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A series of para-substituted phenylethylamine analogues bound to the enzyme aromatic amine dehydrogenase have been simulated using quantum mechanical electronic structure calculations and molecular mechanical molecular dynamics simulations. Trends have been verified connecting bond dissociation energy (and thus driving force) to observed rate constants and activation enthalpy. Trends have been identified in connecting statistics drawn from molecular dynamics simulations and the temperature dependence of the kinetic isotope effect, notably that as the temperature dependence of the kinetic isotope effect increases the flexibility of the promoting vibration decreases. This is explained as being more effected by thermal energy put into the system, and therefore more affected by temperature.

No tubo digestivo das larvas de Anastrepha fraterculus e Anastrepha pickeli há β-glicosidases capazes de clivar dissacarideos, β-glicosídeos tóxicos produzidos por plantas e substratos sintéticos. As β-glicosidases de A. fraterculus são pouco ativas e as de A. pickeli são bastante ativas sobre alguns compostos, entre eles linamarina, um glicosídeo cianogênico. Esse composto está presente, em altas concentrações, no fruto da mandioca do qual a larva se alimenta. A. fraterculus alimenta-se do fruto da goiaba e aparentemente consegue o carboidrato que necessita por ação de α-glicosidases, que são bem mais ativas do que as β. O fruto da mandioca não é tão nutritivo e A. pickeli deve aproveitar a glicose da linamarina para obter energia e consegue desintoxicar-se do aglicone tóxico. Rhynchosciara americana apresenta quatro β-glicosidases nas membranas microvilares intestinais, sendo três delas β-galactosidases. Dessas, duas são ativadas por Triton X-100 sendo que a glicosidase, de maior mobilidade eletroforética é ativada por este composto, com uma Ka de 4µM, um α de 0,5 e um β de 2. β-tioglicosidases foram demonstradas em afideos. Nós verificamos que ocorre a clivagem do tioglicosídeo sinigrina após separação das β-glicosidases digestivas do Lepidoptera Diatraea saccharalis por cromatografia hidrofóbica. Nesse inseto, a mesma enzima é capaz de clivar O- e S-glicosídeos com atividades semelhantes. Enzimas com essas características nunca foram descritas anteriormente. Esses experimentos ilustram a viabilidade das adaptações dos insetos na utilização de compostos formados for ligações β-glicosídicas, viabilizando a exploração de nutrientes normalmente inacessíveis a outros animais. / Anastrepha fraterculus and Anastrepha pickeli have in their midguts 13-glycosidases able to hydrolase dissaccharides, synthetic substrate and plant toxic β-glucosides. β-glycosidases from A. fraterculus have low activity and the enzymes from A. pickeli may be highly active depending on the substrate used. Linamarin, a cyanogenic β-glucoside present in A. pickeli food (Manihot fruit) is easly hydrolysed by A. pickeli β-glycosidases (A. fraterculus eats on guava fruits and may obtain carbohydrate through the action of α-glycosidases, that are much more active them the β-glycosidases). A. pickeli probably uses glucose derived from linamarinan avoiding the effects of the toxic aglycon. Rhynchosciara americana has 4 β-glycosidases (3 galactosidases and I glucosidase) in their intestinal microvilar membranes. Two of these enzymes are activated by Triton X-100. In β glucosidase the activation has Ka= 4µM, α=0,5 e β=2. β-thioglycosidases occur in Aphids. One digestive β-glucosidase from Diatraea saccharalis resolved by hydrofobic chrornatography hydrolyses sinigrin. The same enzyme may hydrolyse O- and S-glucosides with the same efficienly. Enzymes with this specificity have never been described before. In this study we shown some adaptations of insects to use substrates with β-glycosidic bonds, allowing these organisrns to explore nutrients usualy avoided by other animals.

Spiders and scorpions are efficient predators arachnid (PA) consuming preys larger than themselves. Few studies reported, molecularly, the digestion in PA. This work describes a biochemical, transcriptomic and proteomic analysis of the midgut and midgut glands (MMG) and digestive juice (DJ) from Nephilengys cruentata and Tityus serrulatus MMG. Cathepsin L, B, D and F, legumain, trypsin, astacin, carbohydrases and lipases were identified by these approaches. Peptide isomerase and ctenitoxins, which are venom proteins were identified, showing a correlation among digestive and venom enzymes. Summarily, PA relies in multi peptidase system mainly constituted of astacins for extracellular prey liquefaction and cathepsin L for intracellular digestion, describing a molecular model for digestion. Probably, during evolution, gene duplication led a diversification of astacins in the derived groups of Arachnida, like spiders, distinctly from what is observed in basal groups like scorpions. These data on Arachnida digestion will allow detailed multi disciplinary studies. / Aranhas e escorpiões são aracnídeos predadores eficientes (AP) consumindo presas maiores que eles mesmos. Poucos estudos descrevem molecularmente a digestão em AP. Neste trabalho caracterizamos bioquimicamente, por transcriptoma e proteoma o intestino e glândulas digestivas (IGD) e suco digestivo (SD) de Nephilengys cruentata e o IGD de Tityus serrulatus. Catepsinas L, B, D e F, legumaína, tripsinas, astacinas, carboidrases e lipases foram identificadas. Peptídeo isomerase e ctenitoxina foram identificadas no IGD. Estas proteínas podem indicar uma correlação entre enzimas digestivas e do veneno. Portanto, AP apresentam várias peptidases principalmente astacinas para liquefazer a presa extraoralmente e catepsinas L para digestão intracelular, descrevendo um modelo molecular para a digestão. Provavelmente, durante a evolução, eventos duplicação gênica levaram à diversificação das astacinas aracnídeos derivados, como as aranhas, diferentemente dos grupos basais, como os escorpiões. Estes dados sobre a digestão em Arachnida permitirão estudos multidisciplinares.

