Redox Properties of Flavin in BLUF and LOV Photoreceptor Proteins from Hybrid QM/MM Molecular Dynamics Simulation

Flavins play an important role in many oxidation and reduction processes in biological systems. For example, flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) are common cofactors found in enzymatic proteins that use the special redox properties of these flavin molecules for their catalytic or photoactive functions. The redox potential of the flavin is strongly affected by its (protein) environment; however, the underlying molecular interactions of this effect are still unknown. Using hybrid quantum mechanics/molecular mechanics (QM/MM) simulation techniques, we have studied the redox properties of flavin in the gas phase, aqueous solution, and two different protein environments, in particular, a BLUF and a LOV photoreceptor domain. By mapping the changes in electrostatic potential and solvent structure, we gain insight into how specific polarization of the flavin by its environment tunes the reduction potential. We find also that accurate calculation of the reduction potentials of these systems by using the hybrid QM/MM approach is hampered by a too limited sampling of the counterion configurations and by artifacts at the QM/MM boundary. We make suggestions for how these issues can be overcome.

Mediating the performance of anaerobic granular sludge by exogenous flavin supplementation: Flavin binding capacity and behavior, interspecies electron transfer, and methane production

Although flavins are known as effective electron mediators, the binding capacity of exogenous flavins by anaerobic granular sludge (AGS) and their role in interspecies electron transfer (IET) remains unknown. In this study, AGS was mediated by using three exogenous flavins of riboflavin (RF), flavin mononucleotide (FMN), and flavin adenine dinucleotide (FAD). Results showed that the total amounts of flavins associated with extracellular polymeric substance (EPS) of AGS increased by 2.03-2.42 and 3.83-4.94 folds, after exposure to 50 and 200 μM of exogenous flavins, respectively. A large portion of FMN and FAD was transformed into RF by AGS. Exogenous flavin mediation also stimulated the production of EPS and cytochrome c (c-Cyts) as well as cytochrome-bound flavins. The increased abundance of these electron mediators led to a reduced electrochemical impedance of EPS and improved extracellular electron transfer capacity. The methane production of AGS after mediation with exogenous RF, FMN, and FAD increased by 19.03-31.71%, 22.86-26.04%, and 28.51-33.44%, respectively. This study sheds new light on the role of exogenous flavins in promoting the IET process of a complex microbial aggregate of AGS.

Shining a Spotlight on Methyl Groups: Photochemically Induced Dynamic Nuclear Polarization Spectroscopy of 5-Deazariboflavin and Its Nor Analogs

5-Deazaflavins are analogs of naturally occurring flavin cofactors. They serve as substitutes for natural flavin cofactors to investigate and modify the reaction pathways of flavoproteins. Demethylated 5-deazaflavins are potential candidates for artificial cofactors, allowing us to fine-tune the reaction kinetics and absorption characteristics of flavoproteins. In this contribution, demethylated 5-deazariboflavin radicals are investigated (1) to assess the influence of the methyl groups on the electronic structure of the 5-deazaflavin radical and (2) to explore their photophysical properties with regard to their potential as artificial cofactors. We determined the proton hyperfine structure of demethylated 5-deazariboflavins using photochemically induced dynamic nuclear polarization (photo-CIDNP) spectroscopy, as well as density functional theory (DFT). To provide context, we compare our findings to a study of flavin mononucleotide (FMN) derivatives. We found a significant influence of the methylation pattern on the absorption properties, as well as on the proton hyperfine coupling ratios of the xylene moiety, which appears to be solvent-dependent. This effect is enhanced by the replacement of N5 by C5-H in 5-deazaflavin derivatives compared to their respective flavin counterparts.

Development and Characterization of Flavin-Binding Fluorescent Proteins, Part II: Advanced Characterization

Flavin-based fluorescent proteins (FbFPs), a class of small fluorescent proteins derived from light-oxygen-voltage (LOV) domains, bind ubiquitous endogenous flavins as chromophores. Due to their unique properties, they can be used as versatile in vivo reporter proteins under aerobic and anaerobic conditions. This chapter presents methodologies for in-depth characterization of the biochemical, spectroscopic, photophysical, and photochemical properties of FbFPs.

