Cofactor trapping, a new method to produce flavin mononucleotide

We have purified flavin mononucleotide (FMN) from a flavoprotein-overexpressing Escherichia coli strain by cofactor trapping. This approach uses an overexpressed flavoprotein to trap FMN, which is thus removed from the cascade regulating FMN production in E. coli. This, in turn, allows the isolation of highly pure FMN.     

A thermodynamic description of the self-association of flavin mononucleotide.

Systematic heat of dilution studies of the self-association of flavin mononucleotide (FMN) have been conducted as a function of ionic strength (0.05 – 2.0 m) and pH (5–9) in aqueous solution. The data are adequately described by the expression $\text{Q}{}_{\mathrm{T}}\text{= ΔH ? (}\text{ΔH}\text{K}\text{)}{}^{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}\text{(}\text{Q}{}_{\mathrm{T}}\text{c}{}_{\mathrm{T}}\text{)}{}^{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}$ for an isodesmic self-association. Q_T is the molar heat of dilution, ΔH and K are the derived enthalpy and equilibrium constants for the process FMN + (FMN)_i?1 ? (FMN)_i, and c_T is the concentration of FMN expressed in monomer units. Typical values derived for the various thermodynamic parameters at 25 °C are ΔG = ?3.56 kcal mol^?1, ΔH = ?3.72 kcal mol^?1, and ΔS = ?0.54 cal (mol · deg)^?1. These data, plus nuclear magnetic resonance evidence (Yagi, K., Ohishi, N., Takai, A., Kawano, K., and Kyogoku, Y., 1976, Biochemistry15, 2877–2880) argue in favor of an open-ended association of flavin molecules. The signs of the various thermodynamic parameters suggest that both hydrophobic and surface energy forces contribute significantly to the association, while the lack of any significant ionic strength dependence indicates the lack of any ionic centers in the association.     

A conformational approach to study the mode of binding of flavin mononucleotide to flavodoxin

Energetically preferred conformers of Flavin mononucleotide (FMN) were determined using empirical potential energy functions. The minimum energy conformers were used to study the mode of its binding to apoflavodoxin. This study indicates that the conformers of FMN that initiate the binding process undergo significant changes in the position of the phosphate group to reach the final bound conformation. In the bound conformation the phosphate group leads to the formation of a network of hydrogen bonds with the apoflavodoxin and contributes significantly to the binding energy. This extra energy is required for FMN to overcome the repulsion from Met 56 and Glu 59 and to bind tightly to apoflavodoxin.     

A postulated mechanism for the bioluminescent oxidation of reduced flavin mononucleotide

A mechanism is presented for the luciferase catalyzed oxidation of reduced flavin mononucleotide with oxygen in the presence of long-chain aldehyde. The mechanism involves the formation of a flavin peroxy anion which attacks aldehyde. A Baeyer-Villiger type shift leads to oxidation of aldehyde to acid, and to formation of hydroxide and excited protonated flavin which emits a photon. The mechanism is consistent with known details of the bioluminescent reaction and with known reactions of flavins and allows several verifiable predictions to be made.     

Evidence for direct interaction between cysteine 138 and the flavin in thioredoxin reductase. A study using flavin analogs

The flavoenzyme thioredoxin reductase from Escherichia coli contains an oxidation-reduction active disulfide made up of Cys135 and Cys138. Mutations changing each Cys residue to a Ser residue have been effected (Prongay, A. J., engelke, D. R., and Williams, C. H., Jr. (1989) J. Biol. Chem. 264, 2656-2664). The FAD prosthetic group of each altered thioredoxin reductase has been replaced with 1-deaza-FAD (a flavin analog with carbon substituted for nitrogen at position 1), 4-thio-FAD (a flavin analog with sulfur substituted for oxygen at position 4), and 6-thiocyanato-FAD. 1-Deaza-FAD-TRR(Cys135,Ser138) has absorbance and fluorescence spectral properties similar to the oxidized form of wild type apothioredoxin reductase reconstituted with 1-deaza-FAD. The absorbance spectrum of 1-deaza-FAD-TRR(Ser135,Cys138) is similar to the spectrum of the two-electron reduced form of wild type apothioredoxin reductase reconstituted with 1-deaza-FAD, indicating that it is a mixture of two species (O'Donnell, M. E., and Williams, C. H., Jr. (1984) J. Biol. Chem. 259, 2243-2251). The spectrum of one of these species of 1-deaza-FAD-TRR(Ser135,Cys138) resembles the spectrum of oxidized 1-deaza-FAD bound to wild type apothioredoxin reductase. The other species has an absorbance spectrum with a single peak at 400 nm (epsilon 400 = 11,100 M-1 cm-1) and resembles the spectrum of a thiolate adduct at the C4a position of the 1-deaza-FAD. The equilibrium between these species is pH-dependent, with a maximum of 50% C4a-adduct formation at low pH, and is linked to pK alpha values at 8.2 and 9.3. The absorbance spectrum of 4-thio-FAD-TRR(Cys135,Ser138) resembles the spectrum of the unbound 4-thio-FAD, whereas 4-thio-FAD-TRR(Ser135,Cys138) has a spectrum indicative of a mixture of 4-thio-FAD and FAD, suggesting a reaction between the 4-position of the flavin and Cys138. The binding of 6-thiocyanato-FAD to the apoprotein of the mutated enzymes showed no evidence for a reaction between the thiols and the group at the 6-position of the flavin.     

