Kinetic study of a substrate cycle involving a chemical step: highly amplified determination of phenolic compounds

A kinetic analysis of a substrate cycle in which one of the two steps was substituted by a chemical reaction has been made. The model is illustrated by the amplified determination, in a continuous assay, of phenolic compounds at low concentrations using the enzyme tyrosinase and β-NADH to reduce the o-quinone product of catalytic activity. Progress curves corresponding to β-NADH disappearance were not linear and followed first-order kinetics. Knowledge of the kinetics of the reaction has allowed us to achieve detection limits as low as 50 nM in a simple 10-min assay. There is no analytical solution to the non-linear differential equation system that describes the kinetics of the reaction, therefore, computer simulations of its dynamic behaviour are also presented, good agreement with the experimental results being obtained. The method is applicable to the measurement of any other metabolite, and its amplification capacity as well as the simplicity of determining kinetic parameters enable it to be implemented in a bioreactor for automation purposes.     

Kinetic resonance Raman spectroscopy of carotenoids: A sensitive kinetic monitor of bacteriorhodopsin mediated membrane potential changes

A rapid (14 – 22 μs) light-induced, bacteriorhodopsin mediated membrane potential has been detected using the technique of kinetic resonance Raman spectroscopy and the model system of β-carotene incorporated into reconstituted vesicles containing bacteriorhodopsin. Our data demonstrate that the kinetic resonance Raman spectrum of β-carotene is an extremely sensitive monitor of kinetic alterations in membrane potential with micron spatial resolution in a highly scattering medium. In addition, our Raman results indicate that the potential sensitivity of β-carotene is an excited state property of the molecule, thus making it an electrochromic monitor of membrane potential. We feel the techniques illustrated in this paper have the advantage of being a native probe of kinetic membrane potential changes and will be applicable to a wide variety of biological systems without the perturbing side-effects which often accompany the use of non-biological, potential-sensitive dyes.     

Specific enzyme complex of beta-1,4-galactosyltransferase-II and glucuronyltransferase-P facilitates biosynthesis of N-linked human natural killer-1 (HNK-1) carbohydrate

Human natural killer-1 (HNK-1) carbohydrate is highly expressed in the nervous system and is involved in synaptic plasticity and dendritic spine maturation. This unique carbohydrate, consisting of a sulfated trisaccharide (HSO(3)-3GlcAβ1-3Galβ1-4GlcNAc-), is biosynthesized by the successive actions of β-1,4-galactosyltransferase (β4GalT), glucuronyltransferase (GlcAT-P and GlcAT-S), and sulfotransferase (HNK-1ST). A previous study showed that mice lacking β4GalT-II, one of seven β4GalTs, exhibited a dramatic loss of HNK-1 expression in the brain, although β4GalT-I-deficient mice did not. Here, we investigated the underlying molecular mechanism of the regulation of HNK-1 expression. First, focusing on a major HNK-1 carrier, neural cell adhesion molecule, we found that reduced expression of an N-linked HNK-1 carbohydrate caused by a deficiency of β4GalT-II is not likely due to a general loss of the β1,4-galactose residue as an acceptor for GlcAT-P. Instead, we demonstrated by co-immunoprecipitation and endoplasmic reticulum-retention analyses using Neuro2a (N2a) cells that β4GalT-II physically and specifically associates with GlcAT-P. In addition, we revealed by pulldown assay that Golgi luminal domains of β4GalT-II and GlcAT-P are sufficient for the complex to form. With an in vitro assay system, we produced the evidence that the kinetic efficiency k(cat)/K(m) of GlcAT-P in the presence of β4GalT-II was increased about 2.5-fold compared with that in the absence of β4GalT-II. Finally, we showed that co-expression of β4GalT-II and GlcAT-P increased HNK-1 expression on various glycoproteins in N2a cells, including neural cell adhesion molecule. These results indicate that the specific enzyme complex of β4GalT-II with GlcAT-P plays an important role in the biosynthesis of HNK-1 carbohydrate.     

