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Enzyme Reaction (enzyme + reaction)
Selected AbstractsPoly(ADP-Ribose)-Polymerase-Catalyzed Hydrolysis of NAD+: QM/MM Simulation of the Enzyme ReactionCHEMMEDCHEM, Issue 5 2006Daniele Bellocchi Dr. Abstract Poly(ADP-ribose) polymerase (PARP) is a nuclear enzyme which uses NAD+ as substrate and catalyzes the transfer of multiple units of ADP-ribose to target proteins. PARP is an attractive target for the discovery of novel therapeutic agents and PARP inhibitors are currently evaluated for the treatment of a variety of pathological conditions such as brain ischemia, inflammation, and cancer. Herein, we use the PARP-catalyzed reaction of NAD+ hydrolysis as a model for gaining insight into the molecular details of the catalytic mechanism of PARP. The reaction has been studied in both the gas-phase and in the enzyme environment through a QM/MM approach. Our results indicate that the cleavage reaction of the nicotinamide-ribosyl bond proceeds through an SN2 dissociative mechanism via an oxacarbenium transition structure. These results confirm the importance of the structural water molecule in the active site and may constitute the basis for the design of transition-state-based PARP inhibitors. [source] Adenosyl Radical: Reagent and Catalyst in Enzyme ReactionsCHEMBIOCHEM, Issue 5 2010E. Neil G. Marsh Prof. Abstract Adenosine is undoubtedly an ancient biological molecule that is a component of many enzyme cofactors: ATP, FADH, NAD(P)H, and coenzyme A, to name but a few, and, of course, of RNA. Here we present an overview of the role of adenosine in its most reactive form: as an organic radical formed either by homolytic cleavage of adenosylcobalamin (coenzyme B12, AdoCbl) or by single-electron reduction of S -adenosylmethionine (AdoMet) complexed to an iron,sulfur cluster. Although many of the enzymes we discuss are newly discovered, adenosine's role as a radical cofactor most likely arose very early in evolution, before the advent of photosynthesis and the production of molecular oxygen, which rapidly inactivates many radical enzymes. AdoCbl-dependent enzymes appear to be confined to a rather narrow repertoire of rearrangement reactions involving 1,2-hydrogen atom migrations; nevertheless, mechanistic insights gained from studying these enzymes have proved extremely valuable in understanding how enzymes generate and control highly reactive free radical intermediates. In contrast, there has been a recent explosion in the number of radical-AdoMet enzymes discovered that catalyze a remarkably wide range of chemically challenging reactions; here there is much still to learn about their mechanisms. Although all the radical-AdoMet enzymes so far characterized come from anaerobically growing microbes and are very oxygen sensitive, there is tantalizing evidence that some of these enzymes might be active in aerobic organisms including humans. [source] Bioelectrochemical Characterization of Horseradish and Soybean PeroxidasesELECTROANALYSIS, Issue 21 2009Marco Frasconi Abstract Heme peroxidase are ubiquitous enzymes catalyzing the oxidation of a broad range of substrates by hydrogen peroxide. In this paper the bioelectrochemical characterization of horseradish peroxidase (HRP) and soybean peroxidase (SBP), belonging to class III of the plant peroxidase superfamily, was studied. The homogeneous reactions between peroxidases and some common redox mediators in the presence of hydrogen peroxide have been carried out by cyclic voltammetry. The electrochemical characterization of the reactions involving enzyme, substrate and mediators concentrations allowed us to calculate the kinetic parameters for the substrate,enzyme reaction (KMS) and for the redox mediator,enzyme reaction (KMM). A full characterization of the direct electron transfer kinetic parameters between the electrode and enzyme active site was also performed by opportunely modeling data obtained from cyclic voltammetry and square wave voltammetry experiments. The experimental data obtained with immobilized peroxidases show enhanced direct electron transfer and excellent electrocatalytical performance for H2O2. Despite the structural similarities and common catalytic cycle, HRP and SBP exhibit differences in their substrate affinity and catalytic efficiency. Basing on our results, it can be concluded that peroxidase from soybean represents an interesting alternative to the classical and largely employed one obtained from horseradish as biorecognition element of electrochemical mediated biosensors. [source] Composite Multienzyme Amperometric Biosensors for an Improved Detection of Phenolic CompoundsELECTROANALYSIS, Issue 22 2003B. Serra Abstract A biosensor design, in which glucose oxidase and peroxidase are coimmobilized by simple physical inclusion into the bulk of graphite-Teflon pellets, is reported for the detection of phenolic compounds. This design allows the "in situ" generation of the H2O2 needed for the enzyme reaction with the phenolic compounds, which avoids several problems detected in the performance of single peroxidase biosensors as a consequence of the