Analysis of the reduction of nitroxides by flavin mononucleotide

This article describes a simle method to prepare hydroxylamines from nitroxides by photo-activated flavin mononucleotide. The half-time of reduction varied from 2 to 38.4 s for a series of nitroxides. For most nitroxides short exposures to light (min) were sufficient to produce significant amounts of hydroxylamine; longer periods of exposure increased the yields of other products. Proxyl (2,2,5-trimethyl-5-alkylpyrrolidine-N-oxy) nitroxides were unsually reactive with a much higher yield of products which could not be reoxidized by ferricyanide to the nitroxides. Optimum conditions for reversible reduction depend on the nitroxide and the amounts of other reducible substances such as oxygen and ferricyanide that may be present.     

A discrete time stochastic model of a two prey, one predator species interaction

A stochastic discrete time model of a two prey, one predator interaction, an extension of one and two species models proposed by Leslie (1958) and Leslie and Gower, 1958, Leslie and Gower, 1960, is studied. Monte Carlo simulations and the stability properties of the analogous continuous time deterministic model suggest the following hypotheses. (1) The two prey, one predator interaction is in general unstable. The range of parameters allowing coexistence of all three species is small. (2) Deterministically the predator always survives. (3) If the parameters defining the effects of density on the rates of population growth are large, the simulations lead to the rapid extinction of all three species or all but one of the prey species even if the interaction is deterministically stable. (4) The outcome of this three species interaction is largely probabilistic over a wide range of parameters. (5) A prey species with a competitive advantage over a second prey species may still find it difficult to invade and displace the second prey species if the density of the second prey species is high. Increasing the density of the predator offsets this numerical advantage somewhat. (6) The introduction of a predator common to two noncompeting species of prey usually leads to the extinction of one of the prey species. (7) In a stable two prey, one predator interaction the fluctuations of the two prey species are nonperiodic and erratic. The fluctuations of the rarer prey species are damped relative to the commoner species and the fluctuations of the rarer prey species behave as if the series has no fixed mean abundance. The predator population fluctuates with a remarkably constant period. The relevance of these hypotheses to the problem of relating population stability and persistence with the number of species in a community is discussed.     

Association of two nuclear proteins, Npw38 and NpwBP, via the interaction between the WW domain and a novel proline-rich motif containing glycine and arginine

We have previously reported a nuclear protein possessing a WW domain, Npw38 (Komuro, A., Saeki, M., and Kato, S. (1999) Nucleic Acids Res. 27, 1957-1965). Here we report a Npw38-binding protein, NpwBP, isolated from HeLa cell nuclear extracts and its characterization using a cloned cDNA. NpwBP contains two proline-rich regions that are capable of binding to the WW domain of Npw38. The binding analysis using an oligopeptide-immobilized membrane revealed that the WW domain of Npw38 preferentially recognizes a short proline-rich sequence, PPGPPP, surrounded by an arginine residue, so we named it a PGR motif. Localization analysis using green fluorescent protein fusion protein and immunostaining showed that Npw38 and NpwBP are colocalized in the same subnuclear region. Coimmunoprecipitation experiments confirmed the association between Npw38 and NpwBP, which were expressed as epitope-tagged forms in COS7 cells. Furthermore, the N-terminal region of NpwBP has binding ability for poly(rG) and G-rich single-stranded DNA. These results suggest that NpwBP is a physiological ligand of Npw38 and that the Npw38-NpwBP complex may function as a component of an mRNA factory in the nucleus.     