Identification of DypB from Rhodococcus jostii RHA1 as a lignin peroxidase

Rhodococcus jostii RHA1, a polychlorinated biphenyl-degrading soil bacterium whose genome has been sequenced, shows lignin degrading activity in two recently developed spectrophotometric assays. Bioinformatic analysis reveals two unannotated peroxidase genes present in the genome of R. jostii RHA1 with sequence similarity to open reading frames in other lignin-degrading microbes. They are members of the Dyp peroxidase family and were annotated as DypA and DypB, on the basis of bioinformatic analysis. Assay of gene deletion mutants using a colorimetric lignin degradation assay reveals that a ΔdypB mutant shows greatly reduced lignin degradation activity, consistent with a role in lignin breakdown. Recombinant DypB protein shows activity in the colorimetric assay and shows Michaelis-Menten kinetic behavior using Kraft lignin as a substrate. DypB is activated by Mn(2+) by 5-23-fold using a range of assay substrates, and breakdown of wheat straw lignocellulose by recombinant DypB is observed over 24-48 h in the presence of 1 mM MnCl(2). Incubation of recombinant DypB with a β-aryl ether lignin model compound shows time-dependent turnover, giving vanillin as a product, indicating that C(α)-C(β) bond cleavage has taken place. This reaction is inhibited by addition of diaphorase, consistent with a radical mechanism for C-C bond cleavage. Stopped-flow kinetic analysis of the DypB-catalyzed reaction shows reaction between the intermediate compound I (397 nm) and either Mn(II) (k(obs) = 2.35 s(-1)) or the β-aryl ether (k(obs) = 3.10 s(-1)), in the latter case also showing a transient at 417 nm, consistent with a compound II intermediate. These results indicate that DypB has a significant role in lignin degradation in R. jostii RHA1, is able to oxidize both polymeric lignin and a lignin model compound, and appears to have both Mn(II) and lignin oxidation sites. This is the first detailed characterization of a recombinant bacterial lignin peroxidase.     

Kinetic determination of cellular LacZ expression

A kinetic assay for the expression of β-galactosidase in cells transfected with the LacZ gene was developed using a 96-well-plate format. The assay involves solubilization of the cells followed by measuring hydrolytic rates of o-nitrophenyl β-D-galactoside on a standard 96-well-plate reader without other manipulations. The protocol requires only that reagent be added sequentially to the wells at ambient temperatures, thus permitting a semiautomated or fully automated determination of reporter expression. The rates of chromophore development were found to be linear over a 6-log enzyme concentration range, from 0.001 to 100 mU. Additionally, the use of kinetic data avoids the complications of non-enzymatic, background optical density.     

Highly sensitive solid-phase enzyme immunoassay for terminal deoxynucleotidyl transferase

A highly sensitive and specific solid-phase enzyme immunoassay system for terminal deoxynucleotidyl transferase (TdT, EC 2.7.7.31) has been developed by the use of monospecific antibody against calf thymus TdT and β-d-galactosidase from Escherichia coli as label. The immunoassay system was composed of solid phase (polystyrene beads) with immobilized F(ab′)₂ antibody fragments and the antibody Fab′ fragments labeled with β-d-galactosidase. The minimum detectable concentration of calf TdT was 0.1 ng/ml (0.01 ng/assay), making it more sensitive than the radioimmunoassay or enzyme immunoassay methods that use alkaline phosphatase as label, as reported previously. The assay system cross-reacted with human TdT, and TdT in neoplastic cells or sera from leukemic patients was successfully detected by the present immunoassay method.     

Kinetic investigation of a solvent-free, chemoenzymatic reaction sequence towards enantioselective synthesis of a β-amino acid ester

A solvent-free, chemoenzymatic reaction sequence for the enantioselective synthesis of β-amino acid esters has been kinetically and thermodynamically characterized. The coupled sequence comprises a thermal aza-Michael addition of cheap starting materials and a lipase catalyzed aminolysis for the kinetic resolution of the racemic ester. Excellent ee values of >99% were obtained for the β-amino acid ester at 60% conversion. Kinetic constants for the aza-Michael addition were obtained by straightforward numerical integration of second-order rate equations and nonlinear fitting of the progress curves. A different strategy had to be devised for the biocatalytic reaction. Initially, a simplified Michaelis-Menten model including product inhibition was developed for the reaction running in THF as an organic solvent. Activity based parameters were used instead of concentrations in order to facilitate the transfer of the kinetic model to the solvent-free system. Observed solvent effects not accounted for by the use of thermodynamic activities were incorporated into the kinetic model. Enzyme deactivation was observed to depend on the ratio of the applied substrates and also included in the kinetic model. The developed simple model is in very good agreement with the experimental data and allows the simulation and optimization of the solvent-free process.     

