Showing papers on "Substrate (chemistry) published in 1987"

Effect of severe burn injury on substrate cycling by glucose and fatty acids.

Abstract: Increases in metabolic rate and core temperature are common responses to severe injury. We have investigated the hypothesis that these responses are due to increases in substrate cycling. A substrate cycle exists when opposing, nonequilibrium reactions catalyzed by different enzymes are operating simultaneously. At least one of the reactions must involve the hydrolysis of ATP. Thus, a substrate cycle both liberates heat and increases energy expenditure, yet there is no net conversion of substrate to product. In studies in volunteers (n = 18) and in patients with severe burns who were in a hypermetabolic state (n = 18), we used stable-isotope tracers to quantify substrate cycling in the pathways of glycolysis and gluconeogenesis and a cycle involving the simultaneous breakdown and synthesis of stored triglyceride (triglyceride–fatty acid cycle). The total rates of triglyceride–fatty acid and glycolytic–gluconeogenic cycling were elevated in the patients by 450 and 250 percent, respectively (P<0.01...

Engineering enzyme specificity by "substrate-assisted catalysis"

Abstract: A novel approach to engineering enzyme specificity is presented in which a catalytic group from an enzyme is first removed by site-directed mutagenesis causing inactivation. Activity is then partially restored by substrates containing the missing catalytic functional group. Replacement of the catalytic His with Ala in the Bacillus amyloliquefaciens subtilisin gene (the mutant is designated His64Ala) by site-directed mutagenesis reduces the catalytic efficiency (kcat/Km) by a factor of a million when assayed with N-succinyl-L-Phe-L-Ala-L-Ala-L-Phe-p-nitroanilide (sFAAF-pNA). Model building studies showed that a His side chain at the P2 position of a substrate bound at the active site of subtilisin could be virtually superimposed on the catalytic His side chain of this serine protease. Accordingly, the His64Ala mutant hydrolyzes a His P2 substrate (sFAHF-pNA) up to 400 times faster than a homologous Ala P2 or Gln P2 substrate (sFAAF-pNA or sFAQF-pNA) at pH 8.0. In contrast, the wild-type enzyme hydrolyzes these three substrates with similar catalytic efficiencies. Additional data from substrate-dependent pH profiles and hydrolysis of large polypeptides indicate that the His64Ala mutant enzyme can recover partially the function of the lost catalytic histidine from a His P2 side chain on the substrate. Such "substrate-assisted catalysis" provides a new basis for engineering enzymes with very narrow and potentially useful substrate specificities. These studies also suggest a possible functional intermediate in the evolution of the catalytic triad of serine proteases.

Computer simulations of the diffusion of a substrate to an active site of an enzyme.

Abstract: Computer simulations of the diffusion of a substrate to an enzyme active site were performed. They included the detailed shape of the protein and an accurate description of its electrostatic potential. Application of the method to the diffusion of the superoxide anion to the protein superoxide dismutase revealed that the electric field of the enzyme enhances the association rate of the anion by a factor of 30 or more. Calculated changes in the association rate as a function of ionic strength and amino acid modification paralleled the observed behavior. Design principles of superoxide dismutase are considered with respect to insights provided by the simulations. A possible means of enhancing the enzyme turnover rate through site-directed mutagenesis is proposed.

Lipase-catalyzed ester exchange reactions in organic media with controlled humidity.

Abstract: Immobilized lipase activity is studied in organic solvent systems of controlled water content under the influence of a variety of reaction parameters, such as temperature, relative humidity, substrate concentrations, and type of fatty acid used. Control of the amount of water in the reaction system was found to be a valuable tool for the orientation of the reaction process and for the determination of the final reaction products. The properties of the immobilized lipase were studied using the interesterification of triolein and palmitic acid as the model system.

A rapid, sensitive, and inexpensive assay for chloramphenicol acetyltransferase.

