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31.
Ruth Nussinov Akinori Sarai Gary W. Smythers David Wang Robert L. Jernigan 《Journal of biomolecular structure & dynamics》2013,31(3):707-722
Abstract Previous studies of the dinucleotides flanking both the 5′ and 3′ ends of homooligomer tracts have shown that some flanks are consistently preferred over others (1,2). In the first preferred group, the homooligomer tracts are flanked by the same nucleotide and/or the complementary nucleotides, e.g., ATAn, TTAn, CCGn, where n=2–5. Runs flanked by nucleotides with which they cannot base pair are distinctly disfavored. (In this group A/Tn are flanked by C and/or G; Gn/Cn are flanked by A/T, e.g., CGAn, TnGG, G., AT). The frequencies of runs flanked by AorT, and G or C (“mixed” group) are as expected. Here we seek the origin of this effect and its relevance to protein-DNA interactions. Surprisingly, within the first group, runs flanked by their complements with a pyrimidine-purine junction (e.g., TTAn, CnGG) are greatly preferred. The frequencies of their purine-pyrimidine junction mirror-images is just as expected. This effect, as well as additional ones enumerated below, is seen universally in eukaryotes and in prokaryotes, although it is stronger in the former. Detailed analysis of regulatory regions shows these strong trends, particularly in GC sequences. The potential relationship to DNA conformation and DNA-protein interaction is discussed. 相似文献
32.
Robert L. Jernigan Akinori Sarai Bruce Shapiro Ruth Nussinov 《Journal of biomolecular structure & dynamics》2013,31(4):561-567
Abstract We propose some specific DNA conformations that explain, in terms of molecular conformations, the anomalous gel electrophoretic behavior of the sequences (VA4T4X)1, and (V2A3X2)1 where V and X are either G or C. Previously (J. Biomole. Struct. Dyn. 4, 41, 1986) we considered hydrophobic interactions a mong aliphatic hydrocarbon groups in A/T sequences. In the sequences (T)n · (A)n, the T's are slightly bent to yield structures with tightly stacked methyl groups along one side of the major groove. By folding together the two pairs of stacked methyls on the opposite sides of the major groove, TTAA might yield a relatively sharp bend. On this basis, we show below that the sequences (VT4A4X)1 might form a very tightly coiled super-helix whereas the sequences (VA4T4X)1 form a broad super-helix of radius ~ 120 A for i = 25. The sequence (V2A3T3X2)1 forms a slightly smaller radius super-helix. The time of passage through the gel has been taken to be inversely proportional to the smallesuiimension of the molecule. Specifically we are taking the ratio of the apparent molecular weight to the actual molecular weight to be related to the moment of inertia I1 about the smallest principal axis of the molecular conformation. We find a good fit to the experimental gel mobility data of Hagerman (2) if we assume this ratio to be proportional to (I1)1/5. 相似文献
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Shogo Matsumoto Akira Isogai Akinori Suzuki 《Bioscience, biotechnology, and biochemistry》2013,77(9):2401-2403
Two types of glycerol dehydrogenase (GDH) were found on DEAE-cellulose column chromatography of cell-free extracts of methylotrophic yeasts. One type, designated as GDH I, showed only the reductive activity which was detected in the reaction system containing dihydroxyacetone and NADH, at pH 6.0. The other type, designated as GDH II, showed the oxidative activity which was detected in the system containing glycerol and NAD +, at pH 9.0, together with the reductive activity.Candida boidinii No. 2201, which possesses the phosphorylative pathway for glycerol dissimilation, had only GDH I when grown on glycerol or methanol as the carbon source. Hansenula ofunaensis, which has the oxidative pathway, had both GDH I and GDH II when grown on glycerol, but only GDH I when grown on methanol. Hansenula polymorpha Dl-1, which has both pathways, had both GDH I and GDH II when grown on glycerol or methanol. 相似文献
35.
Nobutaka Takahashi Akinori Suzuki Yasuo Kimura Satoshi Miyamoto Saburo Tamura Takashi Mitsui 《Bioscience, biotechnology, and biochemistry》2013,77(9):1115-1122
Piericidin B was isolated from mycellia of Streptomyces mobaraensis besides piericidin A. On the basis of IR, NMR and mass spectral studies together with chemical evidences, its structure was assigned as Id. Its physiological activities are also deescribd. 相似文献
36.
Hiromichi Nagasawa Akira Isogai Akinori Suzuki Saburo Tamura 《Bioscience, biotechnology, and biochemistry》2013,77(8):1759-1763
13C-NMR spectra of isoechinulins A, B and C, metabolites from Aspergillus ruber, were fully assigned on the basis of chemical shifts and multiplicities and comparison with their analogues. Taking advantage of the symmetrical structure of the diketopiperazine ring, the stereochemistry of the trisubstituted carbon-carbon double bond in a dehydrotryptophyl moiety was determined as Z (cis) by measuring the coupling constants, , in the proton nondecoupled spectrum of isoechinulin B. 相似文献
37.
Akinori Suzuki Hiroko Taguchi Saburo Tamura 《Bioscience, biotechnology, and biochemistry》2013,77(5):813-816
A multi-channel continuous-flow analyzer equipped with biosensing devices was developed for multi-component measurement and its use in automating routine analysis was evaluated.Biosensing was achieved by the aid of an immobilized enzyme reactor installed in the channel, and the channel switching process for the sensing of a different compound was made by using a column-switching rotary valve. Another rotary valve was used for auto-sampling. Both of the two rotary valves were interfaced to a system controller and work conjugatively in a programmed manner. Signal subtraction between different channels was found to be more precise compared with the multi-channel flow-injection analysis method, which is of merit for an analysis utilizing enzyme relay reaction (as for sucrose analysis) or for background signal subtraction. Glucose, lactate, and sucrose content in real samples were measured automatically with high reproducibility, and the results agree well with the kit method. 相似文献
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40.
Akira Isogai Akinori Suzuki Shizuo Higashikawa Shimpei Kuyama Saburo Tamura 《Bioscience, biotechnology, and biochemistry》2013,77(4):1023-1024
The structure of the xyloglucan synthesised in vitro by the particulate fraction of suspension-cultured soybean (Glycine max) cells from UDP-glucose and UDP-xylose is mainly composed of two kinds of oligosaccharide-building blocks, a heptasaccharide unit and a pentassaccharide unit [T. Hayashi and K. Matsuda, J. Biol Chem., 256, 11117 (1981)]. The synthesis of the pentasaccharide unit is probably the first step in the construction of oligosaccharide building blocks to elongate the ²-1,4-glucan backbone. This enzymatically synthesized xyloglucan was shown to have the same molecular size (Mw, 180,000) as the xyloglucan prepared from soybean cell walls by gel filtration on a Sepharose CL-6B column, and the same building blocks distributed among each fraction. A pulse-chase experiment indicated that the pentasaccharide unit was converted into the heptasaccharide unit. The conversion was regulated by the concentration of UDP-xylose. 相似文献