Flavin Domain Research Articles

In Support of Nitric Oxide Dioxygenase Function: Algal Hemoglobins and their Reduction Partners

The ubiquity of hemoglobins as a superfamily to life has enthused the field with renewed vigor. Reactions like oxygen binding and nitric oxide (NO) dioxygenation appear to be characteristic to the hemoglobin superfamily, as revealed from investigation of recombinant globins, irrespective of whether they are associated to any particular function like oxygen transport/storage, sensing, electron transport, protection against hypoxia and other possibilities. NO dioxygenase reaction, common in vitro, however, was limited by lack of report of specific enzymes that can convert ferric hemoglobin, formed during reaction of oxy hemoglobin with NO, into ferrous hemoglobin - the species that reacts with NO. Absence of a known cognate reductase would prevent reduction of ferric species of hemoglobin to ferrous form and the oxidation-reduction cycle would be incomplete for NO related function to be fruitful. Assignment of NO dioxygenase activity as a physiological function requires the design of experiments that address reduction mechanisms. We used Chlamydomonas reinhardtii as model system since we have identified 12 globins and 3 putative genes that can potentially function as reductase of ferric hemoglobin. Organism database annotated these reductases as dihydrolipoamide dehydrogenase, cytochrome b5reductase and monodehydroascorbate reductase. So far, we have characterized 3 hemoglobins and 3 putative cognate reductases using biochemical and biophysical methods. Spectroscopic studies reveal that Chlamydomonas contains both pentacoordinate and hexacoordinate hemoglobins. The enzymes were found to contain flavin domain and could reduce ferric Chlamydomonas hemoglobins in vitro to their functional ferrous state. The interactions between hemoglobins and these reductases might support NO scavenging/detoxification function of globins with potential implications in biotechnology.

Characterization of cellobiose dehydrogenase and its FAD-domain from the ligninolytic basidiomycete Pycnoporus sanguineus

Cellobiose dehydrogenase (CDH), an extracellular flavocytochrome produced by several wood-degrading fungi, was detected in the culture supernatant of the selective delignifier Pycnoporus sanguineus maintained on a cellulose-based liquid medium. Cellobiose dehydrogenase was purified as two active fractions: CDH1-FAD (flavin domain) (40.4 fold) with recovery of 10.9% and CDH1 (flavo-heme enzyme) (54.7 fold) with recovery of 9.8%. As determined by SDS-PAGE, the molecular mass of the purified enzyme was found to be 113.4kDa and its isoelectric point was 4.2, whereas these values for the FAD-domain were 82.7kDa and pI=6.7. The carbohydrate content of the purified enzymes was 9.2%. In this work, the cellobiose dehydrogenase gene cdh1 and its corresponding cDNA from fungus P. sanguineus were isolated, cloned, and characterized. The 2310bp full-length cDNA of cdh1 encoded a mature CDH protein containing 769 amino acids, which was preceded by a signal peptide of 19 amino acids. Moreover, both active fractions were characterized in terms of kinetics, temperature and pH optima, and antioxidant properties.

On the use of advanced modelling techniques to investigate the conformational discrepancy between two X-ray structures of the AppA BLUF domain

The conformation of the blue light utilising flavin domain of the signalling protein AppA in the dark state is a matter of intensive research, both experimental and theoretical, and has not yet unambiguously been determined. Two contradicting X-ray structures of the dark state have been published previously. We aim at resolving this seeming contradiction by exploring conformational pathways between the two X-ray structures using advanced modelling techniques, such as local-elevation searching and sampling, soft-core non-bonded interactions and protocols of successively biasing the sampling of sets of torsional angles which adopt different values in the two alternative X-ray structures. The results suggest a high energetic barrier for a change in the Trp104 side chain from a ‘Trp-in’ to a ‘Trp-out’ conformation or vice versa, and illustrate the complexity to model conformational transitions involving a large number of degrees of freedom.

