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Lysine acetylation sites prediction using an ensemble of support vector machine classifiers 总被引:1,自引:0,他引:1
Lysine acetylation is an essentially reversible and high regulated post-translational modification which regulates diverse protein properties. Experimental identification of acetylation sites is laborious and expensive. Hence, there is significant interest in the development of computational methods for reliable prediction of acetylation sites from amino acid sequences. In this paper we use an ensemble of support vector machine classifiers to perform this work. The experimentally determined acetylation lysine sites are extracted from Swiss-Prot database and scientific literatures. Experiment results show that an ensemble of support vector machine classifiers outperforms single support vector machine classifier and other computational methods such as PAIL and LysAcet on the problem of predicting acetylation lysine sites. The resulting method has been implemented in EnsemblePail, a web server for lysine acetylation sites prediction available at http://www.aporc.org/EnsemblePail/. 相似文献
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NAD+ had a biphasic effect on the NADH oxidase activity in electron transport particles from Mycobacterium phlei. The oxidase was inhibited competitively by NAD+ at concentrations above 0.05 mM. NAD+ in concentrations from 0.02 to 0.05 mM resulted in maximum stimulation of both NADH oxidation and oxygen uptake with concentrations of substrate both above and below the apparent K-M. Oxygen uptake and cyanide sensitivity indicated that the NAD+ stimulatory effect was linked to the terminal respiratory chain. The stimulatory effect was specific for NAD+. NAD+ was also specific in protecting the oxidase during heating at 50 degrees and against inactivation during storage at 0 degrees. NAD+ glycohydrolase did not affect stimulation nor heat protection of the NADH oxidase activity if the particles were previously preincubated with NAD+. Binding studies revealed that the particles bound approximately 3.6 pmol of [14C1NAD+ per mg of electron transport particle protein. Although bound NAD+ represented only a small fraction of the total added NAD+ necessary for maximal stimulation, removal of the apparently unbound NAD+ by Sephadex chromatography revealed that particles retained the stimulated state for at least 48 hours. Further addition of NAD+ to stimulated washed particles resulted in competitive inhibition of oxidase activity. Desensitization of the oxidase to the stimulatory effect of NAD+ was achieved by heating the particles at 50 degrees for 2 min without appreciable loss of enzymatic activity. Kinetic studies indicated that addition of NADH to electron transport particles prior to preincubation with NAD+ inhibited stimulation. In addition, NADH inhibited binding of [14C]NAD+. The utilization of artificial electron acceptors, which act as a shunt of the respiratory chain at or near the flavoprotein component, indicated that NAD+ acts as at the level of the NADH dehydrogenase at a site other than the catalytic one resulting in a conformational change which causes restoration as well as protection of oxidase activity. 相似文献
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Light-induced conversion of nicotinamide adenine dinucleotide to nicotinamide adenine dinucleotide phosphate in higher plant leaves 总被引:4,自引:1,他引:4
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Light-induced conversion of NAD to NADP was investigated in higher plants. Upon illumination, conversion of NAD to NADP was observed in intact leaves of wheat and pea following incubation in the dark. This conversion was also observed in mesophyll protoplasts of wheat leaves when they were isolated in the dark or isolated in light and then preincubated in the dark. Chloroplasts isolated from wheat protoplasts prepared in the dark carried out the conversion. The conversion in the mechanically isolated spinach chloroplasts was observed only when they were isolated in the dark from leaves preincubated in darkness. 相似文献
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Masuo Aizawa Robert W. Coughlin Marvin Charles 《Biochimica et Biophysica Acta (BBA)/General Subjects》1975,385(2):362-370
Reduced nicotinamide adenine dinucleotide (NADH) has been characterized electrochemically by solid electrode voltammetry and controlled potential electrolysis. Photometric and enzymatic assay showed that enzymatically active nicotinamide adenine dinucleotide (NAD+) could be regenerated electrolytically from its reduced form without the use of so-called electron mediators. Complete regeneration of enzymatically active NAD can be expected in pyrophosphate buffers and phosphate buffers during the electrolysis. Advantages of electrochemical regeneration of coenzymes are discussed, especially with regard to immobilization of enzymes. 相似文献
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J. B. Jackson 《Journal of bioenergetics and biomembranes》1991,23(5):715-741
H+-transhydrogenase couples the reversible transfer of hydride ion equivalents between NAD(H) and NADP(H) to the translocation of protons across a membrane. There are separate sites on the enzyme for the binding of NAD(H) and of NADP(H). There are some indications of the position of the binding sites in the primary sequence of the enzymes from mitochondria andEscherichia coli. Transfer of hydride ion equivalents only proceeds when a reduced and an oxidized nucleotide are simultaneously bound to the enzyme. When p=0 the rate of interconversion of the ternary complexes of enzyme and nucleotide substrates is probably limiting. An increase in p accelerates the rate of interconversion in the direction of NADH NADP+ until another kinetic component, possibly product release, becomes limiting. The available data are consistent with either direct or indirect mechanisms of energy coupling.Abbreviations DCCD
N N1-dicyclohexylcarbodiimide
- FSBA
51-[p-(fluorosulfonyl)benzoyl] adenosine
- FCCP
carbonylcyanide-p-fluoromethoxyphenylhydrazone
- H+-Thase
H+-transhydrogenase
- thio-NADP+
thionicotinamide adenine dinucleotide phosphate
- AcPdAd+
3-acetylpyridine adenine dinucleotide
- p
proton electrochemical gradient
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membane potential
- pH
pH difference across the membrane 相似文献