Abstract: We present a rapid, sensitive enzymatic assay for chloramphenicol acetyltransferase (CAT) that does not require chromatography, HPLC, or autoradiography. The assay is based on the use of an inexpensive substrate, tritiated acetate, instead of [14C]chloramphenicol. The method is adapted from one originally used by de Crombrugghe et al. (1973) and by Shaw (1975), but with simplifications appropriate for routine use. In our hands, the method is as sensitive as the customary thin-layer chromatography assay and is far more efficient for the performance of many assays, both in terms of labor and expense.

Kinetic studies on ammonia and methane oxidation by Nitrosococcus oceanus

Abstract: The kinetics of ammonia oxidation and the ability of a marine ammonia-oxidizing bacterium, Nitrosococcus oceanus, to metabolize methane were investigated in semicontinuous batch culture. The effects of inhibitors (acetylene and nitrapyrin) and coreactants were determined in order to elucidate the behavior of the ammonia oxygenase enzyme in N. oceanus. Acetylene and nitrapyrin were potent inhibitors and their effects were not mitigated by increased ammonia concentrations. Oxygen concentration had the effect of a mixed-type inhibitor; reduced oxygen inhibited the rate or ammonia oxidation at high substrate concentration but may enhance the rate at low substrate concentrations. Substrate affinity in terms of NH 4 + increased (K m decreased) with increasing pH. Optimal pH was about 8. Methane inhibited ammonia oxidation; the interaction was not simple competitive inhibition and the presence of multiple active sites on the enzyme was indicated by the behaviour of the inhibited treatments. Half-saturation constants for methane (K i=6.6 μM) and ammonia (K m=8.1 μM) were similar. N. oceanus oxidized methanol and methane linearly over time, with CO2 and cell material being produced at approximately equal rates.

Production of flavor esters by immobilized lipase

Abstract: Candidacylindracea lipase adsorbed to silica gel produced a variety of flavor esters when hydrated and shaken in n-heptane containing substrates. Scale-up production of ethyl butyrate was examined in a packed column with recycling of n-hexane containing substrates. Increased substrate concentrations were stimulatory up to a point after which inhibition and enzyme destabilization in repeated runs occurred.

A kinetic model for lipoxygenases based on experimental data with the lipoxygenase of reticulocytes

Abstract: A comprehensive kinetic model for lipoxygenase catalysis is proposed which includes the simultaneous occurrence of dioxygenase and hydroperoxidase activities and is based on the assumption of a single binding site for substrate fatty acid and product. The aerobic reaction of purified lipoxygenase from rabbit reticulocytes with 9,12(Z,Z)-octadecadienoic acid (linoleic acid) as substrate was studied. The rate constants and the dissociation constants of this enzyme were calculated for the model from progress curves; the model describes correctly the experimental data. The following kinetic features of the reticulocyte enzyme are assumed to apply generally to lipoxygenases. (a) The enzyme shows autoactivation by its product. (b) The rate-limiting step is the hydrogen abstraction. (c) Both substrate fatty acid and its product are competitive inhibitors of the lipoxygenase. (d) Lowering the oxygen concentration enhances the degree of substrate inhibition, whereas product inhibition is not influenced. (e) If substrate is in excess the oxygen concentration determines the share of dioxygenase and hydroperoxidase activities of the enzyme. As predicted from the model it was found that at low concentrations of oxygen the regio- and stereo-specificities of the dioxygenation are diminished. During the autoactivation phase the steady-state approximation does not hold.

Chemical vapor deposition of zinc oxide films and products

Abstract: Zinc oxide is applied to a substrate at a low temperature by using a mixture of an organozinc compound and water carried in an inert gas. The resulting zinc oxide film has a relatively low resistivity which can be varied by addition of a group III element.

Isolation of a membrane-associated Bacteroides gingivalis glycylprolyl protease.

