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1

Enzyme Catalyzed Synthetic Reactions.  

National Technical Information Service (NTIS)

Use of an enzyme attached to a cellulosic carrier in organic synthesis is described. Cellulose matrix-supported enzymes constitute useful biological catalysts with broad potential applications in the food, chemical, and pharmaceutical industries. In the c...

G. J. Bartling

1974-01-01

2

Ceramic forming using enzyme catalyzed reactions  

Microsoft Academic Search

A new colloidal processing method for near net shaping ceramic components is outlined. The Direct Coagulation Casting (DCC) process offers the opportunity to produce complex shaped components of high mechanical strength and high reliability at low costs.The process relies on electrostatic stabilized ceramic suspensions and it’s destabilization by time delayed in situ reactions. Enzyme catalyzed reactions may be used either

L. J. Gauckler; Th. Graule; F. Baader

1999-01-01

3

Representing Rate Equations for Enzyme-Catalyzed Reactions  

ERIC Educational Resources Information Center

|Rate equations for enzyme-catalyzed reactions are derived and presented in a way that makes it easier for the nonspecialist to see how the rate of an enzyme-catalyzed reaction depends upon kinetic constants and concentrations. This is done with distribution equations that show how the rate of the reaction depends upon the relative quantities of…

Ault, Addison

2011-01-01

4

Generalized rate equation for single-substrate enzyme catalyzed reactions.  

PubMed

The most widely used rate expression for single-substrate enzyme catalyzed reactions, namely the Michaelis-Menten kinetics is based upon the assumption that enzyme concentration is in excess of the substrate in the medium and the rate is mainly limited by the substrate concentration according to saturation kinetics. However, this is only a special case and the actual rate expression varies depending on the initial enzyme/substrate ratio (E(0)/S(0)). When the substrate concentration exceeds the enzyme concentration the limitation is due to low enzyme concentration and the rate increases with the enzyme concentration according to saturation kinetics. The maximum rate is obtained when the initial concentrations of the enzyme and the substrate are equal. A generalized rate equation was developed in this study and special cases were discussed for enzyme catalyzed reactions. PMID:19265680

Kargi, Fikret

2009-03-03

5

Generalized rate equation for single-substrate enzyme catalyzed reactions  

Microsoft Academic Search

The most widely used rate expression for single-substrate enzyme catalyzed reactions, namely the Michaelis–Menten kinetics is based upon the assumption that enzyme concentration is in excess of the substrate in the medium and the rate is mainly limited by the substrate concentration according to saturation kinetics. However, this is only a special case and the actual rate expression varies depending

Fikret Kargi

2009-01-01

6

Thermodynamic Property Values for Enzyme-catalyzed Reactions  

Microsoft Academic Search

This chapter deals with how one can obtain values of thermodynamic properties - specifically the apparent equilibrium constant K', the stan- dard molar transformed Gibbs energy change DrG', and the standard molar transformed enthalpy change DrH' for biochemical reactions - and, in particular, for enzyme-catalyzed reactions. In addition to direct measurement, these property values can be obtained in a variety

Robert N. Goldberg

2008-01-01

7

Molecular Mechanism by which One Enzyme Catalyzes Two Reactions  

NASA Astrophysics Data System (ADS)

Unlike ordinary enzymes, fructose-1,6-bisphosphate (FBP) aldolase/phosphatase (FBPA/P) catalyzes two distinct reactions : (1) the aldol condensation of dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate to FBP, and (2) the dephosphorylation of FBP to fructose-6-phosphate. We solved the crystal structures of FBPA/P in complex with DHAP (its aldolase form) and FBP (its phosphatase form). The crystal structures revealed that FBPA/P exhibits the dual activities through a dramatic conformational change in the active-site architecture. Our findings expand the conventional concept that one enzyme catalyzes one reaction.

Nishimasu, Hiroshi; Fushinobu, Shinya; Wakagi, Takayoshi

8

Components and coupling in enzyme-catalyzed reactions.  

PubMed

Many enzyme-catalyzed reactions involve coupling of two or more reactions that could otherwise be catalyzed separately. When biochemical reactions are coupled, the equilibrium composition is very different from that when the reactions are not coupled. The number of components in a chemical reaction is equal to the number of independent conservation equations for atoms of elements, but the number of components in an enzyme-catalyzed reaction that is coupled is larger than the number of independent conservation equations for atoms of elements. The investigation of these additional conservation equations by use of linear algebra is complicated by the fact that in dilute aqueous solutions, the activity of water is taken to be unity. This causes an incompatibility of conservation matrices and stoichiometric number matrices that can be avoided by use of the further transformed Gibbs energy G' ' that provides the criterion for spontaneous change and equilibrium when the standard transformed Gibbs energy of water is constant. In the most striking example discussed, the enzyme mechanism of a ligase reaction introduces three constraints in addition to conservation of atoms of elements. This is completely unheard of in chemical reaction thermodynamics. PMID:16851187

Alberty, Robert A

2005-02-10

9

Oxidative tailoring reactions catalyzed by nonheme iron-dependent enzymes: streptorubin B biosynthesis as an example.  

PubMed

Tailoring enzymes catalyze reactions that modify natural product backbone structures before, during, or after their biosynthesis to create a final product with specific biological activities. Such reactions can be catalyzed by a myriad of different enzyme families and are responsible for a wide variety of transformations including regio- and/or stereospecific acylation, alkylation, glycosylation, halogenation, and oxidation. Within a broad group of oxidative tailoring enzymes, there is a rapidly growing family of nonheme iron- and oxygen-dependent enzymes that catalyze a variety of remarkable hydroxylation, desaturation, halogenation, and oxidative cyclization reaction in the biosynthesis of several important metabolites, including carbapenems, penicillins, cephalosporins, clavams, prodiginines, fosfomycin, syringomycin, and coronatine. In this chapter, we report an expedient method for analyzing tailoring enzymes that catalyze oxidative cyclization reactions in prodiginine biosynthesis via expression of the corresponding genes in a heterologous host, feeding of putative biosynthetic intermediates to the resulting strains, and liquid chromatography-mass spectrometry analyses of the metabolites produced. PMID:23034230

Sydor, Paulina K; Challis, Gregory L

2012-01-01

10

Pericyclic reactions catalyzed by chorismate-utilizing enzymes  

PubMed Central

One of the fundamental questions of enzymology is how catalytic power is derived. This review focuses on recent developments in the structure-function relationships of chorismate-utilizing enzymes involved in siderophore biosynthesis to provide insight into the biocatalysis of pericyclic reactions. Specifically, salicylate synthesis by the two-enzyme pathway in Pseudomonas aeruginosa is examined. The isochorismate-pyruvate lyase is discussed in the context of its homologues, the chorismate mutases, and the isochorismate synthase is compared to its homologues in the MST-family (menaquinone, siderophore or tryptophan biosynthesis) of enzymes. The tentative conclusion is that the activities observed cannot be reconciled by inspection of the active site participants alone. Instead, individual activities must arise from unique dynamic properties of each enzyme that are tuned to promote specific chemistries.

Lamb, Audrey L.

2011-01-01

11

Thermodynamics of Enzyme-Catalyzed Reactions: Part 7-2007 Update  

NASA Astrophysics Data System (ADS)

This review serves to update previously published evaluations of equilibrium constants and enthalpy changes for enzyme-catalyzed reactions. For each reaction, the following information is given: the reference for the data, the reaction studied, the name of the enzyme used and its Enzyme Commission number, the method of measurement, the conditions of measurement [temperature, pH, ionic strength, and the buffer(s) and cofactor(s) used], the data and their evaluation, and, sometimes, commentary on the data and on any corrections which have been applied to the data or any calculations for which the data have been used. The review contains data from 119 references which have been examined and evaluated. Chemical Abstract Service registry numbers are given for the substances involved in these various reactions. There is also a cross reference between the substances and the Enzyme Commission numbers of the enzymes used to catalyze the reactions in which the substances participate.

Goldberg, Robert N.; Tewari, Yadu B.; Bhat, Talapady N.

2007-12-01

12

Aldol reaction catalyzed by a hydrophilic catalyst in aqueous micelle as an enzyme mimic system.  

PubMed

Chitosan-supported L-proline complex was synthesized and applied as a catalyst for the direct asymmetric aldol reaction in various organic solvents and water as well. It was found that the novel synthesized catalyst was able to efficiently catalyze the aldol reaction in various media. The catalytic capacity and stereoselectivity of the catalyst were obviously improved with the introduction of aqueous micelle, possibly because the micelle functioned as a hydrophobic pocket, like the hydrophobic portion in enzymes. Moreover, the present synthetic catalyst showed performance similar to that of enzymes and could be used as a model of enzyme catalysis to help better understand the mystic mechanism of enzymes. PMID:18655166

Zhang, Hefeng; Zhao, Wenshan; Zou, Jun; Liu, Yi; Li, Runtao; Cui, Yuanchen

2009-05-01

13

Changes in Binding of Hydrogen Ions in Enzyme-Catalyzed Reactions  

PubMed Central

Most enzyme-catalyzed reactions produce or consume hydrogen ions, and this is expressed by the change in the binding of hydrogen ions in the biochemical reaction, as written in terms of reactants (sums of species). This property of a biochemical reaction is important because it determines the change in the apparent equilibrium constant K? with pH. This property is also important because it is the number of moles of hydrogen ions that can be produced by a biochemical reaction for passage through a membrane, or can be accepted from a transfer through a membrane. There are two ways to calculate the change in binding of hydrogen ions for an enzyme-catalyzed reaction. The first, which has been used for a long time, involves calculating the partial derivative of the standard transformed Gibbs energy of reaction with respect to pH. The second involves calculating the average numbers of hydrogen ions in each reactant and adding and subtracting these average numbers. The changes in binding of hydrogen ions calculated by the second method at pHs 5, 6, 7, 8, and 9 are given for 23 enzyme-catalyzed reactions. Values are given for 206 more reactions on the web. This database can be extended to include more reactions for which pKs of reactants are known or can be estimated.

Alberty, Robert A.

2007-01-01

14

Mutagenicity screening of reaction products from the enzyme-catalyzed oxidation of phenolic pollutants  

SciTech Connect

Phenol-oxidizing enzymes such as peroxidases, laccases, and mushroom polyphenol oxidase are capable of catalyzing the oxidation of a wide range of phenolic pollutants. Although the use of these enzymes in waste-treatment applications has been proposed by a number of investigators, little information exists on the toxicological characteristics of the oxidation products. The enzymes chloroperoxidase, horseradish peroxidase, lignin peroxidase, and mushroom polyphenol oxidase were used in this study to catalyze the oxidation of phenol, several mono-substituted phenols, and pentachlorophenol. Seventeen reaction mixtures representing selected combinations of enzyme and parent phenol were subjected to mutagenicity screening using the Ames Salmonella typhimurium plate incorporation assay; five selected mixtures were also incubated with the S9 microsomal preparation to detect the possible presence of promutagens. The majority of reaction mixtures tested were not directly mutagenic, and none of those tested with S9 gave a positive response. Such lack of mutagenicity of enzymatic oxidation products provides encouragement for establishing the feasibility of enzyme-catalyzed oxidation as a waste-treatment process. The only positive responses were obtained with reaction products from the lignin peroxidase-catalyzed oxidation of 2-nitrophenol and 4-nitrophenol. Clear positive responses were observed when strain TA100 was incubated with 2-nitrophenol reaction-product mixtures, and when strain TA98 was incubated with the 4-nitrophenol reaction mixture. Additionally, 2,4-dinitrophenol was identified as a reaction product from 4-nitrophenol, and preliminary evidence indicates that both 2,4- and 2,6-dinitrophenol are produced from the oxidation of 2-nitrophenol. Possible mechanism by which these nitration reactions occur are discussed.

Massey, I.J.; Aitken, M.D.; Ball, L.M.; Heck, P.E. (Univ. of North Carolina, Chapel Hill, NC (United States). Dept. of Environmental Sciences and Engineering)

1994-11-01

15

Mechanistic studies of an unprecedented enzyme-catalyzed 1,2-phosphono migration reaction  

PubMed Central

(S)-2-Hydroxypropylphosphonate ((S)-2-HPP) epoxidase (HppE) is a mononuclear non-heme iron-dependent enzyme1,2,3 responsible for the last step in the biosynthesis of the clinically useful antibiotic fosfomycin4. Enzymes of this class typically catalyze oxygenation reactions that proceed via the formation of substrate radical intermediates. In contrast, HppE catalyzes an unusual dehydrogenation reaction while converting the secondary alcohol of (S)-2-HPP to the epoxide ring of fosfomycin1,5. HppE is shown here to also catalyze a biologically unprecedented 1,2-phosphono migration with the alternative substrate (R)-1-HPP. This transformation likely involves an intermediary carbocation based on observations with additional substrate analogues, such as (1R)-1-hydroxy-2-aminopropylphosphonate, and model reactions for both radical- and carbocation-mediated migration. The ability of HppE to catalyze distinct reactions depending on the regio- and stereochemical properties of the substrate is given a structural basis using X-ray crystallography. These results provide compelling evidence for the formation of a substrate-derived cation intermediate in the catalytic cycle of a mononuclear non-heme iron-dependent enzyme. The underlying chemistry of this unusual phosphono migration may represent a new paradigm for the in vivo construction of phosphonate-containing natural products that can be exploited for the preparation of novel phosphonate derivatives.

Chang, Wei-chen; Dey, Mishtu; Liu, Pinghua; Mansoorabadi, Steven O.; Moon, Sung-Ju; Zhao, Zongbao K.; Drennan, Catherine L.; Liu, Hung-wen

2013-01-01

16

A transition path sampling study of the reaction catalyzed by the enzyme chorismate mutase.  

PubMed

The study of the chemical steps in enzyme-catalyzed reactions represents a challenge for molecular simulation techniques. One concern is how to calculate paths for the reaction. Common techniques include the definition of a reaction coordinate in terms of a small set of (normally) geometrical variables or the determination of minimum energy paths on the potential energy surface of the reacting system. Both have disadvantages, the former because it presupposes knowledge of which variables are likely to be important for reaction and the latter because it provides a static picture and dynamical effects are ignored. In this paper, we employ the transition path sampling method developed by Chandler and co-workers, which overcomes some of these limitations. The reaction that we have chosen is the chorismate-mutase-catalyzed conversion of chorismate into prephenate, which has become something of a test case for simulation studies of enzyme mechanisms. We generated an ensemble of approximately 1000 independent transition paths for the reaction in the enzyme and another approximately 500 for the corresponding reaction in solution. A large variety of analyses of these paths was performed, but we have concentrated on characterizing the transition state ensemble, particularly the flexibility of its structures with respect to other ligands of the enzyme and the time evolution of various geometrical and energetic properties as the reaction proceeds. We have also devised an approximate technique for locating transition state structures along the paths. PMID:17474768

Crehuet, Ramon; Field, Martin J

2007-05-03

17

Energy Diagrams for Enzyme-Catalyzed Reactions: Concepts and Misconcepts  

ERIC Educational Resources Information Center

|Despite the utility that energy diagrams have as a teaching and learning tool, a survey of their use, in seven popular Biochemistry textbooks, reveals that there is certain confusion around this topic. In our opinion, this confusion arises from the reluctance of authors to consider and indicate the conditions under which the reaction being…

Aledo, J. Carlos; Lobo, Carolina; del Valle, Alicia Esteban

2003-01-01

18

Energy Diagrams for Enzyme-Catalyzed Reactions: Concepts and Misconcepts  

ERIC Educational Resources Information Center

Despite the utility that energy diagrams have as a teaching and learning tool, a survey of their use, in seven popular Biochemistry textbooks, reveals that there is certain confusion around this topic. In our opinion, this confusion arises from the reluctance of authors to consider and indicate the conditions under which the reaction being…

Aledo, J. Carlos; Lobo, Carolina; del Valle, Alicia Esteban

2003-01-01

19

Haloperoxidase reactions catalyzed by lignin peroxidase, an extracellular enzyme from the basidiomycete Phanerochaete chrysosporium  

Microsoft Academic Search

Lignin peroxidase (ligninase, LiP) an HâOâ-dependent lignin-degrading heme enzyme from the basidiomycetous fungus Phanerochaete chrysosporium, catalyzes the oxidation of a variety of lignin model compounds. In this paper the authors examine the haloperoxidase reactions of LiP. In the presence of HâOâ, homogeneous LiP oxidized bromide and iodide but not chloride. Halide oxidation was measured by the halogenation of monochlorodimedone (MCD)

V. Renganathan; Keiji Miki; Michael H. Gold

1987-01-01

20

Temperature effects on enzyme-catalyzed reactions within a cell: Monte Carlo simulations for coupled reaction and diffusion  

NASA Astrophysics Data System (ADS)

We report Monte Carlo simulations of temperature effects on single-step enzymatic reactions with varied rate constants and diffusion coefficients. For typical systems, where the intrinsic reaction rate is more sensitive to temperature than diffusion, the overall reaction is rate-limited at low temperatures and diffusion-limited at high temperatures. The effective activation energy shifts to a much lower value as temperature is increased. Our results show that the temperature dependence of enzyme-catalyzed reactions within a cell may be only loosely related to a potential energy barrier height. The effective activation energy may be strongly affected by coupling of reaction and diffusion.

Nangia, Shivangi; Anderson, James B.

2013-01-01

21

Isotope effects as probes for enzyme catalyzed hydrogen-transfer reactions.  

PubMed

Kinetic Isotope effects (KIEs) have long served as a probe for the mechanisms of both enzymatic and solution reactions. Here, we discuss various models for the physical sources of KIEs, how experimentalists can use those models to interpret their data, and how the focus of traditional models has grown to a model that includes motion of the enzyme and quantum mechanical nuclear tunneling. We then present two case studies of enzymes, thymidylate synthase and alcohol dehydrogenase, and discuss how KIEs have shed light on the C-H bond cleavages those enzymes catalyze. We will show how the combination of both experimental and computational studies has changed our notion of how these enzymes exert their catalytic powers. PMID:23673528

Roston, Daniel; Islam, Zahidul; Kohen, Amnon

2013-05-14

22

Triosephosphate isomerase: energetics of the reaction catalyzed by the yeast enzyme expressed in Escherichia coli  

SciTech Connect

Triosephosphate isomerase from bakers' yeast, expressed in Escherichia coli strain DF502(p12), has been purified to homogeneity. The kinetics of the reaction in each direction have been determined at pH 7.5 and 30 degrees C. Deuterium substitution at the C-2 position of substrate (R)-glyceraldehyde phosphate and at the 1-pro-R position of substrate dihydroxyacetone phosphate results in kinetic isotope effects on kcat of 1.6 and 3.4, respectively. The extent of transfer of tritium from (1(R)-TH)dihydroxyacetone phosphate to product (R)-glyceraldehyde phosphate during the catalyzed reaction is only 3% after 66% conversion to product, indicating that the enzymic base that mediates proton transfer is in rapid exchange with solvent protons. When the isomerase-catalyzed reaction is run in tritiated water in each direction, radioactivity is incorporated both into the remaining substrate and into the product. In the exchange-conversion experiment with dihydroxyacetone phosphate as substrate, the specific radioactivity of remaining dihydroxyacetone phosphate rises as a function of the extent of reaction with a slope of about 0.3, while the specific radioactivity of the products is 54% that of the solvent. In the reverse direction with (R)-glyceraldehyde phosphate as substrate, the specific radioactivity of the product formed is only 11% that of the solvent, while the radioactivity incorporated into the remaining substrate (R)-glyceraldehyde phosphate also rises as a function of the extent of reaction with a slope of 0.3. These results have been analyzed according to the protocol described earlier to yield the free energy profile of the reaction catalyzed by the yeast isomerase.

Nickbarg, E.B.; Knowles, J.R.

1988-08-09

23

Enzyme-catalyzed organic syntheses: transesterification reactions of chlorophyl a, bacteriochlorophyll a, and derivatives with chlorophyllase  

SciTech Connect

The green plant enzyme chlorophyllase (EC 3.1.1.14, chlorophyll chlorophyllido-hydroase) has been used for the synthesis of a variety of primary alcohol and diol esters of chlorophyll a, bacteriochlorophyll a, and pyrobacteriochlorophyll a. Green plant chlorophyllase accepts a much larger range of alcohol and chlorophyll substrates than had previously been realized. Thus, chlorophyllide and bacteriochlorophyllide esters of primary alcohols such as retinol and the detergent Triton X-100 and of dihydric alcohols such as ethylene glycol, butanediol, or 2-hydroxyethyl disulfide can readily be obtained by enzyme-assisted transesterification. The diol chlorophyllide esters are valuable intermediates for the synthesis of reaction center special pair models. Chlorophyllase-assisted reactions can be carried out in media containing up to 95% of organic solvents without the concomitant side reactions that important chlorophyll functional groups readily undergo even under mild conditions in conventional chemical synthetic procedures. In competitive chlorophyllase-catalyzed transesterification reactions, long-chain alcohols such as farnesol and retinol vs simple aliphatic alcohols and diols, the enzyme shows a definite preference for the long-chain alcohol. 37 references, 1 figure, 2 tables.

Michalski, T.J.; Hunt, J.E.; Bradshaw, C.; Wagner, A.M.; Norris, J.R.; Katz, J.J.

1988-08-17

24

Enzyme-catalyzed direct three-component aza-Diels-Alder reaction using hen egg white lysozyme.  

PubMed

The direct three-component aza-Diels-Alder reaction of aromatic aldehyde, aromatic amine, and 2-cyclohexen-1-one was catalyzed by hen egg white lysozyme for the first time. Under the optimized conditions investigated in this paper, the enzyme-catalyzed aza-Diels-Alder reaction gave yields up to 98% and stereoselectivity of endo/exo ratios up to 90:10. PMID:22106947

He, Yan-Hong; Hu, Wen; Guan, Zhi

2011-12-02

25

Isopentenyl diphosphate isomerase catalyzed reactions in D2O: product release limits the rate of this sluggish enzyme-catalyzed reaction.  

PubMed

The E. coli isopentenyl diphosphate isomerase (IDI) catalyzed reaction of isopentenyl diphosphate (IPP) in D(2)O gives a 66% yield of dimethylallyl diphosphate labeled with deuterium at the (E)-methyl group (d-DMAPP) and a 34% yield of IPP labeled with 1 mol of deuterium at C-2 (d-IPP). This shows that the release to D(2)O of the initial product of the IDI-catalyzed reaction (d-DMAPP) is slower than its conversion to d-IPP. Product dissociation is therefore rate determining for isomerization of IPP with a rate constant k(dis) ? k(cat) = 0.08 s(-1). The data provide an estimated rate constant of k(as) = 6 × 10(3) M(-1) s(-1) for binding of DMAPP to E. coli IDI that is similar to rate constants determined for the binding of N-protonated 2-amino ethyl diphosphate intermediate analogs to IDI from yeast [Reardon, J. E.; Abeles, R. H. Biochemistry1986, 25, 5609-5616]. We propose that ligand binding to IDI is relatively slow because there is a significant kinetic barrier to reorganization of the initial encounter complex between enzyme, substrate, and an essential Mg(2+) to form the Michaelis complex where the metal cation bridges the protein and the substrate diphosphate group. PMID:22471428

Jonnalagadda, Venkatadurga; Toth, Krisztina; Richard, John P

2012-04-05

26

Haloperoxidase reactions catalyzed by lignin peroxidase, an extracellular enzyme from the basidiomycete Phanerochaete chrysosporium  

SciTech Connect

Lignin peroxidase (ligninase, LiP) an H/sub 2/O/sub 2/-dependent lignin-degrading heme enzyme from the basidiomycetous fungus Phanerochaete chrysosporium, catalyzes the oxidation of a variety of lignin model compounds. In this paper the authors examine the haloperoxidase reactions of LiP. In the presence of H/sub 2/O/sub 2/, homogeneous LiP oxidized bromide and iodide but not chloride. Halide oxidation was measured by the halogenation of monochlorodimedone (MCD) and a variety of other aromatic compounds. Bromination of MCD produced monochloromonobromodimedone. The pH optimum for the bromination of MCD was 3.5. Both chloride and fluoride inhibited the bromination reaction. LiP binds halides to produce characteristic optical difference spectra. From these spectra apparent dissociation constants for fluoride and chloride were determined to be 0.3 and 20 mM, respectively. Incubation of LiP with bromide and H/sub 2/O/sub 2/ in the absence of organic substrate led to the bleaching of the heme as measured by a decrease in Soret maximum. LiP brominated a variety of aromatic substrates including 3,4-dimethoxybenzyl alcohol (veratryl alcohol) to produce 6-bromoveratryl alcohol (VII). LiP hydrobrominated cinnamic acid (IV) to produce 2-bromo-3-hydroxy-3-phenylpropionic acid (XII). In an analogous reaction LiP hydrobrominated 1-(4-ethoxy-3-methoxyphenyl)propene (II) to produce 2-bromo-1-(4-ethoxy-3-methoxyphenyl)-1-hydroxypropane (XIII). Finally, with 3,4-dimethoxycinnamic acid as the substrate, three bromination products were identified: trans-2-bromo-1-(3,4-dimethoxyphenyl)ethylene (IX), 2,2-dibromo-1-(3,4-dimethoxyphenyl)-1-hydroxyethane (X), and 2-bromo-3-(3,4-dimethoxyphenyl)-3-hydroxypropionic acid (XI).

Renganathan, V.; Miki, K.; Gold, M.H.

1987-08-11

27

Structural characterization of tartrate dehydrogenase: a versatile enzyme catalyzing multiple reactions  

PubMed Central

The first structure of an NAD-dependent tartrate dehydrogenase (TDH) has been solved to 2?Å resolution by single anomalous diffraction (SAD) phasing as a complex with the intermediate analog oxalate, Mg2+ and NADH. This TDH structure from Pseudomonas putida has a similar overall fold and domain organization to other structurally characterized members of the hydroxy-acid dehydrogenase family. How­ever, there are considerable differences between TDH and these functionally related enzymes in the regions connecting the core secondary structure and in the relative positioning of important loops and helices. The active site in these complexes is highly ordered, allowing the identification of the substrate-binding and cofactor-binding groups and the ligands to the metal ions. Residues from the adjacent subunit are involved in both the substrate and divalent metal ion binding sites, establishing a dimer as the functional unit and providing structural support for an alternating-site reaction mechanism. The divalent metal ion plays a prominent role in substrate binding and orientation, together with several active-site arginines. Functional groups from both subunits form the cofactor-binding site and the ammonium ion aids in the orientation of the nicotinamide ring of the cofactor. A lysyl amino group (Lys192) is the base responsible for the water-mediated proton abstraction from the C2 hydroxyl group of the substrate that begins the catalytic reaction, followed by hydride transfer to NAD. A tyrosyl hydroxyl group (Tyr141) functions as a general acid to protonate the enolate inter­mediate. Each substrate undergoes the initial hydride transfer, but differences in substrate orientation are proposed to account for the different reactions catalyzed by TDH.

Malik, Radhika; Viola, Ronald E.

2010-01-01

28

Structural characterization of tartrate dehydrogenase: a versatile enzyme catalyzing multiple reactions  

SciTech Connect

The first structure of an NAD-dependent tartrate dehydrogenase (TDH) has been solved to 2 {angstrom} resolution by single anomalous diffraction (SAD) phasing as a complex with the intermediate analog oxalate, Mg{sup 2+} and NADH. This TDH structure from Pseudomonas putida has a similar overall fold and domain organization to other structurally characterized members of the hydroxy-acid dehydrogenase family. However, there are considerable differences between TDH and these functionally related enzymes in the regions connecting the core secondary structure and in the relative positioning of important loops and helices. The active site in these complexes is highly ordered, allowing the identification of the substrate-binding and cofactor-binding groups and the ligands to the metal ions. Residues from the adjacent subunit are involved in both the substrate and divalent metal ion binding sites, establishing a dimer as the functional unit and providing structural support for an alternating-site reaction mechanism. The divalent metal ion plays a prominent role in substrate binding and orientation, together with several active-site arginines. Functional groups from both subunits form the cofactor-binding site and the ammonium ion aids in the orientation of the nicotinamide ring of the cofactor. A lysyl amino group (Lys192) is the base responsible for the water-mediated proton abstraction from the C2 hydroxyl group of the substrate that begins the catalytic reaction, followed by hydride transfer to NAD. A tyrosyl hydroxyl group (Tyr141) functions as a general acid to protonate the enolate intermediate. Each substrate undergoes the initial hydride transfer, but differences in substrate orientation are proposed to account for the different reactions catalyzed by TDH.

Malik, Radhika; Viola, Ronald E. (Toledo)

2010-10-28

29

Reactions catalyzed by purified L-glutamine: keto-scyllo-inositol aminotransferase, an enzyme required for biosynthesis of aminocyclitol antibiotics.  

PubMed

Dialyzed extracts of the gentamicin producer Micromonospora purpurea catalyze reactions which represent transaminations proposed for 2-deoxystreptamine biosynthesis. To determine whether these transaminations were catalyzed by a single aminotransferase or by multiple enzymes, we purified and characterized an L-glutamine:keto-scyllo-inositol aminotransferase from M. purpurea. This enzyme was purified 130- to 150-fold from late-log-phase mycelia of both wild-type M. purpurea and a 2-deoxystreptamine-less idiotroph. The cofactor pyridoxal phosphate was found to be tightly bound to the enzyme, and spectral analysis demonstrated its participation in the transamination reactions of this enzyme. The major physiological amino donor for the enzyme appears to be L-glutamine; the keto acid product derived from glutamine was characterized as 2-ketoglutaramate, indicating that the alpha amino group of glutamine participates in the transamination. We found that crude extracts contained omega-amidase activity, which may render transaminations with glutamine irreversible in vivo. The substrate specificity of the aminotransferase was shown to be restricted to deoxycyclitols, monoaminocyclitols, and diaminocyclitols, glutamine, and 2-ketoglutaramate, which contrasts with the broader substrate specificity of mammalian glutamine aminotransferase. The appearance of the enzyme in late-log phase, coupled with its narrow substrate specificity, indicates that it participates predominantly in 2-deoxystreptamine biosynthesis rather than in general metabolism. The enzyme catalyzes reactions which represent both transamination steps of 2-deoxystreptamine biosynthesis. Although copurification of two aminotransferases cannot be ruled out, our data are consistent with the participation of a single aminotransferase in the formation of both amino groups of 2-deoxystreptamine during biosynthesis by M. purpurea. We propose that this aminotransferase participates in a key initial step in the biosynthesis of most aminocyclitol antibiotics. PMID:2729940

Lucher, L A; Chen, Y M; Walker, J B

1989-04-01

30

Nuclear quantum effects on an enzyme-catalyzed reaction with reaction path potential: Proton transfer in triosephosphate isomerase  

Microsoft Academic Search

Nuclear quantum mechanical effects have been examined for the proton transfer reaction catalyzed by triosephosphate isomerase, with the normal mode centroid path integral molecular dynamics based on the potential energy surface from the recently developed reaction path potential method. In the simulation, the primary and secondary hydrogens and the C and O atoms involving bond forming and bond breaking were

Mingliang Wang; Zhenyu Lu; Weitao Yang

2006-01-01

31

Formation of covalent ?-linked carbohydrate–enzyme intermediates during the reactions catalyzed by ?-amylases  

Microsoft Academic Search

Porcine pancreatic and Bacillus amyloliquefaciens ?-amylases were examined for the formation of covalent carbohydrate intermediates during reaction. The enzymes were precipitated and denatured by adding 10 volumes of acetone. When these denatured enzymes were mixed with methyl ?-6-[3H]-maltooligosaccharide glycosides and chromatographed on BioGel P-2, no carbohydrate was found in the protein void volume peak. When the enzymes were added to

Seung-Heon Yoon; D. Bruce Fulton; John F. Robyt

2007-01-01

32

Reformulation of the Michaelis-Menten Equation: How Enzyme-Catalyzed Reactions Depend on Gibbs Energy  

ERIC Educational Resources Information Center

|The impact of raising Gibbs energy of the enzyme-substrate complex (G[subscript 3]) and the reformulation of the Michaelis-Menten equation are discussed. The maximum velocity of the reaction (v[subscript m]) and characteristic constant for the enzyme (K[subscript M]) will increase with increase in Gibbs energy, indicating that the rate of…

Bozlee, Brian J.

2007-01-01

33

Catalyzed enzyme electrodes  

SciTech Connect

An enzyme electrode is prepared with a composite coating on an electrical conductor. The composite coating is formed from a casting solution of a perfluorosulfonic acid polymer, an enzyme, and a carbon supported catalyst. The solution may be cast directly on the conductor surface or may be formed as a membrane and applied to the surface. The perfluorosulfonic acid ionomer formed from the casting solution provides an insoluble biocompatible protective matrix for the enzyme and acts to retain the enzyme for long term availability in the electrode structure. The carbon supported catalyst provides catalytic sites throughout the layer for the oxidation of hydrogen peroxide from the enzyme reactions. The carbon support then provides a conductive path for establishing an electrical signal to the electrical conductor. In one embodiment, the electrical conductor is a carbon cloth that permits oxygen or other gas to be introduced to the perfluorosulfonic polymer to promote the enzyme reaction independent of oxygen in the solution being tested.

Zawodzinski, T.A.; Wilson, M.S.; Rishpon, J.; Gottesfeld, S.

1993-07-13

34

Catalyzed enzyme electrodes  

DOEpatents

An enzyme electrode is prepared with a composite coating on an electrical conductor. The composite coating is formed from a casting solution of a perfluorosulfonic acid polymer, an enzyme, and a carbon supported catalyst. The solution may be cast directly on the conductor surface or may be formed as a membrane and applied to the surface. The perfluorosulfonic acid ionomer formed from the casting solution provides an insoluble biocompatible protective matrix for the enzyme and acts to retain the enzyme for long term availability in the electrode structure. The carbon supported catalyst provides catalytic sites throughout the layer for the oxidation of hydrogen peroxide from the enzyme reactions. The carbon support then provides a conductive path for establishing an electrical signal to the electrical conductor. In one embodiment, the electrical conductor is a carbon cloth that permits oxygen or other gas to be introduced to the perfluorosulfonic polymer to promote the enzyme reaction independent of oxygen in the solution being tested.

Zawodzinski, Thomas A. (Los Alamos, NM); Wilson, Mahlon S. (Los Alamos, NM); Rishpon, Judith (Ramat-Aviv, IL); Gottesfeld, Shimshon (Los Alamos, NM)

1993-01-01

35

Catalyzed enzyme electrodes  

DOEpatents

An enzyme electrode is prepared with a composite coating on an electrical conductor. The composite coating is formed from a casting solution of a perfluorosulfonic acid, polymer, an enzyme, and a carbon supported catalyst. The solution may be cast directly on the conductor surface or may be formed as a membrane and applied to the surface. The perfluorosulfonic acid ionomer formed from the casting solution provides an insoluble biocompatible protective matrix for the enzyme and acts to retain the enzyme for long term availability in the electrode structure. The carbon supported catalyst provides catalytic sites throughout the layer for the oxidation of hydrogen peroxide from the enzyme reactions. The carbon support then provides a conductive path for establishing an electrical signal to the electrical conductor. In one embodiment, the electrical conductor is a carbon cloth that permits oxygen or other gas to be introduced to the perfluorosulfonic polymer to promote the enzyme reaction independent of oxygen in the solution being tested.

Zawodzinski, T.A.; Wilson, M.S.; Rishpon, J.; Gottesfeld, S.

1992-12-31

36

Monte Carlo simulations of single- and multistep enzyme-catalyzed reaction sequences: Effects of diffusion, cell size, enzyme fluctuations, colocalization, and segregation  

NASA Astrophysics Data System (ADS)

Following the discovery of slow fluctuations in the catalytic activity of an enzyme in single-molecule experiments, it has been shown that the classical Michaelis-Menten (MM) equation relating the average enzymatic velocity and the substrate concentration may hold even for slowly fluctuating enzymes. In many cases, the average velocity is that given by the MM equation with time-averaged values of the fluctuating rate constants and the effect of enzyme fluctuations is simply averaged out. The situation is quite different for a sequence of reactions. For colocalization of a pair of enzymes in a sequence to be effective in promoting reaction, the second must be active when the first is active or soon after. If the enzymes are slowly varying and only rarely active, the product of the first reaction may diffuse away before the second enzyme is active, and colocalization may have little value. Even for single-step reactions the interplay of reaction and diffusion with enzyme fluctuations leads to added complexities, but for multistep reactions the interplay of reaction and diffusion, cell size, compartmentalization, enzyme fluctuations, colocalization, and segregation is far more complex than for single-step reactions. In this paper, we report the use of stochastic simulations at the level of whole cells to explore, understand, and predict the behavior of single- and multistep enzyme-catalyzed reaction systems exhibiting some of these complexities. Results for single-step reactions confirm several earlier observations by others. The MM relationship, with altered constants, is found to hold for single-step reactions slowed by diffusion. For single-step reactions, the distribution of enzymes in a regular grid is slightly more effective than a random distribution. Fluctuations of enzyme activity, with average activity fixed, have no observed effects for simple single-step reactions slowed by diffusion. Two-step sequential reactions are seen to be slowed by segregation of the enzymes for each step, and results of the calculations suggest limits for cell size. Colocalization of enzymes for a two-step sequence is seen to promote reaction, and rates fall rapidly with increasing distance between enzymes. Low frequency fluctuations of the activities of colocalized enzymes, with average activities fixed, can greatly reduce reaction rates for sequential reactions.

Anderson, James B.; Anderson, Louise E.; Kussmann, Jörg

2010-07-01

37

Microwave-assisted enzyme-catalyzed reactions in various solvent systems  

Microsoft Academic Search

The work describes the accelerated enzymatic digestion of several proteins in various solvent systems under microwave irradiation.\\u000a The tryptic fragments of the proteins were analyzed by matrix-assisted laser desorption\\/ionization mass spectrometry. Under\\u000a the influence of rapid microwave heating, these enzymatic reactions can proceed in a solvent such as chloroform, which, under\\u000a traditional digestion conditions, renders the enzyme inactive. The digestion

Shan-Shan Lin; Chi-Hong Wu; Mei-Chuan Sun; Chung-Ming Sun; Yen-Peng Ho

2005-01-01

38

The lactate dehydrogenase catalyzed pyruvate adduct reaction: simultaneous general acid-base catalysis involving an enzyme and an external catalyst.  

PubMed

The pH dependence of the reaction catalyzed by lactate dehydrogenase, where pyruvate adds covalently to NAD to yield a NAD-Pyr adduct, together with published data on the pH dependence of parameters in the normal redox reaction suggests similar binding modes for enolpyruvate and lactate in their complexes with E X NAD (where E is one-fourth of the tetramer), for ketopyruvate in its complexes with the protonated species, E X H X NAD and E X H X NADH, and for the NAD--Pyr adduct and NADH plus pyruvate in their complexes with E X H. These similarities, together with previous data, suggest a reaction scheme for the formation of the enzyme-adduct complex that includes the relevant proton-transfer steps. Seven different amine chloride buffers were used in a study of the reverse adduct reaction, i.e., the decomposition of E X H X NAD--Pyr. These act with varying efficiencies as external general acid catalysts; the enzyme apparently acts as a (internal) general base. The involvement of the amine chloride buffers as external general catalysts is supported by the concentration dependence of the buffer effect, by a Brönsted plot, and by solvent deuterium isotope effects. The involvement of the enzyme as an internal general catalyst is inferred from the pH dependence of the reaction and the identities of the nearby groups in the E X H X NAD--Pyr complex (from crystallographic studies). The dependence of the adduct reaction on chloride concentration indicates the presence of dead-end inhibitor complexes of E X H X Cl and E X H X NAD X Cl. Chloride also accelerates the decomposition of the adduct in the complex E X H X NAD--Pyr by binding to this complex. PMID:6477888

Burgner, J W; Ray, W J

1984-07-31

39

Enzyme Reactions  

NSDL National Science Digital Library

The enzyme reaction rate activity allows students to simulate the effects of variables such as temperature and pH on the reaction rate of the enzyme catalase. This computer simulation is best used after the students have done a wet lab experiment. The value of the simulation is that it requires the students to interpret and analyze the graphical representation of data and it enables the running of mutiple experiments in a short amount of time.

School, Maryland V.

40

A paper-based surface-enhanced resonance Raman spectroscopic (SERRS) immunoassay using magnetic separation and enzyme-catalyzed reaction.  

PubMed

In this study, a novel paper-based SERRS immunoassay based on magnetic separation and alkaline phosphatase (ALP) enzyme catalyzed hydrolysis reaction was developed. By using modified antibodies conjugated to magnetic beads, capture of mouse IgG followed by addition of ALP-labeled antibodies would form a sandwich-like immunoconjugate. After magnetic separation, 5-bromo-4-chloro-3-indolyl phosphate (BCIP), a low SERRS active compound, was added as the substrate for ALP to generate a high SERRS response. Detection was conducted on a silver colloid/PVP/filter paper SERS substrate by spotting a pre-aggregated silver colloid sol onto polyvinyl pyrrolidone (PVP) modified filter paper using a semi-automatic TLC sample applicator. The optimization of the highly SERS active paper-based substrate, dynamic hydrolysis process of BCIP, quantitative detection of IgG, and selectivity of the assay was studied in detail. By taking advantage of magnetic separation in order to decrease the background interference, the selective enzyme reaction involved in producing a highly SERRS active product could detect mouse IgG from 1 to 500 ng mL(-1) with a LOD of 0.33 ng mL(-1). PMID:23486763

Chen, Yuanyuan; Cheng, Hanwen; Tram, Kha; Zhang, Shengfeng; Zhao, Yanhua; Han, Liyang; Chen, Zengping; Huan, Shuangyan

2013-05-01

41

Stoichiometry of the Redox Neutral Deamination and Oxidative Dehydrogenation Reactions Catalyzed by the Radical SAM Enzyme DesII  

PubMed Central

DesII from Streptomyces venezuelae is a radical SAM (S-adenosyl-l-methionine) enzyme that catalyzes the deamination of TDP-4-amino-4,6-dideoxy-d-glucose to form TDP-3-keto-4,6-dideoxy-d-glucose in the biosynthesis of TDP-d-desosamine. DesII also catalyzes the dehydrogenation of the non-physiological substrate TDP-d-quinovose to TDP-3-keto-6-deoxy-d-glucose. These properties prompted an investigation of how DesII handles SAM in the redox neutral deamination versus the oxidative dehydrogenation reactions. This work was facilitated by the development of an enzymatic synthesis of TDP-4-amino-4,6-dideoxy-d-glucose that couples a transamination equilibrium to the thermodynamically favorable oxidation of formate. In this study, DesII is found to consume SAM versus TDP-sugar with stoichiometries of 0.96 ± 0.05 and 1.01 ± 0.05 in the deamination and dehydrogenation reactions, respectively, using Na2S2O4 as the reductant. Importantly, no significant change in stoichiometry is observed when the flavodoxin/flavodoxin NADP+ oxidoreductase/NADPH reducing system is used in place of Na2S2O4. Moreover, there is no evidence of an uncoupled or abortive process in the deamination reaction, as indicated by the observation that dehydrogenation can take place in the absence of an external source of reductant whereas deamination cannot. Mechanistic and biochemical implications of these results are discussed.

Ruszczycky, Mark W.; Choi, Sei-hyun; Liu, Hung-wen

2010-01-01

42

Thermodynamics of reactions catalyzed by PABA synthase  

Microsoft Academic Search

Microcalorimetry and high-performance liquid chromatography (HPLC) have been used to conduct a thermodynamic investigation of reactions catalyzed by PABA synthase, the enzyme located at the first step in the shikimic acid metabolic pathway leading from chorismate to 4-aminobenzoate (PABA). The overall biochemical reaction catalyzed by the PabB and PabC components of PABA synthase is: chorismate(aq)+ammonia(aq)=4-aminobenzoate(aq)+pyruvate(aq)+H2O(l). This reaction can be divided

Yadu B. Tewari; Pia Y. Jensen; Nand Kishore; Martin P. Mayhew; James F. Parsons; Edward Eisenstein; Robert N. Goldberg

2002-01-01

43

Enzyme-catalyzed organic syntheses: transesterification reactions of chlorophyl a, bacteriochlorophyll a, and derivatives with chlorophyllase  

Microsoft Academic Search

The green plant enzyme chlorophyllase (EC 3.1.1.14, chlorophyll chlorophyllido-hydroase) has been used for the synthesis of a variety of primary alcohol and diol esters of chlorophyll a, bacteriochlorophyll a, and pyrobacteriochlorophyll a. Green plant chlorophyllase accepts a much larger range of alcohol and chlorophyll substrates than had previously been realized. Thus, chlorophyllide and bacteriochlorophyllide esters of primary alcohols such as

T. J. Michalski; J. E. Hunt; C. Bradshaw; A. M. Wagner; J. R. Norris; J. J. Katz

1988-01-01

44

The Effect of Temperature on the Enzyme-Catalyzed Reaction: Insights from Thermodynamics  

ERIC Educational Resources Information Center

|When teaching the effect of temperature on biochemical reactions, the problem is usually oversimplified by confining the thermal effect to the catalytic constant, which is identified with the rate constant of the elementary limiting step. Therefore, only positive values for activation energies and values greater than 1 for temperature…

Aledo, Juan Carlos; Jimenez-Riveres, Susana; Tena, Manuel

2010-01-01

45

Photoelectrochemical sensor for the rapid detection of in situ DNA damage induced by enzyme-catalyzed fenton reaction.  

PubMed

Photoelectrochemical sensors were developed for the rapid detection of oxidative DNA damage induced by Fe2+ and H2O2 generated in situ by the enzyme glucose oxidase. The sensor is a multilayer film prepared on a tin oxide nanoparticle electrode by layer-by-layer self-assembly and is composed of separate layers of a photoelectrochemical indicator, DNA, and glucose oxidase. The enzyme catalyzes the formation of H2O2 in the presence of glucose, which then reacts with Fe2+ and generates hydroxyl radicals by the Fenton reaction. The radicals attack DNA in the sensor film, mimicking metal toxicity pathways in vivo. The DNA damage is detected by monitoring the change of photocurrent of the indicator. In one sensor configuration, a DNA intercalator, Ru(bpy)2(dppz)2+ (bpy = 2,2'-bipyridine, dppz = dipyrido[3,2-a:2',3'-c]phenazine), was employed as the photoelectrochemical indicator. The damaged DNA on the sensor bound less Ru(bpy)2(dppz)2+ than the intact DNA, resulting in a drop in photocurrent. In another configuration, ruthenium tris(bipyridine) was used as the indicator and was immobilized on the electrode underneath the DNA layer. After oxidative damage, the DNA bases became more accessible to photoelectrochemical oxidation than the intact DNA, producing a rise in photocurrent. Both sensors displayed substantial photocurrent change after incubation in Fe2+/glucose in a time-dependent manner. And the detection limit of the first sensor was less than 50 microM. The results were verified independently by fluorescence and gel electrophoresis experiments. When fully integrated with cell-mimicking components, the photoelectrochemical DNA sensor has the potential to become a rapid, high-throughput, and inexpensive screening tool for chemical genotoxicity. PMID:18284175

Liang, Minmin; Jia, Suping; Zhu, Shengchao; Guo, Liang-Hong

2008-01-15

46

Janus-faced Enzymes Yeast Tgl3p and Tgl5p Catalyze Lipase and Acyltransferase Reactions  

PubMed Central

In the yeast, mobilization of triacylglycerols (TAGs) is facilitated by the three TAG lipases Tgl3p, Tgl4p, and Tgl5p. Motif search analysis, however, indicated that Tgl3p and Tgl5p do not only contain the TAG lipase motif GXSXG but also an H-(X)4-D acyltransferase motif. Interestingly, lipid analysis revealed that deletion of TGL3 resulted in a decrease and overexpression of TGL3 in an increase of glycerophospholipids. Similar results were obtained with TGL5. Therefore, we tested purified Tgl3p and Tgl5p for acyltransferase activity. Indeed, both enzymes not only exhibited lipase activity but also catalyzed acylation of lysophosphatidylethanolamine and lysophosphatidic acid, respectively. Experiments using variants of Tgl3p created by site-directed mutagenesis clearly demonstrated that the two enzymatic activities act independently of each other. We also showed that Tgl3p is important for efficient sporulation of yeast cells, but rather through its acyltransferase than lipase activity. In summary, our results demonstrate that yeast Tgl3p and Tgl5p play a dual role in lipid metabolism contributing to both anabolic and catabolic processes.

Rajakumari, Sona

2010-01-01

47

Mechanism of enzyme-catalyzed phospho group transfer  

SciTech Connect

To understand more fully the mechanism of enzyme-catalyzed phospho group transfer, the stereochemical course at phosphorus of four enzymes has been determined. First, using adenosine (..gamma..-(S)-/sup 16/O, /sup 17/O, /sup 18/O)triphosphate as the substrate, the reaction catalyzed by creatine kinase has been found to proceed with overall inversion of configuration at phosphorus. Second, using adenosine (..beta..-(S)-/sup 16/O, /sup 17/O, /sup 18/O)diphosphate as the substrate, the reaction catalyzed by adenylate kinase has been found also to proceed with overall inversion. Third, the reaction catalyzed by phosphoenolpyruvate carboxylase has been studied using ((S/sub p/)-/sup 16/O, /sup 17/O)thiophospoenolpyruvate as the substrate in H/sub 2/ /sup 18/O. Fourth, using adenosine 5'-O-((..gamma..S/sub p/)-..beta gamma..-/sup 17/O,..gamma..-/sup 17/O,/sup 18/O)(3-thiotriphosphate) as the substrate, the reaction catalyzed by pyruvate carboxylase has been shown to proceed with inversion at phosphorus. This results rules out the chemically and enzymatically precendented composite mechanism that had been proposed for this enzyme and supports a stepwise pathway again involving the intermediacy of carboxyphosphate. The first pair of results supports the growing body of evidence that enzyme-catalyzed phospho group transfer proceeds by an in-line associative mechanism. The second pair of results eliminate mechanistic suggestions of concerted electrocyclic processes in bicarbonate dependent carboxylation reactions.

Hansen, D.E.

1986-01-01

48

Regioselective bromohydroxylation of alkenes catalyzed by chloroperoxidase: Advantages of the immobilization of enzyme on talc  

Microsoft Academic Search

The bromohydroxylation of alkenes catalyzed by chloroperoxidase (CPO) from the mould Caldariomyces fumago adsorbed on different types of talc or in reverse micelles was compared to that of the same reaction catalyzed by the free enzyme in buffer. High reactivity was observed in all media, but the reaction was optimized with an enzyme-talc combination that produced the halohydrin with no

Salim Aoun; Michel Baboulène

1998-01-01

49

4-alkyl-o-quinone/2-hydroxy-p-quinone methide isomerase from the larval hemolymph of Sarcophaga bullata. I. Purification and characterization of enzyme-catalyzed reaction.  

PubMed

An enzyme which catalyzes the conversion of certain 4-alkyl-o-benzoquinones to 2-hydroxy-p-quinone methides has been purified to apparent homogeneity from the hemolymph of Sarcophaga bullata by employing conventional protein purification techniques. The purified enzyme migrated with an approximate molecular weight of 98,000 on gel filtration chromatography. On sodium dodecyl sulfate-polyacrylamide gel electrophoresis, it migrated as a single band with a molecular weight of 46,000, indicating that it is made up of two identical subunits. It exhibited a pH optimum of 6.0 and readily converted chemically synthesized as well as enzymatically generated quinones derived from N-acetyldopamine, N-beta-alanyldopamine, and 3,4-dihydroxyphenethyl alcohol to highly unstable 2-hydroxy-p-quinone methides. The quinone methides thus formed were rapidly and nonenzymatically hydrated to form side chain hydroxylated o-diphenols as the stable product. In support of this proposition, when the enzyme reaction with N-acetyldopamine quinone was conducted in the presence of 10% methanol, racemic beta-methoxy-N-acetyldopamine was recovered as an additional product. The quinones of N-acetylnorepinephrine, N-beta-alanylnorepinephrine, and 3,4-dihydroxyphenylglycol were also attacked by the isomerase, resulting in the formation of N-acetylarterenone, N-beta-alanylarterenone and 2-hydroxy-3',4'-dihydroxyacetophenone, respectively as the stable products. The isomerase converted the dihydrocaffeiyl methyl amide quinone to its quinone methide analog which rapidly tautomerized to yield caffeiyl methyl amide. The importance of quinone isomerase in insect immunity and sclerotization of insect cuticle is discussed. PMID:2211605

Saul, S J; Sugumaran, M

1990-10-01

50

Enzyme Catalyzed 2-D Polymerization of Phenol and Aniline Derivatives on a Langmuir-Blodgett Through.  

National Technical Information Service (NTIS)

Previous studies have shown that polymeric materials may be synthesized from substituted phenols and aromatic amine compounds through a Horseradish Peroxidase (HRP) enzyme catalyzed reaction in the bulk. We have developed a novel approach for this enzyme ...

F. Bruno J. A. Akkara L. A. Samuelson B. K. Mandal D. L. Kaplan

1992-01-01

51

Stereochemical course of the reaction catalyzed by the pyridoxal phosphate-dependent enzyme 1-aminocyclopropane-1-carboxylate synthase  

SciTech Connect

(+/-)-S-adenosyl-DL-(3R*,4S*)-(3,4-/sup 2/H/sub 2/)-methionine(a 1:1 mixture of (3R,4S) and (3S,4R) and (+/-)-S-adenosyl-DL-(3R*,4R*)-(3,4-/sup 2/H/sub 2/)methionine (a 1:1 mixture of (3R,4R) and (3S,4S)) were synthesized from (Z)- and (E)-(1,2-/sup 2/H/sub 2/)ethene, respectively. Key steps in the synthesis were the antiperiplanar addition of methanesulfenyl chloride to (Z)-(1,2-/sup 2/H/sub 2/)ethene, to give a 1:1 mixture of (R,R)- and (S,S)-1-chloro-2-(methylthio)(1,2-/sup 2/H/sub 2/)ethane, followed by alkylation with soldium acetamidomalonate and hydrolysis to give an equal mixture of four stereoisomers of (3,4-/sup 2/H/sub 2/)methionine ((2R,3R,4S), (2R,3S,4R), (2S,3R,4S), and (2S,3S,4R)). The other four stereoisomers of (3,4-/sup 2/H/sub 2/)methionine were prepared from (E)-(1,2-/sup 2/H/sub 2/)ethene. The two sets of stereoisomers of (3,4-/sup 2/H/sub 2/)methionine were chemically converted to S-adenosylhomocysteine, methylated to give the corresponding (+/-)-S-adenosyl-DL-methionines, and then incubated with 1-aminocyclopropane-1-carboxylate synthase partially purified from tomato (Lycopersicon esculentum, L.)pericarp tissue. The stereochemistry of the resulting samples of 1-aminocyclopropane-1-carboxylic acid was determined by comparison with the /sup 1/H NMR of the chemically synthesized and regio- and stereo-specifically deuterated compound. The results indicate that the hydrogens at the ..beta.. carbon of the methionine portion of S-adenosylmethionine do not participate in the reaction and that the ring closure occurs with inversion of configuration at the ..gamma.. carbon of the methionine portion of S-adenosyl-methionine, probably through a direct S/sub N/2-type displacement of the 5'-methylthio-5'-deoxyadenosine moiety by a carbanion equivalent formed at the ..cap alpha.. carbon of the methionine portion of S-adenosylmethionine.

Ramalingam, K.; Lee, K.M.; Woodard, R.W.; Bleecker, A.B.; Kende, H.

1985-12-01

52

Potassium Phosphate Catalyzed Nitroaldol Reaction  

Microsoft Academic Search

Potassium phosphate was found to catalyze condensation of nitroalkanes with various aliphatic and aromatic aldehydes to form nitroaldols in excellent yields in acetonitrile medium at room temperature.