Development and Characterization of Flavin-Binding Fluorescent Proteins, Part I: Basic Characterization

Flavin-based fluorescent proteins (FbFPs) are small fluorescent proteins derived from light-oxygen-voltage (LOV) domains. The proteins bind ubiquitous endogenous flavins as chromophores and can be used as versatile in vivo reporter proteins under aerobic and anaerobic conditions. This chapter presents the methodology to identify LOV domain sequences in genomic databases; design new FbFPs; characterize their biochemical, spectroscopic, photophysical, and photochemical properties; and conduct basic fluorescence microscopy experiments.

Arsenic Oxidation by Flavin-Derived Reactive Species under Oxic and Anoxic Conditions: Oxidant Formation and pH Dependence

Flavins are ubiquitous redox-active compounds capable of producing reactive oxygen (O₂^•-, ^•OH, and H₂O₂) and flavin radical species in natural environments, yet their roles in the redox transformations of environmental contaminants, such as arsenic (As), remain to be investigated. Here, we show that reduced flavins can be a source of effective oxidants for As(III) under both oxic and anoxic conditions. For instance, in the presence of 15 μM reduced riboflavin (RBFH₂), 22% of 30 μM As(III) is oxidized in aerated solution at pH 7.0. The co-oxidation of As(III) with RBFH₂ is pH-dependent, with a faster reaction rate under mildly acidic relative to alkaline conditions. Quencher tests with 2-propanol (for ^•OH) and catalase (for H₂O₂) indicate that As(III) oxidation under oxic conditions is likely controlled by flavin-derived ^•OH at pH 5.2 and 7.0, and by H₂O₂ at pH 9.0. Kinetic modeling further implies that flavin-derived reactive oxygen species are mainly responsible for As(III) oxidation under oxic conditions, whereas oxidation of As(III) under anoxic conditions at pH 9.0 is attributed to riboflavin radicals (RBFH^•) generated from co-existing oxidized and reduced riboflavin. The demonstrated ability of flavins to catalyze As(III) oxidation has potential implications for As redox cycling in the environment.

Acute toxicity of organic chemicals to Gammarus pulex correlates with sensitivity of Daphnia magna across most modes of action

We investigated the sensitivity of the freshwater crustacean amphipod Gammarus pulex towards organic xenobiotic compounds in comparison to the sensitivity of the crustacean cladoceran Daphnia magna. In addition we studied the influence of the chemical's mode of action on the relationship between the sensitivity of G. pulex and that of D. magna. We tested the acute toxicity of twelve compounds (Malathion, Aldicarb, Carbofuran, 2,4-dichloroaniline, 2,4-dichlorophenol, 1,2,3-trichlorobenzene, 4,6-dinitro-o-cresol, 2,4,5-trichlorophenol, Ethylacrylate, 4-nitrobenzyl-chloride, Sea-nine, Imidacloprid) with different modes of action and physicochemical properties towards the freshwater amphipod G. pulex in laboratory experiments. Additional toxicity data was collected from the peer-reviewed literature and databases (data pairs for 44 chemicals in total). The chemicals were assigned to seven mode of action groups. The relationship between the sensitivity of G. pulex (48h-LC50s and 96h-LC50s) and that of D. magna (48h-EC50s) was investigated using regression analysis and correlation plots. G. pulex is two to three orders of magnitude more sensitive towards neonicotinoids than D. magna (P=0.0046, n=3). For organophosphates we found that D. magna is more sensitive than G. pulex by approximately a factor of six (P=0.0256, n=6). There was no significant difference between the sensitivity of D. magna and that of G. pulex in any of the other mode of action groups; however chemicals with the same mode of action grouped together in the same area of the correlation plot. Without the neonicotinoids 75% of all G. pulex toxicity data were within one order of magnitude of the D. magna data and 100% within two orders of magnitude. The regressions with all data and with all data minus neonicotinoids were both significant linear relationships with slopes around one and intercept around zero. Thus, G. pulex is generally equally sensitive towards organic xenobiotics as D. magna.

