Reduced Flavin Mononucleotide Research Articles

Photoenzymatic Enantioselective Intermolecular Radical Hydroamination.

Since the discovery of Hofmann-Löffler-Freytag reaction more than 130 years ago, nitrogen-centered radicals have been widely studied in both structures and reactivities1-2. Nevertheless, catalytic enantioselective intermolecular radical hydroamination remains a challenge due to the existence of side reactions, short lifetime of nitrogen-centered radicals, and lack of understanding of the fundamental catalytic steps. In chemistry, nitrogen-centered radicals are produced with radical initiators, photocatalysts, or electrocatalysts. On the other hand, the generation and reaction of nitrogen-centered radicals are unknown in nature. Here we report a pure biocatalytic system by successfully repurposing an ene-reductase through directed evolution for the photoenzymatic production of nitrogen-centered radicals and enantioselective intermolecular radical hydroaminations. These reactions progress efficiently at room temperature under visible light without any external photocatalysts and exhibit excellent enantioselectivities. Detailed mechanistic study reveals that the enantioselectivity originates from the radical-addition step while the reactivity originates from the ultrafast photoinduced electron transfer (ET) from reduced flavin mononucleotide (FMNH-) to nitrogen-containing substrates.

Exploration of Optimal pH in Hypothermic Machine Perfusion for Rat Liver Grafts Retrieved after Circulatory Death.

Ex vivo hypothermic machine perfusion (HMP) is a strategy for controlling ischemia-reperfusion injury in donation after circulatory death (DCD) liver transplantation. The pH of blood increases with a decrease in temperature and water dissociation, leading to a decrease in [H+]. This study aimed to verify the optimal pH of HMP for DCD livers. Rat livers were retrieved 30 min post-cardiac arrest and subjected to 3-h cold storage (CS) in UW solution (CS group) or HMP with UW-gluconate solution (machine perfusion [MP] group) of pH 7.4 (original), 7.6, 7.8, and 8.0 (MP-pH 7.6, 7.8, 8.0 groups, respectively) at 7-10 °C. The livers were subjected to normothermic perfusion to simulate reperfusion after HMP. All HMP groups showed greater graft protection compared to the CS group due to the lower levels of liver enzymes in the former. The MP-pH 7.8 group showed significant protection, evidenced by bile production, diminished tissue injury, and reduced flavin mononucleotide leakage, and further analysis by scanning electron microscopy revealed a well-preserved structure of the mitochondrial cristae. Therefore, the optimum pH of 7.8 enhanced the protective effect of HMP by preserving the structure and function of the mitochondria, leading to reduced reperfusion injury in the DCD liver.

QM/MM Modeling of the Flavin Functionalization in the RutA Monooxygenase

Oxygenase activity of the flavin-dependent enzyme RutA is commonly associated with the formation of flavin-oxygen adducts in the enzyme active site. We report the results of quantum mechanics/molecular mechanics (QM/MM) modeling of possible reaction pathways initiated by various triplet state complexes of the molecular oxygen with the reduced flavin mononucleotide (FMN) formed in the protein cavities. According to the calculation results, these triplet-state flavin-oxygen complexes can be located at both re-side and si-side of the isoalloxazine ring of flavin. In both cases, the dioxygen moiety is activated by electron transfer from FMN, stimulating the attack of the arising reactive oxygen species at the C4a, N5, C6, and C8 positions in the isoalloxazine ring after the switch to the singlet state potential energy surface. The reaction pathways lead to the C(4a)-peroxide, N(5)-oxide, or C(6)-hydroperoxide covalent adducts or directly to the oxidized flavin, depending on the initial position of the oxygen molecule in the protein cavities.