The nucleotide 2'-deoxythymidine 5'-monophosphate (thymidylate, dTMP) is phosphorylated twice to become a substrate for DNA polymerases, which copy a cell’s genetic information in advance of cell division. The main route to dTMP is mediated by the enzyme thymidylate synthase (TSase) and goes through 2'-deoxyuridine 5'-monophosphate (dUMP); dUMP’s heterocyclic aromatic pyrimidine ring loses a proton from its C5 position and gains a methylene and a hydride from the other reactant, methylene tetrahydrofolate (MTHF). In general, intricate knowledge of an enzyme’s mechanism can yield insight that leads to the development of precision-targeted inhibitors tailored exactly to thymidylate synthase. In fact, even more careful targeting could be achievable: Although E. coli TSase has served as a model system, investigators have increasingly been directing their lines of inquiry toward human TSase. A general enzymatic catalytic cascade is complex, comprising substrate binding, the chemical steps and product release; typically, the product release step is rate-limiting. TSase, however, is partially rate-limited by the chemistry portion of the process. The enzymatic mechanism has been considered for decades, yet recently has undergone a reassessment. After substrate binding – for which there is strong evidence for preference to dUMP as the first ligand in the wild-type E. coli enzyme – the important events are methylene transfer from MTHF to dUMP, proton abstraction and hydride transfer. The last of these – hydride transfer – is irreversible and rate-limiting (to a large degree without Mg2+, and to a small but noticeable degree with Mg2+). The studies described here are aimed at three therapeutically relevant questions: (a) determining the extent of negative charge accumulation at the O4 position of the hydride transfer acceptor; (b) expanding knowledge of the differential properties of E. coli and human TSase; and (c) gaining insight into the molecular origin of the drug resistance seen in a clinically relevant human TSase mutant. The properties touched on in this work include steady-state kinetics; inhibition constants toward 5-fluoro dUMP, substrate binding sequence and the temperature dependency of intrinsic hydride transfer kinetic isotope effects (KIEs). Intrinsic KIEs are a specialized measurement that permits the investigator to examine a particular hydrogen transfer step in isolation; it is achieved by labeling the bond to hydrogen broken in the reaction with protium (1H, also written as H), deuterium (2H, also written as D) or tritium (3H, also written as T). The latter is radioactive. The reaction is conducted with a mixture of two hydrogen isotopes at a time, and the extent to which the heavier isotope is disfavored against reaction is assessed; this covers multiple steps. Heavier isotopes directly participating in a chemical step react slower both because of zero-point vibrational energies if a semi-classical view is taken and because of the mass-dependence of tunneling probabilities if a quantum-mechanical view is taken. Each of the two-way isotopic comparisons mentioned above furnishes an observed KIE for that competition between two isotopes. Mathematical combination of two isotopic comparisons cancels out the effect of isotopically insensitive steps and provides rich insight into the hydride transfer alone. The ultimate result is the ratio of rate constants for the isotopologues; this ratio’s magnitude and variation with temperature report on the compactness of the active site and its resistance to thermal fluctuation, respectively. Our results reveal a possible role for E. coli asparagine 177 (N177) in the hydride transfer transition state (TS) stabilization, as revealed by its disruption in the aspartate mutant, N177D. This disruption was found to be alleviated to a high extent when the substrate was changed to dCMP, consistent with the N177 stabilizing partial negative charge at the TS for hydride transfer. This has drug design implications. Our work on human TSase underscores slightly weaker substrate binding preference, insensitivity to Mg2+ and mild alteration of hydride transfer TS when compared with E. coli TSase. Finally, analysis of the Y33H mutant of human TSase – the affected residue being remote from the active site – indicated the drug resistance was because of a higher inhibition constant for 5F-dUMP and that the hydride transfer step is disrupted, with a wider variation among donor-acceptor distances (between the two carbons involved in the hydride transfer at the TS for that step). Other researchers’ crystallographic evidence reveals greater positional uncertainty for a set of active-site side chains in the E. coli equivalent mutant. In totality, the data available implicate enzyme motions as relevant to drug binding and to catalysis for human TSase. In summary, the research described herein enriches the understanding of several aspects of the behavior of multiple TSase variants – the overall performance as seen via steady-state kinetics; the pattern of substrate binding as seen with observed KIEs for the proton abstraction step; and the efficiency of active site preparation for hydride transfer as evidenced in the temperature dependency of intrinsic hydride transfer KIEs.