Uday V. Desai; D. M. Pore; R. B. Mane; S. B. Solabannavar; P. P. Wadgaonkar

2004-01-01

53

Controlling reaction specificity in pyridoxal phosphate enzymes  

PubMed Central

Pyridoxal 5'-phosphate enzymes are ubiquitous in the nitrogen metabolism of all organisms. They catalyze a wide variety of reactions including racemization, transamination, decarboxylation, elimination, retro-aldol cleavage, Claisen condensation, and others on substrates containing an amino group, most commonly ?-amino acids. The wide variety of reactions catalyzed by PLP enzymes is enabled by the ability of the covalent aldimine intermediate formed between substrate and PLP to stabilize carbanionic intermediates at C? of the substrate. This review attempts to summarize the mechanisms by which reaction specificity can be achieved in PLP enzymes by focusing on three aspects of these reactions: stereoelectronic effects, protonation state of the external aldimine intermediate, and interaction of the carbanionic intermediate with the protein side chains present in the active site.

Toney, Michael D.

2012-01-01

54

Cobalt-catalyzed cross-coupling reactions  

Microsoft Academic Search

In the last few years, we and other groups have demonstrated that economical cobalt salts can advantageously replace expensive and toxic catalysts for cross coupling reactions. These cobalt- catalyzed reactions have considerably extended the range of functionalized compounds. A variety of sensitive functional groups can be tolerated in these coupling reactions and various organic compounds RX could be involved (R

Corinne Gosmini; Jeanne-Marie Begouin; Aurélien Moncomble

2008-01-01

55

Potential of mean force calculation for the proton and hydride transfer reactions catalyzed by medium-chain acyl-CoA dehydrogenase: effect of mutations on enzyme catalysis.  

PubMed

Potential of mean force calculations have been performed on the wild-type medium-chain acyl-CoA dehydrogenase (MCAD) and two of its mutant forms. Initial simulation and analysis of the active site of the enzyme reveal that an arginine residue (Arg256), conserved in the substrate-binding domain of this group of enzymes, exists in two alternate conformations, only one of which makes the enzyme active. This active conformation was used in subsequent computations of the enzymatic reactions. It is known that the catalytic alpha,beta-dehydrogenation of fatty acyl-CoAs consists of two C-H bond dissociation processes: a proton abstraction and a hydride transfer. Energy profiles of the two reaction steps in the wild-type MCAD demonstrate that the reaction proceeds by a stepwise mechanism with a transient species. The activation barriers of the two steps differ by only approximately 2 kcal/mol, indicating that both may contribute to the rate-limiting process. Thus this may be a stepwise dissociation mechanism whose relative barriers can be tuned by suitable alterations of the substrate and/or enzyme. Analysis of the structures along the reaction path reveals that Arg256 plays a key role in maintaining the reaction center hydrogen-bonding network involving the thioester carbonyl group, which stabilizes transition states as well as the intervening transient species. Mutation of this arginine residue to glutamine increases the activation barrier of the hydride transfer reaction by approximately 5 kcal/mol, and the present simulations predict a substantial loss of catalytic activity for this mutant. Structural analysis of this mutant reveals that the orientation of the thioester moiety of the substrate has been changed significantly as compared to that in the wild-type enzyme. In contrast, simulation of the active site of the Thr168Ala mutant shows no significant change in the relative orientation of the substrate and the cofactor in the active site; as a result, this mutation has very little effect on the overall reaction barrier, and this is consistent with the experimental data. This study demonstrates that significant insights into the catalytic mechanism can be obtained from simulation studies, and the results can be used to design novel mechanistic probes for the enzyme. PMID:16342946

Bhattacharyya, Sudeep; Ma, Shuhua; Stankovich, Marian T; Truhlar, Donald G; Gao, Jiali

2005-12-20

56

Spectroscopic, steady-state kinetic, and mechanistic characterization of the radical SAM enzyme QueE, which catalyzes a complex cyclization reaction in the biosynthesis of 7-deazapurines.  

PubMed

7-Carboxy-7-deazaguanine (CDG) synthase (QueE) catalyzes the complex heterocyclic radical-mediated conversion of 6-carboxy-5,6,7,8-tetrahydropterin (CPH(4)) to CDG in the third step of the biosynthetic pathway to all 7-deazapurines. Here we present a detailed characterization of QueE from Bacillus subtilis to delineate the mechanism of conversion of CPH(4) to CDG. QueE is a member of the radical S-adenosyl-l-methionine (SAM) superfamily, all of which use a bound [4Fe-4S](+) cluster to catalyze the reductive cleavage of the SAM cofactor to generate methionine and a 5'-deoxyadenosyl radical (5'-dAdo(•)), which initiates enzymatic transformations requiring hydrogen atom abstraction. The ultraviolet-visible, electron paramagnetic resonance, and Mössbauer spectroscopic features of the homodimeric QueE point to the presence of a single [4Fe-4S] cluster per monomer. Steady-state kinetic experiments indicate a K(m) of 20 ± 7 ?M for CPH(4) and a k(cat) of 5.4 ± 1.2 min(-1) for the overall transformation. The kinetically determined K(app) for SAM is 45 ± 1 ?M. QueE is also magnesium-dependent and exhibits a K(app) for the divalent metal ion of 0.21 ± 0.03 mM. The SAM cofactor supports multiple turnovers, indicating that it is regenerated at the end of each catalytic cycle. The mechanism of rearrangement of QueE was probed with CPH(4) isotopologs containing deuterium at C-6 or the two prochiral positions at C-7. These studies implicate 5'-dAdo(•) as the initiator of the ring contraction reaction catalyzed by QueE by abstraction of the H atom from C-6 of CPH(4). PMID:23194065

McCarty, Reid M; Krebs, Carsten; Bandarian, Vahe

2012-12-24

57

Infrared Laser Catalyzed Chemical Reactions  

Microsoft Academic Search

The development of the laser some twelve years ago has resulted in the creation and\\/or the resuscitation of a number of experimental disciplines involving measurements of energy transfer, chemical reaction rates, high resolution spectroscopy as well as nonlinear effects. In the last three years more and more work involving the use of lasers has been reported on in the literature

A. M. Ronn

1975-01-01

58

Unusual cytochrome p450 enzymes and reactions.  

PubMed

Cytochrome P450 enzymes primarily catalyze mixed-function oxidation reactions, plus some reductions and rearrangements of oxygenated species, e.g. prostaglandins. Most of these reactions can be rationalized in a paradigm involving Compound I, a high-valent iron-oxygen complex (FeO(3+)), to explain seemingly unusual reactions, including ring couplings, ring expansion and contraction, and fusion of substrates. Most P450s interact with flavoenzymes or iron-sulfur proteins to receive electrons from NAD(P)H. In some cases, P450s are fused to protein partners. Other P450s catalyze non-redox isomerization reactions. A number of permutations on the P450 theme reveal the diversity of cytochrome P450 form and function. PMID:23632016

Guengerich, F Peter; Munro, Andrew W

2013-04-30

59

An antibody-catalyzed bimolecular Diels-Alder reaction  

SciTech Connect

There exist over 1,500 known enzymes which carry out a vast array of chemical reactions with remarkable specificity and reaction rates. It is surprising then that there are no documented examples of enzyme-catalyzed pericyclic cycloaddition reactions, yet there are among the most powerful and commonly used reactions in synthetic organic chemistry. The most important of these is the Diels-Alder reaction of a diene with a dienophile, which provides a straightforward and highly stereospecific route to cyclohexene derivatives. Given the importance of this reaction in organic chemistry and its novel mechanism, it was of interest to ask whether a Diels-Alderase enzymatic catalyst could be evolved from an antibody combining site. Generation of antibodies to a structure that mimics the pericyclic transition state for a Diels-Alder reaction should result in an antibody combining site that lowers the entropy of activation {Delta}S{sup {double dagger}} by binding both the diene and the dienophile in a reactive conformation. The authors approach toward the design of a transition-state analogue involves incorporation of an ethano bridge, which locks the cyclohexene ring of hapten in a conformation that resembles the proposed pericyclic transition state for the Diels-Alder reaction of cisoid diene with dienophile. The authors now report that antibodies generated to the transition-state analogue catalyze the addition of the acyclic water-soluble diene to the maleimide derivative to give the cyclohexene product.

Braisted, A.C.; Schultz, P.G. (Lawrence Berkeley Laboratory, CA (USA))

1990-09-26

60

A Link between Protein Structure and Enzyme Catalyzed Hydrogen Tunneling  

NASA Astrophysics Data System (ADS)

We present evidence that the size of an active site side chain may modulate the degree of hydrogen tunneling in an enzyme-catalyzed reaction. Primary and secondary kH/kT and kD/kT kinetic isotope effects have been measured for the oxidation of benzyl alcohol catalyzed by horse liver alcohol dehydrogenase at 25 degrees C. As reported in earlier studies, the relationship between secondary kH/kT and kD/kT isotope effects provides a sensitive probe for deviations from classical behavior. In the present work, catalytic efficiency and the extent of hydrogen tunneling have been correlated for the alcohol dehydrogenase-catalyzed hydride transfer among a group of site-directed mutants at position 203. Val-203 interacts with the opposite face of the cofactor NAD+ from the alcohol substrate. The reduction in size of this residue is correlated with diminished tunneling and a two orders of magnitude decrease in catalytic efficiency. Comparison of the x-ray crystal structures of a ternary complex of a high-tunneling (Phe-93 --> Trp) and a low-tunneling (Val-203 --> Ala) mutant provides a structural basis for the observed effects, demonstrating an increase in the hydrogen transfer distance for the low-tunneling mutant. The Val-203 --> Ala ternary complex crystal structure also shows a hyperclosed interdomain geometry relative to the wild-type and the Phe-93 --> Trp mutant ternary complex structures. This demonstrates a flexibility in interdomain movement that could potentially narrow the distance between the donor and acceptor carbons in the native enzyme and may enhance the role of tunneling in the hydride transfer reaction.

Bahnson, Brian J.; Colby, Thomas D.; Chin, Jodie K.; Goldstein, Barry M.; Klinman, Judith P.

1997-11-01

61

Surface catalyzed mercury transformation reactions  

NASA Astrophysics Data System (ADS)

Mercury is a known pollutant that has detrimental effect on human health and environment. The anthropogenic emissions of mercury account for 10 to 30% of worldwide mercury emissions. There is a need to control/reduce anthropogenic mercury emissions. Many mercury control technologies are available but their effectiveness is dependent on the chemical form of mercury, because different chemical forms of mercury have different physical and chemical properties. Mercury leaves the boiler in its elemental form but goes through various transformations in the post-combustion zone. There is a need to understand how fly ash and flue gas composition affect speciation, partitioning, and reactions of mercury under the full range of post-combustion zone conditions. This knowledge can then be used to predict the chemical transformation of mercury (elemental, oxidized or particulate) in the post combustion zone and thus help with the control of mercury emissions from coal-burning power plants. To accomplish this goal present study was conducted using five coal fly ashes. These ashes were characterized and their catalytic activity was compared under selected reaction conditions in a fixed bed reactor. Based on the results from these fly ash experiments, three key components (carbon, iron oxide and calcium oxide) were chosen. These three components were then used to prepare model fly ashes. Silica/alumina was used as a base for these model fly ashes. One, two or three component model fly ashes were then prepared to investigate mercury transformation reactions. The third set of experiments was performed with five different oxidation catalysts to further understand the mercury oxidation process. Based on the results of these three studies the key components were predicted for different fly ash compositions under variety of flue gas conditions. A fixed bed reactor system was used to conduct this study. In all the experiments, the inlet concentration of Hg0(g) was maintained at 35 mug/m 3 using a diffusion tube as the source of Hg0(g). All experiments were conducted using 4% O2 in nitrogen mix as a reaction gas, and other reactants (HCl, H2O and SO2, NO 2, Br2) were added as required. The fixed bed reactor was operated over a temperature range of 200 to 400°C. In each experiment, the reactor effluent was analyzed using the modified Ontario-Hydro method. After each experiment, fly ash particles were also analyzed for mercury. The results show that the ability of fly ash to adsorb and/or oxidize mercury is primarily dependent on its carbon, iron and calcium content. There can be either one or more than one key component at a particular temperature and flue gas condition. Surface area played a secondary role in effecting the mercury transformations when compared to the concentration of the key component in the fly ash. Amount carbon and surface area played a key important role in the adsorption of mercury. Increased concentration of gases in the flue gas other than oxygen and nitrogen caused decreased the amount of mercury adsorbed on carbon surface. Mercury adsorption by iron oxide primarily depended on the crystalline structure of iron oxide. alpha-iron oxide had no effect on mercury adsorption or oxidation under most of the flue gas conditions, but gamma-iron oxide adsorbed mercury under most of the flue gas conditions. Bromine is a very good oxidizing agent for mercury. But in the presence of calcium oxide containing fly ashes, all the oxidized mercury would be reduced to elemental form. Among the catalysts, it was observed that presence of free lattice chlorine in the catalyst was very important for the oxidation of mercury. But instead of using the catalyst alone, using it along with carbon may better serve the purpose by providing the adsorption surface for mercury and also some extra surface area for the reaction to occur (especially for fly ashes with low surface area).

Varanasi, Patanjali

62

Hydrogen Location in Stages of an Enzyme-Catalyzed Reaction: Time-of-Flight Neutron Structure of D-Xylose Isomerase with Bound D-Xylulose  

SciTech Connect

The time-of-flight neutron Laue technique has been used to determine the location of hydrogen atoms in the enzyme D-xylose isomerase (XI). The neutron structure of crystalline XI with bound product, D-xylulose, shows, unexpectedly, that O5 of D-xylulose is not protonated but is hydrogen-bonded to doubly protonated His54. Also, Lys289, which is neutral in native XI, is protonated (positively charged), while the catalytic water in native XI has become activated to a hydroxyl anion which is in the proximity of C1 and C2, the molecular site of isomerization of xylose. These findings impact our understanding of the reaction mechanism.

Coates, Leighton [ORNL

2009-01-01

63

Hydrogen location in stages of an enzyme-catalyzed reaction: time-of-flight neutron structure of d-xylose isomerase with bound d-xylulose+?  

PubMed Central

The time-of-flight neutron Laue technique has been used to determine the location of hydrogen atoms in the enzyme D-xylose isomerase (XI). The neutron structure of crystalline XI with bound product, D-xylulose, shows, unexpectedly, that O5 of D-xylulose is not protonated but is hydrogen-bonded to doubly protonated His54. Also, Lys289, which is neutral in native XI, is protonated (positively charged), while the catalytic water in native XI has become activated to a hydroxyl anion which is in close proximity to C1 and C2, the molecular site of isomerization of xylose. These findings impact our understanding of the reaction mechanism.

Kovalevsky, Andrey Y.; Katz, Amy K.; Carrell, H. L.; Hanson, Leif; Mustyakimov, Marat; Fisher, S. Zoe; Coates, Leighton; Schoenborn, Benno P.; Bunick, Gerard J.; Glusker, Jenny. P.; Langan, Paul

2008-01-01

64

Enzyme Catalysis of Synthesis Reactions in Non-Aqueous Solvents by Reversal of Nominally Hydrolytic Reactions.  

National Technical Information Service (NTIS)

This project is an extension of an effort to develop new methods of chemical synthesis by using hydrolytic enzymes to catalyze condensations , the reverse of usual hydrolysis reactions. In conventional aqueous media the thermodynamic equilibrium of hydrol...

L. G. Butler R. G. Squires F. Reithel

1974-01-01

65

[Synthesis of carbohydrate related compounds by using aldolase catalyzed reaction].  

PubMed

Enzymes proceed the reaction with high regio- and stereoselectivity under mild conditions, i.e. in an aqueous medium at room temperature. However, enzymatic reactions that catalyze carbon-carbon bond formation have not been utilized in organic synthesis until recently. We had an interest in an aldolase-catalyzed reaction which proceed carbon-carbon bond formation referred to aldol condensation, by which many bioactive compounds have been rationally synthesized. On the other hand, recent biological studies on cell recognition (cell adhesion) have disclosed the important roles of oligosaccharides on cell surfaces, especially which include glucuronic acid, 3-deoxy-D-manno-oct-2-ulosonic acid (KDO), and sialic acid in the structures e.g., sialyl Lewis X and endotoxins, in differentiation, induction, viral and bacterial infections, and immune response. As well as acidic oligosaccharides, basic ones have been utilized as practical medicines in the clinical level, like acarbose that acts as an amylase inhibitor. Based on these background, we embarked the synthesis of carbohydrate related compounds which can control the interaction between carbohydrates and carbohydrate recognition protein by the use of several aldolases. Azasugars, potent inhibitors toward glycosidases, were synthesized using fructose-1,6-diphosphate (FDP)-aldolase and other dihdroxyacetonephosphate (DHAP)-dependent aldolases in the key step. Sialyl Lewis X mimetic, peptidic mimetic of RNA having anti-Vero toxin activity, mycestericin D, and aza-idulonic acid were prepared by taking advantage of L-threonine aldolase catalyzed reaction, which afford beta-hydroxy-alpha-L-amino acids. A precursor of KDO, featured acidic sugar of endotoxins was provided by the reaction catalyzed with kynureninase, which generates beta-anion of L-alanine in its active site during the metabolic reaction from kynurenine to anthranilic acid. PMID:10655781

Kajimoto, T

2000-01-01

66

Exploring Transition Metal Catalyzed Reactions via AB Initio Reaction Pathways  

NASA Astrophysics Data System (ADS)

The study and prediction of chemical reactivity is one of the most influential contributions of quantum chemistry. A central concept in the theoretical treatment of chemical reactions is the reaction pathway, which can be quite difficult to integrate accurately and efficiently. This talk will outline our developments in the integration of these pathways on ab initio potential energy surfaces. We will also describe results from recent studies on the kinetics of transition metal catalyzed reactions, including the importance of vibrational coupling to the reaction coordinate and the role of this coupling in catalytic rate enhancement.

Hratchian, Hrant P.

2011-06-01

67

Olefin cyclopropanation via carbene transfer catalyzed by engineered cytochrome P450 enzymes.  

PubMed

Transition metal-catalyzed transfers of carbenes, nitrenes, and oxenes are powerful methods for functionalizing C=C and C-H bonds. Nature has evolved a diverse toolbox for oxene transfers, as exemplified by the myriad monooxygenation reactions catalyzed by cytochrome P450 enzymes. The isoelectronic carbene transfer to olefins, a widely used C-C bond-forming reaction in organic synthesis, has no biological counterpart. Here we report engineered variants of cytochrome P450(BM3) that catalyze highly diastereo- and enantioselective cyclopropanation of styrenes from diazoester reagents via putative carbene transfer. This work highlights the capacity to adapt existing enzymes for the catalysis of synthetically important reactions not previously observed in nature. PMID:23258409

Coelho, Pedro S; Brustad, Eric M; Kannan, Arvind; Arnold, Frances H

2012-12-20

68

Biginelli Reaction Catalyzed by Copper Nanoparticles  

PubMed Central

We recently reported a novel synthesis of copper nanoparticles from copper sulphate utilizing the charge-compensatory effect of ionic liquid [bmim]BF4 and ethylene glycol. The nanoparticles were characterized and found to be stable for one year. Here we hypothesize that the stabilized nanoparticles should be able to catalyze one-pot multicomponent organic reactions. We show that the nanoparticles catalyzed Biginelli reaction at room temperature to give the product 3,4-dihydopyrimidinone (>90% yield in ?15 minutes) from aldehydes, ?-diketoester (ethylacetoacetate) and urea (or thiourea). ). Remarkably, such high yields and rapid kinetics was found to be independent of the electronic density on the reactant aryl-aldehyde. This was probably because even the surface-active particles reacted faster in the presence of ionic liquid as compared to conventional methods. The heterocyclic dihydropyrimidinones (DHPMs) and their derivatives are widely used in natural and synthetic organic chemistry due to their wide spectrum of biological and therapeutic properties (resulting from their antibacterial, antiviral, antitumor and anti-inflammatory activities. Our method has an easy work-up procedure and the nanoparticles could be recycled with minimal loss of efficiency.

Dewan, Manika; Kumar, Ajeet; Saxena, Amit; De, Arnab; Mozumdar, Subho

2012-01-01

69

Thermodynamic limitations on microbially catalyzed reaction rates  

NASA Astrophysics Data System (ADS)

Quantification of global biogeochemical cycles requires knowledge of the rates at which microorganisms catalyze chemical reactions. In order for models that describe these processes to capture global patterns of change, the underlying formulations in them must account for biogeochemical transformations over seasonal and millennial time scales in environments characterized by different energy levels. Building on existing models, a new thermodynamic limiting function is introduced. With only one adjustable parameter, this function that can be used to model microbial metabolism throughout the range of conditions in which organisms are known to be active. The formulation is based on a comparison of the amount of energy available from any redox reaction to the energy required to maintain a membrane potential, a proxy for the minimum amount of energy required by an active microorganism. This function does not require species- or metabolism-specific parameters, and can be used to model metabolisms that capture any amount of energy. The utility of this new thermodynamic rate limiting term is illustrated by applying it to three low-energy processes: fermentation, methanogenesis and sulfate reduction. The model predicts that the rate of fermentation will be reduced by half once the Gibbs energy of the catalyzed reaction reaches -12 kJ (mol e-)-1, and then slowing exponentially until the energy yield approaches zero. Similarly, the new model predicts that the low energy yield of methanogenesis, -4 to -0.5 kJ (mol e-)-1, for a partial pressure of H2 between 11 and 0.6 Pa decreases the reaction rate by 95-99%. Finally, the new function's utility is illustrated through its ability to accurately model sulfate concentration data in an anoxic marine sediment.

LaRowe, Douglas E.; Dale, Andrew W.; Amend, Jan P.; Van Cappellen, Philippe

2012-08-01

70

Iridium-Catalyzed Hydrogen Transfer Reactions  

NASA Astrophysics Data System (ADS)

This chapter describes the application of iridium complexes to catalytic hydrogen transfer reactions. Transfer hydrogenation reactions provide an alternative to direct hydrogenation for the reduction of a range of substrates. A hydrogen donor, typically an alcohol or formic acid, can be used as the source of hydrogen for the reduction of carbonyl compounds, imines, and alkenes. Heteroaromatic compounds and even carbon dioxide have also been reduced by transfer hydrogenation reactions. In the reverse process, the oxidation of alcohols to carbonyl compounds can be achieved by iridium-catalyzed hydrogen transfer reactions, where a ketone or alkene is used as a suitable hydrogen acceptor. The reversible nature of many hydrogen transfer processes has been exploited for the racemization of alcohols, where temporary removal of hydrogen generates an achiral ketone intermediate. In addition, there is a growing body of work where temporary removal of hydrogen provides an opportunity for using alcohols as alkylating agents. In this chemistry, an iridium catalyst "borrows" hydrogen from an alcohol to give an aldehyde or ketone intermediate, which can be transformed into either an imine or alkene under the reaction conditions. Return of the hydrogen from the catalyst provides methodology for the formation of amines or C-C bonds where the only by-product is typically water.

Saidi, Ourida; Williams, Jonathan M. J.

71

Enzyme-catalyzed regioselective transesterification of peracylated sophorolipids  

Microsoft Academic Search

Regioselective transesterifications and hydrolysis of peracylated sophorolipid (SL) derivatives catalyzed by lipases was investigated. This study is the first evaluation of the lipase-catalyzed reactions on the non-lactonic SL derivatives. Four lipases, namely from porcine pancreas (PPL, Type II), Candida rugosa (AYS, TypeVII), Pseudomonas cepacia (PS-30), and Candida antarctica (Novozym 435, carrier fixed lipase fraction B) were used in anhydrous THF

Jason A Carr; Kirpal S Bisht

2003-01-01

72

Nucleoside diphosphate kinase from Mycobacterium tuberculosis cleaves single strand DNA within the human c-myc promoter in an enzyme-catalyzed reaction  

Microsoft Academic Search

The reason for secretion of nucleoside diphosphate kinase (NdK), an enzyme involved in maintaining the cellular pool of nucleoside triphosphates in both prokaryotes and eukaryotes, by Mycobacterium tuberculosis is intriguing. We recently observed that NdK from M.tuberculosis (mNdK) localizes within nuclei of HeLa and COS-1 cells and also nicks chro- mosomal DNA in situ (A. K. Saini, K. Maithal, P.

Praveen Kumar; Anjali Verma; Adesh Kumar Saini; Puneet Chopra; Pradip K. Chakraborti; Yogendra Singh; Shantanu Chowdhury

2005-01-01

73

Immobilized enzymes: Electrokinetic effects on reaction rates under external diffusion.  

PubMed

The rates of reactions catalyzed by enzymes immobilized on a nonporous solid surface have been computed employing a Nernst film model. The Nernst-Planck equations for the transport of the charged substrate and product species in the film and the Poisson equation for the distribution of electrical potential are solved numerically with the appropriate boundary conditions. The electrical charge at the surface is assumed to arise from the dissociation equilibria of the acidic and basic surface groups of the enzyme. The pH at the surface affects both the surface charge as well as the intrinsic kinetics of the enzyme-catalyzed reaction. Factors which determine the pH at the surface include the pH in the bulk solution and the release of H(+) ions in the enzyme-catalyzed reaction. The latter causes a lowering of pH at the surface, causing the reaction rate to differ from that computed assuming an equilibrium distribution of electrical potential. Another kind of nonequilibrium contribution is caused by unequal charges or diffusivities of the substrate and products, which results in a diffusion potential being set up. Two moduli are introduced to evaluate the significance of the reaction-generated lowering of pH and the diffusion potential effect. The effect of changing various parameters, e.g., reaction rate constant, substrate concentration, enzyme concentration, pH, etc., on the overall reaction rate are studied. PMID:18546127

Kalthod, D G; Uckenstein, E

1982-10-01

74

Flavoenzymes catalyzing oxidative aromatic ring-cleavage reactions.  

PubMed

2-Methyl-3-hydroxypyridine-5-carboxylic acid (MHPC) oxygenase (MHPCO) and 5-pyridoxic acid oxygenase are flavoenzymes catalyzing an aromatic hydroxylation and a ring-cleavage reaction. Both enzymes are involved in biodegradation of vitamin B6 in bacteria. Oxygen-tracer experiments have shown that the enzymes are monooxygnases since only one atom of molecular oxygen is incorporated into the products. Kinetics of MHPCO has shown that the enzyme is similar to single-component flavoprotein hydroxylases in that the binding of MHPC is required prior to the flavin reduction by NADH, and C4a-hydroperoxy-FAD and C4a-hydroxy-FAD are found as intermediates. Investigation on the protonation status of the substrate upon binding to the enzyme has shown that only the tri-ionic form of MHPC is bound at the MHPCO active site. Using a series of FAD analogues with substituents at the 8-position of the isoalloxazine ring, the oxygenation of MHPC by the C4a-hydroperoxy-FAD was shown to occur via an electrophilic aromatic substitution mechanism. Recently, the X-ray structures of MHPCO and a complex of MHPC-MHPCO at 2.1A have been reported and show the presence of nine water molecules in the enzyme active site. Based on structural data, a few residues, Tyr82, Tyr223, Arg181, were suggested to be important for catalysis of MHPCO. PMID:19728986

Chaiyen, Pimchai

2009-09-01

75

Detoxification of sulfur mustard by enzyme-catalyzed oxidation using chloroperoxidase.  

PubMed

One of the most interesting methods for the detoxification of sulfur mustard is enzyme-catalyzed oxidation. This study examined the oxidative destruction of a sulfur mustard by the enzyme chloroperoxidase (EC 1.11.1.10). Chloroperoxidase (CPO) belongs to a group of enzymes that catalyze the oxidation of various organic compounds by peroxide in the presence of a halide ion. The enzymatic oxidation reaction is affected by several factors: pH, presence or absence of chloride ion, temperature, the concentrations of hydrogen peroxide and enzyme and aqueous solubility of the substrate. The optimum reaction conditions were determined by analyzing the effects of all factors, and the following conditions were selected: solvent, Britton-Robinson buffer (pH=3) with tert-butanol (70:30 v/v); CPO concentration, 16U/mL; hydrogen peroxide concentration, 40mmol/L; sodium chloride concentration, 20mmol/L. Under these reaction conditions, the rate constant for the reaction is 0.006s(-1). The Michaelis constant, a measure of the affinity of an enzyme for a particular substrate, is 1.87×10(-3)M for this system. The Michaelis constant for enzymes with a high affinity for their substrate is in the range of 10(-5) to 10(-4)M, so this value indicates that CPO does not have a very high affinity for sulfur mustard. PMID:24034427

Popiel, S; Nawa?a, J

2013-07-05

76

Enzyme-catalyzed synthesis of heptyl-?-glycosides: Effect of water coalescence at high temperature.  

PubMed

Alkyl glycosides can be synthesized by glycosidases in organic media with limited amounts of water. These systems, however, limit the solubility of the sugar substrates and decrease reaction yields. Herein we report the enzymatic synthesis of heptyl-?-glycosides in heptanol catalyzed by a hyperthermophilic ?-glycosidase at 90°C. Our results indicate that dispersion of water in heptanol changes with time producing coalescence of water at the bottom of the reactor, playing a key role in the reaction yield. Water-soluble substrate, enzyme and products are concentrated in the aqueous phase, according to their partition coefficients, promoting side reactions that inactivate the enzyme. Reaction yield of heptyl-?-glycosides was 35% relative to lactose, at 7% water. The increase in the water phase to 12% diminished the enzyme inactivation and increased the heptyl-?-glycosides yield to 52%. Surface-active compounds, SDS and octyl glucoside, increased water dispersion but were unable to prevent coalescence. PMID:23863873

Montiel, Carmina; Bustos-Jaimes, Ismael; Bárzana, Eduardo

2013-06-28

77

Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function  

Microsoft Academic Search

Functionally analogous enzymes are those that catalyze similar reactions on similar substrates but do not share common ancestry, providing a window on the different structural strategies nature has used to evolve required catalysts. Identification and use of this information to improve reaction classification and computational annotation of enzymes newly discovered in the genome projects would benefit from systematic determination of

Daniel E. Almonacid; Emmanuel R. Yera; John B. O. Mitchell; Patricia C. Babbitt

2010-01-01

78

Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction  

Microsoft Academic Search

The Diels-Alder reaction is a cornerstone in organic synthesis, forming two carbon-carbon bonds and up to four new stereogenic centers in one step. No naturally occurring enzymes have been shown to catalyze bimolecular Diels-Alder reactions. We describe the de novo computational design and experimental characterization of enzymes catalyzing a bimolecular Diels-Alder reaction with high stereoselectivity and substrate specificity. X-ray crystallography

Justin B. Siegel; Alexandre Zanghellini; Helena M. Lovick; Gert Kiss; Abigail R. Lambert; Jennifer L. St. Clair; Jasmine L. Gallaher; Donald Hilvert; Michael H. Gelb; Barry L. Stoddard; Kendall N. Houk; Forrest E. Michael; David Baker

2010-01-01

79

Methanogen Homoaconitase Catalyzes Both Hydrolyase Reactions in Coenzyme B Biosynthesis*S?  

PubMed Central

Homoaconitase enzymes catalyze hydrolyase reactions in the ?-aminoadipate pathway for lysine biosynthesis or the 2-oxosuberate pathway for methanogenic coenzyme B biosynthesis. Despite the homology of this iron-sulfur protein to aconitase, previously studied homoaconitases catalyze only the hydration of cis-homoaconitate to form homoisocitrate rather than the complete isomerization of homocitrate to homoisocitrate. The MJ1003 and MJ1271 proteins from the methanogen Methanocaldococcus jannaschii formed the first homoaconitase shown to catalyze both the dehydration of (R)-homocitrate to form cis-homoaconitate, and its hydration is shown to produce homoisocitrate. This heterotetrameric enzyme also used the analogous longer chain substrates cis-(homo)2aconitate, cis-(homo)3aconitate, and cis-(homo)4aconitate, all with similar specificities. A combination of the homoaconitase with the M. jannaschii homoisocitrate dehydrogenase catalyzed all of the isomerization and oxidative decarboxylation reactions required to form 2-oxoadipate, 2-oxopimelate, and 2-oxosuberate, completing three iterations of the 2-oxoacid elongation pathway. Methanogenic archaeal homoaconitases and fungal homoaconitases evolved in parallel in the aconitase superfamily. The archaeal homoaconitases share a common ancestor with isopropylmalate isomerases, and both enzymes catalyzed the hydration of the minimal substrate maleate to form d-malate. The variation in substrate specificity among these enzymes correlated with the amino acid sequences of a flexible loop in the small subunits.

Drevland, Randy M.; Jia, Yunhua; Palmer, David R. J.; Graham, David E.

2008-01-01

80

Enzyme Catalyzed Regioselective Synthesis of Sucrose Fatty Acid Ester Surfactants  

Microsoft Academic Search

A commercial subtilisin preparation was used in pyridine to catalyze the regioselective conversion of sucrose and fatty acid vinyl esters into the 1?-O-acyl sucrose derivatives. The 1?-O-laury sucrose, 1?-O-myristyl sucrose and 1?-O-stearyl sucrose were obtained as the major products of these reactions. The 1?,6-di-O-acyl sucrose derivatives were also obtained as minor products. The critical micellar concentration (CMC) of each of

Tulay Polat; Hélène G. Bazin; Robert J. Linhardt

1997-01-01

81

Pressure effects on enzyme-catalyzed quantum tunneling events arise from protein-specific structural and dynamic changes.  

PubMed

The rate and kinetic isotope effect (KIE) on proton transfer during the aromatic amine dehydrogenase-catalyzed reaction with phenylethylamine shows complex pressure and temperature dependences. We are able to rationalize these effects within an environmentally coupled tunneling model based on constant pressure molecular dynamics (MD) simulations. As pressure appears to act anisotropically on the enzyme, perturbation of the reaction coordinate (donor-acceptor compression) is, in this case, marginal. Therefore, while we have previously demonstrated that pressure and temperature dependences can be used to infer H-tunneling and the involvement of promoting vibrations, these effects should not be used in the absence of atomistic insight, as they can vary greatly for different enzymes. We show that a pressure-dependent KIE is not a definitive hallmark of quantum mechanical H-tunneling during an enzyme-catalyzed reaction and that pressure-independent KIEs cannot be used to exclude tunneling contributions or a role for promoting vibrations in the enzyme-catalyzed reaction. We conclude that coupling of MD calculations with experimental rate and KIE studies is required to provide atomistic understanding of pressure effects in enzyme-catalyzed reactions. PMID:22632111

Hay, Sam; Johannissen, Linus O; Hothi, Parvinder; Sutcliffe, Michael J; Scrutton, Nigel S

2012-06-05

82

beta-D-Galactosidase from Paenibacillus thiaminolyticus catalyzing transfucosylation reactions.  

PubMed

A genomic library of bacterial strain Paenibacillus thiaminolyticus was constructed and the plasmid DNA of the clone, containing the gene encoding beta-d-galactosidase with beta-d-fucosidase activity, detected by 5-bromo-4-chloro-3-indoxyl beta-d-galactopyranoside, was sequenced. Cells of Escherichia coli BL21 (DE3) were used for production of the enzyme in the form of a histidine-tagged protein. This recombinant fusion protein was purified using Ni-NTA agarose affinity chromatography and characterized by using p-nitrophenyl beta-d-fucopyranoside (K(m) value of (1.18 +/- 0.06) mmol/L), p-nitrophenyl beta-d-galactopyranoside (K(m) value of (250 +/- 40) mmol/L), p-nitrophenyl beta-d-glucopyranoside (K(m) value of (77 +/- 6) mmol/L), and lactose (K(m) value of (206 +/- 5) mmol/L) as substrates. Optimal pH and temperature were estimated as 5.5 and 65 degrees C, respectively. According to the amino acid sequence, the molecular weight of the fusion protein was calculated to be 68.6 kDa and gel filtration chromatography confirmed the presence of the enzyme in a monomeric form. In the following step, its ability to catalyze transfucosylation reactions was tested. The enzyme was able to catalyze the transfer of fucosyl moiety to different p-nitrophenyl glycopyranosides (producing p-nitrophenyl beta-d-fucopyranosyl-(1,3)-beta-d-fucopyranoside, p-nitrophenyl beta-d-fucopyranosyl-(1,3)-alpha-d-glucopyranoside, p-nitrophenyl beta-d-fucopyranosyl-(1,3)-alpha-d-mannopyranoside, and p-nitrophenyl beta-d-fucopyranosyl-(1,6)-alpha-d-galactopyranoside) and alcohols (producing methyl beta-d-fucopyranoside, ethyl beta-d-fucopyranoside, 1-propyl beta-d-fucopyranoside, 2-propyl beta-d-fucopyranoside, 1-octyl beta-d-fucopyranoside, and 2-octyl beta-d-fucopyranoside). These results indicate the possibility of utilizing this enzyme as a promising tool for enzymatic synthesis of beta-d-fucosylated molecules. PMID:20008517

Benesová, Eva; Lipovová, Petra; Dvoráková, Hana; Králová, Blanka

2009-12-14

83

Improved enzyme stability in lipase-catalyzed synthesis of fatty acid ethyl ester from soybean oil.  

PubMed

In this work, we describe the optimization of the ethanolysis of soybean oil by the enzyme Lipozyme TL-IM in the lipase-catalyzed biodiesel synthesis and the improvement of the enzyme stability over repeated batches. The studied process variables were: reaction temperature, substrate molar ratio, enzyme content, and volume of added water. Fractional factorial design was used to analyze the variables so as to select those with higher influence on the reaction and then perform a central composite design to find the optimal reaction conditions. The optimal conditions found were: temperature, 26 degrees C; substrate molar ratio, 7.5:1 (ethanol/oil); enzyme content, 25% in relation to oil weight; and added water, 4% in relation to oil weight. Under these conditions, the yield conversion obtained was 69% in 12 h. The enzyme stability assessment in repeated batches was carried out by washing the immobilized enzyme with different solvents (n-hexane, water, ethanol, and propanol) after each batch. In the treatment with n-hexane, around 80% of the enzyme activity still remains after seven cycles of synthesis, suggesting its economical application on biodiesel production. PMID:18548204

Costa Rodrigues, Rafael; Volpato, Giandra; Wada, Keiko; Záchia Ayub, Marco Antônio

2008-06-12

84

Steroid hydroxylations: A paradigm for cytochrome P450 catalyzed mammalian monooxygenation reactions  

SciTech Connect

The present article reviews the history of research on the hydroxylation of steroid hormones as catalyzed by enzymes present in mammalian tissues. The report describes how studies of steroid hormone synthesis have played a central role in the discovery of the monooxygenase functions of the cytochrome P450s. Studies of steroid hydroxylation reactions can be credited with showing that: (a) the adrenal mitochondrial enzyme catalyzing the 11{beta}-hydroxylation of deoxycorticosterone was the first mammalian enzyme shown by O{sup 18} studies to be an oxygenase; (b) the adrenal microsomal enzyme catalyzing the 21-hydroxylation of steroids was the first mammalian enzyme to show experimentally the proposed 1:1:1 stoichiometry (substrate:oxygen:reduced pyridine nucleotide) of a monooxygenase reaction; (c) application of the photochemical action spectrum technique for reversal of carbon monoxide inhibition of the 21-hydroxylation of 17{alpha}-OH progesterone was the first demonstration that cytochrome P450 was an oxygenase; (d) spectrophotometric studies of the binding of 17{alpha}-OH progesterone to bovine adrenal microsomal P450 revealed the first step in the cyclic reaction scheme of P450, as it catalyzes the 'activation' of oxygen in a monooxygenase reaction; (e) purified adrenodoxin was shown to function as an electron transport component of the adrenal mitochondrial monooxygenase system required for the activity of the 11{beta}-hydroxylase reaction. Adrenodoxin was the first iron-sulfur protein isolated and purified from mammalian tissues and the first soluble protein identified as a reductase of a P450; (f) fractionation of adrenal mitochondrial P450 and incubation with adrenodoxin and a cytosolic (flavoprotein) fraction were the first demonstration of the reconstitution of a mammalian P450 monooxygenase reaction.

Estabrook, Ronald W. [Virginia Lazenby O'Hara Professor of Biochemistry, Ida and Cecil Green Chair in the Biomedical Sciences, Department of Biochemistry, Room Y7.206B, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX 75390-9038 (United States)]. E-mail: Ronald.estabrook@utsouthwestern.edu

2005-12-09

85

Enzyme-catalyzed oxidation facilitates the return of fluorescence for single-walled carbon nanotubes.  

PubMed

In this work, we studied enzyme-catalyzed oxidation of single-walled carbon nanotubes (SWCNTs) produced by the high-pressure carbon monoxide (HiPco) method. While oxidation via strong acids introduced defect sites on SWCNTs and suppressed their near-infrared (NIR) fluorescence, our results indicated that the fluorescence of SWCNTs was restored upon enzymatic oxidation, providing new evidence that the reaction catalyzed by horseradish peroxidase (HRP) in the presence of H2O2 is mainly a defect-consuming step. These results were further supported by both UV-vis-NIR and Raman spectroscopy. Therefore, when acid oxidation followed by HRP-catalyzed enzyme oxidation was employed, shortened (<300 nm in length) and NIR-fluorescent SWCNTs were produced. In contrast, upon treatment with myeloperoxidase, H2O2, and NaCl, the oxidized HiPco SWCNTs underwent complete oxidation (i.e., degradation). The shortened, NIR-fluorescent SWCNTs resulting from HRP-catalyzed oxidation of acid-cut HiPco SWCNTs may find applications in cellular NIR imaging and drug delivery systems. PMID:23672715

Chiu, Cheuk Fai; Barth, Brian A; Kotchey, Gregg P; Zhao, Yong; Gogick, Kristy A; Saidi, Wissam A; Petoud, Stéphane; Star, Alexander

2013-05-29

86

Iron-catalyzed asymmetric haloamination reactions.  

PubMed

The first iron(iii)/N,N'-dioxide-catalyzed asymmetric haloamination of 3-alkylidene- and 3-arylidene-indolin-2-ones was developed, affording the corresponding chiral oxindole derivatives bearing vicinal haloamine substituents with excellent results (up to 99% yield, 99% ee, >19?:?1 dr). This iron catalyst also exhibits perfect enantioselectivity for chalcone derivatives. The cooperative activation of the substrate and the reagent in concert guarantees the high stereoselectivity. PMID:23903004

Cai, Yunfei; Liu, Xiaohua; Zhou, Pengfei; Kuang, Yulong; Lin, Lili; Feng, Xiaoming

2013-08-01

87

Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction  

PubMed Central

The Diels-Alder reaction is a cornerstone in organic synthesis, forming two carbon-carbon bonds and up to four new stereogenic centers in one step. No naturally occurring enzymes have been shown to catalyze bimolecular Diels-Alder reactions. We describe the de novo computational design and experimental characterization of enzymes catalyzing a bimolecular Diels-Alder reaction with high stereoselectivity and substrate specificity. X-ray crystallography confirms that the structure matches the design for the most active of the enzymes, and binding site substitutions reprogram the substrate specificity. Designed stereoselective catalysts for carbon-carbon bond forming reactions should be broadly useful in synthetic chemistry.

Siegel, Justin B.; Zanghellini, Alexandre; Lovick, Helena M.; Kiss, Gert; Lambert, Abigail R.; St.Clair, Jennifer L.; Gallaher, Jasmine L.; Hilvert, Donald; Gelb, Michael H.; Stoddard, Barry L.; Houk, Kendall N.; Michael, Forrest E.; Baker, David

2011-01-01

88

Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction.  

PubMed

The Diels-Alder reaction is a cornerstone in organic synthesis, forming two carbon-carbon bonds and up to four new stereogenic centers in one step. No naturally occurring enzymes have been shown to catalyze bimolecular Diels-Alder reactions. We describe the de novo computational design and experimental characterization of enzymes catalyzing a bimolecular Diels-Alder reaction with high stereoselectivity and substrate specificity. X-ray crystallography confirms that the structure matches the design for the most active of the enzymes, and binding site substitutions reprogram the substrate specificity. Designed stereoselective catalysts for carbon-carbon bond-forming reactions should be broadly useful in synthetic chemistry. PMID:20647463

Siegel, Justin B; Zanghellini, Alexandre; Lovick, Helena M; Kiss, Gert; Lambert, Abigail R; St Clair, Jennifer L; Gallaher, Jasmine L; Hilvert, Donald; Gelb, Michael H; Stoddard, Barry L; Houk, Kendall N; Michael, Forrest E; Baker, David

2010-07-16

89

Atom transfer and rearrangement reactions catalyzed by methyltrioxorhenium, MTO  

SciTech Connect

Methyltrioxorhenium (MTO) catalyzes the desulfurization of thiiranes by triphenylphosphine. Enormous enhancement in rate is observed when the catalyst is pretreated with hydrogen sulfide prior to the reaction. Using 2-mercaptomethylthiophenol as a ligand, the author synthesized several model complexes to study the mechanism of this reaction. With suitable model systems, they were able to show that the active catalyst is a Re(V) species. The reactions are highly stereospecific and very tolerant to functional groups. As part of the studies, he synthesized and crystallographically characterized the first examples of neutral terminal and bridging Re(V)sulfidocomplexes. Some of these complexes undergo fast oxygen atom transfer reactions with organic and inorganic oxidants. Studies on these model complexes led them to the discovery that MTO catalyzes the selective oxidation of thiols to disulfides. This report contains the Introduction; ``Chapter 6: Isomerization of Propargylic Alcohols to Enones and Enals Catalyzed by Methylrhenium Trioxide``; and Conclusions.

Jacob, J.

1999-05-10

90

An Enzyme-Catalyzed Multistep DNA Refolding Mechanism in Hairpin Telomere Formation  

PubMed Central

Hairpin telomeres of bacterial linear chromosomes are generated by a DNA cutting–rejoining enzyme protelomerase. Protelomerase resolves a concatenated dimer of chromosomes as the last step of chromosome replication, converting a palindromic DNA sequence at the junctions between chromosomes into covalently closed hairpins. The mechanism by which protelomerase transforms a duplex DNA substrate into the hairpin telomeres remains largely unknown. We report here a series of crystal structures of the protelomerase TelA bound to DNA that represent distinct stages along the reaction pathway. The structures suggest that TelA converts a linear duplex substrate into hairpin turns via a transient strand-refolding intermediate that involves DNA-base flipping and wobble base-pairs. The extremely compact di-nucleotide hairpin structure of the product is fully stabilized by TelA prior to strand ligation, which drives the reaction to completion. The enzyme-catalyzed, multistep strand refolding is a novel mechanism in DNA rearrangement reactions.

Shi, Ke; Huang, Wai Mun; Aihara, Hideki

2013-01-01

91

Adventures in Gold-Catalyzed Cascade Reactions and Rearrangements  

Microsoft Academic Search

Gold-catalyzed organic transformations have been a hot topic of research in synthetic organic community over the last few years. Amazingly, most of the reactions can be performed under mild conditions using a catalytic amount of gold complexes. One of the widely reported reactions using gold catalysts is heterocyclization that involves an activation of a pi-system followed by a nucleophilic attack

Dinesh Vinod Vidhani

2010-01-01

92

Insights into the "free state" enzyme reaction kinetics in nanoconfinement.  

PubMed

The investigation of enzyme reaction kinetics in nanoconfined spaces mimicking the conditions in living systems is of great significance. Here, a nanofluidics chip integrated with an electrochemical detector has been designed for studying "free state" enzyme reaction kinetics in nanoconfinement. The nanofluidics chip is fabricated using the UV-ablation technique developed in our group. The enzyme and substrate solutions are simultaneously supplied from two single streams into a nanochannel through a Y-shaped junction. The laminar flow forms in the front of the nanochannel, then the two liquids fully mix at their downstream where a homogeneous enzyme reaction occurs. The "free state" enzyme reaction kinetics in nanoconfinement can thus be investigated in this laminar flow based nanofluidics device. For demonstration, glucose oxidase (GOx) is chosen as the model enzyme, which catalyzes the oxidation of beta-d-glucose. The reaction product hydrogen peroxide (H2O2) can be electrochemically detected by a microelectrode aligning to the end of nanochannel. The steady-state electrochemical current responding to various glucose concentrations is used to evaluate the activity of the "free state" GOx under nanoconfinement conditions. The effect of liquid flow rate, enzyme concentration, and nanoconfinement on reaction kinetics has been studied in detail. Results show that the "free state" GOx activity increases significantly compared to the immobilized enzyme and bath system, and the GOx reaction rate in the nanochannel is two-fold faster than that in bulk solution, demonstrating the importance of "free state" and spatial confinement for the enzyme reaction kinetics. The present approach provides an effective method for exploiting the "free state" enzyme activity in nanospatial confinement. PMID:23429726

Wang, Chen; Ye, De-Kai; Wang, Yun-Yi; Lu, Tao; Xia, Xing-Hua

2013-04-21

93

Diffusion and reaction in an immobilized enzyme starch saccharification catalyst  

Microsoft Academic Search

Effectiveness factors were predicted from measurements of basic parameters made on single oligosaccharides, and the prediction\\u000a was compared to experimental effec tiveness factors for the reaction of each oligosaccharide in the immobilized enzyme catalyst.\\u000a Kinetic parameters were obtained for the hydrolysis of each oligosaccharide catalyzed by soluble glucoamylase, and were fit\\u000a with a subsite model equation capable of generalization to

D. A. Sirotti; A. H. Emery

1984-01-01

94

Stereochemistry and mechanism of a new single-turnover, half-transamination reaction catalyzed by the tryptophan synthase alpha 2 beta 2 complex  

SciTech Connect

Tryptophan synthase is a versatile enzyme that catalyzes a wide variety of pyridoxal phosphate dependent reactions that are also catalyzed in model systems. These include beta-replacement, beta-elimination, racemization, and transamination reactions. We now show that the apo-alpha 2 beta 2 complex of tryptophan synthase will bind two unnatural substrates, pyridoxamine phosphate and indole-3-pyruvic acid, and will convert them by a single-turnover, half-transamination reaction to pyridoxal phosphate and L-tryptophan, the natural coenzyme and a natural product, respectively. This enzyme-catalyzed reaction is more rapid and more stereospecific than an analogous model reaction. The pro-S 4'-methylene proton of pyridoxamine phosphate is removed during the reaction, and the product is primarily L-tryptophan. We conclude that pyridoxal phosphate enzymes may be able to catalyze some unnatural reactions involving bound reactants and bound coenzyme since the coenzyme itself has the intrinsic ability to promote a variety of reactions.

Miles, E.W.

1987-01-27

95

Enantioselective aldol reactions catalyzed by chiral phosphine oxides.  

PubMed

The development of enantioselective aldol reactions catalyzed by chiral phosphine oxides is described. The aldol reactions presented herein do not require the prior preparation of the masked enol ethers from carbonyl compounds as aldol donors. The reactions proceed through a trichlorosilyl enol ether intermediate, formed in situ from carbonyl compounds, which then acts as the aldol donor. Phosphine oxides activate the trichlorosilyl enol ethers to afford the aldol adducts with high stereoselectivities. This procedure was used to realize a directed cross-aldol reaction between ketones and two types of double aldol reactions (a reaction at one/two ? position(s) of a carbonyl group) with high diastereo- and enantioselectivities. PMID:23828817

Kotani, Shunsuke; Sugiura, Masaharu; Nakajima, Makoto

2013-07-04

96

Rearrangement Reactions Catalyzed by Cytochrome P450s  

PubMed Central

Cytochrome P450s promote a variety of rearrangement reactions both as a consequence of the nature of the radical and other intermediates generated during catalysis, and of the neighboring structures in the substrate that can interact either with the initial radical intermediates or with further downstream products of the reactions. This article will review several kinds of previously published cytochrome P450-catalyzed rearrangement reactions, including changes in stereochemistry, radical clock reactions, allylic rearrangements, “NIH” and related shifts, ring contractions and expansions, and cyclizations that result from neighboring group interactions. Although most of these reactions can be carried out by many members of the cytochrome P450 superfamily, some have only been observed with select P450s, including some reactions that are catalyzed by specific endoperoxidases and cytochrome P450s found in plants.

Ortiz de Montellano, Paul R.; Nelson, Sidney D.

2010-01-01

97

Electrostatic effects on the rates of DNA-catalyzed reactions  

Microsoft Academic Search

Diol-epoxide metabolites of many genotoxic polycyclic aromatic hydrocarbons are hydrolyzed to tetraols in a detoxification reaction. The hydrolysis reaction has both spontaneous and acid-catalyzed components; moreover, the reaction rate increases in the presence of DNA. The best studied of these diol epoxide metabolites are the trans 7,8 diol-9,10 epoxides of benzo[a]pyrene: anti-BPDE, the proximate carcinogen, in which the oxirane ring

George R. Pack; Linda Wong

1996-01-01

98

Enzyme catalyzed electricity-driven water softening system.  

PubMed

Hardness in water, which is caused by divalent cations such as calcium and magnesium ions, presents a major water quality problem. Because hard water must be softened before use in residential applications, there is great interest in the saltless water softening process because, unlike ion exchange softeners, it does not introduce additional ions into water. In this study, a saltless hardness removal driven by bioelectrochemical energy produced through enzymatic oxidation of glucose was proposed and investigated. Glucose dehydrogenase was coated on a carbon electrode to catalyze glucose oxidation in the presence of NAD? as a cofactor/mediator and methylene green as an electrocatalyst. The results showed that electricity generation stimulated hardness removal compared with non-electricity conditions. The enzymatic water softener worked upon a 6h batch operation per day for eight days, and achieved an average hardness removal of 46% at a high initial concentration of 800 mg/L as CaCO?. More hardness was removed at a lower initial concentration. For instance, at 200mg/L as CaCO? the enzymatic water softener removed 76.4±4.6% of total hardness. The presence of magnesium ions decreased hardness removal because of its larger hydrated radius than calcium ions. The enzymatic water softener removed 70-80% of total hardness from three actual hard water samples. These results demonstrated a proof-of-concept that enzyme catalyzed electricity generation can be used to soften hard water. PMID:23040397

Arugula, Mary A; Brastad, Kristen S; Minteer, Shelley D; He, Zhen

2012-08-29

99

Nickel-catalyzed coupling reactions of alkenes  

Microsoft Academic Search

Several reactions of simple, unactivated alkenes with electrophiles under Ni(0) catalysis are discussed. The coupling of olefins with aldehydes and silyl triflates provides allylic or homoallylic alcohol derivatives, depending on the supporting ligands and, to a lesser extent, the substrates employed. Reaction of alkenes with isocyanates yields N-alkyl acrylamides. In these methods, alkenes act as the functional equivalents of alkenyl-

Sze-Sze Ng; Chun-Yu Ho; Kristin D. Schleicher; Timothy F. Jamison

2008-01-01

100

Nickel-Catalyzed Coupling Reactions of Alkenes.  

PubMed

Several reactions of simple, unactivated alkenes with electrophiles under nickel(0) catalysis are discussed. The coupling of olefins with aldehydes and silyl triflates provides allylic or homoallylic alcohol derivatives, depending on the supporting ligands and, to a lesser extent, the substrates employed. Reaction of alkenes with isocyanates yields N-alkyl acrylamides. In these methods, alkenes act as the functional equivalents of alkenyl- and allylmetal reagents. PMID:21814295

Ng, Sze-Sze; Ho, Chun-Yu; Schleicher, Kristin D; Jamison, Timothy F

2008-01-01

101

Nickel-Catalyzed Coupling Reactions of Alkenes  

PubMed Central

Several reactions of simple, unactivated alkenes with electrophiles under nickel(0) catalysis are discussed. The coupling of olefins with aldehydes and silyl triflates provides allylic or homoallylic alcohol derivatives, depending on the supporting ligands and, to a lesser extent, the substrates employed. Reaction of alkenes with isocyanates yields N-alkyl acrylamides. In these methods, alkenes act as the functional equivalents of alkenyl- and allylmetal reagents.

Ng, Sze-Sze; Ho, Chun-Yu; Schleicher, Kristin D.; Jamison, Timothy F.

2011-01-01

102

Microemulsions as vehicles for lipase catalyzed reactions  

Microsoft Academic Search

Microemulsions have proved to be excellent reaction media for several types of enzymatic lipid trnasformations. Using a 1,3-specific\\u000a lipase transesterification, selective hydrolysis and glycerolysis reactions have been performed in good yield with a high\\u000a degree of regioselectivity. The rate of transesterification was found to be highly dependent on the type of unsaturation of\\u000a the fatty acid residues; a double bond

K. Holmberg; E. Österberg

103

Enzyme dynamics and tunneling enhanced by compression in the hydrogen abstraction catalyzed by soybean lipoxygenase-1.  