H2-Driven Reduction of Flavin by Hydrogenase Enables Cleaner Operation of Nitroreductases for Nitro-Group to Amine Reductions

Hydrogenase-mediated reduction of flavin mononucleotide by H2 is exploited to enable cleaner application of nitroreductase enzymes for reduction of aromatic nitro functional groups. This turns the overall reaction into a biocatalytic hydrogenation. Use of flavin-containing nitroreductases in industrial biotechnology typically relies upon NADH or NADPH as reductant, together with glucose dehydrogenase and glucose as a regeneration system for the reduced nicotinamide cofactor, with 3 equivalents of the carbon-intensive glucose required for a single 6-electron nitro to amine conversion. We show here that reduced flavin mononucleotide is an alternative reductant for nitroreductases, and by combining this with H2-driven recycling of reduced flavin, we avoid glucose, thereby enabling atom-efficient biocatalytic nitro reductions. We compare this biocatalytic system, via green chemistry metrics, to existing strategies for biocatalytic nitro-group reductions, particularly with respect to replacing glucose with H2 gas. We take steps towards demonstrating industrial viability: we report an overexpression system for E. coli hydrogenase 1, giving a 12-fold improvement in enzyme yield; we show a reaction in which the hydrogenase exhibits > 26,000 enzyme turnovers; and we demonstrate reasonable solvent tolerance of the hydrogenase and flavin reduction system which would enable reaction intensification.

Cryo-EM structure of the fatty acid reductase LuxC–LuxE complex provides insights into bacterial bioluminescence

The discovery of reduced flavin mononucleotide and fatty aldehydes as essential factors of light emission facilitated study of bacterial luminescence. Although the molecular mechanisms underlying bacterial luminescence have been studied for more than 60 years, the structure of the bacterial fatty acid reductase complex remains unclear. Here, we report the cryo-EM structure of the Photobacterium phosphoreum fatty acid reductase complex LuxC–LuxE to a resolution of 2.79 Å. We show that the active site Lys238/Arg355 pair of LuxE is >30 Å from the active site Cys296 of LuxC, implying that catalysis relies on a large conformational change. Furthermore, mutagenesis and biochemical experiments support that the L-shaped cleft inside LuxC plays an important role in substrate binding and reaction. We obtained a series of mutants with significantly improved activity as measured by in vitro bioluminescence assays and demonstrated that the double mutant W111A/F483K displayed the highest activity (370% of the WT). Our results indicated that the activity of LuxC significantly affects the bacterial bioluminescence reaction. Finally, we expressed this mutated lux operon in Escherichia coli but observed that the in vivo concentrations of ATP and NADPH limited the enzyme activity; thus, we conclude that the luminous intensity mainly depends on the level of metabolic energy.

QM/MM Molecular Modeling Reveals Mechanism Insights into Flavin Peroxide Formation in Bacterial Luciferase.

Bacterial luciferase (Lux) catalyzes oxidation of reduced flavin mononucleotide (FMN) and aldehyde to form oxidized FMN and carboxylic acid via molecular oxygen with concomitant light generation. The enzyme is useful for various detection applications in biomedical experiments. Upon reacting with oxygen, the reduced FMN generates C4a-peroxy-FMN (FMNH-C4a-OO-) as a reactive intermediate, which is required for light generation. However, the mechanism and control of FMNH-C4a-OO- formation are not clear. This work investigated the reaction of FMNH-C4a-OO- formation in Lux using QM/MM methods. The B3LYP/6-31G*/CHARMM27 calculations indicate that Lux controls the formation of FMNH-C4a-OO- via the conserved His44 residue. The steps in intermediate formation are found to be as follows: (i) H+ reacts with O2 to generate +OOH. (ii) +OOH attacks C4a of FMNH- to generate FMNH-C4a-OOH. (iii) H+ is transferred from FMNH-C4a-OOH to His44 to generate FMNH-C4a-OO- while His44 stabilizes FMNH-C4a-OO- by forming a hydrogen bond to an oxygen atom. This controlling key mechanism for driving the change from FMNH-C4a-OOH to the FMNH-C4a-OO- adduct is confirmed because FMNH-C4a-OO- is more stable than FMNH-C4a-OOH in the luciferase active site.

Mechanism of the Reaction between Cyanocobalamin and Reduced Flavin Mononucleotide

Mechanism of the Reaction between Cyanocobalamin and Reduced Flavin Mononucleotide

Solar-Assisted eBiorefinery: Photoelectrochemical Pairing of Oxyfunctionalization and Hydrogenation Reactions.

