• 한국당과학회:학술대회논문집
• /
• 2006.11a
• /
• pp.35-36
• /
• 2006

• Journal of Microbiology
• /
• v.44 no.5
• /
• pp.508-514
• /
• 2006

In this study, the double-stranded DNA-dependent activities of Deinococcus radiodurans RecA protein (Dr RecA) were characterized. The interactions of the Dr RecA protein with double-stranded DNA were determined, especially dsDNA-dependent ATP hydrolysis by the Dr RecA protein and the DNA strand exchange reaction, in which multiple branch points exist on a single RecA protein-DNA complex. A nucleotide cofactor (ATP or dATP ) was required for the Dr RecA protein binding to duplex DNA. In the presence of dATP, the nucleation step in the binding process occurred more rapidly than in the presence of ATP. Salts inhibited the binding of the Dr RecA protein to double-stranded DNA. Double-stranded DNA-dependent ATPase activities showed a different sensitivity to anion species. Glutamate had only a minimal effect on the double-stranded DNA-dependent ATPase activities, up to a concentration of 0.7 M. In the competition experiment for Dr RecA protein binding, the Dr RecA protein manifested a higher affinity to double-stranded DNA than was observed for single-stranded DNA.

• International Journal of Fuzzy Logic and Intelligent Systems
• /
• v.15 no.2
• /
• pp.111-120
• /
• 2015

Protein named entity identification is one of the most essential and fundamental predecessor for extracting information about protein-protein interactions from biomedical literature. In this paper, we explore the use of abstracts of biomedical literature in MEDLINE for protein name identification and present the results of the conducted experiments. We present a robust and effective approach to classify biomedical named entities into protein and non-protein classes, based on a rich set of features: orthographic, keyword, morphological and newly introduced Protein-Score features. Our procedure shows significant performance in the experiments on GENIA corpus using Random Forest, achieving the highest values of precision 92.7%, recall 91.7%, and F-measure 92.2% for protein identification, while reducing the training and testing time significantly.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2005.09a
• /
• pp.294-299
• /
• 2005

We have studied unbound docking for 12 protein-protein complexes using conformational space annealing (CSA) combined along with statistical pair potentials. The CSA, a powerful global optimization tool, is used to search the conformational space represented by a translational vector and three Euler amgles between two proteins. The energy function consists of three statistical pair-wise energy terms; one from the distance-scaled finite ideal-gas reference state (DFIRE) approach by Zhou and the other two derived from residue-residue contacts. The residue-residue contact terms describe both attractive and repulsive interactions between two residues in contact. The performance of the CSA docking is compared with that of ZDOCK, a well-established protein-protein docking method. The results show that the application of CSA to the protein-protein docking is quite successful, indicating that the CSA combined with a good scoring function is a promising method for the study of protein-protein interaction.

• BMB Reports
• /
• v.38 no.1
• /
• pp.97-103
• /
• 2005

Under the condition of expression of $\lambda$ P protein at lethal level, the oriC DNA-binding activity is significantly affected in wild-type E. coli but not in the rpl mutant. In purified system, the $\lambda$ P protein inhibits the binding of both oriC DNA and ATP to the wild-type DnaA protein but not to the rpl DnaA protein. We conclude that the $\lambda$ P protein inhibits the binding of oriC DNA and ATP to the wild-type DnaA protein, which causes the inhibition of host DNA synthesis initiation that ultimately leads to bacterial death. A possible beneficial effect of this interaction of $\lambda$ P protein with E. coli DNA initiator protein DnaA for phage DNA replication has been proposed.

