SciCombinator

Discover the most talked about and latest scientific content & concepts.

Concept: Product

163

The specificity for the α-1,4- and α-1,6-glucosidic linkages varies among glycoside hydrolase family 31 α-glucosidases. This difference in substrate specificity has been considered to be due to the difference in an aromatic residue on β→α loop 1 in the catalytic domain with a (β/α)8 barrel fold; i.e., the enzymes having Tyr and Trp on β→α loop 1 were respectively described as α-1,4-specific and α-1,6-specific α-glucosidases. Schwanniomyces occidentalis α-glucosidase, however, prefers the α-1,4-glucosidic linkage, although the enzyme possesses Trp324 at the corresponding position. The mutation of Trp324 to Tyr decreased the ability for hydrolysis of the α-1,6-glucosidic linkage and formation of the α-1,6-glucosidic linkage in transglycosylation, indicating Trp324 to be closely associated with α-1,6 specificity, even if the enzyme preferred the α-1,4-glucosidic linkage. The mutant enzyme was found to catalyze the production of the branched oligosaccharide, 2,4-di-O-(α-D-glucopyranosyl)-D-glucopyranose, more efficiently than the wild-type enzyme.

Concepts: Protein, Metabolism, Enzyme, Enzyme substrate, Product, Catalysis, Ribozyme, Hydrolysis

106

E-cigarettes are largely unregulated and internet sales are substantial. This study examines how the online market for e-cigarettes has changed over time: in product design and in marketing messages appearing on websites.

Concepts: Product, Marketing, Graphic design

45

Reaction prediction remains one of the major challenges for organic chemistry and is a prerequisite for efficient synthetic planning. It is desirable to develop algorithms that, like humans, “learn” from being exposed to examples of the application of the rules of organic chemistry. We explore the use of neural networks for predicting reaction types, using a new reaction fingerprinting method. We combine this predictor with SMARTS transformations to build a system which, given a set of reagents and reactants, predicts the likely products. We test this method on problems from a popular organic chemistry textbook.

Concepts: Product, Chemical reaction, Chemistry, Organic reaction, Biochemistry, Sodium, Organic chemistry, Forecasting

28

A highly diastereoselective (d.r. >99:1) and enantioselective (ee value up to 96 %) synthesis of trisubstituted cyclohexanols was achieved by using a one-pot sequential organocatalysis that involved a quinidine thiourea-catalyzed tandem Henry-Michael reaction between nitromethane and 7-oxo-hept-5-en-1-als followed by a tetramethyl guanidine (TMG)-catalyzed tandem retro-Henry-Henry reaction on the reaction products of the tandem Henry-Michael reaction. Through a mechanistic study, it has also been demonstrated that similar results may also be achieved with this one-pot sequential organocatalysis by using the racemic Henry product as the substrate.

Concepts: Product, Chemical reaction, Stereochemistry, Chemical synthesis, Enantiomer, Aldol reaction, Racemic mixture, Chiral resolution

27

OTUB1 is a Lys48-specific deubiquitinating enzyme that forms a complex in vivo with E2 ubiquitin (Ub)-conjugating enzymes including UBC13 and UBCH5. OTUB1 binds E2~Ub thioester intermediates and prevents ubiquitin transfer, thereby noncatalytically inhibiting accumulation of polyubiquitin. We report here that a second role of OTUB1-E2 interactions is to stimulate OTUB1 cleavage of Lys48 polyubiquitin. This stimulation is regulated by the ratio of charged to uncharged E2 and by the concentration of Lys48-linked polyubiquitin and free ubiquitin. Structural and biochemical studies of human and worm OTUB1 and UBCH5B show that the E2 enzyme stimulates binding of the Lys48 polyubiquitin substrate by stabilizing folding of the OTUB1 N-terminal ubiquitin-binding helix. Our results suggest that OTUB1-E2 complexes in the cell are poised to regulate polyubiquitin chain elongation or degradation in response to changing levels of E2 charging and available free ubiquitin.

Concepts: Protein, Cell, Enzyme, Glucose, Enzyme substrate, Product, Chemical equilibrium, Ratio

27

LipPks1, a polyketide synthase subunit of the lipomycin synthase, is believed to catalyze polyketide chain initiation reaction using isobutyryl-CoA as a substrate, and elongate once with methylmalonyl-CoA to start the biosynthesis of antibiotic α-lipomycin in Streptomyces aureofaciens Tü117. Recombinant LipPks1, containing the thioesterase domain from the 6-deoxyerythronolide B synthase, was produced in Escherichia coli and its substrate specificity was investigated in vitro. Surprisingly, several different acyl-CoAs including isobutyryl-CoA were accepted as the starter substrates while no product was observed with acetyl-CoA. These results demonstrate the broad substrate specificity of LipPks1 and may be applied to producing new antibiotics.