Fenton degradation of 4,6-dinitro-o-cresol with Fe(2+)-substituted ion-exchange resin

The Fenton degradation of 4,6-dinitro-o-cresol (DNOC) was studied under different experimental conditions using Amberlyst 15 ion-exchange resin containing ferrous ion. DNOC was found to be effectively degraded under most conditions, and it was observed that, with the addition of HCl, the desorption of ferrous ion from the resin into the solution played a major role in this degradation. The total iron concentration in the reaction solution was found to increase with the addition of HCl, and a pseudo-first-order kinetic model was applied to the desorption of ferrous ion from the resin on the basis of the assumption of a first-order ion-exchange process. The degradation rate of DNOC also increased as a function of HCl. A kinetic model was developed to simulate the degradation of DNOC under different operating conditions, assuming the first-order desorption of ferrous ion. Different cations were compared with H(+), and H(+) was found to be the most efficient at facilitating the degradation reaction at low concentrations, whereas Ca(2+) was found to be most efficient at high concentrations. pH was measured during the reaction, and its effect on degradation was explored. It was found that a lower pH could lead to faster degradation of the target compound. Degradation of DNOC under different delivery rates of H(2)O(2) was studied, and optimal conditions were determined. The results also showed that the delivery rate of H(2)O(2) did not affect the ion-exchange process of the resin.

Synchronous-scan fluorescence of algal cells for toxicity assessment of heavy metals and herbicides

Synchronous-scan spectrofluorometry was applied to Chlorella vulgaris cells to assess the toxicity of heavy metals and herbicides in water. Simultaneous scan of both the excitation and emission spectra was done at a constant wavelength difference Deltalambda (20-140 nm) between the emission and excitation wavelengths in the range of 420-700 nm emission, where a peak of fluorescence was observed. Its position depends on Deltalambda. Fluorescence measurements were conducted with algal cells in suspension in water and immobilized in a translucent silica matrix. The influence of toxic chemicals was tested with cadmium as a heavy metal and with atrazine, diuron, DNOC and paraquat as herbicides. The toxic effect of those chemicals mainly results in a quenching of algal cells fluorescence by reducing their photosynthetic activity.

Dinitrocresol and phosphate stimulation of the oxygen consumption of a cell-free oxidative system obtained from sea urchin eggs

1. A cell-free system capable of using oxygen with oxalacetate as substrate has been prepared from both unfertilized and fertilized sea urchin eggs. The oxygen uptake by this system is about twice that of an equivalent quantity of intact unfertilized eggs and half that of an equivalent quantity of intact fertilized eggs. 2. The oxygen consumption of this cell-free oxidative system can be stimulated by addition of suitable concentrations of 4,6-dinitro-o-cresol or by inorganic phosphate. This confirms, with a cell-free system obtained from sea urchin eggs, the observations of Loomis and Lipmann regarding stimulation of oxygen consumption by a system obtained from rabbit kidney. 3. A preliminary but unsuccessful attempt has been made to determine the conditions under which cell-free, aerobic, phosphorylating systems may be obtained from either unfertilized or fertilized sea urchin eggs.

Pathogenetic transition in the morphology of abnormal sperm in the testes and the caput, corpus, and cauda epididymides of male rats after treatment with 4,6-dinitro-o-cresol

