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Various Amino Acids (various + amino_acids)
Selected AbstractsModulation of activity and substrate specificity by modifying the backbone length of the distant interdomain loop of D-amino acid aminotransferaseFEBS JOURNAL, Issue 24 2000Aldo Gutierrez The activity and substrate specificity of d -amino acid aminotransferase ( d -AAT) (EC 2.6.1.21) can be rationally modulated by replacing the loop core (P119-R120-P121) with glycine chains of different lengths: 1, 3, or 5 glycines. The mutant enzymes were much more active than the wild-type enzyme in the overall reactions between various amino acids and pyruvate. The presteady-state kinetic analyses of half-reactions revealed that the 5-glycine mutant has the highest affinity (Kd) among all mutant enzymes and the wild-type enzyme towards various amino acids except d -aspartate. The 5-glycine mutant was much more efficient as a catalyst than the wild-type enzyme because the mutant enzyme showed the highest value of specificity constant (kmax/Kd) for all amino acids except d -aspartate and d -glutamate. The kmax/Kd values of the three mutants decreased with decrease in glycine chain length for each amino acid examined. Our findings may provide a new approach to rational modulation of enzymes. [source] Phylogenetic analysis of condensation domains in the nonribosomal peptide synthetasesFEMS MICROBIOLOGY LETTERS, Issue 1 2005Niran Roongsawang Abstract Condensation (C) domains in the nonribosomal peptide synthetases are capable of catalyzing peptide bond formation between two consecutively bound various amino acids. C-domains coincide in frequency with the number of peptide bonds in the product peptide. In this study, a phylogenetic approach was used to investigate structural diversity of bacterial C-domains. Phylogenetic trees show that the C-domains are clustered into three functional groups according to the types of substrate donor molecules. They are l -peptidyl donors, d -peptidyl donors, and N -acyl donors. The fact that C-domain structure is not subject to optical configuration of amino acid acceptor molecules supports an idea that the conversion from l to d -form of incorporating amino acid acceptor occurs during or after peptide bond formation. l -peptidyl donors and d -peptidyl donors are suggested to separate before separating the lineage of Gram-positive and Gram-negative bacteria in the evolution process. [source] Photoheterotrophy and light-dependent uptake of organic and organic nitrogenous compounds by Planktothrix rubescens under low irradianceFRESHWATER BIOLOGY, Issue 10 2003Tatiana Zotina Summary 1. Planktothrix rubescens is the dominant photoautotrophic organism in Lake Zürich, a prealpine, deep, mesotrophic freshwater lake with an oxic hypolimnion. Over long periods of the year, P. rubescens accumulates at the metalimnion and growth occurs in situ at irradiance near the photosynthesis compensation point. Experiments were conducted to evaluate the contribution of photoheterotrophy, heterotrophy and light-dependent uptake of nitrogenous organic compounds to the carbon and nitrogen budget of this cyanobacterium under conditions of restricted availability of light quanta. 2. We used both purified natural populations of P. rubescens from the depth of 9 m and an axenic culture grown under low irradiance at 11 ,mol m,2 s,1 on a light : dark cycle (10 : 14 h) to determine the uptake rates of various amino acids, urea, glucose, fructose, acetate and inorganic carbon. The components were added to artificial lake water in low amounts that simulated the naturally occurring potential concentrations. 3. The uptake rates of acetate and amino acids (glycine, serine, glutamate and aspartate) were strongly enhanced at low irradiance as compared with the dark. However, no difference was observed in the uptake of arginine, which was taken up at high rates under both treatments. The uptake rates of glucose, fructose and urea were very low under all conditions. Similar results were obtained for both axenic P. rubescens and for purified natural populations of P. rubescens that were separated from bacterioplankton and other phytoplankton. 4. Metalimnetic P. rubescens that was stratified at low irradiance for weeks exhibited much higher uptake rates than filaments that were entrained in the deepening surface mixed layer and experienced higher irradiance. The added organic compounds contributed up to 62% to the total carbon uptake of metalimnetic P. rubescens. On the basis of a molar C : N ratio of 4.9, the nitrogen uptake as organic compounds satisfied up to 84% of the nitrogen demand. 5. The experiments indicate that photoheterotrophy and light-dependent uptake of nitrogenous organic compounds may contribute significantly to the carbon and nitrogen budget of filaments at low irradiance typical for growth of P. rubescens in the metalimnion and at the bottom of the surface mixed layer. [source] Modified Cyclodextrins as Enantioselective Hosts for Amino AcidsHELVETICA CHIMICA ACTA, Issue 4 2008Pavan Kumar, Vydyula Abstract Two modified , -cyclodextrins, H-2 and H-3, having a flexible appended moiety were studied for the chiral discrimination of the enantiomers of various amino acids by means of fluorescence as signaling option. These hosts quenched the fluorescence intensities of amino acids upon binding. The d- enantiomers were better recognized by these hosts. The association constants (Ks) and enantioselectivity factors (,) of the host,guest complexes were calculated. [source] Off-line combination of reversed-phase liquid chromatography and laser desorption/ionization time-of-flight mass spectrometry with seamless post-source decay fragment ion analysis for characterization of square-planar nickel(II) complexesJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 4 2006Pavel, ehulka Abstract Characterization of square-planar nickel(II) complexes of the Schiff base of (S)- N -benzylproline (2-benzoylphenyl)amide and various amino acids that are used as efficient ,-amino acids synthons was carried out using laser desorption/ionization time-of-flight mass spectrometry (LDI-TOF MS) in off-line combination with liquid chromatography. A mixture of four square-planar nickel(II) complexes was separated using reversed-phase liquid chromatography (RPLC) and the separated fractions from the chromatographic run were spotted on the metal target directly from the column outlet using a lab-made sample deposition device. The separated fractions were then analyzed by LDI-TOF MS. Seamless postsource decay (sPSD) fragment ion analysis was used for their structural characterization, which made possible the confirmation of expected chemical structures of the analyzed compounds. The off-line combination of the separation by RPLC and analysis by LDI-TOF MS allowed successful separation, sensitive detection and structure elucidation of the square-planar nickel(II) complexes. Copyright © 2006 John Wiley & Sons, Ltd. [source] Differential interactions of plasmid DNA, RNA and genomic DNA with amino acid-based affinity matricesJOURNAL OF SEPARATION SCIENCE, JSS, Issue 17-18 2010Angela Sousa Abstract The development of a strategy to plasmid DNA (pDNA) purification has become necessary for the development of gene therapy and DNA vaccine production processes in recent years, since this nucleic acid and most of contaminants, such as RNA, genomic DNA and endotoxins, are negatively charged. An ideal separation methodology may be achieved with the use of affinity interactions between immobilized amino acids and nucleic acids. In this study, the binding behaviour of nucleic acids under the influence of different environmental conditions, such as the composition and ionic strength of elution buffer, and the temperature, is compared with various amino acids immobilized on chromatography resins. Supercoiled (sc) plasmid isoform was isolated with all matrices used, but in some cases preferential interactions with other nucleic acids were found. Particularly, lysine chromatography showed to be an ideal technology mainly on RNA purification using low salt concentration. On the other hand, arginine ligands have shown a greater ability to retain the sc isoform comparatively to the other nucleic acids retention, becoming this support more adequate to sc pDNA purification. The temperature variation, competitive elution and oligonucleotides affinity studies also allowed to recognize the dominant interactions inherent to biorecognition of pDNA molecule and the affinity matrices. [source] Functional analysis of the large periplasmic loop of the Escherichia coli K-12 WaaL O-antigen ligaseMOLECULAR MICROBIOLOGY, Issue 6 2008José M. Pérez Summary WaaL is a membrane enzyme implicated in ligating undecaprenyl-diphosphate (Und-PP)-linked O antigen to lipid A-core oligosaccharide. We determined the periplasmic location of a large (EL5) and small (EL4) adjacent loops in the Escherichia coli K-12 WaaL. Structural models of the EL5 from the K-12, R1 and R4 E. coli ligases were generated by molecular dynamics. Despite the poor amino acid sequence conservation among these proteins, the models afforded similar folds consisting of two pairs of almost perpendicular ,-helices. One ,-helix in each pair contributes a histidine and an arginine facing each other, which are highly conserved in WaaL homologues. Mutations in either residue rendered WaaL non-functional, since mutant proteins were unable to restore O antigen surface expression. Replacements of residues located away from the putative catalytic centre and non-conserved residues within the centre itself did not affect ligation. Furthermore, replacing a highly conserved arginine in EL4 with various amino acids inactivates WaaL function, but functionality reappears when the positive charge is restored by a replacement with lysine. These results lead us to propose that the conserved amino acids in the two adjacent periplasmic loops could interact with Und-PP, which is the common component in all WaaL substrates. [source] Dependence of Apparent Viscosity on Mycelial Morphology of Streptomyces fradiae Culture in Various Nitrogen SourcesBIOTECHNOLOGY PROGRESS, Issue 4 2000Du Bok Choi To examine what causes increased viscosity in culture broth in Streptomyces fradiae culture, various natural nitrogen sources were investigated. Extracellular protease activity increased with culture time and decomposed the natural nitrogen source into amino acids. In the case of gluten meal, after a culture time of 5 d, concentrations of glutamic acid and aspartic acid had increased to 600 and 200 mg/L, respectively, which were about 3- and 2-fold as high as levels in cultures under similar conditions using Pharmamedia. For various amino acids tested, the addition of glutamic acid or aspartic acid mixture to the culture medium raised the apparent viscosity to its highest demonstrated value, 260 mPa·s after 5 d of culture, which was 3-fold higher than without amino acids. Consumption of the decomposed glutamic acid and aspartic acid was dependent on the activities of glutamate dehydrogenase and aspartate aminotransferase, respectively. When ammonium ion was used as the nitrogen source, cell concentration reached 1.75 g/L measured as an intracellular nucleic acid concentration,which was about 2.3-fold higher than that with any other natural nitrogen source. However, apparent viscosity was only 75 mPa·s, a value one-third that of the amino acid mixture, and 70% of the pellets were bigger than 1.2 × 104 ,m2. In the case of gluten meal or the amino acid mixture, pellets bigger than 1.2 × 104 ,m2 comprised only 8%. This demonstrates that consumption of some amino acids affected the formation of filamentous morphology, which caused an increase in the apparent viscosity of the culture broth, and the apparent viscosity was not caused by the mycelial concentration but the mycelial morphology. [source] | |||||||||||||