β-Galactosidase activity assay using far-red-shifted fluorescent substrate DDAOG

β-Galactosidase (β-gal) is commonly used as a reporter gene in biological research, and a wide variety of substrates have been developed to assay its activity. One substrate, 9H-(1,3-dichloro-9,9-dimethylacridin-2-one-7-yl) β-d-galactopyranoside (DDAOG), can be cleaved by β-gal to produce 7-hydroxy-9H(I,3-dichloro-9,9-dimethylacridin-2-one) (DDAO). On excitation, DDAO generates a far-red-shifted fluorescent signal. Using this substrate, we developed a β-gal activity assay method. The DDAO signal was stable for at least 18 h. The signal intensity was linearly related to both the enzyme amount and substrate concentration. An optimized buffer for the β-gal/DDAOG assay was also formulated. When compared with the colorimetric substrate o-nitrophenyl-β-d-galactopyranoside (ONPG), the signal-to-background ratio of the DDAOG method was approximately 12-fold higher. The β-gal/DDAOG assay method was also tested in transiently transfected cells employing both pharmacologically and genetically inducible gene expression systems. The ability to detect signal induction is comparable to a similar assay using luciferase as the signal generating moiety. The β-gal/DDAOG assay method should provide a fluorescent reporter assay system for the wide variety of β-gal systems currently in use.     

The green tea polyphenol (2)-epigallocatechin-3-gallate (EGCG) is not a β-secretase inhibitor

(2)-Epigallocatechin-3-gallate (EGCG) is a major polyphenolic component of green tea. A number of studies have demonstrated EGCG has the possibility for delaying the onset or retarding the progression of Alzheimer's disease (AD) and indicated EGCG possess inhibition of β-secretase activity. We utilized homogeneous time-resolved fluorescence assay with a substrate Eu-CEVNLDAEFK-Qsy7 to screen β-secretase inhibitor in a cell-free system and AlphaLISA assay in cell system. The results first showed that EGCG had significant inhibition of β-secretase activity with IC(50) value of 7.57 × 10(-7)M in screening assay, but then we found EGCG had significant fluorescence-quenching effect in confirming assay, this indicates EGCG has the false positive β-secretase inhibitory activity. Furthermore, the followed AlphaLISA assay based on cell showed EGCG did not reduce the β-amyloid 1-40 secretion in HuAPPswe/HuBACE1 Chinese hamster ovary cell without affecting cell viability. Therefore our findings indicate EGCG do not inhibit β-secretase cleavage activity. Overall this study illustrates that EGCG is not a β-secretase inhibitor based on the compelling data. This provides further support that the choice of complementary assay format or technology is a critical factor in molecular screening and drug development for improving the hit-finding capability and efficiency.     

A quantitative continuous enzyme assay of intramolecularly quenched fluorogenic phospholipase substrates for molecular imaging

There has been recent growth in the development of activatable near-infrared (NIR) fluorescent probes for molecular imaging, generally designed by placing fluorochromes on a cleavable substrate in close proximity to one another, such that they self-quench, but fluoresce on separation via enzymatic cleavage of the substrate. Although these probes offer excellent contrast, the detection of enzyme activity has largely only been described qualitatively. In order to assess the effectiveness of a probe, it is useful to have a quantitative measure, such as the enzyme-substrate kinetic parameters. We have developed an assay to determine kinetic parameters and applied it to an intramolecularly quenched molecule, Pyro-PtdEtn-BHQ, a NIR fluorescent probe specific to phosphatidylcholine-specific phospholipase C. The development of this assay includes corrections for intermolecular quenching, calibration, optimization of reaction mixtures, and determination of kinetic and inhibition parameters. This assay can easily be extended to analyze and compare the efficiency of other fluorescent activatable phospholipase probes as suitable molecular imaging agents.     

ENZYMATIC ISOTOPIC ASSAY FOR AND PRESENCE OF β-PHENYLETHYLAMINE IN BRAIN

Abstract— An enzymatic isotopic assay for the measurement of β-phenylethylamine in brain, with a sensitivity of 100-200 pg, has been developed. With this assay, the endogenous β-phenylethylamine content (1.5 ng/g) in the rat brain has been determined. Phenylalanine administration increases the brain levels of this amine; inhibition of monoamine oxidase causes a 40-fold increase in brain β-phenylethylamine. After a combined treatment with a monoamine oxidase inhibitor and phenylalanine, the β-phenylethylamine content in the brain increases to about 400-fold. This increase can be blocked by the central decarboxylase inhibitor NSD-1055. p-Chlorophenylalanine also increases β-phenylethylamipe concentration in the brain, and this effect is potentiated by a simultaneous administration of phenylalanine.     

