton spectroscopy and in fluorescence lifetime imaging microscopy (FLIM).

Effect of quinone on the fluorescence decay dynamics of endogenous flavin bound to bacterial luciferase

The interaction of quinone with luciferase from Photobacterium leiognathi was studied based on the fluorescence decay measurements of the endogenous flavin bound to the enzyme. Homologous 1,4-quinones, 1,4-benzoquinone, methyl-1,4-benzoquinone, 2-methyl-5-isopropyl-1,4-benzoquine and 1,4-naphthoquinone, were investigated. In the absence of quinone, the fluorescence intensity and anisotropy decays of the endogenous flavin exhibited two intensity decay lifetimes (~1 and 5 ns) and two anisotropy decay lifetimes (~0.2 and 20 ns), suggesting a heterogeneous quenching and a rotational mobility microenvironment of the active site of the luciferase, respectively. In the presence of quinone, the intensity decay heterogeneity was largely maintained, whereas the fraction of the short anisotropy decay component and the averaged rotational rate of FMN increased with the increasing hydrophobicity of the quinone. We hypothesize that the hydrophobicity of the quinone plays a role in the non-specific inhibition mechanism of xenobiotic molecules in the bacterial bioluminescence system via altering the rotational mobility of the endogenous flavin in the luciferase.

Redox compounds influence on the NAD(P)H:FMN-oxidoreductase-luciferase bioluminescent system

A review of the mechanisms of the exogenous redox compounds influence on the bacterial coupled enzyme system: NAD(P)H:FMN-oxidoreductase-luciferase has been done. A series of quinones has been used as model organic oxidants. The three mechanisms of the quinones' effects on bioluminescence were suggested: (1) inhibition of the NADH-dependent redox reactions; (2) interactions between the compounds and the enzymes of the coupled enzyme system; and (3) intermolecular energy migration. The correlation between the kinetic parameters of bioluminescence and the standard redox potential of the quinones proved that the inhibition of redox reactions was the key mechanism by which the quinones decrease the light emission intensity. The changes in the fluorescence anisotropy decay of the endogenous flavin of the enzyme preparations showed the direct interaction between quinones and enzymes. It has been demonstrated that the intermolecular energy migration mechanism played a minor role in the effect of quinones on the bioluminescence. A comparative analysis of the effect of quinones, phenols and inorganic redox compounds on bioluminescent coupled enzyme systems has been carried out.

Bioluminescence and exogenous compounds: physico-chemical basis for bioluminescent assay

Bioluminescent systems are convenient objects to study mechanisms of influence of exogenous molecules on living organisms. Classification of physical and physico-chemical mechanisms of the effects of luminous bacteria Photobacterium leiognathi on bioluminescent reactions is suggested. Five mechanisms are discussed: (1) change of electron-excited states' population and energy transfer, (2) change of efficiency of S-T conversion in the presence of external heavy atom, (3) change of rates of coupled reactions, (4) interactions with enzymes and variation of enzymatic activity, (5) nonspecific effects of electron acceptors. Effects of various groups of chemical compounds are discussed according to the classification suggested. The compounds are: a series of fluorescent dyes, organic oxidizers, organic and inorganic heavy-atom containing compounds, and metallic salts. Applications of fluorescence time-resolved and steady-state techniques, as well as bioluminescence kinetics study, are discussed. The patterns of exogenous compounds' influence form a physico-chemical basis for bioluminescent ecological assay.

Characteristics of endogenous flavin fluorescence of Photobacterium leiognathi luciferase and Vibrio fischeri NAD(P)H:FMN-oxidoreductase

The bioluminescent bacterial enzyme system NAD(P)H:FMN-oxidoreductase-luciferase has been used as a test system for ecological monitoring. One of the modes to quench bioluminescence is the interaction of xenobiotics with the enzymes, which inhibit their activity. The use of endogenous flavin fluorescence for investigation of the interactions of non-fluorescent compounds with the bacterial luciferase from Photobacterium leiognathi and NAD(P)H:FMN-oxidoreductase from Vibrio fischeri has been proposed. Fluorescence spectroscopy methods have been used to study characteristics of endogenous flavin fluorescence (fluorophore lifetime, the rotational correlation time). The fluorescence anisotropy behaviour of FMN has been analysed and compared to that of the enzyme-bound flavin. The fluorescence characteristics of endogenous flavin of luciferase and NAD(P)H:FMN-oxidoreductase have been shown to be applicable in studying enzymes' interactions with non-fluorescent compounds.

