Showing papers on "Substrate (chemistry) published in 1993"

Slow- and tight-binding inhibitors of the 85-kDa human phospholipase A2.

Abstract: A trifluoromethyl ketone analogue of arachidonic acid in which the COOH group is replaced with COCF3 (AACOCF3) was prepared and found to be a tight- and slow-binding inhibitor of the 85-kDa cytosolic human phospholipase A2 (cPLA2). Enzyme inhibition was observed when AACOCF3 was tested in assays using either phospholipid vesicles or phospholipid/Triton X-100 mixed micelles. The fact that the inhibition developed over several minutes in both assays establishes that AACOCF3 inhibits by direct binding to the enzyme rather than by decreasing the fraction of enzyme bound to the substrate interface. From the measured values of the inhibitor association and dissociation rate constants, an upper limit of the equilibrium dissociation constant for the Ca(2+).AACOCF3.PLA2 complex of 5 x 10(-5) mole fraction was obtained. Thus, detectable inhibition of cPLA2 by AACOCF3 occurs when this compound is present in the assay at a level of one inhibitor per several thousand substrates. Arachidonic acid analogues in which the COOH group is replaced by COCH3, CH(OH)CF3, CHO, or CONH2 did not detectably inhibit the cPLA2. The arachidonyl ketones AACOCF2CF3 and AACOCF2Cl were found by 19F NMR to be less hydrated than AACOCF3 in phospholipid/Triton X-100 mixed micelles, and compared to AACOCF3 these compounds are also weaker inhibitors of cPLA2. In keeping with the fact that cPLA2 displays substrate specificity for arachidonyl-containing phospholipids, the arachidic acid analogue C19H39COCF3 is a considerably less potent inhibitor compared to AACOCF3.(ABSTRACT TRUNCATED AT 250 WORDS)

Crystal structure of Escherichia coli TEM1 beta-lactamase at 1.8 A resolution.

Abstract: The X-ray structure of Escherichia coli TEM1 beta-lactamase has been refined to a crystallographic R-factor of 16.4% for 22,510 reflections between 5.0 and 1.8 A resolution; 199 water molecules and 1 sulphate ion were included in refinement. Except for the tips of a few solvent-exposed side chains, all protein atoms have clear electron density and refined to an average atomic temperature factor of 11 A2. The estimated coordinates error is 0.17 A. The substrate binding site is located at the interface of the two domains of the protein and contains 4 water molecules and the sulphate anion. One of these solvent molecules is found at hydrogen bond distance from S70 and E166. S70 and S130 are hydrogen bonded to K73 and K234, respectively. It was found that the E. coli TEM1 and Staphylococcus aureus PC1 beta-lactamases crystal structures differ in the relative orientations of the two domains composing the enzymes, which result in a narrowed substrate binding cavity in the TEM1 enzyme. Local but significant differences in the vicinity of this site may explain the occurrence of TEM1 natural mutants with extended substrate specificities.

Purification and preliminary characterization of the extracellular lipase of Bacillus subtilis 168, an extremely basic pH‐tolerant enzyme

Abstract: The extracellular lipase of Bacillus subtilis 168 was purified from the growth medium of an overproducing strain by ammonium sulfate precipitation followed by phenyl-Sepharose and hydroxyapatite column chromatography. The purified lipase had a strong tendency to aggregate. It exhibited a molecular mass of 19,000 Da by SDS-PAGE and a pI of 9.9 by chromatofocusing. The enzyme showed maximum stability at pH 12 and maximum activity at pH 10. The lipase was active toward p-nitrophenyl esters and triacylglycerides with a marked preference for esters with C8 acyl groups. Using trioleyl glycerol as substrate, the enzyme preferentially cleaved the 1(3)-position ester bond. No interfacial activation effect was observed with triacetyl glycerol as substrate.

Kinetics of competitive inhibition and cometabolism in the biodegradation of benzene, toluene, and p‐xylene by two Pseudomonas isolates.