Vibrational Assignment of the Ultrafast Infrared Spectrum of the Photoactivatable Flavoprotein AppA

The blue light using flavin (BLUF) domain proteins, such as the transcriptional antirepressor AppA, are a novel class of photosensors that bind flavin noncovalently in order to sense and respond to high-intensity blue (450 nm) light. Importantly, the noncovalently bound flavin chromophore is unable to undergo large-scale structural change upon light absorption, and thus there is significant interest in understanding how the BLUF protein matrix senses and responds to flavin photoexcitation. Light absorption is proposed to result in alterations in the hydrogen-bonding network that surrounds the flavin chromophore on an ultrafast time scale, and the structural changes caused by photoexcitation are being probed by vibrational spectroscopy. Here we report ultrafast time-resolved infrared spectra of the AppA BLUF domain (AppA(BLUF)) reconstituted with isotopes of FAD, specifically [U-(13)C(17)]-FAD, [xylene-(13)C(8)]-FAD, [U-(15)N(4)]-FAD, and [4-(18)O(1)]-FAD both in solution and bound to AppA(BLUF). This allows for unambiguous assignment of ground- and excited-state modes arising directly from the flavin. Studies of model compounds and DFT calculations of the ground-state vibrational spectra reveal the sensitivity of these modes to their environment, indicating they can be used as probes of structural dynamics.

The Central Role of Gln63 for the Hydrogen Bonding Network and UV–Visible Spectrum of the AppA BLUF Domain

In blue-light sensing using flavin (BLUF) domains, the side-chain orientation of key residues close to the flavin chromophore is still under debate. We report quantum refinements of the wild-type AppA BLUF protein from Rhodobacter sphaeroides starting from two published X-ray structures (1YRX and 2IYG) with different arrangements of the residues around the chromophore. Quantum refinement uses the same experimental X-ray raw data as conventional refinement, but includes data from quantum mechanics/molecular mechanics (QM/MM) calculations as restraints, which is expected to be more reliable than the normally employed MM data. In addition to quantum refinement, pure QM/MM geometry optimizations are performed for the 1YRX and 2IYG structures and for five models derived therefrom. Vertical excitation energies are computed at the QM(DFT/MRCI)/MM level to assess the resulting structures. The experimental absorption maximum of the dark state of wild-type AppA is well reproduced for structures that contain the Gln63 residue in 1YRX-type orientation. The computed excitation energies are red-shifted for structures with a flipped Gln63 residue in 2IYG-type orientation. The calculated 1YRX- and 2IYG-type hydrogen-bonding networks are discussed in detail, particularly with regard to the orientation of the chromophore and the Gln63, Trp104, and Met106 residues.

New insights into the mechanism of electron transfer within flavohemoglobins: tunnelling pathways, packing density, thermodynamic and kinetic analyses

Flavohemoglobins (FlavoHb) are metalloenzymes catalyzing the reaction of nitric oxide dioxygenation. The iron cation of the heme group needs to be preliminarily reduced to the ferrous state to be catalytically competent. This reduction is triggered by a flavin adenine dinucleotide (FAD) prosthetic group which is localized in a distinct domain of the protein. In this paper we obtain new insights into the internal long range electron transfer (over ca. 12 Å) using a combination of experimental and computational approaches. Employing a time-resolved pulse radiolysis technique we report the first direct measurement of the FADH˙→ HemeFe(III) electron transfer rate. A rate constant of (6.8 ± 0.5) × 10(3) s(-1) is found. A large panel of computational approaches are used to provide the first estimation of the thermodynamic characteristics of the internal electron transfer step within flavoHb: both the driving force and the reorganization energy are estimated as a function of the protonated state of the flavin semi-quinone. We also report an analysis of the electron pathways involved in the tunnelling of the electron through the aqueous interface between the globin and the flavin domains.