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Flagyl and reduced nicotinamide adenine dinucleotide 总被引:1,自引:0,他引:1
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Reduced nicotinamide adenine dinucleotide (NADH) has been characterized electrochemically by solid electrode voltammetry and controlled potential electrolysis. Photometric and enzymatic assay showed that enzymatically active nicotinamide adenine dinucleotide (NAD-+) could be regenerated electrolytically from its reduced form without the use of so-called electron mediators. Complete regeneration of enzymatically active NAD can be expected in pyrophosphate buffers and phosphate buffers during the electrolysis. Advantages of electrochemical regeneration of coenzymes are discussed, especially with regard to immobilization of enzymes. 相似文献
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Formation of reduced nicotinamide adenine dinucleotide peroxide 总被引:1,自引:0,他引:1
Incubation of NADH at neutral and slightly alkaline pH leads to the gradual absorption of 1 mol of H+. This uptake of acid requires oxygen and mainly yields anomerized NAD+ (NAD+), with only minimal formation od acid-modified NADH. The overall stoichiometry of the reaction is: NADH + H+ + 1/2O2 leads to H2O + NAD+, with NADH peroxide (HO2-NADH+) serving as the intermediate that anomerizes and breaks down to give NAD+ and H2O2. The final reaction reaction mixture contains less than 0.1% of the generated H2O2, which is nonenzymically reduced by NADH. The latter reaction is inhibited by catalase, leading to a decrease in the overall rate of acid absorption, and stimulated by peroxidase, leading to an increase in the overall rate of acid absorption. Although oxygen can attack NADH at either N-1 or C-5 of the dihydropyridine ring, the attack appears to occur primarily at N-1. This assignment is based on the inability of the C-5 peroxide to anomerize, whereas the N-1 peroxide, being a quaternary pyridinium compound, can anomerize via reversible dissociation of H2O2. The peroxidase-catalyzed oxidation of NADH by H2O2 does not lead to anomerization, indicating that anomerization occurs prior to the release of H2O2. Chromatography of reaction mixtures on Dowex 1 formate shows the presence of two major and several minor neutral and cationic degradation products. One of the major products is nicotinamide, which possibly arises from breakdown of nicotinamide-1-peroxide. The other products have not been identified, but may be derived from other isomeric nicotinamide peroxides. 相似文献
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Shiao-Chun Tu 《Archives of biochemistry and biophysics》1981,208(2):487-494
Both absorption and fluorescence properties of 3-amino pyridine adenine dinucleotide (AAD) were examined. The shape of the AAD fluorescence emission spectrum, maximal at 425 nm, remains unchanged over the pH range 2 to 11, indicating that there is only one detectable emitting species. AAD fluorescence increases as the pH decreases, with an apparent pKa of about 3.5. The absorption-pH profile indicates a pKa of about 3.3 for the ground state of AAD. Effects of organic solvents on AAD fluorescence are somewhat diverse. The low fluorescence quantum yield of 0.022 corresponds well with the short lifetime of 1.15 ns at 23 °C in neutral aqueous solution. The steady-state polarization of AAD in water and that at infinite viscosity were determined at 23 °C to be 0.037 and 0.083, respectively. Since a smaller value of polarization for either donor or acceptor leads to a better estimate of the orientation factor for dipole-dipole interaction, AAD appears to be particularly suitable for energy transfer studies. Similar to NADH, AAD also assumes a folded conformation in aqueous solution. This is evident from effects of temperature and hydrolysis by phosphodiesterase on absorption and/or fluorescence properties of AAD. Energy transfer from the adenine group to the 3-aminopyridine ring has been detected to occur in aqueous solution at 23 °C with an efficiency of about 0.12, corresponding to a distance of 7.5 Å between these two ring moieties. 相似文献
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The binding of NADH to bull semen NAD nucleosidase was observed to be accompanied by a considerable enhancement of the fluorescence of NADH. The fluorescence enhancement observed in the binding of NADH to the enzyme was utilized to study the stoichiometry of binding of this compound to the enzyme. Results obtained from the fluorescence titration of the enzyme with NADH indicated the binding of one mole of NADH per mole of enzyme (36,000 g). The dissociation constant for the enzyme-NADH complex was determined to be 2.52 × 10?6m. NADH was also found to be a very effective competitive inhibitor of the NADase-catalyzed hydrolysis of NAD, and the inhibitor dissociation constant (KI) for the enzyme-NADH complex was determined to be 2.99 × 10?6m which was in good agreement with the value obtained from the fluorescence titration experiments. 相似文献
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Gel-permeation chromatography and ultrafiltration have been used to study the free and bound forms of NAD in crude extracts prepared from rabbit muscle. Both techniques indicate that over 80% of the endogenous NAD is free.Nicotinamide inhibits the destruction of NAD in muscle homogenates (50% inhibition at 1.6 mm nicotinamide). In the absence of nicotinamide, there is a rapid destruction of free NAD, but a more gradual destruction of bound NAD. The latter result confirms earlier findings that bound NAD is protected from the hydrolytic action of NADase. However, this protection is unlikely to constitute an important mechanism for controlling NADase activity in muscle homogenates because such a small proportion of the endogenous NAD is bound.In the absence of nicotinamide, NAD also disappears rapidly from minced muscle. Interestingly, the NAD/NADH ratio remains constant (NAD/NADH = 18.1–18.5) during the disappearance of NAD in minced muscle. Upon homogenization of the mince, the NAD/NADH ratio abruptly decreases, then slowly increases during subsequent incubation. The latter rise in NAD/NADH ratio appears to be independent of absolute changes in NAD concentration brought about by the action of NADase or the addition of exogenous NAD. 相似文献
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M H Van Woert 《Life sciences》1967,6(24):2605-2612