Abstract: Two Pseudomonas species (designated strains B1 and X1) were isolated from an aerobic pilot-scale fluidized bed reactor treating groundwater containing benzene, toluene, and p-xylene (BTX). Strain B1 grew with benzene and toluene as the sole sources of carbon and energy, and it cometabolized p-xylene in the presence of toluene. Strain X1 grew on toluene and p-xylene, but not benzene. In single substrate experiments, the appearance of biomass lagged the consumption of growth substrates, suggesting that substrate uptake may not be growth-rate limiting for these substrates. Batch tests using paired substrates (BT, TX, or BX) revealed competitive inhibition and cometabolic degradation patterns. Competitive inhibition was modeled by adding a competitive inhibition term to the Monod expression. Cometabolic transformation of nongrowth substrate (p-xylene) by strain B1 was quantified by coupling xylene transformation to consumption of growth substrate (toluene) during growth and to loss of biomass during the decay phase. Coupling was achieved by defining two transformation capacity terms for the cometabolizing culture: one that relates consumption of growth substrate to the consumption of nongrowth substrate, and second that relates consumption of biomass to the consumption of nongrowth substrate. Cometabolism increased decay rates, and the observed yield for strain B1 decreased in the presence of p-xylene.

Substrate specificity of the protein tyrosine phosphatases.

Abstract: The substrate specificity of a recombinant protein tyrosine phosphatase (PTPase) was probed using synthetic phosphotyrosine-containing peptides corresponding to several of the autophosphorylation sites in epidermal growth factor receptor (EGFR). The peptide corresponding to the autophosphorylation site, EGFR988-998, was chosen for further study due to its favorable kinetic constants. The contribution of individual amino acid side chains to the binding and catalysis was ascertained utilizing a strategy in which each amino acid within the undecapeptide EGFR988-998 (DADEpYLIPQQG) was sequentially substituted by an Ala residue (Ala-scan). The resulting effects due to singular Ala substitution were assessed by kinetic analysis with two widely divergent homogeneous PTPases. A "consensus sequence" for PTPase recognition may be suggested from the Ala-scan data as DADEpYAAPA, and the presence of acidic residues proximate to the NH2-terminal side of phosphorylation is critical for high-affinity binding and catalysis. The Km value for EGFR988-998 decreased as the pH increased, suggesting that phosphate dianion is favored for substrate binding. The results demonstrate that chemical features in the primary structure surrounding the dephosphorylation site contribute to PTPase substrate specificity.

Molecular recognition in cytochrome P-450 : mechanism for the control of uncoupling reactions

Abstract: The pathway for utilization of pyridine nucleotide derived reducing equivalents in the cytochrome P-450 monooxygenase systems has three major branch points. The first is a partitioning between autoxidation of a ferrous, oxygenated heme adduct and input of the second reducing equivalent required for monooxygenase stoichiometry. The second is between dioxygen bond scission and release of two-electron-reduced O2 as hydrogen peroxide. The third is between substrate hydrogen abstraction initiated by a putative higher valent iron-oxo species and reduction of this intermediate by two additional electrons to produce water in an overall oxidase stoichiometry. For all substrates investigated, the direct release of superoxide at the first branch point never competes with second electron input. In order to elucidate the aspects of molecular recognition of a substrate-P-450 complex which affect these individual branch points in the catalytic cycle, we have measured the NADH-derived reducing equivalents recovered in hydroxylated substrate, hydrogen peroxide, and water for a series of active-site mutants designed to alter the coupling of ethylbenzene hydroxylation. We find that the reaction specificity at the second and third branch points is affected by site-directed mutations that alter the topology of the binding pocket. The increased commitment to catalysis observed for all mutants suggests that active-site hydration is important in the uncoupling to form hydrogen peroxide at the second branch point. The liberation of hydrogen peroxide does not correlate with the location of the mutation in the pocket, as expected if the two-electron-reduced dioxygen-bound intermediate is not directly participating in the substrate activation step.(ABSTRACT TRUNCATED AT 250 WORDS)

A covalent enzyme-substrate intermediate with saccharide distortion in a mutant T4 lysozyme.