Effect of inorganic phosphate on FMN binding and loop flexibility in Desulfovibrio desulfuricans apo-flavodoxin

The complex between flavin mononucleotide (FMN) and apo-flavodoxin is dominated by isoalloxazine-stacking interactions and 5'-phosphate hydrogen bonds. We show here that FMN binding to Desulfovibrio desulfuricans apo-flavodoxin is faster and the affinity is higher in the presence of inorganic phosphate as compared to in its absence (I=110 mM, pH 7, 20 degrees C). The transition-state of complex formation was investigated by phi-value analysis using Trp60Ala and Tyr98Ala apo-flavodoxin variants. We find that Tyr98 is highly involved in the FMN/protein transition state independent of inorganic phosphate, whereas the participation of Trp60 is modulated by inorganic phosphate. The phi-value for Trp60 is higher without phosphate, implying that at this condition stronger binding of Trp60 is required in the transition state to assure successful complex formation. Consistent with the experimental data, all-atom molecular dynamic simulations reveal that the presence of an anion in the phosphate subsite restricts the mobility of the Trp60-containing loop in terms of both backbone and side-chain movements, but has no effect on the Tyr98-containing loop. The overall thermodynamic stability of apo-flavodoxin is higher in the presence of inorganic phosphate as compared to in its absence (I=110 mM, pH 7, 20 degrees C). Kinetic experiments reveal that the additional stability originates in slower unfolding. The combined experimental and computational observations demonstrate that phosphate has an ordering effect on the Trp60-containing loop, which positions Trp60 favorably for FMN binding and increases the barrier for protein unfolding.

Mechanism of flavin mononucleotide cofactor binding to the Desulfovibrio vulgaris flavodoxin. 1. Kinetic evidence for cooperative effects associated with the binding of inorganic phosphate and the 5'-phosphate moiety of the cofactor

The pathway(s) by which the flavin cofactor binds to the apoflavoprotein is the subject of some debate. The crystal and NMR structures of several different flavodoxins have provided some insight, although there is disagreement about the location of the initial interaction between the flavin mononucleotide (FMN) and the apoflavodoxin and the degree of protein conformational change associated with cofactor binding [Genzor, C. G., Perales-Alcon, A., Sancho, J., and Romero, A. (1996) Nat. Struct. Biol. 3, 329-332; Steensma, E., and van Mierlo, C. P. M. (1998) J. Mol. Biol. 282, 653-666]. Binding kinetics using stopped-flow spectrofluorimetry and phosphate competition studies were used to develop a model for flavin binding to the flavodoxin from Desulfovibrio vulgaris. In the presence of phosphate, the time course of fluorescence quenching associated with FMN binding to apoflavodoxin was biphasic, whereas riboflavin, which lacks the 5'-phosphate group of FMN, displayed monophasic binding kinetics. When the concentration of phosphate in solution was increased, the FMN binding rates of the two phases behaved differently; the rate of one phase decreased, while the rate of the other increased. A similar increase in the single phase associated with riboflavin binding was also observed. This has led to the following model. The binding of the flavin isoalloxazine ring to its subsite is dependent on the presence of a phosphate group in the phosphate-binding subsite. When phosphate is in the buffer solution, FMN can bind in either of two ways: by the initial insertion of the 5'-phosphate group followed by ring binding or, when inorganic phosphate from solution is bound, the insertion of the isoalloxazine ring first. Riboflavin, which lacks the phosphate moiety of FMN, binds only in the presence of inorganic phosphate, presumably due to the binding of this group in the phosphate-binding subsite. These results suggest that cooperative interactions exist between the phosphate subsite and the ring-binding region in the D. vulgaris flavodoxin that are necessary for isoalloxazine ring binding.

Advances in flavin and flavoprotein optical spectroscopy

Flavins and flavoproteins are versatile redox cofactors that can perform both one- and two-electron transfer. Because they are highly colored in all three oxidation states, optical spectroscopy has been exploited for decades to study these redox changes. This review summarizes the application of optical spectroscopies to flavins and flavoproteins since 1990. Special emphasis is placed on new techniques, such as Stark spectroscopy, as well as significant refinements in more well known techniques, such as resonance Raman spectroscopy and ultrafast spectroscopy.

