PDBML: the representation of archival macromolecular structure data in XML

Summary: The Protein Data Bank (PDB) has recently released versionsof the PDB Exchange dictionary and the PDB archival data filesin XML format collectively named PDBML. The automated generationof these XML files is driven by the data dictionary infrastructurein use at the PDB. The correspondences between the PDB dictionaryand the XML schema metadata are described as well as the XMLrepresentations of PDB dictionaries and data files. Availability: The current software translated XML schema fileis located at http://deposit.pdb.org/pdbML/pdbx-v1.000.xsd,and on the PDB mmCIF resource page at http://deposit.pdb.org/mmcif/.PDBML files are stored on the PDB beta ftp site at ftp://beta.rcsb.org/pub/pdb/uniformity/data/XML Contact: jwest{at}rcsb.rutgers.edu     

Synthesis of a bioprobe for elucidation of target molecule of spongean anti-malarial peroxides

The reactants of an anti-malarial peroxide having a 6-carbomethoxymethyl-3-methoxy-1,2-dioxane moiety treated with FeSO4 were analyzed. For mechanistic study of the anti-malarial peroxide, two biotinylated probes to elucidate the target molecules were designed and synthesized. The two synthesized probes showed potent anti-malarial activity, and one of them was proved to form an irreversible binding with protein in a model experiment.     

Post-column enzyme reactors for chemiluminometric detection of glucose, 1,5-anhydroglucitol and 3-hydroxybutyrate in an anion-exchange chromatographic system

A liquid chromatographic system consisting of a co-immobilized 3-hydroxybutyrate dehydrogenase-NADH oxidase reactor and an immobilized pyranose oxidase reactor in series and a chemiluminometer was developed for the simultaneous determination of glucose, 1,5-anhydroglucitol and 3-hydroxybutyrate in plasma. The enzymes were immobilized on toresylated poly(vinyl alcohol) beads. Separation was achieved on a TSK gel SAX column (40×4 mm I.D.) with an eluent of 50 mM NaOH containing 30 mM sodium butyrate. The hydrogen peroxide produced was detected by measuring the chemiluminescence emitted on admixing with luminol and potassium hexacyanoferrate(III). The calibration curves were linear from 0.8 to 500 μM (7 ng−4 μg) for glucose, from 0.8 to 400 μM (7 ng−3 μg) for 1,5-anhydroglucitol and from 1 to 700 μM (5 ng−4 μg in a 50-μl injection) for 3-hydroxybutyrate. The sample throughput was four per hour. The reactors were stable for at least ten days.     

Optimum Culture Conditions for Production of Exfoliative Toxin by Staphylococcus hyicus

Optimum culture conditions for the production of exfoliative toxin by Staphylococcus hyicus (shET) were examined. High shET activity was obtained from the culture filtrate of HI and TY broth inoculated with S. hyicus. The pH in these two media ranged from 7 to 8.5 during bacterial culture, while the lowest pH in TS and BHI broth was less than 6. shET activity in the culture filtrate from TY broth inoculated with 10⁷ CFU of S. hyicus per ml was higher than that in TY broth inoculated with 10⁶ and 10⁸ CFU of bacteria per ml. When shET activity in the culture filtrate was measured under various shaking conditions, the culture filtrate shaken at 75 oscillations per min had the highest shET activity of the five shaking conditions. shET activity of the culture filtrate of TY broth to which protease inhibitor had been added was the same as that of TY broth without inhibitor. shET activity in a shaking culture in an Erlenmeyer flask was also the same as that in sac culture and that in shaking culture using a shaking (Sakaguchi) flask. shET activity in TY broth supplemented with 100 mM glucose was significantly lower than that in TY broth without glucose. Based on the above results, the optimum culture conditions for the production of shET were as follows: inoculation of 3 × 10⁹ CFU of S. hyicus strain P-1 into 300 ml of TY broth in a 2,000-ml Erlenmeyer flask, and incubation at 37 C with shaking at 75 oscillations per min. Then shET activity of the culture filtrate under appropriate culture conditions was measured after various incubation periods. shET activity was detected 6 hr after inoculation, reached the maximum (2⁵³ exfoliative unit/0.1 ml) at 16 hr and decreased between 20 and 48 hr. Thus, the optimum incubation period was determined to be 16 hr. Then the optimum concentration of ammonium sulfate for isolation of shET from the culture filtrate under appropriate culture conditions was examined. The greatest shET activity was obtained from the fraction salted out with 90% saturated ammonium sulfate. Thus, the optimum concentration of ammonium sulfate for the isolation of shET was determined to be 90% saturation.