Conformational Changes of NADPH-Cytochrome P450 Oxidoreductase Are Essential for Catalysis and Cofactor Binding

The crystal structure of NADPH-cytochrome P450 reductase (CYPOR) implies that a large domain movement is essential for electron transfer from NADPH via FAD and FMN to its redox partners. To test this hypothesis, a disulfide bond was engineered between residues Asp(147) and Arg(514) in the FMN and FAD domains, respectively. The cross-linked form of this mutant protein, designated 147CC514, exhibited a significant decrease in the rate of interflavin electron transfer and large (≥90%) decreases in rates of electron transfer to its redox partners, cytochrome c and cytochrome P450 2B4. Reduction of the disulfide bond restored the ability of the mutant to reduce its redox partners, demonstrating that a conformational change is essential for CYPOR function. The crystal structures of the mutant without and with NADP(+) revealed that the two flavin domains are joined by a disulfide linkage and that the relative orientations of the two flavin rings are twisted ∼20° compared with the wild type, decreasing the surface contact area between the two flavin rings. Comparison of the structures without and with NADP(+) shows movement of the Gly(631)-Asn(635) loop. In the NADP(+)-free structure, the loop adopts a conformation that sterically hinders NADP(H) binding. The structure with NADP(+) shows movement of the Gly(631)-Asn(635) loop to a position that permits NADP(H) binding. Furthermore, comparison of these mutant and wild type structures strongly suggests that the Gly(631)-Asn(635) loop movement controls NADPH binding and NADP(+) release; this loop movement in turn facilitates the flavin domain movement, allowing electron transfer from FMN to the CYPOR redox partners.

Another look at the interaction between mitochondrial cytochrome c and flavocytochrome b 2

Yeast flavocytochrome b (2) tranfers reducing equivalents from lactate to oxygen via cytochrome c and cytochrome c oxidase. The enzyme catalytic cycle includes FMN reduction by lactate and reoxidation by intramolecular electron transfer to heme b (2). Each subunit of the soluble tetrameric enzyme consists of an N terminal b (5)-like heme-binding domain and a C terminal flavodehydrogenase. In the crystal structure, FMN and heme are face to face, and appear to be in a suitable orientation and at a suitable distance for exchanging electrons. But in one subunit out of two, the heme domain is disordered and invisible. This raises a central question: is this mobility required for interaction with the physiological acceptor cytochrome c, which only receives electrons from the heme and not from the FMN? The present review summarizes the results of the variety of methods used over the years that shed light on the interactions between the flavin and heme domains and between the enzyme and cytochrome c. The conclusion is that one should consider the interaction between the flavin and heme domains as a transient one, and that the cytochrome c and the flavin domain docking areas on the heme b (2) domain must overlap at least in part. The heme domain mobility is an essential component of the flavocytochrome b (2) functioning. In this respect, the enzyme bears similarity to a variety of redox enzyme systems, in particular those in which a cytochrome b (5)-like domain is fused to proteins carrying other redox functions.

Ultrafast Infrared Spectroscopy of an Isotope-Labeled Photoactivatable Flavoprotein

The blue light using flavin (BLUF) domain photosensors, such as the transcriptional antirepressor AppA, utilize a noncovalently bound flavin as the chromophore for photoreception. Since the isoalloxazine ring of the chromophore is unable to undergo large-scale structural change upon light absorption, there is intense interest in understanding how the BLUF protein matrix senses and responds to flavin photoexcitation. Light absorption is proposed to result in alterations in the hydrogen-bonding network that surrounds the flavin chromophore on an ultrafast time scale, and the structural changes caused by photoexcitation are being probed by vibrational spectroscopy. Here we report ultrafast time-resolved infrared spectra of the AppA BLUF domain (AppA(BLUF)) reconstituted with isotopically labeled riboflavin (Rf) and flavin adenine dinucleotide (FAD), which permit the first unambiguous assignment of ground and excited state modes arising directly from the flavin carbonyl groups. Studies of model compounds and DFT calculations of the ground state vibrational spectra reveal the sensitivity of these modes to their environment, indicating that they can be used as probes of structural dynamics.