PubMed

A fully microscopical simulation of the rate-limiting hydrogen abstraction catalyzed by soybean lipoxygenase-1 (SLO-1) has been carried out. This enzyme exhibits the largest, and weakly temperature dependent, experimental H/D kinetic isotope effect (KIE) reported for a biological system. The theoretical model used here includes the complete enzyme with a solvation shell of water molecules, the Fe(III)-OH- cofactor, and the linoleic acid substrate. We have used a hybrid QM(PM3/d-SRP)/MM method to describe the potential energy surface of the whole system, and the ensemble-averaged variational transition-state theory with multidimensional tunneling (EA-VTST/MT) to calculate the rate constant and the primary KIE. The computational results show that the compression of the wild-type active site enzyme results in the huge contribution of tunneling (99%) to the rate of the hydrogen abstraction. Importantly, the active site becomes more flexible in the Ile553Ala mutant reactant complex simulation (for which a markedly temperature dependent KIE has been experimentally determined), thus justifying the proposed key role of the gating promoting mode in the reaction catalyzed by SLO-1. Finally, the results indicate that the calculated KIE for the wild-type enzyme has an important dependence on the barrier width. PMID:17134234

Tejero, Ismael; Garcia-Viloca, Mireia; Gonzalez-Lafont, Angels; Lluch, José M; York, Darrin M

2006-12-01

104

Palladium-Catalyzed Coupling Reactions of Aryl Chlorides  

Microsoft Academic Search

Collectively, palladium-catalyzed cou- pling reactions represent some of the most powerful and versatile tools avail- able to synthetic organic chemists. Their widespread popularity stems in part from the fact that they are gen- erally tolerant to a large number of functional groups, which allows them to be employed in a wide range of applications. However, for many years a major

Adam F. Littke; Gregory C. Fu

2002-01-01

105

Adenosyl radical: reagent and catalyst in enzyme reactions.  

PubMed

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 B(12), 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. PMID:20191656

Marsh, E Neil G; Patterson, Dustin P; Li, Lei

2010-03-22

106

Cross-ligation and exchange reactions catalyzed by hairpin ribozymes.  

PubMed Central

The negative strand of the satellite RNA of tobacco ringspot virus (sTobRV(-)) contains a hairpin catalytic domain that shows self-cleavage and self-ligation activities in the presence of magnesium ions. We describe here that the minimal catalytic domain can catalyze a cross-ligation reaction between two kinds of substrates in trans. The cross-ligated product increased when the reaction temperature was decreased during the reaction from 37 degrees C to 4 degrees C. A two-stranded hairpin ribozyme, divided into two fragments between G45 and U46 in a hairpin loop, showed higher ligation activity than the nondivided ribozyme. The two stranded ribozyme also catalyzed an exchange reaction of the 3'-portion of the cleavage site. Images

Komatsu, Y; Koizumi, M; Sekiguchi, A; Ohtsuka, E

1993-01-01

107

Investigation of the rh-catalyzed asymmetric reductive aldol reaction. Expanded scope based on reaction analysis.  

PubMed

[reaction: see text] A series of experiments are described that suggest that the Rh-catalyzed reductive aldol reaction proceeds by addition of a Rh(I) hydride, generated in situ, to the reacting acrylate followed by a stereochemistry-controlling aldol addition reaction. On the basis of this hypothesis, reaction conditions are engineered that allow for increased substrate scope. PMID:15228266

Russell, Albert E; Fuller, Nathan O; Taylor, Steven J; Aurriset, Pauline; Morken, James P

2004-07-01

108

(Ligand intermediates in metal-catalyzed reactions)  

SciTech Connect

This report consists of sections on sigma bond complexes of alkenes, a new carbon-hydrogen bond activation reaction of alkene complexes, carbon-hydrogen bond migrations in alkylidene complexes, carbon- hydrogen bond migrations in alkyne complexes, synthesis, structure and reactivity of C{sub x} complexes, synthesis and reactivity of alcohol and ether complexes, new catalysts for the epimerization of secondary alcohols; carbon-hydrogen bond activation in alkoxide complexes, pi/sigma equilibria in metal/O=CXX' complexes, and other hydrocarbon ligands; miscellaneous.(WET)

Not Available

1992-01-01

109

Mild and efficient cyanuric chloride catalyzed Pictet-Spengler reaction  

PubMed Central

Summary A practical, mild and efficient protocol for the Pictet–Spengler reaction catalyzed by cyanuric chloride (trichloro-1,3,5-triazine, TCT) is described. The 6-endo cyclization of tryptophan/tryptamine and modified Pictet–Spengler substrates with both electron-withdrawing and electron-donating aldehydes was carried out by using a catalytic amount of TCT (10 mol %) in DMSO under a nitrogen atmosphere. TCT catalyzed the Pictet–Spengler reaction involving electron-donating aldehydes in excellent yield. Thus, it has a distinct advantage over the existing methodologies where electron-donating aldehydes failed to undergo 6-endo cyclization. Our methodology provided broad substrate scope and diversity. This is indeed the first report of the use of TCT as a catalyst for the Pictet–Spengler reaction.

Sharma, Ashish; Singh, Mrityunjay; Rai, Nitya Nand

2013-01-01

110

Stau-catalyzed big-bang nucleosynthesis reactions  

SciTech Connect

We study the new type of big-bang nucleosynthesis (BBN) reactions that are catalyzed by a hypothetical long-lived negatively charged, massive leptonic particle (called X{sup -}) such as the supersymmetric (SUSY) particle stau, the scalar partner of the tau lepton. It is known that if the X{sup -} particle has a lifetime of tau{sub X} > or approx. 10{sup 3} s, it can capture a light element previously synthesized in standard BBN and form a Coulombic bound state and induces various types of reactions in which X{sup -} acts as a catalyst. Some of these X{sup -} catalyzed reactions have significantly large cross sections so that the inclusion of the reactions into the BBN network calculation can markedly change the abundances of some elements. We use a high-accuracy three-body calculation method developed by the authors and provide precise cross sections and rates of these catalyzed BBN reactions for use in the BBN network calculation.

Kamimura, Masayasu [Department of Physics, Kyushu University, Fukuoka 812-8581 (Japan); Kino, Yasushi [Department of Physics, Tohoku University, Sendai 980-8578 (Japan); Hiyama, Emiko [RIKEN Nishina Center, Wako 351-0198 (Japan)

2010-06-01

111

Mammalian cytochrome P450 enzymes catalyze the phenol-coupling step in endogenous morphine biosynthesis.  

PubMed

A cytochrome P450 (P450) enzyme in porcine liver that catalyzed the phenol-coupling reaction of the substrate (R)-reticuline to salutaridine was previously purified to homogeneity (Amann, T., Roos, P. H., Huh, H., and Zenk, M. H. (1995) Heterocycles 40, 425-440). This reaction was found to be catalyzed by human P450s 2D6 and 3A4 in the presence of (R)-reticuline and NADPH to yield not a single product, but rather (-)-isoboldine, (-)-corytuberine, (+)-pallidine, and salutaridine, the para-ortho coupled established precursor of morphine in the poppy plant and most likely also in mammals. (S)-Reticuline, a substrate of both P450 enzymes, yielded the phenol-coupled alkaloids (+)-isoboldine, (+)-corytuberine, (-)-pallidine, and sinoacutine; none of these serve as a morphine precursor. Catalytic efficiencies were similar for P450 2D6 and P450 3A4 in the presence of cytochrome b(5) with (R)-reticuline as substrate. The mechanism of phenol coupling is not yet established; however, we favor a single cycle of iron oxidation to yield salutaridine and the three other alkaloids from (R)-reticuline. The total yield of salutaridine formed can supply the 10 nm concentration of morphine found in human neuroblastoma cell cultures and in brain tissues of mice. PMID:19561069

Grobe, Nadja; Zhang, Baichen; Fisinger, Ursula; Kutchan, Toni M; Zenk, Meinhart H; Guengerich, F Peter

2009-06-26

112

Mammalian Cytochrome P450 Enzymes Catalyze the Phenol-coupling Step in Endogenous Morphine Biosynthesis*  

PubMed Central

A cytochrome P450 (P450) enzyme in porcine liver that catalyzed the phenol-coupling reaction of the substrate (R)-reticuline to salutaridine was previously purified to homogeneity (Amann, T., Roos, P. H., Huh, H., and Zenk, M. H. (1995) Heterocycles 40, 425–440). This reaction was found to be catalyzed by human P450s 2D6 and 3A4 in the presence of (R)-reticuline and NADPH to yield not a single product, but rather (?)-isoboldine, (?)-corytuberine, (+)-pallidine, and salutaridine, the para-ortho coupled established precursor of morphine in the poppy plant and most likely also in mammals. (S)-Reticuline, a substrate of both P450 enzymes, yielded the phenol-coupled alkaloids (+)-isoboldine, (+)-corytuberine, (?)-pallidine, and sinoacutine; none of these serve as a morphine precursor. Catalytic efficiencies were similar for P450 2D6 and P450 3A4 in the presence of cytochrome b5 with (R)-reticuline as substrate. The mechanism of phenol coupling is not yet established; however, we favor a single cycle of iron oxidation to yield salutaridine and the three other alkaloids from (R)-reticuline. The total yield of salutaridine formed can supply the 10 nm concentration of morphine found in human neuroblastoma cell cultures and in brain tissues of mice.

Grobe, Nadja; Zhang, Baichen; Fisinger, Ursula; Kutchan, Toni M.; Zenk, Meinhart H.; Guengerich, F. Peter

2009-01-01

113

Enzyme-catalyzed assembly of gold nanoparticles for visualized screening of DNA base excision repair.  

PubMed

Activity screening of DNA base excision repair (BER) enzymes is a crucial step for understanding numerous fundamental biochemical processes. A novel label-free homogeneous technique is developed for visualized uracil-DNA glycosylase (UDG) activity assay using gold nanoparticles (AuNPs). This strategy relies on the enzyme-catalyzed assembly of AuNPs decorated with DNA probes. In the presence of endonuclease IV (an enzyme which can further hydrolyze the products from UDG-catalyzed reaction), the substrate DNA selectively interacts with UDG followed by the efficient release of a single-strand probe. The released single-strand probe then makes the network-like assembly of decorated AuNPs to provide a visible signal for UDG activity. This strategy that can be performed in a label-free homogeneous assay format improved the duration, the simplicity and the throughput of UDG activity screening. The results provided in the present study revealed that this strategy could hold great potential as a robust, convenient and visualized platform for activity screening of uracil-DNA glycosylases with high selectivity and desirable sensitivity. PMID:23141341

Nguyen, Van-Trong; Le, Dinh-Vu; Nie, Chan; Zhou, Dian-Ming; Wang, Yu-Zhi; Tang, Li-Juan; Jiang, Jian-Hui; Yu, Ru-Qin

2012-08-01

114

Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction.  

PubMed

The proton transfer reaction between the substrate nitroethane and Asp-402 catalyzed by nitroalkane oxidase and the uncatalyzed process in water have been investigated using a path-integral free-energy perturbation method. Although the dominating effect in rate acceleration by the enzyme is the lowering of the quasiclassical free energy barrier, nuclear quantum effects also contribute to catalysis in nitroalkane oxidase. In particular, the overall nuclear quantum effects have greater contributions to lowering the classical barrier in the enzyme, and there is a larger difference in quantum effects between proton and deuteron transfer for the enzymatic reaction than that in water. Both experiment and computation show that primary KIEs are enhanced in the enzyme, and the computed Swain-Schaad exponent for the enzymatic reaction is exacerbated relative to that in the absence of the enzyme. In addition, the computed tunneling transmission coefficient is approximately three times greater for the enzyme reaction than the uncatalyzed reaction, and the origin of the difference may be attributed to a narrowing effect in the effective potentials for tunneling in the enzyme than that in aqueous solution. PMID:19926855

Major, Dan T; Heroux, Annie; Orville, Allen M; Valley, Michael P; Fitzpatrick, Paul F; Gao, Jiali

2009-11-19

115

Differential Quantum Tunneling Contributions in Nitroalkane Oxidase Catalyzed and the Uncatalyzed Proton Transfer Reaction  

SciTech Connect

The proton transfer reaction between the substrate nitroethane and Asp-402 catalyzed by nitroalkane oxidase and the uncatalyzed process in water have been investigated using a path-integral free-energy perturbation method. Although the dominating effect in rate acceleration by the enzyme is the lowering of the quasiclassical free energy barrier, nuclear quantum effects also contribute to catalysis in nitroalkane oxidase. In particular, the overall nuclear quantum effects have greater contributions to lowering the classical barrier in the enzyme, and there is a larger difference in quantum effects between proton and deuteron transfer for the enzymatic reaction than that in water. Both experiment and computation show that primary KIEs are enhanced in the enzyme, and the computed Swain-Schaad exponent for the enzymatic reaction is exacerbated relative to that in the absence of the enzyme. In addition, the computed tunneling transmission coefficient is approximately three times greater for the enzyme reaction than the uncatalyzed reaction, and the origin of the difference may be attributed to a narrowing effect in the effective potentials for tunneling in the enzyme than that in aqueous solution.

Major , D.; Heroux , A; Orville , A; Valley , M; Fitzpatrick , P; Gao , J

2009-01-01

116

Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction  

PubMed Central

The proton transfer reaction between the substrate nitroethane and Asp-402 catalyzed by nitroalkane oxidase and the uncatalyzed process in water have been investigated using a path-integral free-energy perturbation method. Although the dominating effect in rate acceleration by the enzyme is the lowering of the quasiclassical free energy barrier, nuclear quantum effects also contribute to catalysis in nitroalkane oxidase. In particular, the overall nuclear quantum effects have greater contributions to lowering the classical barrier in the enzyme, and there is a larger difference in quantum effects between proton and deuteron transfer for the enzymatic reaction than that in water. Both experiment and computation show that primary KIEs are enhanced in the enzyme, and the computed Swain-Schaad exponent for the enzymatic reaction is exacerbated relative to that in the absence of the enzyme. In addition, the computed tunneling transmission coefficient is approximately three times greater for the enzyme reaction than the uncatalyzed reaction, and the origin of the difference may be attributed to a narrowing effect in the effective potentials for tunneling in the enzyme than that in aqueous solution.

Major, Dan T.; Heroux, Annie; Orville, Allen M.; Valley, Michael P.; Fitzpatrick, Paul F.; Gao, Jiali

2009-01-01

117

Spectroscopy of an Enzyme Reaction  

Microsoft Academic Search

IF a suitable amount of monoethyl-hydrogen peroxide is added to an active preparation of liver catalase at pH 7, the enzyme spectrum disappears instantly, and two new absorption bands in the green range of the spectrum appear. In the course of a few minutes, at room temperature, the new absorption bands decrease in intensity, and simultaneously the original enzyme spectrum

Kurt G. Stern

1935-01-01

118

Enzyme-free colorimetric bioassay based on gold nanoparticle-catalyzed dye decolorization.  

PubMed

A novel, enzyme-free and aptamer-based colorimetric platform for protein detection has been developed, which takes advantage of aptamer-functionalized magnetic beads (MBs) for target capture, concentration and separation, and aptamer-conjugated gold nanoparticle (AuNP)-catalyzed color bleaching reaction of methyl orange (MO) to generate the colorimetric signals. It was demonstrated that the proposed colorimetric sensing strategy enables simple, cost-effective, sensitive and specific thrombin detection without the use of any enhancing solutions and enzymes. Herein, by naked eye observation, we can detect the human thrombin with a detection limit of approximately 320 pM, which can be further decreased to 30 pM with the help of a UV-vis instrument. In addition, this method also works for targets with two or more binding sites. PMID:23223492

Li, Wei; Li, Jie; Qiang, Weibing; Xu, Jingjuan; Xu, Danke

2012-12-05

119

Lipase-catalyzed reactions at different surfaces.  

PubMed

Starting from gold chips, we have tailor-made three surfaces by the self-assembly monolayer technique: one entirely hydrophobic, one hydrophobic with dispersed carboxyl groups, and one hydrophilic, containing hydroxyl groups. Rhizomucor miehei lipase has been adsorbed to the hydrophobic and the hydrophilic surfaces and covalently bound to the surface containing carboxyl groups. The adsorption of two substrates-capric acid (decanoic acid) and monocaprin-on the lipase-covered surfaces was monitored by the surface plasmon resonance (SPR) technique. Biocatalysis was also performed in the SPR instrument by circulating a solution of the substrate, dissolved in an 85:15 water-glycerol mixture at a(w) = 0.81, through the instrument, thus exposing the capric acid or the monocaprin to the lipase-covered surfaces. The product composition was found to depend on the type of surface used. Lipase adsorbed at the hydrophilic surface favored hydrolysis, and capric acid was the main product formed when monocaprin was used as substrate. Lipase adsorbed at a hydrophobic surface and, in particular, lipase covalently bound to a hydrophobic surface favored condensation. More dicaprin than capric acid was formed in experiments with monocaprin as the substrate. Reactions performed outside the SPR instrument showed that small amounts of triglyceride were also formed under these conditions. We believe that this work constitutes the first example of the SPR instrument being used for in-situ biotransformation. PMID:16952258

Reis, P; Holmberg, K; Debeche, T; Folmer, B; Fauconnot, L; Watzke, H

2006-09-12

120

Density Functional Study of Mo-Carbonyl-Catalyzed Alkynol Cycloisomerization: Comparison with W-Catalyzed Reaction  

PubMed Central

Mo-catalyzed endo-cycloisomerizations of alkynes tethered to alcohols have been studied using density functional theory, and comparisons were made with the W-catalyzed reaction. The cycloisomerization is initiated with the formation of metal alkyne ? complex and is followed by the rate-determining step, which transforms the ? complex to a vinylidene carbene complex, considered to be critical for endo-mode cyclization. Several different alkynols have been selected to investigate five- and six-membered ring endo-cycloisomerizations in the presence of Mo(CO)5 catalyst. The energy barriers calculated for five- and six-membered ring cycloisomerizations are within a range of 25–30 kcal/mol for most cases studied, showing no significant energy difference between the two metals. The stabilization effect of THF and Et3N solvents and the substitution reaction of THF by alkynol substrates in the reaction process with Mo and W complexes are studied as well. The principal difference between Mo- and W-catalyzed cycloisomerization processes appears to be the initial formation of a ? complex, which is more stabilizing for formation of the W-alkyne vs Mo-alkyne complexes.

Nowroozi-Isfahani, Taraneh; Musaev, Djamaladdin G.; McDonald, Frank E.; Morokuma, Keiji

2006-01-01

121

Mechanism-based modulator discovery for sirtuin-catalyzed deacetylation reaction.  

PubMed

Silent information regulator 2 (Sir2) enzymes or sirtuins are a family of evolutionarily conserved intracellular protein deacetylases that can catalyze the acetyl group removal from the specific N?-acetyl-lysine (AcK) side chains on a variety of proteins from all kingdoms of life. Yeast Sir2 was the first sirtuin identified, and so far seven sirtuins (i.e. SIRT1-7) have been found in mammals including humans. The sirtuin-catalyzed deacetylation reaction has captured tremendous interest during the past a few years because of (i) its increasingly demonstrated importance in many crucial biological processes such as gene transcription, metabolism, and aging, and thus its therapeutic potential for metabolic and age-related diseases and cancer, and (ii) its unique deacetylation chemistry. Specifically, the sirtuin-catalyzed AcK side chain deacetylation is not merely an amide hydrolysis reaction, instead is coupled to the nicotinamide cleavage from ?-nicotinamide adenine dinucleotide (?-NAD+ or NAD+) with the generation of three enzymatic products, i.e. the deacetylated protein species, nicotinamide, and 2'-O-acetyl-ADP-ribose (2'-O-AADPR). Here the author would like to review the past endeavors on developing mechanism-based sirtuin modulators (inhibitors and activators). The first part of this article will provide an updated mechanistic picture of the sirtuin-catalyzed deacetylation reaction. The second part will be focused on how the mechanistic knowledge has been exploited for the design of effective sirtuin modulators. PMID:22876953

Zheng, Weiping

2013-01-01

122

Adenosyl radical: reagent and catalyst in enzyme reactions  

PubMed Central

Lead in 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. In contrast, there has been a recent explosion in the number radical AdoMet enzymes discovered that catalyze a remarkably wide range of chemically challenging reactions. 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 may be active in aerobic organisms including humans.

Patterson, Dustin P.

2010-01-01

123

Flavoprotein hydroxylase PgaE catalyzes two consecutive oxygen-dependent tailoring reactions in angucycline biosynthesis.  

PubMed

A simplified model system composed of a NADPH-dependent flavoprotein hydroxylase PgaE and a short-chain alcohol dehydrogenase/reductase (SDR) CabV was used to dissect a multistep angucycline modification redox cascade into several subreactions in vitro. We demonstrate that the two enzymes are sufficient for the conversion of angucycline substrate 2,3-dehydro-UWM6 to gaudimycin C. The flavoenzyme PgaE is shown to be responsible for two consecutive NADPH- and O(2)-dependent reactions, consistent with the enzyme-catalyzed incorporation of oxygen atoms at C-12 and C-12b in gaudimycin C. The two reactions do not significantly overlap, and the second catalytic cycle is initiated only after the original substrate 2,3-dehydro-UWM6 is nearly depleted. This allowed us to isolate the product of the first reaction at limiting NADPH concentrations and allowed the study of the qualitative and kinetic properties of the separated reactions. Dissection of the reaction cascade also allowed us to establish that the SDR reductase CabV catalyzes the final biosynthetic step, which is closely coupled to the second PgaE reaction. In the absence of CabV, the complete PgaE reaction leads invariably to product degradation, whereas in its presence, the reaction yields the final product, gaudimycin C. The result implies that the C-6 ketoreduction step catalyzed by CabV is required for stabilization of a reactive intermediate. The close relationship between PgaE and CabV would explain previous in vivo observations: why the absence of a reductase gene may result in the lack of C-12b-oxygenated species and, vice versa, why all C-12b-oxygenated angucyclines appear to have undergone reduction at position C-6. PMID:21595438

Kallio, Pauli; Patrikainen, Pekka; Suomela, Jukka-Pekka; Mäntsälä, Pekka; Metsä-Ketelä, Mikko; Niemi, Jarmo

2011-05-27

124

Enzyme reactions in a multicompartment electrolyzer with isoelectrically trapped enzymes.  

PubMed

The possibility of performing bioconversions under an electric field is here reported. A system is described by which the enzyme is trapped by an isoelectric mechanism between two zwitterionic membranes having pI values encompassing the isoelectric point of the enzyme. The enzyme is loaded into a multicompartment electrolyzer and kept operating under an electric field, which will continuously harvest the reaction product. Since, under focusing conditions, all buffering ions will vacate the reaction chamber at steady state, the buffering ion is trapped into the enzyme chamber by using amphoteric buffers co-isoelectric with the enzyme. As an example of such "isoelectrically immobilized' reactor, the enzyme beta-hydroxysteroid dehydrogenase is blocked into an isoelectric trap delimited by a pI 8.0 and a pI 6.5 membranes. 100 mM histidine (pI 7.47) is co-immobilized by the same isoelectric mechanism into the enzyme chamber. The dehydrocholic acid substrate (3,7,12-trioxo-5 beta-cholanoic acid) and reduced co-factor (NADH) are continuously infused into the enzyme chamber and the product (3 beta-hydroxy-7,12-dioxo- 5 beta-cholanoic acid, a compound of pharmaceutical interest) and the oxidized co-factor (NAD+) collected, separately, into the two neighbouring chambers at the anodic side. Advantages: in a soluble form, the enzyme maintains the reaction kinetics of the free soluble form. Additionally, the reaction product and exhausted co-factor can be recovered by electrophoretic transport. PMID:8675964

Chiari, M; Dell'Orto, N; Mendozza, M; Carrea, G; Righetti, P G

1996-02-01

125

ENZYME-CATALYZED GEL-FORMATION OF GELATIN AND CHITOSAN. POTENTIAL FOR IN SITU APPLICATIONS  

Technology Transfer Automated Retrieval System (TEKTRAN)

We compared the ability of two enzymes to catalyze the formation of gels from solutions of gelatin and chitosan. A microbial transglutaminase, currently under investigation for food applications, was observed to catalyze the formation of strong and permanent gels from gelatin solutions. Chitosan w...

126

Arabidopsis mutants affected in the transcriptional control of allene oxide synthase, the enzyme catalyzing the entrance step in octadecanoid biosynthesis  

Microsoft Academic Search

Allene oxide synthase (AOS) catalyzes the entrance reaction in the biosynthesis of the octadecanoids 12-oxophytodienoic acid (OPDA) and jasmonic acid (JA). The enzyme is feedback-regulated by JA and thus a target of the JA-signalling pathway. A fusion genetic approach was used to isolate mutants in this signalling pathway. Seeds from transgenic Arabidopsis thaliana plants expressing the Escherichia coli uidA gene

Ines I. Kubigsteltig; Elmar W. Weiler

2003-01-01

127

An Immobilized-EnzymeFlow-EnthalpimetricAnalyzer: Applicationto GlucoseDeterminationby Direct PhosphorylationCatalyzed by Hexokinase  

Microsoft Academic Search

A novel flow-enthalpimetric analyzer is described and its use demonstrated by an analysis in which glucose is de- termined by its hexokinase-catalyzed phosphorylation reaction. The method depends on measurement of the temperature differential across a column packed with glass-supported immobilized enzyme. Sample volumes of 120 tl can be usedto obtain a calibration curve that is linear up to 25 mmol

Larry D. Bowers; Peter W. Carr

128

Hydrogen Tunneling in Enzyme Reactions  

NASA Astrophysics Data System (ADS)

Primary and secondary protium-to-tritium (H/T) and deuterium-to-tritium (D/T) kinetic isotope effects for the catalytic oxidation of benzyl alcohol to benzaldehyde by yeast alcohol dehydrogenase (YADH) at 25 degrees Celsius have been determined. Previous studies showed that this reaction is nearly or fully rate limited by the hydrogen-transfer step. Semiclassical mass considerations that do not include tunneling effects would predict that kH/kT = (kD/kT)3.26, where kH, kD, and kT are the rate constants for the reaction of protium, deuterium, and tritium derivatives, respectively. Significant deviations from this relation have now been observed for both primary and especially secondary effects, such that experimental H/T ratios are much greater than those calculated from the above expression. These deviations also hold in the temperature range from 0 to 40 degrees Celsius. Such deviations were previously predicted to result from a reaction coordinate containing a significant contribution from hydrogen tunneling.

Cha, Yuan; Murray, Christopher J.; Klinman, Judith P.

1989-03-01

129

Enhancement of photosensitivity in the alcohol-added ferroin-catalyzed Belousov-Zhabotinsky reaction system  

Microsoft Academic Search

The observation of photoinduced image formation in the alcohol-added ferroin-catalyzed Belousov-Zhabotinsky (BZ) reaction is reported. It is found that alcohol acts as a reagent that reduces the activation energy both of the ferroin-catalyzed and the Ce-catalyzed BZ reaction system and enhances the photosensitivity. By comparing the photosensitivity and photoinduced image formation for the ferroin-catalyzed BZ system with and without alcohol,

Jiro Abe; Kazuhisa Matsuda; Masakazu Taka; Yasuo Shirai

1995-01-01

130

Asymptotic Expansion in Enzyme Reactions with High Enzyme Concentrations  

Microsoft Academic Search

In this paper we find a new asymptotic expansion valid in enzymatic reactions where the total amount of enzyme exceeds greatly the total amount of substrate. In such case it is well known that the Michelis-Menten approximation is no longer valid; therefore our asymptotic expansion is a new tool to approximate in a closed form the concentrations of the reactants

Alberto Maria Bersani; Guido Dell'Acqua

2010-01-01

131

Enzyme-catalyzed hydrolysis of the supported phospholipid bilayers studied by atomic force microscopy.  

PubMed

Atomic force microscopy (AFM) is employed to reveal the morphological changes of the supported phospholipid bilayers hydrolyzed by a phospholipase A(2) (PLA(2)) enzyme in a buffer solution at room temperature. Based on the high catalytic selectivity of PLA(2) toward l-enantiomer phospholipids, five kinds of supported bilayers made of l- and D-dipalmitoylphosphatidylcholines (DPPC), including l-DPPC (upper leaflet adjacent to solution)/l-DPPC (bottom leaflet) (or l/l in short), l/d, d/l, d/d, and racemic ld/ld, were prepared on a mica surface in gel-phase, to explicate the kinetics and mechanism of the enzyme-induced hydrolysis reaction in detail. AFM observations for the l/l bilayer show that the hydrolysis rate for l-DPPC is significantly increased by PLA(2) and most of the hydrolysis products desorb from substrate surface in 40 min. As d-enantiomers are included in the bilayer, the hydrolysis rate is largely decreased in comparison with the l/l bilayer. The time used to hydrolyze the as-prepared bilayers by PLA(2) increases in the sequence of l/l, l/d, ld/ld, and d/l (d/d is inert to the enzyme action). d-enantiomers in the enantiomer hybrid bilayers remain on the mica surface at the end of the hydrolysis reaction. It was confirmed that the hydrolysis reaction catalyzed by PLA(2) preferentially occurs at the edges of pits or defects on the bilayer surface. The bilayer structures are preserved during the hydrolysis process. Based on these observations, a novel kinetics model is proposed to quantitatively account for the PLA(2)-catalyzed hydrolysis of the supported phospholipid bilayers. The model simulation demonstrates that PLA(2) mainly binds with lipids at the perimeter of defects in the upper leaflet and leads to a hydrolysis reaction, yielding species soluble to the solution phase. The lipid molecules underneath subsequently flip up to the upper leaflet to maintain the hydrophilicity of the bilayer structure. Our analysis shows that d-enantiomers in the hybrid bilayers considerably reduce the hydrolysis rate by its ineffective binding with PLA(2). PMID:22995243

Wu, HengLiang; Yu, Le; Tong, Yujin; Ge, Aimin; Yau, Shuehlin; Osawa, Masatoshi; Ye, Shen

2012-09-17

132

Kinetics of Imidazole Catalyzed Ester Hydrolysis: Use of Buffer Dilutions to Determine Spontaneous Rate, Catalyzed Rate, and Reaction Order.  

ERIC Educational Resources Information Center

|Described is an advanced undergraduate kinetics experiment using buffer dilutions to determine spontaneous rate, catalyzed rate, and reaction order. The reaction utilized is hydrolysis of p-nitro-phenyl acetate in presence of imidazole, which has been shown to enhance rate of the reaction. (Author/JN)|

Lombardo, Anthony

1982-01-01

133

Reaction conditions for laccase catalyzed polymerization of catechol  

Microsoft Academic Search

Poly(catechol) was synthesized in batch runs with laccase from Trametes versicolor (ATCC 200801). The polymerization reaction was conducted in a closed, temperature controlled system containing acetone and sodium acetate buffer for pH control. The effects of the solvent mixture, monomer (catechol), enzyme, medium pH and temperature on the polymerization rate were investigated with respect to initial reaction conditions and depletion

Nahit Akta?; Abdurrahman Tanyolaç

2003-01-01

134

Online Electrospray Ionization Mass Spectrometric Monitoring of Protease-Catalyzed Reactions in Real Time  

NASA Astrophysics Data System (ADS)

Although there are a lot of well established methods for monitoring enzyme-catalyzed reactions, most of them are based on changes in spectroscopic properties during the conversion of substrates to products. However, reactions without optical changes are common, which are inapplicable to these spectroscopic methods. As an alternative technique for enzymologic research, mass spectrometry (MS) is favored due to its specificity, sensitivity, and the ability to obtain stoichiometric information. In this work, probe electrospray ionization (PESI) source coupled with a time of flight mass spectrometer was employed to monitor some typical protease-catalyzed reactions, including pepsinolysis and trypsinolysis of cytochrome c in real time. Due to the high electrical conductivity of each reaction system, corona discharges are likely to occur, which would decrease intensities of mass spectrometric signals. An ultra-fine sampling probe and an auxiliary vapor spray were adopted to prevent corona discharges. Experimental results from peptic and tryptic digestions of cytochrome c showed different and characteristic catalytic pathways. With the data presented in this study, PESI-MS can be considered as a potential tool for real-time monitoring of enzymatic reactions because of its simplicity in instrumental configuration, wide applicability under harsh conditions, and flexibility in combination with other techniques.

Yu, Zhan; Chen, Lee Chuin; Mandal, Mridul Kanti; Nonami, Hiroshi; Erra-Balsells, Rosa; Hiraoka, Kenzo

2012-04-01

135

Online electrospray ionization mass spectrometric monitoring of protease-catalyzed reactions in real time.  

PubMed

Although there are a lot of well established methods for monitoring enzyme-catalyzed reactions, most of them are based on changes in spectroscopic properties during the conversion of substrates to products. However, reactions without optical changes are common, which are inapplicable to these spectroscopic methods. As an alternative technique for enzymologic research, mass spectrometry (MS) is favored due to its specificity, sensitivity, and the ability to obtain stoichiometric information. In this work, probe electrospray ionization (PESI) source coupled with a time of flight mass spectrometer was employed to monitor some typical protease-catalyzed reactions, including pepsinolysis and trypsinolysis of cytochrome c in real time. Due to the high electrical conductivity of each reaction system, corona discharges are likely to occur, which would decrease intensities of mass spectrometric signals. An ultra-fine sampling probe and an auxiliary vapor spray were adopted to prevent corona discharges. Experimental results from peptic and tryptic digestions of cytochrome c showed different and characteristic catalytic pathways. With the data presented in this study, PESI-MS can be considered as a potential tool for real-time monitoring of enzymatic reactions because of its simplicity in instrumental configuration, wide applicability under harsh conditions, and flexibility in combination with other techniques. PMID:22314937

Yu, Zhan; Chen, Lee Chuin; Mandal, Mridul Kanti; Nonami, Hiroshi; Erra-Balsells, Rosa; Hiraoka, Kenzo

2012-04-01

136

Clay-catalyzed reactions of coagulant polymers during water chlorination  

USGS Publications Warehouse

The influence of suspended clay/solid particles on organic-coagulant reactions during water chlorination was investigated by analyses of total product formation potential (TPFP) and disinfection by-product (DBP) distribution as a function of exchanged clay cation, coagulant organic polymer, and reaction time. Montmorillonite clays appeared to act as a catalytic center where the reaction between adsorbed polymer and disinfectant (chlorine) was mediated closely by the exchanged clay cation. The transition-metal cations in clays catalyzed more effectively than other cations the reactions between a coagulant polymer and chlorine, forming a large number of volatile DBPs. The relative catalytic effects of clays/solids followed the order Ti-Mont > Fe-Mont > Cu-Mont > Mn-Mont > Ca-Mont > Na-Mont > quartz > talc. The effects of coagulant polymers on TPFP follow the order nonionic polymer > anionic polymer > cationic polymer. The catalytic role of the clay cation was further confirmed by the observed inhibition in DBP formation when strong chelating agents (o-phenanthroline and ethylenediamine) were added to the clay suspension. Moreover, in the presence of clays, total DBPs increased appreciably when either the reaction time or the amount of the added clay or coagulant polymer increased. For volatile DBPs, the formation of halogenated methanes was usually time-dependent, with chloroform and dichloromethane showing the greatest dependence. ?? 2003 Elsevier Inc. All rights reserved.

Lee, J. -F.; Liao, P. -M.; Lee, C. -K.; Chao, H. -P.; Peng, C. -L.; Chiou, C. T.

2004-01-01

137

Ab initio study of ice catalyzation of HOCl + HCl reaction  

SciTech Connect

The observations by Farman et al. revealed remarkable depletions in the total atmospheric ozone content in Antarctica. The observed total ozone decreased smoothing during the spring season from about 1975. Satellite observations have proved Antarctic ozone depletions over a very extended region, in general agreement with the local ground-based data of Farman et al. It was suggested that heterogeneous reactions occurring on particles in polar stratospheric clouds (PSCs) play a central role in the depletion of stratospheric ozone. Experiments proved that the reaction of HOCl + HCl was very slow in the gas phase, but on ice surface it was rapid. In this work the ice catalysis of HOCl + HCl reaction was investigated by using ab initio molecular orbital theory. The authors applied the Hartree-Fock self-consistent field and the second-order Moeller-Plesset perturbation theory with the basis sets of 6-31G* to the model system. The complexes and transition state were obtained along the reaction with and without the presence of ice surface. By comparing the results, a possible catalyzation mechanism of ice on the reaction is proposed.

Zhou, Y.F.; Liu, C.B.

2000-06-15

138

Kinetic modeling of interesterification reactions catalyzed by immobilized lipase.  

PubMed

Kinetic data for lipase-catalyzed interesterification reactions between free fatty acids and triglycerides were collected and the dynamics of the interesterification reactions were successfully modeled using tow rate experssions requiring a total of five adjustable parameters. One rate expression describes the disappearance of the free fatty acid (octanoic or linolenic acid), and the second describes the rate of release of fatty acid residues from the triglycerides (olive oil or milkfat). This model is able to account for the effects of the concentration of all chemical species participating in interesterification throughout the entire reaction. When the data for both milkfat and olive oil were subjected to nonlinear regression analyses using the same mathematical model, the parameter estimates for both systems were comparable. In addition to reproducing the tendencies observed experimentally, simulations of the interesterification system under a variety of initial conditions provided insight into the effects of several reaction variables which could not be examined experimentally. Among the most significant findings of the simulation work are (1) there is a limit beyond which increasing the initial concentration of water produces no further increase in the initial rate of the interesterification reaction; (2) an increase in the initial concentration of lower glycerides produces a concomitant increase in the rate of the interesterification reaction; (3) the free fatty acids inhibit the rate of hydrolysis of the fatty acid residues of the triglycerides; (4) there is a limit beyond which increasing the initial concentration of triglycerides produces no significant increase in the rate of either the hydrolysis reaction or the interesterification reaction. PMID:18615612

Reyes, H R; Hill, C G

1994-01-20

139

Kinetic Parameters for the Noncatalyzed and Enzyme-Catalyzed Mutarotation of Glucose Using a Blood Glucometer  

ERIC Educational Resources Information Center

|The kinetic parameters for the conversion of alpha-D-glucose to beta-D-glucose were measured using a blood glucometer. The reaction order, rate constant, and Arrhenius activation energy are reported for the noncatalyzed reaction and turnover number and Michaelis constant are reported for the reaction catalyzed by porcine kidney mutarotase. The…

Hardee, John R.; Delgado, Bryan; Jones, Wray

2011-01-01

140

A paradigm for enzyme-catalyzed proton transfer at carbon: triosephosphate isomerase.  

PubMed

Triosephosphate isomerase (TIM) catalyzes the stereospecific 1,2-proton shift at dihydroxyacetone phosphate (DHAP) to give (R)-glyceraldehyde 3-phosphate through a pair of isomeric enzyme-bound cis-enediolate phosphate intermediates. The chemical transformations that occur at the active site of TIM were well understood by the early 1990s. The mechanism for enzyme-catalyzed isomerization is similar to that for the nonenzymatic reaction in water, but the origin of the catalytic rate acceleration is not understood. We review the results of experimental work that show that a substantial fraction of the large 12 kcal/mol intrinsic binding energy of the nonreacting phosphodianion fragment of TIM is utilized to activate the active site side chains for catalysis of proton transfer. Evidence is presented that this activation is due to a phosphodianion-driven conformational change, the most dramatic feature of which is closure of loop 6 over the dianion. The kinetic data are interpreted within the framework of a model in which activation is due to the stabilization by the phosphodianion of a rare, desolvated, loop-closed form of TIM. The dianion binding energy is proposed to drive the otherwise thermodynamically unfavorable desolvation of the solvent-exposed active site. This reduces the effective local dielectric constant of the active site, to enhance stabilizing electrostatic interactions between polar groups and the anionic transition state, and increases the basicity of the carboxylate side chain of Glu-165 that functions to deprotonate the bound carbon acid substrate. A rebuttal is presented to the recent proposal [Samanta, M., Murthy, M. R. N., Balaram, H., and Balaram, P. (2011) ChemBioChem 12, 1886-1895] that the cationic side chain of K12 functions as an active site electrophile to protonate the carbonyl oxygen of DHAP. PMID:22409228

Richard, John P

2012-03-20

141

Direct detection of enzyme-catalyzed products by FET sensor with ferrocene-modified electrode  

Microsoft Academic Search

An FET-based biosensor with a ferrocene-modified gold electrode detects the enzyme-produced electrons by using mediators that transfer the electrons from the enzyme to the sensor. Since an extended-gate FET sensor with a light-shielding mask can be operated without a light-shielding box, a small portable instrument will soon be realised. However, when the FET sensor detected enzyme-catalyzed products with the mediators

Yu Ishige; Sizu Takeda; Masao Kamahori

2010-01-01

142

Enzyme-catalyzed processes of first-pass hepatic and intestinal drug extraction  

Microsoft Academic Search

Oral bioavailability of pharmacologically effective drugs is often limited by first-pass biotransformation. In humans, both hepatic and intestinal enzymes can catalyze the metabolism of a drug as it transits between the gastrointestinal lumen and systemic blood for the first time. Although a spectrum of drug biotransformations can occur during first-pass, the most common are oxidations catalyzed by cytochromes P450. It

Kenneth E. Thummel; Kent L. Kunze; Danny D. Shen

1997-01-01

143

Cobalt(II)-catalyzed atom\\/group transfer reaction: Stereoselective carbene and nitrene transfer reactions  

Microsoft Academic Search

Metalloporphyrins have been shown to catalyze many fundamental and practically important chemical transformations, some of which represent the first demonstrations of these catalytic processes. The most notable examples include an assortment of atom\\/group transfer reactions, such as oxene, nitrene, and carbene transfers. Atom\\/group transfer reactions allow for the direct conversion of abundant and inexpensive alkenes and alkanes into value-added functional

Joshua V Ruppel

2008-01-01

144

A thermodynamic investigation of reactions catalyzed by tryptophan synthase.  

PubMed

Microcalorimetry and high-performance liquid chromatography have been used to conduct a thermodynamic investigation of the following reactions catalyzed by the tryptophan synthase alpha 2 beta 2 complex (EC 4.2.1.20) and its subunits: indole(aq) + L-serine(aq) = L-tryptophan(aq) + H2O(1); L-serine(aq) = pyruvate(aq) + ammonia(aq); indole(aq) + D-glyceraldehyde 3-phosphate(aq) = 1-(indol-3-yl)glycerol 3-phosphate(aq); L-serine(aq) + 1-(indol-3-yl)glycerol 3-phosphate(aq) = L-tryptophan(aq) + D-glyceraldehyde 3-phosphate(aq) + H2O(1). The calorimetric measurements led to standard molar enthalpy changes for all four of these reactions. Direct measurements yielded an apparent equilibrium constant for the third reaction; equilibrium constants for the remaining three reactions were obtained by using thermochemical cycle calculations. The results of the calorimetric and equilibrium measurements were analyzed in terms of a chemical equilibrium model that accounted for the multiplicity of the ionic states of the reactants and products. Thermodynamic quantities for chemical reference reactions involving specific ionic forms have been obtained. These quantities permit the calculation of the position of equilibrium of the above four reactions as a function of temperature, pH, and ionic strength. Values of the apparent equilibrium constants and standard transformed Gibbs free energy changes delta r G'(m) degree under approximately physiological conditions are given. Le Châtelier's principle provides an explanation as to why, in the metabolic pathway leading to the synthesis of L-tryptophan, the third reaction proceeds in the direction of formation of indole and D-glyceraldehyde 3-phosphate even though the apparent equilibrium constant greatly favors the formation of 1-(indol-3-yl)glycerol 3-phosphate. PMID:9700925

Kishore, N; Tewari, Y B; Akers, D L; Goldberg, R N; Miles, E W

1998-07-27

145

Enzyme Reactions in Nanoporous, Picoliter Volume Containers  

PubMed Central

Advancements in nanoscale fabrication allow creation of small volume reaction containers that can facilitate the screening and characterization of enzymes. A porous, ~19 pL volume vessel has been used in this work to carry out enzyme reactions under varying substrate concentrations. Assessment of small molecule and Green Fluorescent Protein diffusion from the vessels indicates that pore sizes on order of 10 nm can be obtained, allowing capture of proteins and diffusive exchange of small molecules. Glucose oxidase and horseradish peroxidase can be contained in these structures and diffusively fed with a solution containing glucose and the fluorogenic substrate Amplex Red™ through the engineered nanoscale pore structure. Fluorescent microscopy was used to monitor the reaction, which was carried out under microfluidic control. Kinetic characteristics of the enzyme (Km and Vmax) were evaluated and compared with results from conventional scale reactions. These picoliter, nanoporous containers can facilitate quick determination of enzyme kinetics in microfluidic systems without the requirement of surface tethering and can be used for applications in drug discovery, clinical diagnostics and high-throughput screening.

Siuti, Piro; Retterer, Scott T.; Choi, Chang-Kyoung; Doktycz, Mitchel J.

2012-01-01

146

Scaling and Continuum Percolation Model for Enzyme-Catalyzed Gel Degradation  

NASA Astrophysics Data System (ADS)

Enzyme-catalyzed gel degradation is inherently controlled by diffusion of enzymes in the gel. We report kinetics measurements on the gelatin-thermolysin system, varying solvent viscosity as well as gel and enzyme concentrations. Scaling relations and reduced variables are proposed which are shown to account for the experimental results. Finally, we argue that the nontrivial experimental dependence on enzyme concentration for the degradation time demonstrates that enzyme random walk is self-attracting, leading to a continuum percolation model for gel degradation.

Lairez, D.; Carton, J.-P.; Zalczer, G.; Pelta, J.

2007-06-01

147

Deep eutectic solvents (DESs) are viable cosolvents for enzyme-catalyzed epoxide hydrolysis.  

PubMed

A special group of ionic liquids, deep eutectic solvents (DESs) have been tested as cosolvents in enzyme-catalyzed hydrolysis of a chiral (1,2)-trans-2-methylstyrene oxide. The choline chloride:ethane diol (ET), choline chloride:glycerol (GLY) and choline:chloride:urea (REL) DESs were included in the reaction mixtures with epoxide and the potato epoxide hydrolase StEH1. The effect of the DESs on enzyme function was primarily elevations of K(M) (up to 20-fold) and with lesser effects on turnover numbers (twofold variation). The regioselectivity in hydrolysis of the (1R,2R)-2-trans-methylstyrene oxide was altered in the presence of GLY or ET to favor epoxide ring opening at the benzylic carbon (R=2.33), enhancing the regioselectivity observed in buffer-only systems (R=1.35). The DES solutions dissolved 1.5-fold higher epoxide concentrations as compared to phosphate buffer. The total conversion of high concentration (40 g/l) of (1S,2S)-MeSO was not negatively affected by addition of 40% GLY. PMID:20438773

Lindberg, Diana; de la Fuente Revenga, Mario; Widersten, Mikael

2010-05-07

148

Effect of enzyme dehydration on alcalase-catalyzed dipeptide synthesis in near-anhydrous organic media.  

PubMed

The effect of enzyme dehydration by molecular sieves on the coupling of phenylalanine amide and the carbamoylmethyl ester of N-protected phenylalanine in near-anhydrous tetrahydrofuran was investigated. This coupling was catalyzed by Alcalase covalently immobilized onto macroporous acrylic beads (Cov); these immobilized enzymes were hydrated prior to use. The dehydration kinetics of Cov by molecular sieve powder were determined by incubating Cov with different amounts of molecular sieve powder for different periods of time (0-80 h). Subsequently, the remaining coupling activity of Cov was measured. Dehydration-induced inactivation of Cov by molecular sieve powder was found to occur in three phases: (1) an initial, rapid, major dehydration-induced inactivation that takes place during the first activity measurement, (2) a phase of first-order inactivation, and (3) a plateau phase in activity. These dehydration kinetics were incorporated into a previously found reaction kinetics model. The resulting model was then used to fit progress curve data of the coupling in the presence of different amounts of molecular sieve powder. Upon establishment of parameter values, the model was used to predict independent data sets and found to work well. PMID:23554404

Vossenberg, Petra; Beeftink, Rik; Stuart, Martien Cohen; Tramper, Hans

2013-05-02

149

Probing the regiospecificity of enzyme-catalyzed steroid glycosylation.  

PubMed

The potential of a uniquely permissive engineered glycosyltransferase (OleD ASP) as a catalyst for steroid glycosylation is highlighted. The ability of OleD ASP to glucosylate a range of cardenolides and bufadienolides was assessed using a rapid LC-UV/MS-SPE-NMR analytical platform. While a bias toward OleD-catalyzed C3 monoglucosylation was observed, subtle alterations of the steroidal architecture, in some cases, invoked diglucosylation or, in one case (digoxigenin), C12 glucosylation. This latter case represents the first, and highly efficient, synthesis of digoxigenin 12-O-?-D-glucoside. PMID:23075289

Zhou, Maoquan; Hou, Yanpeng; Hamza, Adel; Pain, Christophe; Zhan, Chang-Guo; Bugni, Tim S; Thorson, Jon S

2012-10-18

150

Good vibrations in enzyme-catalysed reactions  

NASA Astrophysics Data System (ADS)

Fast motions (femtosecond to picosecond) and their potential involvement during enzyme-catalysed reactions have ignited considerable interest in recent years. Their influence on reaction chemistry has been inferred indirectly from studies of the anomalous temperature dependence of kinetic isotope effects and computational simulations. But can such motion reduce the width and height of energy barriers along the reaction coordinate, and contribute to quantum mechanical and/or classical nuclear-transfer chemistry? Here we discuss contemporary ideas for enzymatic reactions invoking a role for fast 'promoting' (or 'compressive') motions that, in principle, can aid hydrogen-transfer reactions. Of key importance is the direct demonstration of a role for compressive motions and the ability to understand in atomic detail the structural origin of these fast motions, but so far this has not been achieved. Here we discuss both indirect experimental evidence that supports a role for compressive motion and the additional insight gained from computational simulations.

Hay, Sam; Scrutton, Nigel S.

2012-03-01

151

TBAF-catalyzed deacylation of cellulose esters: Reaction scope and influence of reaction parameters.  

PubMed

In order to expand its utility and understand how to carry it out most efficiently, the scope of the highly regioselective, tetrabutylammonium fluoride (TBAF) catalyzed deacylation of cellulose acetates has been investigated, including the influence of key process parameters: solvent, temperature, and water content. Reactions in DMSO, THF, MEK and acetone afforded similar extents of deacylation and regioselectivity. Reaction with TBAF in DMSO at 50°C for 18h was the most efficient process providing regioselective deacylation at O-2/3. All results were consistent with our previous mechanistic proposals. Furthermore, we demonstrate that TBAF-catalyzed deacylation is also effective and regioselective with cellulose acetate, butyrate, and hexanoate triesters, and even with a cellulose ester devoid of alpha protons, cellulose tribenzoate. These reactions displayed regioselectivity for deacylation at O-2/3 similar to that observed earlier with cellulose acetate (DS 2.4). PMID:23987400

Zheng, Xueyan; Gandour, Richard D; Edgar, Kevin J

2013-06-20

152

The Enzyme-Catalyzed Synthesis of Sucrose from Starch.  

National Technical Information Service (NTIS)

The most abundant food sugar is sucrose and world demand for sucrose and other sweeteners has outstripped production. Commercial processes have been developed for enzymic production of glucose-fructose mixtures from cornstarch. This report very briefly de...

S. J. Kelly L. G. Butler R. G. Squires

1976-01-01

153

Selenophosphate synthetase. Enzyme properties and catalytic reaction.  

PubMed

Selenophosphate synthetase, the product of the selD gene, produces the biologically active selenium donor compound, monoselenophosphate, from ATP and selenide. Isolation of the enzyme and characterization of some of its physical and catalytic properties are described. Magnesium ion and a monovalent cation, K+, NH4+, or Rb+, are required for catalytic activity. Polyphosphates and other common nucleotide triphosphates do not replace ATP as substrate. The stoichiometry of the catalytic reaction (Reaction 1) was established using 31P NMR, anaerobic molecular sieve chromatography, and radiochemical labeling procedures. ATP+selenide+H2O-->selenophosphate+Pi+AMP. In the absence of selenide, ATP is converted completely to AMP and orthophosphate upon prolonged incubation with elevated levels of enzyme. AMP is a competitive inhibitor of ATP, Ki = 170 microM, whereas selenophosphate and orthophosphate are weak inhibitors indicating a multistep reaction. Attempts to obtain direct evidence for a postulated enzyme-pyrophosphate intermediate using several experimental approaches are described. No exchange of [14C]AMP with ATP could be detected after the enzyme was freed of traces of contaminating adenylate kinase by chromatography on phenyl-Sepharose. PMID:8144648

Veres, Z; Kim, I Y; Scholz, T D; Stadtman, T C

1994-04-01

154

Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function  

PubMed Central

Functionally analogous enzymes are those that catalyze similar reactions on similar substrates but do not share common ancestry, providing a window on the different structural strategies nature has used to evolve required catalysts. Identification and use of this information to improve reaction classification and computational annotation of enzymes newly discovered in the genome projects would benefit from systematic determination of reaction similarities. Here, we quantified similarity in bond changes for overall reactions and catalytic mechanisms for 95 pairs of functionally analogous enzymes (non-homologous enzymes with identical first three numbers of their EC codes) from the MACiE database. Similarity of overall reactions was computed by comparing the sets of bond changes in the transformations from substrates to products. For similarity of mechanisms, sets of bond changes occurring in each mechanistic step were compared; these similarities were then used to guide global and local alignments of mechanistic steps. Using this metric, only 44% of pairs of functionally analogous enzymes in the dataset had significantly similar overall reactions. For these enzymes, convergence to the same mechanism occurred in 33% of cases, with most pairs having at least one identical mechanistic step. Using our metric, overall reaction similarity serves as an upper bound for mechanistic similarity in functional analogs. For example, the four carbon-oxygen lyases acting on phosphates (EC 4.2.3) show neither significant overall reaction similarity nor significant mechanistic similarity. By contrast, the three carboxylic-ester hydrolases (EC 3.1.1) catalyze overall reactions with identical bond changes and have converged to almost identical mechanisms. The large proportion of enzyme pairs that do not show significant overall reaction similarity (56%) suggests that at least for the functionally analogous enzymes studied here, more stringent criteria could be used to refine definitions of EC sub-subclasses for improved discrimination in their classification of enzyme reactions. The results also indicate that mechanistic convergence of reaction steps is widespread, suggesting that quantitative measurement of mechanistic similarity can inform approaches for functional annotation.

Almonacid, Daniel E.; Yera, Emmanuel R.; Mitchell, John B. O.; Babbitt, Patricia C.

2010-01-01

155

In situ regeneration of NADH via lipoamide dehydrogenase-catalyzed electron transfer reaction evidenced by spectroelectrochemistry  

PubMed Central

NAD/NADH is a coenzyme found in all living cells, carrying electrons from one reaction to another. We report on characterizations of in situ regeneration of NADH via lipoamide dehydrogenase (LD)-catalyzed electron transfer reaction to regenerate NADH using UV-vis spectroelectrochemistry. The Michaelis-Menten constant (Km) and maximum velocity (Vmax) of NADH regeneration were measured as 0.80 ± 0.15 mM and 1.91 ± 0.09 ?M s-1 in a 1-mm thin-layer spectroelectrochemical cell using gold gauze as the working electrode at the applied potential -0.75 V (vs. Ag/AgCl). The electrocatalytic reduction of the NAD system was further coupled with the enzymatic conversion of pyruvate to lactate by lactate dehydrogenase to examine the coenzymatic activity of the regenerated NADH. Although the reproducible electrocatalytic reduction of NAD into NADH is known to be difficult compared to the electrocatalytic oxidation of NADH, our spectroelectrochemical results indicate that the in situ regeneration of NADH via LD-catalyzed electron transfer reaction is fast and sustainable and can be potentially applied to many NAD/NADH-dependent enzyme systems.