Inspired by natural photosynthesis, biocatalytic photoelectrochemical (PEC) platforms are gaining prominence for the conversion of solar energy into useful chemicals by combining redox biocatalysis and photoelectrocatalysis. Herein, we report a dual biocatalytic PEC platform consisting of a molybdenum (Mo)-doped BiVO4 (Mo:BiVO4 ) photoanode and an inverse opal ITO (IO-ITO) cathode that gives rise to the coupling of peroxygenase and ene-reductase-mediated catalysis, respectively. In the PEC cell, the photoexcited electrons generated from the Mo:BiVO4 are transferred to the IO-ITO and regenerate reduced flavin mononucleotides to drive ene-reductase-catalyzed trans-hydrogenation of ketoisophrone to (R)-levodione. Meanwhile, the photoactivated Mo:BiVO4 evolves H2 O2 in situ via a two-electron water-oxidation process with the aid of an applied bias, which simultaneously supplies peroxygenases to drive selective hydroxylation of ethylbenzene into enantiopure (R)-1-phenyl-1-hydroxyethane. Thus, the deliberate integration of PEC systems with redox biocatalytic reactions can simultaneously produce valuable chemicals on both electrodes using solar-powered electrons and water.

Solar‐Assisted eBiorefinery: Photoelectrochemical Pairing of Oxyfunctionalization and Hydrogenation Reactions

AbstractInspired by natural photosynthesis, biocatalytic photoelectrochemical (PEC) platforms are gaining prominence for the conversion of solar energy into useful chemicals by combining redox biocatalysis and photoelectrocatalysis. Herein, we report a dual biocatalytic PEC platform consisting of a molybdenum (Mo)‐doped BiVO4 (Mo:BiVO4) photoanode and an inverse opal ITO (IO‐ITO) cathode that gives rise to the coupling of peroxygenase and ene‐reductase‐mediated catalysis, respectively. In the PEC cell, the photoexcited electrons generated from the Mo:BiVO4 are transferred to the IO‐ITO and regenerate reduced flavin mononucleotides to drive ene‐reductase‐catalyzed trans‐hydrogenation of ketoisophrone to (R)‐levodione. Meanwhile, the photoactivated Mo:BiVO4 evolves H2O2 in situ via a two‐electron water‐oxidation process with the aid of an applied bias, which simultaneously supplies peroxygenases to drive selective hydroxylation of ethylbenzene into enantiopure (R)‐1‐phenyl‐1‐hydroxyethane. Thus, the deliberate integration of PEC systems with redox biocatalytic reactions can simultaneously produce valuable chemicals on both electrodes using solar‐powered electrons and water.

Exploring the FMN binding site in the mitochondrial outer membrane protein mitoNEET

MitoNEET is a mitochondrial outer membrane protein that hosts a redox active [2Fe-2S] cluster in the C-terminal cytosolic domain. Increasing evidence has shown that mitoNEET has an essential role in regulating energy metabolism in human cells. Previously, we reported that the [2Fe-2S] clusters in mitoNEET can be reduced by the reduced flavin mononucleotide (FMNH2) and oxidized by oxygen or ubiquinone-2, suggesting that mitoNEET may act as a novel redox enzyme catalyzing electron transfer from FMNH2 to oxygen or ubiquinone. Here, we explore the FMN binding site in mitoNEET by using FMN analogs and find that lumiflavin, like FMN, at nanomolar concentrations can mediate the redox transition of the mitoNEET [2Fe-2S] clusters in the presence of flavin reductase and NADH (100 μM) under aerobic conditions. The electron paramagnetic resonance (EPR) measurements show that both FMN and lumiflavin can dramatically change the EPR spectrum of the reduced mitoNEET [2Fe-2S] clusters and form a covalently bound complex with mitoNEET under blue light exposure, suggesting that FMN/lumiflavin has specific interactions with the [2Fe-2S] clusters in mitoNEET. In contrast, lumichrome, another FMN analog, fails to mediate the redox transition of the mitoNEET [2Fe-2S] clusters and has no effect on the EPR spectrum of the reduced mitoNEET [2Fe-2S] clusters under blue light exposure. Instead, lumichrome can effectively inhibit the FMNH2-mediated reduction of the mitoNEET [2Fe-2S] clusters, indicating that lumichrome may act as a potential inhibitor to block the electron transfer activity of mitoNEET.