Abstract: A low-molecular-weight proteolytic enzyme was purified 47-fold from outer membranes of Bacteroides gingivalis ATCC 33277 by preparative polyacrylamide gel electrophoresis. The enzyme was present in all B. gingivalis strains tested but was not found in other species of black-pigmented Bacteroides. The molecular weight, determined by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis, was 19,500 when the enzyme was heated to 100 degrees C in SDS before electrophoresis and 29,000 when it was mixed with SDS but not heated. The optimum pH, with azocasein as the substrate, was between 6.0 and 6.5. The activity was inhibited by phenylmethylsulfonyl fluoride, N-alpha-p-tosyl-L-lysine chloromethyl ketone, Hg2+, and various reducing agents. The enzyme was active against azocasein, azocoll, proline-rich protein from saliva, and the synthetic peptide glycyl-L-proline-p-nitroanilide. The enzyme did not degrade acid-soluble collagen nor did it hydrolyze various arginine- and lysine-containing synthetic substrates.

Fungal growth response to carbon and nitrogen limitation: A theoretical model

Abstract: A model of fungal growth in soil is described. Two biomass components, cell walls and cytoplasm are considered. Allocation of assimilates to cell wall and cytoplasm synthesis and the relative rate of cytoplasm translocation vary according to C and N availabilities. Model behaviour in relation to substrate supply is examined. For single substrate additions, active mycelium (cytoplasm-filled hyphae) shows a positive correlation to substrate availability, while total hyphal length (cytoplasm-filled + evacuated hyphae) shows an inverse response. For continuous substrate additions, the model predicts that equilibrium levels of active mycelium depend primarily on substrate input rate and yield efficiency and are independent of other parameters controlling substrate availability. Model assumptions about biosynthate allocation and cytoplasm translocation influence N mineralization and immobilization patterns. The model suggests that critical C:N ratios change during decomposition as the fungal biomass develops. The advantages conferred by the mycclial growth form, in terms of conserving energy and nutrient elements in resource-poor environments, are discussed.

Oxidation of protoporphyrinogen to protoporphyrin, a step in chlorophyll and haem biosynthesis. Purification and partial characterization of the enzyme from barley organelles.

Abstract: The protoporphyrinogen-oxidizing enzyme from Triton X-100 extracts of the mitochondrial and etioplast fractions of etiolated barley was purified by using ion-exchange and hydroxyapatite chromatography. The purified enzyme from both organelle fractions exhibited a Km of 5 microM and was labile to mild heat and acidification. The pH optimum (5-6) and the substrate-specificity (mesoporphyrinogen was oxidized as rapidly as protoporphyrinogen) revealed properties very different from the protoporphyrinogen-oxidizing enzyme of rat liver or yeast mitochondria, which is specific for protoporphyrinogen as substrate. The purest fractions showed a polypeptide band corresponding to an Mr of approx. 36,000 on SDS/polyacrylamide-gel electrophoresis. This is the first purification and characterization of the enzyme from a plant, and indicates no readily detectable differences between the enzyme isolated from mitochondrial or etioplast fractions, although only the latter organelle has the capacity for both haem and chlorophyll synthesis.

Measurement of electroactive species in solution

Abstract: In order to improve the sensitivity of electrochemical assays based on an electrochemical system capable of generating a current, where the system comprises as components an enzyme, a substrate, and a mediator, with the mediator mediating transfer of electrons between the enzyme and an electrode while the enzyme is catalysing a reaction of the substrate, the mediator is indirectly linked with the electrode by a compound capable of accumulating electrical charge for measurement after a delay period.

Purification and characterization of an 8‐hydroxy‐5‐deazaflavin‐reducing hydrogenase from the archaebacterium Methanococcus voltae

Abstract: A methylviologen and 8-hydroxy-5-deazaflavin(F420)-reducing hydrogenase was purified over 800-fold to near homogeneity from the archaebacterium Methanococcus voltae with 10 U mg−1 F420-reducing activity. It is the only hydrogenase in this organism. The enzyme showed Km values of 16 μM for F420 and 1.2 mM for methylviologen. A turnover number of 1050 min−1 was calculated for the minimal active unit. The protein tends to aggregate. The molecular mass of the minimal active unit is 105 kDa. Larger molecules of 745 kDa were regularly observed. The enzyme was resolved into subunits with molecular masses of 55 kDa, 45 kDa, 37 kDa and 27 kDa by SDS/polyacrylamide gel electrophoresis. Reversible conversion of an anionic into an uncharged form was observed by DEAE-cellulose chromatography with concomitant changes in substrate specifities. The methylviologen-reducing activity was heat-resistant up to 65°C and was not affected by antiserum raised against the native enzyme, while F420 reduction was inactivated by both treatments. Nickel and selenium contents were determined as 0.6–0.7 mol each, FAD content as 1 mol and iron as 4.5 mol/mol protein (105 kDa), respectively. Electron micrographs taken from the purified enzyme show ring-shaped molecules of 18 nm diameter, which represent the high-molecular-mass species of the enzyme.