Shining a Light on an Opportunistic Pathogen

Shining a Light on an Opportunistic Pathogen

The Opportunistic Human PathogenAcinetobacter baumanniiSenses and Responds to Light

Light is a ubiquitous environmental signal that many organisms sense and respond to by modulating their physiological responses accordingly. While this is an expected response among phototrophic microorganisms, the ability of chemotrophic prokaryotes to sense and react to light has become a puzzling and novel issue in bacterial physiology, particularly among bacterial pathogens. In this work, we show that the opportunistic pathogen Acinetobacter baumannii senses and responds to blue light. Motility and formation of biofilms and pellicles were observed only when bacterial cells were incubated in darkness. In contrast, the killing of Candida albicans filaments was enhanced when they were cocultured with bacteria under light. These bacterial responses depend on the expression of the A. baumannii ATCC 17978 A1S_2225 gene, which codes for an 18.6-kDa protein that contains an N-terminal blue-light-sensing-using flavin (BLUF) domain and lacks a detectable output domain(s). Spectral analyses of the purified recombinant protein showed its ability to sense light by a red shift upon illumination. Therefore, the A1S_2225 gene, which is present in several members of the Acinetobacter genus, was named blue-light-sensing A (blsA). Interestingly, temperature plays a role in the ability of A. baumannii to sense and respond to light via the BlsA photoreceptor protein.

Flavin-containing reductase: new perspective on the detoxification of nitrobenzodiazepine

Importance of the field: Nitrobenzodiazepines (NBDZs) are important hypnotic-sedative drugs prescribed in clinic for treating sleeping disorders. The long-lasting efficacy of NBDZs has made them to be used purposely resulting in neurophysiological impairment and internal toxicity. While many studies have investigated the biotransformation of NBDZs, studies seldom are found on their reductive metabolism or the enzymes that act on these drugs.Areas covered in this review: In this review, we describe the finding of human hepatic NADPH-cytochrome P450 reductase (EC 1.6.2.4) and Escherichia coli nitroreductase NfsB (EC 1.5.1.34) in the reductive conversion of NBDZ to a harmless metabolite 7-aminobenzodiazepine and present the facts of reductive activity in other flavin-containing reductases. A historic investigation on the reduction of nitroaromatics and quinones by the selected flavoenzymes is performed. In addition, flavin domain structures of these enzymes are discussed.What the reader will gain: The reader will gain a comprehensive understanding of the reductive metabolism of NBDZs including the structure–activity relationship of the selected flavoproteins.Take home message: The discovery of novel flavin-containing reductase on NBDZ in the body is essential for the development of more active nitroreductases which may find applications in the detoxification of NBDZ.

Determining Structural Differences in the Dark and Light States of AppA using Vibrational and Ultrafast Fluorescence Spectroscopy

The blue light using flavin (BLUF) domain proteins are a novel class of photosensors that bind flavin noncovalently in order to sense and respond to high intensity blue (450 nm) light. The transcriptional antirepressor AppA, is a BLUF photosensor that utilizes a non‐covalently bound flavin chromophore which is unable to undergo large scale structural change upon light absorption. This is in contrast to most photoreceptors which undergo structural reformations such as trans/cis isomerization upon irradiation. It is of great interest to understand how the BLUF protein matrix senses and responds to flavin photoexcitation. Light absorption is thought to result in alterations in a hydrogen bonding network that surrounds the flavin chromophore on the picosecond time scale. The excited photochemistry of wild‐type AppA and several mutants of AppA in which the hydrogen bonding network has been altered, has been analyzed using ultrafast (100 fs) time resolved fluorescence spectroscopy and picosecond time resolved infrared spectroscopy. Reconstitution of the protein with isotopically‐labeled flavin has permitted unambiguous assignment of the ground and excited state modes associated with the flavin C2=O and C4=O groups, and together the data provide a more detailed understanding of the photoexcitation mechanism.