Creating Flavin Reductase Variants with Thermostable and Solvent-Tolerant Properties by Rational-Design Engineering.

We have employed computational approaches-FireProt and FRESCO-to predict thermostable variants of the reductase component (C1 ) of (4-hydroxyphenyl)acetate 3-hydroxylase. With the additional aid of experimental results, two C1 variants, A166L and A58P, were identified as thermotolerant enzymes, with thermostability improvements of 2.6-5.6 °C and increased catalytic efficiency of 2- to 3.5-fold. After heat treatment at 45 °C, both of the thermostable C1 variants remain active and generate reduced flavin mononucleotide (FMNH- ) for reactions catalyzed by bacterial luciferase and by the monooxygenase C2 more efficiently than the wild type (WT). In addition to thermotolerance, the A166L and A58P variants also exhibited solvent tolerance. Molecular dynamics (MD) simulations (6 ns) at 300-500 K indicated that mutation of A166 to L and of A58 to P resulted in structural changes with increased stabilization of hydrophobic interactions, and thus in improved thermostability. Our findings demonstrated that improvements in the thermostability of C1 enzyme can lead to broad-spectrum uses of C1 as a redox biocatalyst for future industrial applications.

Cloning and expression of the flavin reductase LuxG from Photobacterium leiognathi YL and its improvement for NADH detection.

In the present study, we aimed to purify and characterize LuxG obtained from Photobacterium leiognathi YL and examine its improvement for NADH detection. To this end, we cloned and expressed the putative luxG gene of P. leiognathi YL in the Escherichia coli BL21 strain. The product of luxG is a flavin reductase that consists of 206 amino acids, corresponding to a subunit molecular mass of ∼26 kDa. Phylogenetic analysis demonstrated that P. leiognathi YL LuxG has a rather distant evolutionary relationship with Frase I of Aliivibrio fischeri and Frp of Vibrio harveyi, but a close evolutionary relationship with Fre from Escherichia coli, which are all enzymes related to oxido-reductase. Further comparison shows that the changes in the functionally conserved sites may contribute to the functional divergence of LuxG and Fre. LuxG could supply reduced flavin mononucleotide (FMN) for bacterial luminescence by catalyzing the oxidation of nicotinamide adenine dinucleotide hydrogen (NADH). Based on this, a coupled pure enzyme bioluminescent system was established and used for NADH detection. The NADH samples with concentrations of 0.1-1 nM were used to validate the linear relationship, and it was found that the logarithmic deviations were less than 3%, which showed more sensitive and stable results than the NADH detection by recombinant E. coli including the exogenously expressed luciferase and intrinsic Fre. Investigation of P. leiognathi YL LuxG would provide a basic understanding of its evolution, and structural and functional properties, which might contribute to the development of a NADH detection kit in the future.

Bacterial luciferase: Molecular mechanisms and applications.

Bacterial luciferase is a flavin-dependent monooxygenase which is remarkable for its distinctive feature in transforming chemical energy to photons of visible light. The bacterial luciferase catalyzes bioluminescent reaction using reduced flavin mononucleotide, long-chain aldehyde and oxygen to yield oxidized flavin, corresponding acid, water and light at λmax around 490nm. The enzyme comprises of two non-identical α and β subunits, where α subunit is a catalytic center and β subunit is crucially required for maintaining catalytic function of the α subunit. The crystal structure with FMN bound and mutagenesis studies have assigned a number of amino acid residues that are important in coordinating critical reactions and stabilizing intermediates to attain optimum reaction efficiency. The enzyme achieves monooxygenation by generating C4a-hydroperoxyflavin intermediate that later changes its protonation status to become C4a-peroxyflavin, which is necessary for the nucleophilic attacking with aldehyde substrate. The decomposing of C4a-peroxyhemiacetal produces excited C4a-hydroxyflavin and acid product. The chemical basis regrading bioluminophore generation in Lux reaction remains an inconclusive issue. However, current data can, at least, demonstrate the involvement of electron transfer to create radical molecules which is the key step in this mechanism. Lux is a self-sufficient bioluminescent system in which all substrates can be recycled and produced by a group of enzymes from the lux operon. This makes Lux distinctively advantageous over other luciferases for reporter enzyme application. The progression of understanding of Lux catalysis is beneficial to improve light emitting efficiency in order to expand the robustness of Lux application.