Enzyme-catalyzed, gas-phase reactions.

Abstract: Dehydrated preparations of alcohol oxidase adsorbed on DEAEcellulose vigorously catalyze a gas-phase oxidation of ethanol vapors with molecular oxygen. The gas-phase reaction is strongly dependent on the water activity of the system. The enzymatic activity is severely inhibited by the product hydrogen peroxide. This inhibition can be alleviated, however, by an addition of catalase or peroxidase to the dry preparation. Such dehydrated, bienzymic catalysts afford a complete and selective conversion of the substrate to acetaldehyde. Dry alcohol oxidase is much more thermostable than in aqueous solution. The results of this work suggest that dehydrated enzymes have potential applications in the analysis of gaseous compounds and in the development of novel gas-solid bioreactors.

Purification and characterization of an exo-beta-1,4-glucanase from Ruminococcus flavefaciens FD-1.

Abstract: An exo-beta-1,4-glucanase (Exo A) from Ruminococcus flavefaciens FD-1 was purified to homogeneity and characterized. Enzyme activity was monitored during purification by using the substrate p-nitrophenyl-beta-D-cellobioside (NPC). Over 85% of the NPC activity was found to be extracellular once the filter paper was degraded (7 days). Culture supernatant was harvested, and the protein was concentrated by ultrafiltration. The retentate (greater than or equal to 300,000 Mr), containing most of the activity against NPC, was then fractionated with a TSK DEAE-5PW column. This yielded a sharp major peak of NPC enzyme activity, followed by a broader, less active area that appeared to contain at least six minor peaks of lower enzymatic activity. Further purification was achieved by chromatography with a hydroxylapatite column. Finally, gel filtration chromatography yielded a homogeneous enzyme (Exo A) as determined by silver stains of both sodium dodecyl sulfate- and nondenaturing electrophoresis gels. Substrate specificity experiments and the products of cellulose digestion indicate that the enzyme was an exo-beta-1,4-glucanase. Exo A required Ca2+ for maximal activity and had an apparent Km of 3.08 mM for NPC, with a Vmax of 0.298 mumol/min per mg of protein. The enzyme had an Mr of 230,000, as determined by gel filtration chromatography, and was a dimer of 118,000-Mr subunits. The N-terminal amino acid sequence of the enzyme is presented.

Mode of substrate carboxyl binding to the [4Fe-4S]+ cluster of reduced aconitase as studied by 17O and 13C electron-nuclear double resonance spectroscopy.

Abstract: The active form of aconitase has a diamagnetic [4Fe-4S]2+ cluster. A specific iron ion (Fea, which is lost during inactivation) is the binding site for substrate, as shown by Mossbauer spectroscopy. We have studied the mode of substrate and analogue binding at equilibrium to the paramagnetic [4Fe-4S]+ cluster of the reduced active form by 17O and 13C electron-nuclear double resonance spectroscopy with specifically labeled substrates. The data show that with substrate, only the carboxyl at C-2 of the propane backbone is strongly bound in addition to H2O or OH- (HxO) from the solvent, whereas in an isocitrate analogue that has a nitro group at C-2, the carboxyl and hydroxyl at C-1 are bound along with solvent HxO. We conclude from these data that, on addition of any one of the three substrates, cis-aconitate is the predominant species bound to Fea of the cluster along with solvent HxO and that cis-aconitate is bound in the citrate mode (carboxyl at C-2). The results with the nitro analogue show that the enzyme can also bind a substrate-like ligand to the cluster in the alternative isocitrate mode (carboxyl at C-1), as is implicit in models proposed for the aconitase reaction.