In order to elucidate the pathogenesis of tailless sperm, 4,6-dinitro-o-cresol (DNOC) was administered to Jcl:SD male rats at daily oral doses of 0, 10 or 15mg/kg for 5 days. Sperm were collected from the caput, corpus, and cauda epididymides on days 1, 7 and 14 after the last dosing (D1, D7 and D14, respectively), counted and examined morphologically by phase-contrast and scanning electron microscopy. The incidence of abnormal sperm was significantly increased in the DNOC 15mg/kg group. On D1, peeled sperm (loss of mitochondrial sheath at the proximal end of the middle piece) was frequently observed in the caput epididymides, whereas sperm in the corpus and cauda epididymides had normal morphology. Distribution of the peeled sperm changed as time passed and the corpus epididymides showed a peak incidence on D7. On D14, the highest incidence of abnormal sperm was observed in the cauda epididymides, where the major abnormality was tailless. Similar effects were also found in the 10mg/kg group but were less potent. Transmission electron microscopy of testicular sperm on D1 revealed the presence of elongated spermatids that lacked the mitochondrial sheath at the proximal end of the middle piece, although the round and elongating spermatids looked normal. These results suggest that DNOC exposure of male rats primarily causes partial loss of the mitochondrial sheath in the testicular elongated spermatids, and that the affected sperm become tailless by D14 after reaching the cauda epididymides.

Comparative studies on the spermatotoxic effects of dinoseb and its structurally related chemicals

Three dinitrophenolic compounds, dinoseb (DNBP; 7.5 mg/kg b.w.), 4,6-dinitro-o-cresol (DNOC; 4, 7.5, 15 mg/kg b.w.), and 2,4-dinitrophenol (DNP; 7.5, 15, 30 mg/kg b.w.) were administered orally to sexually matured Jcl:SD male rats for 5 consecutive days. Half of the males in each group were necropsied at 3 (D3) and 14 (D14) days after the last dosing, respectively, and examined for the effects of dinitrophenols on spermato-/spermiogenesis. DNBP (7.5 mg/kg), DNOC (15 mg/kg), and DNP (30 mg/kg) caused 1, 5, and 0 deaths, respectively, as well as a decreased body weights during the treatment. Although examinations on D3 revealed no treatment-related alterations, DNBP and DNOC resulted in reduced sperm motility and increased incidence of tailless sperm in the cauda epididymis on D14. DNP also caused slightly increased incidence of tailless sperm on D14. These results demonstrate that DNBP, DNOC, and DNP manifest similar spermatotoxic effects at or around a lethal dose in rats.

Effects of dinoseb, 4,6-dinitro-o-cresol, and 2,4-dinitrophenol on rat Sertoli-germ cell co-cultures

The effects of dinoseb (DNBP), a known testicular toxicant in the rat, on germ cells were investigated in Sertoli-germ cell co-cultures. Two DNBP-related dinitrophenolic compounds, 4,6-dinitro-o-cresol (DNOC) and 2,4-dinitrophenol (DNP), were also examined, as testicular toxicity of these compounds had not been elucidated. Cultures were exposed to each compound (10(-7)-10(-4)M) for 24h and examined for the number and viability of detached cells and morphologic alterations under a light microscope. DNBP significantly increased the number of detached cells (10(-5) and 10(-4)M) and suppressed their viability (10(-6)-10(-4)M). Morphologic observations revealed degenerative alterations in the germ cells and Sertoli cells. Similar effects as observed after DNBP exposure were evident at 10(-4)M DNOC and 10(-4)M DNP. These results demonstrate that DNBP, DNOC, and DNP have in vitro toxicity to these cell populations at high concentration, and suggest the possibility that DNOC and DNP also cause testicular damage in experimental animals and humans.