Abstract: The glycosyl-enzyme intermediate in lysozyme action has long been considered to be an oxocarbonium ion, although precedent from other glycosidases and theoretical considerations suggest it should be a covalent enzyme-substrate adduct. The mutation of threonine 26 to glutamic acid in the active site cleft of phage T4 lysozyme (T4L) produced an enzyme that cleaved the cell wall of Escherichia coli but left the product covalently bound to the enzyme. The crystalline complex was nonisomorphous with wild-type T4L, and analysis of its structure showed a covalent linkage between the product and the newly introduced glutamic acid 26. The covalently linked sugar ring was substantially distorted, suggesting that distortion of the substrate toward the transition state is important for catalysis, as originally proposed by Phillips. It is also postulated that the adduct formed by the mutant is an intermediate, consistent with a double displacement mechanism of action in which the glycosidic linkage is cleaved with retention of configuration as originally proposed by Koshland. The peptide part of the cell wall fragment displays extensive hydrogen-bonding interactions with the carboxyl-terminal domain of the enzyme, consistent with previous studies of mutations in T4L.

Purification and characterization of the α‐agarase from Alteromonas agarlyticus (Cataldi) comb. nov., strain GJ1B

Abstract: The phenotypic features of strain GJ1B, an unidentified marine bacterium that degrades agar [Young, K. S., Bhattacharjee, S. S. & Yaphe, W. (1978) Carbohydr. Res. 66, 207–212], were investigated and its agarolytic system was characterized using 13C-NMR spectroscopy to analyse the agarose degradation products. The bacterium was assigned to the genus Alteromonas and the new combination A. agarlyticus (Cataldi) is proposed. An α-agarase, i.e specific for the α(13) linkages present in agarose, was purified to homogeneity from the culture supernatant by affinity chromatography on cross-linked agarose (Sepharose CL-6B) and by anion-exchange chromatograpy (Mono Q column). The major end product of agarose hydrolysis using the purified enzyme was agarotetraose. Using SDS/PAGE, the purified α-agarase was detected as a single band with a molecular mass of 180 kDa. After the affinity-chromatography step, however, the native molecular mass was approximately 360 kDa, suggesting that the native enzyme is a dimer which is dissociated to active subunits by anion-exchange chromatography. The isolectric point was estimated to be 5.3. Enzyme activity was observed using agar as the substrate over the pH range 6.0–9.0 with a maximum value at pH 7.2 in Mops or Tris buffer. The enzyme was inactivated by prolonged treatment at a pH below 6.5, or by temperatures over 45°C or by removing calcium. In addition, a β-galactosidase specific for the end products of the α-agarase was present in the α-agarase affinity-chromatography fraction, probably as part of a complex with this enzyme. The degradation of agarose by this agarase complex yielded a mixture of oligosaccharides in the agarotetraose series and the agarotriose series, the latter consisting of oligosaccharides with an odd number of galactose residues.

A mechanism for rotamase catalysis by the FK506 binding protein (FKBP).

Abstract: A detailed mechanism for the catalysis of prolyl isomerization by the rotamase enzyme FKBP is proposed on the basis of a model constructed from the known structure of the FK506/FKBP complex. The model substrate is bound as a type VIa proline turn with the ends exposed to permit longer polypeptide chains (e.g., protein loops) to act as substrates. An ab initio potential for the isomerized imide bond is combined with a molecular mechanics representation of the rest of the system to calculate the reaction path. The resulting activation energy for the enzymatic cis-->trans isomerization is equal to about 6 kcal/mol, in good agreement with experiment. The lowering of the barrier relative to the solution value of 19 kcal/mol is found to arise from a combination of desolvation of the imide carbonyl, ground-state destabilization, substrate autocatalysis, and preferential transition-state binding. Minimal rearrangements are required in the enzyme and the substrate along the reaction path. The enzyme residues that participate in catalysis agree with the available mutation data. The type VIa turn model corresponds to a sequence-specific structural motif commonly found on the surface of proteins. It is likely to have a role in the formation of protein complexes with FKBP-like domains that function as foldases or chaperones.