A fluorometric method for determination of catalytic activity of CYP51b1 (sterol 14α-demethylase) with coumarin derivatives

A method for direct registration of CYP51b1 (sterol-14α-demethylase) activity with coumarin derivatives as substrate has been proposed. Determination of catalytic activity of this enzyme with 7-aminocoumarin-4-acetic acid (ACAC) is based on registration of the increase of fluorescence (λexcitation = 360 nm and λemission = 435 nm) at 30°C. In the model system for assay of CYP51b1 activity BMR (a flavin domain of the bacterial cytochrome P450BM-3) may serve as the electron donor. The developed method is simple, highly sensitive and accurate; it can be used for screening of sterol 14α-demethylase inhibitors.

Functional expression of Phanerochaete chrysosporium cellobiose dehydrogenase flavin domain in Escherichia coli

Cellobiose dehydrogenase (CDH; EC 1.1.99.18) is an extracellular glycosylated protein composed of two distinct domains, a C-terminal catalytic flavin domain and an N-terminal cytochrome-b-type heme domain, which transfers electrons from the flavin domain to external electron acceptors. The soluble flavin domain of the Phanerochaete chrysosporium CDH was successfully expressed in Escherichia coli. The enzyme showed dye-mediated CDH activity higher than that of the complete CDH, composed of flavin domain and heme domain, prepared using Pichia pastoris as the host microorganism. The ability to conveniently express the recombinant CDH flavin domain in E. coli provides great opportunities for the molecular engineering of the catalytic properties of CDH.

A QM/MM study on the fast photocycle of blue light using flavin photoreceptors in their light-adapted/active form

Based on QM/MM calculations using a combination of time-dependent Hartree-Fock and coupled cluster response theory a mechanism is proposed for the photocycle of blue light using flavin (BLUF) domains in the signaling/light adapted conformation. In analogy to the dark-adapted form, a charge transfer state drives proton transfer from the highly conserved tyrosine residue to the flavin chromophore. The latter step is mediated by the adjacent glutamine residue, which, in the light adapted conformation, exists as its imidic tautomer. However, before the proton transfer is even halfway completed, a conical intersection seam between the charge transfer and ground state is reached. Two channels for the decay back to the initial light-adapted conformation are open, a rapid one leading directly through the funnel of the conical intersection, bypassing the formation of the biradical intermediate, and a slower one via the biradical intermediate. The mechanism as proposed here: (i) explains the very rapid photocycle; and (ii) confirms the concept of photoirreversibility, both of which have been experimentally observed for BLUF domains in their light-adapted conformations.

Electron transfer in the complex of membrane-bound human cytochrome P450 3A4 with the flavin domain of P450BM-3: The effect of oligomerization of the heme protein and intermittent modulation of the spin equilibrium

We studied the kinetics of NADPH-dependent reduction of human CYP3A4 incorporated into Nanodiscs (CYP3A4–ND) and proteoliposomes in order to probe the effect of P450 oligomerization on its reduction. The flavin domain of cytochrome P450-BM3 (BMR) was used as a model electron donor partner. Unlike CYP3A4 oligomers, where only 50% of the enzyme was shown to be reducible by BMR, CYP3A4–ND could be reduced almost completely. High reducibility was also observed in proteoliposomes with a high lipid-to-protein ratio (L/P = 910), where the oligomerization equilibrium is displaced towards monomers. In contrast, the reducibililty in proteoliposomes with L/P = 76 did not exceed 55 ± 6%. The effect of the surface density of CYP3A4 in proteoliposomes on the oligomerization equilibrium was confirmed with a FRET-based assay employing a cysteine-depleted mutant labeled on Cys-468 with BODIPY iodoacetamide. These results confirm a pivotal role of CYP3A4 oligomerization in its functional heterogeneity. Furthermore, the investigation of the initial phase of the kinetics of CYP3A4 reduction showed that the addition of NADPH causes a rapid low-to-high-spin transition in the CYP3A4–BMR complex, which is followed by a partial slower reversal. This observation reveals a mechanism whereby the CYP3A4 spin equilibrium is modulated by the redox state of the bound flavoprotein.