Spectroscopic study of nitroaromatic-smectite sorption mechanisms

Sorption mechanisms of 1,3- and 1,4-dinitrobenzene, 1,3,5-trinitrobenzene (TNB), dinitro-o-creasol, and 6-sec-butyl-2,4-dinitrophenol (DINOSEB) on smectite were investigated using FTIR spectroscopy and HPLC methods. A quantitative method was developed that established a direct link between the HPLC and the FTIR data. Freundlich sorption values ranged from 47 (L g(-1)) for 1,3,5-TNB to 3.7 for DINOSEB and showed that the extent of nitroaromatic compounds (NAC) sorption was strongly dependent on the number and position of the nitro substituents as well as other substituents and steric effects. The amount of 1,3,5-TNB sorbed to smectite was strongly influenced by the nature of the exchangeable cation. Furthermore, the exchangeable cation significantly influenced the positions and relative intensities of the vibrational modes of the -NO2 groups. The strongest perturbations were observed for cations with lower enthalpies of hydration (e.g., K+) and included a red shift of the v(asym)(NO) band, a concomitant blue shift of the v(sym)(NO) band. These changes were accompanied by a 2-fold increase in the relative intensity of the v(asym)(NO) band relative to the intensity of the v(sym) (NO) band. Molecular quantum mechanics calculations were used to rationalize frequency shifts in terms of nitroaromatic interactions with interlayer cations. Results indicate that the sorption of NACs to smectite surfaces is controlled largely by the hydration characteristics of the exchangeable cation, which regulates both cation-nitroaromatic complexation and swelling of the smectite.

Rapid and sensitive determination of 4-nitrophenol, 3-methyl-4-nitrophenol, 4,6-dinitro-o-cresol, parathion-methyl, fenitrothion, and parathion-ethyl by liquid chromatography with electrochemical detection

Liquid chromatography with electrochemical detection has been used to determine various nitropesticides, DNOC, fenitrothion, and parathion (methyl and ethyl), and some of their main metabolites, 4-nitrophenol for parathion (methyl and ethyl) and 3-methyl-4-nitrophenol for fenitrothion, by using indirect detection. Analysis of them in river water samples has been performed without a preconcentration step. The recovery efficiencies of the tested compounds yielded values between 96 and 112% at the fortification level of 0.5 ppb in a river water sample, and their relative standard deviations were between 1 and 15%. The detection limits of these compounds ranged between 0.05 and 0.14 ppb.

Biodegradation of the pesticide 4,6-dinitro-ortho-cresol by microorganisms in batch cultures and in fixed-bed column reactors

A mixed culture of microorganisms able to utilize 4,6-dinitro-ortho-cresol (DNOC) as the sole source of carbon, nitrogen and energy was isolated from soil contaminated with pesticides and from activated sludge. DNOC was decomposed aerobically in batch cultures as well as in fixed-bed column reactors. Between 65% and 84% of the substrate nitrogen was released as nitrate into the medium, and 61% of the carbon from uniformly 14C-labelled DNOC was recovered as 14CO2. The mixed microbial culture also decomposed 4-nitrophenol and 2,4-dinitrophenol but not 2,3-dinitrophenol, 2,6-dinitrophenol, 2,4-dinitrotoluene, 2,4-dinitrobenzoic acid or 2-sec-butyl-4,6-dinitrophenol (Dinoseb). Maximal degradation rates for DNOC by the bacterial biofilm immobilized on glass beads in fixed-bed column reactors were 30 mmol day-1 (1 reactor volume)-1, leaving an effluent concentration of less than 5 micrograms l-1 DNOC in the outflowing medium. The apparent Ks value of the immobilized mixed culture for DNOC was 17 microM. Degradation was inhibited at DNOC concentrations above 30 microM and it ceased at 340 microM, possibly because of the uncoupling action of the nitroaromatic compound on the cellular energy-transducing mechanism.

Flavin Sensitized Photoreactions: Effects of 3-(p-Chlorophenyl)-1,1-Dimethylurea

Photooxidation reactions, which were inhibited by high concentrations of oxygen, were affected by the addition of 3-(p-chlorophenyl)-1,1-dimethylurea (CMU), but the response varied with the substrate being oxidized. With ascorbic acid and 2,3-diketogulonic acid, CMU reversed the inhibition caused by high concentrations of oxygen. With ethylenediaminetetraacetic acid (EDTA), tetraethylene tetramine, or Mn(++) as reductant, CMU itself inhibited the reactions. The photoreduction of flavins by EDTA and the bleaching of flavin mononucleotide under anaerobic conditions were also inhibited by CMU. Corresponding photoreactions sensitized by phthaleine dyes or methylene blue were completely insensitive to CMU. This compound therefore seems to change specifically the reactivity of excited flavin molecules.