Hydrodynamic interaction between two copepods: a numerical study

Numerical simulations were carried out to compute the flow fieldaround two tethered, stationary or swimming model-copepods withvaried separation distances between them and for different relativebody positions and orientations. Based on each simulated flowfield, the power expended by each copepod in generating theflow field and volumetric flux through the capture area of eachcopepod were calculated. The geometry of the flow field aroundeach copepod was visualized by tracking fluid particles to constructstream tubes. The hydrodynamic force on each copepod was calculated.Also, velocity magnitudes and deformation rates were calculatedalong a line just above the antennules of each copepod. Allthe results were compared to the counterpart results for a solitarycopepod (stationary or swimming) to evaluate the hydrodynamicinteraction between the two copepods. The calculations of thepower and volumetric flux show that no energetic benefits areavailable for two copepods in close proximity. The results ofthe stream tube and force calculations show that when two copepodsare in close proximity, the hydrodynamic interaction betweenthem distorts the geometry of the flow field around each copepodand changes the hydrodynamic force on each copepod. Two beneficialroles of the hydrodynamic interactions are suggested for copepodswarms: (1) to maintain the integrity of the swarms and (2)to separate the swarming members with large nearest neighbourdistances (usually more than five body lengths). To preventstrong hydrodynamic interactions, copepods in swarms have toavoid positions of strong interactions, such as those directlyabove or below their neighbours. The results of the velocitymagnitudes and deformation rates demonstrate that the hydrodynamicinteraction between two copepods generates the hydrodynamicsignals detectable by the setae on each copepod's antennules.Based on the threshold of Yen et al. (1992), the results showthat the detection distance between two copepods of comparablesize is about two to five body lengths. Copepods may employa simple form of pattern recognition to detect the distance,speed and direction of an approaching copepod of comparablesize.     

Electrochemical reduction of methemoglobin either directly or with flavin mononucleotide as a mediator

Electrochemical reduction of methemoglobin on a platinum electrode is studied by means of thin layer spectroelectrochemistry. For methemoglobin alone in solution, direct reduction is very slow even for potentials close to those of the reduction of the solvent. The reduction of a methemoglobin-oxyhemoglobin mixture with an imposed potential causes the electrochemical reduction of oxygen, the conversion of oxyhemoglobin into deoxyhemoglobin, and a simultaneous transformation of part of the molecules into methemoglobin. When fixed oxygen has disappeared, reduction of methemoglobin takes place. The reduction of methemoglobin and deoxyhemoglobin is catalyzed by the presence of flavin mononucleotide (FMN). For the oxyhemoglobin-methemoglobin mixture, flavin makes a fast deoxygenation of oxyhemoglobin without a change in the oxidation state of the iron. It also allows the rapid reduction of methemoglobin. In each case, the resulting deoxyhemoglobin solutions do not show any electrolysis-induced modification of the equilibrium curves for oxygen binding.     

A novel glycolate oxidase requiring flavin mononucleotide as the cofactor in the prasinophycean alga Mesostigma viride

A new type of glycolate-oxidizing enzyme was found in the prasinophycean alga Mesostigma viride. This enzyme was characterized as the glycolate oxidase that strongly requires FMN, thus distinguishing it from most other Prasinophytes that possess glycolate dehydrogenase instead.     

Insights into the mode of flavin mononucleotide binding and catalytic mechanism of bacterial chromate reductases: A molecular dynamics simulation study

Enzymes from natural sources protect the environment via complex biological mechanisms, which aid in reductive immobilization of toxic metals including chromium. Nevertheless, progress was being made in elucidating high-resolution crystal structures of reductases and their binding with flavin mononucleotide (FMN) to understand the underlying mechanism of chromate reduction. Therefore, herein, we employed molecular dynamics (MD) simulations, principal component analysis (PCA), and binding free energy calculations to understand the dynamics behavior of these enzymes with FMN. Six representative chromate reductases in monomeric and dimeric forms were selected to study the mode, dynamics, and energetic component that drive the FMN binding process. As evidenced by MD simulation, FMN prefers to bind the cervix formed between the catalytic domain surrounded by strong conserved hydrogen bonding, electrostatic, and hydrophobic contacts. The slight movement and reorientation of FMN resulted in breakage of some crucial H-bonds and other nonbonded contacts, which were well compensated with newly formed H-bonds, electrostatic, and hydrophobic interactions. The critical residues aiding in tight anchoring of FMN within dimer were found to be strongly conserved in the bacterial system. The molecular mechanics combined with the Poisson-Boltzmann surface area binding free energy of the monomer portrayed that the van der Waals and electrostatic energy contribute significantly to the total free energy, where, the polar solvation energy opposes the binding of FMN. The proposed proximity relationships between enzyme and FMN binding site presented in this study will open up better avenues to engineer enzymes with optimized chromate reductase activity for sustainable bioremediation of heavy metals.     