β-Neo-endorphin,a new hypothalamic “big” Leu-enkephalin of porcine origin: Its purification and the complete amino acid sequence

A new hypothalamic “big” Leu-enkephalin of porcine origin, designated as β-neo-endorphin, has been isolated from a side fraction, obtained in our previous isolation of α-neo-endorphin and PH-8P (dynorphin[1–8]). The complete amino acid sequence has been elucidated to be : Tyr-Gly-Gly-Phe-Leu-Arg-Lys-Tyr-Pro. The sequence has been confirmed by the comparison of natural β-neo-endorphin with a synthetic peptide. In addition, β-neo-endorphin exhibits potent opioid activity in guinea-pig ileum assay.     

A bioassay for determination of lipopolysaccharide in environmental samples

Although the limulus amebocyte lysate (LAL) assay is widely used to determine the concentration of LPS in biological samples, it is known to be susceptible to interference caused by substances of non-bacterial origin. In particular, polysaccharides such as β-glucans and pectic polysaccharides from fungi or plants, respectively, were shown to give higher LPS readings than were actually present in the sample. Here, we describe an assay for the determination of LPS in biological samples based on the stimulation of TLR4/MD2/CD14 transfected HEK293 cells which dose dependently release IL-8 upon stimulation with increasing concentrations of highly purified Escherichia coli LPS. The resulting standard curve is used to determine the LPS concentration in unknown samples. We show that the outcome of the LPS stimulation is not affected by the presence of β-glucans or other environmental substances found in dust extracts. Although, we present evidence that the LPS concentration measured with the kinetic chromogenic LAL test correlates with data from the TLR4 assay, the LAL test displays higher LPS readings. We conclude that the described TLR4 assay is a reliable alternative to assess the concentration of LPS in environmental samples without being influenced by polysaccharides such as β-glucans and other environmental substances found in dust extracts.     

Acid β-Glucosidase: Enzymology and Molecular Biology of Gaucher Diseas

Abstract

Human lysosomal β-glucosidase (D-glucosyl-acylsphingo-sine glucohydrolase, EC 3.2.1.45) is a membrane-associated enzyme that cleaves the β-glucosidic linkage of glucosylcer-amide (glucocerebroside), its natural substrate, as well as synthetic β-glumsides. Experiments with cultured cells suggest that in vivo this glycoprotein requires interaction with negatively charged lipids and a small acidic protein, SAP-2, for optimal glucosylceramide hydrolytic rates. In vitro, detergents (Triton? X-100 or bile acids) or negatively charged gangliosides or phos-pholipids and one of several “activator proteins” increase hydrolytic rate of lipid and water-soluble substrates. Using such in vitro assay systems and active site-directed covalent inhibitors, kinetic and structural properties of the active site have been elucidated. The defective activity of this enzyme leads to the variants of Gaucher disease, the most prevalent lysosomal storage disease. The nonneuronopathic (type 1) and neuronopathic (types 2 and 3) variants of this inherited (autosomal recessive) disease but panethnic, but type 1 is most prevalent in the Ashkenazi Jewish population. Several missense mutations, identified in the structural gene for lysosomal β-glucosidase from Gaucher disease patients, are presumably casual to the specifically altered post-translational oligosaccharide processing or stability of the enzyme as well as the alterecA in vitro kinetic properties of the residual enzyme from patient tissues.     

Highly selective recognition of naphthol isomers based on the fluorescence dye-incorporated SH-β-cyclodextrin functionalized gold nanoparticles

In present work, a rhodamine 6G (Rh 6G)-incorporated β-cyclodextrin functionalized gold nanoparticle (Rh 6G-CD-AuNP) based fluorescent assay has been successfully developed for recognizing/detecting the structural isomers, α-naphthol and β-naphthol, in aqueous solution. The β-cyclodextrin functionalized gold nanoparticles (CD-AuNPs) are achieved by conjugating the thiolated β-cyclodextrin (SH-β-CD) with AuNPs via S-Au covalent bonds. Rhodamine 6G (Rh 6G) is chosen as a fluorescent probe in this approach because it can be strongly absorbed on the surface of AuNP by noncovalent interaction. After binding with β-CD cavity, the naphthols enable to act as electron transfer quenchers of Rh 6G, which lead to significant fluorescence quenching of the dye. Because of different association ability of naphthol isomers with the β-CD cavity, the assay can selectively distinguish α-naphthol and β-naphthol with reasonable sensitivity. Detection of naphthols down to 8 nM with a dynamic range of nearly three orders of magnitude (0.01-8 μM) for α-naphthol and 50 nM with two orders of magnitude (0.1-20 μM) for β-naphthol is demonstrated, respectively. The ability of the method for detecting the content of α-naphthol or β-naphthol in the different naphthol mixtures has also been evaluated.     