Tam, Tsz Kin; Chen, Baowei; Lei, Chenghong; Liu, Jun

2012-01-01

156

Implicit versus explicit solvent in free energy calculations of enzyme catalysis: Methyl transfer catalyzed by catechol O-methyltransferase  

NASA Astrophysics Data System (ADS)

We compare free energy calculations for the methyl transfer reaction catalyzed by catechol O-methyltransferase using the quantum mechanical/molecular mechanical free energy method with implicit and explicit solvents. An analogous methylation reaction in a solution is also studied. For the explicit solvent model, we use the three-point transferable intermolecular potential model, and for the implicit model, we use the generalized Born molecular volume model as implemented in CHARMM. We find that activation and reaction free energies calculated with the two models are very similar, despite some structural differences that exist. A significant change in the polarization of the environment occurs as the reaction proceeds. This is more pronounced for the reaction in a solution than for the enzymatic reaction. For the enzymatic reaction, most of the changes take place in the protein rather than in the solvent, and, hence, the benefit of having an instantaneous relaxation of the solvent degrees of freedom is less pronounced for the enzymatic reaction than for the reaction in a solution. This is a likely reason why energies of the enzyme reaction are less sensitive to the choice of atomic radii than are energies of the reaction in a solution.

Rod, Thomas H.; Rydberg, Patrik; Ryde, Ulf

2006-05-01

157

Investigations of Surface-Catalyzed Reactions in a Mars Mixture  

NASA Astrophysics Data System (ADS)

In the design of a thermal protection system (TPS) for a planetary entry vehicle, accurate modeling of the trajectory aero-heating poses a significant challenge owing to large uncertainties in chemical processes taking place at the surface. Even for surface-catalyzed reactions, which have been investigated extensively, there is no consensus on how they should be modeled; or, in some cases, on which reactions are likely to occur. Current TPS designs for Mars missions rely on a super-catalytic boundary condition, which assumes that all dissociated species recombine to the free stream composition.While this is recognized to be the the most conservative approach, discrepancies in aero-heating measurements in ground test facilities preclude less conservative design options, resulting in an increased TPS mass at the expense of scientific payload.Using two-photon absorption laser induced fluorescence in a 30 kW inductively coupled plasma torch facility, preliminary studies have been performed to obtain spatially-resolved measurements of the dominant species in a plasma boundary layer for a Martian atmosphere mixture over catalytic and non-catalytic surfaces.

Dougherty, M.; Owens, W.; Meyers, J.; Fletcher, D. G.

2011-08-01

158

Reaction Pathway and Free Energy Profile for Cocaine Hydrolase-Catalyzed Hydrolysis of (-)-Cocaine  

PubMed Central

Reaction pathway of (?)-cocaine hydrolysis catalyzed by our recently discovered most efficient cocaine hydrolase, which is the A199S/F227A/S287G/A328W/Y332G mutant of human butyrylcholinesterase (BChE), and the corresponding free energy profile have been studied by performing first-principles pseudobond quantum mechanical/molecular mechanical (QM/MM)-free energy (FE) calculations. Based on the QM/MM-FE results, the catalytic hydrolysis process consists of four major reaction steps, including the nucleophilic attack on carbonyl carbon of (?)-cocaine benzoyl ester by hydroxyl group of S198, dissociation of (?)-cocaine benzoyl ester, nucleophilic attack on carbonyl carbon of (?)-cocaine benzoyl ester by water, and finally the dissociation between (?)-cocaine benzoyl group and S198 of the enzyme. The second reaction step is rate-determining. The calculated free energy barrier associated with the transition state for the rate-determining step is ~15.0 kcal/mol, which is in excellent agreement with the experimentally-derived activation free energy of ~14.7 kcal/mol. The mechanistic insights obtained from the present study will be valuable for rational design of more active cocaine hydrolase against (?)-cocaine. In particular, future efforts aiming at further increasing the catalytic activity of the enzyme against (?)-cocaine should focus on stabilization of the transition state for the second reaction step in which the benzoyl ester of (?)-cocaine dissociates.

Liu, Junjun; Zhan, Chang-Guo

2012-01-01

159

Mechanism of maltal hydration catalyzed by. beta. -amylase: Role of protein structure in controlling the steric outcome of reactions catalyzed by a glycosylase  

Microsoft Academic Search

Crystalline (monomeric) soybean and (tetrameric) sweet potato β-amylase were shown to catalyze the cis hydration of maltal (α-D-glucopyranosyl-2-deoxy-D-arabino-hex-1-enitol) to form β-2-deoxymaltose. As reported earlier with the sweet potato enzyme, maltal hydration in DâO by soybean β-amylase was found to exhibit an unusually large solvent deuterium kinetic isotope effect (V{sub H}\\/V{sub D}=6.5), a reaction rate linearly dependent on the mole fraction

Sumio Kitahata; Seiya Chiba; Curtis F. Brewer; Edward J. Hehre

1991-01-01

160

Plausible novel ribose metabolism catalyzed by enzymes of the methionine salvage pathway in Bacillus subtilis.  

PubMed

The methionine salvage pathway (MSP) recycles reduced sulfur from 5-methylthioribose. Here we propose a novel ribose metabolic pathway performed by MSP enzymes of Bacilli. MtnK, an initial catalyst of MSP, had significant ribose kinase activity, with Vmax and Km values of 2.9 µmol min(-1) mg of protein(-1) and 4.8 mM. Downstream enzymes catalyzed the isomerization of ribose-1-phosphate and subsequent dehydration, enolization, dephosphorylation, and dioxygenation. PMID:23649237

Nakano, Toshihiro; Saito, Yohtaro; Yokota, Akiho; Ashida, Hiroki

2013-05-07

161

Transition Path Sampling Study of the Reaction Catalyzed by Purine Nucleoside Phosphorylase.  

PubMed

The Transition Path Sampling (TPS) method is a powerful technique for studying rare events in complex systems, that allows description of reactive events in atomic detail without prior knowledge of reaction coordinates and transition states. We have applied TPS in combination with a hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) method to study the enzyme human purine nucleoside phosphorylase (hPNP). This enzyme catalyzes the reversible phosphorolysis of 6-oxypurine (deoxy)nucleosides to generate the corresponding purine base and (deoxy)ribose 1-phosphate. Hundreds of reactive trajectories were generated. Analysis of this transition path ensembles provides insight into the detailed mechanistic dynamics of reaction in the enzyme. Our studies have indicated a reaction mechanism involving the cleavage of the N-ribosidic bond to form transition states with substantial ribooxacarbenium ion character, that is then followed by conformational changes in the enzyme and the ribosyl group leading to migration of the anomeric carbon of the ribosyl group toward phosphate to form the product ribose 1-phosphate. This latter process is crucial in PNP, because several strong H-bonds form between active site residues in order to capture and align the phosphate nucleophile. Calculations of the commitment probability along reactive paths demonstrated the presence of a broad energy barrier at the transition state. Analysis of these transition state structures showed that bond-breaking and bond-forming distances are not a good choice for the reaction coordinate, but that the pseudorotational phase of the ribose ring is also a significant variable. PMID:20664707

Saen-Oon, Suwipa; Schramm, Vern L; Schwartz, Steven D

2008-01-01

162

Does enzyme-catalyzed formation of sulfate complexes cause oxygen isotope exchange during dissimilatory microbial sulfate reduction?  

NASA Astrophysics Data System (ADS)

We have experimentally tested the hypothesis that oxygen isotope exchange may occur between sulfate and water during enzyme-catalyzed formation of the sulfate complex adenosine phosphosulfate (APS). This reaction is the initial step in the dissimilatory microbial sulfate reduction process. It has been suggested that the enzyme-catalyzed formation of APS could facilitate oxygen isotope exchange between the cell internal water and the residual sulfate pool. This is important because only a fraction of the APS is then further reduced to sulfite, the remainder of which could be reintroduced to the sulfate pool, resulting in significant resetting of the sulfate oxygen isotope compositions. This study isolated the enzyme-catalyzed formation of APS in vitro, in a solution of 17O-labeled water, in order to quantify the degree of oxygen isotope exchange between the complexed sulfate and water. The use of ?17O as an indicator of exchange is more rigorous than the commonly used ?18O parameter. We observed no oxygen isotope exchange between the APS and water during a set of experimental runs at 30° C with time varying from 2 to 48 hours. A subsequent study will confirm and describe the dynamics of APS formation during this reaction using spectroscopic methods. The lack of oxygen isotope exchange between APS and water suggests that the discrepancy seen in the literature between the level of enrichment for ?34S vs. ?18O is not due to oxygen isotope exchange during APS formation, but other processes, i.e. the re-oxidation of sulfite to sulfate or oxygen exchange between sulfite and water during the later steps of dissimilatory microbial sulfate reduction.

Bao, H.; Kohl, I. E.

2006-12-01

163

The Structural Basis for a Coordinated Reaction Catalyzed by a Bifunctional Glycosyltransferase in Chondroitin Biosynthesis*  

PubMed Central

Bifunctional chondroitin synthase K4CP catalyzes glucuronic acid and N-acetylgalactosamine transfer activities and polymerizes a chondroitin chain. Here we have determined that an N-terminal region (residues 58–134) coordinates two transfer reactions and enables K4CP to catalyze polymerization. When residues 58–107 are deleted, K4CP loses polymerase activity while retaining both transfer activities. Peptide 113DWPSDL118 within this N-terminal region interacts with C-terminal peptide 677YTWEKI682. The deletion of either sequence abolishes glucuronic acid but not N-acetylgalactosamine transfer activity in K4CP. Both donor bindings and transfer activities are lost by mutating 677YTWEKI682 to 677DAWEDI682. On the other hand, acceptor substrates retain their binding to K4CP mutants. The characteristics of these K4CP mutants highlight different states of the enzyme reaction, providing an underlying structural basis for how these peptides play essential roles in coordinating the two glycosyltransferase activities for K4CP to elongate the chondroitin chain.

Sobhany, Mack; Kakuta, Yoshimitsu; Sugiura, Nobuo; Kimata, Koji; Negishi, Masahiko

2012-01-01

164

CuCl/bipyridine-catalyzed addition reactions of arylboroxines with aldehydes, ?,?-unsaturated ketones, and N-tosyl aldimines.  

PubMed

CuCl/bipyridine-catalyzed addition reactions of arylboroxines with aldehydes and ?,?-unsaturated ketones at elevated temperatures were described. By using the microwave energy, CuCl/bipyridine-catalyzed addition reactions of arylboroxines with aldimines were also realized. PMID:21827191

Liao, Yuan-Xi; Hu, Qiao-Sheng

2011-08-23

165

Optimal temperature and concentration profiles in a cascade of CSTR's performing Michaelis-Menten reactions with first order enzyme deactivation  

Microsoft Academic Search

A necessary condition is found for the intermediate temperatures and substrate concentrations in a series of CSTR's performing an enzyme-catalyzed reaction which leads to the minimum overall volume of the cascade for given initial and final temperatures and substrate concentrations. The reaction is assumed to occur in a single phase under steady state conditions. The common case of Michaelis-Menten kinetics

A. L. Paiva; F. X. Malcata

1993-01-01

166

Isolation and partial purification of an enzyme catalyzing the formation of O-xylosylzeatin in Phaseolus vulgaris embryos.  

PubMed

An enzyme catalyzing the formation of a cytokinin metabolite, an O-pentosyl derivative of zeatin [Lee, Y. H., Mok, M. C., Mok, D. W. S., Griffin, D. A. & Shaw, G. (1985) Plant Physiol. 77, 635-641], was isolated from Phaseolus vulgaris embryos. Of all the potential pentose donors tested, UDP-xylose was the only substrate recognized by the enzyme. This indicates that the O-pentosyl derivatives previously obtained are O-xylosylzeatin and its ribonucleoside. The enzyme (UDP-xylose:zeatin O-xylosyltransferase, EC 2.4.2.-) has high affinity for trans-zeatin (K(m) 2 muM) and dihydrozeatin (K(m) 10 muM) but does not recognize cis-zeatin or ribosylzeatin. The molecular weight of the enzyme is approximately 50,000 and the pH optimum of the reaction is 8-8.5. Under comparable isolation and reaction conditions, similar enzyme activity could not be detected in P. lunatus embryos, confirming the genetic differences observed in vivo. PMID:16593839

Turner, J E; Mok, D W; Mok, M C; Shaw, G

1987-06-01

167

Nanoparticle-catalyzed reductive bleaching for fabricating turn-off and enzyme-free amplified colorimetric bioassays.  

PubMed

Nanoparticle-catalyzed reductive bleaching reactions of colored substrates are emerging as a class of novel indicator reactions for fabricating enzyme-free amplified colorimetric biosensing (turn-off mode), which are exactly opposite to the commonly used oxidative coloring processes of colorless substrates in traditional enzyme-catalyzed amplified colorimetric bioassays (turn-on mode). In this work, a simple theoretical analysis shows that the sensitivity of this colorimetric bioassay can be improved by increasing the amplification factor (kcat?t), or enhancing the binding affinity between analyte and receptor (Kd), or selecting the colored substrates with high extinction coefficients (?). Based on this novel strategy, we have developed a turn-off and cost-effective amplified colorimetric thrombin aptasensor. This aptasensor made full use of sandwich binding of two affinity aptamers for increased specificity, magnetic particles for easy separation and enrichment, and gold nanoparticle (AuNP)-catalyzed reductive bleaching reaction to generate the amplified colorimetric signal. With 4-nitrophenol (4-NP) as the non-dye colored substrate, colorimetric bioassay of thrombin was achieved by the endpoint method with a detection limit of 91pM. In particular, when using methylene blue (MB) as the substrate, for the first time, a more convenient and efficient kinetic-based colorimetric thrombin bioassay was achieved without the steps of acidification termination and magnetic removal of particles, with a low detection limit of 10pM, which was superior to the majority of the existing colorimetric thrombin aptasensors. The proposed colorimetric protocol is expected to hold great promise in field analysis and point-of-care applications. PMID:23962710

Li, Wei; Qiang, Weibing; Li, Jie; Li, Hui; Dong, Yifan; Zhao, Yaju; Xu, Danke

2013-08-02

168

Structure of a Novel Enzyme That Catalyzes Acyl Transfer to Alcohols in Aqueous Conditions  

SciTech Connect

The unusual architecture of the enzyme (MsAcT) isolated from Mycobacterium smegmatis forms the mechanistic basis for favoring alcoholysis over hydrolysis in water. Unlike hydrolases that perform alcoholysis only under anhydrous conditions, MsAcT demonstrates alcoholysis in substantially aqueous media and, in the presence of hydrogen peroxide, has a perhydrolysis:hydrolysis ratio 50-fold greater than that of the best lipase tested. The crystal structures of the apoenzyme and an inhibitor-bound form have been determined to 1.5 {angstrom} resolution. MsAcT is an octamer in the asymmetric unit and forms a tightly associated aggregate in solution. Relative to other structurally similar monomers, MsAcT contains several insertions that contribute to the oligomerization and greatly restrict the shape of the active site, thereby limiting its accessibility. These properties create an environment by which MsAcT can catalyze transesterification reactions in an aqueous medium and suggests how a serine hydrolase can be engineered to be an efficient acyltransferase.

Mathews, I.; Soltis, M.; Saldajeno, M.; Ganshaw, G.; Sala, R.; Weyler, W.; Cervin, M.A.; Whited, G.; Bott, R.

2009-06-03

169

New palladium-catalyzed reactions of unsaturated triflates with alkenes and alkyenes  

Microsoft Academic Search

The palladium-catalyzed reaction of vinyl triflates with P-substituted-a,P- unsaturated carbonyl compounds affords regio- and stereoselectively the corresponding vinylic substitution derivatives. The application of this reaction to the synthesis of quinolines, coumarins, and cardenolides is described. The palladium- catalyzed reaction of unsaturated triflates with functionalized internal and terminal alkynes produces a variety of heterocyclic compounds such as furans, benzo(hIfurans, indoles, butenolides,

Sandro Cacchi

1996-01-01

170

Adrenodoxin supports reactions catalyzed by microsomal steroidogenic cytochrome P450s  

SciTech Connect

The interaction of adrenodoxin (Adx) and NADPH cytochrome P450 reductase (CPR) with human microsomal steroidogenic cytochrome P450s was studied. It is found that Adx, mitochondrial electron transfer protein, is able to support reactions catalyzed by human microsomal P450s: full length CYP17, truncated CYP17, and truncated CYP21. CPR, but not Adx, supports activity of truncated CYP19. Truncated and the full length CYP17s show distinct preference for electron donor proteins. Truncated CYP17 has higher activity with Adx compared to CPR. The alteration in preference to electron donor does not change product profile for truncated enzymes. The electrostatic contacts play a major role in the interaction of truncated CYP17 with either CPR or Adx. Similarly electrostatic contacts are predominant in the interaction of full length CYP17 with Adx. We speculate that Adx might serve as an alternative electron donor for CYP17 at the conditions of CPR deficiency in human.

Pechurskaya, Tatiana A. [Institute of Bioorganic Chemistry, Academy of Sciences of Belarus, Kuprevicha st., 5/2, Minsk 220141 (Belarus); Harnastai, Ivan N. [Institute of Bioorganic Chemistry, Academy of Sciences of Belarus, Kuprevicha st., 5/2, Minsk 220141 (Belarus); Grabovec, Irina P. [Institute of Bioorganic Chemistry, Academy of Sciences of Belarus, Kuprevicha st., 5/2, Minsk 220141 (Belarus); Gilep, Andrei A. [Institute of Bioorganic Chemistry, Academy of Sciences of Belarus, Kuprevicha st., 5/2, Minsk 220141 (Belarus); Usanov, Sergey A. [Institute of Bioorganic Chemistry, Academy of Sciences of Belarus, Kuprevicha st., 5/2, Minsk 220141 (Belarus)]. E-mail: usanov@iboch.bas-net.by

2007-02-16

171

Activation Energies for an Enzyme-Catalyzed and Acid-Catalyzed Hydrolysis: An Introductory Interdisciplinary Experiment for Chemists and Biochemists.  

ERIC Educational Resources Information Center

|Background information, procedures used, and typical results obtained are provided for an experiment in which students determine and compare the Arrhenius activation energies (Ea) for the hydrolysis of salicin. This reaction is subject to catalysis both by acid and by the enzyme emulsin (beta-d-glucoside glycohydrolase). (JN)|

Adams, K. R.; Meyers, M. B.

1985-01-01

172

Activation Energies for an Enzyme-Catalyzed and Acid-Catalyzed Hydrolysis: An Introductory Interdisciplinary Experiment for Chemists and Biochemists.  

ERIC Educational Resources Information Center

Background information, procedures used, and typical results obtained are provided for an experiment in which students determine and compare the Arrhenius activation energies (Ea) for the hydrolysis of salicin. This reaction is subject to catalysis both by acid and by the enzyme emulsin (beta-d-glucoside glycohydrolase). (JN)

Adams, K. R.; Meyers, M. B.

1985-01-01

173

Nickel-catalyzed Arbuzov reactions of aryl triflates with triethyl phosphite  

Microsoft Academic Search

An efficient method was developed for the nickel-catalyzed phosphonylation of aryl triflates with triethyl phosphite, in which KBr as an additive promoted the SN2 catalytic step. To the best of our knowledge, this is the first example of nickel-catalyzed Arbuzov reactions of aryl triflates. Most of the substrates showed good reactivity under this catalytic system.

Guoqiang Yang; Chaoren Shen; Liang Zhang; Wanbin Zhang

2011-01-01

174

Recent developments in gold-catalyzed cycloaddition reactions  

PubMed Central

Summary In the last years there have been extraordinary advances in the development of gold-catalyzed cycloaddition processes. In this review we will summarize some of the most remarkable examples, and present the mechanistic rational underlying the transformations.

2011-01-01

175

Recent Developments in Pd-Catalyzed Alkene Aminoarylation Reactions for the Synthesis of Nitrogen Heterocycles  

PubMed Central

This short review describes new developments in Pd-catalyzed aminoarylation reactions between aryl halides and alkenes bearing pendant nitrogen nucleophiles. These transformations provide a novel and powerful method for accessing numerous 3-, 5-, 6-, and 7-membered nitrogen heterocycles.

Schultz, Danielle M.; Wolfe, John P.

2012-01-01

176

Rh-catalyzed reductive coupling reaction of aldehydes with conjugated dienes promoted by triethylborane.  

PubMed

Rh(I) catalyzes the reductive coupling reaction of a wide variety of aldehydes with conjugated dienes in the presence of a stoichiometric amount of triethylborane to provide homoallyl alcohols in a single operation. PMID:19663391

Kimura, Masanari; Nojiri, Daisuke; Fukushima, Masahiro; Oi, Shuichi; Sonoda, Yusuke; Inoue, Yoshio

2009-09-01

177

Acid-catalyzed reactions of hexanal on sulfuric acid particles: Identification of reaction products  

NASA Astrophysics Data System (ADS)

While it is well established that organics compose a large fraction of the atmospheric aerosol mass, the mechanisms through which organics are incorporated into atmospheric aerosols are not well understood. Acid-catalyzed reactions of compounds with carbonyl groups have recently been suggested as important pathways for transfer of volatile organics into acidic aerosols. In the present study, we use the aerodyne aerosol mass spectrometer (AMS) to probe the uptake of gas-phase hexanal into ammonium sulfate and sulfuric acid aerosols. While both deliquesced and dry non-acidic ammonium sulfate aerosols showed no organic uptake, the acidic aerosols took up substantial amounts of organic material when exposed to hexanal vapor. Further, we used 1H-NMR, Fourier transform infrared (FTIR) spectroscopy and GC-MS to identify the products of the acid-catalyzed reaction of hexanal in acidic aerosols. Both aldol condensation and hemiacetal products were identified, with the dominant reaction products dependent upon the initial acid concentration of the aerosol. The aldol condensation product was formed only at initial concentrations of 75-96 wt% sulfuric acid in water. The hemiacetal was produced at all sulfuric acid concentrations studied, 30-96 wt% sulfuric acid in water. Aerosols up to 88.4 wt% organic/11.1 wt% H 2SO 4/0.5 wt% water were produced via these two dimerization reaction pathways. The UV-VIS spectrum of the isolated aldol condensation product, 2-butyl 2-octenal, extends into the visible region, suggesting these reactions may impact aerosol optical properties as well as aerosol composition. In contrast to previous suggestions, no polymerization of hexanal or its products was observed at any sulfuric acid concentration studied, from 30 to 96 wt% in water.

Garland, Rebecca M.; Elrod, Matthew J.; Kincaid, Kristi; Beaver, Melinda R.; Jimenez, Jose L.; Tolbert, Margaret A.

178

Intensity Oscillation of Chemiluminescence in Ferroin-Catalyzed Belousov-Zhabotinsky Reaction  

Microsoft Academic Search

A weak chemiluminescence phenomenon was observed in ferroin-catalyzed Belousov-Zhabotinsky (BZ) reaction. The luminescence intensity oscillated with the self- oscillation of the visible color change and redox potential change in anti phase. A periodic signal of the luminescence was also detected even after the extinction of the self- oscillation. These results showed that the ferroin-catalyzed system has additional oscillatory reaction which

Osamu INOMOTO; Tomoyuki OHYA; Shoichi KAI

2000-01-01

179

Iron-catalyzed cross-coupling reactions of alkyl Grignards with aryl sulfamates and tosylates.  

PubMed

The iron-catalyzed cross-coupling of aryl sulfamates and tosylates has been achieved with primary and secondary alkyl Grignards. This study of iron-catalyzed cross-coupling reactions also examines the isomerization and ?-hydride elimination problems that are associated with the use of isopropyl nucleophiles. While a variety of iron sources were competent in the reaction, the use of FeF(3)•3H(2)O was critical to minimize nucleophile isomerization. PMID:23244161

Agrawal, Toolika; Cook, Silas P

2012-12-17

180

Enzyme reactions in a multicompartment electrolyzer with isoelectrically trapped enzymes  

Microsoft Academic Search

The possibility of performing bioconversions under an electric field is here reported. A system is described by which the enzyme is trapped by an isoelectric mechanism between two zwitterionic membranes having pI values encompassing the isoelectric point of the enzyme. The enzyme is loaded into a multicompartment electrolyzer and kept operating under an electric field, which will continuously harvest the

Marcella Chiari; Norma Dell'Orto; Monica Mendozza; Giacomo Carrea; Pier Giorgio Righetti

1996-01-01

181

Fundamental reaction pathway and free energy profile for butyrylcholinesterase-catalyzed hydrolysis of heroin.  

PubMed

The pharmacological function of heroin requires an activation process that transforms heroin into 6-monoacetylmorphine (6-MAM), which is the most active form. The primary enzyme responsible for this activation process in human plasma is butyrylcholinesterase (BChE). The detailed reaction pathway of the activation process via BChE-catalyzed hydrolysis has been explored computationally, for the first time, in this study via molecular dynamics simulation and first-principles quantum mechanical/molecular mechanical free energy calculations. It has been demonstrated that the whole reaction process includes acylation and deacylation stages. The acylation consists of two reaction steps, i.e., the nucleophilic attack on the carbonyl carbon of the 3-acetyl group of heroin by the hydroxyl oxygen of the Ser198 side chain and the dissociation of 6-MAM. The deacylation also consists of two reaction steps, i.e., the nucleophilic attack on the carbonyl carbon of the acyl-enzyme intermediate by a water molecule and the dissociation of the acetic acid from Ser198. The calculated free energy profile reveals that the second transition state (TS2) should be rate-determining. The structural analysis reveals that the oxyanion hole of BChE plays an important role in the stabilization of rate-determining TS2. The free energy barrier (15.9 ± 0.2 or 16.1 ± 0.2 kcal/mol) calculated for the rate-determining step is in good agreement with the experimentally derived activation free energy (?16.2 kcal/mol), suggesting that the mechanistic insights obtained from this computational study are reliable. The obtained structural and mechanistic insights could be valuable for use in the future rational design of a novel therapeutic treatment of heroin abuse. PMID:23992153

Qiao, Yan; Han, Keli; Zhan, Chang-Guo

2013-08-30

182

A novel palladium-catalyzed homocoupling reaction initiated by transmetallation of palladium enolates  

Microsoft Academic Search

Palladium-catalyzed homocoupling reaction of aryl boronic acids has been developed using a protocol similar to the well-documented crosscoupling reaction. ?-Halocarbonyl compounds are applied to initiate the reaction via oxidative addition to a palladium(0) species. The resulting palladium enolate halide can promote the double transmetallation. Reductive elimination generates the desire homocoupling product.

Aiwen Lei; Xumu Zhang

2002-01-01

183

Iridium-catalyzed allylic vinylation and asymmetric allylic amination reactions with o-aminostyrenes.  

PubMed

An Ir-catalyzed allylic vinylation reaction of allyl carbonates with o-aminostyrene derivatives has been realized, providing skipped (Z,E)-diene derivatives. With (E)-but-2-ene-1,4-diyl dimethyl dicarbonate as the substrate, an efficient enantioselective synthesis of 1-benzazepine derivatives via an Ir-catalyzed domino allylic vinylation/intramolecular allylic amination reaction has been developed. Mechanistic studies of the allylic vinylation reaction have been carried out, and the results suggest that the leaving group of the allylic precursor plays a key role in directing the reaction pathway. Screening of various allylic precursors showed that Ir-catalyzed reactions of allyl diethyl phosphates with o-aminostyrene derivatives proceed via an allylic amination pathway. A subsequent ring-closing metathesis (RCM) reaction of the amination products led to a series of enantiomerically enriched 1,2-dihydroquinoline derivatives. Their utility is indicated by an asymmetric total synthesis of (-)-angustureine. PMID:21995503

Ye, Ke-Yin; He, Hu; Liu, Wen-Bo; Dai, Li-Xin; Helmchen, Günter; You, Shu-Li

2011-11-02

184

Diverse reactions catalyzed by naphthalene dioxygenase from Pseudomonas sp strain NCIB 9816  

Microsoft Academic Search

Naphthalene dioxygenase (NDO) fromPseudomonas sp strain NCIB 9816 is a multicomponent enzyme system which initiates naphthalene catabolism by catalyzing the addition of both atoms of molecular oxygen and two hydrogen atoms to the substrate to yield enantiomerically pure (+)-cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene. NDO has a relaxed substrate specificity and catalyzes the dioxygenation of many related 2- and 3-ring aromatic and hydroaromatic (benzocyclic) compounds

SM Resnick; K Lee; DT Gibson

1996-01-01

185

Oxidation reactions catalyzed by vanadium chloroperoxidase from Curvularia inaequalis  

Microsoft Academic Search

Vanadium haloperoxidases have been reported to mediate the oxidation of halides to hypohalous acid and the sulfoxidation of organic sulfides to the corresponding sulfoxides in the presence of hydrogen peroxide. However, traditional heme peroxidase substrates were reported not to be oxidized by vanadium haloperoxidases. Surprisingly, we have now found that the recombinant vanadium chloroperoxidase from the fungus Curvularia inaequalis catalyzes

Hilda B ten Brink; Henk L Dekker; Hans E Schoemaker; Ron Wever

2000-01-01

186

The reaction mechanism for dehydration process catalyzed by type I dehydroquinate dehydratase from Gram-negative Salmonella enterica  

NASA Astrophysics Data System (ADS)

The fundamental reaction mechanism for the dehydration process catalyzed by type I dehydroquinate dehydratase from Gram-negative Salmonella enterica has been studied by density functional theory calculations. The results indicate that the dehydration process undergoes a two-step cis-elimination mechanism, which is different from the previously proposed one. The catalytic roles of both the highly conserved residue His143 and the Schiff base formed between the substrate and Lys170 have also been elucidated. The structural and mechanistic insight presented here may direct the design of type I dehydroquinate dehydratase enzyme inhibitors as non-toxic antimicrobials, anti-fungals, and herbicides.

Yao, Yuan; Li, Ze-Sheng

2012-01-01

187

A free-standing condensation enzyme catalyzing ester bond formation in C-1027 biosynthesis  

PubMed Central

Nonribosomal peptide synthetases (NRPSs) catalyze the biosynthesis of many biologically active peptides and typically are modular, with each extension module minimally consisting of a condensation, an adenylation, and a peptidyl carrier protein domain responsible for incorporation of an amino acid into the growing peptide chain. C-1027 is a chromoprotein antitumor antibiotic whose enediyne chromophore consists of an enediyne core, a deoxy aminosugar, a benzoxazolinate, and a ?-amino acid moiety. Bioinformatics analysis suggested that the activation and incorporation of the ?-amino acid moiety into C-1027 follows an NRPS mechanism whereby biosynthetic intermediates are tethered to the peptidyl carrier protein SgcC2. Here, we report the biochemical characterization of SgcC5, an NRPS condensation enzyme that catalyzes ester bond formation between the SgcC2-tethered (S)-3-chloro-5-hydroxy-?-tyrosine and (R)-1-phenyl-1,2-ethanediol, a mimic of the enediyne core. SgcC5 uses (S)-3-chloro-5-hydroxy-?-tyrosyl-SgcC2 as the donor substrate and exhibits regiospecificity for the C-2 hydroxyl group of the enediyne core mimic as the acceptor substrate. Remarkably, SgcC5 is also capable of catalyzing amide bond formation, albeit with significantly reduced efficiency, between (S)-3-chloro-5-hydroxy-?-tyrosyl-(S)-SgcC2 and (R)-2-amino-1-phenyl-1-ethanol, an alternative enediyne core mimic bearing an amine at its C-2 position. Thus, SgcC5 is capable of catalyzing both ester and amide bond formation, providing an evolutionary link between amide- and ester-forming condensation enzymes.

Lin, Shuangjun; Van Lanen, Steven G.; Shen, Ben

2009-01-01

188

Cobalt-catalyzed hydrosilation/hydrogen-transfer cascade reaction: a new route to silyl enol ethers.  

PubMed

Capitalizing on cobalt: A new route to silyl enol ethers employing a Co-catalyzed cascade reaction featuring a tandem hydrosilation/hydrogen-transfer reaction is reported. The low catalyst loading, mild reaction conditions, and unique ?(2)-silane resting state showcase the impressive utility of this seldom used transition-metal catalyst in C-H activation reactions (see scheme; VTMS?=?vinyltrimethylsilane; Cp*? = ?1,2,3,4,5-pentamethylcyclopentadiene). PMID:23780615

Lyons, Thomas W; Brookhart, Maurice

2013-06-18

189

Explaining the Atypical Reaction Profiles of Heme Enzymes with a Novel Mechanistic Hypothesis and Kinetic Treatment  

PubMed Central

Many heme enzymes show remarkable versatility and atypical kinetics. The fungal extracellular enzyme chloroperoxidase (CPO) characterizes a variety of one and two electron redox reactions in the presence of hydroperoxides. A structural counterpart, found in mammalian microsomal cytochrome P450 (CYP), uses molecular oxygen plus NADPH for the oxidative metabolism (predominantly hydroxylation) of substrate in conjunction with a redox partner enzyme, cytochrome P450 reductase. In this study, we employ the two above-mentioned heme-thiolate proteins to probe the reaction kinetics and mechanism of heme enzymes. Hitherto, a substrate inhibition model based upon non-productive binding of substrate (two-site model) was used to account for the inhibition of reaction at higher substrate concentrations for the CYP reaction systems. Herein, the observation of substrate inhibition is shown for both peroxide and final substrate in CPO catalyzed peroxidations. Further, analogy is drawn in the “steady state kinetics” of CPO and CYP reaction systems. New experimental observations and analyses indicate that a scheme of competing reactions (involving primary product with enzyme or other reaction components/intermediates) is relevant in such complex reaction mixtures. The presence of non-selective reactive intermediate(s) affords alternate reaction routes at various substrate/product concentrations, thereby leading to a lowered detectable concentration of “the product of interest” in the reaction milieu. Occam's razor favors the new hypothesis. With the new hypothesis as foundation, a new biphasic treatment to analyze the kinetics is put forth. We also introduce a key concept of “substrate concentration at maximum observed rate”. The new treatment affords a more acceptable fit for observable experimental kinetic data of heme redox enzymes.

Manoj, Kelath Murali; Baburaj, Arun; Ephraim, Binoy; Pappachan, Febin; Maviliparambathu, Pravitha Parapurathu; Vijayan, Umesh K.; Narayanan, Sivaprasad Valiyaveettil; Periasamy, Kalaiselvi; George, Ebi Ashley; Mathew, Lazar T.

2010-01-01

190

Bulk Gold-Catalyzed Reactions of Isocyanides, Amines, and Amine N-Oxides  

SciTech Connect

Bulk gold powder (5–50 ?m particles) catalyzes the reactions of isocyanides with amines and amine N-oxides to produce ureas. The reaction of n-butyl isocyanide (nBu–N?C) with di-n-propylamine and N-methylmorpholine N-oxide in acetonitrile, which was studied in the greatest detail, produced 3-butyl-1,1-dipropylurea (O?C(NHnBu)(NnPr2)) in 99% yield at 60 °C within 2 h. Sterically and electronically different isocyanides, amines, and amine N-oxides react successfully under these conditions. Detailed studies support a two-step mechanism that involves a gold-catalyzed reaction of adsorbed isocyanide with the amine N-oxide to form an isocyanate (RN?C?O), which rapidly reacts with the amine to give the urea product. These investigations show that bulk gold, despite its reputation for poor catalytic activity, is capable of catalyzing these reactions.

Klobukowski, Erik; Angelici, Robert; Woo, Keith L.

2012-01-26

191

Palladium-catalyzed cross-coupling reaction of secondary benzylic bromides with grignard reagents.  

PubMed

A mild palladium-catalyzed Kumada-Corriu reaction of secondary benzylic bromides with aryl and alkenyl Grignard reagents has been developed. In the presence of the Xantphos ligand, the undesired beta-elimination pathway is minimized, affording the corresponding cross-coupling products in acceptable to good yields. The reaction proceeds with inversion of the configuration. PMID:19943702

López-Pérez, Ana; Adrio, Javier; Carretero, Juan C

2009-12-01

192

Iridium-catalyzed reaction of enones with alcohols affording 1,3-diketones.  

PubMed

An iridium-catalyzed coupling reaction of alcohols with enones has been successfully developed providing access to 1,3-diketones with high selectivity in good yields. This reaction provides an atom-economical route to 1,3-diketones from readily available alcohols. PMID:22641102

Obora, Yasushi; Nakamura, Kazuhiro; Hatanaka, Shintaro

2012-05-28

193

A deep cavitand catalyzes the Diels-Alder reaction of bound maleimides.  

PubMed

A deep cavitand catalyzes Diels-Alder reactions of bound maleimides via activation of the dienophile by interaction with the organized hydrogen bonding network at the cavitand rim. Rapid in-out exchange of reactant and product allows efficient turnover. The increase in steric bulk of the reaction product lessens its binding affinity, reducing (and in some cases completely eliminating) product inhibition. PMID:17971992

Hooley, Richard J; Rebek, Julius

2007-10-04

194

Enzyme electrochemical sensor electrode.  

National Technical Information Service (NTIS)

An electrochemical sensor electrode is formed from an electronic conductor coated with a casting solution containing a perfluorosulfonic acid ionomer and a selected enzyme. The selected enzyme catalyzes a reaction between a predetermined substance in a so...

J. Rishpon S. Gottesfeld T. A. Zawodzinski

1989-01-01

195

In Vivo Identification of Intermediate Stages of the DNA Inversion Reaction Catalyzed by the Salmonella Hin Recombinase  

Microsoft Academic Search

The Hin recombinase catalyzes a site-specific recombination reaction that results in the reversible inversion of a 1-kbp segment of the Salmonella chromosome. The DNA inversion reaction catalyzed by the Salmonella Hin recombinase is a dynamic process proceeding through many intermediate stages, requiring multiple DNA sites and the Fis accessory protein. Biochemical analysis of this reaction has identified intermediate steps in

Oliver Z. Nanassy; Kelly T. Hughes

196

Iron and xanthine oxidase catalyze formation of an oxidant species distinguishable from OH. : comparison with the Haber-Weiss reaction  

SciTech Connect

O2- was produced by gamma irradiation of formate solutions, by the action of xanthine oxidase on hypoxanthine and O2, and by the action of ferredoxin reductase on NADPH and paraquat in the presence of O2. Its reaction with H2O2 and various iron chelates was studied. Oxidation of deoxyribose to thiobarbituric acid-reactive products that was appropriately inhibited by OH. scavengers, or formate oxidation to CO2, was used to detect OH(.). With each source of O2-, and by these criteria, Fe(EDTA) efficiently catalyzed this (Haber-Weiss) reaction, but little catalysis was detectable with iron bound to DTPA, citrate, ADP, ATP, or pyrophosphate, or without chelator in phosphate buffer. O2- produced from xanthine oxidase, but not from the other sources, underwent another iron-dependent reaction with H2O2, to produce an oxidant that did not behave as free OH(.). It was formed in phosphate or bicarbonate buffer, and caused deoxyribose oxidation that was readily inhibited by mannitol or Tris, but not by benzoate, formate, or dimethyl sulfoxide. It did not oxidize formate to CO2. Addition of EDTA changed the pattern of inhibition to that expected for a reaction of OH(.). The other chelators all inhibited deoxyribose oxidation, provided their concentrations were high enough. The results are compatible with iron bound to xanthine oxidase catalyzing production of a strong oxidant (which is not free OH.) from H2O2 and O2- produced by the enzyme.

Winterbourn, C.C.; Sutton, H.C.

1986-01-01

197

An ester appending multifunctional ionic liquid for Pd(II) catalyzed Heck reaction  

Microsoft Academic Search

A basic, ester functionalized, imidazolium based ionic liquid (IL2), 3-Methyl-1-(ethoxycarbonylmethyl)imidazolium hydroxide was designed eyeing in situ generation and stabilization of palladium nanoparticles for palladium catalyzed Heck reaction of haloarenes and olefins. This phosphine-free Pd-IL catalyst demonstrated excellent activity and reusability at relatively low reaction temperature (80°C) for a wide spectrum of haloarenes including chloroarenes. The relatively low reaction temperature could

Anand D. Sawant; Dilip G. Raut; Nitin B. Darvatkar; Uday V. Desai; Manikrao M. Salunkhe

2010-01-01

198

Cu-Catalyzed Cross-Dehydrogenative Coupling Reactions of (Benzo)thiazoles with Cyclic Ethers.  

PubMed

Copper-catalyzed cross-dehydrogenative coupling (CDC) reactions of (benzo)thiazoles with cyclic ethers were developed under mild conditions. In particular, the formation of C-C bonds via the CDC reactions between non-benzo-fused azoles and ethers are reported for the first time. In addition, the acetals, known as the masked 2-thiazolecarboxaldehydes, could be successfully obtained by this CDC reaction. The preliminary mechanism and supportive DFT calculations are discussed as well. PMID:23967877

Xie, Zengyang; Cai, Yuping; Hu, Hongwen; Lin, Chen; Jiang, Juli; Chen, Zhaoxu; Wang, Leyong; Pan, Yi

2013-08-22

199

Nuclear physics of the muon-catalyzed d+d reactions  

SciTech Connect

A Coulomb-corrected, charge independent R-matrix calculation of the four-nucleon reactions accounts for the surprisingly large branching ratio, as well as for the absolute fusion rate measured for the muon- catalyzed d{plus}d reactions. Reaction constants are given for both S-wave and P-wave transitions that would result in the sort of temperature dependence for the branching ratio that has recently been observed. 6 refs., 1 fig., 1 tab.

Hale, G.M.

1990-01-01

200

Tandem Aldol Condensation - Platinacycle-Catalyzed Addition Reactions of Aldehydes, Methyl Ketones and Arylboronic Acids  

PubMed Central

Tandem aldol condensation of aldehydes with methyl ketones followed by anionic four-electron donor-based (Type I) platinacycle-catalyzed addition reactions of arylboronic acids to form ?-arylated ketones is described. Good to excellent yields of ?-arylated ketones were obtained for the tandem reactions of aromatic/aliphatic aldehydes, methyl ketones and arylboronic acids, and moderate yields were observed for the tandem reaction with ?, ?-unsaturated aldehydes as the aldehyde source.

Liao, Yuan-Xi; Hu, Qiao-Sheng

2013-01-01

201

Tandem Aldol Condensation - Platinacycle-Catalyzed Addition Reactions of Aldehydes, Methyl Ketones and Arylboronic Acids.  

PubMed

Tandem aldol condensation of aldehydes with methyl ketones followed by anionic four-electron donor-based (Type I) platinacycle-catalyzed addition reactions of arylboronic acids to form ?-arylated ketones is described. Good to excellent yields of ?-arylated ketones were obtained for the tandem reactions of aromatic/aliphatic aldehydes, methyl ketones and arylboronic acids, and moderate yields were observed for the tandem reaction with ?, ?-unsaturated aldehydes as the aldehyde source. PMID:23335856

Liao, Yuan-Xi; Hu, Qiao-Sheng

2012-09-01

202

Efficient Biginelli Reaction Catalyzed by Sulfamic Acid or Silica Sulfuric Acid under Solvent?Free Conditions  

Microsoft Academic Search

Sulfamic acid efficiently catalyzes the three?component condensation reaction of aldehydes, 1,3?dicarbonyl compounds, and urea\\/thiourea under solvent?free conditions to afford the corresponding dihydropyrimidinones and thio?derivatives in high yields. Silica sulfuric acid is also found to be an efficient catalyst for the Biginelli reaction under solvent?free conditions. Compared to the classical Biginelli reaction conditions, this new method consistently has the advantage of

2007-01-01

203

A natural vanishing act: the enzyme-catalyzed degradation of carbon nanomaterials.  

PubMed

Over the past three decades, revolutionary research in nanotechnology by the scientific, medical, and engineering communities has yielded a treasure trove of discoveries with diverse applications that promise to benefit humanity. With their unique electronic and mechanical properties, carbon nanomaterials (CNMs) represent a prime example of the promise of nanotechnology with applications in areas that include electronics, fuel cells, composites, and nanomedicine. Because of toxicological issues associated with CNMs, however, their full commercial potential may not be achieved. The ex vitro, in vitro, and in vivo data presented in this Account provide fundamental insights into the biopersistence of CNMs, such as carbon nanotubes and graphene, and their oxidation/biodegradation processes as catalyzed by peroxidase enzymes. We also communicate our current understanding of the mechanism for the enzymatic oxidation and biodegradation. Finally, we outline potential future directions that could enhance our mechanistic understanding of the CNM oxidation and biodegradation and could yield benefits in terms of human health and environmental safety. The conclusions presented in this Account may catalyze a rational rethinking of CNM incorporation in diverse applications. For example, armed with an understanding of how and why CNMs undergo enzyme-catalyzed oxidation and biodegradation, researchers can tailor the structure of CNMs to either promote or inhibit these processes. In nanomedical applications such as drug delivery, the incorporation of carboxylate functional groups could facilitate biodegradation of the nanomaterial after delivery of the cargo. On the other hand, in the construction of aircraft, a CNM composite should be stable to oxidizing conditions in the environment. Therefore, pristine, inert CNMs would be ideal for this application. Finally, the incorporation of CNMs with defect sites in consumer goods could provide a facile mechanism that promotes the degradation of these materials once these products reach landfills. PMID:22824066

Kotchey, Gregg P; Hasan, Saad A; Kapralov, Alexander A; Ha, Seung Han; Kim, Kang; Shvedova, Anna A; Kagan, Valerian E; Star, Alexander

2012-07-23

204

A Natural Vanishing Act: The Enzyme-Catalyzed Degradation of Carbon Nanomaterials  

PubMed Central

CONSPECTUS Over the past three decades, revolutionary research in nanotechnology by the scientific, medical, and engineering communities has yielded a treasure trove of discoveries with diverse applications that promise to benefit humanity. With their unique electronic and mechanical properties, carbon nanomaterials (CNMs) represent a prime example of the promise of nanotechnology with applications in areas that include electronics, fuel cells, composites, and nanomedicine. Because of toxicological issues associated with CNMs, however, their full commercial potential may not be achieved. The ex vitro, in vitro, and in vivo data presented in this Account provide fundamental insights into the biopersistence of CNMs, such as carbon nanotubes and graphene, and their oxidation/biodegradation processes as catalyzed by peroxidase enzymes. We also communicate our current understanding of the mechanism for the enzymatic oxidation/biodegradation. Finally, we outline potential future directions that could enhance our mechanistic understanding of the CNM oxidation/biodegradation and could yield benefits in terms of human health and environmental safety. The conclusions presented in this Account may catalyze a rational rethinking of CNM incorporation in diverse applications. For example, armed with an understanding of how and why CNMs undergo enzyme-catalyzed oxidation/biodegradation, researchers can tailor the structure of CNMs to either promote or inhibit these processes. In nanomedical applications such as drug delivery, the incorporation of carboxylate functional groups could facilitate biodegradation of the nanomaterial after delivery of the cargo. On the other hand, in the construction of aircraft, a CNM composite material should be stable to oxidizing conditions in the environment. Therefore, pristine, inert CNMs would be ideal for this application. Finally, the incorporation of CNMs with defect sites in consumer goods could provide a facile mechanism that promotes the degradation of these materials once these products reach landfills.

Kotchey, Gregg P.; Hasan, Saad A.; Kapralov, Alexander A.; Ha, Seung Han; Kim, Kang; Shvedova, Anna A.; Kagan, Valerian E.; Star, Alexander

2012-01-01

205

Concise, convergent syntheses of (±)-trichostatin A utilizing a Pd-catalyzed ketone enolate ?-alkenylation reaction.  

PubMed

Two concise, convergent syntheses of (±)-trichostatin A (1), a potent histone deacetylase inhibitor, have been accomplished. The key step in both is a Pd-catalyzed ?-alkenylation reaction between ketone 2 and either dienyl bromide 3 or alkenyl bromide 9 using a modification of cross-coupling conditions described by Negishi and Hartwig. A brief investigation has shown the potential utility of a Ni-catalyzed version of this reaction. The overall synthetic routes are short and amenable to scaleup, providing access to trichostatin A via trichostatic acid as a direct precursor. PMID:21688856

Cosner, Casey C; Helquist, Paul

2011-06-21

206

Gold-catalyzed reactions between alkenyldiazo carbonyl species and acetals.  

PubMed

In the presence of catalyst IPrAuSbF6 catalyst (IPr = 1,3-bis(diisopropylphenyl)imidazol-2-ylidene), alkenyldiazo carbonyl species react with organic acetals to give E-configured alkyl 3,5-dimethoxy-5-pent-2-enoates stereoselectively. This reaction sequence comprises an initial Prins-type reaction, followed by gold carbene formation. PMID:23641859

Pagar, Vinayak Vishnu; Jadhav, Appaso M; Liu, Rai-Shung

2013-05-14

207

Enzyme-Catalyzed Ring-Opening Polymerization of ?-Caprolactone in Supercritical Carbon Dioxide  

Microsoft Academic Search

We report the ring-opening polymerization reaction of -caprolactone in supercritical carbon dioxide (scCO2) using an enzyme catalyst, Lipase B from Candida antarctica supported on macroporous beads (Novozym-435). Ring-opening polymerization of lactones is more commonly performed in organic solvents or in bulk using a Lewis acid catalyst. Recently there has been much interest in the replacement of such catalysts by enzymes.

Frank C. Loeker; Christopher J. Duxbury; Rajesh Kumar; Wei Gao; Richard A. Gross; Steven M. Howdle

2004-01-01

208

Global Conformational Change Associated with the Two-step Reaction Catalyzed by Escherichia coli Lipoate-Protein Ligase A*  

PubMed Central

Lipoate-protein ligase A (LplA) catalyzes the attachment of lipoic acid to lipoate-dependent enzymes by a two-step reaction: first the lipoate adenylation reaction and, second, the lipoate transfer reaction. We previously determined the crystal structure of Escherichia coli LplA in its unliganded form and a binary complex with lipoic acid (Fujiwara, K., Toma, S., Okamura-Ikeda, K., Motokawa, Y., Nakagawa, A., and Taniguchi, H. (2005) J Biol. Chem. 280, 33645–33651). Here, we report two new LplA structures, LplA·lipoyl-5?-AMP and LplA·octyl-5?-AMP·apoH-protein complexes, which represent the post-lipoate adenylation intermediate state and the pre-lipoate transfer intermediate state, respectively. These structures demonstrate three large scale conformational changes upon completion of the lipoate adenylation reaction: movements of the adenylate-binding and lipoate-binding loops to maintain the lipoyl-5?-AMP reaction intermediate and rotation of the C-terminal domain by about 180°. These changes are prerequisites for LplA to accommodate apoprotein for the second reaction. The Lys133 residue plays essential roles in both lipoate adenylation and lipoate transfer reactions. Based on structural and kinetic data, we propose a reaction mechanism driven by conformational changes.

Fujiwara, Kazuko; Maita, Nobuo; Hosaka, Harumi; Okamura-Ikeda, Kazuko; Nakagawa, Atsushi; Taniguchi, Hisaaki

2010-01-01

209

Phospholipids chiral at phosphorus. Steric course of the reactions catalyzed by phosphatidylserine synthase from Escherichia coli and yeast  

SciTech Connect

The steric courses of the reactions catalyzed by phosphatidylserine (PS) synthase from Escherichia coli and yeast were elucidated by the following procedure. R/sub P/ and S/sub P/ isomers of 1,2-dipalmitoyl-sn-glycero-3-(/sup 17/O, /sup 18/O)phosphoethanolamine ((/sup 17/O, /sup 18/O)DPPE) were synthesized and converted to (R/sub P/)- and (S/sub P/)-1,2-dipalmitoyl-sn-glycero-3-(/sup 16/O, /sup 17/O, /sup 18/O)DPPA), respectively, by incubating with phospholipase D. Condensation of (/sup 16/O, /sup 17/O, /sup 18/O)DPPA with cytidine 5'-monophosphomorpholidate in pyridine gave the desired substrate for PS synthase, (/sup 17/O, /sup 18/O)cytidine 5'-diphospho-1,2-dipalmitoyl-sn-glycerol ((/sup 17/O,/sup 18/O)CDP-DPG), as a mixture of several isotopic and configurational isomers. Incubation of (/sup 17/O, /sup 18/O)CDP-DPG), as a mixture of several isotopic and configurational isomers. Incubation of (/sup 17/O, /sup 18/O) CDP-DPG with a mixture of L-serine, PS synthase and PS decarboxylase gave (/sup 17/O, /sup 18/O)DPPE. The configuration and isotopic enrichments of the starting (/sup 17/O, /sup 18/O)DPPE and the product were analyzed by /sup 31/P NMR following trimethylsilylation of the DPPE. The results indicate that the reaction of E. coli PS synthase proceeds with retention of configuration at phosphorus, which suggests a two-step mechanism involving a phosphatidyl-enzyme intermediate, while the yeast PS synthase catalyzes the reaction with inversion of configuration, which suggests a single-displacement mechanism. Such results lend strong support to the ping-pong mechanism proposed for the E. coli enzyme and the sequential Bi-Bi mechanism proposed for the yeast enzyme, both based on previous isotopic exchange experiments.

Raetz, C.R.H.; Carman, G.M.; Dowhan, W.; Jiang, R.T.; Waszkuc, W.; Loffredo, W.; Tsai, M.D.

1987-06-30

210

Mineral catalyzed hydrothermal reactions as precursors to extant anabolic pathways  

NASA Astrophysics Data System (ADS)

Investigations into hydrothermal reactions under conditions of moderate hydrostatic pressure and in the presence of transition metal sulfides reveal reaction pathways the bear remarkable similarity with extant anabolic reactions. First, it is seen that most common transition metal sulfides are capable of promoting all of the key reactions at the core of Acetyl Co-A synthesis. These include CO reduction to methyl groups and carbonyl insertion to form transferable acetyl groups. The synthesis of alpha-keto acids are also promoted, presumably by double carbonylation. A pathway starting with CO2 and H2 has been identified leading to the synthesis of citric acid. Citric acid provides a crucial abiotic, anabolic, branch point to the prebiotic synthesis of various amino acids, as well. As the pyrimidines, orotic acid and uracil. In many cases the abiotic reaction pathways differ slightly from extant anabolic pathways by shunting past particularly reactive intermediates, e.g. oxaloacetic acid. These reactions have the capacity to provide the prebiotic world with many, but not all, of the molecular constituents to aid the emergence of an RNA world.

Cody, G. D.

211

Carbocyclization versus oxycyclization on the metal-catalyzed reactions of oxyallenyl C3-linked indoles.  

PubMed

The preparation of previously unknown (indol-3-yl)-?-allenols and -allenones was accomplished from indole-3-carbaldehydes, through indium-mediated Barbier allenylation reaction taking advantage of the N-(2-pyridyl)sulfonyl group. Metal-catalyzed cyclizations of oxyallenyl C3-linked indoles proceeded in two ways depending on the presence or absence of the N-(2-pyridyl)sulfonyl group. For allenols, gold-catalyzed oxycyclization occurred in the presence of the protecting group; in the absence of the protecting group, palladium- and gold-catalyzed benzannulations operated. On the contrary, under gold catalysis furyl-indoles were obtained as exclusive products from NH-allenones, while 5-endo carbocyclization adducts were the major components starting from N-SO2py-protected allenones. These cyclization reactions have been developed experimentally, and their mechanisms have additionally been investigated by a computational study. PMID:23738835

Alcaide, Benito; Almendros, Pedro; Alonso, José M; Fernández, Israel

2013-06-18

212

Nonperfect synchronization of reaction center rehybridization in the transition state of the hydride transfer catalyzed by dihydrofolate reductase.  

PubMed

It has been suggested that the magnitudes of secondary kinetic isotope effects (2 degrees KIEs) of enzyme-catalyzed reactions are an indicator of the extent of reaction-center rehybridization at the transition state. A 2 degrees KIE value close to the corresponding secondary equilibrium isotope effects (2 degrees EIE) is conventionally interpreted as indicating a late transition state that resembles the final product. The reliability of using this criterion to infer the structure of the transition state is examined by carrying out a theoretical investigation of the hybridization states of the hydride donor and acceptor in the Escherichia coli dihydrofolate reductase (ecDHFR)-catalyzed reaction for which a 2 degrees KIE close to the 2 degrees EIE was reported. Our results show that the donor carbon at the hydride transfer transition state resembles the reactant state more than the product state, whereas the acceptor carbon is more productlike, which is a symptom of transition state imbalance. The conclusion that the isotopically substituted carbon is reactant-like disagrees with the conclusion that would have been derived from the criterion of 2 degrees KIEs and 2 degrees EIEs, but the breakdown of the correlation with the equilibrium isotope effect can be explained by considering the effect of tunneling. PMID:16231943

Pu, Jingzhi; Ma, Shuhua; Garcia-Viloca, Mireia; Gao, Jiali; Truhlar, Donald G; Kohen, Amnon

2005-10-26

213

The spliceosome catalyzes debranching in competition with reverse of the first chemical reaction.  