presence of a high H2O2 concentration. So, a much lower surface fouling was found at the GOD-HRP biosensor in comparison with a graphite-Teflon-HRP electrode, suggesting that the controlled generation of H2O2 makes more difficult the formation of polymers from the enzyme reaction products. The construction of trienzyme biosensors, in which GOD, HRP and tyrosinase were coimmobilized into the graphite-Teflon matrix is also reported, and their performance was compared with that of GOD-HRP bienzyme electrodes. The practical applicability of the composite multienzyme amperometric biosensors was evaluated by the estimation of the phenolic compounds content in waste waters from a refinery, and the results were compared with those obtained by using a colorimetric official method based on the reaction with 4-aminoantipyrine. [source] MCE enzyme immunoassay for carcinoembryonic antigen and alpha-fetoprotein using electrochemical detectionELECTROPHORESIS, Issue 19 2009Shusheng Zhang Abstract An MCE electrochemical enzyme immunoassay protocol for the determination of carcinoembryonic antigen (CEA) and alpha-fetoprotein (AFP) was reported. Two antigens (Ag), CEA and AFP, were incubated simultaneously with an excess amount of horseradish peroxidase-labeled antibody (Ab*). The free Ab* and the Ab*,Ag complex produced in the solution were first separated through a postcolumn reaction and then traced by the enzyme substrate o -aminophenol. The 3-aminophenoxazine produced in enzyme reaction was detected with downstream amperometric detection. The separations were performed at a separation voltage of +1.4,kV and were completed in less than 60,s. The better analytical performance and distinct miniaturization/portability for MCE at less assay time and sample volume consumption was achieved. The detection limit of CEA and AFP was calculated to be 0.25 and 0.13,ng/mL, respectively. Therefore, MCE could be used as a sensitive and new tool in separation science and offered considerable promise in biological sample analysis or quick clinical diagnosis. [source] Novel polyketides synthesized with a higher plant stilbene synthaseFEBS JOURNAL, Issue 13 2001Hiroyuki Morita The physiological function of the stilbene synthase (STS) from groundnut (Arachis hypogaea) is the formation of resveratrol. The enzyme uses 4-coumaroyl-CoA, performs three condensations with malonyl-CoA, and folds the resulting tetraketide into a new aromatic ring system. We investigated the capacity for building novel and unusual polyketides from alternative substrates. Three types of products were obtained: (a) complete reaction (stilbene-type), (b) three condensations without formation of an aromatic ring (CTAL-type pyrone derailment), and (c) two condensations (BNY-type pyrone derailment). All product types were obtained from 4-fluorocinnamoyl-CoA and analogs in which the coumaroyl moiety was replaced by furan or thiophene. Only type (b) and (c) products were synthesized from other 4-substituted 4-coumaroyl-CoA analogs (-Cl, -Br, -OCH3). Benzoyl-CoA, phenylacetyl-CoA, and medium chain aliphatic CoA esters were poor substrates, and the majority of the products were of type (c). The results show that minor modifications can be used to direct the enzyme reaction to form a variety of different and new products. Manipulation of the biosynthesis of polyketides by synthetic analogs could lead to the development of a chemical library of pharmaceutically interesting novel polyketides. [source] Creating a mutant luciferase resistant to HPV chemical inhibition by random mutagenesis and colony-level screeningLUMINESCENCE: THE JOURNAL OF BIOLOGICAL AND CHEMICAL LUMINESCENCE, Issue 3 2006Eileen Kim-Choi Abstract Firefly luciferase covers a wide range of applications. One common usage of the bioluminescence assay is the measurement of intracellular concentration of adenosine triphosphate (ATP) for cell viability. However, inhibition of the enzyme reaction by chemicals in the assay has so far limited the application of luciferase for high production volume (HPV) chemical testing. The objective of this research was to obtain a mutant luciferase with increased stability to inhibition by HPV chemicals, yet retaining specific activity comparable to, or better than, wild-type luciferase. The enzymatic properties of the wild-type luciferase were improved by random mutagenesis and colony-level screening. In this paper, the detailed process of creating mutant luciferases for testing the toxicity of HPV chemicals is described. As a result, two mutant luciferases were created, with different degrees of improved tolerance to inhibition by chloroform and other HPV chemicals. Copyright © 2006 John Wiley & Sons, Ltd. [source] Facile synthesis of functional polyperoxides by radical alternating copolymerization of 1,3-dienes with oxygenTHE CHEMICAL RECORD, Issue 5 2009Eriko Sato Abstract We have developed a facile synthesis of degradable polyperoxides by the radical alternating copolymerization of 1,3-diene monomers with molecular oxygen at an atmospheric pressure. In this review, the synthesis, the degradation behavior, and the applications of functional