Transesterification of an RNA model in buffer solutions in H2O and D2O

Transesterification of a phosphodiester bond of RNA models has been studied in various buffer solutions, under neutral and slightly alkaline conditions in H₂O and D₂O. The results show that imidazole is the only buffer system where a clear buffer catalysis on the cleavage of a phosphodiester bond is observed. The rate enhancement in sulphonic acid buffers is smaller, and a sulphonate base, particularly, is inactive as a catalyst. The rate‐enhancing effect of imidazole is, however, catalytic, and the catalytic inactivity of sulphonate buffers can be attributed to their structure and/or charge. The catalysis by imidazole is a complex system which, in addition to first‐order reactions, involves a process that shows a second‐order dependence in imidazole concentration. The latter reaction becomes significant in acidic imidazole buffers (pH < pK_a), as the buffer concentration increases. The kinetic solvent deuterium isotope effect k_H/k_D, referring to first‐order catalysis by imidazole base, is 2.3 ± 0.3. That referring to second‐order catalysis is most probably much larger, but an accurate value could not be obtained. Copyright © 2007 John Wiley & Sons, Ltd.     

Crystallization of Arthrobacter sp. strain 1C N-(1-D-carboxyethyl)-L-norvaline dehydrogenase and its complex with NAD+

The novel NAD+-linked opine dehydrogenase from a soil isolate Arthrobacter sp. strain 1C belongs to an enzyme superfamily whose members exhibit quite diverse substrate specificites. Crystals of this opine dehydrogenase, obtained in the presence or absence of co-factor and substrates, have been shown to diffract to beyond 1.8 ? resolution. X-ray precession photographs have established that the crystals belong to space group P21212, with cell parameters a = 104.9, b = 80.0, c = 45.5 ? and a single subunit in the asymmetric unit. The elucidation of the three-dimensional structure of this enzyme will provide a structural framework for this novel class of dehydrogenases to enable a comparison to be made with other enzyme families and also as the basis for mutagenesis experiments directed towards the production of natural and synthetic opine-type compounds containing two chiral centres.     

Production of recombinant bleaching enzymes from thermophilic microorganisms in fungal hosts

Cost-effective production of enzymes for industrial processes makes the appropriate selection of the host-vector expression system critical. We have developed two systems for the bulk production of bleaching enzymes from thermophiles. Kluyveromyces lactis has been developed as a secretion host employing expression vectors based on the 2μ-like plasmid pKD1 of Kluyveromyces drosophilarium. Our second system involves the filamentous fungus Trichoderma reesei. Fusion and nonfusion vectors have been constructed using the strong cellobiohydrolase 1 (cbh1) promoter. The KEX2 protease cleavage site and a 6 × HIS-tag have been incorporated to facilitate both cleavage and purification of the mature foreign proteins.     

Analysis of similarity of electrophoretic patterns in mRNA differential display

We present a novel method of statistical analysis for the comparison of electrophoretic data. The method is based on the squared Euclidian distance of normalized signal data vectors of electrophoretic lanes. The differences in the electrophoretic patterns are evaluated by a statistical test based on Hubert's statistics which measures the significance of the signal grouping. We demonstrate the validity and applicability of the method in a large data set derived from automated fluorescent mRNA differential display analysis of the expression of acute-phase proteins during experimental Escherichia coli infection in mice. The current testing method is capable of finding theoretically similar natural groupings to be similar in a statistically significant way whereas theoretically dissimilar or random groupings can be recognized to be artifactual. We also show how the calculated pairwise signal distances can be utilized in methodological problem solving. These analytical methods can be applied to the study of other related problems of similarity analysis of electrophoretic patterns, and also provide useful tools for the development of automated recognition of differentially expressed mRNAs.     

Antibacterial activity of methylated chitosan and chitooligomer derivatives: Synthesis and structure activity relationships

The purpose of this study was to synthesize series of methylated chitosaccharide derivatives, possessing various degree of methylation, and to determine their structure activity relationship (SAR) with regard to their antibacterial effect against Staphylococcus aureus. Chitosan polymer and chitooligomers were used as starting materials and were methylated by reaction with methyl iodide. Depending on the reaction conditions the degree of N-quaternization ranged from 0% to 74%, with varying degree of N,N-dimethylation, N-monomethylation and O-methylation. More selective N-quaternization could be obtained with protection group strategy. At pH 5.5 the chitosaccharide polymers and their methylated derivatives were active against S. aureus with minimal inhibitory concentration (MIC) ranging from 16 to 512 μg/mL. At pH 7.2 the non-quaternized derivatives were inactive but their highly N-quaternized derivatives showed MIC as low as 8 μg/mL. The chitooligomers, as well as their derivatives, were inactive at both pH’s. The SAR studies revealed that N-quaternization was mainly responsible for the antibacterial effects at pH 7.2, whereas it did not contribute to the antibacterial activity under acidic conditions.     

The identification of vicinally substituted cyclohexane isomers in their mixtures by 1H and 13C NMR spectroscopy

The radical addition reactions of organobromine compounds, XBr (X = CH2COOMe, PhCH2, CHBr2 and CCl3) with cyclohexene afforded mixtures of cis/trans isomer pairs of 1-X-2-Br-cyclohexanes. In addition to benzyl benzoyloxy derivatives are formed also, when benzoyl peroxide is used as an initiator. Owing to the great difficulties in separating these cis/trans isomer pairs, they are identified directly in their mixtures by NMR spectroscopy. In addition to one-dimensional (ID) 1H, proton decoupled 13C and DEPT-135, also two-dimensional (2D) 13C-13C INADEQUATE as well as 1H-13C HMQC experiments have been used in assigning the signals of each compound in their mixtures. The identification of each isomer was based on comparison of experimental 3J(H,H) coupling constants with theoretical ones based on the well-known Karplus type relationship. The more stable conformation for each isomer was estimated using the semiempirical AM1 molecular orbital method. The calculations support the isomer pair elucidations.