Modulation of the Cytochrome P450 Reductase Redox Potential by the Phospholipid Bilayer

Cytochrome P450 reductase (CPR) is a tethered membrane protein which transfers electrons from NADPH to microsomal P450s. We show that the lipid bilayer has a role in defining the redox potential of the CPR flavin domains. In order to quantitate the electrochemical behavior of this central redox protein, full-length CPR was incorporated into soluble nanometer scale discoidal membrane bilayers (nanodiscs), and potentials were measured using spectropotentiometry. The redox potentials of both FMN and FAD were found to shift to more positive values when in a membrane bilayer as compared to a solubilized version of the reductase. The potentials of the semiquinone/hydroquinone couple of both FMN and FAD are altered to a larger extent than the oxidized/semiquinone couple which is understood by a simple electrostatic model. When anionic lipids were used to change the membrane composition of the CPR-nanodisc, the redox potential of both flavins became more negative, favoring electron transfer from CPR to cytochrome P450.

Comparison of Direct and Mediated Electron Transfer for Cellobiose Dehydrogenase from Phanerochaete sordida

Direct and mediated electron transfer (DET and MET) between the enzyme and electrodes were compared for cellobiose dehydrogenase (CDH) from the basidiomycete Phanerochaete sordida (PsCDH). For DET, PsCDH was adsorbed at pyrolytic graphite (PG) electrodes while for MET the enzyme was covalently linked to a low potential Os redox polymer. Both types of electrodes were prepared in the presence of single walled carbon nanotubes (SWCNTs). DET requires the oxidation of the heme domain, while MET occurs partially via the heme and the flavin domain at pH 3.5. At pH 6 MET occurs solely via the flavin domain. Most probably, the interaction of the domains decreases from pH 3.5 to 6.0 due to electrostatic repulsion of deprotonated amino acid residues, covering the surfaces of both domains. MET starts at a lower potential than DET. The midpoint potentials at pH 3.5 for the flavin (40 mV) and the heme domain (170 mV) were determined with spectroelectrochemistry. The electrochemical and spectroelectrochemical measurements presented in this work are in conformity. The pH dependency of DET and MET was investigated for PsCDH. The optimum was observed between pH 4 and 4.5 pH for DET and in the range of pH 5-6 for MET. The current densities obtained by MET are 1 order of magnitude higher than by DET. During multicycle cyclic voltammetry experiments carried out at different pHs, the PsCDH modified electrode working by MET turned out to be very stable. In order to characterize a PsCDH modified anode working by MET with respect to biofuel cell applications, this electrode was combined with a Pt-black cathode as model for a membraneless biofuel cell. In comparison to DET, a 10 times higher maximum current and maximum power density in a biofuel cell application could be achieved by MET. While CDH modified electrodes working by DET are highly qualified for applications in amperometric biosensors, a much better performance as biofuel cell anodes can be obtained by MET. The use of CDH modified electrodes working by MET for biofuel cell applications results in a less positive onset of the electrocatalytic current (which may lead to an increased cell voltage), higher current and power density, and much better long-term stability over a broad range of pH.

A Conclusive Mechanism of the Photoinduced Reaction Cascade in Blue Light Using Flavin Photoreceptors

On the basis of extensive first-principle calculations within the framework of quantum mechanics/molecular mechanics (QM/MM), a conclusive mechanism for the formation of the signaling state of blue light using flavin (BLUF) domain proteins is proposed which is compatible with the experimental data presently available. Time-dependent density functional, as well as advanced coupled cluster response theory was employed for the QM part in order to describe the relevant excited states. One of the key residues involved in the mechanism is the glutamine adjacent to the flavin chromophore. The reaction cascade, triggered by the initial photoexcitation of the flavin chromophore, involves isomerization of this residue but no rotation as assumed previously. The fact that only the environment, but not the flavin chromophore by itself, is chemically transformed along the individual steps of the mechanism is unique for biological photoreceptors. The final isomer of the glutamine tautomer, i.e., the imidic acid, is further stabilized by the interchange of a methionine residue in the binding pocket with a tryptophan residue. The flip of these two residues might be the trigger for the large conformational change of this protein which is consequently transmitted as the signal to the biological environment.