Studies on glycolysis in vitro: role of glucose phosphorylation and phosphofructokinase activity on total velocity

An in vitro glycolysis system has been developed to study the regulation of glycolysis on kinetic structure basis, in order to determine the extent of regulatory effects on the whole system of individual enzymes according to their kinetic data, in rat liver and muscle. Hexokinase or glucose-6-phosphate addition to the system with glucose as substrate increases lactate production rate by 2.5 in liver and by 10 in muscle, which suggest glucose phosphorylation step is a limiting step in this system. Fructose 2,6-bisphosphate addition to the system increases lactate production rate in liver only when glucose is the substrate, but not with glucose-6-phosphate as substrate. There is a linear relationship between glycolytic activity, as lactate produced per min and protein quantity, which suggests that this system can also be used to assay glycolytic activity in tissue extracts. Specific glycolytic activity found, as mumol of L-lactate produced per min, per protein mg was 0.1 for muscle and 0.01 for liver.     

A nonradioactive high-performance liquid chromatographic microassay for uridine 5'-monophosphate synthase, orotate phosphoribosyltransferase, and orotidine 5'-monophosphate decarboxylase.

A novel nonradioactive, microassay method has been developed to determine simultaneously the two enzymatic activities of orotate phosphoribosyltransferase (OPRTase) and orotidine 5'-monophosphate decarboxylase (ODCase), either as a bifunctional protein (uridine 5'-monophosphate synthase, UMPS) or as separate enzymes. Substrates (orotate for OPRTase or orotidine 5'-monophosphate for ODCase) and a product (UMP) of the enzymatic assay were separated by high-performance liquid chromatography (HPLC) using a reversed-phase column and an ion-pairing system; the amount of UMP was quantified by dual-wavelength uv detection at 260 and 278 nm. This HPLC assay can easily detect picomole levels of UMP in enzymatic reactions using low specific activity UMPS of mammalian cell extracts, which is difficult to do with the other nonradioactive assays that have been described. The HPLC assay is suitable for use in protein purification and for kinetic study of these enzymes.     

ZNRF1 interacts with tubulin and regulates cell morphogenesis

The ubiquitin-proteasome system has been implicated in neuronal degeneration and regeneration. We demonstrated that overexpression of ZNRF1, which has been identified as a crucial molecule in nerve regeneration, causes morphological changes such as neurite-like elongation. Molecular dissections showed that both the RING finger domain and zinc finger domain are required for morphological changes. Furthermore, we identified β-tubulin type 2 (Tubb2) as a ZNRF1-binding protein by yeast two-hybrid screening. In vivo binding assay showed that ZNRF1 interacts with Tubb2 and immunofluorescent staining suggests that ZNRF1 is colocalized with Tubb2. These results suggest that ZNRF1 mediates regulation of neuritogenesis via interaction with tubulin.     

A direct spectrophotometric assay for peptide deformylase.

A direct UV-VIS spectrophotometric assay has been developed for peptide deformylase. This assay employs a novel class of peptide mimetics as deformylase substrates which, upon enzymatic removal of the N-terminal formyl group, rapidly release free thiols. The released thiols are quantitated using Ellman's reagent. A variety of peptide analogues that contain beta-thiaphenylalanine or beta-thiamethionine as the N-terminal residue were synthesized and found to be excellent substrates of the peptide deformylase from Escherichia coli (k(cat)/K(M) = 6.9 x 10(5) M(-1) s(-1) for the most reactive substrate). The deformylase reaction is conveniently monitored on a UV-VIS spectrophotometer in a continuous fashion. The versatility of the assay has been demonstrated by its application to kinetic characterization of the deformylase, pH profile studies, and enzyme inhibition assays. The assay can also be performed in an end-point fashion. The results demonstrate that this assay is a simple, highly sensitive, and rapid method to study kinetic properties of deformylases without the use of any coupling enzymes.     

In Vivo Evolution of a β-lactamase-like Activity Throughout the Idiotypic Pathway

Abstract

An abzyme (9G4H9) displaying a β-lactamase activity was obtained through the idiotypic pathway and has been previously described. Analysis of the catalytic mechanism by kinetic measurements with various substrates, chemical modifications, and three dimensional modeling, led us to conclude that IgG 9G4H9 displays an activity at the crossroads of β-lactamases and penicillin-binding proteins (PBPs). Penicillin-binding proteins and βlactamases are two closely related enzymes arising from a common ancestral gene. We herein propose that the idiotypic network has allowed the generation of a catalyst with unique catalytic properties, but that could behave as an intermediate between both enzymes.