PubMed

Splicing of nuclear pre-mRNA occurs via two steps of the transesterification reaction, forming a lariat intermediate and product. The reactions are catalyzed by the spliceosome, a large ribonucleoprotein complex composed of five small nuclear RNAs and numerous protein factors. The spliceosome shares a similar catalytic core structure with that of fungal group II introns, which can self-splice using the same chemical mechanism. Like group II introns, both catalytic steps of pre-mRNA splicing can efficiently reverse on the affinity-purified spliceosome. The spliceosome also catalyzes a hydrolytic spliced-exon reopening reaction as observed in group II introns, indicating a strong link in their evolutionary relationship. We show here that, by arresting splicing after the first catalytic step, the purified spliceosome can catalyze debranching of lariat-intron-exon 2. The debranching reaction, although not observed in group II introns, has similar monovalent cation preferences as those for splicing catalysis of group II introns. The debranching reaction is in competition with the reverse Step 1 reaction influenced by the ionic environment and the structure of components binding near the catalytic center, suggesting that the catalytic center of the spliceosome can switch between different conformations to direct different chemical reactions. PMID:23681507

Tseng, Chi-Kang; Cheng, Soo-Chen

2013-05-16

214

Base-catalyzed feedback in the urea-urease reaction.  

PubMed

The bell-shaped rate-pH curve coupled to production of base in the urea-urease reaction was utilized to give feedback-driven behavior: an acid-to-base pH clock (a kinetic switch), bistability and hysteresis between an acid/base state when the initial pH was adjusted by a strong acid, and aperiodic pH oscillations when the initial pH was adjusted by a weak acid in an open reactor. A simple model of the reaction reproduced most of the experimental results and provided insight into the role of self-buffering in the dynamics. This reaction suggests new possibilities in the development of biocompatible feedback to couple to pH-sensitive processes for bioinspired applications in medicine, engineering, or materials science. PMID:20954690

Hu, Gang; Pojman, John A; Scott, Stephen K; Wrobel, Magdalena M; Taylor, Annette F

2010-11-11

215

Particle growth by acid-catalyzed heterogeneous reactions of organic carbonyls on preexisting aerosols.  

PubMed

Aerosol growth by the heterogeneous reactions of different aliphatic and alpha,beta-unsaturated carbonyls in the presence/absence of acidified seed aerosols was studied in a 2 m long flow reactor (2.5 cm i.d.) and a 0.5-m3 Teflon film bag under darkness. For the flow reactor experiments, 2,4-hexadienal, 5-methyl-3-hexen-2-one, 2-cyclohexenone, 3-methyl-2-cyclopentenone, 3-methyl-2-cyclohexenone, and octanal were studied. The carbonyls were selected based on their reactivity for acid-catalyzed reactions, their proton affinity, and their similarity to the ring-opening products from the atmospheric oxidation of aromatics. To facilitate acid-catalyzed heterogeneous hemiacetal/acetal formation, glycerol was injected along with inorganic seed aerosols into the flow reactor system. Carbonyl heterogeneous reactions were accelerated in the presence of acid catalysts (H2SO4), leading to higher aerosol yields than in their absence. Aldehydes were more reactive than ketones for acid-catalyzed reactions. The conjugated functionality also resulted in higher organic aerosol yieldsthan saturated aliphatic carbonyls because conjugation with the olefinic bond increases the basicity of the carbonyl leading to increased stability of the protonated carbonyl. Aerosol population was measured from a series of sampling ports along the length of the flow reactor using a scanning mobility particle sizer. Fourier transform infrared spectrometry of either an impacted liquid aerosol layer or direct reaction of carbonyls as a thin liquid layer on a zinc selenide FTIR disk was employed to demonstrate the direct transformation of chemical functional groups via the acid-catalyzed reactions. These results strongly indicate that atmospheric multifunctional organic carbonyls, which are created by atmospheric photooxidation reactions, can contribute significantly to secondary organic aerosol formation through acid-catalyzed heterogeneous reactions. Exploratory studies in 25- and 190-m3 outdoor chambers were also implemented to demonstrate the formation of high molecular weight organic structures. The reaction of ozone with alpha-pinene to generate secondary organic aerosols (SOAs) was performed in the presence of background aerosol consisting of a mixture of wood soot and diesel soot. Results strongly suggest that indigenous sulfuric acid associated with the combustion of fossil fuels (e.g., diesel soot) can initiate acid-catalyzed heterogeneous reactions of SOAs on the particle phase. PMID:12967102

Jang, Myoseon; Carroll, Brian; Chandramouli, Bharadwaj; Kamens, Richard M

2003-09-01

216

From vinyl pyranoses to carbasugars by an iron-catalyzed reaction complementary to classical Ferrier carbocyclization.  

PubMed

Starting from vinyl pyranoses an iron-catalyzed tandem isomerization-intramolecular aldolization reaction was developed to prepare cyclohexenone derivatives bearing substituents on the double bond, and it has been applied in a short synthesis of 4-epi-gabosines A and B, from d-glucose. PMID:19641820

Mac, Dinh Hung; Samineni, Ramesh; Petrignet, Julien; Srihari, Pabbaraja; Chandrasekhar, Srivari; Yadav, Jhillu Singh; Grée, René

2009-06-24

217

N-heterocyclic carbene-catalyzed stereoselective cascade reaction: synthesis of functionalized tetrahydroquinolines.  

PubMed

The first N-heterocyclic carbene-catalyzed stereoselective aza-Michael-Michael-lactonization cascade reaction of 2'-aminophenylenones and 2-bromoenals for the construction of chiral functionalized tetrahydroquinolines with three consecutive stereogenic centers has been achieved in high yields (up to 98%) with excellent diastereo- (>25:1) and enantioselectivities (up to 98.7% ee). PMID:24020617

Zhang, Hai-Rui; Dong, Zhen-Wen; Yang, Yu-Jie; Wang, Ping-Luan; Hui, Xin-Ping

2013-09-10

218

Efficient Chromium(II)-Catalyzed Cross-Coupling Reactions between Csp(2) Centers.  

PubMed

Low-toxicity chromium(II) chloride catalyzes at 25 °C within minutes the coupling reactions of various (hetero)arylmagnesium reagents with N-heterocyclic halides, aromatic halogenated ketones or imines, and alkenyl iodides. Remarkably, much lower amounts of homo-coupling side products are obtained compared to related iron, cobalt, or manganese cross-couplings. PMID:24053764

Steib, Andreas K; Kuzmina, Olesya M; Fernandez, Sarah; Flubacher, Dietmar; Knochel, Paul

2013-10-07

219

An inexpensive fluorescent labeling protocol for bioactive natural products utilizing Cu(I)-catalyzed Huisgen reaction  

Microsoft Academic Search

Labeling of bioactive small molecules with organic dyes for various applications in cell biology has been emerging as an attractive research field. Using an easily prepared and inexpensive fluorescein derivative 1 and a Cu(I)-catalyzed Huisgen reaction, an efficient fluorescent labeling strategy is developed generally for bioactive natural products. Essentials of a successful labeling include the personalized introduction of an azido

Yan-Hong Zhang; Zheng-Xi Gao; Chun-Long Zhong; Hai-Bin Zhou; Lei Chen; Wen-Min Wu; Xin-Jun Peng; Zhu-Jun Yao

2007-01-01

220

Ag(I)-catalyzed cyclization reaction of ethyl o-hydroxyphenylethynylphosphinates to phosphachromones  

Microsoft Academic Search

An Ag(I)-catalyzed intramolecular cyclization of ethyl o-hydroxyphenylethynylphosphinate to phosphachromones has been developed with high regioselectivity and good yields. The present reaction represents the first example of intramolecular addition of phenol to 1-alkynylphosphonates, which provides an approach to synthesize new phosphorus heterocycles. The resulting phosphachromones could have potential bioactivities.

Liang Xie; Jing Ma; Yi-Xiang Ding

2008-01-01

221

Oscillating luminescence in the Belousov-Zhabotinsky reaction catalyzed by Ru(bpy) 3 2+  

Microsoft Academic Search

Oscillations in the Ru(bpy)32+ catalyzed Belousov-Zhabotinsky reaction were followed by monitoring the absorbance, photoand chemiluminescence intensity, lifetime of the luminescent excited state, and bromide concentration. The formation of a species (most probably Br2) which quenches the Ru(bpy)32+ luminescence is followed.

F. Bolletta; L. Prodi; N. Zaccheroni

1995-01-01

222

Highly stereoselective synthesis of trisubstituted cyclohexanols using a guanidine-catalyzed tandem Henry-Michael reaction.  

PubMed

A highly diastereoselective (dr >99:1) and enantioselective (ee value up to 98%) synthesis of trisubstituted cyclohexanols was achieved by using a tandem Henry--Michael reaction between nitromethane and 7-oxo-hept-5-enals catalyzed by the Misaki-Sugimura guanidine. PMID:23544418

Dai, Qipu; Huang, Huicai; Zhao, John Cong-Gui

2013-04-09

223

Asymmetric Mannich reaction of ?-keto imines catalyzed by diarylprolinol silyl ether.  

PubMed

Synthetic methods: An asymmetric catalytic, desulfonylative Mannich reaction of ?-keto imines with aldehydes, as catalyzed by diarylprolinol silyl ether 1, was developed. It gave the Mannich product in good yield with excellent anti and enantioselectivity (see scheme; Boc = tert-butoxycarbonyl, TMS = trimethylsilyl). PMID:23633408

Hayashi, Yujiro; Sakamoto, Daisuke; Shomura, Hiroki; Hashizume, Daisuke

2013-04-30

224

Eutectic Salt Catalyzed Environmentally Benign and Highly Efficient Biginelli Reaction  

PubMed Central

A simple deep eutectic solvent based on tin (II) chloride was used as a dual catalyst and environmentally benign reaction medium for an efficient synthesis of 3,4-dihydropyrimidin-2(1H)-one derivatives, from aromatic and aliphatic aldehydes, 1,3-dicarbonyl compounds, and urea in good-to-excellent yields and short reaction time. This simple ammonium deep eutectic solvent, easily synthesized from choline chloride and tin chloride, is relatively inexpensive and recyclable, making it applicable for industrial applications.

Azizi, Najmadin; Dezfuli, Sahar; Hahsemi, Mohmmad Mahmoodi

2012-01-01

225

Eutectic salt catalyzed environmentally benign and highly efficient Biginelli reaction.  

PubMed

A simple deep eutectic solvent based on tin (II) chloride was used as a dual catalyst and environmentally benign reaction medium for an efficient synthesis of 3,4-dihydropyrimidin-2(1H)-one derivatives, from aromatic and aliphatic aldehydes, 1,3-dicarbonyl compounds, and urea in good-to-excellent yields and short reaction time. This simple ammonium deep eutectic solvent, easily synthesized from choline chloride and tin chloride, is relatively inexpensive and recyclable, making it applicable for industrial applications. PMID:22649326

Azizi, Najmadin; Dezfuli, Sahar; Hahsemi, Mohmmad Mahmoodi

2012-04-29

226

Ru(II)-catalyzed RCM reactions with electrophilic diene substrates  

Microsoft Academic Search

Electrophilic dienes from ?,?-unsaturated ketones readily undergo the Ru(II)-benzylidene initiated RCM reaction. Cyclohexenone spirane formation was faster than cycloheptenone spirane formation. The products were pure stereoisomers. The products after hydrolysis were ?,?-unsaturated oxo derivatives of cyclic ?-amino acids.

Sonata Krikstolaitytè; Kristin Hammer; Kjell Undheim

1998-01-01

227

Iodide-catalyzed halocyclization/cycloaddition/elimination cascade reaction.  

PubMed

An iodocyclization reaction of o-alkynylphenyl carboxaldehydes is reported that is truly catalytic with respect to the electrophilic iodine source. With a combination of tetrabutylammonium iodide (TBAI), Oxone as non-nucleophilic and easy to handle co-oxidant, and fluorinated protic solvents, highly substituted 1-naphthalenones could be prepared in high yields of up to 91%. PMID:23373844

Kloeckner, Ulrich; Finkbeiner, Peter; Nachtsheim, Boris J

2013-02-13

228

Eu(fod) 3-catalyzed tandem regiospecific rearrangement of divinyl alkoxyacetates and Diels–Alder reaction  

Microsoft Academic Search

Unsymmetrical divinyl alkoxyacetates (such as 7a) undergo a Eu(fod)3-catalyzed regiospecific allylic rearrangement to form C5-substituted (E)-2-ethoxy-1,3-dienes at room temperature. When the rearrangement of 7a was carried out in the presence of maleic anhydride, a tandem allylic rearrangement and Diels–Alder reaction occurred to give the adduct 11. Reactions of other dienophiles in this tandem procedure were examined.

Wei-Min Dai; Wing Leung Mak; Anxin Wu

2000-01-01

229

Enrichment of ?-linolenic acid from borage oil via lipase-catalyzed reactions  

Microsoft Academic Search

Three lipase-catalyzed reactions were utilized to enrich ?-linolenic acid in borage oil: (i) selective hydrolysis in isooctane\\u000a by Candida rugosa lipase immobilized on microporous polypropylene, (ii) selective esterification of free fatty acid from saponified borage\\u000a oil and n-butanol by Lipozyme IM-20, and (iii) acidolysis of the products of the previous two reactions, that is, unhydrolyzed acylglycerols\\u000a and unesterified free fatty

Fang-Cheng Huang; Yi-Hsu Ju; Cheng-Wei Huang

1997-01-01

230

Selectivity of montmorillonite catalyzed prebiotic reactions of D, L-nucleotides  

Microsoft Academic Search

The montmorillonite-catalyzed reactions of the 5?-phosphorimidazolides of D, L-adenosine (D, L-ImpA) (Figure 1a. N = A, R\\u000a = H) and D, L-uridine (Figure 1a., N = U, R = H) yields oligomers that were as long as 7 mers and 6 mers, respectively. The\\u000a reactions of dilute solutions of D-ImpA and D-ImpU under the same conditions gave oligomers as long

Prakash C. Joshi; Stefan Pitsch; James P. Ferris

2007-01-01

231

Uncovering the enzymes that catalyze the final steps in oxytetracycline biosynthesis.  

PubMed

Tetracyclines are a group of natural products sharing a linearly fused four-ring scaffold, which is essential for their broad-spectrum antibiotic activities. Formation of the key precursor anhydrotetracycline 3 during oxytetracycline 1 biosynthesis has been previously characterized. However, the enzymatic steps that transform 3 into 1, including the additional hydroxylation at C5 and the final C5a-C11a reduction, have remained elusive. Here we report two redox enzymes, OxyS and OxyR, are sufficient to convert 3 to 1. OxyS catalyzes two sequential hydroxylations at C6 and C5 positions of 3 with opposite stereochemistry, while OxyR catalyzes the C5a-C11a reduction using F420 as a cofactor to produce 1. The crystal structure of OxyS was obtained to provide insights into the tandem C6- and C5-hydroxylation steps. The substrate specificities of OxyS and OxyR were shown to influence the relative ratio of 1 and tetracycline 2. PMID:23621493

Wang, Peng; Bashiri, Ghader; Gao, Xue; Sawaya, Michael R; Tang, Yi

2013-05-01

232

Determination of initial velocities of enzymic reactions from progress curves.  

PubMed Central

The present communication describes a novel method for estimating initial velocities (v) of enzyme-catalysed reactions. It is based on an approximation of experimental data obtained by the cubic spline function. The initial velocity of a reaction is calculated as a derivative of the approximating function at a time value equal to zero. The proposed method is usable on a computer with a FORTRAN IV program. The method can be successfully used in such cases as substantial extents of substrate conversion, the inactivation of an enzyme in the course of a reaction, the existence of large experimental error or when the reaction mechanism is unknown.

Dagys, R; Pauliukonis, A; Kazlauskas, D; Mankevicius, M; Simutis, R

1986-01-01

233

Efficient palladium-catalyzed Heck reactions mediated by the diol-functionalized imidazolium ionic liquids  

Microsoft Academic Search

The diol-functionalized imidazolium ionic liquids, 1-(2,3-dihydroxypropyl)-3-methylimidazolium hexafluorophosphate (1) and 2,2-bis(1-methyl-methylimidazolium) propane-1,3-diol hexafluorophosphate (2), were synthesized and used as the phosphine-free ligands in the palladium-catalyzed Heck reaction of aryl bromides with electron-deficient olefins. Under aerobic conditions, the efficient arylation of acrylates could be accomplished when catalyzed by PdCl2-2 (or 1) in DMF with Et3N as a base, in terms of good

Yueqin Cai; Ye Liu

2009-01-01

234

Tritium Secondary Kinetic Isotope Effect on Phenylalanine Ammonia-Lyase-Catalyzed Reaction  

Microsoft Academic Search

The mechanism by which phenylalanine ammonia-lyase (PAL, EC 4.3.1.5) catalyzes the reversible elimination of ammonia from phenylalanine yielding (E)-cinnamic acid has gained much attention in the recent years. Dehydroalanine is essential for the catalysis. It was assumed that this prostetic group acts as the electrophile, leading to a covalently bonded enzyme–intermediate complex with quarternary nitrogen of phenylalanine. Recently, an alternative

Andrzej Lewandowicz; Jacek Jemielity; Marianna Ka?ska; Jerzy Zo?; Piotr Paneth

1999-01-01

235

Stereospecificity for pro-( R) hydrogen of NAD(P)H during enzyme-catalyzed hydride transfer to CL20  

Microsoft Academic Search

A dehydrogenase from Clostridium sp. EDB2 and a diaphorase from Clostridium kluyveri were reacted with CL-20 to gain insights into the enzyme-catalyzed hydride transfer to CL-20, and the enzyme’s stereo-specificity for either pro-R or pro-S hydrogens of NAD(P)H. Both enzymes biotransformed CL-20 at rates of 18.5 and 24nmol\\/h\\/mg protein, using NADH and NADPH as hydride-source, respectively, to produce a N-denitrohydrogenated

Bharat Bhushan; Annamaria Halasz; Jalal. Hawari

2005-01-01

236

First principle kinetic studies of zeolite-catalyzed methylation reactions.  

PubMed

Methylations of ethene, propene, and butene by methanol over the acidic microporous H-ZSM-5 catalyst are studied by means of state of the art computational techniques, to derive Arrhenius plots and rate constants from first principles that can directly be compared with the experimental data. For these key elementary reactions in the methanol to hydrocarbons (MTH) process, direct kinetic data became available only recently [J. Catal.2005, 224, 115-123; J. Catal.2005, 234, 385-400]. At 350 °C, apparent activation energies of 103, 69, and 45 kJ/mol and rate constants of 2.6 × 10(-4), 4.5 × 10(-3), and 1.3 × 10(-2) mol/(g h mbar) for ethene, propene, and butene were derived, giving following relative ratios for methylation k(ethene)/k(propene)/k(butene) = 1:17:50. In this work, rate constants including pre-exponential factors are calculated which give very good agreement with the experimental data: apparent activation energies of 94, 62, and 37 kJ/mol for ethene, propene, and butene are found, and relative ratios of methylation k(ethene)/k(propene)/k(butene) = 1:23:763. The entropies of gas phase alkenes are underestimated in the harmonic oscillator approximation due to the occurrence of internal rotations. These low vibrational modes were substituted by manually constructed partition functions. Overall, the absolute reaction rates can be calculated with near chemical accuracy, and qualitative trends are very well reproduced. In addition, the proposed scheme is computationally very efficient and constitutes significant progress in kinetic modeling of reactions in heterogeneous catalysis. PMID:21182253

Van Speybroeck, Veronique; Van der Mynsbrugge, Jeroen; Vandichel, Matthias; Hemelsoet, Karen; Lesthaeghe, David; Ghysels, An; Marin, Guy B; Waroquier, Michel

2010-12-23

237

Development of Safe and Scalable Continuous-Flow Methods for Palladium-Catalyzed Aerobic Oxidation Reactions  

PubMed Central

Summary The synthetic scope and utility of Pd-catalyzed aerobic oxidation reactions has advanced significantly over the past decade, and these reactions have potential to address important green-chemistry challenges in the pharmaceutical industry. This potential has been unrealized, however, because safety concerns and process constraints hinder large-scale applications of this chemistry. These limitations are addressed by the development of a continuous-flow tube reactor, which has been demonstrated on several scales in the aerobic oxidation of alcohols. Use of a dilute oxygen gas source (8% O2 in N2) ensures that the oxygen/organic mixture never enters the explosive regime, and efficient gas-liquid mixing in the reactor minimizes decomposition of the homogeneous catalyst into inactive Pd metal. These results provide the basis for large-scale implementation of palladium-catalyzed (and other) aerobic oxidation reactions for pharmaceutical synthesis.

Ye, Xuan; Diao, Tianning

2010-01-01

238

Antioxidant activity of minimally processed red chicory (Cichorium intybus L.) evaluated in xanthine oxidase-, myeloperoxidase-, and diaphorase-catalyzed reactions.  

PubMed

Minimally processed red chicory products (Cichorium intybus L. var. silvestre) were studied for their polyphenol content and antioxidant activity evaluated by using the synthetic 2,2-diphenyl-1-(2,4,6-trinitrophenyl)hydrazyl radical and three model reactions catalyzed by relevant enzymatic sources of reactive oxygen species, namely, xanthine oxidase, myeloperoxidase, and diaphorase. Products were analyzed at the time of production and after storage at 4 degrees C within either a gas permeable film or a gas barrier film. The antioxidant activity and contents of hydroxycinnamic acids and flavonoids decreased by less than 20% during storage of the minimally processed red chicory products. Total phenolics were significantly correlated with the antioxidant activity evaluated with both the synthetic radical and the enzyme-catalyzed reactions. On a molar basis, red chicory phenolics were as efficient as the reference compound Trolox in scavenging the synthetic radical. However, red chicory phenolics had a much higher inhibitory activity than Trolox in the model enzymatic systems. PMID:18680376

Lavelli, Vera

2008-08-05

239

Evidence for a transient peroxynitro acid in the reaction catalyzed by nitronate monooxygenase with propionate 3-nitronate.  

PubMed

Nitronate monooxygenase is a flavin-dependent enzyme that catalyzes the denitrification of propionate 3-nitronate (P3N) and other alkyl nitronates. The enzyme was previously known as 2-nitropropane dioxygenase, until its reclassification in 2010 by the IUBMB. Physiologically, the monooxygenase from fungi protects the organism from the environmental occurrence of P3N, which shuts down the Krebs cycle by inactivating succinate dehydrogenase and fumarase. The inhibition of these enzymes yields severe neurological disorders or death. Here, we have used for the first time steady-state and rapid kinetics, viscosity and pH effects, and time-resolved absorbance spectroscopy of the enzyme in turnover with P3N and the substrate analogue ethyl nitronate (EN) to elucidate the mechanism of the reaction. A transient increase in absorbance at ?300 nm, never reported before, was seen during steady-state turnover of the enzyme with P3N and oxygen, with no concomitant changes between 400 and 600 nm. The transient species was not detected when oxygen was absent. Anaerobic reduction of the enzyme with P3N yielded anionic flavosemiquinone and was fast (e.g., ?1900 s(-1)). Steady-state kinetics demonstrated that oxygen reacts before the release of the product of P3N oxidation from the enzyme. No pH effects were seen with P3N on kcat/Km, kcat/Koxygen, and kcat; in contrast, with EN, the kcat/Km and kcat decreased with increasing pH defining two plateaus and a pKa ? 8.0. Solvent viscosity at the pH optima suggested product release as being partially controlling the overall rate of turnover with the physiological substrate and its analogue. A mechanism that satisfies the kinetic results is proposed. PMID:23530838

Smitherman, Crystal; Gadda, Giovanni

2013-04-05

240

Enzyme-catalyzed processes of first-pass hepatic and intestinal drug extraction.  

PubMed

Oral bioavailability of pharmacologically effective drugs is often limited by first-pass biotransformation. In humans, both hepatic and intestinal enzymes can catalyze the metabolism of a drug as it transits between the gastrointestinal lumen and systemic blood for the first time. Although a spectrum of drug biotransformations can occur during first-pass, the most common are oxidations catalyzed by cytochromes P450. It is the isozymes CYP2D6, CYP3A4, CYP1A2, CYP2C9 and CYP2C19 that are most often implicated in first-pass drug elimination. For any given substrate, enzyme specificity, enzyme content, substrate binding affinity and sensitivity to irreversible catalytic events all play a role in determining the overall efficiency, or intrinsic clearance, of elimination. Several models have been proposed over the past twenty-five years that mathematically describe the process of drug extraction across the liver. The most widely used, the well-stirred model, has also been considered for depiction of first-pass drug elimination across the intestinal wall. With these models it has been possible to examine sources of interindividual variability in drug bioavailability including, variable constitutive enzyme expression (both genetic and environmentally determined), enzyme induction by drugs, disease and diet, and intrinsic or acquired differences in plasma protein binding and organ blood flow (food and drug effects). In recent years, the most common application of hepatic clearance models has been the determination of maximum organ availability of a drug from in vitro derived estimates of intrinsic metabolic clearance. The relative success of the in vitro-in vivo approach for both low and highly extracted drugs has led to a broader use by the drug industry for a priori predictions as part of the drug selection process. A considerable degree of effort has also been focused on gut wall first-pass metabolism. Important pathways of intestinal Phase II first-pass metabolism include the sulfation of terbutaline and isoproterenol and glucuronidation of morphine and labetalol. It is also clear that some of the substrates for CYP3A4 (e.g., cyclosporine, midazolam, nifedipine, verapamil and saquinavir) undergo significant metabolic extraction by the gut wall. For example, the first-pass extraction of midazolam by the intestinal mucosa appears, on average, to be comparable to extraction by the liver. However, many other CYP3A substrates do not appear susceptible to a gut wall first-pass, possibly because of enzyme saturation during first-pass or a limited intrinsic metabolic clearance. Both direct biochemical and indirect in vivo clearance data suggest significant inter-individual variability in gut wall CYP3A-dependent metabolism. The source of this constitutive variability is largely unknown. Because of their unique anatomical location, enzymes of the gut wall may represent an important and highly sensitive site of metabolically-based interactions for orally administered drugs. Again, interindividual variability may make it impossible to predict the likelihood of an interaction in any given patient. Hopefully, though, newer models for studying human gut wall metabolic extraction will provide the means to predict the average extraction ratio and maximum first-pass availability of a putative substrate, or the range of possible inhibitory or inductive changes for a putative inhibitor/inducer. PMID:10837554

Shen; Kunze; Thummel

1997-09-15

241

Bisphosphine-Catalyzed Mixed Double-Michael Reactions: Asymmetric Synthesis of Oxazolidines, Thiazolidines, and Pyrrolidines  

PubMed Central

Bisphosphine-catalyzed mixed double-Michael reactions have been developed to afford ?-amino carbonyl derivatives of oxazolidines, thiozolidines, and pyrrolidines in excellent yields and with high diastereoselectivities. Efficient reactions between amino acid-derived pronucleophiles, e.g., ?-amino alcohols,?-amino thiols, and ?-amino diesters, as Michael donors and electron-deficient acetylenes, e.g., propiolates, acetylacetylene, and tosylacetylene, as Michael acceptors provided access to azolidines containing both diversity of substituents and asymmetry. This methodology—the first examples of mixed double-Michael reactions of acetylenes—is operationally simple and involves mild conditions. Mechanistically, it constitutes a rare example of the anchimeric assistance of bisphosphines in organocatalysis.

Sriramurthy, Vardhineedi; Barcan, Gregg A.; Kwon, Ohyun

2008-01-01

242

Click reactions in protein chemistry: from the preparation of semisynthetic enzymes to new click enzymes.  

PubMed

Click-chemistry is an approach based on cycloaddition reactions which has been successfully used as a chemical approach for complex organic molecules and which has recently starred in a boom in the world of protein chemistry. The advantage of the use of this technique in protein chemistry is based on a very high and efficient chemoselectivity, which usually requires simple or no purification and is extremely rate-accelerated in aqueous media. The perspective discusses some of the most recent advances in the application of this reaction in selective enzyme surface modification for the creation of new semisynthetic enzymes (fluorescence labeled enzymes, peptide-enzyme conjugates, glycosylated enzymes), and interestingly, the recent design and creation of "click" enzymes. PMID:23023600

Palomo, Jose M

2012-10-01

243

A computational study of acid catalyzed aerosol reactions of atmospherically relevant epoxides.  

PubMed

Epoxides are important intermediates of atmospheric isoprene oxidation. Their subsequent reactions in the particle phase lead to the production of organic compounds detected in ambient aerosols. We apply density functional theory to determine the important kinetic factors that drive epoxide reactions in the particle phase. Specifically, the importance of acid catalysis and solvent polarity are investigated using a variety of epoxides and nucleophiles. The condensed phase is modeled using molecular clusters immersed in a dielectric continuum and a majority of the calculations are performed with the M062x density functional and the 6-311++G** basis set. Calculations of acid catalyzed epoxide hydrolysis transition states for simple primary, secondary and tertiary epoxides are consistent with an A-2 mechanism where the nucleophile (water) interacts with an epoxide carbon in the transition state. By applying transition state theory to this mechanism, the overall rate constants of epoxide reactions such as hydrolysis, organosulfate formation, organonitrate formation and oligomerization are determined. The calculations indicate that the acid catalyzed hydrolysis rate constant of 2-methyl-2,3-epoxybutane-1,4-diol (?-IEPOX - an isoprene epoxide produced under low NOx conditions) is approximately 30 times greater than 2-methyl-2,3-epoxypropanoic acid (MAE - methacrylic acid epoxide derived from isoprene and produced at high NOx concentrations). Furthermore, acid catalyzed organosulfate formation and epoxide oligomerization reactions are competitive and appear to be kinetically favorable over the hydrolysis of IEPOX. PMID:24061334

Piletic, Ivan R; Edney, Edward O; Bartolotti, Libero J

2013-10-01

244

Spectral and Kinetic Characterization of Intermediates in the Aromatization Reaction Catalyzed by NikD, an Unusual Amino Acid Oxidase†  

PubMed Central

The flavoenzyme nikD, a 2-electron acceptor, catalyzes a remarkable aromatization of piperideine-2-carboxylate (P2C) to picolinate, an essential component of nikkomycin antibiotics. Steady-state kinetic data are indicative of a sequential mechanism where oxygen reacts with a reduced enzyme•dihydropicolinate (DHP) complex. The kinetics observed for complex formation with competitive inhibitors are consistent with a one-step binding mechanism. The anaerobic reaction with P2C involves three steps. The first step yields an enzyme•substrate charge transfer complex likely to contain the electron-rich P2C enamine. Calculated rates of formation and dissociation of the nikD•P2C complex are similar to those observed for the enzyme•1-cyclohexenoate complex. Formation of a reduced enzyme•DHP complex, (EH2•DHP)ini, occurs in a second step that exhibits a hyperbolic dependence on substrate concentration. The limiting rate of nikD reduction is at least 10-fold faster than the turnover rate observed with unlabeled or [4, 4, 5, 5, 6, 6-D6]-P2C and exhibits a kinetic isotope effect (KIE = 6.4). The observed KIE on Kd apparent (4.7) indicates that P2C is a sticky substrate. Formation of a final reduced species, (EH2•DHP)fin, occurs in a third step that is independent of P2C concentration and equal to the observed turnover rate. The observed KIE (3.3) indicates that the final step involves cleavage of at least one C-H bond. Tautomerization, followed by isomerization, of the initial DHP intermediate can produce an isomer that could be oxidized to picolinate in a reaction that satisfies known steric constraints of flavoenzyme reactions without the need to reposition a covalently tethered flavin or tightly bound intermediate.

Bruckner, Robert C.; Jorns, Marilyn Schuman

2009-01-01

245

Role of water in mukaiyama-aldol reaction catalyzed by lanthanide lewis Acid: a computational study.  

PubMed

Carbon-carbon bond formations, such as Kobayashi modification of the Mukaiyama-Aldol reaction, catalyzed by lanthanide (Ln) Lewis acid in aqueous solution comprise one of the most attractive types of reactions in terms of green chemistry. However, their detailed mechanisms and the role of water molecules remained unclear. In order to explore complex potential energy surfaces for the water and substrate coordination around Eu(3+) as well as the detailed mechanism of the Mukaiyama-Aldol reaction between trimethylsilyl (TMS) cylcohexenolate and benzaldehyde (BA) catalyzed by Eu(3+), the recently developed anharmonic downward distortion following (ADDF) and artificial force-induced reaction (AFIR) methods were used with the B3LYP-D3 theory. The most favorable water coordination structures are Eu(3+)(H2O)8 and Eu(3+)(H2O)9; they are comparable in free energy and are likely to coexist, with an effective coordination number of 8.3. Eu(3+)(H2O)8(BA) is the best aldehyde coordinated structure. Starting with this complex, the Mukaiyama-Aldol reaction proceeds via a stepwise mechanism, first C-C bond formation between the substrates, followed by proton transfer from water to BA and then TMS dissociation caused by nucleophilic attack by bulk water molecules. Why did the yield of the Mukaiyama-Aldol reaction catalyzed by Ln(3+) in organic solvent dramatically increase upon addition of water? Without water, the reverse reaction (C-C cleavage) takes place easily. Why did this reaction show syn-preference in water? The anti transition state for C-C formation in water is entropically less favored relative to the syn transition state because of the existence of a rigid hydrogen bond between the TMS part and coordination water around Eu(3+) in the former. PMID:24006879

Hatanaka, Miho; Morokuma, Keiji

2013-09-05

246

Practical synthesis of 1,3-oleoyl 2-docosahexaenoylglycerol by lipase-catalyzed reactions: An evaluation of different reaction routes  

Microsoft Academic Search

Three new synthetic routes were critically evaluated for the lipase-catalyzed production of 1,3-oleoyl-2 docosahexaenoylglycerol (ODO) in relatively large-scale (approximately 200g). First, the production of 1,3-diolein by the reaction of glycerol and oleic acid followed by incorporation of docosahexaenoic (DHA) ethyl ester at the sn-2 position was studied. 1,3-Diolein was produced in 68.3% and 84.6% yield when stoichiometric amounts of the

H. Zhang; G. Önal; C. Wijesundera; X. Xu

2009-01-01

247

Organic reactions catalyzed by methylrhenium trioxide: Dehydration, amination, and disproportionation of alcohols  

SciTech Connect

Methylrhenium trioxide (MTO) is the first transition metal complex in trace quantity to catalyze the direct formation of ethers from alcohols. The reactions are independent of the solvents used: benzene, toluene, dichloromethane, chloroform, acetone, and in the alcohols themselves. Aromatic alcohols gave better yields than aliphatic. Reactions between two different alcohols could also be used to prepare unsymmetric ethers, the best yields being obtained when one of the alcohols is aromatic alcohols proceeding in better yield. When primary (secondary) amines were used as the limiting reagent, direct amination of alcohols catalyzed by MTO gave good yields of the expected secondary (tertiary) amines at room temperature. Disproportionation of alcohols to alkanes and carbonyl compounds was also observed for aromatic alcohols in the presence of MTO. On the basis of the results of this investigation and a comparison with the interaction between MTO and water, a concerted process and a mechanism involving carbocation intermediates have been suggested. 5 tabs.

Zhu, Zuolin; Espenson, J.H. [Iowa State Univ., Ames, IA (United States)

1996-01-12

248

Pre-Steady-State Kinetic Analysis of Enzyme-monitored Turnover during Cystathionine ?-Synthase-catalyzed H2S-Generation†  

PubMed Central

Cystathionine ?-synthase (CBS) catalyzes the first step in the transsulfuration pathway in mammals, i.e., the condensation of serine and homocysteine to produce cystathionine and water. Recently, we have reported a steady-state kinetic analysis of the three hydrogen sulfide (H2S)-generating reactions that are catalyzed by human and yeast CBS (Singh et al (2009) J Biol Chem 284: 22457-66). In the current study, we report a pre-steady-state kinetic analysis of intermediates in the H2S-generating reactions catalyzed by yeast CBS (yCBS). Because yCBS does not have a heme cofactor, in contrast to human CBS, it is easier to observe reaction intermediates with yCBS. The most efficient route for H2S generation by yCBS is the ?-replacement of the cysteine thiol by homocysteine. In this reaction, yCBS first reacts with cysteine to release H2S and forms an aminoacrylate intermediate (kobs=1.61 ± 0.04 mM?1 s?1 at low cysteine and 2.8 ± 0.1 mM?1 s?1 at high cysteine concentrations, at 20 °C), which has an absorption maximum at 465 nm. Homocysteine binds to the E•aminoacrylate intermediate with a bimolecular rate constant of 142 mM?1 s?1 and rapidly condenses to form the enzyme-bound external aldimine of cystathionine. The reactions could be partially rate limited by release of the products, cystathionine and H2S.

Singh, Sangita; Ballou, David P.; Banerjee, Ruma

2010-01-01

249

Envisioning an enzymatic Diels-Alder reaction by in situ acid-base catalyzed diene generation.  

PubMed

We present and evaluate a new and potentially efficient route for enzyme-mediated Diels-Alder reactions, utilizing general acid-base catalysis. The viability of employing the active site of ketosteroid isomerase is demonstrated. PMID:22547054

Linder, Mats; Johansson, Adam Johannes; Manta, Bianca; Olsson, Philip; Brinck, Tore

2012-05-01

250

Phthalocyanine-peptide conjugates via palladium-catalyzed cross-coupling reactions.  

PubMed

Phthalocyanines (Pc) were conjugated with peptide moieties to improve their target selectivity for potential use as fluorescence and/or positron emission tomography (PET) probes in medical imaging. Three synthetic methods based on palladium-catalyzed cross-coupling reactions (Sonogashira, Buchwald-Hartwig, and Suzuki-Miyaura) were investigated. Using these methods, a series of peptides monofunctionalized with Pc at the N/C-terminal position or on a phenylalanine side chain was obtained in good yields and characterized. PMID:21302913

Ali, Hasrat; Ait-Mohand, Samia; Gosselin, Simon; van Lier, Johan E; Guérin, Brigitte

2011-02-08

251

Ultra low momentum neutron catalyzed nuclear reactions on metallic hydride surfaces  

Microsoft Academic Search

Ultra low momentum neutron catalyzed nuclear reactions in metallic hydride system surfaces are discussed. Weak interaction\\u000a catalysis initially occurs when neutrons (along with neutrinos) are produced from the protons that capture “heavy” electrons.\\u000a Surface electron masses are shifted upwards by localized condensed matter electromagnetic fields. Condensed matter quantum\\u000a electrodynamic processes may also shift the densities of final states, allowing an

A. Widom; L. Larsen

2006-01-01

252

Organic Reactions in Ionic Liquids: Gewald Synthesis of 2?Aminothiophenes Catalyzed by Ethylenediammonium Diacetate  

Microsoft Academic Search

Ionic liquids based on 1?butyl?3?methylimidazolium tetrafluoroborate (BmimBF4) and 1?butyl?3?methylimidazolium hexafluorophosphate (BmimPF6) were used as reusable alternatives to volatile organic solvents (VOCs) for ethylenediammonium diacetate (EDDA) catalyzed Gewald synthesis of 2?aminothiophenes. Significant rate enhancement and improvement of the yield were observed. The ionic liquids containing catalyst EDDA were recycled several times with no decreases in yields and reaction rates.

Yi Hu

2004-01-01

253

Highly Diastereoselective Pd-Catalyzed Carboetherification Reactions of Acyclic Internal Alkenes. Stereoselective Synthesis of Polysubstituted Tetrahydrofurans  

PubMed Central

A highly diastereoselective synthesis of substituted tetrahydrofurans bearing stereocenters at C2 and C1? via Pd-catalyzed carboetherification reactions of acyclic internal alkenes is described. Use of an improved catalyst composed of Pd2(dba)3/S-Phos provides products with up to >20:1 dr. The stereoselective preparation of tetrahydrofurans containing three stereocenters, including a molecule structurally related to simplakidine A, is also reported.

Ward, Amanda F.; Wolfe, John P.

2010-01-01

254

Use of Aryl Chlorides as Electrophiles in Pd-Catalyzed Alkene Difunctionalization Reactions  

PubMed Central

The development of conditions that allow use of inexpensive aryl chlorides as electrophiles in Pd-catalyzed alkene carboamination and carboetherification reactions is described. A catalyst composed of Pd(OAc)2 and S-Phos minimizes N-arylation of the substrate and prevents formation of mixtures of regioisomeric products. A number of heterocycles, including pyrrolidines, isoxazolidines, tetrahydrofurans, and pyrazolidines, are efficiently generated with this method.

Rosen, Brandon R.; Ney, Joshua E.; Wolfe, John P.

2010-01-01

255

Gold-Catalyzed Cycloisomerization of 1,5-Allenynes via Dual Activation of an Ene Reaction  

PubMed Central

A tris-triphenylphosphinegold oxonium tetrafluoroborate, [(Ph3PAu)3O]BF4, catalyzes the rearrangement of 1,5-allenynes to produce cross-conjugated trienes. Experimental and computational evidence shows that the ene reaction proceeds through a unique nucleophilic addition of an allene double bond to a cationic phosphinegold(I) complexed phosphinegold(I) acetylide, followed by a 1,5-hydrogen shift.

Cheong, Paul Ha-Yeon; Morganelli, Philip; Luzung, Michael R.; Houk, K. N.; Toste, F. Dean

2010-01-01

256

Efficient Heck reactions catalyzed by a palladium\\/diol–imidazolium salt in aerial atmosphere  

Microsoft Academic Search

A new diol–imidazolium salt, 1-(2,3-dihydroxypropyl)-3-methylimidazolium hexafluorophosphate (1), was found to be an efficient and reusable phosphine-free ligand for palladium catalyzed Heck reactions. The couplings of a variety of aryl iodides\\/aryl bromides with acrylates generated the corresponding products in good\\/excellent yields even in aerial atmosphere. In addition, the palladium catalyst mediated by 1 could be easily recovered and reused for ten

Yueqin Cai; Yong Lu; Ye Liu; Mingyuan He; Qingxia Wan

2008-01-01

257

Oscillating chemiluminescence in rhodamine B-induced Belousov-Zhabotinsky reaction catalyzed by Ce(IV)  

Microsoft Academic Search

It was found that rhodamine B could induce oscillating chemiluminescence (OCL) from the Ce4+-catalyzed Belousov-Zhabotinsky reaction. This new OCL system, i.e., rhodamine B-malonic acid-bromate-Ce(IV)-sulfuric acid,\\u000a exhibited two clearly distinguished emission peaks in each oscillation period. The initial concentrations of the reactants\\u000a strongly influenced the oscillation pattern. For the study of the CL mechanism, a platform for a versatile and simultaneous

ChunFeng Duan; GuangMing Liu; ZhiFeng Zhang; Hua Cui

2009-01-01

258

Laccase from Basidiomycetous Fungus–Catalyzed Synthesis of Substituted Benzopyranocoumarins via Domino Reaction  

Microsoft Academic Search

The present investigation provides a simple and convenient route to organic synthesis of substituted benzopyranocoumarin, which is important because it is a probable HIV protease inhibitor. The reaction of ?,?-unsaturated derivatives of coumarins with catechol or 1,4-hydroquinones was catalyzed using laccase in an aqueous medium. Quinones, generated in situ by the oxidation of the corresponding catechol or 1,4-hydroquinones, underwent a

Mazaahir Kidwai; Roona Poddar; Sarika Diwaniyan; Ramesh Chander Kuhad

2011-01-01

259

Iron-Catalyzed Reaction between Nitrosyl Disulfonate and Hydroxylamine Monosulfonate Ions  

Microsoft Academic Search

An investigation of the kinetics of the iron-catalyzed reaction between the purple-colored, paramagnetic nitrosyl disulfonate (ON(SO3)2=) ions and hydroxylamine monosulfonate (HONHSO3—) ions has been made. [W. J. Ramsey and D. M. Yost, J. Chem. Phys. 21, 957 (1953)]. At a temperature of 20°C, an ionic strength of 0.026, and total added iron concentrations less than 3.5×10—7VF, the initial rate of

William J. Ramsey; Don M. Yost

1955-01-01

260

Big-Bang Nucleosynthesis Reactions Catalyzed by a Long-Lived Negatively Charged Leptonic Particle  

Microsoft Academic Search

An accurate quantum three-body calculation is performed for the new type of big-bang nucleosynthesis (BBN) reactions that are catalyzed by a hypothetical long-lived negatively charged, massive leptonic particle (called X^-) such as the supersymmetric (SUSY) particle stau, the scalar partner of the tau lepton. It is known that if the X^- particle has a lifetime tau_X ≳ 10^3 s, it

Masayasu Kamimura; Yasushi Kino; Emiko Hiyama

2009-01-01

261

Novel method to detect DNA methylation using gold nanoparticles coupled with enzyme-linkage reactions.  

PubMed

DNA methylation, catalyzed by methylases, plays a critical role in many biological processes, and methylases have been regarded as promising targets for antimicrobial drugs. In this paper, we propose a simple and sensitive colorimetric assay method to detect the activity of methylases so as to monitor DNA methylation using DNA-modified gold nanoparticles (AuNPs) coupled with enzyme-linkage reactions. The duplex DNA molecules modified on the surface of AuNPs are first methylated by DNA adenine methylation (Dam) methyltransferase (MTase) and then cut by methylation-sensitive restriction endonuclease Dpn I. Removal of duplex from the AuNP surfaces by the methylation/cleavage process will destabilize the nanoparticles, resulting in aggregation of AuNPs and a red-to-blue color change. Consequently, the enzyme activity of Dam MTase can be assayed and DNA methylation can be detected. Furthermore, this study may provide a sensitive platform to screen inhibitors for Dam MTase. PMID:19954204

Liu, Tao; Zhao, Jing; Zhang, Dongmei; Li, Genxi

2010-01-01

262

Barrier compression and tunneling in enzyme catalysed reactions  

NASA Astrophysics Data System (ADS)

Nuclear quantum mechanical tunneling is important in enzyme-catalysed H-transfer reactions. This viewpoint has arisen after a number of experimental studies have described enzymatic reactions with kinetic isotope effects that are significantly larger than the semi-classical limit. Other experimental evidence for tunneling, and the potential role of promoting vibrations that transiently compress the reaction barrier, is more indirect, being derived from the interpretation of e.g. mutational analyses of enzyme systems and temperature perturbation studies of reaction rates/kinetic isotope effects. Computational simulations have, in some cases, determined exalted kinetic isotope effects and tunneling contributions, and identified putative promoting vibrations. In this presentation, we present the available evidence -- both experimental and computational -- for environmentally-coupled H-tunneling in several enzyme systems, from our recent work on redox enzyme systems. We then consider the relative importance of tunneling contributions to these reactions. We find that the tunneling contribution to these reactions confers a rate enhancement of approx. 1000-fold. Without tunneling, a 1000-fold reduction in activity would seriously impair cellular metabolism. We infer that tunneling is crucial to host organism viability thereby emphasising the general importance of tunneling in biology.

Scrutton, Nigel

2011-03-01

263

Synthesis of quinolines via Friedländer reaction catalyzed by CuBTC metal-organic-framework.  

PubMed

Friedländer condensation between 2-aminoaryl ketones and different carbonyl compounds, catalyzed by CuBTC was investigated by a combination of various experimental techniques and by density functional theory based modelling. CuBTC exhibiting hard Lewis acid character showed highly improved catalytic activity when compared with other molecular sieves showing high concentraion of Lewis acid sites, e.g. in BEA and (Al)SBA-15. Polysubstituted quinolines were synthesized via a Friedländer reaction catalyzed by CuBTC under the solvent-free conditions. High concentration of active sites in CuBTC together with the concerted effect of a pair of adjacent Cu(2+) coordinatively unsaturated active sites are behind a very high quinoline yield reached within a short reaction time. Results reported here make CuBTC a promising catalyst for other Lewis acid-promoted condensations, including those leading to biologically active compounds with a particular relevance for the pharmaceutical industry. The mechanism of a catalyzed Friedländer reaction investigated computationally is also reported. PMID:22293862

Pérez-Mayoral, Elena; Musilová, Zuzana; Gil, Barbara; Marszalek, Bartosz; Položij, Miroslav; Nachtigall, Petr; ?ejka, Jiri

2012-02-01

264

Purification of the two-enzyme system catalyzing the oxidation of the D-proline residue of pristinamycin IIB during the last step of pristinamycin IIA biosynthesis.  

PubMed Central

High levels of conversion of 14C-labelled pristinamycin IIB (PIIB) to pristinamycin IIA (PIIA) were obtained in vivo in Streptomyces pristinaespiralis and in some other streptogramin A producers. This established that PIIB was an intermediate on the pathway to PIIA. In addition, in vitro studies with cell-free protein preparations demonstrated that the oxidation of PIIB to PIIA is a complex process requiring NADH, riboflavin 5'-phosphate (FMN), and molecular oxygen. Two enzymes were shown to be necessary to catalyze this reaction. Both were purified to homogeneity from S. pristinaespiralis by a coupled enzyme assay based on the formation of PIIA and by requiring addition of the complementing enzyme. One enzyme was purified about 3,000-fold by a procedure including a decisive affinity chromatography step on FMN-agarose. It was shown to be a NADH:FMN oxidoreductase (E.C. 1.6.8.1.) (hereafter called FMN reductase), providing reduced FMN (FMNH2) to the more abundant second enzyme. The latter was purified only 160-fold and was called PIIA synthase. Our data strongly suggest that this enzyme catalyzes a transient hydroxylation of PIIB by molecular oxygen immediately followed by a dehydration leading to PIIA. The native PIIA synthase consists of two different subunits with Mrs of around 50,000 and 35,000, as estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, while the FMN reductase seems to be a monomer with a Mr of around 28,000 and containing one molecule of tightly bound FMN. Stepwise Edman degradation of the entire polypeptides or some of their trypsin-digested fragments provided amino acid sequences for the two isolated proteins.

Thibaut, D; Ratet, N; Bisch, D; Faucher, D; Debussche, L; Blanche, F

1995-01-01

265

Detoxification of substituted phenols by oxidoreductive enzymes through polymerization reactions  

Microsoft Academic Search

Laccases from the fungiRhizoctonia praticola andTrametes versicolor as well as horseradish peroxidase and tyrosinase were evaluated for their ability to polymerize phenolic contaminants. The removal of phenols through polymerization depended on the chemical structure and concentration of the substrate, pH of the reaction mixture, activity of the enzyme, length of incubation, and temperature. The enzymes retained their activity throughout a

J. Dec; J.-M. Bollag

1990-01-01

266

Facile one-pot assembly of imidazotriazolobenzodiazepines via indium(III)-catalyzed multicomponent reactions.  

PubMed

An operationally simple, one-pot multicomponent reaction has been developed for the assembly of 9H-benzo[f]imidazo[1,2-d][1,2,3]triazolo[1,5-a][1,4]diazepines adorned with three diversification points via an atom-economical transformation incorporating ?-diketones, o-azidobenzaldehydes, propargylic amines, and ammonium acetate. This process involves tandem InCl3-catalyzed cyclocondensation and intramolecular azide-alkyne 1,3-dipolar cycloaddition reactions; optimization data, substrate scope, and mechanistic insights are discussed. PMID:23961714

Nguyen, Huy H; Palazzo, Teresa A; Kurth, Mark J

2013-08-20

267

Mechanisms of reactions of organoaluminium compounds with alkenes and alkynes catalyzed by Zr complexes  

NASA Astrophysics Data System (ADS)

The results of studies dealing with mechanisms of hydro-, carbo- and cycloalumination of alkenes and alkynes catalyzed by zirconium complexes are generalized and systematized for the first time. Data about the structures of intermediates responsible for the formation of the target compounds are presented and the available data on the effect of the structure of organoaluminium compounds and the electronic and steric factors determining the catalytic activity of metal complexes in these reactions are considered in detail. Much attention is paid to studies of the influence of reaction conditions on the chemo-, regio- and stereoselectivity of the Zr-containing complex catalysts. The bibliography includes 217 references.

Parfenova, L. V.; Khalilov, Leonard M.; Dzhemilev, Usein M.

2012-06-01

268

Transition-metal-catalyzed laboratory-scale carbon-carbon bond-forming reactions of ethylene.  

PubMed

Ethylene, the simplest alkene, is the most abundantly synthesized organic molecule by volume. It is readily incorporated into transition-metal-catalyzed carbon-carbon bond-forming reactions through migratory insertions into alkylmetal intermediates. Because of its D2h symmetry, only one insertion outcome is possible. This limits byproduct formation and greatly simplifies analysis. As described within this Minireview, many carbon-carbon bond-forming reactions incorporate a molecule (or more) of ethylene at ambient pressure and temperature. In many cases, a useful substituted alkene is incorporated into the product. PMID:24105881

Saini, Vaneet; Stokes, Benjamin J; Sigman, Matthew S

2013-09-17

269

Zinc Enzymes.  

ERIC Educational Resources Information Center

|Discusses the role of zinc in various enzymes concerned with hydration, hydrolysis, and redox reactions. The binding of zinc to protein residues, properties of noncatalytic zinc(II) and catalytic zinc, and the reactions catalyzed by zinc are among the topics considered. (JN)|

Bertini, I.; And Others

1985-01-01

270

Crystal structure of glycogen synthase: homologous enzymes catalyze glycogen synthesis and degradation  

PubMed Central

Glycogen and starch are the major readily accessible energy storage compounds in nearly all living organisms. Glycogen is a very large branched glucose homopolymer containing about 90% ?-1,4-glucosidic linkages and 10% ?-1,6 linkages. Its synthesis and degradation constitute central pathways in the metabolism of living cells regulating a global carbon/energy buffer compartment. Glycogen biosynthesis involves the action of several enzymes among which glycogen synthase catalyzes the synthesis of the ?-1,4-glucose backbone. We now report the first crystal structure of glycogen synthase in the presence and absence of adenosine diphosphate. The overall fold and the active site architecture of the protein are remarkably similar to those of glycogen phosphorylase, indicating a common catalytic mechanism and comparable substrate-binding properties. In contrast to glycogen phosphorylase, glycogen synthase has a much wider catalytic cleft, which is predicted to undergo an important interdomain ‘closure' movement during the catalytic cycle. The structures also provide useful hints to shed light on the allosteric regulation mechanisms of yeast/mammalian glycogen synthases.

Buschiazzo, Alejandro; Ugalde, Juan E; Guerin, Marcelo E; Shepard, William; Ugalde, Rodolfo A; Alzari, Pedro M

2004-01-01

271

Arylation of 2-substituted pyridines via Pd-catalyzed decarboxylative cross-coupling reactions of 2-picolinic acid.  

PubMed

The novel palladium-catalyzed decarboxylative cross-coupling reactions of 2-picolinic acid with aryl and heteroaryl bromides including benzenes, naphthalenes, pyridines and quinolines for C-C bond formation have been successfully achieved. PMID:23172107

Li, Xinjian; Zou, Dapeng; Leng, Faqiang; Sun, Chunxia; Li, Jingya; Wu, Yangjie; Wu, Yusheng

2012-11-22

272

p-Toluene Sulfonic Acid–Catalyzed, Solvent-Free Synthesis of Symmetrical Bisamides by Reaction Between Aldehydes and Amides  

Microsoft Academic Search

Reaction between aldehydes and amides catalyzed by p-toluene sulfonic acid in solvent-free conditions provided a simple and efficient one-pot route for the synthesis of symmetrical bisamide derivatives in excellent yields.