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No description available.

Flavonoid glycosides are required for a number of crucial roles in planta and have the potential for development in a variety of agricultural, medicinal, and biotechnological applications. A number of recent advancements have been made in characterizing glycosyltransferases, the enzymes that are responsible for the synthesis of these important molecules. In this review, glycosyltransferases are considered with regard to biochemical properties, expression patterns, levels of enzyme activity during development, and structure/function relationships. This is presented with historical context to highlight critical findings, particularly with regard to the innovative work that has come from research on citrus species. The plant glycosyltransferase crystal structures that have been solved over the past decade, either alone or in complex with sugar donor and/or acceptor molecules, are discussed. The application of results from these structures to inform current structure/function work as well as implications and goals for future crystallography and tertiary modeling studies are considered. A thorough understanding of the properties of glycosyltransferases will be a critical step in any future biotechnological application of these enzymes in areas such as crop improvement and custom design of enzymes to produce desired compounds for nutritional and/or medicinal usage.

Glucosylation is a predominant flavonoid modification reaction affecting the solubility, stability, and subsequent bioavailability of these metabolites. Flavonoid glycosides affect taste characteristics in citrus making the associated glucosyltransferases particularly interesting targets for biotechnology applications in these species. In this work, a Citrus paradisi glucosyltransferase gene was identified, cloned, and introduced into the pET recombinant protein expression system utilizing primers designed against a predicted flavonoid glucosyltransferase gene (AY519364) from Citrus sinensis. The encoded C. paradisi protein is 51.2 kDa with a predicted pI of 6.27 and is 96% identical to the C. sinensis homologue. A number of compounds from various flavonoid subclasses were tested, and the enzyme glucosylated only the flavonol aglycones quercetin (Kmapp = 67 μ M; Vmax = 20.45 pKat/μg), kaempferol (Kmapp = 12 μ M; Vmax = 11.63 pKat/μg), and myricetin (Kmapp = 33 μ M; Vmax = 12.21 pKat/μg) but did not glucosylate the anthocyanidin, cyanidin. Glucosylation occurred at the 3 hydroxyl position as confirmed by HPLC and TLC analyses with certified reference compounds. The optimum pH was 7.5 with a pronounced buffer effect noted for reactions performed in Tris-HCl buffer. The enzyme was inhibited by Cu2+, Fe2+, and Zn2+ as well as UDP (Kiapp = 69.5 μ M), which is a product of the reaction. Treatment of the enzyme with a variety of amino acid modifying compounds suggests that cysteine, histidine, arginine, tryptophan, and tyrosine residues are important for activity. The thorough characterization of this C. paradisi flavonol 3-O-glucosyltransferase adds to the growing base of glucosyltransferase knowledge, and will be used to further investigate structure-function relationships.

Les glycosaminoglycanes (GAGs) sont des polymères de sucres linéaires, présents chez tous les animaux. Certaines bactéries pathogènes synthétisent également des polysaccharides identiques ou très similaires aux GAGs humains. Cette thèse a porté en particulier sur la synthèse de la chondroïtine sulfate et de l’héparosan qui font partie de cette famille de polysaccharides. L’intérêt pour ces deux GAGs est grandissant dans l’industrie pharmaceutique du fait des nombreuses applications médicales qu’ils pourraient permettre. La chondroïtine sulfate est d’ores et déjà extraite de tissus animaux ce qui peut engendrer des problèmes sanitaires, notamment des contaminations virales ou aux prions. En revanche, le procédé de production pour l’héparosan reste à mettre en place. Il est donc nécessaire de développer des procédés de production pour ces deux molécules. La synthèse enzymatique est une voie particulièrement prometteuse pour la production de la chondroïtine sulfate et de l’héparosan, et a fait l’objet de ce travail de thèse. / Glycosaminoglycans (GAGs) are long linear polysaccharide chains, found in all animals. Some pathogenic bacteria also synthesize polysaccharides identical or similar to human GAGs. This thesis deals with chondroitin sulfate and heparosan syntheses, members of the GAGs family. There is a growing interest in these two GAGs in the pharmaceutical industry due to numerous potential applications they offer. Chondroitin sulfate is currently extracted from animal tissues which can lead to sanitary problems such as viral or prion contaminations. On the other hand, a production process still needs to be developed for heparosan. Therefore, it is necessary to develop new methods for the production of these two polymers. Enzymatic synthesis, which is a promising alternative for the production of chondroitin sulfate and heparosan, was the subject of this thesis.