Solvent variation inverts substrate specificity of an enzyme

Abstract: The substrate specificity of the serine protease subtilisin Carlsberg in the transesterification reaction of N-Ac-L-Ser-OEt and N-Ac-L-Phe-OEt with 1-propanol was examined in 20 anhydrous solvents. The serine substrate was strongly favored in some solvents, while the phenylalanine substrate was greatly preferred in others. A thermodynamic model was derived which correctly predicted the substrate specificity as a function of the solvent-to-water partition coefficients of the substrates and the substrate specificity of the enzyme-catalyzed hydrolysis of the esters in water. This model is independent of the substrates and and the substrate, so long as the latter is removed from the solvent in the transition state

Method for the determination of the concentration of an enzyme substrate and a sensor for carrying out the method

Abstract: A method for the continuous and reversible determination of the concentration of an enzyme substrate such as glucose in an specimen, wherein the specimen is brought into contact with a corresponding enzyme selected from oxidases and oxygenases and to which a flavin coenzyme (FMN, FAD) is bonded, the flavin coenzyme changing to a reduced form by the enzyme substrate and to an oxidized form by molecular oxygen dissolved in the specimen, and the change in the fluorescence spectrum, produced by means of the reduction of the flavin coenzyme, is measured.

The divalent cation is obligatory for the binding of ligands to the catalytic site of secreted phospholipase A2.

Abstract: The divalent cation requirement for partial reactions of the catalytic turnover cycle during interfacial catalysis by pig pancreatic phospholipase A2 (PLA2) is investigated. Results show that the specific role of calcium in all the events of the catalytic cycle at the active site is not shared by other divalent cations. Cations such as calcium, barium, and cadmium bind to the enzyme in the aqueous phase. The active-site-directed ligands (substrate, products, and transition-state mimics) do not bind to the enzyme in the absence of a divalent cation. The synergistic binding of such ligands to the active site of PLA2 bound to the interface is, however, observed only in the presence of isosteric ions like calcium and cadmium, but not with larger ions like strontium or barium. The equilibrium constants for ligands bound to the enzyme in the presence of calcium and cadmium are virtually the same. However, only calcium supports the catalytic turnover; the rate of hydrolysis in the presence of cadmium is less than 1% of that observed with calcium. The role of divalent ions on the interfacial catalytic turnover cycle of PLA2 is not only due to the cation-assisted binding of the substrate but also due to its participation in the chemical step. Other roles of divalent ions in the events of interfacial catalytic turnover are also identified. For example, the binding of the enzyme to the interface is apparently promoted because the divalent cation is required for the sequential step, i.e., the binding of the substrate to the active site of PLA2.(ABSTRACT TRUNCATED AT 250 WORDS)

Combined use of β-galactosidase and sialyltransferase coupled with in situ regeneration of CMP-sialic acid for one pot synthesis of oligosaccharides

Abstract: A single reaction vessel process for the synthesis of a sialylated galactoside is disclosed. The synthesis utilizes a β-galactosidase to catalyze the reaction of a galactose-containing substrate and an acceptor to form a new galactosyl glycoside that is then sialylated using a cyclic multienzyme synthesis system to form CMP-sialic acid that sialylates the formed galactosyl glycoside in the presence of an α-sialyltransferase. The value of Km /Vmax for the formed galactosyl glycoside as a substrate for the α-sialyltransferase is less than one-third the Km /Vmax value for the galactose-containing substrate for that α-sialyltransferase.

Partial Purification of a cis-trans-Isomerase of Zeatin from Immature Seed of Phaseolus vulgaris L

Abstract: Investigation of the conversion of exogenous cis-zeatin to trans-zeatin in immature seeds of Phaseolus vulgaris L. led to the isolation of a cis-trans-isomerase from the endosperm. The enzyme was purified more than 2000-fold by chromatography on a series of fast protein liquid chromatography (anion exchange, gel filtration, and hydrophobic interaction) and concanavalin A columns. The enzymic reaction favors conversion from the cis to the trans form and requires flavin, light, and dithiothreitol. cis-Zeatin riboside is also a substrate for the enzyme. Retention on the concanavalin A column indicated that the enzyme is a glycoprotein. The enzyme was stable for at least 8 weeks when stored at -80[deg] C. The occurrence of cis-trans-isomerization suggests that cis-zeatin and cis-zeatin riboside formed by tRNA degradation could be precursors of biologically active cytokinins.