Concepts: Bacteria, Enzyme, Enzyme substrate, Product, Antibiotic resistance, Catalysis, Escherichia coli, Antibiotic

27

Lactate dehydrogenase from the thermophilic organism Geobacillus stearothermophilus (formerly Bacillus stearothermophilus) (bsLDH) has a crucial role in producing chirally pure hydroxyl compounds. α-Hydroxy acids are used in many industrial situations, ranging from pharmaceutical to cosmetic dermatology products. One drawback of this enzyme is its limited substrate specificity. For instance, l-lactate dehydrogenase exhibits no detectable activity towards the large side chain of 2-hydroxy acid l-mandelic acid, an α-hydroxy acid with anti-bacterial activity. Despite many attempts to engineer bsLDH to accept α-hydroxy acid substrates, there have been no attempts to introduce the industrially important l-mandelic acid to bsLDH. Herein, we describe attempts to change the reactivity of bsLDH towards l-mandelic acid. Using the Insight II molecular modelling programme (except ‘program’ in computers) and protein engineering techniques, we have successfully introduced substantial mandelate dehydrogenase activity to the enzyme. Energy minimisation modelling studies suggested that two mutations, T246G and I240A, would allow the enzyme to utilise l-mandelic acid as a substrate. Genes encoding for the wild-type and mutant enzymes were constructed, and the resulting bsLDH proteins were overexpressed in Escherichia coli and purified using the TAGZyme system. Enzyme assays showed that insertion of this double mutation into highly purified bsLDH switched the substrate specificity from lactate to l-mandelic acid.

Concepts: Protein, Gene, Bacteria, Enzyme, Enzyme substrate, Product, Escherichia coli, Lactic acid

27

Commercial inulinase from Aspergillus niger was immobilized in montmorillonite and then treated in pressurized propane and liquefied petroleum gas (LPG). Firstly, the effects of system pressure, exposure time, and depressurization rate, using propane and LPG, on enzymatic activity were evaluated through central composite design 2(3). Residual activities of 145.1 and 148.5 % were observed for LPG (30 bar, 6 h, and depressurization rate of 20 bar min(-1)) and propane (270 bar, 1 h, and depressurization rate of 100 bar min(-1)), respectively. The catalysts treated at these conditions in both fluids were then used for the production of fructooligosaccharides (FOS) using sucrose and inulin as substrates in aqueous and organic systems. The main objective of this step was to evaluate the yield and productivity in FOS, using alternatives for enhancing enzyme activity by means of pressurized fluids and also using low-cost supports for enzyme immobilization, aiming at obtaining a stable biocatalyst to be used for synthesis reactions. Yields of 18 % were achieved using sucrose as substrate in aqueous medium, showing the potential of this procedure, hence suggesting a further optimization step to increase the process yield.

Concepts: Enzyme, Glucose, Enzyme substrate, Product, Catalysis, Enzymes, Immobilized enzyme, Liquefied petroleum gas

26

Human tyrosinase is the first enzyme of the multistep process of melanogenesis. It catalyzes the hydroxylation of L-tyrosine to L-dihydroxyphenylalanine and the following oxidation of o-diphenol to the corresponding quinone, L-dopaquinone. In spite of its biomedical relevance, its reactivity is far from being fully understood, mostly because of the lack of a suitable expression system. Indeed, until now, studies on substrates and inhibitors of tyrosinases have been performed in vitro almost exclusively using mushroom or bacterial enzymes. We report on the production of a recombinant human tyrosinase in insect cells (Sf9 line). Engineering the protein, improving cell culture conditions, and setting a suitable purification protocol optimized product yield. The obtained active enzyme was truthfully characterized with a number of substrate and inhibitor molecules. These results were compared to those gained from a parallel analysis of the bacterial (Streptomyces antibioticus) enzyme and those acquired from the literature for mushroom tyrosinase, showing that the reactivity of the human enzyme appears unique and pointing out the great bias introduced when using non-human tyrosinases to measure the inhibitory efficacy of new molecules. The described enzyme is therefore an indispensable paradigm in testing pharmaceutical or cosmetic agents addressing tyrosinase activity.

Concepts: DNA, Gene expression, Cell, Bacteria, Enzyme, Enzyme substrate, Product, Tyrosinase

26

Indoleamine 2,3-dioxygenase-2 (IDO2) is one of three enzymes (alongside tryptophan 2,3-dioxygenase and indoleamine 2,3-dioxygenase (IDO1)) that catalyse dioxygenation of L-tryptophan as the first step in the kynurenine pathway. Despite the reported expression of IDO2 in tumours, some fundamental characteristics of the enzyme, such as substrate specificity and inhibition selectivity, are still to be clearly defined. In this study, we report the kinetic and inhibition characteristics of recombinant human IDO2. Choosing from a series of likely IDO2 substrates, we screened 54 tryptophan derivatives and tryptophan-like molecules, and characterised the 8 with which the enzyme was most active. Specificity of IDO2 for the two isomers of 1-methyltryptophan was also evaluated and the findings compared with those obtained in other studies on IDO2 and IDO1. Interestingly, IDO2 demonstrates behaviour distinct from that of IDO1 in terms of substrate specificity and affinity, such that we have identified tryptophan derivatives that are mutually exclusive as substrates for IDO1 and IDO2. Our results support the idea that the antitumour activity of 1-Me-D-Trp is unlikely to be related with competitive inhibition of IDO2, and also imply that there are subtle differences in active site structure in the two enzymes that may be exploited in the development of specific inhibitors of these enzymes, a route which may prove important in defining their role(s) in cancer.

Concepts: Enzyme kinetics, Enzyme, Enzyme substrate, Product, Catalysis, Enzyme inhibitor, Tryptophan, Biomolecules