Structural insights into the mechanism defining substrate affinity in Arabidopsis thaliana dUTPase: the role of tryptophan 93 in ligand orientation

Background: Deoxyuridine triphosphate nucleotidohydrolase (dUTPase) hydrolyzes dUTP to dUMP and pyrophosphate to maintain the cellular thymine-uracil ratio. dUTPase is also a target for cancer chemotherapy. However, the mechanism defining its substrate affinity remains unclear. Sequence comparisons of various dUTPases revealed that Arabidopsis thaliana dUTPase has a unique tryptophan at position 93, which potentially contributes to its degree of substrate affinity. To better understand the roles of tryptophan 93, A. thaliana dUTPase was studied. Results: Enzyme assays showed that A. thaliana dUTPase belongs to a high-affinity group of isozymes, which also includes the enzymes from Escherichia coli and Mycobacterium tuberculosis. Enzymes from Homo sapiens and Saccharomyces cerevisiae are grouped as low-affinity dUTPases. The structure of the homo-trimeric A. thaliana dUTPase showed three active sites, each with a different set of ligand interactions between the amino acids and water molecules. On an α-helix, tryptophan 93 appears to keep serine 89 in place via a water molecule and to specifically direct the ligand. Upon being oriented in the active site, the C-terminal residues close the active site to promote the reaction. Conclusions: In the high-affinity group, the prefixed direction of the serine residues was oriented by a positively charged residue located four amino acids away, while low-affinity enzymes possess small hydrophobic residues at the corresponding sites

Thioacetalization of aldehydes and ketones catalyzed by hexabromoacetone

<p></p> <p>Protection of <i>p</i>-anisaldehyde with 1,3-propanedithiol under UV irradiation without a catalyst resulted in 87% yield of 1,3-dithiane in 20 min. Addition of hexabromoacetone further reduced the reaction time and UV irradiation also accelerated the formation of dithianes, yielding 95% of 1,3-dithiane in only 1 min. Aromatic aldehydes or ketones with electron-donating substituents at the <i>ortho</i> or <i>para</i> position increased the yield of the corresponding dithianes, while electron-withdrawing group decelerated the reaction. Aldehydes were easier to protect than ketones, and aliphatic ketones were also more readily protected than aromatic ketones. The protection was highly selective towards an aldehyde compared to a ketone.</p

Biotinyl-methyl 4-(amidomethyl)benzoate is a competitive inhibitor of human biotinidase

Posttranslational modification of histones by biotinylation can be catalyzed by both biotinidase (BTD) and holocarboxylase synthetase. Biotinylation of histones is an important epigenetic mechanism to regulate gene expression, DNA repair, and chromatin remodeling. The role of BTD in histone biotinylation is somewhat ambiguous, given that BTD also catalyzes removal of the biotin tag from histones. Here, we sought to develop BTD inhibitors for future studies of the role of BTD in altering chromatin structure. We adopted an existing colorimetric BTD assay for use in a novel 96-well plate format to permit high-throughput screening of potential inhibitors. Biotin analogs were chemically synthesized and tested for their ability to inhibit human BTD. Seven of these compounds inhibited BTD by 26–80%. Biotinyl-methyl 4-(amidomethyl)benzoate had the largest effect on BTD, causing an 80% inhibition at 1 mM concentration. Enzyme kinetics studies were conducted to determine Vmax, Km and Kifor the seven inhibitors; kinetics were consistent with the hypothesis that biotinyl-methyl 4-(amidomethyl)benzoate and the other compounds acted by competitive inhibition of BTD. Finally, biotinyl-methyl 4-(amidomethyl) benzoate did not affect biotin transport in human cells, suggesting specificity in regard to biotin-related processes

Gold Nanoparticles Supported on Alumina as a Catalyst for Surface Plasmon-Enhanced Selective Reductions of Nitrobenzene

Au nanoparticles supported on alumina (Au/Al₂O₃) with average particle size of 3.9 ± 0.7 nm and surface plasmon band centerned at 516.5 nm were prepared by deposition–precipitation method, and their photocatalytic activities for the reduction of nitrobenzene using either formic acid in acetonitrile (method A) or KOH in 2-propanol (method B) were investigated. Even at room temperature, the Au/Al₂O₃ was found to be highly active and selective for conversion of nitrobenzene to aniline when used with formic acid in acetonitrile or to azobenzene when performed with KOH in 2-propanol under irradiation with green light-emitting diode (517 nm)

Conversion of Bivalve Shells to Monocalcium and Tricalcium Phosphates: An Approach to Recycle Seafood Wastes

The search for sustainable resources remains a subject of global interest and the conversion of the abundantly available bivalve shell wastes to advanced materials is an intriguing method. By grinding, calcium carbonate (CaCO3) powder was obtained from each shell of bivalves (cockle, mussel, and oyster) as revealed by FTIR and XRD results. Each individual shell powder was reacted with H3PO4 and H2O to prepare Ca(H2PO4)2·H2O giving an anorthic crystal structure. The calcination of the mixture of each shell powder and its produced Ca(H2PO4)2·H2O, at 900 °C for 3 h, resulted in rhombohedral crystal β-Ca3(PO4)2 powder. The FTIR and XRD data of the CaCO3, Ca(H2PO4)2·H2O, and Ca3(PO4)2 prepared from each shell powder are quite similar, showing no impurities. The thermal behaviors of CaCO3 and Ca(H2PO4)2·H2O produced from each shell were slightly different. However, particle sizes and morphologies of the same products obtained from different shells were slightly different—but those are significantly different for the kind of the obtained products. Overall, the products (CaCO3, Ca(H2PO4)2·H2O, and Ca3(PO4)2) were obtained from the bivalve shell wastes by a rapidly simple, environmentally benign, and low-cost approach, which shows huge potential in many industries providing both economic and ecological benefits

Rhodium-catalyzed asymmetric hydrogenation using self-assembled chiral bidentate ligands

The chirality-directed self-assembly of bifunctional subunits around a structural metal-typically, zinc(II)-is used to form a heteroleptic complex in which a second set of ligating groups are suitably disposed to bind a second metal, forming a heterobimetallic catalyst system. We find that subtle changes in the structural backbone (i.e., ligand scaffold) of such chiral bidentate self-assembled ligands (SALs) can be used to manipulate the ligand topography and chiral environment around catalytic metal; thus, the scaffold can be optimized to maximize asymmetric induction. Using this combinatorial strategy for ligand synthesis, a preliminary study was carried out in which a library of 110 SALs was evaluated in the rhodium-catalyzed asymmetric hydrogenation of a simple N-acyl enamide. The level of enantioselectivity obtained varies from near racemic to greater than 80% ee as a function of the ligand scaffold, with the possibility of further improvement yet to be explored