Mohammad Anary-Abbasinejad; Mohammad H. Mosslemin; Alireza Hassanabadi; Safiyeh Tajik Safa

2010-01-01

273

REtools: A laboratory program for restriction enzyme work: enzyme selection and reaction condition assistance  

PubMed Central

Background Restriction enzymes are one of the everyday tools used in molecular biology. The continuously expanding panel of known restriction enzymes (several thousands) renders their optimal use virtually impossible without computerized assistance. Several manufacturers propose on-line sites that assist scientists in their restriction enzyme work, however, none of these sites meet all the actual needs of laboratory workers, and they do not take into account the enzymes actually present in one's own laboratory. Results Using FileMaker Pro, we developed a stand-alone application which can run on both PCs and Macintoshes. We called it REtools, for Restriction Enzyme tools. This program, which references all currently known enzymes (>3500), permits the creation and update of a personalized list of restriction enzymes actually available in one's own laboratory. Upon opening the program, scientists will be presented with a user friendly interface that will direct them to different menus, each one corresponding to different situations that restriction enzyme users commonly encounter. We particularly emphasized the ease of use to make REtools a solution that laboratory members would actually want to use. Conclusion REtools, a user friendly and easily customized program to organize any laboratory enzyme stock, brings a software solution that will make restriction enzyme use and reaction condition determination straightforward and efficient. The usually unexplored potential of isoschizomers also becomes accessible to all, since REtools proposes all possible enzymes similar to the one(s) chosen by the user. Finally, many of the commonly overlooked subtleties of restriction enzyme work, such as methylation requirement, unusual reaction conditions, or the number of flanking bases required for cleavage, are automatically provided by REtools.

Martin, Patrick; Boulukos, Kim E; Pognonec, Philippe

2006-01-01

274

Palladium-Catalyzed Aryl Amination Reactions of 6-Bromo- and 6-Chloropurine Nucleosides  

PubMed Central

Palladium-catalyzed C–N bond forming reactions of 6-bromo- as well as 6-chloropurine ribonucleosides and the 2’-deoxy analogues with aryl amines are described. Efficient conversions were observed with Pd(OAc)2/Xantphos/Cs2CO3, in PhMe at 100 °C. Reactions of the bromo nucleoside derivatives could be conducted at a lowered catalytic loading (5 mol % Pd(OAc)2/7.5 mol % Xantphos), whereas good product yields were obtained with a higher catalyst load (10 mol % Pd(OAc)2/15 mol % Xantphos) when the chloro analogue was employed. Among the examples evaluated, silyl protection for the hydroxyls appears better as compared to acetyl. The methodology has been evaluated via reactions with a variety of aryl amines and by synthesis of biologically relevant deoxyadenosine and adenosine dimers. This is the first detailed analysis of aryl amination reactions of 6-chloropurine nucleosides, and comparison of the two halogenated nucleoside substrates.

Thomson, Paul F.; Lagisetty, Pallavi; Balzarini, Jan; De Clercq, Erik; Lakshman, Mahesh K.

2011-01-01

275

Differential Selectivity of the Escherichia coli Cell Membrane Shifts the Equilibrium for the Enzyme-Catalyzed Isomerization of Galactose to Tagatose?  

PubMed Central

An Escherichia coli galactose kinase gene knockout (?galK) strain, which contains the l-arabinose isomerase gene (araA) to isomerize d-galactose to d-tagatose, showed a high conversion yield of tagatose compared with the original galK strain because galactose was not metabolized by endogenous galactose kinase. In whole cells of the ?galK strain, the isomerase-catalyzed reaction exhibited an equilibrium shift toward tagatose, producing a tagatose fraction of 68% at 37°C, whereas the purified l-arabinose isomerase gave a tagatose equilibrium fraction of 36%. These equilibrium fractions are close to those predicted from the measured equilibrium constants of the isomerization reaction catalyzed in whole cells and by the purified enzyme. The equilibrium shift in these cells resulted from the higher uptake and lower release rates for galactose, which is a common sugar substrate, than for tagatose, which is a rare sugar product. A ?mglB mutant had decreased uptake rates for galactose and tagatose, indicating that a methylgalactoside transport system, MglABC, is the primary contributing transporter for the sugars. In the present study, whole-cell conversion using differential selectivity of the cell membrane was proposed as a method for shifting the equilibrium in sugar isomerization reactions.

Kim, Jin-Ha; Lim, Byung-Chul; Yeom, Soo-Jin; Kim, Yeong-Su; Kim, Hye-Jung; Lee, Jung-Kul; Lee, Sook-Hee; Kim, Seon-Won; Oh, Deok-Kun

2008-01-01

276

Adenine Phosphoribosyl Transferase 1 is a Key Enzyme Catalyzing Cytokinin Conversion from Nucleobases to Nucleotides in Arabidopsis.  

PubMed

In plants, the cytokinin metabolic processes, including cytokinin biosynthesis, interconversion, inactivation, and degradation, play critical roles in the regulation of cytokinin homeostasis and plant development. Purine metabolic enzymes have been implied to catalyze the cytokinin interconversion in previous works. In this study, we report that Adenine Phosphoribosyl Transferase 1 (APT1) is the causal gene of the high-dose cytokinin-resistant mutants. APT1 catalyzes the cytokinin conversion from free bases to nucleotides, and is functionally predominant among the five members of the Arabidopsis Adenine Phosphoribosyl Transferase family. Loss of APT1 activity in plants leads to excess accumulation of cytokinin bases, thus evoking myriad cytokinin-regulated responses, such as delayed leaf senescence, anthocyanin accumulation, and downstream gene expression. Thus, our study defines APT1 as a key metabolic enzyme participating in the cytokinin inactivation by phosphoribosylation. PMID:23658065

Zhang, Xinyan; Chen, Yutao; Lin, Xin; Hong, Xinyu; Zhu, Ying; Li, Wenyang; He, Wenrong; An, Fengying; Guo, Hongwei

2013-05-08

277

Diastereoselectivity in Lewis-Acid Catalyzed Mukaiyama Aldol Reactions: A DFT Study  

PubMed Central

The basis for diastereoselectivity in Lewis acid-catalyzed Mukaiyama aldol reactions was studied using density functional theory. By exploring the conformations of the transition structures for the diastereodifferentiating step of seven different reactions, simple models were generated. The effects of varying the substituents on the enol carbon and the ?-carbon of the silyl enol ether from methyl to tert-butyl groups and the substituent on the aldehyde between methyl and phenyl groups were investigated by comparison of the transition structures for different reactions. Expanding on the previous qualitative models by Heathcock and Denmark, we found that while the pro-anti pathways takes place via antiperiplanar transition structures, the pro-syn pathways prefer synclinal transition structures. The relative steric effects of the Lewis acid and trimethyl silyl groups and the influence of E/Z isomerism on the aldol transition state were investigated. By calculating 36 transition structures at the M06/6-311G*//B3LYP/6-31G* level of theory and employing the IEFPCM polarizable continuum model for solvation effects, this study expands the mechanistic knowledge and provides a model for understanding the diastereoselectivity in Lewis acid-catalyzed Mukaiyama aldol reactions.

Lee, Joshua M.; Helquist, Paul; Wiest, Olaf

2012-01-01

278

Sulfuric, hydrochloric, and nitric acid-catalyzed triacetone triperoxide (TATP) reaction mixtures: an aging study.  

PubMed

The organic peroxide explosive triacetone triperoxide (TATP) is regularly encountered by law enforcement agents in various stages of its production. This study utilizes solid-phase microextraction (SPME) and gas chromatography/mass spectrometry (GC/MS) to examine sulfuric acid-, hydrochloric acid-, and nitric acid-catalyzed TATP syntheses during the initial 24 h of these reactions at low temperatures (5-9°C). Additionally, aging of the reaction mixtures was examined at both low and ambient temperatures (19-21°C) for a further 9 days. For each experiment, TATP could be readily identified in the headspace above the reaction mixture 1 h subsequent to the combination of reagents; at 24 h, TATP and diacetone diperoxide (DADP) were prominent. TATP degraded more rapidly than DADP. Additionally, chlorinated acetones chloroacetone and 1,1,-dichloroacetone were identified in the headspace above the hydrochloric acid-catalyzed TATP reaction mixture. These were not present when the catalyst was sulfuric acid or nitric acid. PMID:21595692

Fitzgerald, Mark; Bilusich, Daniel

2011-05-19

279

Influence of Hydroxylamine Conformation on Stereocontrol in Pd-Catalyzed Isoxazolidine-Forming Reactions  

PubMed Central

Palladium-catalyzed carboamination reactions between N-Boc-O-(but-3-enyl)hydroxylamine derivatives and aryl or alkenyl bromides afford cis-3,5- and trans-4,5-disubstituted isoxazolidines in good yield with up to >20:1 dr. The diastereoselectivity observed in the formation of cis-3,5-disubstituted isoxazolidines is superior to selectivities typically obtained in other transformations, such as 1,3-dipolar cycloaddition reactions, that provide these products. In addition, the stereocontrol in the C–N bond-forming Pd-catalyzed carboamination reactions of N-Boc-O-(but-3-enyl)hydroxylamines is significantly higher than related C–O bond-forming carboetherification reactions of N-benzyl-N-(but-3-enyl)hydroxylamine derivatives. This is likely due to a stereoelectronic preference for cyclization via transition states in which the Boc-group is placed in a perpendicular orientation relative to the plane of the developing ring, which derives from the conformational equilibria of substituted hydroxylamines.

Lemen, Georgia S.; Giampietro, Natalie C.; Hay, Michael B.

2009-01-01

280

Kinetics of acid-catalyzed aldol condensation reactions of aliphatic aldehydes  

NASA Astrophysics Data System (ADS)

Field observations of atmospheric aerosols have established that organic compounds compose a large fraction of the atmospheric aerosol mass. However, the physical/chemical pathway by which organic compounds are incorporated into atmospheric aerosols remains unclear. The potential role of acid-catalyzed reactions of organic compounds on acidic aerosols has been explored as a possible chemical pathway for the incorporation of organic material into aerosols. In the present study, ultraviolet-visible (UV-vis) spectroscopy was used to monitor the kinetics of formation of the products of the acid-catalyzed aldol condensation reaction of a range of aliphatic aldehydes (C 2-C 8). The experiments were carried out at various sulfuric acid concentrations and a range of temperatures in order to estimate the rate constants of such reactions on sulfuric acid aerosols under tropospheric conditions. The rate constants were generally found to decrease as the chain length of the aliphatic aldehyde increased (except for acetaldehyde, which had an unusually small rate constant), increase as a function of sulfuric acid concentration as predicted by excess acidity theory, and showed normal Arrhenius behavior as a function of temperature. While the kinetic data are generally consistent with previous laboratory reports of aldehyde reactivity in various sulfuric acid media, the aldol condensation reactions involving aliphatic aldehydes do not appear fast enough to be responsible for significant transfer of organic material into atmospheric aerosols.

Casale, Mia T.; Richman, Aviva R.; Elrod, Matthew J.; Garland, Rebecca M.; Beaver, Melinda R.; Tolbert, Margaret A.

281

Asymmetric 1,3-Dipolar Cycloaddition Reactions Catalyzed by Heterocycle-Based Metal Complexes  

NASA Astrophysics Data System (ADS)

Highly enantioselective 1,3-dipolar cycloaddition reactions of several 1,3-dipoles, such as nitrones, nitrile oxides, nitrile imines, diazoalkanes, azomethine imines and carbonyl ylides, catalyzed by heterocyclic supramolecular type of metal complexes consisting of chiral heterocyclic compounds and metal salts were described in terms of their ability of asymmetric induction and enantioface differentiation. The scope and limitations of each cycloaddition reactions were also briefly described. Of the chiral hererocycle-based ligands, chiral bisoxazoline, 2,6-bis(oxazolinyl)pyridine, and related oxazoline ligands are shown to be quite effective in obtaining high levels of asymmtric induction. The combination of the bisoxazoline ligand derived from (1S,2R)-cis-1-amino-2-indanol and metal salts was especially efficient for asymmetric cycloaddition reactions of a number of 1,3-dipoles, such as nitrones, nitrile oxide, nitrile imines, diazoacetates and azomethine imines. The metals utilized for the heterocycle-based complexes show a crucial role for degree of asymmetric induction depending upon the 1,3-dipole used. High levels of enantioselectivity were achieved in 1,3-dipolar cycloaddition reactions of unstable carbonyl ylides with benzyloxyacetaldehyde derivatives, ?-keto esters, 3-(2-alkenoyl)-2-oxazolidinones, and even vinyl ethers, which were catalyzed by Pybox-lanthanoid metal complexes.

Suga, Hiroyuki

282

Enantioselective intramolecular c?h amination catalyzed by engineered cytochrome p450 enzymes in?vitro and in?vivo.  

PubMed

Nitrogen activation: Though P450 enzymes are masters of oxygen activation and insertion into C?H bonds, their ability to use nitrogen for the same purpose has so far not been explored. Engineered variants of cytochrome P450BM3 have now been found to catalyze intramolecular C?H aminations in azide substrates. Mutations to two highly conserved residues significantly increased this activity. PMID:23893546

McIntosh, John A; Coelho, Pedro S; Farwell, Christopher C; Wang, Z Jane; Lewis, Jared C; Brown, Tristan R; Arnold, Frances H

2013-07-24

283

On-line characterization using ultrasound of pectin hydrolysis catalyzed by the enzyme pectinmethylesterase  

NASA Astrophysics Data System (ADS)

The major problem in the fruit juice industry is associated with juice quality deterioration due to the cloud loss of juice concentrates by the enzymatic reaction of pectinmethylesterase enzyme (PME, EC 3.1.1.11). During pectin hydrolysis, pectin and water are transformed into polygalacturonic acid (pectate) and methanol by the action of PME. In this work, a low-intensity ultrasonic technique is used to monitor this enzymatic reaction, with PME both from orange peel and from Aspergillus niger. Changes in sound velocity during pectin hydrolysis (1% concentration of pectin, T = 30°C and pH = 4.5 and 7) with 0.25 ml of enzyme solution (PME) have been measured using a through-transmission technique. Sound velocity decreases as pectin is transformed into pectate and methanol and at the end of the process, the change in sound velocity reaches 0.3 m/s with PME from orange peel and 0.33 m/s with PME from Aspergillus niger.

Aparicio, C.; Resa, P.; Sierra, C.; Elvira, L.

2012-12-01

284

Enzyme-Catalyzed Oxidation of 17?-Estradiol Using Immobilized Laccase from Trametes versicolor  

PubMed Central

Many natural and synthetic estrogens are amenable to oxidation through the catalytic action of oxidative enzymes such as the fungal laccase Trametes versicolor. This study focused on characterizing the conversion of estradiol (E2) using laccase that had been immobilized by covalent bonding onto silica beads contained in a bench-scale continuous-flow packed bed reactor. Conversion of E2 accomplished in the reactor declined when the temperature of the system was changed from room temperature to just above freezing at pH 5 as a result of a reduced rate of reaction rather than inactivation of the enzyme. Similarly, conversion increased when the system was brought to warmer temperatures. E2 conversion increased when the pH of the influent to the immobilized laccase reactor was changed from pH 7 to pH 5, but longer-term experiments showed that the enzyme is more stable at pH 7. Results also showed that the immobilized laccase maintained its activity when treating a constant supply of aqueous E2 at a low mean residence time over a 12-hour period and when treating a constant supply of aqueous E2 at a high mean residence time over a period of 9 days.

Cardinal-Watkins, Chantale; Nicell, Jim A.

2011-01-01

285

Mechanism of the intramolecular Claisen condensation reaction catalyzed by MenB, a crotonase superfamily member.  

PubMed

MenB, the 1,4-dihydroxy-2-naphthoyl-CoA synthase from the bacterial menaquinone biosynthesis pathway, catalyzes an intramolecular Claisen condensation (Dieckmann reaction) in which the electrophile is an unactivated carboxylic acid. Mechanistic studies on this crotonase family member have been hindered by partial active site disorder in existing MenB X-ray structures. In the current work the 2.0 Å structure of O-succinylbenzoyl-aminoCoA (OSB-NCoA) bound to the MenB from Escherichia coli provides important insight into the catalytic mechanism by revealing the position of all active site residues. This has been accomplished by the use of a stable analogue of the O-succinylbenzoyl-CoA (OSB-CoA) substrate in which the CoA thiol has been replaced by an amine. The resulting OSB-NCoA is stable, and the X-ray structure of this molecule bound to MenB reveals the structure of the enzyme-substrate complex poised for carbon-carbon bond formation. The structural data support a mechanism in which two conserved active site Tyr residues, Y97 and Y258, participate directly in the intramolecular transfer of the substrate ?-proton to the benzylic carboxylate of the substrate, leading to protonation of the electrophile and formation of the required carbanion. Y97 and Y258 are also ideally positioned to function as the second oxyanion hole required for stabilization of the tetrahedral intermediate formed during carbon-carbon bond formation. In contrast, D163, which is structurally homologous to the acid-base catalyst E144 in crotonase (enoyl-CoA hydratase), is not directly involved in carbanion formation and may instead play a structural role by stabilizing the loop that carries Y97. When similar studies were performed on the MenB from Mycobacterium tuberculosis, a twisted hexamer was unexpectedly observed, demonstrating the flexibility of the interfacial loops that are involved in the generation of the novel tertiary and quaternary structures found in the crotonase superfamily. This work reinforces the utility of using a stable substrate analogue as a mechanistic probe in which only one atom has been altered leading to a decrease in ?-proton acidity. PMID:21830810

Li, Huei-Jiun; Li, Xiaokai; Liu, Nina; Zhang, Huaning; Truglio, James J; Mishra, Shambhavi; Kisker, Caroline; Garcia-Diaz, Miguel; Tonge, Peter J

2011-10-11

286

A novel method for chemo-enzymatic synthesis of elicitor-active chitosan oligomers and partially N-deacetylated chitin oligomers using N-acylated chitotrioses as substrates in a lysozyme-catalyzed transglycosylation reaction system  

Microsoft Academic Search

N,N?,N?-Tri(monochloro)acetylchitotriose prepared by N-monochloroacetylation of chitotriose trihydrochloride was successfully polymerized into higher-molecular-weight oligomers by a lysozyme-catalyzed transglycosylation reaction, and a following base-catalyzed N-demonochloroacetylation gave a chitosan oligomer mixture mainly composed of oligomers with dp >6. Partially N-deacetylated chitin oligomers (DAC oligomers) with dp 4–12 were synthesized by the enzyme reaction using N,N?,N?-tri(monochloro)acetylchitotriose and N,N?,N?-triacetylchitotriose (chitin trimer) as initial substrates followed

Kohki Akiyama; Kazuyoshi Kawazu; Akio Kobayashi

1995-01-01

287

Recent advancements and challenges of palladiumII-catalyzed oxidation reactions with molecular oxygen as the sole oxidant  

PubMed Central

During the past 10 years there have been significant advances in PdII-catalyzed oxidation reactions where the use of ligands has led to the development of catalytic systems capable of achieving high turnover numbers, which employ molecular oxygen as the sole stoichiometric oxidant. This Feature article will highlight some of the recent developments in direct molecular oxygen-coupled PdII-catalyzed oxidation reactions with an emphasis on enhanced catalytic systems and new reactions. Additionally, limitations of current catalytic systems, such as ligand oxidation, are presented and their implications for the development of new reactions are discussed.

Gligorich, Keith M.; Sigman, Matthew S.

2010-01-01

288

Imparting catalyst control upon classical palladium-catalyzed alkenyl C-H bond functionalization reactions.  

PubMed

The functional group transformations carried out by the palladium-catalyzed Wacker and Heck reactions are radically different, but they are both alkenyl C-H bond functionalization reactions that have found extensive use in organic synthesis. The synthetic community depends heavily on these important reactions, but selectivity issues arising from control by the substrate, rather than control by the catalyst, have prevented the realization of their full potential. Because of important similarities in the respective selectivity-determining nucleopalladation and ?-hydride elimination steps of these processes, we posit that the mechanistic insight garnered through the development of one of these catalytic reactions may be applied to the other. In this Account, we detail our efforts to develop catalyst-controlled variants of both the Wacker oxidation and the Heck reaction to address synthetic limitations and provide mechanistic insight into the underlying organometallic processes of these reactions. In contrast to previous reports, we discovered that electrophilic palladium catalysts with noncoordinating counterions allowed for the use of a Lewis basic ligand to efficiently promote tert-butylhydroperoxide (TBHP)-mediated Wacker oxidation reactions of styrenes. This discovery led to the mechanistically guided development of a Wacker reaction catalyzed by a palladium complex with a bidentate ligand. This ligation may prohibit coordination of allylic heteroatoms, thereby allowing for the application of the Wacker oxidation to substrates that were poorly behaved under classical conditions. Likewise, we unexpectedly discovered that electrophilic Pd-?-alkyl intermediates are capable of distinguishing between electronically inequivalent C-H bonds during ?-hydride elimination. As a result, we have developed E-styrenyl selective oxidative Heck reactions of previously unsuccessful electronically nonbiased alkene substrates using arylboronic acid derivatives. The mechanistic insight gained from the development of this chemistry allowed for the rational design of a similarly E-styrenyl selective classical Heck reaction using aryldiazonium salts and a broad range of alkene substrates. The key mechanistic findings from the development of these reactions provide new insight into how to predictably impart catalyst control in organometallic processes that would otherwise afford complex product mixtures. Given our new understanding, we are optimistic that reactions that introduce increased complexity relative to simple classical processes may now be developed based on our ability to predict the selectivity-determining nucleopalladation and ?-hydride elimination steps through catalyst design. PMID:22111756

Sigman, Matthew S; Werner, Erik W

2011-11-23

289

Imparting Catalyst-Control upon Classical Palladium-Catalyzed Alkenyl C-H Bond Functionalization Reactions  

PubMed Central

Conspectus The functional group transformations carried out by the palladium-catalyzed Wacker and Heck reactions are radically different, but they are both alkenyl C-H bond functionalization reactions that have found extensive use in organic synthesis. The synthetic community depends heavily on these important reactions, but selectivity issues arising from control by the substrate, rather than control by the catalyst, have prevented the realization of their full potential. Because of important similarities in the respective selectivity-determining nucleopalladation and ?-hydride elimination steps of these processes, we posit that the mechanistic insight garnered through the development of one of these catalytic reactions may be applied to the other. In this Account, we detail our efforts to develop catalyst-controlled variants of both the Wacker oxidation and the Heck reaction to address synthetic limitations and provide mechanistic insight into the underlying organometallic processes of these reactions. In contrast to previous reports, we discovered that electrophilic palladium catalysts with non-coordinating counterions allowed for the use of a Lewis basic ligand to efficiently promote TBHP-mediated Wacker oxidation reactions of styrenes. This discovery led to the mechanistically guided development of a Wacker reaction catalyzed by a palladium complex with a bidentate ligand. This ligation may prohibit coordination of allylic heteroatoms, thereby allowing for the application of the Wacker oxidation to substrates that were poorly behaved under classical conditions. Likewise, we unexpectedly discovered that electrophilic Pd-?-alkyl intermediates are capable of distinguishing between electronically inequivalent C–H bonds during ?-hydride elimination. As a result, we have developed E-styrenyl selective oxidative Heck reactions of previously unsuccessful electronically non-biased alkene substrates using arylboronic acid derivatives. The mechanistic insight gained from the development of this chemistry allowed for the rational design of a similarly E-styrenyl selective classical Heck reaction using aryldiazonium salts and a broad range of alkene substrates. The key mechanistic findings from the development of these reactions provide new insight into how to predictably impart catalyst control in organometallic processes that would otherwise afford complex product mixtures. Given our new understanding, we are optimistic that reactions that introduce increased complexity relative to simple classical processes may now be developed based on our ability to predict the selectivity-determining nucleopalladation and ?-hydride elimination steps through catalyst design.

Sigman, Matthew S.; Werner, Erik W.

2011-01-01

290

Exploiting Acyl and Enol Azolium Intermediates via NHeterocyclic Carbene Catalyzed Reactions of Alpha-Reducible Aldehydes  

PubMed Central

N-heterocyclic carbenes are well known for their role in catalyzing benzoin and Stetter reactions: the generation of acyl anion equivalents from simple aldehydes to react with a variety of electrophiles. However, when an aldehyde bearing a leaving group or unsaturation adjacent to the acyl anion equivalent is subjected to an NHC, a new avenue of reactivity is unlocked, leading to a number of novel transformations which can generate highly complex products from simple starting materials, many of which are assembled through unconventional bond disconnections. The field of these new reactions - those utilizing ?-reducible aldehydes to access previously unexplored catalytic intermediates – has expanded rapidly in the past eight years. This review aims to provide the reader with a historical perspective on the underlying discoveries that led to the current state of the art, a mechanistic description of these reactions, and a summary of the recent advances in this area.

Vora, Harit U.; Wheeler, Philip

2013-01-01

291

Iron-catalyzed oxidation of thioethers by iodosylarenes: stereoselectivity and reaction mechanism.  

PubMed

Catalytic properties of a series of iron(III)-salen (salen=N,N'-bis(salicylidene)ethylenediamine dianion) and related complexes in asymmetric sulfoxidation reactions, with iodosylarenes as terminal oxidants, have been explored. These catalysts have been found to efficiently catalyze oxidation of alkyl aryl sulfides to sulfoxides with high chemoselectivity (up to 100 %) and moderate-to-high enantioselectivity (up to 84 % with isopropylthiobenzene and iodosylmesitylene), the TON (TON=turnover number) approaching 500. The influence of the ligand (electronic and steric effects of the substituents), oxidant, and substrate structures on the oxidation stereoselectivity has been investigated systematically. The structure of the reactive intermediates (complexes of the type [Fe(III)(ArIO)(salen)] and the reaction mechanism have been revealed by both mechanistic studies with different iodosylarenes and direct in situ (1)H NMR observation of the formation of the reactive species and its reaction with the substrate. PMID:17611952

Bryliakov, Konstantin P; Talsi, Evgenii P

2007-01-01

292

Chemiluminescent Reactions Catalyzed by Nanoparticles of Gold, Silver, and Gold/Silver Alloys  

NASA Astrophysics Data System (ADS)

Chemiluminescence (CL) reactions are catalyzed by metals nanoparticles, which display unique catalytic properties due to an increased surface area. The present study describes the catalytic effects of nanoparticles (NP) of silver, gold, and alloys of Au/Ag nanoparticles on the chemiluminescent reaction taking place between luminol and potassium ferricyanide. It was found that silver nanoparticles and alloy nanoparticles enhance the CL process when their sizes remained in the range of 30 nm to 50 nm. The data show that the intensity and rate of chemiluminescence were influenced by the mole fraction of gold and silver in the alloy. Data to this chemiluminescence reaction are modeled by a double exponential curve, which indicates that two competing processes are occurring.

Abideen, Saqib Ul

293

Asymmetric syn-selective Henry reaction catalyzed by the sulfonyldiamine-CuCl-pyridine system.  

PubMed

A catalytic asymmetric Henry reaction has been developed with use of a sulfonyldiamine-CuCl complex as a catalyst. A series of new binaphthyl-containing sulfonyldiamine ligands (2a-h) were readily synthesized in two steps starting from commercially available chiral 1,2-diamines. The (R,R)-diamine-(R)-binaphthyl ligand (2d)-CuCl complex smoothly catalyzed the enantioselective Henry reaction with the assistance of pyridine to give the corresponding adduct with high enantiomeric excess (up to 93%). Moreover, the 2d-CuCl-pyridine system promotes the diastereoselective Henry reaction in syn-selective manner to give the adduct in up to 99% yield with 92:8 syn/ anti selectivity. The enantiomeric excess of the syn-adduct was 84% ee. PMID:18512989

Arai, Takayoshi; Takashita, Ryuta; Endo, Yoko; Watanabe, Masahiko; Yanagisawa, Akira

2008-05-31

294

Enzyme Catalysis and the Gibbs Energy  

ERIC Educational Resources Information Center

Gibbs-energy profiles are often introduced during the first semester of organic chemistry, but are less often presented in connection with enzyme-catalyzed reactions. In this article I show how the Gibbs-energy profile corresponds to the characteristic kinetics of a simple enzyme-catalyzed reaction. (Contains 1 figure and 1 note.)

Ault, Addison

2009-01-01

295

Enzyme Catalysis and the Gibbs Energy  

ERIC Educational Resources Information Center

|Gibbs-energy profiles are often introduced during the first semester of organic chemistry, but are less often presented in connection with enzyme-catalyzed reactions. In this article I show how the Gibbs-energy profile corresponds to the characteristic kinetics of a simple enzyme-catalyzed reaction. (Contains 1 figure and 1 note.)|

Ault, Addison

2009-01-01

296

Evolutionary optimization of the catalytic effectiveness of an enzyme  

Microsoft Academic Search

The kinetic and thermodynamic features of reactions catalyzed by present-day enzymes appear to be the consequence of the evolution of these proteins toward maximal catalytic effectiveness. These features are identified and analyzed (in detail for one substrate-one product enzymes) by using ideas that link the energetics of the reaction catalyzed by an enzyme to the maximization of its catalytic efficiency.

Jonathan J. Burbaum; Ronald T. Raines; Jeremy R. Knowles

1989-01-01

297

Spontaneous high-yield hydrogen production from cellulosic materials and water catalyzed by enzyme cocktail  

SciTech Connect

Carbon-neutral hydrogen gas is a compelling energy carrier, especially for the transportation section. Low-cost hydrogen can be produced from abundant renewable lignocellulosic biomass through a number of methods employing chemical catalysis, biocatalysis or a combination of both, but these technologies suffer from low hydrogen yields (well below the theoretical yield of 12 H2 per glucose), undesired side-products and/or required severe reaction conditions. Here we present a novel in vitro synthetic biology approach for producing near theoretical hydrogen yields from cellulosic materials (cellodextrins) and water at 32oC and 1 atm. These non-natural catabolic pathways containing up to 14 enzymes and one coenzyme degrade cellodextrins initially to glucose-1-phosphate and eventually to CO2, split water and finally release the chemical energy in the form of hydrogen gas. Up to 11.2 H2 per anhydroglucose was produced in a batch reaction. This spontaneous endothermic reaction is driven by entropy gain, suggesting that the thermal energy is adsorbed for generating more chemical energy (hydrogen gas) than that in cellodextrins, i.e., output/input of chemical energy > 1, with an input of ambient-temperature thermal energy.

Ye, Xinhao [Virginia Polytechnic Institute and State University (Virginia Tech); Wang, Yiran [Virginia Polytechnic Institute and State University (Virginia Tech); Hopkins, Robert C. [University of Georgia, Athens, GA; Adams, Michael W. W. [University of Georgia, Athens, GA; Evans, Barbara R [ORNL; Mielenz, Jonathan R [ORNL; Zhang, Y.-H. Percival [Virginia Polytechnic Institute and State University (Virginia Tech)

2009-01-01

298

Synthesis of tetrasubstituted alkenes through a palladium-catalyzed domino carbopalladation/C-H-activation reaction.  

PubMed

Helical tetrasubstituted alkenes (7) were obtained in a highly efficient way through a palladium-catalyzed domino-carbopalladation/CH-activation reaction of propargylic alcohols 6 in good to excellent yields. Electron-withdrawing- and electron-donating substituents can be introduced onto the upper and lower aromatic rings. The substrates (6) for the domino process were synthesized by addition of the lithiated alkyne (20) to various aldehydes (19); moreover, the substrates were accessible enantioselectively (in 95% ee) by reduction of the corresponding ketone using the Noyori procedure. PMID:22259072

Tietze, Lutz F; Hungerland, Tim; Düfert, Alexander; Objartel, Ina; Stalke, Dietmar

2012-01-19

299

Stereochemistry and Mechanism of Reactions Catalyzed by Tryptophanase from Escherichia coZi  

Microsoft Academic Search

Several p replacement and cu,p elimination reactions catalyzed by tryptophanase from Escherichia coli are shown to proceed stereospecifically with retention of configuration. These conversions include synthesis of tryptophan from (2S,3R)- and (2S,3S)-(3-3H)serine in the presence of indole, deamination of these serines in DzO to pyruvate and ammonia, and cleavage of (2S,3R)- and (2S,3S)-(3-3H)tryptophan in DzO to indole, pyru- vate, and

John C. Vederas; Erwin Schleicher; Ming-Daw Tsai; Heinz G. Floss

300

How does Pin1 catalyze the cis-trans prolyl peptide bond isomerization? A QM/MM and mean reaction force study.  

PubMed

Pin1 represents an enzyme that specifically catalyzes the isomerization of peptide bonds between phosphorylated threonine or serine residues and proline. Despite its relevance as molecular timer in a number of biological processes related to cancer and Alzheimer disease, a detailed understanding of the factors contributing to the catalysis is still missing. In this study, we employ extensive QM/MM molecular dynamics simulations in combination with the mean reaction force (MRF) to discern the influence of the enzyme on the reaction mechanism and the origin of the catalysis. As a recently introduced method, the MRF separates the activation free energy barrier to reach the transition state into structural and electronic contributions providing a more detailed description of the enzyme's function. As a reference, we first study the isomerization starting from the cis form in solution and obtain a free energy barrier and a reaction free energy, which are in agreement with previous studies and experiment. With the new mean reaction force method, intramolecular hydrogen bonds in the peptide were identified that stabilize the transition state and reduce the electronic contribution to the free energy barrier. To elucidate the mechanism of catalysis of Pin1, the reaction in solution and in the catalytic cavity of the enzyme were compared. Both yield the same free energy barrier for the isomerization of the cis form, but with different decomposition in structural and electronic contributions by the mean reaction force. The enzyme reduces the energy required for structural rearrangements to reach the transition state, pointing to a destabilization of the reactant, but increases the electronic contribution to the barrier through specific enzyme-peptide hydrogen bonds. In the reverse reaction, the isomerization of the trans form, the enzyme alters the energetics and the mechanism of the reaction considerably. Unfavorable enzyme-peptide interactions in the catalytic cavity during the isomerization change the reaction coordinate, resulting in two minima with small energy differences to the transition state. These small free energy barriers should in principle make the reaction feasible at room temperature once the conformer is bound in the right conformation. PMID:23030417

Vöhringer-Martinez, Esteban; Duarte, Fernanda; Toro-Labbé, Alejandro

2012-10-18

301

Role of Valine 464 in the Flavin Oxidation Reaction Catalyzed by Choline Oxidase  

SciTech Connect

The oxidation of reduced flavin cofactors by oxygen is a very important reaction that is central to the chemical versatility of hundreds of flavoproteins classified as monooxygenases and oxidases. These enzymes are characterized by bimolecular rate constants {ge} 10{sup 5} M{sup -1} s{sup -1} and produce water and hydrogen peroxide, respectively. A hydrophobic cavity close to the reactive flavin C(4a) atom has been previously identified in the 3D structure of monooxygenases but not in flavoprotein oxidases. In the present study, we have investigated by X-ray crystallography, mutagenesis, steady-state, and rapid reaction approaches the role of Val464, which is <6 {angstrom} from the flavin C(4a) atom in choline oxidase. The 3D structure of the Val464Ala enzyme was essentially identical to that of the wild-type enzyme as shown by X-ray crystallography. Time-resolved anaerobic substrate reduction of the enzymes showed that replacement of Val464 with alanine or threonine did not affect the reductive half-reaction. Steady-state and rapid kinetics as well as enzyme-monitored turnovers indicated that the oxidative half-reaction in the Ala464 and Thr464 enzymes was decreased by 50-fold with respect to the wild-type enzyme. We propose that the side chain of Val464 in choline oxidase provides a nonpolar site that is required to guide oxygen in proximity of the C(4a) atom of the flavin, where it will subsequently react via electrostatic catalysis. Visual analysis of available structures suggests that analogous nonpolar sites are likely present in most flavoprotein oxidases. Mechanistic considerations provide rationalization for the differences between sites in monooxygenases and oxidases.

Finnegan, Steffan; Agniswamy, Johnson; Weber, Irene T.; Gadda, Giovanni (GSU)

2010-11-03

302

Brain chemistry: how does P450 catalyze the O-demethylation reaction of 5-methoxytryptamine to yield serotonin?  

PubMed

Density functional theory has been applied to elucidate the mechanism of the O-demethylation reaction that generates serotonin from 5-methoxytryptamine (5-MT); a process that is efficiently catalyzed by P450 CYP2D6. Two substrates, the neutral 5-MT and the protonated 5-MTH(+), were used to probe the reactivity of CYP2D6 compound I. Notably, the H-abstraction process is found to be slightly more facile for 5-MT. However, our DFT augmented by docking results show that the amino acid Glu216 in the active site holds the NH(3)(+) tail of the 5-MTH(+) substrate in an upright conformation and thereby controls the regioselectivity of the bond activation. Thus, the substrate protonation serves an important function in maximizing the yield of serotonin. This finding is in accord with experimental conclusions that 5-MTH(+) serves as the substrate for the CYP2D6 enzyme. The study further shows that the H-abstraction follows two-state reactivity (TSR), whereas the rebound path may involve more states due to the appearance of both Fe(IV) and Fe(III) electromers during the reaction of 5-MTH(+). PMID:20405876

Schyman, Patric; Usharani, Dandamudi; Wang, Yong; Shaik, Sason

2010-05-27

303

Structure and function of metal cations in light alkane reactions catalyzed by modified H-ZSM5  

Microsoft Academic Search

The rate of propane dehydrocyclodimerization to form C6 aromatics is limited by a sequence of irreversible dehydrogenation reactions leading to propene, higher alkenes, dienes, trienes, and aromatics. Quasi-equilibrated acid—catalyzed cracking, oligometization, and cyclization reactions of alkene intermediates occur in sequence with these dehydrogenation reactions. Each dehydrogenation reaction is in turn limited by the rate of elementary steps that dispose of

Joseph A. Biscardi; Enrique Iglesia

1996-01-01

304

ZnS quantum dots as pH probes for study of enzyme reaction kinetics.  

PubMed

Water soluble ZnS quantum dots (QDs) modified by mercaptoacetic acid (MAA) were used to determinate proton concentration in aqueous solutions by fluorescence spectroscopic technique. The results showed that the fluorescence of the water-soluble QDs could be quenched by proton concentration and the fluorescence intensity of the water-soluble QDs decreased linearly as the pH varied from 4.5 to 7.0. Based on this phenomenon, a convenient, rapid and specific method to determine of enzyme reaction kinetics was proposed. The modified ZnS QDs were successfully used as pH probes in monitoring the hydrolysis of glycidyl butyrate catalyzed by porcine pancreatic lipase (PPL). The proposed method was found to improve stability, sensitivity and a monitoring range for determination proton concentration as compared to the already described analytical methods based on p-Nitrophenoxide (PNP). PMID:22579390

Wu, Dudu; Chen, Zhi

2012-04-05

305

Transition-metal-catalyzed Suzuki-Miyaura cross-coupling reactions: a remarkable advance from palladium to nickel catalysts.  

PubMed

In the transition-metal-catalyzed cross-coupling reactions, the use of the first row transition metals as catalysts is much more appealing than the precious metals owing to the apparent advantages such as cheapness and earth abundance. Within the last two decades, particularly the last five years, explosive interests have been focused on the nickel-catalyzed Suzuki-Miyaura reactions. This has greatly advanced the chemistry of transition-metal-catalyzed cross-coupling reactions. Most notably, a broad range of aryl electrophiles such as phenols, aryl ethers, esters, carbonates, carbamates, sulfamates, phosphates, phosphoramides, phosphonium salts, and fluorides, as well as various alkyl electrophiles, which are conventionally challenging, by applying palladium catalysts can now be coupled efficiently with boron reagents in the presence of nickel catalysts. In this review, we would like to summarize the progress in this reaction. PMID:23460083

Han, Fu-She

2013-06-21

306

Enzyme Reactions on a 27 MHz Quartz Crystal Microbalance  

Microsoft Academic Search

A quartz crystal microbalance (QCM) is known as a useful tool to detect gravimetric molecular interactions. We have developed\\u000a a 27-MHz QCM (Affinix Q4) to detect various biomolecular interactions such as DNA-DNA hybridization, DNA-protein interactions, glycolipid-protein\\u000a interactions, and protein-protein interactions. In this chapter, we show that the 27-MHz QCM is also useful to detect the\\u000a kinetics of enzyme reactions, because

Yoshio Okahata; Toshiaki Mori; Hiroyuki Furusawa; Takanori Nihira

307

Evaluation of the role of His447 in the reaction catalyzed by cholesterol oxidase.  

PubMed

Cholesterol oxidase catalyzes the oxidation and isomerization of cholesterol to cholest-4-en-3-one via cholest-5-en-3-one. It has been proposed that His447 acts as the general base catalyst for oxidation, and that the resulting imidazolium ion formed acts as an electrophile for isomerization. In this work, we undertook an assessment of the proposed dual roles of His447 in the oxidation and isomerization reactions. To test its role, we constructed five mutants, H447Q, H447N, H447E, H447D, and H447K, that introduce hydrogen bond donors and acceptors and carboxylate bases at this position, and a sixth mutant, E361Q, to test the interplay between His447 and Glu361. These mutants were characterized using steady-state kinetics and deuterium substrate and solvent isotope effects. For those mutants that catalyze either oxidation of cholesterol or isomerization of cholest-5-en-3-one, the Km's vary no more than 3-fold relative to wild type. H447K is inactive in both oxidation (> 100,000-fold reduced) and isomerization assays (> 10,000-fold reduced). H447E and H447D do not catalyze oxidation (> 100,000-fold reduced), but do catalyze isomerization, 10(4) times slower than wild type. The k(cat) for H447Q is 120-fold lower than wild type for oxidation, and the same as wild type for isomerization. The k(cat) for H447N is 4400-fold lower than wild type for oxidation, and is 30-fold lower than wild type for isomerization. E361Q does not catalyze isomerization (> 10,000-fold reduced), and the k(cat) for oxidation is 30-fold lower than wild type. The substrate deuterium kinetic isotope effects for the wild-type and mutant-catalyzed oxidation reactions suggest that mutation of His447 to an amide results in a change of the rate-determining step from hydride transfer to hydroxyl deprotonation. The deuterium solvent and substrate kinetic isotope effects for isomerization indicate that an amide at position 447 is an effective electrophile to catalyze formation of a dienolic intermediate. Moreover, consideration of kinetic and structural results together suggests that a hydrogen bonding network involving His447, Glu361 and Asn485, Wat541, and substrate serves to position the substrate and coordinate general base and electrophilic catalysis. That is, in addition to its previously demonstrated role as base for deprotonation of carbon-4 during isomerization, Glu361 has a structural role and may act as a general base during oxidation. The His447, Asn485, Glu361, and Wat541 residues are conserved in other GMC oxidoreductases. Observation of this catalytic tetrad in flavoproteins of unknown function may be diagnostic for an ability to oxidize unactivated alcohols. PMID:9922167

Kass, I J; Sampson, N S

1998-12-22

308

A specific affinity reagent to distinguish aldehyde dehydrogenases and oxidases. Enzymes catalyzing aldehyde oxidation in an adult moth  

SciTech Connect

Aldehyde dehydrogenase (ALDH) and oxidase (AO) enzymes from the tissue extracts of male and female tobacco budworm moth (Heliothis virescens) were identified after electrophoretic protein separation. AO activity was visualized using formazan- or horseradish peroxidase-mediated staining coupled to the AO-catalyzed oxidation of benzaldehyde. A set of six soluble AO enzymes with isoelectric points from pI 4.6 to 5.3 were detected primarily in the antennal extracts. Partially purified antennal AO enzymes also oxidized both (Z)-9-tetradecenal and (Z)-11-hexadecenal, the two major pheromone components of this moth. ALDH activity was detected using a tritium-labeled affinity reagent based on a known irreversible inhibitor of this enzyme. This labeled vinyl ketone, (3H)(Z)-1,11-hexadecadien-3-one, was synthesized and used to covalently modify the soluble ALDH enzymes from tissue extracts. Molecular subunits of potential ALDH enzymes were visualized in the fluorescence autoradiograms of sodium dodecyl sulfate-polyacrylamide gel electrophoresis-separated proteins of the antenna, head, and leg tissues. Covalent modification of these protein subunits decreased specifically in the presence of excess pheromone aldehyde or benzaldehyde. Labeled vinyl ketones are thus novel tools for the identification of molecular subunits of ALDH enzymes.

Tasayco, M.L.; Prestwich, G.D. (State Univ. of New York, Stony Brook (USA))

1990-02-25

309

Copper-catalyzed enantioselective Henry reaction of enals and subsequent iodocyclization: stereoselective construction of chiral azatricyclic frameworks.  

PubMed

In the frame: A cascade sequence combining an asymmetric Henry reaction and a stereoselective intramolecular iodocyclization provides direct access to an enantioenriched tricyclic hexahydrochromeno[4,3-b]pyrrole framework. The Henry reaction is catalyzed by copper in the presence of L1. PMID:23934727

Zhou, Yirong; Zhu, Yuequan; Yan, Shaobai; Gong, Yuefa

2013-08-09

310

One-pot synthesis of 4-methylisoquinolines via a sequential Pd-catalyzed Heck reaction and intramolecular cyclization.  

PubMed

An efficient, one-pot synthesis of 4-methylisoquinolines via a cascade Pd-catalyzed Heck reaction, intramolecular cyclization and isomerization has been developed. This reaction has a wide range of substrates with various functional groups, and the corresponding products have been obtained in good yields. PMID:24068319

Tian, Yulin; Qi, Jianguo; Sun, Chenbin; Yin, Dali; Wang, Xiaojian; Xiao, Qiong

2013-10-01

311

Label-free SERS monitoring of chemical reactions catalyzed by small gold nanoparticles using 3D plasmonic superstructures.  

PubMed

Label-free in situ surface-enhanced Raman scattering (SERS) monitoring of reactions catalyzed by small gold nanoparticles using rationally designed plasmonic superstructures is presented. Catalytic and SERS activities are integrated into a single bifunctional 3D superstructure comprising small gold satellites self-assembled onto a large shell-isolated gold core, which eliminates photocatalytic side reactions. PMID:23186150

Xie, Wei; Walkenfort, Bernd; Schlücker, Sebastian

2012-11-29

312

The Palladium-Catalyzed Cross-Coupling Reaction of Phenylboronic Acid with Haloarenes in the Presence of Bases  

Microsoft Academic Search

The transition metal-catalyzed reactions of organometallics with organic halides have been extensively studied to prove a new approach to selective formation of carbon-carbon bonds. Recently, such coupling reactions of haloarenes with aryl magnesium and zinc compounds in the presence of palladium or nickel complexes have been reported for the synthesis of biaryls. Davidson and Triggs have previously reported that arylboronic

N. Miyaura; T. Yanagi; A. Suzuki

1981-01-01

313

Secondary sup 15 N isotope effects on the reactions catalyzed by alcohol and formate dehydrogenases  

SciTech Connect

Secondary {sup 15}N isotope effects at the N-1 position of 3-acetylpyridine adenine dinucleotide have been determined, by using the internal competition technique, for horse liver alcohol dehydrogenase (LADH) with cyclohexanol as a substrate and yeast formate dehydrogenase (FDH) with formate as a substrate. On the basis of less precise previous measurements of these {sup 15}N isotope effects, the nicotinamide ring of NAD has been suggested to adopt a boat conformation with carbonium ion character at C-4 during hydride transfer. If this mechanism were valid, as N-1 becomes pyramidal an {sup 15}N isotope effect for the reaction catalyzed by LADH was measured. These values suggest that a significant {sup 15}N kinetic isotope effect is not associated with hydride transfer for LADH and FDH. Thus, in contrast with the deformation mechanism previously postulated, the pyridine ring of the nucleotide apparently remains planar during these dehydrogenase reactions.

Rotberg, N.S.; Cleland, W.W. (Univ. of Wisconsin, Madison (USA))

1991-04-23

314

Negative resists for i-line lithography utilizing acid-catalyzed intramolecular dehydration reaction  

NASA Astrophysics Data System (ADS)

Chemical amplification negative resist system composed of a novolak resin, a carbinol and an acid generator is investigated for i-line phase-shift lithography. The reaction in this resist is based on an acid-catalyzed intramolecular dehydration reaction. The dehydration products act as aqueous-base dissolution inhibitors, and carbinol compounds in unexposed areas work as dissolution promoters. The resist composed of a novolak resin, 1,4-bis((alpha) -hydroxyisopropyl) benzene (DIOL-1) and 2- naphthoylmethyltetramethylenesulfonium triflate (PAG-2) gives the best lithographic performance in terms of sensitivity and resolution. Line-and-space patterns of 0.275 micrometers are obtained using an i-line stepper (NA:0.45) in conjunction with a phase shifting mask.

Ueno, Takumi; Uchino, Shou-ichi; Hattori, K. T.; Onozuka, T.; Shirai, Sei-ichiro; Moriuchi, Noboru; Hashimoto, Michiaki; Koibuchi, S.

1994-05-01

315

The Palladium-Catalyzed Aerobic Kinetic Resolution of Secondary Alcohols: Reaction Development, Scope, and Applications  

PubMed Central

The first palladium-catalyzed enantioselective oxidation of secondary alcohols has been developed, utilizing the readily available diamine (?)-sparteine as chiral ligand and molecular oxygen as the stoichiometric oxidant. Mechanistic insights regarding the role of base and hydrogen bond donors have resulted in several improvements to the original system. Namely, addition of cesium carbonate and tert-butyl alcohol greatly enhances reaction rates, promoting rapid resolutions. The use of chloroform as solvent allows the use of ambient air as the terminal oxidant at 23 °C, resulting in enhanced catalyst selectivity. These improved reaction conditions have permitted the successful kinetic resolution of benzylic, allylic, and cyclopropyl secondary alcohols to high enantiomeric excess with good to excellent selectivity factors. This catalyst system has also been applied to the desymmetrization of meso-diols, providing high yields of enantioenriched hydroxyketones.

Ebner, David C.; Bagdanoff, Jeffrey T.; Ferreira, Eric M.; McFadden, Ryan M.; Caspi, Daniel D.; Trend, Raissa M.

2010-01-01

316

The Escherichia coli multidrug transporter MdfA catalyzes both electrogenic and electroneutral transport reactions  

PubMed Central

The resistance of cells to many drugs simultaneously (multidrug resistance) often involves the expression of membrane transporters (Mdrs); each recognizes and expels a broad spectrum of chemically unrelated drugs from the cell. The Escherichia coli Mdr transporter MdfA is able to transport differentially charged substrates in exchange for protons. This includes neutral compounds, namely chloramphenicol and thiamphenicol, and lipophilic cations such as tetraphenylphosphonium and ethidium. Here we show that the chloramphenicol and thiamphenicol transport reactions are electrogenic, whereas the transport of several monovalent cationic substrates is electroneutral. Therefore, unlike with positively charged substrates, the transmembrane electrical potential (negative inside) constitutes a major part of the driving force for the transport of electroneutral substrates by MdfA. These results demonstrate an unprecedented ability of a single secondary transporter to catalyze discrete transport reactions that differ in their electrogenicity and are governed by different components of the proton motive force.

Lewinson, Oded; Adler, Julia; Poelarends, Gerrit J.; Mazurkiewicz, Piotr; Driessen, Arnold J. M.; Bibi, Eitan

2003-01-01

317

Palladium-catalyzed alkene carboamination reactions for the synthesis of substituted piperazines  

PubMed Central

A strategy for the stereoselective preparation of enantiomerically enriched cis-2,6-disubstituted piperazines from amino acid precursors is described. The target compounds are generated in 95–99% ee with good to excellent levels of diastereoselectivity (usually 14:1 to >20:1) using Pd-catalyzed carboamination reactions between aryl or alkenyl halides and substituted ethylenediamine derivatives to form the heterocyclic rings. The synthesis requires only 4–5 steps from commercially available amino acids, and allows for the modular construction of piperazines bearing different substituents at N1, N4, C2, and C6. The use of this strategy for the construction of 2,3-disubstituted piperazines, fused bicyclic piperazines, and tetrahydroquinoxalines is also reported. In addition, the mechanism of the key carboamination reactions are discussed, and new models that predict and explain the stereochemical outcome of these transformations are presented.

Nakhla, Josephine S.; Schultz, Danielle M.; Wolfe, John P.

2009-01-01

318

Gold- and silver-catalyzed reactions of propargylic alcohols in the presence of protic additives.  

PubMed

A wide range of primary, secondary and tertiary propargylic alcohols undergo a Meyer-Schuster rearrangement to give enones at room temperature in the presence of a gold(I) catalyst and small quantities of MeOH or 4-methoxyphenylboronic acid. The syntheses of the enone natural products isoegomaketone and daphenone were achieved using this reaction as the key step. The rearrangement of primary propargylic alcohols can readily be combined in a one-pot procedure with the addition of a nucleophile to the resulting terminal enone, to give ?-aryl, ?-alkoxy, ?-amino or ?-sulfido ketones. Propargylic alcohols bearing an adjacent electron-rich aryl group can also undergo silver-catalyzed substitution of the alcohol with oxygen, nitrogen and carbon nucleophiles. This latter reaction was initially observed with a batch of gold catalyst that was probably contaminated with small quantities of silver salt. PMID:22374879

Pennell, Matthew N; Turner, Peter G; Sheppard, Tom D

2012-02-28

319

Inhibition of adenylate cyclase by transglutaminase-catalyzed reactions in pigeon erythrocyte ghosts.  

PubMed

We report the occurrence in pigeon erythrocytes of a soluble Ca2+-dependent transglutaminase (TGase) activity. The effect of the erythrocyte ghost protein modifications, determined by TGase-catalyzed reactions, on adenylate cyclase, phospholipid methyltransferase I and II activities and on the lipidic matrix fluidity of the membrane was investigated by using a purified guinea pig liver TGase preparation. The results showed a significant inhibitory effect of such modifications both on the basal and on the variously stimulated (by NaF, Gpp(NH)p alone or in the presence of 1-isoproterenol) adenylate cyclase activity. By contrast, both the phospholipid methylation and the fluidity of the lipidic matrix of the membrane were unaffected by TGase-mediated reactions. These data suggest a new possible inhibitory mechanism of the cyclic AMP synthesis which might be triggered by the enhancement of the cytosolic Ca2+ concentration. PMID:2874804

Porta, R; De Santis, A; Esposito, C; Draetta, G F; Di Donato, A; Illiano, G

1986-07-31

320

Palladium-catalyzed C-F activation of polyfluoronitrobenzene derivatives in Suzuki-Miyaura coupling reactions.  

PubMed

Highly fluorinated nitrobenzene derivatives are suitable substrates for palladium-catalyzed C-F bond arylation using readily available palladium catalysts under both conventional heating and microwave conditions. Arylation occurs ortho to the nitro group offering a synthetic route to polyfluorinated 2-arylnitrobenzene systems. The regiochemistry of the arylation reactions suggests that there is a significant directing interaction between the nitro group and the incoming nucleophilic palladium catalyst which is facilitated by the presence of several fluorine atoms attached the ring. Investigations into the regioselectivity and reactivity of several tetrafluoro- and trifluoronitrobenzene derivatives provides further evidence for the highly nucleophilic character of the oxidative addition step in contrast to the concerted mechanism of more conventional Suzuki-Miyaura coupling reactions involving aryl iodides and bromides. PMID:20704342

Cargill, Matthew R; Sandford, Graham; Tadeusiak, Andrezj J; Yufit, Dmitrii S; Howard, Judith A K; Kilickiran, Pinar; Nelles, Gabrielle

2010-09-01

321

Reaction of ethyl diazoacetate with N-2,7-octadienylanilines catalyzed by compounds of copper  

SciTech Connect

The reaction of EDA with N-2,7-octadienyl derivatives of aniline, catalyzed by the complex copper bis(N-(R,S)-..cap alpha..-phenylethylsalicylaldiminate), was studied. The reaction of N-2,7-octadienylanilines, and also of bis(N-2,7-octadienyl)- and N-acetyle-N-2-7-octadienylanilines, with EDA proceeds with the formation of the products of the cyclopropanation at the terminal vinyl group or the disubstituted double bond. In the case of the N-alkyl-N-2,7-octadienyl anilines, the skeletal isomerization of the octadienyl anilines, the skeletal isomerization of the octadienyl radical in the initial amine with the simultaneous introduction of ethoxycarbonylcarbene at the allylic C-H bond takes place.

Fakhretdinov, R.N.; Marvanov, R.M.; Dzhemilev, U.M.; Tolstikov, G.A.