Chorismate synthase from malaria parasites is bifunctional enzyme

Chorismate synthase (Cs) is the last enzyme of the main trunk of shikimate pathway and catalyzes formation of chorismate, a major aromatic metabolite precursor. We have previously reported that Cs is highly conserved across different Plasmodium sp. Here we report that Cs from malaria parasites are bifunctional enzymes through expression and functional studies of two recombinant proteins rPfCs (Cs from P. falciparum) and rPvCs (Cs from P. vivax). We confirm bifunctional activity of both rPfCs and rPvCs based on their ability to catalyze formation of chorismate under aerobic conditions as well as their ability to catalyze generation of reduced flavin mononucleotide (FMN) as assessed through diaphorase assay.

QM/MM molecular modelling on mutation effect of chorismate synthase enzyme catalysis

Chorismate synthase (CS) catalyzes the conversion of 5-enolpyruvylshikimate-3-phosphate (EPSP) to chorismate which is a key intermediate in the biosynthesis of aromatic amino acids. CS enzyme is a new target for antibacterial drugs. Even though several reaction mechanisms have been proposed, the catalytic mechanism is still unclear. QM/MM adiabatic mapping calculations were performed in order to investigate roles of this enzyme. High-accuracy SCS-MP2/aVDZ/CHARMM27 calculations indicated that the reaction pathway has three steps; (i) proton transfer from reduced flavin mononucleotide (FMNH2) to D339, (ii) proton transfer from EPSP to FMNH– and (iii) phosphate elimination. Adiabatic mapping calculations indicated that H110 and R48 residues play essential catalyst roles for CS enzyme catalysis by transition state (TS) and product stabilizations via charge polarization and hydrogen bonding to EPSP and/or FMNH2. A high accuracy calculation - SCS-MP2/aVDZ/CHARMM27 method was employed to obtain the accurate reaction mechanism pathway and to evaluate the effect of amino acid residues in the active site on the enzyme catalysis. The potential energy barriers of the reactions of H110A and R48A were found to increase. The CS catalysis was consequently slowed down due to missing the TS and product stabilizations.

Revisiting the Origin of Bacterial Bioluminescence: QM/MM Study on Oxygenation Reaction of Reduced Flavin in Protein.

Bacterial bioluminescence is initiated by the oxygenation reaction of reduced flavin mononucleotide in luciferase. This enzymatic oxygenation occurs in a wide range of biological processes including cellular redox metabolism, biocatalysis, biosynthesis and homeostasis. However, little is known about the mechanism of the enzymatic reaction between singlet reduced flavin and triplet oxygen. To explore the enigmatic oxygenation, for the first time, the reaction of reduced flavin anion with oxygen was studied in bacterial luciferase by a combined quantum mechanics and molecular mechanics method as well as molecular dynamics simulation. The calculated results demonstrate that the reaction proceeds via a proton-coupled electron transfer (PCET) pathway, and the essential αHis44 acts as a catalytic acid to provide the proton. The currently proposed PCET mechanism clearly describes the initial steps of bacterial bioluminescence, and could be suitable for the other flavin oxygenation reactions in enzymes.

Crystal structure of the dimethylsulfide monooxygenase DmoA from Hyphomicrobium sulfonivorans.

DmoA is a monooxygenase which uses dioxygen (O2) and reduced flavin mononucleotide (FMNH2) to catalyze the oxidation of dimethylsulfide (DMS). Although it has been characterized, the structure of DmoA remains unknown. Here, the crystal structure of DmoA was determined to a resolution of 2.28 Å and was compared with those of its homologues LadA and BdsA. The results showed that their overall structures are similar: they all share a conserved TIM-barrel fold which is composed of eight α-helices and eight β-strands. In addition, they all have five additional insertions. Detailed comparison showed that the structures have notable differences despite their high sequence similarity. The substrate-binding pocket of DmoA is smaller compared with those of LadA and BdsA.