polyperoxides are summarized. The alkyl sorbates as the conjugated 1,3-dienes gave a regiospecific alternating copolymer by exclusive 5,4-addition during polymerization and the resulting polyperoxides decomposed by the homolysis of a peroxy linkage followed by successive , -scissions. The preference of 5,4-addition was well rationalized by theoretical calculations. The degradation of the polyperoxides occurred with various stimuli, such as heating, UV irradiation, a redox reaction with amines, and an enzyme reaction. The various functional polyperoxides were synthesized by following two methods, one is the direct copolymerization of functional 1,3-dienes, and the other is the functionalization of the precursor polyperoxides. Water soluble polyperoxides were also prepared, and the LCST behavior and the application to a drug carrier in the drug delivery system were investigated. In order to design various types of degradable polymers and gels we developed a method for the introduction of dienyl groups into the precursor polymers. The resulting dienyl-functionalized polymers were used for the degradable gels. The degradable branched copolymers showed a microphase-separated structure, which changed owing to the degradation of the polyperoxide segments. © 2009 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 9: 000,000; 2009: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.200900009 [source] Biosynthesis reaction mechanism and kinetics of deoxynucleoside triphosphates, dATP and dGTPBIOTECHNOLOGY & BIOENGINEERING, Issue 4 2005Jie Bao Abstract The enzyme reaction mechanism and kinetics for biosyntheses of deoxyadenosine triphosphate (dATP) and deoxyguanosine triphosphate (dGTP) from the corresponding deoxyadenosine diphosphate (dADP) and deoxyguanosine diphosphate (dGDP) catalyzed by pyruvate kinase were studied. A kinetic model for this synthetic reaction was developed based on a Bi-Bi random rapid equilibrium mechanism. Kinetic constants involved in this pyruvate kinase catalyzed phosphorylation reactions of deoxynucleoside diphosphates including the maximum reaction velocity, Michaelis-Menten constants, and inhibition constants for dATP and dGTP biosyntheses were experimentally determined. These kinetic constants for dATP and dGTP biosyntheses are of the same order of magnitude but significantly different between the two reactions. Kinetic constants involved in ATP and GTP biosyntheses as reported in literature are about one order of magnitude different from those involved in dATP and dGTP biosyntheses. This enzyme reaction requires Mg2+ ion and the optimal Mg2+ concentration was also determined. The experimental results showed a very good agreement with the simulation results obtained from the kinetic model developed. This kinetic model can be applied to the practical application of a pyruvate kinase reaction system for production of dATP and dGTP. There is a significant advantage of using enzymatic biosyntheses of dATP and dGTP as compared to the chemical method that has been in commercial use. © 2005 Wiley Periodicals, Inc. [source] Synthesis of [2,- 2H1]-RibonucleosidesHELVETICA CHIMICA ACTA, Issue 3 2004András Földesi New syntheses of C(2,)-deuterated ribonucleosides have been accomplished starting either from 3,5-di- O -benzyl-1- O -methyl- ,,, - D -ribofuranose (1b) or 2,3- O -isopropylidene- D -ribose (14), with >97 atom-% D incorporation in both cases. The former is suited to the demands of multiple-site deuteration or uniform 13C/multiple 2H double labeling of the ribofuranose moiety, whereas the latter is particularly appropriate for single-site 2H labeling for mechanistic studies of enzyme reactions. [source] Modeling aspects of mechanisms for reactions catalyzed by metalloenzymesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2001P. E. M. Siegbahn Different models to treat metal-catalyzed enzyme reactions are investigated. The test case chosen is the recently suggested full catalytic cycle of manganese catalase including eight different steps. This cycle contains OO and OH activations, as well as electron transfer steps and redox active reactions, and is therefore believed to be representative of many similar systems. Questions concerning modeling of ligands and the accuracy of the computational model are studied. Imidazole modeling of histidines are compared to ammonia modeling, and formate modeling compared to acetate modeling of glutamates. The basis set size required for the geometry optimization and for the final energy evaluation is also investigated. The adequacy of the model is judged in relation to the inherent accuracy achievable with the hybrid DFT method B3LYP. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1634,1645, 2001 [source] A potential role for isothermal calorimetry in studies of the effects of thermodynamic non-ideality in enzyme-catalyzed reactions,JOURNAL OF MOLECULAR RECOGNITION, Issue 5 2004Thierry G. A. Lonhienne Abstract Attention is drawn to the feasibility of using isothermal calorimetry for the characterization of enzyme reactions under conditions bearing greater relevance to the crowded biological environment, where kinetic parameters are likely to differ significantly from those obtained by classical enzyme kinetic studies in dilute solution. An outline of the application of isothermal calorimetry to the determination of enzyme kinetic parameters is followed by considerations of the nature and consequences of crowding effects in enzyme catalysis. Some of those effects of thermodynamic non-ideality are then illustrated by means of experimental results from calorimetric studies of the effect of molecular crowding on the kinetics of catalysis by rabbit muscle pyruvate kinase. This review concludes with a discussion of the potential of isothermal calorimetry for the experimental determination of kinetic parameters for enzymes either in biological environments or at least in media that should provide reasonable approximations of the crowded conditions encountered in vivo. Copyright © 2004 John Wiley & Sons, Ltd. [source] Stereospecificity for the hydrogen transfer of pyridoxal enzyme reactionsTHE CHEMICAL RECORD, Issue 5 2001Kenji Soda Abstract We have studied the stereospecificities of various pyridoxal 5,-phosphate dependent enzymes for the hydrogen transfer between the C-4, of a bound coenzyme and the C-2 of a substrate in the transamination catalyzed by the enzymes. Prior to our studies, pyridoxal enzymes so far studied were reported to catalyze the hydrogen transfer only on the si -face of the planar imine intermediate formed from substrate and coenzyme. This finding had been considered as the evidence that pyridoxal enzymes have evolved divergently from a common ancestral protein, because identity in the stereospecificity reflects the similarity in the active-site structure, in particular in the geometrical relationship between the coenzyme and the active site base participating in the hydrogen transfer. However, we found that d -amino acid aminotransferase, branched-chain l -amino acid aminotransferase, and 4-amino-4-deoxychorismate lyase catalyze the re -face specific hydrogen transfer, and that amino acid racemases catalyze the nonstereospecific hydrogen transfer. These findings suggest the convergent evolution of pyridoxal enzymes. Crystallographical studies have shown that the stereospecificity reflects the active-site structure of the enzymes, and that the enzymes with the same fold exhibit the same stereospecificity. The active site structure with the catalytic base being situated on the specific face of the cofactor has been conserved during the evolution among the pyridoxal enzymes of the same family. © 2001 John Wiley & Sons, Inc. and The Japan Chemical Journal Forum Chem Rec 1:373,384, 2001 [source] Analysis of Classical and Quantum Paths for Deprotonation of Methylamine by Methylamine DehydrogenaseCHEMPHYSCHEM, Issue 12 2007Kara E. Ranaghan Abstract The hydrogen-transfer reaction catalysed by methylamine dehydrogenase (MADH) with methylamine (MA) as substrate is a good model system for studies of proton tunnelling in enzyme reactions,an area of great current interest,for which atomistic simulations will be vital. Here, we present a detailed analysis of the key deprotonation step of the MADH/MA reaction and compare the results with experimental observations. Moreover, we compare this reaction with the related aromatic amine dehydrogenase (AADH) reaction with tryptamine, recently studied by us, and identify possible causes for the differences observed in the measured kinetic isotope effects (KIEs) of the two systems. We have used combined quantum mechanics/molecular mechanics (QM/MM) techniques in molecular dynamics simulations and variational transition state theory with multidimensional tunnelling calculations averaged over an ensemble of paths. The results reveal important mechanistic complexity. We calculate activation barriers and KIEs for the two possible proton transfers identified,to either of the carboxylate oxygen atoms of the catalytic base (Asp428,),and analyse the contributions of quantum effects. The activation barriers and tunnelling contributions for the two possible proton transfers are similar and lead to a phenomenological activation free energy of 16.5±0.9 kcal,mol,1 for transfer to either oxygen (PM3-CHARMM calculations applying PM3-SRP specific reaction parameters), in good agreement with the experimental value of 14.4 kcal,mol,1. In contrast, for the AADH system, transfer to the equivalent OD1 was found to be preferred. The structures of the enzyme complexes during reaction are analysed in detail. The hydrogen bond of Thr474,(MADH)/Thr172,(AADH) to the catalytic carboxylate group and the nonconserved active site residue Tyr471,(MADH)/Phe169,(AADH) are identified as important factors in determining the preferred oxygen acceptor. The protein environment has a significant effect on the reaction energetics and hence on tunnelling contributions and KIEs. These environmental effects, and the related clearly different preferences for the two carboxylate oxygen atoms (with different KIEs) in MADH/MA and AADH/tryptamine, are possible causes of the differences observed in the KIEs between these two important enzyme reactions. [source] |