1986-06-20

322

Study of enzyme adsorption and reaction kinetics for cellulose hydrolysis  

SciTech Connect

Enzymatic hydrolysis of cellulose occurs due to the combined catalytic action of two types of cellulase components commonly referred to as C/sub 1/ and C/sub x/. However, before the hydrolysis reaction can begin, it is necessary for these enzymes to first adsorb onto the accessible surfaces of the insoluble cellulose substrate. The objective of the study was to gain a better understanding of the relationships between the adsorption of these enzyme components, the hydrolysis kinetics, the cellulosic surface area accessible to the enzymes, and the cellulose crystallinity. These relationships were investigated by passing a Trichoderma viride cellulase solution through columns of cellulose powder having different accessibility and crystallinity, and then analyzing the quantities of the different enzyme components and the hydrolysis product in the effluent. The amounts of the different cellulase components were analyzed using high-performance anion-exchange chromatography. Additional adsorption and hydrolysis experiments were done using columns of cellulose beads specially developed to provide amodel substrate for this analysis. A mathematical model has been formulated to describe the kinetics of enzyme adsorption and the resultant, initial hydrolysis rate in cellulose column. The analytical solutions obtained have been linearized into a convenient form so that the kinetic parameters of the model can be readily determined from experimental breakthrough curves.

Gilbert, I.G.

1982-01-01

323

Nickel-catalyzed methanation reactions studied with an in situ magnetic induction method: Experiments and modeling  

SciTech Connect

Methanation reactions of CO or CO{sub 2} catalyzed by a commercial Ni/kiesel-guhr catalyst, and the adsorption of the relevant reactants and products, were studied with an in situ magnetic induction method using a low-field ac permeameter. At the conditions studied, CH{sub 4} was the only product observed and both reactions exhibited similar rates and trends. Comparison of the magnetic data under reaction to the individual contributions expected from adsorption suggests that adsorbed CO was the dominant surface species in CO methanation, while adsorbed CH{sub 4} was the dominant species in CO{sub 2} methanation. The reaction rate and relative magnetic loss were modeled using parameters obtained from single-species magnetic-adsorption data. Adsorptions were modeled with a Langmuir-type isotherm. Rates of methanation were successfully described by a Langmuir-Hinshelwood rate expression using the single-species magnetic-adsorption parameters and extracting the surface-reaction rate constant. The magnetic loss was predicted then, using predetermined parameters, and compared to observations. Adequate prediction was observed for CO{sub 2} methanation whereas significant deviation exists for CO methanation. The latter result is die to the falsification of CO and possibly CH{sub 4} adsorption parameters by irreversible processes.

Yesgar, P.W.; Sheintuch, M. (Technion-Israel Inst. of Tech., Haifa, (Israel))

1991-02-01

324

Characteristics of the nitric oxide synthase-catalyzed conversion of arginine to N-hydroxyarginine, the first oxygenation step in the enzymic synthesis of nitric oxide.  

PubMed

The nitric oxide synthase-catalyzed conversion of L-arginine to L-citrulline and nitric oxide is known to be the sum of two partial reactions: oxygenation of arginine to N-hydroxyarginine, followed by oxygenation of N-hydroxyarginine to citrulline and nitric oxide. Whereas the conversion of N-hydroxyarginine to citrulline and nitric oxide has been the subject of a number of studies, the oxygenation of arginine to N-hydroxyarginine has received little attention. Here we show that substrate amounts of rat cerebellar nitric oxide synthase, in the absence of added NADPH, catalyze the conversion of arginine to N-hydroxyarginine as the dominant product. The product appears not to be tightly bound to the enzyme. A maximum of 0.16 mol of N-hydroxyarginine/mol of nitric oxide synthase subunit was formed. The reaction requires oxygen and the addition of Ca2+/calmodulin and is stimulated 3-fold by tetrahydrobiopterin. Upon addition of NADPH, citrulline is formed exclusively. Conversion of N-hydroxyarginine to citrulline, like the first partial reaction, requires Ca2+/calmodulin and is stimulated by tetrahydrobiopterin but differs from the first partial reaction in being completely dependent upon addition of NADPH. These results indicate that brain nitric oxide synthase contains an endogenous reductant that can support oxygenation of arginine but not of N-hydroxyarginine. The reductant is not NADPH, since the amount of nitric oxide synthase-bound NADPH is appreciably less than the amount required for N-hydroxyarginine synthesis. Possible candidates for this role are discussed in relation to proposed mechanisms of action of nitric oxide synthase. PMID:7530247

Campos, K L; Giovanelli, J; Kaufman, S

1995-01-27

325

Evidence that both protium and deuterium undergo significant tunneling in the reaction catalyzed by bovine serum amine oxidase  

SciTech Connect

The magnitudes of primary and secondary H/T and D/T kinetic isotope effects have been measured in the bovine serum amine oxidase catalyzed oxidation of benzylamine from 0 to 45{degree}C. Secondary H/T and D/T kinetic effects are small and in the range anticipated from equilibrium isotope effects; Arrhenius preexponential factors (A{sub H}/A{sub T} and A{sub D}/A{sub T}) determined from the temperature dependence of isotope effects also indicate semiclassical behavior. By contrast, primary H/T and D/T isotope effects, 35.2 {plus minus} 0.8 and 3.07 {plus minus} 0.07, respectively, at 25{degree}C, are larger than semiclassical values and give anomalously low preexponential factor rations, A{sub H}/A{sub T} = 0.12 {plus minus} 0.04 and A{sub D}/A{sub T} = 0.51 {plus minus} 0.10. Stopped-flow studies indicate similar isotope effects on cofactor reduction as seen in the steady state, consistent with a single rate-limiting C-H bond cleavage step for V{sub max}/K{sub m}. The comparison of primary and secondary isotope effects allows the authors to rule out appreciable coupling between the primary and secondary hydrogens at C-1 of the substrate. From the properties of primary isotope effects, they conclude that both protium and deuterium undergo significant tunneling in the course of substrate oxidation. These finding represent the first example of quantum mechanical effects in an enzyme-catalyzed proton abstraction reaction.

Grant, K.L.; Klinman, J.P. (Univ. of California, Berkeley (USA))

1989-08-08

326

Understanding bistability in complex enzyme-driven reaction networks.  

PubMed

Much attention has been paid recently to bistability and switch-like behavior that might be resident in important biochemical reaction networks. There is, in fact, a great deal of subtlety in the relationship between the structure of a reaction network and its capacity to engender bistability. In common physicochemical settings, large classes of extremely complex networks, taken with mass action kinetics, cannot give rise to bistability no matter what values the rate constants take. On the other hand, bistable behavior can be induced in those same settings by certain very simple and classical mass action mechanisms for enzyme catalysis of a single overall reaction. We present a theorem that distinguishes between those mass action networks that might support bistable behavior and those that cannot. Moreover, we indicate how switch-like behavior results from a well-studied mechanism for the action of human dihydrofolate reductase, an important anti-cancer target. PMID:16735474

Craciun, Gheorghe; Tang, Yangzhong; Feinberg, Martin

2006-05-30

327

Mesoscopic statistical properties of multistep enzyme-mediated reactions.  

PubMed

Enzyme-mediated reactions may proceed through multiple intermediate conformational states before creating a final product molecule, and one often wishes to identify such intermediate structures from observations of the product creation. In this study, the authors address this problem by solving the chemical master equations for various enzymatic reactions. A perturbation theory analogous to that used in quantum mechanics allows the determination of the first (n) and the second (?2) cumulants of the distribution of created product molecules as a function of the substrate concentration and the kinetic rates of the intermediate processes. The mean product flux V=d(n)/dt (or 'dose-response' curve) and the Fano factor F= ?2/(n) are both realistically measurable quantities, and whereas the mean flux can often appear the same for different reaction types, the Fano factor can be quite different. This suggests both qualitative and quantitative ways to discriminate between different reaction schemes, and the authors explore this possibility in the context of four sample multistep enzymatic reactions. Measuring both the mean flux and the Fano factor can not only discriminate between reaction types, but can also provide some detailed information about the internal, unobserved kinetic rates, and this can be done without measuring single-molecule transition events. PMID:21028932

de Ronde, W H; Daniels, B C; Mugler, A; Sinitsyn, N A; Nemenman, I

2009-09-01

328

Statistical properties of multistep enzyme-mediated reactions  

SciTech Connect

Enzyme-mediated reactions may proceed through multiple intermediate conformational states before creating a final product molecule, and one often wishes to identify such intermediate structures from observations of the product creation. In this paper, we address this problem by solving the chemical master equations for various enzymatic reactions. We devise a perturbation theory analogous to that used in quantum mechanics that allows us to determine the first () and the second (variance) cumulants of the distribution of created product molecules as a function of the substrate concentration and the kinetic rates of the intermediate processes. The mean product flux V=d/dt (or 'dose-response' curve) and the Fano factor F=variance/ are both realistically measurable quantities, and while the mean flux can often appear the same for different reaction types, the Fano factor can be quite different. This suggests both qualitative and quantitative ways to discriminate between different reaction schemes, and we explore this possibility in the context of four sample multistep enzymatic reactions. We argue that measuring both the mean flux and the Fano factor can not only discriminate between reaction types, but can also provide some detailed information about the internal, unobserved kinetic rates, and this can be done without measuring single-molecule transition events.

Nemenman, Ilya [Los Alamos National Laboratory; Sinitsyn, Nikolai A [Los Alamos National Laboratory; De Ronde, Wiet H [AMOLF; Daniels, Bryan C [CORNELL; Mugler, Andrew [COLUMBIA

2008-01-01

329

Effect of osmolytes on protein dynamics in the lactate dehydrogenase-catalyzed reaction.  

PubMed

Laser-induced temperature jump relaxation spectroscopy was used to probe the effect of osmolytes on the microscopic rate constants of the lactate dehydrogenase-catalyzed reaction. NADH fluorescence and absorption relaxation kinetics were measured for the lactate dehydrogenase (LDH) reaction system in the presence of varying amounts of trimethylamine N-oxide (TMAO), a protein-stabilizing osmolyte, or urea, a protein-destabilizing osmolyte. Trimethylamine N-oxide (TMAO) at a concentration of 1 M strongly increases the rate of hydride transfer, nearly nullifies its activation energy, and also slightly increases the enthalpy of hydride transfer. In 1 M urea, the hydride transfer enthalpy is almost nullified, but the activation energy of the step is not affected significantly. TMAO increases the preference of the closed conformation of the active site loop in the LDH·NAD(+)·lactate complex; urea decreases it. The loop opening rate in the LDH·NADH·pyruvate complex changes its temperature dependence to inverse Arrhenius with TMAO. In this complex, urea accelerates the loop motion, without changing the loop opening enthalpy. A strong, non-Arrhenius decrease in the pyruvate binding rate in the presence of TMAO offers a decrease in the fraction of the open loop, pyruvate binding competent form at higher temperatures. The pyruvate off rate is not affected by urea but decreases with TMAO. Thus, the osmolytes strongly affect the rates and thermodynamics of specific events along the LDH-catalyzed reaction: binding of substrates, loop closure, and the chemical event. Qualitatively, these results can be understood as an osmolyte-induced change in the energy landscape of the protein complexes, shifting the conformational nature of functional substates within the protein ensemble. PMID:21306147

Zhadin, Nickolay; Callender, Robert

2011-02-09

330

Palladium-Catalyzed Aryl Amination Reactions of 6-Bromo- and 6-Chloropurine Nucleosides.  

PubMed

Palladium-catalyzed C-N bond forming reactions of 6-bromo- as well as 6-chloropurine ribonucleosides and the 2'-deoxy analogues with aryl amines are described. Efficient conversions were observed with Pd(OAc)(2)/Xantphos/Cs(2)CO(3), in PhMe at 100 °C. Reactions of the bromo nucleoside derivatives could be conducted at a lowered catalytic loading (5 mol % Pd(OAc)(2)/7.5 mol % Xantphos), whereas good product yields were obtained with a higher catalyst load (10 mol % Pd(OAc)(2)/15 mol % Xantphos) when the chloro analogue was employed. Among the examples evaluated, silyl protection for the hydroxyls appears better as compared to acetyl. The methodology has been evaluated via reactions with a variety of aryl amines and by synthesis of biologically relevant deoxyadenosine and adenosine dimers. This is the first detailed analysis of aryl amination reactions of 6-chloropurine nucleosides, and comparison of the two halogenated nucleoside substrates. PMID:21818182

Thomson, Paul F; Lagisetty, Pallavi; Balzarini, Jan; De Clercq, Erik; Lakshman, Mahesh K

2010-07-01

331

Unraveling the role of water in the stereoselective step of aqueous proline-catalyzed aldol reactions.  

PubMed

A multiscale computational study was performed with the aim of tracing the source of stereoselectivity and disclosing the role of water in the stereoselective step of propionaldehyde aldol self-condensation catalyzed by proline amide in water, a reaction that serves as a model for aqueous organocatalytic aldol condensations. Solvent mixing and hydration behavior were assessed by classical molecular dynamics simulations, which show that the reaction between propanal and the corresponding enamine takes place in a fully hydrated environment. First-principles molecular dynamics simulations were used to study the free-energy profile of four possible reaction paths, each of which yields a different stereoisomer, and high-level static first-principles calculations were employed to characterize the transition states for microsolvated species. The first solvation shell of the oxygen atom of the electrophilic aldehyde at the transition states contains two water molecules, each of which donates one hydrogen bond to the nascent alkoxide and thereby largely stabilizes its excess electron density. The stereoselectivity originates in an extra hydrogen bond donated by the amido group of proline amide in two reaction paths. PMID:23074080

Ribas-Arino, Jordi; Carvajal, Maria Angels; Chaumont, Alain; Masia, Marco

2012-10-16

332

Fenton-Like Reaction Catalyzed by the Rare Earth Inner Transition Metal Cerium  

PubMed Central

Cerium (Ce) is a rare earth metal that is not known to have any biological role. Cerium oxide materials of several sizes and shapes have been developed in recent years as a scaffold for catalysts. Indeed even cerium oxide nanoparticles themselves have displayed catalytic activities and antioxidant properties in tissue culture and animal models. Because of ceria's ability to cycle between the +3 and +4 states at oxygen vacancy sites, we investigated whether cerium metal would catalyze a Fenton-like reaction with hydrogen peroxide. Indeed, cerium chloride did exhibit radical production in the presence of hydrogen peroxide, as assessed by relaxation of supercoiled plasmid DNA. Radical production in this reaction was also followed by production of radical cation of 2,2?-azinobis-(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS). Radical scavengers and spin traps were capable of competing with ABTS for radicals produced in this cerium dependent Fenton-like reaction. Electron paramagnetic resonance experiments reveal both hydroxyl radical and superoxide anion in a reaction containing cerium and hydrogen peroxide. Based on these results we propose that cerium is capable of redox-cycling with peroxide to generate damaging oxygen radicals.

HECKERT, ERIC G.; SEAL, SUDIPTA; SELF, WILLIAM T.

2011-01-01

333

Silver-catalyzed tandem synthesis of naphthyridines and thienopyridines via three-component reaction.  

PubMed

An efficient approach for the silver-catalyzed regioselective tandem synthesis of highly functionalized 1,2-dihydrobenzo[1,6]naphthyridines 6a-z and 7a-e by the reaction of ortho-alkynylaldehydes 3a-n with amines 4a-d and ketones 5a-c/active methylene compounds 5d-g, under mild reaction conditions, is described. The scope of the developed chemistry was successfully extended for the direct synthesis of 1,2-dihydrobenzo[4,5]thieno[2,3-c]pyridines 8a-e, which is known as the sulfur analogue of ?-carbolines. Naphthyridines 6a-z and thienopyridines 8a-e were obtained via dual activation concept using l-proline as organocatalyst; however, naphthyridines 7a-e were synthesized without using organocatalyst. The reaction shows selective N-C bond formation on the more electrophilic alkynyl carbon, resulting in the regioselective 6-endo-dig-cyclized products. Reactivity behavior of electron-deficient and electron-rich ortho-alkynylaldehydes in the synthesis of naphthyridines and thienopyridine by three-component reaction is supported by the control experiment. PMID:23565804

Verma, Akhilesh K; Kotla, Siva K Reddy; Choudhary, Deepak; Patel, Monika; Tiwari, Rakesh K

2013-04-17

334

Acid-catalyzed reactions of twisted amides in water solution: competition between hydration and hydrolysis.  

PubMed

The acid-catalyzed reactions of twisted amides in water solution were investigated by using cluster-continuum model calculations. In contrast to the previous widely suggested concerted hydration of the C=O group, our calculations show that the reaction proceeds in a practically stepwise manner, and that the hydration and hydrolysis channels of the C-N bond compete. The Eigen ion (H(3)O(+)) is the key species involved in the reaction, and it modulates the hydration and hydrolysis reaction pathways. The phenyl substitution in the twisted amide not only activates the N-CO bond, but also stabilizes the hydrolysis product through n(N)??(phenyl) delocalization, leading exclusively to the hydrolysis product of the ring-opened carboxylic acid. Generally, the twisted amides are more active than the planar amides, and such a rate acceleration results mainly from the increase in exothermicity in the first N-protonation step; the second step of the nucleophilic attack is less affected by the twisting of the amide bond. The present results show good agreement with the available experimental observations. PMID:21901771

Wang, Binju; Cao, Zexing

2011-09-07

335

Efficient approach to 4-sulfonamidoquinolines via copper(I)-catalyzed cascade reaction of sulfonyl azides with alkynyl imines.  

PubMed

A novel and efficient approach to 4-sulfonamidoquinolines via copper-catalyzed cascade reaction of sulfonyl azides with alkynyl imines has been developed in which a 1,3-dipole cycloaddition/ketenimine formation/6?-electrocyclization/[1,3]-H shift cascade reaction was involved. Various 4-sulfonamidoquinolines were afforded in up to 84% yield for 19 examples. This synthetic strategy features with atom economy, concise steps, easy operation, and mild reaction conditions. PMID:23521106

Cheng, Guolin; Cui, Xiuling

2013-03-22

336

Enhancement of enzyme activity and enantioselectivity by cyclopentyl methyl ether in the transesterification catalyzed by Pseudomonas cepacia lipase co-lyophilized with cyclodextrins.  

PubMed

The solvent effects of cyclopentyl methyl ether (CPME) on the reaction rates and enzyme enantioselectivity in the enantioselective transesterifications of racemic 6-methyl-5-hepten-2-ol (racemic sulcatol: SUL) and racemic 2,2-dimethyl-1,3-dioxolane-4-methanol (racemic solketal: SOL) with a series of enol esters catalyzed by Pseudomonas cepacia lipase co-lyophilized with cyclodextrins (alpha-, beta-, gamma-, partially methylated beta-, and 2,3,6-tri-O-methyl-beta-cyclodextrin: alphaCyD; betaCyD; gammaCyD; Me1.78betaCyD; Me3betaCyD) were investigated and compared with those in diisopropyl ether (IPE). In the case of SUL, enzyme activities of the co-lyophilizate with Me1.78betaCyD in CPME were lower than those in IPE with every acyl source, however, the absolute enantiopreference was shown in the transesterification with vinyl butyrate (VBR) in IPME. When the substrates were SOL and VBR, the enzyme activities in CPME were greatly enhanced as high as 1.6-9.8-fold, while the enantioselectivities in CPME were comparable to those in IPE. PMID:15834802

Mine, Yurie; Zhang, Lin; Fukunaga, Kimitoshi; Sugimura, Yoshiaki

2005-03-01

337

An enzyme catalyzing O-prenylation of the glucose moiety of fusicoccin A, a diterpene glucoside produced by the fungus Phomopsis amygdali.  

PubMed

Isoprenoids form the largest family of compounds found in nature. Isoprenoids are often attached to other moieties such as aromatic compounds, indoles/tryptophan, and flavonoids. These reactions are catalyzed by three phylogenetically distinct prenyltransferases: soluble aromatic prenyltransferases identified mainly in actinobacteria, soluble indole prenyltransferases mostly in fungi, and membrane-bound prenyltransferases in various organisms. Fusicoccin A (FC A) is a diterpene glycoside produced by the plant-pathogenic fungus Phomopsis amygdali and has a unique O-prenylated glucose moiety. In this study, we identified for the first time, from a genome database of P. amygdali, a gene (papt) encoding a prenyltransferase that reversibly transfers dimethylallyl diphosphate (DMAPP) to the 6'-hydroxy group of the glucose moiety of FC A to yield an O-prenylated sugar. An in vitro assay with a recombinant enzyme was also developed. Detailed analyses with recombinant PAPT showed that the enzyme is likely to be a monomer and requires no divalent cations. The optimum pH and temperature were 8.0 and 50?°C, respectively. K(m) values were calculated as 0.49±0.037 ?M for FC P (a plausible intermediate of FC A biosynthesis) and 8.3±0.63 ?M for DMAPP, with a k(cat) of 55.3±3.3×10?³ s. The enzyme did not act on representative substrates of the above-mentioned three types of prenyltransferase, but showed a weak transfer activity of geranyl diphosphate to FC P. PMID:22287087

Noike, Motoyoshi; Liu, Chengwei; Ono, Yusuke; Hamano, Yoshimitsu; Toyomasu, Tomonobu; Sassa, Takeshi; Kato, Nobuo; Dairi, Tohru

2012-01-27

338

The radical SAM enzyme AlbA catalyzes thioether bond formation in subtilosin A.  

PubMed

Subtilosin A is a 35-residue, ribosomally synthesized bacteriocin encoded by the sbo-alb operon of Bacillus subtilis. It is composed of a head-to-tail circular peptide backbone that is additionally restrained by three unusual thioether bonds between three cysteines and the ?-carbon of one threonine and two phenylalanines, respectively. In this study, we demonstrate that these bonds are synthesized by the radical S-adenosylmethionine enzyme AlbA, which is encoded by the sbo-alb operon and comprises two [4Fe-4S] clusters. One [4Fe-4S] cluster is coordinated by the prototypical CXXXCXXC motif and is responsible for the observed S-adenosylmethionine cleavage reaction, whereas the second [4Fe-4S] cluster is required for the generation of all three thioether linkages. On the basis of the obtained results, we propose a new radical mechanism for thioether bond formation. In addition, we show that AlbA-directed substrate transformation is leader-peptide dependent, suggesting that thioether bond formation is the first step during subtilosin A maturation. PMID:22366720

Flühe, Leif; Knappe, Thomas A; Gattner, Michael J; Schäfer, Antje; Burghaus, Olaf; Linne, Uwe; Marahiel, Mohamed A

2012-02-26

339

Synthesis of 1-hydroperoxy-1'-alkoxyperoxides by the iodine-catalyzed reactions of geminal bishydroperoxides with acetals or enol ethers.  

PubMed

It was found that iodine-catalyzed reactions of geminal bishydroperoxides with acetals proceed with the replacement of only one alkoxy group by the peroxide group to give previously unknown structures of 1-hydroperoxy-1'-alkoxyperoxides in yields up to 64%. The same compounds are formed in the iodine-catalyzed reactions of geminal bishydroperoxides with enol ethers. The nature of the solvent has a decisive influence on the formation of 1-hydroperoxy-1'-alkoxyperoxides. In the series of Et(2)O, THF, EtOH, CHCl(3), CH(3)CN, and hexane, the best results were obtained with the use of Et(2)O or THF as the solvent. PMID:19005604

Terent'ev, Alexander O; Platonov, Maxim M; Krylov, Igor B; Chernyshev, Vladimir V; Nikishin, Gennady I

2008-10-20

340

Lipase-catalyzed degradation of polyesters in organic solvents. A new methodology of polymer recycling using enzyme as catalyst.  

PubMed

Enzymatic hydrolytic degradation of aliphatic polyesters in organic solvents has been examined. The degradation of poly(epsilon-caprolactone) took place using Candida antarctica lipase as catalyst in toluene at 60 degrees C to give oligomers with molecular weight of less than 500. The degradation behavior catalyzed by lipase was quite different than an acid-catalyzed degradation (random bond cleavage of polymer). After the removal of the solvent from the reaction mixture, the residual oligomer was polymerized in the presence of the same catalyst of lipase. These data provide a basic concept that the degradation-polymerization could be controlled by presence or absence of the solvent, providing a new methodology of plastics recycling. PMID:11709839

Kobayashi, S; Uyama, H; Takamoto, T

2000-01-01

341

MuteinDB: the mutein database linking substrates, products and enzymatic reactions directly with genetic variants of enzymes  

PubMed Central

Mutational events as well as the selection of the optimal variant are essential steps in the evolution of living organisms. The same principle is used in laboratory to extend the natural biodiversity to obtain better catalysts for applications in biomanufacturing or for improved biopharmaceuticals. Furthermore, single mutation in genes of drug-metabolizing enzymes can also result in dramatic changes in pharmacokinetics. These changes are a major cause of patient-specific drug responses and are, therefore, the molecular basis for personalized medicine. MuteinDB systematically links laboratory-generated enzyme variants (muteins) and natural isoforms with their biochemical properties including kinetic data of catalyzed reactions. Detailed information about kinetic characteristics of muteins is available in a systematic way and searchable for known mutations and catalyzed reactions as well as their substrates and known products. MuteinDB is broadly applicable to any known protein and their variants and makes mutagenesis and biochemical data searchable and comparable in a simple and easy-to-use manner. For the import of new mutein data, a simple, standardized, spreadsheet-based data format has been defined. To demonstrate the broad applicability of the MuteinDB, first data sets have been incorporated for selected cytochrome P450 enzymes as well as for nitrilases and peroxidases. Database URL: http://www.MuteinDB.org

Braun, Andreas; Halwachs, Bettina; Geier, Martina; Weinhandl, Katrin; Guggemos, Michael; Marienhagen, Jan; Ruff, Anna J.; Schwaneberg, Ulrich; Rabin, Vincent; Torres Pazmino, Daniel E.; Thallinger, Gerhard G.; Glieder, Anton

2012-01-01

342

MuteinDB: the mutein database linking substrates, products and enzymatic reactions directly with genetic variants of enzymes.  

PubMed

Mutational events as well as the selection of the optimal variant are essential steps in the evolution of living organisms. The same principle is used in laboratory to extend the natural biodiversity to obtain better catalysts for applications in biomanufacturing or for improved biopharmaceuticals. Furthermore, single mutation in genes of drug-metabolizing enzymes can also result in dramatic changes in pharmacokinetics. These changes are a major cause of patient-specific drug responses and are, therefore, the molecular basis for personalized medicine. MuteinDB systematically links laboratory-generated enzyme variants (muteins) and natural isoforms with their biochemical properties including kinetic data of catalyzed reactions. Detailed information about kinetic characteristics of muteins is available in a systematic way and searchable for known mutations and catalyzed reactions as well as their substrates and known products. MuteinDB is broadly applicable to any known protein and their variants and makes mutagenesis and biochemical data searchable and comparable in a simple and easy-to-use manner. For the import of new mutein data, a simple, standardized, spreadsheet-based data format has been defined. To demonstrate the broad applicability of the MuteinDB, first data sets have been incorporated for selected cytochrome P450 enzymes as well as for nitrilases and peroxidases. Database URL: http://www.MuteinDB.org. PMID:22730453

Braun, Andreas; Halwachs, Bettina; Geier, Martina; Weinhandl, Katrin; Guggemos, Michael; Marienhagen, Jan; Ruff, Anna J; Schwaneberg, Ulrich; Rabin, Vincent; Torres Pazmiño, Daniel E; Thallinger, Gerhard G; Glieder, Anton

2012-06-21

343

The determination of specificity constants in enzyme-catalysed reactions.  

PubMed Central

A convenient and accurate procedure for determining the kinetic parameter Vmax./Km is described. This avoids the error in the usual method of taking the observed first-order rate constant of an enzymic reaction at low substrate concentration as Vmax./Km. A series of reactions is used in which the initial concentration of substrate is below Km (e.g. from 5% to 50% of Km). Measurements are taken over the same extent of reaction (e.g. 70%) for each member of the series, and treated as if the kinetics were truly first-order. The reciprocal of the observed first-order rate constant is then plotted against the initial concentration of substrate: the reciprocal of the ordinate intercept is Vmax./Km. The procedure, as well as being applicable to simple reactions, is shown to be valid when there is competitive inhibition by the product, or when the reaction is reversible, or when there is competitive or mixed inhibition. The hydrolysis of cephalosporin C by a beta-lactamase from Pseudomonas aeruginosa is used to illustrate the method.

Crompton, I E; Waley, S G

1986-01-01

344

Optimal distribution of immobilized enzyme in a pellet for a substrate-inhibited reaction  

SciTech Connect

This article sets out to show how the enzyme should be distributed within a porous pellet so that the enzyme effectiveness is maximized, given a fixed total amount of enzyme and a set of diffusion and reaction parameters. The general behaviour of substrate-inhibited reactions and application and function of the optimal enzyme distribution is discussed.

Morbidelli, M.; Servida, A.; Varma, A.

1984-12-01

345

A thiocyanate hydrolase of Thiobacillus thioparus. A novel enzyme catalyzing the formation of carbonyl sulfide from thiocyanate  

SciTech Connect

A thiocyanate hydrolase that catalyzes the first step in thiocyanate degradation was purified to homogeneity from Thiobacillus thioparus, an obligate chemolithotrophic eubacterium metabolizing thiocyanate to sulfate as an energy source. The thiocyanate hydrolase was purified 52-fold by steps involving ammonium sulfate precipitation, DEAE-Sephacel column chromatography, and hydroxylapatite column chromatography. The enzyme hydrolyzed 1 mol of thiocyanate to form 1 mol of carbonyl sulfide and 1 mol of ammonia as follows: SCN- + 2H2O----COS + NH3 + OH-. This is the first report describing the hydrolysis of thiocyanate to carbonyl sulfide by an enzyme. The enzyme had a molecular mass of 126 kDa and was composed of three different subunits: alpha (19 kDa), beta (23 kDa), and gamma (32 kDa). The enzyme exhibited optimal activities at pH 7.5-8.0 and at temperatures ranging from 30 to 40 degrees C. The Km value for thiocyanate was approximately 11 mM. Immunoblot analysis with polyclonal antibodies against the purified enzyme suggested that it was induced in T. thioparus cells when the cells were grown with thiocyanate.

Katayama, Y.; Narahara, Y.; Inoue, Y.; Amano, F.; Kanagawa, T.; Kuraishi, H. (Faculty of Agriculture, Tokyo University of Agriculture and Technology, (Japan))

1992-05-05

346

Palladium-catalyzed reactions in the synthesis of 3- and 4-substituted indoles. 4  

SciTech Connect

4-Bromo-1-tosylindole (1) was converted to tricyclic indole enone 11, a potential intermediate in the synthesis of tetracyclic ergot alkaloids, by a series of palladium-catalyzed processes. Attempts to construct the ergot D ring by the hetero-Diels-Alder reaction of enone 11 and 1-azabutadiene 12 produced not the expected (4 + 2) adduct 13 but the benz(cd)indoline derivative 14 resulting from attack of the aza diene at the indole 2-position. The thermodynamic stability of the naphthol nucleus makes enone 11 generally susceptible to attack at the indole 2-position, as evidenced by the attack of hydride and methyl cuprate nucleophiles at this portion forming indolines 16 and 17, respectively.

Hegedus, L.S.; Sestrick, M.R.; Michaelson, E.T.; Harrington, P.J. (Colorado State Univ., Fort Collins (USA))

1989-08-18

347

The base catalyzed hydrolysis and condensation reactions of dilute and concentrated TEOS (Tetraethylorthosilicate) solutions: Draft  

SciTech Connect

The synthesis of submicron silica particles by the hydrolysis and condensation of dilute and concentrated solutions of tetraethylorthosiliate (TEOS) has been studied in low-molecular weight alcohols (C/sub 1/--C/sub 4/). A base (ammonia) is used to catalyze the reaction. Raman spectroscopy, gas chromatography and the molybdate method are used to establish the hydrolysis and condensation kinetics. Dynamic and classical light-scattering techniques are employed to monitor particle growth and particle number concentration kinetics, and particle size distribution. The effects of solvent and TEOS concentration on the degree of monodispersity of the particles will be discussed. Furthermore, the chemical and particle growth data will be used to test the theories of homogeneous nucleation and coagulative nucleation, which have been proposed as the mechanisms that govern the growth of submicron monodisperse silica particle by TEOS hydrolysis. 13 refs., 4 figs., 1 tab.

Harris, M.T.; Byers, C.H.; Brunson, R.R.

1989-01-01

348

Enzyme Reactions on a 27 MHz Quartz Crystal Microbalance  

Microsoft Academic Search

A quartz crystal microbalance (QCM) is known as a useful tool to detect gravimetric molecular\\u000a interactions. We have developed a 27-MHz QCM (Affinix Q4) to detect\\u000a various biomolecular interactions such as DNA–DNA hybridization, DNA–protein interactions, glycolipid–protein\\u000a interactions, and protein–protein interactions. In this chapter, we show that the 27-MHz QCM is also\\u000a useful to detect the kinetics of enzyme reactions, because all the steps of

Yoshio Okahata; Toshiaki Mori; Hiroyuki Furusawa; Takanori Nihira

349

Mapping the reaction pathway in palladium-catalyzed cross-coupling reactions  

SciTech Connect

The formation of the cyclooctatetraene (COT) complex Pd(dppf)(COT) (dppf = 1,1{prime}-bis(diphenylphosphino)ferrocene) from Pd(dppf)X{sub 2} (X = Cl, Sr, I) and dilithium cyclooctatetraenide in situ affords an entry into the cross-coupling chemistry of this system. The reaction of Pd(dppf)(COT) with an alkenyl bromide or iodide results in the formation of the appropriate ({eta}{sup 1}-alkenyl)palladium halide via an oxidative addition of a {eta}{sup 2}-coordinated alkene species. The full characterization of the intermediate Pd(dppf)(CH{double bond}CHC{sub 6}H{sub 4}OCHY{sub 3})Br (9) and the norbornene insertion product Pd(dppf)(C{sub 7}H{sub 10}CH{double bond}CHC{sub 6}H{sub 4}OCH{sub 3}) (15) is reported. A set of putative intermediates for the coupling of alkenyl and benzyl moieties by palladium complexes is demonstrated spectroscopically. The cross-coupling cycle for the case of alkenyl-aryl coupling is delineated by an analysis of cross-coupling reactions employing {sup 13}C-labeled catalysts and unlabeled substrates (and vice versa). Platinum analogues of all the intermediates in this cross-coupling catalytic cycle have been observed.

Brown, J.M.; Cooley, N.A. (Dyson Perrins Lab., Oxford (England))

1990-02-01

350

Stochastic theory of large-scale enzyme-reaction networks: Finite copy number corrections to rate equation models  

NASA Astrophysics Data System (ADS)

Chemical reactions inside cells occur in compartment volumes in the range of atto- to femtoliters. Physiological concentrations realized in such small volumes imply low copy numbers of interacting molecules with the consequence of considerable fluctuations in the concentrations. In contrast, rate equation models are based on the implicit assumption of infinitely large numbers of interacting molecules, or equivalently, that reactions occur in infinite volumes at constant macroscopic concentrations. In this article we compute the finite-volume corrections (or equivalently the finite copy number corrections) to the solutions of the rate equations for chemical reaction networks composed of arbitrarily large numbers of enzyme-catalyzed reactions which are confined inside a small subcellular compartment. This is achieved by applying a mesoscopic version of the quasisteady-state assumption to the exact Fokker-Planck equation associated with the Poisson representation of the chemical master equation. The procedure yields impressively simple and compact expressions for the finite-volume corrections. We prove that the predictions of the rate equations will always underestimate the actual steady-state substrate concentrations for an enzyme-reaction network confined in a small volume. In particular we show that the finite-volume corrections increase with decreasing subcellular volume, decreasing Michaelis-Menten constants, and increasing enzyme saturation. The magnitude of the corrections depends sensitively on the topology of the network. The predictions of the theory are shown to be in excellent agreement with stochastic simulations for two types of networks typically associated with protein methylation and metabolism.

Thomas, Philipp; Straube, Arthur V.; Grima, Ramon

2010-11-01

351

Kinetics of Acid-Catalyzed Aldol Condensation Reactions of Aliphatic Aldehydes  

NASA Astrophysics Data System (ADS)

While it is well established that organic compounds compose a large fraction of the atmospheric aerosol mass, the mechanisms through which organics are incorporated into atmospheric aerosols are not well understood. Acid-catalyzed reactions of compounds with carbonyl groups have recently been suggested as important pathways for transfer of volatile organics into acidic aerosols. In the present study, ultraviolet-visible (UV-Vis) spectroscopy was used to monitor the kinetics of formation of the products of the aldol condensation reaction of a range of aliphatic aldehydes (C2-C8) The experiments were carried out at various sulfuric acid concentrations and a range of temperatures in order to estimate the rate constants of such reactions on sulfuric acid aerosols under tropospheric conditions. The rate constants were generally found to decrease as the chain length of the aliphatic aldehyde increased (except for acetaldehyde, which had an unusually small rate constant), increase as a function of sulfuric acid concentration as predicted by excess acidity theory, and showed normal Arrhenius behavior as a function of temperature.

Elrod, M. J.; Casale, M. T.; Richman, A. R.; Beaver, M. R.; Garland, R. M.; Tolbert, M. A.

2006-12-01

352

A preliminary investigation of acid-catalyzed polymerization reactions of shale oil distillates  

SciTech Connect

Sinor (1989) reported that a major specialty market may exist for shale oil as an asphalt blending material. Shale oil can be converted to an asphalt blending material by acid catalyzed condensation and polymerization reactions of the many molecular species comprising the composition of shale oil. To simplify the investigation, crude shale oil was separated by distillation into three distillates of different hydrocarbon and heteroaromatic compositions. These distillates were then treated with two different types of acids to determine the effect of acid type on the end products. Three western shale oil distillates, a naphtha, a middle distillate, and an atmospheric gas oil, were reacted with anhydrous AlCl{sub 3} and 85% H{sub 2}SO{sub 4} under low-severity conditions. At relatively low temperatures, little change in the hydrocarbon composition was noted for the AlCl{sub 3} reactions. AlCl{sub 3}{center_dot} (a polymerized product and/or complex) was formed. However, it is assumed that the sludge was mainly the result of heteroaromatic-AlCl{sub 3} reactions.

Netzel, D.A.

1991-04-01

353

A preliminary investigation of acid-catalyzed polymerization reactions of shale oil distillates  

SciTech Connect

Sinor (1989) reported that a major specialty market may exist for shale oil as an asphalt blending material. Shale oil can be converted to an asphalt blending material by acid catalyzed condensation and polymerization reactions of the many molecular species comprising the composition of shale oil. To simplify the investigation, crude shale oil was separated by distillation into three distillates of different hydrocarbon and heteroaromatic compositions. These distillates were then treated with two different types of acids to determine the effect of acid type on the end products. Three western shale oil distillates, a naphtha, a middle distillate, and an atmospheric gas oil, were reacted with anhydrous AlCl{sub 3} and 85% H{sub 2}SO{sub 4} under low-severity conditions. At relatively low temperatures, little change in the hydrocarbon composition was noted for the AlCl{sub 3} reactions. AlCl{sub 3}{center dot} (a polymerized product and/or complex) was formed. However, it is assumed that the sludge was mainly the result of heteroaromatic-AlCl{sub 3} reactions.

Netzel, D.A.

1991-04-01

354

Negative Resist for i-Line Lithography Utilizing Acid Catalyzed Silanol-Condensation Reaction  

NASA Astrophysics Data System (ADS)

Negative resist systems composed of a novolak resin, diphenylsilanediol (Ph2Si(OH)2) and an acid generator are investigated for i-line lithography. The reaction in this resist system is based on an acid-catalyzed condensation reaction; the acid produced in the exposed area induces a condensation reaction of Ph2Si(OH)2 during post-exposure baking. The condensation product, siloxane, acts as an aqueous-base dissolution inhibitor, while silanol compounds in unexposed areas work as dissolution accelerators. The resist composed of a novolak resin, Ph2Si(OH)2 and 2-naphthoylmethyl-tetramethylenesulfonium hexafluoroantimonate (NMTMS-SbF6) shows a sensitivity of about 200 mJ/cm2 at 365 nm. This sensitivity is lower than that at 248 nm when triphenylsulfonium triflate (Ph3S+OTf-) is used as an acid generator, which can be ascribed to the low quantum yield of acid generation from NMTMS-SbF6. Using this resist, 0.3 ?m space patterns with 1 ?m film thickness were obtained by combining an i-line stepper with a phase-shifting mask.

Hayashi, Nobuaki; Tadano, Keiko; Tanaka, Toshihiko; Shiraishi, Hiroshi; Ueno, Takumi; Iwayanagi, Takao

1990-11-01

355

Comparison Of Reaction Barriers In Energy And Free Energy For Enzyme Catalysis  

NASA Astrophysics Data System (ADS)

Reaction paths on potential energy surfaces obtained from QM/MM calculations of enzymatic or solution reactions depend on the starting structure employed for the path calculations. The free energies associated with these paths should be more reliable for studying reaction mechanisms, because statistical averages are used. To investigate this, the role of enzyme environment fluctuations on reaction paths has been studied with an ab initio QM/MM method for the first step of the reaction catalyzed by 4-oxalocrotonate tautomerase (4OT). Four minimum energy paths (MEPs) are compared, which have been determined with two different methods. The first path (path A) has been determined with a procedure that combines the nudged elastic band (NEB) method and a second order parallel path optimizer recently developed in our group. The second path (path B) has also been determined by the combined procedure, however, the enzyme environment has been relaxed by molecular dynamics (MD) simulations. The third path (path C) has been determined with the coordinate driving (CD) method, using the enzyme environment from path B. We compare these three paths to a previously determined path (path D) determined with the CD method. In all four cases the QM/MM-FE method (Y. Zhang et al., JCP, 112, 3483) was employed to obtain the free energy barriers for all four paths. In the case of the combined procedure, the reaction path is approximated by a small number of images which are optimized to the MEP in parallel, which results in a reduced computational cost. However, this does not allow the FEP calculation on the MEP. In order to perform FEP calculations on these paths, we introduce a modification to the NEB method that enables the addition of as many extra images to the path as needed for the FEP calculations. The calculated potential energy barriers show differences in the activation barrier between the calculated paths of as much as 5.17 kcal/mol. However, the largest free energy barrier difference is 1.58 kcal/mol. These results show the importance of the inclusion of the environment fluctuation in the calculation of enzymatic activation barriers

Andrés Cisneros, G.; Yang, Weitao

356

The mechanism of the reaction catalyzed by uronate isomerase illustrates how an isomerase may have evolved from a hydrolase within the amidohydrolase superfamily.  

PubMed

Uronate isomerase (URI) catalyzes the reversible isomerization of D-glucuronate to D-fructuronate and of D-galacturonate to D-tagaturonate. URI is a member of the amidohydrolase superfamily (AHS), a highly divergent group of enzymes that catalyze primarily hydrolytic reactions. The chemical mechanism and active site structure of URI were investigated in an attempt to improve our understanding of how an active site template that apparently evolved to catalyze hydrolytic reactions has been reforged to catalyze an isomerization reaction. The pH-rate profiles for k(cat) and k(cat)/K(m) for URI from Escherichia coli are bell-shaped and indicate that one group must be unprotonated and another residue must be protonated for catalytic activity. Primary isotope effects on the kinetic constants with [2-2H]-D-glucuronate and the effects of changes in solvent viscosity are consistent with product release being the rate-limiting step. The X-ray structure of Bh0493, a URI from Bacillus halodurans, was determined in the presence of the substrate D-glucuronate. The bound complex showed that the mononuclear metal center in the active site is ligated to the C-6 carboxylate and the C-5 hydroxyl group of the substrate. This hydroxyl group is also hydrogen bonded to Asp-355 in the same orientation as the hydroxide or water is bound in those members of the AHS that catalyze hydrolytic reactions. In addition, the C-2 and C-3 hydroxyl groups of the substrate are hydrogen bonded to Arg-357 and the carbonyl group at C-1 is hydrogen bonded to Tyr-50. A chemical mechanism is proposed that utilizes a proton transfer from C-2 of D-glucuronate to C-1 that is initiated by the combined actions of Asp-355 from the end of beta-strand 8 and the C-5 hydroxyl of the substrate that is bound to the metal ion. The formation of the proposed cis-enediol intermediate is further facilitated by the shuttling of the proton between the C-2 and C-1 oxygens by the conserved Tyr-50 and/or Arg-355. PMID:19678710

Nguyen, Tinh T; Fedorov, Alexander A; Williams, Lakenya; Fedorov, Elena V; Li, Yingchun; Xu, Chengfu; Almo, Steven C; Raushel, Frank M

2009-09-22

357

The Mechanism of the Reaction Catalyzed by Uronate Isomerase Illustrates How an Isomerase May Have Evolved from a Hydrolase within the Amidohydrolase Superfamily†  

PubMed Central

Uronate isomerase (URI) catalyzes the reversible isomerization of D-glucuronate to D-fructuronate and of D-galacturonate to D-tagaturonate. URI is a member of the amidohydrolase superfamily (AHS), a highly divergent group of enzymes that catalyzes primarily hydrolytic reactions. The chemical mechanism and active site structure of URI was investigated in an attempt to obtain a greater understanding of how an active site template that apparently evolved to catalyze hydrolytic reactions has been re-forged to catalyze an isomerization reaction. The pH-rate profiles for kcat and kcat/Km for URI from Escherichia coli are bell-shaped and indicate that one group must be unprotonated and another residue must be protonated for catalytic activity. Primary isotope effects on the kinetic constants with [2-2H]-D-glucuronate and the effects of changes in solvent viscosity are consistent with product release as the rate limiting step. The X-ray structure of Bh0493, a URI from Bacillus halodurans, was determined in the presence of the substrate D-glucuronate. The bound complex showed that the mononuclear metal center in the active site is ligated to the C-6 carboxylate and the C-5 hydroxyl group of the substrate. This hydroxyl group is also hydrogen bonded to Asp-355 in the same orientation as the hydroxide/water is bound in those members of the AHS that catalyze hydrolytic reactions. In addition, the C-2 and C-3 hydroxyl groups of the substrate are hydrogen bonded to Arg-357 and the carbonyl group at C-1 is hydrogen bonded to Tyr-50. A chemical mechanism is proposed that utilizes a proton transfer from C-2 of D-glucuronate to C-1 that is initiated by the combined actions of Asp-355 from the end of ?-strand 8 and the C-5 hydroxyl of the substrate that is bound to the metal ion. The formation of the proposed cis-enediol intermediate is further facilitated by the shuttling of the proton between the C-2 and C-1 oxygens by the conserved Tyr-50 and/or Arg-355.

Nguyen, Tinh T.; Fedorov, Alexander A.; Williams, LaKenya; Fedorov, Elena V.; Li, Yingchun; Xu, Chengfu; Almo, Steven C.; Raushel, Frank M.

2009-01-01

358

X-ray study of the conformational changes in the molecule of phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis during the catalyzed reaction.  

PubMed

Structures of recombinant phosphopantetheine adenylyltransferase (PPAT) from Mycobacterium tuberculosis (PPATMt) in the apo form and in complex with the substrate ATP were determined at 1.62 and 1.70?Å resolution, respectively, using crystals grown in microgravity by the counter-diffusion method. The ATP molecule of the PPATMt-ATP complex was located with full occupancy in the active-site cavity. Comparison of the solved structures with previously determined structures of PPATMt complexed with the reaction product dephosphocoenzyme A (dPCoA) and the feedback inhibitor coenzyme A (CoA) was performed using superposition on C(?) atoms. The peculiarities of the arrangement of the ligands in the active-site cavity of PPATMt are described. The conformational states of the PPAT molecule in the consequent steps of the catalyzed reaction in the apo enzyme and the enzyme-substrate and enzyme-product complexes are characterized. It is shown that the binding of ATP and dPCoA induces the rearrangement of a short part of the polypeptide chain restricting the active-site cavity in the subunits of the hexameric enzyme molecule. The changes in the quaternary structure caused by this rearrangement are accompanied by a variation of the size of the inner water-filled channel which crosses the PPAT molecule along the threefold axis of the hexamer. The molecular mechanism of the observed changes is described. PMID:23151631

Timofeev, Vladimir; Smirnova, Evgenia; Chupova, Larisa; Esipov, Roman; Kuranova, Inna

2012-11-09

359

Study of high glass transition temperature thermosets made from the copper(I)-catalyzed azide–alkyne cycloaddition reaction  

Microsoft Academic Search

Thermal properties of polymers made from the copper(I)-catalyzed cycloaddition reaction between azides and alkynes have been investigated. Differential scanning calorimetry (DSC) and dynamic mechanical analysis (DMA) were used to measure the glass transition temperatures (Tg) of these materials. The polymers were found to have unusually high Tg values, up to 60°C higher than the curing temperature. It has been shown

Nicolas Le Baut; David D. Díaz; Sreenivas Punna; M. G. Finn; Hugh R. Brown

2007-01-01

360

Generation of benzoimidazo[1,5-a]imidazoles via a copper-catalyzed tandem reaction of carbodiimide and isocyanoacetate.  

PubMed

Carbodiimide reacts with isocyanide catalyzed by copper(i) iodide, leading to benzoimidazo[1,5-a]imidazoles in good yields. This reaction is efficient, and proceeds through a formal [3+2] cycloaddition and C-N coupling. PMID:22576575

Qiu, Guanyinsheng; Wu, Jie

2012-05-10

361

Asymmetric Palladium-Catalyzed Carboamination Reactions for the Synthesis of Enantiomerically Enriched 2-(Arylmethyl)- and 2-(Alkenylmethyl) pyrrolidines  

PubMed Central

The enantioselective synthesis of 2-(arylmethyl)- and 2-(alkenylmethyl)pyrrolidine derivatives via Pd-catalyzed alkene carboamination reactions is described. These transformations generate enantiomerically enriched products with up to 94% ee from readily available alkenyl or aryl bromides and N-boc-pent-4-enylamines. The application of this method to a concise asymmetric synthesis of (?)-tylophorine is also discussed.

Mai, Duy N.; Wolfe, John P.

2010-01-01

362

Investigation on 1,4-dichlorophthalazine-derivatized cinchona alkaloids-catalyzed asymmetric "interrupted" Feist-Bénary reaction.  

PubMed

Different 1,4-dichlorophthalazine-cinchona alkaloid derivatives have been used to catalyze the asymmetric "interrupted" Feist-Bénary reaction of ethyl bromopyruvate/substituted bromoketoesters and beta-dicarbonyl compounds. The corresponding hydroxydihydrofurans have been obtained in excellent yields and with up to 91%ee. PMID:17380487

Jin, Ying; Liu, Xue Ying; Jing, Lin Lin; He, Wei; Sun, Xiao Li; Zhang, Sheng Yong

2007-05-15

363

Pd-Catalyzed Suzuki-Miyaura Cross-Coupling Reactions between Sulfamates and Potassium Boc-Protected Aminomethyltrifluoroborates.  

PubMed

Sulfamates were studied as the electrophilic partners in the palladium-catalyzed Suzuki-Miyaura cross-coupling reaction with potassium Boc-protected primary and secondary aminomethyltrifluoroborates. A broad range of substrates was successfully coupled to provide the desired products. Complex molecules containing a new carbon-carbon bond and an aminomethyl moiety could be prepared through this developed method. PMID:23646846

Molander, Gary A; Shin, Inji

2013-05-01

364

Phosphine-catalyzed Rauhut-Currier domino reaction: a facile strategy for the construction of carbocyclic spirooxindoles skeletons.  

PubMed

Push-over: A novel domino reaction of activated conjugated dienes and methyleneindolinones incorporates a phosphine-catalyzed intermolecular Rauhut-Currier to form two C-C bonds and a quaternary carbon center. This method can be used to synthesize spirocyclopenteneoxindoles skeletons, which are potential building blocks for biologically active compounds. PMID:23813882

Hu, Chongchong; Zhang, Qinglong; Huang, You

2013-06-28

365

Assay, purification, and characterization of cobaltochelatase, a unique complex enzyme catalyzing cobalt insertion in hydrogenobyrinic acid a,c-diamide during coenzyme B12 biosynthesis in Pseudomonas denitrificans.  

PubMed Central

Hydrogenobyrinic acid a,c-diamide was shown to be the substrate of cobaltochelatase, an enzyme that catalyzes cobalt insertion in the corrin ring during the biosynthesis of coenzyme B12 in Pseudomonas denitrificans. Cobaltochelatase was demonstrated to be a complex enzyme composed of two different components of M(r) 140,000 and 450,000, which were purified to homogeneity. The 140,000-M(r) component was shown to be coded by cobN, whereas the 450,000-M(r) component was composed of two polypeptides specified by cobS and cobT. Each component was inactive by itself, but cobaltochelatase activity was reconstituted upon mixing CobN and CobST. The reaction was ATP dependent, and the Km values for hydrogenobyrinic acid a,c-diamide, Co2+, and ATP were 0.085 +/- 0.015, 4.2 +/- 0.2, and 220 +/- 36 microM, respectively. Spectroscopic data revealed that the reaction product was cob(II)yrinic acid a,c-diamide, and experiments with a coupled-enzyme incubation system containing both cobaltochelatase and cob(II)yrinic acid a,c-diamide reductase (F. Blanche, L. Maton, L. Debussche, and D. Thibaut, J. Bacteriol. 174:7452-7454, 1992) confirmed this result. This report not only provides the first evidence that hydrogenobyrinic acid and its a,c-diamide derivative are indeed precursors of adenosylcobalamin but also demonstrates that precorrin-6x, precorrin-6y, and precorrin-8x, three established precursors of hydrogenobyrinic acid (D. Thibaut, M. Couder, A. Famechon, L. Debussche, B. Cameron, J. Crouzet, and F. Blanche, J. Bacteriol. 174:1043-1049, 1992), are also on the pathway to cobalamin. Images

Debussche, L; Couder, M; Thibaut, D; Cameron, B; Crouzet, J; Blanche, F

1992-01-01

366

Cobalamin- and Corrinoid-Dependent Enzymes  

PubMed Central

This chapter will review the literature on cobalamin- and corrinoid-containing enzymes. These enzymes fall into two broad classes, those using methylcobalamin or related methylcorrinoids as prosthetic groups and catalyzing methyltransfer reactions, and those using adenosylcobalamin as the prosthetic group and catalyzing the generation of substrate radicals that in turn undergo rearrangements and/or eliminations.

Matthews, Rowena G.

2011-01-01

367

Reaction Pathway and Free Energy Profiles for Butyrylcholinesterase- Catalyzed Hydrolysis of Acetylthiocholine  

PubMed Central

The catalytic mechanism for butyrylcholineserase (BChE)-catalyzed hydrolysis of acetylthiocholine (ATCh) has been studied by performing pseudobond first-principles quantum mechanical/molecular mechanical-free energy (QM/MM-FE) calculations on both acylation and deacylation of BChE. Additional quantum mechanical (QM) calculations have been carried out, along with the QM/MM-FE calculations, to understand the known substrate activation effect on the enzymatic hydrolysis of ATCh. It has been shown that the acylation of BChE with ATCh consists of two reaction steps including the nucleophilic attack on the carbonyl carbon of ATCh and the dissociation of thiocholine ester. The deacylation stage includes nucleophilic attack of a water molecule on the carboxyl carbon of substrate and dissociation between the carboxyl carbon of substrate and hydroxyl oxygen of Ser198 side chain. QM/MM-FE calculation results reveal that the acylation of BChE is rate-determining. It has also been demonstrated that an additional substrate molecule binding to the peripheral anionic site (PAS) of BChE is responsible for the substrate activation effect. In the presence of this additional substrate molecule at PAS, the calculated free energy barrier for the acylation stage (rate-determining step) is decreased by ~1.7 kcal/mol. All of our computational predictions are consistent with available experimental kinetic data. The overall free energy barriers calculated for BChE-catalyzed hydrolysis of ATCh at regular hydrolysis phase and substrate activation phase are ~13.6 and ~11.9 kcal/mol, respectively, which are in reasonable agreement with the corresponding experimentally-derived activation free energies of 14.0 kcal/mol (for regular hydrolysis phase) and 13.5 kcal/mol (for substrate activation phase). .