Taurine dioxygenase (tauD)-independent taurine assimilation in Escherichia coli.

On the basis of previous studies on taurine assimilation in Escherichia coli, TauD, an iron- and α-ketoglutarate-dependent taurine dioxygenase, has been regarded as an indispensable factor for assimilation. However, we found that tauD-deficient strains did not lose their taurine assimilation ability when there was no deletion of ssuD, which encodes a reduced flavin mononucleotide [FMNH(2)]-dependent alkanesulfonate monooxygenase, which is responsible for the desulfonation of alkanesulfonates. There were no significant differences in lag phase time, growth rate and final growth yield between the tauD-deficient strain and the tauD wild-type strain. Iron increased the growth rate and final growth yield of the ssuD mutant, but not those of the tauD mutant. The double deletion of tauD and ssuD resulted in the loss of the ability to assimilate taurine. When ssuD was artificially expressed in the double-deletion mutant, the mutant recovered its taurine assimilation ability. These findings indicate that there is another taurine assimilation pathway that is dependent on ssuD but independent of tauD.

Biological Redox Mediation for Oxygen Reduction Reaction Catalysts in Lithium–Oxygen Batteries

Governing the fundamental reaction of oxygen and lithium in lithium–oxygen batteries is vital to realizing their potentially high energy density. Here, we report novel oxygen reduction reaction (ORR) catalysts that are capable of mediating the lithium and oxygen reaction within a solution-driven discharge, which promotes the solution-phase formation of lithium peroxide (Li2O2), thus enhancing the discharge capacity. The new ORR catalysts are derived from mimicking the biological redox mediation occurring in the respiration system of a bacteria, where biomolecule mediates the oxidation of reduced flavin mononucleotide and the reduction of cytochrome b in the cell membrane. The redox potential of the molecule in the biological environment is demonstrated to coincide with the suitable ORR potential range of lithium–oxygen batteries in aprotic solvent, thereby enabling its successful functioning as a redox mediator (RM) that triggers the solution-based discharge. The use of the catalyst prevents the growth of film-like Li2O2 even in an ether-based electrolyte, which has been reported to induce surface-driven discharge and early passivation of the electrode, thus boosting the discharge capacity by ~30 times. The similarity of the redox mediation in the biological cell and lithium–oxygen ‘cell’ inspires the exploration of various redox active bio-organic compounds for potential high-performance RMs toward achieving high theoretical specific energies for lithium–oxygen batteries.

Crystal structure of the flavin reductase of Acinetobacter baumannii p-hydroxyphenylacetate 3-hydroxylase (HPAH) and identification of amino acid residues underlying its regulation by aromatic ligands

The first step in the degradation of p-hydroxyphenylacetic acid (HPA) is catalyzed by the two-component enzyme p-hydroxyphenylacetate 3-hydroxylase (HPAH). The two components of Acinetobacter baumannii HPAH are known as C1 and C2, respectively. C1 is a flavin reductase that uses NADH to generate reduced flavin mononucleotide (FMNH−), which is used by C2 in the hydroxylation of HPA. Interestingly, although HPA is not directly involved in the reaction catalyzed by C1, the presence of HPA dramatically increases the FMN reduction rate. Amino acid sequence analysis revealed that C1 contains two domains: an N-terminal flavin reductase domain, and a C-terminal MarR domain. Although MarR proteins typically function as transcription regulators, the MarR domain of C1 was found to play an auto-inhibitory role. Here, we report a crystal structure of C1 and small-angle X-ray scattering (SAXS) studies that revealed that C1 undergoes a substantial conformational change in the presence of HPA, concomitant with the increase in the rate of flavin reduction. Amino acid residues that are important for HPA binding and regulation of C1 activity were identified by site-directed mutagenesis. Amino acid sequence similarity analysis revealed several as yet uncharacterized flavin reductases with N- or C-terminal fusions.