Sites of interaction between SecA and the chaperone SecB, two proteins involved in export

SecB, a small tetrameric cytosolic chaperone in Escherichia coli, facilitates the export of precursor poly-peptides by maintaining them in a nonnative conformation and passing them to SecA, which is a peripheral member of the membrane-bound translocation apparatus. It has been proposed by several laboratories that as SecA interacts with various components along the export pathway, it undergoes conformational changes that are crucial to its function. Here we report details of molecular interactions between SecA and SecB, which may serve as conformational switches. One site of interaction involves the final C-terminal 21 amino acids of SecA, which are positively charged and contain zinc. The C terminus of each subunit of the SecA dimer makes contact with the flat beta-sheet that is formed by each dimer of the SecB tetramer. Here we demonstrate that a second interaction exists between the extreme C-terminal alpha-helix of SecB and a site on SecA, as yet undefined but different from the C terminus of SecA. We investigated the energetics of the interactions by titration calorimetry and characterized the hydrodynamic properties of complexes stabilized by both interactions or each interaction singly using sedimentation velocity centrifugation.     

Arrestin binding to calmodulin: a direct interaction between two ubiquitous signaling proteins

Arrestins serve as multi-functional regulators of G-protein coupled receptors, interacting with hundreds of different receptor subtypes and a variety of other signaling proteins. Here we identify calmodulin as a novel arrestin interaction partner using three independent methods in vitro and in cells. Arrestin preferentially binds calcium-loaded calmodulin with a Kd value of approximately 7 microM, which is within range of endogenous calmodulin concentrations. The calmodulin binding site is localized on the concave side of the C-domain and a loop in the center of the arrestin molecule, significantly overlapping with receptor and microtubule-binding sites. Using purified proteins, we found that arrestins sequester calmodulin, preventing its binding to microtubules. Nanomolar affinity of arrestins for their cognate receptors makes calmodulin an ineffective competitor for arrestin binding at relatively high receptor concentrations. The arrestin-calmodulin interaction likely regulates the localization of both proteins and their availability for other interaction partners.     

Segregate or cooperate- a study of the interaction between two species of Dictyostelium

Background

Plastids have inherited their own genomes from a single cyanobacterial ancestor, but the majority of cyanobacterial genes, once retained in the ancestral plastid genome, have been lost or transferred into the eukaryotic host nuclear genome via endosymbiotic gene transfer. Although previous studies showed that cyanobacterial gnd genes, which encode 6-phosphogluconate dehydrogenase, are present in several plastid-lacking protists as well as primary and secondary plastid-containing phototrophic eukaryotes, the evolutionary paths of these genes remain elusive.

Results

Here we show an extended phylogenetic analysis including novel gnd gene sequences from Excavata and Glaucophyta. Our analysis demonstrated the patchy distribution of the excavate genes in the gnd gene phylogeny. The Diplonema gene was related to cytosol-type genes in red algae and Opisthokonta, while heterolobosean genes occupied basal phylogenetic positions with plastid-type red algal genes within the monophyletic eukaryotic group that is sister to cyanobacterial genes. Statistical tests based on exhaustive maximum likelihood analyses strongly rejected that heterolobosean gnd genes were derived from a secondary plastid of green lineage. In addition, the cyanobacterial gnd genes from phototrophic and phagotrophic species in Euglenida were robustly monophyletic with Stramenopiles, and this monophyletic clade was moderately separated from those of red algae. These data suggest that these secondary phototrophic groups might have acquired the cyanobacterial genes independently of secondary endosymbioses.

Conclusion

We propose an evolutionary scenario in which plastid-lacking Excavata acquired cyanobacterial gnd genes via eukaryote-to-eukaryote lateral gene transfer or primary endosymbiotic gene transfer early in eukaryotic evolution, and then lost either their pre-existing or cyanobacterial gene.     

NADH-Ubiquinone oxidoreductase: substrate-dependent oxygen turnover to superoxide anion as a function of flavin mononucleotide

Bovine heart mitochondrial NADH-ubiquinone oxidoreductase (complex I) catalyzed NADH- and ubiquinone-1-dependent oxygen (O2) turnover to hydrogen peroxide that was stimulated by piericidin A and superoxide dismutase (SOD), but was insensitive to antimycin A, myxothiazol, and potassium cyanide. The extent of O2 consumption as a function of ubiquinone-1 did not correlate with piericidin A-sensitive rates of ubiquinone reduction. Decylubiquinone did not stimulate O2 consumption, but did initiate an SOD-sensitive cytochrome c reduction when complex I was isolated away from ubiquinol-cytochrome c oxidoreductase. Rates and extent of O2 turnover (ROS production) and ubiquinone reduction were higher than previously reported for submitochondrial particles (SMP) and isolated complex I. This ROS production was shown to co-isolate with complex I flavin.