Chen, Xi; Fang, Lei; Liu, Junjun; Zhan, Chang-Guo

2012-01-01

368

Cobalt-catalyzed trimethylsilylmethylmagnesium-promoted radical alkenylation of alkyl halides: a complement to the Heck reaction.  

PubMed

A cobalt complex, [CoCl2(dpph)] (DPPH = [1,6-bis(diphenylphosphino)hexane]), catalyzes an intermolecular styrylation reaction of alkyl halides in the presence of Me3SiCH2MgCl in ether to yield beta-alkylstyrenes. A variety of alkyl halides including alkyl chlorides can participate in the styrylation. A radical mechanism is strongly suggested for the styrylation reaction. The sequential isomerization/styrylation reactions of cyclopropylmethyl bromide and 6-bromo-1-hexene provide evidence of the radical mechanism. Crystallographic and spectroscopic investigations on cobalt complexes reveal that the reaction would begin with single electron transfer from an electron-rich (diphosphine)bis(trimethylsilylmethyl)cobalt(II) complex followed by reductive elimination to yield 1,2-bis(trimethylsilyl)ethane and a (diphosphine)cobalt(I) complex. The combination of [CoCl2(dppb)] (DPPB = [1,4-bis(diphenylphosphino)butane]) catalyst and Me3SiCH2MgCl induces intramolecular Heck-type cyclization reactions of 6-halo-1-hexenes via a radical process. On the other hand, the intramolecular cyclization of the prenyl ether of 2-iodophenol would proceed in a fashion similar to the conventional palladium-catalyzed transformation. The nonradical oxidative addition of carbon(sp2)-halogen bonds to cobalt is separately verified by a cobalt-catalyzed cross-coupling reaction of alkenyl halides with Me3SiCH2MgCl with retention of configuration of the starting vinyl halides. The cobalt-catalyzed intermolecular radical styrylation reaction of alkyl halides is applied to stereoselective variants. Styrylations of 1-alkoxy-2-bromocyclopentane derivatives provide trans-1-alkoxy-2-styrylcyclopentane skeletons, one of which is optically pure. PMID:16771523

Affo, Walter; Ohmiya, Hirohisa; Fujioka, Takuma; Ikeda, Yousuke; Nakamura, Tomoaki; Yorimitsu, Hideki; Oshima, Koichiro; Imamura, Yuki; Mizuta, Tsutomu; Miyoshi, Katsuhiko

2006-06-21

369

Development of the ReaxFF Reactive Force Field for Describing Transition Metal Catalyzed Reactions, with Application to the Initial Stages of the Catalytic Formation of Carbon Nanotubes  

Microsoft Academic Search

With the aim of developing a computationally inexpensive method for modeling the high-temperature reaction dynamics of transition metal catalyzed reactions we have developed a ReaxFF reactive force field in which the parameters are fitted to a substantial quantum mechanics (QM) training set, containing full reaction pathways for relevant reactions. In this paper we apply this approach to reactions involving carbon

Kevin D. Nielson; Jonas Oxgaard; Wei-Qiao Deng; William A. Goddard III; William A. Goddard

2005-01-01

370

Dissecting the component reactions catalyzed by the actinorhodin minimal polyketide synthase.  

PubMed

The actinorhodin (act) minimal polyketide synthase (PKS) from Streptomyces coelicolor consists of three proteins: an acyl carrier protein (ACP) and two beta-ketoacyl ACP synthase components known as KSalpha and KSbeta. The act minimal PKS catalyzes at least 18 separate reactions which can be divided into loading, initiation, extension, and cyclization and release phases. Two quantitative kinetic assays were developed and used to measure individual rate and Michaelis constants for loading, initiation and extension steps. In the minimal PKS, the reaction between malonyl CoA and ACP to form malonyl ACP (loading) is the rate-limiting step (kcat = 0.49 min-1, KM = 207 microM). This reaction increases 5-fold in rate in the presence of KSalphaKSbeta (kcat = 2.3 min-1, KM = 215 microM). In the presence of S. coelicolor malonyl CoA:ACP transacylase (MCAT), the rate of loading increases and the kinetic parameters of malonyl-ACP as a substrate of KSalphaKSbeta can be measured (kcat = 20.6 min-1, KM = 2.4 microM). Under these conditions, it appears that decarboxylation of malonyl-ACP to form acetyl-ACP (initiation) is the rate-limiting step. When an excess of acetyl ACP is supplied, either chain extension, cyclization, or release steps become rate limiting (k approximately 60 min-1). No ACP-bound intermediates could be observed, suggesting that partially or fully extended chains do not accumulate because chain extension is rate limiting under these conditions and that cyclization and release are fast. apo-ACP acts as a mixed inhibitor of malonyl ACP binding to KSalpha/KSbeta (Kic = 50 microM, Kiu = 137 microM), but apo-ACP does not appear to inhibit MCAT. PMID:18034463

Beltran-Alvarez, Pedro; Cox, Russell J; Crosby, John; Simpson, Thomas J

2007-11-23

371

Fundamental Reaction Pathways for Cytochrome P450-catalyzed 5?-Hydroxylation and N-Demethylation of Nicotine  

PubMed Central

The reaction pathways for 5?-hydroxylation and N-demethylation of nicotine catalyzed by cytochrome P450 were investigated by performing a series of first-principle electronic structure calculations on a catalytic reaction model system. The computational results indicate that 5?-hydroxylation of nicotine occurs through a two-state stepwise process, i.e. an initial hydrogen atom transfer from nicotine to Cpd I (i.e. the HAT step) followed by a recombination of the nicotine moiety with the iron-bound hydroxyl group (i.e. the rebound step) on both the high-spin (HS) quartet and low-spin (LS) doublet states. The HAT step is the rate-determining one. This finding represents the first case that exhibits genuine rebound transition state species on both the HS and the LS states for C?-H hydroxylation of amines. N-demethylation of nicotine involves a N-methylhydroxylation to form N-(hydroxymethyl)nornicotine, followed by N-(hydroxymethyl)nornicotine decomposition to nornicotine and formaldehyde. The N-methylhydroxylation step is similar to 5?-hydroxylation, namely that a rate-determining HAT step followed by a rebound step. The decomposition process occurs on the deprotonated state of N-(hydroxymethyl)nornicotine assisted by a water molecule and the energy barrier is significantly lower than that of the N-methylhydroxylation process. Comparison of the rate-determining free energy barriers for the two reaction pathways predicts a preponderance of 5?-hydroxylation over the N-demethylation by roughly a factor of 18:1, which is in excellent agreement with the factor of 19:1 derived from available experimental data.

Li, Dongmei; Wang, Yong; Han, Keli; Zhan, Chang-Guo

2010-01-01

372

Kinetic and Molecular Analysis of 5-Epiaristolochene 1,3-Dihydroxylase, a Cytochrome P450 Enzyme Catalyzing Successive Hydroxylations of Sesquiterpenes*S  

PubMed Central

The final step of capsidiol biosynthesis is catalyzed by 5-epiaristolochene dihydroxylase (EAH), a cytochrome P450 enzyme that catalyzes the regio- and stereospecific insertion of two hydroxyl moieties into the bicyclic sesquiterpene 5-epiaristolochene (EA). Detailed kinetic studies using EA and the two possible monohydroxylated intermediates demonstrated the release of 1?-hydroxy-EA ((OH)EA) at high EA concentrations and a 10-fold catalytic preference for 1?(OH)EA versus 3?(OH)EA, indicative of a preferred reaction order of hydroxylation at C-1, followed by that at C-3. Sequence alignments and homology modeling identified active-site residues tested for their contribution to substrate specificity and overall enzymatic activity. Mutants EAH-S368C and EAH-S368V exhibited wild-type catalytic efficiencies for 1?(OH)EA biosynthesis, but were devoid of the successive hydroxylation activity for capsidiol biosynthesis. In contrast to EAH-S368C, EAH-S368V catalyzed the relative equal biosynthesis of 1?(OH)EA, 2?(OH)EA, and 3?(OH)EA from EA with wild-type efficiency. Moreover, EAH-S368V converted ~1.5% of these monohydroxylated products to their respective ketone forms. Alanine and threonine mutations at position 368 were significantly compromised in their conversion rates of EA to capsidiol and correlated with 3.6- and 5.7-fold increases in their Km values for the 1?(OH)EA intermediate, respectively. A role for Ile486 in the successive hydroxylations of EA was also suggested by the EAH-I468A mutant, which produced significant amounts 1?(OH)EA, but negligible amounts of capsidiol from EA. The altered product profile of the EAH-I486A mutant correlated with a 3.6-fold higher Km for EA and a 4.4-fold slower turnover rate (kcat) for 1?(OH)EA. These kinetic and mutational studies were correlated with substrate docking predictions to suggest how Ser368 and Ile486 might contribute to active-site topology, substrate binding, and substrate presentation to the oxo-Fe-heme reaction center.

Takahashi, Shunji; Zhao, Yuxin; O'Maille, Paul E.; Greenhagen, Bryan T.; Noel, Joseph P.; Coates, Robert M.; Chappell, Joe

2010-01-01

373

Rescue of K12G Triosephosphate Isomerase by Ammonium Cations: The Reaction of an Enzyme in Pieces  

PubMed Central

The K12G mutation at yeast triosephosphate isomerase (TIM) results in a 5.5 × 105-fold decrease in kcat/Km for isomerization of glyceraldehyde 3-phosphate, and the activity of this mutant can be successfully “rescued” by NH4+ and primary alkylammonium cations. The transition state for the K12G mutant TIM-catalyzed reaction is stabilized by 1.5 kcal/mol by interaction with NH4+. The larger 3.9 kcal/mol stabilization by CH3CH2CH2CH2NH3+ is due to hydrophobic interactions between the mutant enzyme and the butyl side chain of the cation activator. There is no significant transfer of a proton from alkylammonium cations to GAP at the transition state for the K12G mutant TIM-catalyzed reaction, because activation by a series of RNH3+ shows little or no dependence on the pKa of RNH3+. A comparison of kcat/Km = 6.6 × 106 M?1 s?1 for the wildtype TIM-catalyzed isomerization of GAP and the third-order rate constant of 150 M?2 s?1 for activation by NH4+ of the K12G mutant TIM-catalyzed isomerization shows that stabilization of the bound transition state by the effectively intramolecular interaction of the cationic side chain of Lys-12 at wildtype TIM is 6.3 kcal/mol greater than for the corresponding intermolecular interaction of NH4+ at K12G mutant TIM.

Go, Maybelle K.; Amyes, Tina L.; Richard, John P.

2010-01-01

374

Adenylate-forming enzymes  

PubMed Central

Thioesters, amides and esters are common chemical building blocks in a wide array of natural products. The formation of these bonds can be catalyzed in a variety of ways. For chemists, the use of an activating group is a common strategy and adenylate enzymes are exemplars of this approach. Adenylating enzymes activate the otherwise unreactive carboxylic acid by transforming the normal hydroxyl leaving group into adenosine monophosphate. Recently there have been a number of studies of such enzymes and in this review we suggest a new classification scheme. The review highlights the diversity in enzyme fold, active site architecture and metal coordination that has evolved to catalyze this particular reaction.

Schmelz, Stefan; Naismith, James H.

2012-01-01

375

Rhodium catalyzed chelation-assisted C-H bond functionalization reactions.  

PubMed

Over the last several decades, researchers have achieved remarkable progress in the field of organometallic chemistry. The development of metal-catalyzed cross-coupling reactions represents a paradigm shift in chemical synthesis, and today synthetic chemists can readily access carbon-carbon and carbon-heteroatom bonds from a vast array of starting compounds. Although we cannot understate the importance of these methods, the required prefunctionalization to carry out these reactions adds cost and reduces the availability of the starting reagents. The use of C-H bond activation in lieu of prefunctionalization has presented a tantalizing alternative to classical cross-coupling reactions. Researchers have met the challenges of selectivity and reactivity associated with the development of C-H bond functionalization reactions with an explosion of creative advances in substrate and catalyst design. Literature reports on selectivity based on steric effects, acidity, and electronic and directing group effects are now numerous. Our group has developed an array of C-H bond functionalization reactions that take advantage of a chelating directing group, and this Account surveys our progress in this area. The use of chelation control in C-H bond functionalization offers several advantages with respect to substrate scope and application to total synthesis. The predictability and decreased dependence on the inherent stereoelectronics of the substrate generally result in selective and high yielding transformations with broad applicability. The nature of the chelating moiety can be chosen to serve as a functional handle in subsequent elaborations. Our work began with the use of Rh(I) catalysts in intramolecular aromatic C-H annulations, which we further developed to include enantioselective transformations. The application of this chemistry to the simple olefinic C-H bonds found in ?,?-unsaturated imines allowed access to highly substituted olefins, pyridines, and piperidines. We observed complementary reactivity with Rh(III) catalysts and developed an oxidative coupling with unactivated alkenes. Further studies on the Rh(III) catalysts led us to develop methods for the coupling of C-H bonds to polarized ? bonds such as those in imines and isocyanates. In several cases the methods that we have developed for chelation-controlled C-H bond functionalization have been applied to the total synthesis of complex molecules such as natural products, highlighting the utility of these methods in organic synthesis. PMID:22148885

Colby, Denise A; Tsai, Andy S; Bergman, Robert G; Ellman, Jonathan A

2011-12-08

376

Rhodium catalyzed chelation-assisted C-H bond functionalization reactions  

PubMed Central

Conspectus Over the last several decades, researchers have achieved remarkable progress in the field of organometallic chemistry. The development of metal-catalyzed cross-coupling reactions represents a paradigm shift in chemical synthesis, and today synthetic chemists can readily access carbon-carbon and carbon-heteroatom bonds from a vast array of starting compounds. Although we cannot understate the importance of these methods, the required pre-functionalization to carry out these reactions adds cost and reduces the availability of the starting reagents. The use of C-H bond activation in lieu of pre-functionalization has presented a tantalizing alternative to classical cross-coupling reactions. Researchers have met the challenges of selectivity and reactivity associated with the development of C-H bond functionalization reactions with an explosion of creative advances in substrate and catalyst design. Literature reports on selectivity based on steric effects, acidity, and electronic and directing group effects are now numerous. Our group has developed an array of C-H bond functionalization reactions that take advantage of a chelating directing group, and this Account surveys our progress in this area. The use of chelation control in C-H bond functionalization offers several advantages with respect to substrate scope and application to total synthesis. The predictability and decreased dependence on the inherent stereoelectronics of the substrate generally result in selective and high yielding transformations with broad applicability. The nature of the chelating moiety can be chosen to serve as a functional handle in subsequent elaborations. Our work began with the use of Rh(I) catalysts in intramolecular aromatic C-H annulations, which we further developed to include enantioselective transformations. The application of this chemistry to the simple olefinic C-H bonds found in ?,?-unsaturated imines allowed access to highly substituted olefins, pyridines, and piperidines. We observed complementary reactivity with Rh(III) catalysts and developed an oxidative coupling with unactivated alkenes. Further studies on the Rh(III) catalysts led us to develop methods for the coupling of C-H bonds to polarized ? bonds such as those in imines and isocyanates. In several cases the methods that we have developed for chelation-controlled C-H bond functionalization have been applied to the total synthesis of complex molecules such as natural products, highlighting the utility of these methods in organic synthesis.

Colby, Denise A.; Tsai, Andy S.; Bergman, Robert G.; Ellman, Jonathan A.

2011-01-01

377

Ruthenium-catalyzed ?-(hetero)arylation of saturated cyclic amines: reaction scope and mechanism.  

PubMed

Transition-metal-catalyzed sp(3) C-H activation has emerged as a powerful approach to functionalize saturated cyclic amines. Our group recently disclosed a direct catalytic arylation reaction of piperidines at the ? position to the nitrogen atom. 1-(Pyridin-2-yl)piperidine could be smoothly ?-arylated if treated with an arylboronic ester in the presence of a catalytic amount of [Ru3(CO)12] and one equivalent of 3-ethyl-3-pentanol. A systematic study on the substrate and reagent scope of this transformation is disclosed in this paper. The effect of substitution on both the piperidine ring and the arylboronic ester has been investigated. Smaller (pyrrolidine) and larger (azepane) saturated ring systems, as well as benzoannulated derivatives, were found to be compatible substrates with the ?-arylation protocol. The successful use of a variety of heteroarylboronic esters as coupling partners further proved the power of this direct functionalization method. Mechanistic studies have allowed for a better understanding of the catalytic cycle of this remarkable transformation featuring an unprecedented direct transmetalation on a Ru(II)-H species. PMID:23780756

Peschiulli, Aldo; Smout, Veerle; Storr, Thomas E; Mitchell, Emily A; Eliáš, Zden?k; Herrebout, Wouter; Berthelot, Didier; Meerpoel, Lieven; Maes, Bert U W

2013-06-18

378

Gold(III) Salen complex-catalyzed synthesis of propargylamines via a three-component coupling reaction.  

PubMed

[reaction: see text] Propargylamines have been synthesized by a gold(III) salen complex-catalyzed three-component coupling reaction of aldehydes, amines, and alkynes in water in excellent yields at 40 degrees C. With chiral prolinol derivatives as the amine component, excellent diastereoselectivities (up to 99:1) have been attained. This coupling reaction has been applied to the synthesis of propargylamine-modified artemisinin derivatives with the delicate endoperoxide moieties remaining intact. Cytotoxicities with IC(50) values up to 1.1 microM against a human hepatocellular carcinoma cell line (HepG2) were exhibited by these artemisinin derivatives. PMID:16597102

Lo, Vanessa Kar-Yan; Liu, Yungen; Wong, Man-Kin; Che, Chi-Ming

2006-04-13

379

Relative rates of various steps of NO–CH 4–O 2 reaction catalyzed by Pd\\/H-ZSM-5  

Microsoft Academic Search

Reaction mechanism of the reduction of nitrogen monoxide by methane in an oxygen excess atmosphere (NO–CH4–O2 reaction) catalyzed by Pd\\/H-ZSM-5 has been studied at 623–703K in the absence of water vapor, in comparison with the mechanism for Co-ZSM-5. Kinetic isotope effect for the N2 formation in NO–CH4–O2 vs. NO–CD4–O2 reactions was 1.65 at 673K and decreased with a decrease in

Hidenaga Kato; Chikafumi Yokoyama; Makoto Misono

1998-01-01

380

Cyclohexanone Conversion Catalyzed by Pt\\/?-Al 2 O 3 : Evidence of Oxygen Removal and Coupling Reactions  

Microsoft Academic Search

\\u000a Abstract  The conversion of cyclohexanone, often identified as an intermediate in the conversion of lignin-derived compounds, was catalyzed\\u000a by Pt\\/?-Al2O3 in the presence of H2 at 573 K. Dehydrogenation was a kinetically significant reaction, indicated by a high selectivity for phenol. Oxygen-removal\\u000a reactions are indicated by products including benzene, cyclohexene, and cyclohexene. Bimolecular reactions involving cyclohexanone\\u000a and\\/or products of its conversion led

Tarit Nimmanwudipong; Ron C. Runnebaum; Kevin Tay; David E. Block; Bruce C. Gates

381

Nickel and cobalt-catalyzed coupling of alkyl halides with alkenes via heck reactions and radical conjugate addition.  

PubMed

Cross-coupling of alkyl halides with alkenes leading to Heck-type and addition products is summarized. The development of Heck reaction with aliphatic halides although has made significant progress in the past decade and particularly recently, it was much less explored in comparison with the aryl halides. The use of Ni- and Co-catalyzed protocols allowed efficient Heck coupling of activated and unactivated alkenes with 1°, 2° and 3° alkyl halides. In addition, radical conjugate addition to activated alkenes has become a well-established method that has led to efficient construction of many natural products. The utilization of Ni- and Co-catalyzed strategies would avoid toxic tin reagents, and therefore worth exploring. The recent development of Ni- and Co-catalyzed addition of alkyl halides to alkenes displays much improved reactivity and functional group tolerance. In this mini-review, we also attempt to overview the mechanisms that are proposed in the reactions, aiming at providing insight into the nickel and cobalt-catalyzed coupling of alkyl halides with alkenes. PMID:23544460

Qian, Qun; Zang, Zhenhua; Chen, Yang; Tong, Weiqi; Gong, Hegui

2013-05-01

382

Novel poly-gamma-glutamate-processing enzyme catalyzing gamma-glutamyl DD-amidohydrolysis.  

PubMed

The pgdS gene product of Bacillus subtilis, PgdS, cleaves poly-gamma-glutamate (PGA) in an endo-peptidase-like fashion. However, its catalytic property remains obscure. In this study, a simple assay for the PgdS enzyme using 1-fluoro-2,4-dinitrobenzene was developed, and some characteristics of PgdS, such as optimal pH, were examined. The enzyme was strongly inhibited by a thiol-modifying reagent, suggesting that it possesses essential cysteine residue(s) in catalysis. PgdS exhibited a high affinity to PGA that consisted mainly of D-glutamate residues, but no affinity to PGA composed only of L-glutamate residues (L-PGA). The enzyme processed DL-copolymer-type PGA (DL-PGA) with an average molecular mass of 1,000 kDa to a high-molecular-mass L-glutamate-rich fragment (average 200 kDa), the L-rich PGA fragment, and low-molecular-mass fragment composed mostly of D-glutamate residues (average 5 kDa), D-fragment. To deepen our understanding of the catalytic property of the PgdS enzyme, we analyzed the structures of the N- and C-terminal regions and found that D-glutamyl residues successively lie even at both ends of the L-rich PGA fragment. Our observations indicate that PgdS is a novel endo-peptidase that specifically cleaves the gamma-amide linkage between two D-glutamate residues in PGA, i.e., gamma-glutamyl DD-amidohydrolase. The enzyme is possibly useful in the biochemical processing of B. subtilis DL-PGA. PMID:16952838

Ashiuchi, Makoto; Nakamura, Hisaaki; Yamamoto, Masayoshi; Misono, Haruo

2006-07-01

383

High malic enzyme activity in tumor cells and its cross-reaction with antipigeon liver malic enzyme serum  

Microsoft Academic Search

Summary  Rabbit antibodies against pigeon liver malic enzyme (EC 1.1.1.40) were prepared. The antiserum gave single precipitation line\\u000a with crude pigeon liver extract. Cross reaction was observed with partially purified malic enzyme or crude extract from chicken\\u000a liver. Positive cross reaction was also observed with the concentrated cytosolic fraction of two human carcinoma cell lines\\u000a which were demonstrated to contain high

Pui-ling Kam; Ching-chun Lin; Jue-Cheng Li; Ching-liang Meng; Gu-gang Chang

1988-01-01

384

Lipase-catalyzed optical resolution of racemic naproxen in biphasic enzyme membrane reactors  

Microsoft Academic Search

A lipase-immobilized membrane reactor was applied for the optical resolution of racemic naproxen, and the effect of various operation conditions on reaction rate and enantio-selectivity was examined. The membrane reactor consisted of an organic phase dissolving naproxen ester, a lipase-immobilized polyamide membrane, and an aqueous phase to recover the reaction products. The lipase immobilized in the membrane reactor showed a

Keiji Sakaki; Lidietta Giorno; Enrico Drioli

2001-01-01

385

A novel ortho-dehalogenation reaction of 2-chlorocinnamic acid catalyzed by the pink yeast Rhodotorula rubra Y-1529.  

PubMed

In the present study, a resting cells suspension of Rhodotorula rubra Y-1529 was shown to have the capacity to perform an ortho-dehalogenation reaction on 2-chlorocinnamic acid. The results from the biodegradation of U-[14C]benzoic acid, cinnamic acid, 3-chlorocinnamic acid and 4-chlorocinnamic acid suggest that the first step of the ortho-dehalogenation reaction occurred during the oxidation of the unsaturated C3 side chain of 2-chlorocinnamic acid to 2-chlorobenzoic acid. None of the 2-chlorobenzoic acid was found in the biodegradation system, suggesting that this step was a highly regulated step. After the side-chain oxidation reaction, the hydroxylation of the benzene ring was determined to be at the para-position first, followed by the meta-position. The occurrence of 3:4-position ring fission reactions and the production of the final product, CO2, was proven by the biodegradation of U-[14C] benzoic acid. This oxidative dehalogenation reaction catalyzed by R. rubra was found to be regiospecific for 2-chlorocinnamic acid; the chloride ion was probably removed after the ring fission reaction. A pathway of the ortho-dehalogenation reaction of 2-chlorocinnamic acid catalyzed by R. rubra was proposed based on these data. PMID:10789983

Sun, F M; Wang, J S; Traxler, R W

2000-06-01

386

Choline Monooxygenase, an Unusual Iron-Sulfur Enzyme Catalyzing the First Step of Glycine Betaine Synthesis in Plants: Prosthetic Group Characterization and cDNA Cloning  

Microsoft Academic Search

Plants synthesize the osmoprotectant glycine betaine via the route choline --> betaine aldehyde --> glycine betaine. In spinach, the first step is catalyzed by choline monooxygenase (CMO), a ferredoxin-dependent stromal enzyme that has been hypothesized to be an oligomer of identical subunits and to be an Fe-S protein. Analysis by HPLC and matrix-assisted laser desorption ionization MS confirmed that native

Bala Rathinasabapathi; Michael Burnet; Brenda L. Russell; Douglas A. Gage; Pao-Chi Liao; Gordon J. Nye; Paul Scott; John H. Golbeck; Andrew D. Hanson

1997-01-01

387

Assessment of theoretical procedures for calculating barrier heights for a diverse set of water-catalyzed proton-transfer reactions.  

PubMed

Accurate electronic barrier heights are obtained for a set of nine proton-transfer tautomerization reactions, which are either (i) uncatalyzed, (ii) catalyzed by one water molecule, or (iii) catalyzed by two water molecules. The barrier heights for reactions (i) and (ii) are obtained by means of the high-level ab initio W2.2 thermochemical protocol, while those for reaction (iii) are obtained using the W1 protocol. These three sets of benchmark barrier heights allow an assessment of the performance of more approximate theoretical procedures for the calculation of barrier heights of uncatalyzed and water-catalyzed reactions. We evaluate initially the performance of the composite G4 procedure and variants thereof (e.g., G4(MP2) and G4(MP2)-6X), as well as that of standard ab initio procedures (e.g., MP2, SCS-MP2, and MP4). We find that the performance of the G4(MP2)-type thermochemical procedures deteriorates with the number of water molecules involved in the catalysis. This behavior is linked to deficiencies in the MP2-based basis-set-correction term in the G4(MP2)-type procedures. This is remedied in the MP4-based G4 procedure, which shows good performance for both the uncatalyzed and the water-catalyzed reactions, with mean absolute deviations (MADs) from the benchmark values lying below the threshold of "chemical accuracy" (arbitrarily defined as 1 kcal mol(-1) ? 4.2 kJ mol(-1)). We also examine the performance of a large number of density functional theory (DFT) and double-hybrid DFT (DHDFT) procedures. We find that, with few exceptions (most notably PW6-B95 and B97-2), the performance of the DFT procedures that give good results for the uncatalyzed reactions deteriorates with the number of water molecules involved in the catalysis. The DHDFT procedures, on the other hand, show excellent performance for both the uncatalyzed and catalyzed reactions. Specifically, almost all of them afford MADs below the "chemical accuracy" threshold, with ROB2-PLYP and B2K-PLYP showing the best overall performance. PMID:22497287

Karton, Amir; O'Reilly, Robert J; Radom, Leo

2012-04-12

388

Heck reaction catalyzed by Pd/C, in a triphasic-organic/Aliquat 336/aqueous-solvent system.  

PubMed

The rate of the Pd/C catalyzed Heck coupling of Ar-I with CH(2)=CH-R is accelerated tenfold by the presence of Aliquat 336 (A336), a well known phase transfer catalyst, and an ionic liquid. Both when conducted in A336 as solvent, and in an isooctane/A336/aqueous triphasic mixture, the Heck reaction of aryl iodides with electron deficient olefins, catalyzed by Pd/C, proceeds with high yields and selectivity. When KOH is used instead of Et(3)N, selective formation of the biphenyl rather than the Heck product, is observed. Aryl bromides react more sluggishly, and only the more activated ones undergo the Heck reaction. In the absence of the olefin, aryl halides possessing an electron withdrawing group are reduced to the corresponding Ar-H. PMID:15280963

Perosa, Alvise; Tundo, Pietro; Selva, Maurizio; Zinovyev, Sergei; Testa, Alberto

2004-07-14

389

Atomically dispersed Au-(OH)x species bound on titania catalyze the low-temperature water-gas shift reaction.  

PubMed

We report a new method for stabilizing appreciable loadings (~1 wt %) of isolated gold atoms on titania and show that these catalyze the low-temperature water-gas shift reaction. The method combines a typical gold deposition/precipitation method with UV irradiation of the titania support suspended in ethanol. Dissociation of H2O on the thus-created Au-O-TiO(x) sites is facile. At higher gold loadings, nanoparticles are formed, but they were shown to add no further activity to the atomically bound gold on titania. Removal of this "excess" gold by sodium cyanide leaching leaves the activity intact and the atomically dispersed gold still bound on titania. The new materials may catalyze a number of other reactions that require oxidized active metal sites. PMID:23437858

Yang, Ming; Allard, Lawrence F; Flytzani-Stephanopoulos, Maria

2013-03-01

390

Methane production from the catalyzed reaction of graphite and water vapor at low temperatures (500-600 K)  

SciTech Connect

The steady-state production of methane from the catalyzed reaction of high-density graphite and water vapor at low temperatures (500-600 K) is reported. The reaction is catalyzed by potassium hydroxide and potassium carbonate placed on the graphite surface. The steady-state production of methane has a turnover frequency of 10/sup -3/ sec/sup -1/ at 522 K and as activation energy of 10 +/- 3 kcal/mole. Several other alkali hydroxides, lithium, sodium, and cesium hydroxide, all turned out to be good catalysts for the production of methane from water vapor and graphite. The surface composition and surface texture were characterized by Auger electron spectroscopy and scanning electron microscopy, respectively.

Cabrera, A.L.; Heinemann, H.; Somorjai, G.A.

1982-05-01

391

Structural Insights into E1-Catalyzed Ubiquitin Activation and Transfer to Conjugating Enzymes  

SciTech Connect

Ubiquitin (Ub) and ubiquitin-like proteins (Ubls) are conjugated to their targets by specific cascades involving three classes of enzymes, E1, E2, and E3. Each E1 adenylates the C terminus of its cognate Ubl, forms a E1{approx}Ubl thioester intermediate, and ultimately generates a thioester-linked E2{approx}Ubl product. We have determined the crystal structure of yeast Uba1, revealing a modular architecture with individual domains primarily mediating these specific activities. The negatively charged C-terminal ubiquitin-fold domain (UFD) is primed for binding of E2s and recognizes their positively charged first a helix via electrostatic interactions. In addition, a mobile loop from the domain harboring the E1 catalytic cysteine contributes to E2 binding. Significant, experimentally observed motions in the UFD around a hinge in the linker connecting this domain to the rest of the enzyme suggest a conformation-dependent mechanism for the transthioesterification function of Uba1; however, this mechanism clearly differs from that of other E1 enzymes.

Lee,I.; Schindelin, H.

2008-01-01

392

Factors that Affect Oxygen Activation and Coupling of the Two Redox Cycles in the Aromatization Reaction Catalyzed by NikD, an Unusual Amino Acid Oxidase†‡  

PubMed Central

NikD is a flavoprotein oxidase that catalyzes the oxidation of piperideine-2-carboxylate (P2C) to picolinate in a remarkable aromatization reaction comprising two redox cycles and at least one isomerization step. Tyr258 forms part of an "aromatic cage" that surrounds the ring in picolinate and its precursors. Mutation of Tyr258 to Phe does not perturb the structure of nikD but does affect the coupling of the two redox cycles and causes a 10-fold decrease in turnover rate. Tyr258Phe catalyzes a quantitative 2-electron oxidation of P2C but only 60% of the resulting dihydropicolinate intermediate undergoes a second redox cycle to produce picolinate. The mutation does not affect product yield with an alternate substrate (3,4-dehydro-L-proline) that is aromatized in a single 2-electron oxidation step. Wild-type and mutant enzyme exhibit identical rate constants for P2C oxidation to dihydropicolinate and isomerization of a reduced enzyme•dihydropicolinate complex. The observed rates are 200- and 10-fold faster, respectively, than the mutant turnover rate. Picolinate release from Tyr258Phe is 100-fold faster than turnover. The presence of bound substrate or product is a key factor in oxygen activation by wild-type nikD, as judged by the 10- to 75-fold faster rates observed for complexes of the reduced enzyme with picolinate, benzoate or 1-cyclohexenoate, a 1-deaza P2C analog. The reduced Tyr258Phe•1-cyclohexenoate complex is 25-fold less reactive with oxygen than the wild-type complex. We postulate that mutation of Tyr258 causes subtle changes in active site dynamics that promote release of the reactive dihydropicolinate intermediate and disrupt the efficient synchronization of oxygen activation observed with wild-type nikD.

Kommoju, Phaneeswara-Rao; Bruckner, Robert C.; Ferreira, Patricia; Carrell, Christopher J.; Mathews, F. Scott; Jorns, Marilyn Schuman

2009-01-01

393

Zn(II)/amine-catalyzed coupling reaction of alkylidenemalonates with propargyl alcohol: a one-pot synthesis of methylenetetrahydrofurans.  

PubMed

[reaction: see text] A metal-catalyzed tandem 1,4-addition/cyclization between propargyl alcohol and a Michael acceptor, such as alkylidene malonate, has been developed. In the presence of catalytic amounts of zinc triflate [Zn(OTf)(2)] and triethylamine (Et(3)N), various 2-alkylidene-1,3-dicarbonyl compounds reacted with propargyl alcohol to give 3- or 4-methylene tetrahydrofurans in excellent yields. PMID:15176807

Nakamura, Masaharu; Liang, Chungen; Nakamura, Eiichi

2004-06-10

394

Lewis base-catalyzed conjugate reduction and reductive aldol reaction of alpha,beta-unsaturated ketones using trichlorosilane.  

PubMed

Lewis bases such as Ph3P=O and HMPA catalyze the 1,4-reduction of alpha,beta-unsaturated ketones with trichlorosilane, and because the 1,2-reduction of aldehydes scarcely proceeded under the conditions, one-pot reductive aldol reactions with aldehydes were successfully achieved; preliminary studies using a chiral Lewis base revealed a high potential for enantioselective catalysis. PMID:18802553

Sugiura, Masaharu; Sato, Norimasa; Kotani, Shunsuke; Nakajima, Makoto

2008-07-17

395

Rare earth perfluorooctanoate [RE(PFO) 3] catalyzed one-pot Mannich reaction: three component synthesis of ?-amino carbonyl compounds  

Microsoft Academic Search

Mannich reaction of acetophenone, aldehydes and aromatic amines catalyzed efficiently by RE(PFO)3 was described firstly, which carried out smoothly in high yields with three component one-pot method. Furthermore, it was found these catalysts were completely recovered and reused without loss of their catalytic activities and are thus environmentally conscious, and this procedure is a new choice to synthesis ?-aminocarbonyl compounds.

Limin Wang; Jianwei Han; Jia Sheng; He Tian; Zhaoyu Fan

2005-01-01

396

N-Heterocyclic carbene-catalyzed direct cross-aza-benzoin reaction: Efficient synthesis of ?-amino-?-keto esters  

PubMed Central

Summary An efficient catalytic synthesis of ?-amino-?-keto esters has been newly developed. Cross-coupling of various aldehydes with ?-imino ester, catalyzed by N-heterocyclic carbene, leads chemoselectively to ?-amino-?-keto esters in moderate to good yields with high atom efficiency. The reaction mechanism is discussed, and it is proposed that the ?-amino-?-keto esters are formed under thermodynamic control.

Uno, Takuya; Kobayashi, Yusuke

2012-01-01

397

Kinetic studies on the Rhizomucor miehei lipase catalyzed esterification reaction of oleic acid with 1-butanol in a biphasic system  

Microsoft Academic Search

The kinetics of the esterification of oleic acid with 1-butanol catalyzed by free Rhizomucor miehei lipase in a biphasic system was studied in a batch reactor. The reaction appeared to proceed via a Ping Pong bi–bi mechanism with 1-butanol inhibition. The kinetic constants of the model were determined from experiments at 30°C with initial concentrations of 0.1–0.95?mol?Lorg?1 oleic acid and

G. N. Kraai; J. G. M. Winkelman; J. G. de Vries; H. J. Heeres

2008-01-01

398

Highly sensitive electrochemical detection of proteins using aptamer-coated gold nanoparticles and surface enzyme reactions.  

PubMed

A novel electrochemical detection methodology is described for the femtomolar detection of proteins which utilizes both DNA aptamer-functionalized nanoparticles and a surface enzymatic reaction. Immunoglobulin E (IgE) was used as a model protein biomarker, which possesses two distinct epitopes for antibody (anti-IgE) and DNA aptamer binding. A surface sandwich assay format was utilized involving the specific adsorption of IgE onto a gold electrode surface that was pre-modified with a monolayer of aptamer-nanoparticle conjugates followed by the specific interaction of alkaline phosphatase (ALP) conjugated anti-IgE. To clearly demonstrate the signal enhancement associated with nanoparticle use, anodic current measurements of the ALP catalyzed oxidation of the enzyme substrate 4-aminophenylphosphate (APP) were also compared with electrode surfaces upon which the aptamer was directly attached. The detection of an unlabelled protein at concentrations as low as 5 fM is a significant improvement compared to conventional electrochemical-based immunoassay approaches and provides a foundation for the practical use and incorporation of nanoparticle-enhanced detection into electrochemical biosensing technologies. PMID:22302221

Nam, Eun Ji; Kim, Eum Ji; Wark, Alastair W; Rho, Sangchul; Kim, Hyungi; Lee, Hye Jin

2012-02-02

399

Mn(II)–sodium dodecyl sulphate complex mimic enzyme-catalyzed fluorescence quenching of Pyronine B by hydrogen peroxide  

Microsoft Academic Search

Mn(II)–sodium dodecyl sulphate complex (Mn(II)–SDS) is used to mimic the active group of peroxidase. The catalytic characteristic of this mimic enzyme catalyst in the oxidation reaction of fluorescence substrate, tetraethyldiaminoxanthyl chloride (Pyronine B (PB)), with hydrogen peroxide has been studied. The experimental results show that Mn(II)–SDS complex has similar catalytic activity that of peroxidase. The steady-state catalytic rate depends upon

Li-Hua Chen; Liu-Zhan Liu; Han-Xi Shen

2003-01-01

400

THE REACTION BETWEEN THE ENZYME TYROSINASE AND ITS SPECIFIC ANTIBODY  

PubMed Central

1. Antibodies to the enzyme tyrosinase, obtained from the mushroom Psalliota campestris, have been produced in rabbits and human beings. 2. These antibody preparations, though precipitating the enzyme from solution, do not affect its catalytic activity.

Adams, Mark H.

1942-01-01

401

Pd-catalyzed reaction of allyl carbonate with polyols: the role of CO2 in transesterification versus etherification of glycerol.  

PubMed

An intermolecular Pd/PPh(3)-catalyzed transesterification of diallyl carbonate with glycerol to generate glycerol carbonate has been developed. Analysis of the reaction kinetics in THF indicates a first-order dependence on Pd and diallyl carbonate, that the Pd bears two phosphines during the turnover limiting event, and that increasing the glycerol concentration inhibits reaction, possibly via change in the polarity of the medium. (13)C isotopic labeling studies demonstrate that the Pd-catalyzed transesterification requires at least one allyl carbonate moiety and that there is rapid equilibrium of the allyl carbonate with CO(2) in solution, even when present only at low concentrations. A mechanism that is consistent with these results involves oxidative addition of the allyl carbonate to Pd followed by reversible decarboxylation, with the intermediate ?(1)- and ?(3)-allyl Pd alkoxides mediating direct and indirect transesterification reactions with the glycerol. Using this model, successful simulations of the kinetics of reactions conducted under atmospheres of N(2) or CO(2) could be achieved, including switching in selectivity between etherification and transesterification in the early stages of reaction. Reactions with the higher polyols threitol and erythritol are also efficient, generating the terminal (1,2) monocarbonates with high selectivity. PMID:22266740

Gordillo, Alvaro; Lloyd-Jones, Guy C

2012-01-20

402

Inactivation of Key Metabolic Enzymes by Mixed-Function Oxidation Reactions: Possible Implication in Protein Turnover and Ageing  

Microsoft Academic Search

Several mixed-function oxidation systems catalyze the inactivation of Escherichia coli glutamine synthetase. Inactivation involves modification of a single histidine residue in each enzyme subunit and makes the enzyme susceptible to proteolytic degradation. We show here that 10 key enzymes in metabolism are inactivated by a bacterial NADH oxidase and by an oxidase system comprised of NADPH, cytochrome P-450 reductase, and

Laura Fucci; Cynthia N. Oliver; Minor J. Coon; Earl R. Stadtman

1983-01-01

403

An Improved Method for Studying the Enzyme-Catalyzed Oxidation of Glucose Using Luminescent Probes  

ERIC Educational Resources Information Center

|A new method is presented for measuring the rate of the oxidation of glucose in the presence of glucose oxidase. The improved method employs luminescence measurements to directly determine the concentration of oxygen in real time, thus obviating complicated reaction schemes employed in previous methods. Our method has been used to determine…

Bare, William D.; Pham, Chi V.; Cuber, Matthew; Demas, J. N.

2007-01-01

404

An Improved Method for Studying the Enzyme-Catalyzed Oxidation of Glucose Using Luminescent Probes  

ERIC Educational Resources Information Center

A new method is presented for measuring the rate of the oxidation of glucose in the presence of glucose oxidase. The improved method employs luminescence measurements to directly determine the concentration of oxygen in real time, thus obviating complicated reaction schemes employed in previous methods. Our method has been used to determine…

Bare, William D.; Pham, Chi V.; Cuber, Matthew; Demas, J. N.

2007-01-01

405

Isotope effects in the non enzymic glucation of hemoglobin catalyzed by phosphate.  

National Technical Information Service (NTIS)

The reaction of hemoglobin, mainly at the N-terminal valine, with glucose exhibits identical rates in protium and deuterium oxides, both for the buffer-independent rate and for the first-order rate in phosphate buffer. Under the conditions employed, imine...

H. Gil J. Mata-Segreda R. Schowen

1991-01-01

406

Purification, identification, and cloning of lysoplasmalogenase, the enzyme that catalyzes hydrolysis of the vinyl ether bond of lysoplasmalogen.  

PubMed

Lysoplasmalogenase (EC 3.3.2.2 and EC 3.3.2.5) is an enzyme that catalyzes hydrolytic cleavage of the vinyl ether bond of lysoplasmalogen, forming fatty aldehyde and glycerophosphoethanolamine or glycerophosphocholine and is specific for the sn-2-deacylated form of plasmalogen. Here we report the purification, characterization, identification, and cloning of lysoplasmalogenase. Rat liver microsomal lysoplasmalogenase was solubilized with octyl glucoside and purified 500-fold to near homogeneity using four chromatography steps. The purified enzyme has apparent K(m) values of ?50 ?m for both lysoplasmenylcholine and lysoplasmenylethanolamine and apparent V(m) values of 24.5 and 17.5 ?mol/min/mg protein for the two substrates, respectively. The pH optimum was 7.0. Lysoplasmalogenase was competitively inhibited by lysophosphatidic acid (K(i) ?20 ?m). The predominant band on a gel at ?19 kDa was subjected to trypsinolysis, and the peptides were identified by mass spectrometry as Tmem86b, a protein of unknown function. Transient transfection of human embryonic kidney (HEK) 293T cells showed that TMEM86b cDNA yielded lysoplasmalogenase activity, and Western blot analyses confirmed the synthesis of TMEM86b protein. The protein was localized in the membrane fractions. The TMEM86b gene was also transformed into Escherichia coli, and its expression was verified by Western blot and activity analyses. Tmem86b is a hydrophobic transmembrane protein of the YhhN family. Northern blot analyses demonstrated that liver expressed the highest level of Tmem86b, which agreed with tissue distribution of activity. Overexpression of TMEM86b in HEK 293T cells resulted in decreased levels of plasmalogens, suggesting that the enzyme may be important in regulating plasmalogen levels in animal cells. PMID:21515882

Wu, Lai-Chu; Pfeiffer, Douglas R; Calhoon, Elisabeth A; Madiai, Francesca; Marcucci, Guido; Liu, Shujun; Jurkowitz, Marianne S

2011-04-22

407

Purification, Identification, and Cloning of Lysoplasmalogenase, the Enzyme That Catalyzes Hydrolysis of the Vinyl Ether Bond of Lysoplasmalogen*  

PubMed Central

Lysoplasmalogenase (EC 3.3.2.2 and EC 3.3.2.5) is an enzyme that catalyzes hydrolytic cleavage of the vinyl ether bond of lysoplasmalogen, forming fatty aldehyde and glycerophosphoethanolamine or glycerophosphocholine and is specific for the sn-2-deacylated form of plasmalogen. Here we report the purification, characterization, identification, and cloning of lysoplasmalogenase. Rat liver microsomal lysoplasmalogenase was solubilized with octyl glucoside and purified 500-fold to near homogeneity using four chromatography steps. The purified enzyme has apparent Km values of ?50 ?m for both lysoplasmenylcholine and lysoplasmenylethanolamine and apparent Vm values of 24.5 and 17.5 ?mol/min/mg protein for the two substrates, respectively. The pH optimum was 7.0. Lysoplasmalogenase was competitively inhibited by lysophosphatidic acid (Ki ?20 ?m). The predominant band on a gel at ?19 kDa was subjected to trypsinolysis, and the peptides were identified by mass spectrometry as Tmem86b, a protein of unknown function. Transient transfection of human embryonic kidney (HEK) 293T cells showed that TMEM86b cDNA yielded lysoplasmalogenase activity, and Western blot analyses confirmed the synthesis of TMEM86b protein. The protein was localized in the membrane fractions. The TMEM86b gene was also transformed into Escherichia coli, and its expression was verified by Western blot and activity analyses. Tmem86b is a hydrophobic transmembrane protein of the YhhN family. Northern blot analyses demonstrated that liver expressed the highest level of Tmem86b, which agreed with tissue distribution of activity. Overexpression of TMEM86b in HEK 293T cells resulted in decreased levels of plasmalogens, suggesting that the enzyme may be important in regulating plasmalogen levels in animal cells.

Wu, Lai-Chu; Pfeiffer, Douglas R.; Calhoon, Elisabeth A.; Madiai, Francesca; Marcucci, Guido; Liu, Shujun; Jurkowitz, Marianne S.

2011-01-01

408

Unification of reaction pathway and kinetic scheme for N2 reduction catalyzed by nitrogenase  

PubMed Central

Nitrogenase catalyzes the reduction of N2 and protons to yield two NH3 and one H2. Substrate binding occurs at a complex organo-metallocluster called FeMo-cofactor (FeMo-co). Each catalytic cycle involves the sequential delivery of eight electrons/protons to this cluster, and this process has been framed within a kinetic scheme developed by Lowe and Thorneley. Rapid freezing of a modified nitrogenase under turnover conditions using diazene, methyldiazene (HN = N-CH3), or hydrazine as substrate recently was shown to trap a common intermediate, designated I. It was further concluded that the two N-atoms of N2 are hydrogenated alternately (“Alternating” (A) pathway). In the present work, Q-band CW EPR and 95Mo ESEEM spectroscopy reveal such samples also contain a common intermediate with FeMo-co in an integer-spin state having a ground-state “non-Kramers” doublet. This species, designated H, has been characterized by ESEEM spectroscopy using a combination of 14,15N isotopologs plus 1,2H isotopologs of methyldiazene. It is concluded that: H has NH2 bound to FeMo-co and corresponds to the penultimate intermediate of N2 hydrogenation, the state formed after the accumulation of seven electrons/protons and the release of the first NH3; I corresponds to the final intermediate in N2 reduction, the state formed after accumulation of eight electrons/protons, with NH3 still bound to FeMo-co prior to release and regeneration of resting-state FeMo-co. A proposed unification of the Lowe-Thorneley kinetic model with the “prompt” alternating reaction pathway represents a draft mechanism for N2 reduction by nitrogenase.

Lukoyanov, Dmitriy; Yang, Zhi-Yong; Barney, Brett M.; Dean, Dennis R.; Seefeldt, Lance C.; Hoffman, Brian M.

2012-01-01

409

Unification of reaction pathway and kinetic scheme for N2 reduction catalyzed by nitrogenase.  

PubMed

Nitrogenase catalyzes the reduction of N(2) and protons to yield two NH(3) and one H(2). Substrate binding occurs at a complex organo-metallocluster called FeMo-cofactor (FeMo-co). Each catalytic cycle involves the sequential delivery of eight electrons/protons to this cluster, and this process has been framed within a kinetic scheme developed by Lowe and Thorneley. Rapid freezing of a modified nitrogenase under turnover conditions using diazene, methyldiazene (HN = N-CH(3)), or hydrazine as substrate recently was shown to trap a common S = ½ intermediate, designated I. It was further concluded that the two N-atoms of N(2) are hydrogenated alternately ("Alternating" (A) pathway). In the present work, Q-band CW EPR and (95)Mo ESEEM spectroscopy reveal such samples also contain a common intermediate with FeMo-co in an integer-spin state having a ground-state "non-Kramers" doublet. This species, designated H, has been characterized by ESEEM spectroscopy using a combination of (14,15)N isotopologs plus (1,2)H isotopologs of methyldiazene. It is concluded that: H has NH(2) bound to FeMo-co and corresponds to the penultimate intermediate of N(2) hydrogenation, the state formed after the accumulation of seven electrons/protons and the release of the first NH(3); I corresponds to the final intermediate in N(2) reduction, the state formed after accumulation of eight electrons/protons, with NH(3) still bound to FeMo-co prior to release and regeneration of resting-state FeMo-co. A proposed unification of the Lowe-Thorneley kinetic model with the "prompt" alternating reaction pathway represents a draft mechanism for N(2) reduction by nitrogenase. PMID:22460797

Lukoyanov, Dmitriy; Yang, Zhi-Yong; Barney, Brett M; Dean, Dennis R; Seefeldt, Lance C; Hoffman, Brian M

2012-03-29

410

Real-time detection of dopamine released from a nerve model cell by an enzyme-catalyzed luminescence method and its application to drug assessment.  

PubMed

A real-time observation of neurotransmitter release from a nerve cell is a useful method for not only neuroscience research, but also assessing of the influence of chemicals, including drugs, on the human nervous system. In this study, a more simple and sensitive method for real-time monitoring of dopamine release from a nerve model cell was developed. Highly sensitive detection of dopamine was performed by using tyramine oxidase for dopamine oxidation, which was followed by a luminol luminescence reaction. This enzyme-catalyzed luminescence method was applied to observe dopamine release from the PC12 cell as a nerve model cell upon stimulation with acetylcholine and an acetylcholine receptor agonist. The results demonstrated that the real-time monitoring of the activation of the PC12 cell was easily performed by this method. This method possessed many advantages, such as high sensitivity, rapid measurement and no pretreatment for cells. It might be applied to drug screening and the assessment of harmful influences of food additives and pesticides on the nerves. PMID:17213629

Shinohara, Hiroaki; Wang, Feifei

2007-01-01

411

9-Mercaptodethiobiotin is Generated as a Ligand to the [2Fe-2S]+ Cluster During the Reaction Catalyzed by Biotin Synthase from Escherichia coli  

PubMed Central

Biotin synthase catalyzes formation of the thiophane ring through stepwise substitution of a sulfur atom for hydrogen atoms at the C9 and C6 positions of dethiobiotin. Biotin synthase is a Radical SAM enzyme that reductively cleaves S-adenosylmethionine, generating 5?-deoxyadenosyl radicals that initially abstract a hydrogen atom from the C9 position of dethiobiotin. We have proposed that the resulting dethiobiotinyl radical is quenched by the ?-sulfide of the nearby [2Fe-2S]2+ cluster, resulting in coupled formation of 9-mercaptodethiobiotin and a reduced [2Fe-2S]+ cluster. This reduced FeS cluster is observed by electron paramagnetic resonance spectroscopy as a mixture of two orthorhombic spin systems. In the present work, we use isotopically labeled 9-mercaptodethiobiotin and enzyme to probe the ligand environment of the [2Fe-2S]+ cluster in this reaction intermediate. HYSCORE spectra exhibit strong cross-peaks demonstrating strong isotropic coupling of the nuclear spin with the paramagnetic center. The hyperfine coupling constants are consistent with a structural model for the reaction intermediate in which 9-mercaptodethiobiotin is covalently coordinated to the remnant [2Fe-2S]+ cluster.

Fugate, Corey J.; Stich, Troy A.; Kim, Esther G.; Myers, William K.; Britt, R. David; Jarrett, Joseph T.

2012-01-01

412

9-Mercaptodethiobiotin is generated as a ligand to the [2Fe-2S]+ cluster during the reaction catalyzed by biotin synthase from Escherichia coli.  

PubMed

Biotin synthase catalyzes formation of the thiophane ring through stepwise substitution of a sulfur atom for hydrogen atoms at the C9 and C6 positions of dethiobiotin. Biotin synthase is a radical S-adenosylmethionine (SAM) enzyme that reductively cleaves S-adenosylmethionine, generating 5'-deoxyadenosyl radicals that initially abstract a hydrogen atom from the C9 position of dethiobiotin. We have proposed that the resulting dethiobiotinyl radical is quenched by the ?-sulfide of the nearby [2Fe-2S](2+) cluster, resulting in coupled formation of 9-mercaptodethiobiotin and a reduced [2Fe-2S](+) cluster. This reduced FeS cluster is observed by electron paramagnetic resonance spectroscopy as a mixture of two orthorhombic spin systems. In the present work, we use isotopically labeled 9-mercaptodethiobiotin and enzyme to probe the ligand environment of the [2Fe-2S](+) cluster in this reaction intermediate. Hyperfine sublevel correlation spectroscopy (HYSCORE) spectra exhibit strong cross-peaks demonstrating strong isotropic coupling of the nuclear spin with the paramagnetic center. The hyperfine coupling constants are consistent with a structural model for the reaction intermediate in which 9-mercaptodethiobiotin is covalently coordinated to the remnant [2Fe-2S](+) cluster. PMID:22607542

Fugate, Corey J; Stich, Troy A; Kim, Esther G; Myers, William K; Britt, R David; Jarrett, Joseph T

2012-05-29

413

Synthesis of Cocoa Butter Equivalent from Palm Oil by Carica papaya Lipase-Catalyzed Interesterification  

Microsoft Academic Search

Cocoa butter equivalent could be synthesized by lipase-catalyzed interesterification of oil. The objective of this research was to investigate the synthesis of cocoa butter equivalent from interesterification of palm oil catalyzed by Carica papaya lipase. The study showed that the compositions of cocoa butter equivalent were affected by acyl donor sources, substrate ratio, initial water of enzyme, reaction time, reaction

Porntippa Pinyaphong

2009-01-01

414

Evidence of kinetic control of ligand binding and staged product release in MurA (enolpyruvyl UDP-GlcNAc synthase)-catalyzed reactions .  

PubMed

MurA (enolpyruvyl UDP-GlcNAc synthase) catalyzes the first committed step in peptidoglycan biosynthesis. In this study, MurA-catalyzed breakdown of its tetrahedral intermediate (THI), with a k(cat)/K(M) of 520 M(-1) s(-1), was far slower than the normal reaction, and 3 x 10(5)-fold slower than the homologous enzyme, AroA, reacting with its THI. This provided kinetic evidence of slow binding and a conformationally constrained active site. The MurA cocrystal structure with UDP-N-acetylmuramic acid (UDP-MurNAc), a potent inhibitor, and phosphite revealed a new "staged" MurA conformation in which the Arg397 side chain tracked phosphite out of the catalytic site. The closed-to-staged transition involved breaking eight MurA.ligand ion pairs, and three intraprotein hydrogen bonds helping hold the active site loop closed. These were replaced with only two MurA.UDP-MurNAc ion pairs, two with phosphite, and seven new intraprotein ion pairs or hydrogen bonds. Cys115 appears to have an important role in forming the staged conformation. The staged conformation app