• Journal of Nutrition and Health
• /
• v.29 no.8
• /
• pp.867-873
• /
• 1996

This study was undertaken to determine whether the anabolic steroid nandrolone phenylpropionate(NPP) can inhibit the muscle atrophy and reduction in muscle protein synthesis caused by glucocorticoids in female rates. Daily injections of 50mg/kg of corticosterone for eight days induced significant reductions in body weight gain and protein without affecting food intake. The mass, protein and RNA content, ratio of RNA to protein, and fractional rate of protein synthesis, measured in vivo, of gastrocnemius muscle were all significantly reduced by corticosterone treatement. Simultaneous administration of NPP at a dose of 10mg/kg with corticosteorne (50mg/kg) fully inhibited the reductions in the mass, protein and RNA content of gastrocnemius muscle, and body weight gain and protein with no alteration in food intake but the reduction in fractional rate of muscle protein syntheis was only partially prevented. The results indicate that the anabolic steroid nandrolone phenylpropionate is capable of preventing muscle atrophy in female rats treated with excess corticosterion.

• The Journal of Natural Sciences
• /
• v.9 no.1
• /
• pp.25-29
• /
• 1997

To study the mechanism of lipocortin-1, the 37 kDa protein, one of the annxin superfamily thought to be a second messenger during the Glucocorticoid dependent anti-inflammatory action, the gene for lipocortin-1 binding protein was isolated using the yeast two hybrid assay, the yeast based genetic assay recognizing the protein-protein interaction. The results showed that this gene has a weak homology to the for the human serine proteinase.

• Journal of Nutrition and Health
• /
• v.22 no.6
• /
• pp.497-506
• /
• 1989

To investigate the effect of levels of dietary protein and age on bone metabolism 40% and 5% casein were fed to the rats of 2 & 13 months of age for 12 weeks. High protein groups showed higher bone weight and Ca content than low protein groups and urinary Ca loss was increased in high protein groups but the difference disappeared gradually. A significant increase in urinary hydroxyproline excretion was noted in high protein groups of both age. Another short term study was undertaken to study if the above effect was related with renal function or PTH. Extremely high and low protein diets(60%, 6%) were fed to the rats of different ages(6wks, 6mos.) for 2 weeks, Urinary Ca excretion was significantly increased in high protein groups of young and aged rats and GFR was increased as well. There was no difference in serum iPTH levels between low and high protein groups, but it was elevated in aged rats. Alkaline phosphatase activity was higher in young rats, reflecting faster bone formation. The observed hypercalciuria in high protein groups, especially in aged rats, seems to be related to higher GFR, and PTH dose not appear to be a major mediator.

• Archives of Pharmacal Research
• /
• v.19 no.6
• /
• pp.502-506
• /
• 1996

Protein X is one of the subunits of pyruvate dehydrogenase complex. The biological role of this protein has not been fully elucidated, mainly because of the difficulty in its dissociation from the tightly bound dihydrolipoamide acetyltransferase-protein X subcomplex. We have found that the detachment of protein X from acetyltransferase subunit can be easily accomplished by the cycles of freezing and thawing proces. Several lines of evidence including sodium dodecyl sulfate-polyacrylamide gel electrophoresis, N-terminal amino acid sequence analysis and acetylation with $[2^{14}C]$ pyruvate confirmed that the purified protein is protein X. The purified intact form of protein X was acetylated by $[2^{14}C]$ pyruvate in the presence of py-ruvate dehydrogenase subunit.The acetylation efficiency of this protein was lower than that of acetyltransferase and was not affected by the presence of acetyltransferase.

• YAKHAK HOEJI
• /
• v.42 no.1
• /
• pp.46-52
• /
• 1998

Retroviral integrase is required for integration of viral DNA into the host cell chromosome. Human immunodeficiency virus type-1 integrase was partially purified as a part of a fusion protein linked to a maltose-binding protein and characterized in terms of an endonucleolytic activity. The concentration of the fusion protein purified through an amylose column was about 12mg/ml. Indicating that the solubility of the fusion protein is highly increased by the presence of a maltose-binding protein, considering that the integrase protein alone is poorly solubilized. The endonucleolytic activity of the fusion protein was detected at 0.1 to 1.OmM $Mn^{++}$ ion, but not at any concentrations tested of $Mn^{++}$ ion.