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91.
Using information‐theoretic concepts, we examine the role of the reference state, a crucial component of empirical potential functions, in protein fold recognition. We derive an information‐based connection between the probability distribution functions of the reference state and those that characterize the decoy set used in threading. In examining commonly used contact reference states, we find that the quasi‐chemical approximation is informatically superior to other variant models designed to include characteristics of real protein chains, such as finite length and variable amino acid composition from protein to protein. We observe that in these variant models, the total divergence, the operative function that quantifies discrimination, decreases along with threading performance. We find that any amount of nativeness encoded in the reference state model does not significantly improve threading performance. A promising avenue for the development of better potentials is suggested by our information‐theoretic analysis of the action of contact potentials on individual protein sequences. Our results show that contact potentials perform better when the compositional properties of the data set used to derive the score function probabilities are similar to the properties of the sequence of interest. Results also suggest to use only sequences of similar composition in deriving contact potentials, to tailor the contact potential specifically for a test sequence. Proteins 2010. © 2009 Wiley‐Liss, Inc. 相似文献
92.
Verónica Irazusta Elia Obis Armando Moreno-Cermeño Elisa Cabiscol Joaquim Ros Jordi Tamarit 《Free radical biology & medicine》2010,48(3):411-420
Iron overload is involved in several pathological conditions, including Friedreich ataxia, a disease caused by decreased expression of the mitochondrial protein frataxin. In a previous study, we identified 14 proteins selectively oxidized in yeast cells lacking Yfh1, the yeast frataxin homolog. Most of these were magnesium-binding proteins. Decreased Mn-SOD activity, oxidative damage to CuZn-SOD, and increased levels of chelatable iron were also observed in this model. This study explores the relationship between low SOD activity, the presence of chelatable iron, and protein damage. We observed that addition of copper and manganese to the culture medium restored SOD activity and prevented both oxidative damage and inactivation of magnesium-binding proteins. This protection was compartment specific: recovery of mitochondrial enzymes required the addition of manganese, whereas cytosolic enzymes were recovered by adding copper. Copper treatment also decreased Δyfh1 sensitivity to menadione. Finally, a Δsod1 mutant showed high levels of chelatable iron and inactivation of magnesium-binding enzymes. These results suggest that reduced superoxide dismutase activity contributes to the toxic effects of iron overloading. This would also apply to pathologies involving iron accumulation. 相似文献
93.
Guozhi Tang Denis J. Kertesz Minmin Yang Xianfeng Lin Zhanguo Wang Wentao Li Zongxing Qiu Junli Chen Jianghua Mei Li Chen Taraneh Mirzadegan Seth F. Harris Armando G. Villaseñor Jennifer Fretland William L. Fitch Julie Qi Hang Gabrielle Heilek Klaus Klumpp 《Bioorganic & medicinal chemistry letters》2010,20(20):6020-6023
94.
Diversity and identification of methanogenic archaea and sulphate-reducing bacteria in sediments from a pristine tropical mangrove 总被引:1,自引:0,他引:1
Rodrigo Gouvêa Taketani Caio Augusto Yoshiura Armando Cavalcante Franco Dias Fernando Dini Andreote Siu Mui Tsai 《Antonie van Leeuwenhoek》2010,97(4):401-411
Mangrove sediments are anaerobic ecosystems rich in organic matter. This environment is optimal for anaerobic microorganisms,
such as sulphate-reducing bacteria and methanogenic archaea, which are responsible for nutrient cycling. In this study, the
diversity of these two functional guilds was evaluated in a pristine mangrove forest using denaturing gradient gel electrophoresis
(DGGE) and clone library sequencing in a 50 cm vertical profile sampled every 5.0 cm. DGGE profiles indicated that both groups
presented higher richness in shallow samples (0–30 cm) with a steep decrease in richness beyond that depth. According to redundancy
analysis, this alteration significantly correlated with a decrease in the amount of organic matter. Clone library sequencing
indicated that depth had a strong effect on the selection of dissimilatory sulphate reductase (dsrB) operational taxonomic units (OTUs), as indicated by the small number of shared OTUs found in shallow (0.0 cm) and deep
(40.0 cm) libraries. On the other hand, methyl coenzyme-M reductase (mcrA) libraries indicated that most of the OTUs found in the shallow library were present in the deep library. These results
show that these two guilds co-exist in these mangrove sediments and indicate important roles for these organisms in nutrient
cycling within this ecosystem. 相似文献
95.
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97.
Ochratoxin A is a mycotoxin produced by several Aspergillus and some Penicillium species which may be present in food and feed products. It can be enzymatically hydrolyzed into ochratoxin α and l-β-phenylalanine, thereby decreasing its toxicity. The ochratoxin A degradation capacity of Aspergillus niger is well known and here we report the isolation and purification of a novel enzyme from A. niger that hydrolyzes this mycotoxin. A wheat germ medium supplemented with ochratoxin A was used to produce the enzyme, which
was purified from culture filtrate by acetone precipitation and anion exchange chromatography. An overall purification of
2.5-fold with a recovery of 68% and a final specific activity of 36 U/mg was obtained. The enzyme is a metalloenzyme as it
was inhibited at 10 mM EDTA, whereas PMSF had no effect. The ochratoxin A hydrolytic enzyme presented a V
max of 0.44 μM/min and a K
m of 0.5 mM when the reaction was carried out at pH 7.5 and 37°C. 相似文献
98.
Anopheles aquasalis larvae are salt water tolerant, preferring concentrations between 10 and 20 parts per thousand (ppt). The larvicidal efficacy of two formulations of Bacillus thuringiensis var. israelensis (Vectobac-12AS and Bactivec), was investigated against An. aquasalis at salinities of 0, 10, and 20 ppt. A probit analysis was used to calculate the lethal concentrations (LC50 and LC95) for each product at each salinity. The LC50 and LC95 were higher for Bactivec than Vectobac-12AS, and for Bactivec, the LC50 and LC95 increased with salinity. Vectobac-12AS should thus be preferred to Bactivec for An. aquasalis control, especially in saline breeding habitats. 相似文献
99.
100.
De Santa F Albini S Mezzaroma E Baron L Felsani A Caruso M 《Molecular and cellular biology》2007,27(20):7248-7265
The expression of retinoblastoma (pRb) and cyclin D3 proteins is highly induced during the process of skeletal myoblast differentiation. We have previously shown that cyclin D3 is nearly totally associated with hypophosphorylated pRb in differentiated myotubes, whereas Rb-/- myocytes fail to accumulate the cyclin D3 protein despite normal induction of cyclin D3 mRNA. Here we report that pRb promotes cyclin D3 protein accumulation in differentiating myoblasts by preventing cyclin D3 degradation. We show that cyclin D3 displays rapid turnover in proliferating myoblasts, which is positively regulated through glycogen synthase kinase 3beta (GSK-3beta)-mediated phosphorylation of cyclin D3 on Thr-283. We describe a novel interaction between pRb and cyclin D3 that maps to the C terminus of pRb and to a region of cyclin D3 proximal to the Thr-283 residue and provide evidence that the pRb-cyclin D3 complex formation in terminally differentiated myotubes hinders the access of GSK-3beta to cyclin D3, thus inhibiting Thr-283 phosphorylation. Interestingly, we observed that the ectopic expression of a stabilized cyclin D3 mutant in C2 myoblasts enhances muscle-specific gene expression; conversely, cyclin D3-null embryonic fibroblasts display impaired MyoD-induced myogenic differentiation. These results indicate that the pRb-dependent accumulation of cyclin D3 is functionally relevant to the process of skeletal muscle cell differentiation. 相似文献