Role of methionine 56 in the control of the oxidation-reduction potentials of the Clostridium beijerinckii flavodoxin: effects of substitutions by aliphatic amino acids and evidence for a role of sulfur-flavin interactions

Flavodoxins are small electron transferases that participate in low-potential electron transfer pathways. The flavodoxin protein is able to separate the two redox couples of the noncovalently bound flavin mononucleotide (FMN) cofactor through the differential thermodynamic stabilization or destabilization of each of its redox states. In the flavodoxin from Clostridium beijerinckii, the sulfur atom of methionine 56 is in direct contact with the re or inner face of the isoalloxazine ring of the FMN cofactor. In this study, evidence was sought for a possible role for sulfur-aromatic (flavin) interactions in the regulation of one-electron reduction potentials in flavoproteins. Met56 was systematically replaced with all the naturally occurring aliphatic amino acids by site-directed mutagenesis. Replacement of Met56 with alanine or glycine increased the midpoint potentials at pH 7 for the oxidized-semiquinone couple by up to 20 mV compared to that of the wild type, while replacement by the longer chain aliphatic residues decreased the midpoint potential by >30 mV. The midpoint potential for the semiquinone-hydroquinone couple was less negative than that for the wild type for all the mutants, increasing by as much as 90 mV for the M56I mutant. For the M56A mutant, the loss of approximately 0.5 kcal/mol in the binding energy for oxidized FMN and an increase of 1. 6 kcal/mol for the flavin hydroquinone, relative to that of the wild type, are responsible for the observed changes in the midpoint potentials. The stability of the semiquinone complex of this mutant was not affected. The one-election reduction potentials for the M56L, M56I, and M56V mutants are also influenced by the differential stabilization of the three redox states; however, the semiquinone complex was significantly less stable in these proteins. These differences are likely the consequence of the introduction of additional steric factors and an apparent structural preference for a smaller or more flexible side chain at this position in the semiquinone complex. While the other factors may contribute, it is argued that the results obtained for the entire group of mutants are consistent with the elimination of important sulfur-flavin interactions that contribute in part to the stabilization of the oxidized and destabilization of the hydroquinone states of the cofactor in this flavodoxin. The results of this study also demonstrate unequivocally the functional importance of this methionine residue and that it is unique among the aliphatic amino acids in its capacity to generate the physiologically relevant low reduction potential exhibited by the C. beijerinckii flavodoxin.

A comparative picosecond-resolved fluorescence study of tryptophan residues in iron-sulfur proteins

The fluorescence intensity and anisotropy decays of the intrinsic tryptophan emission from six Fe/S proteins (ranging from the very simplest ones to enzyme complexes containing one, two or more Trp residues) were measured. All proteins were examined in the reduced and the oxidized state. In either redox state each protein exhibits ultrarapid tryptophan fluorescence decay on the picosecond timescale contributing up to 93% of the total decay. Correlation times in the range of 1 ns or less were found for all six iron-sulfur proteins reflecting internal Trp motion. In addition, some proteins exhibit longer correlation times reflecting segmental motion and overall protein tumbling. The ultrarapid fluorescence decay in iron-sulfur proteins indicates efficient radiationless energy transfer between distant tryptophan residues and iron-sulfur clusters. Such an energy transfer mechanism can be accounted for by referring to the three-dimensional structures of rubredoxin and ferredoxin in calculating the transfer efficiency of the single tryptophan-iron-sulfur couple.

Molecular dynamics simulations of oxidized and reduced Clostridium beijerinckii flavodoxin

Molecular dynamics simulations of oxidized and reduced Clostridium beijerinckii flavodoxin in water have been performed in a sphere of 1.4-nm radius surrounded by a restrained shell of 0.8 nm. The flavin binding site, comprising the active site of the flavodoxin, was in the center of the sphere. No explicit information about protein-bound water molecules was included. An analysis is made of the motional characteristics of residues located in the active site. Positional fluctuations, hydrogen bonding patterns, dihedral angle transitions, solvent behavior, and time-dependent correlations are examined. The 375-ps trajectories show that both oxidized and reduced protein-bound flavins are immobilized within the protein matrix, in agreement with earlier obtained time-resolved fluorescence anisotropy data. The calculated time-correlated behavior of the tryptophan residues reveals significant picosecond mobility of the tryptophan side chain located close to the reduced isoalloxazine part of the flavin.