Protective film for articles and method

Abstract: A method of preparing a coated substrate is disclosed. The substrate is coated with a plasma generated polymer containing Si, O, C and H in specific atom ratio wherein the polymer also contains certain functional groups. A power density of 10?6 to 108? J/Kg is employed in the plasma polymerization process.

Reconstituted cartilage tissue

Abstract: The present invention relates to cartilage tissue reconstituted on a substrate; to a method for producing reconstituted cartilage tissue; and to cartilage tissue reconstituted in vitro from isolated chondrocytes cultured on a substrate.

Mathematical treatment of electrophoretically mediated microanalysis.

Abstract: A new concept in reaction-based chemical analysis is introduced and theoretically described. By utilization of the variability in electrophoretic mobilities among charged species, spatially distinct zones of chemical reagents can be electrophoretically merged under the influence of an applied electric field. Electrophoretically mediated microanalysis (EMMA) exploits this phenomenon as a basis for chemical analysis utilizing capillary electrophoretic systems. EMMA is described in terms of the four stages required for reaction-based analysis: (1) analyte and analytical reagent metering; (2) initiation of reaction; (3) control of reaction conditions and product formation; (4) detection of species whose production or depletion is indicative of the concentration or quantity of the analyte of interest. The method is illustrated by the enzymatic oxidation of ethanol to acetaldehyde by alcohol dehydrogenase with the concurrent reduction of NAD+ to NADH monitored at 340 nm. Experimental results for both substrate and enzyme determinations are shown to agree with the presented theory.

Enzyme catalyzed polymerization and precipitation of aromatic compounds from aqueous solution

Abstract: Horseradish peroxidase enzyme (HRP), once activated by hydrogen peroxide, initiates the oxidation of a wide variety of aromatic compounds. Reaction products undergo a non-enzymatic polymerization to form water insoluble aggregates which are readily separated from solution. HRP was selected for application in wastewater treatment systems due to its stability and retention of its catalytic ability over wide ranges of pH and temperature. HRP activity was optimal between pH 5.7 and 8.5 with peak activity occurring at neutral pH. Activity increased with temperature up to 50 °C and declined at higher temperatures due to thermal inactivation. HRP was inactivated rapidly by hydrogen peroxide in the absence of an aromatic substrate. The efficiency of removal that was achieved was dependent on the nature of the aromatic undergoing treatment and the amount of enzyme provided due to the finite lifetime of the catalyst. Optimization of pH significantly improved catalytic efficiency with a corresponding savings in trea...

Substrate interactions between trypanothione reductase and N1-glutathionylspermidine disulphide at 0.28-nm resolution.

Abstract: The enzyme trypanothione reductase has been identified as a prime target for the rational design of inhibitors which may have clinical use in the treatment of tropical diseases caused by the genera Trypanosoma and Leishmania. To aid the design or identification of new inhibitors of this enzyme we have elucidated the structural detail of a trypanothione reductase complexed with one of the naturally occurring substrates, N1-glutathionylspermidine disulphide, by single-crystal X-ray diffraction methods at 0.28-nm resolution. The model for the Crithidia fasciculata enzyme-substrate complex has an R-factor of 14.8% and root-mean-square deviations of 0.0015 nm and 3.3° on bond lengths and angles respectively. Hydrogen bonding and van der Waals interactions between the enzyme and substrate are dominated by the amino acid side chains. The substrate binds in a rigid active site such that one glutathione moiety is in a V-shape, the other in an extended conformation. One spermidine moiety binds closely to a hydrophobic patch in the active site formed by a tryptophan and a methionine. Distances between the methionine Sδ and the terminal N of this spermidine suggest that a hydrogen bond may supplement the hydrophobic interactions in this part of the active site.