• The Journal of the Korea Contents Association
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• v.8 no.1
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• pp.259-271
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• 2008

We propose a protein function finding algorithm that is able to predict specific molecular function for unannotated proteins through domain analysis from protein-protein network. To do this, we first construct protein-protein interaction(PPI) network in Saccharomyces cerevisiae from MIPS databases. The PPI network(proteins; 3,637, interactions; 10,391) shows the characteristics of a scale-free network and a hierarchical network that proteins with a number of interactions occur in small and the inherent modularity of protein clusters. Protein-protein interaction databases obtained from a Y2H(Yeast Two Hybrid) screen or a composite data set include random false positives. To filter the database, we reconstruct the PPI networks based on the cellular localization. And then we analyze Hub proteins and the network structure in the reconstructed network and define structural modules from the network. We analyze protein domains from the structural modules and derive functional modules from them. From the derived functional modules with high certainty, we find tentative functions for unannotated proteins.

• Journal of The Korean Society of Grassland and Forage Science
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• v.20 no.2
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• pp.97-102
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• 2000

To increase thennotolerance of forage crops, transgenic rice plants as a model for transformation of monocots were generated. A cDNA encoding the chloroplast-localized small heat shock protein (small HSP) of rice, Oshsp21, was introduced into rice plants via Agrobacterium-mediated gene transfer system. Calli induced from scutella were co-cultivated with a A. tumefaciens strain EHAlOl canying a plasmid, pIGhsp21. A large number of transgenic plants were regenerated on a medium containing hygromycin. Integration of Oshsp2l gene was confirmed by PCR and Southern blot analyses with genomic DNA. Northern blot and immunoblot analyses revealed that the Oshsp21 gene was constitutively expressed and accumulated as mature protein in transgenic plants. Effects of constitutive expression of the OshspZl on thermotolerance were first probed with the chlorophyll fluorescence. Results indicate that inactivation of electron transport reactions in photosystem I1 (PSII), were mitigated by constitutive expression of the Oshsp21. These results suggest that the chloroplast small HSP plays an important role in protecting photosynthetic machinery during heat stress. (Key words : Thermotolerance, Rice, Transgenic, cDNA)

• Preventive Nutrition and Food Science
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• v.2 no.1
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• pp.42-48
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• 1997

the exocrine pancreatic secretion is an important factor in the maintenance of zinc homeostasis. The daily pancreatic secretion of zinc into the gastrointestinal tract may be two or more times the daily dietary zinc intake. The objective of this study was to examine the distribution of proteins and zinc in pancreatic/biliary fluid following intraperitoneal {TEX}${65}^Zn${/TEX} injection into dietary prepared Sprague-Dawly rats. Distribution of zinc-binding protein in Sephadex G-75 subfractions showed a peak corresponding to the high molecular weight protein standard(<66kDa) in the pancreatic/biliary fluid. Zinc also was associated with the 29~35kDa mole-cular weight proteins. These are similar in size with zinc-containing enzymes, carboxypeptidase A and car-boxypeptidase B. A more remarkable small molecular weight fraction eluted beyond the 6.5kDa standard pro-tein peak. These results show the presence of small molecular weight compound in pancreatic/biliary fluid associated with zinc . These small molecular weight compounds may serve as zinc-binding ligands for the secretion of enogenous zinc into the duodenum. These findings suggest that these lignads may dissociate zinc in the duodenum thus making it vulnerable to complexation with phytate in the upper gastrointestinal tract rendering the zinc unavailable for reabsorption.

• Journal of Pharmaceutical Investigation
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• v.29 no.4
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• pp.315-321
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• 1999

Poly (lactide-co-glycolide) (PLGA) microspheres containing ovalbumin (OVA) as a model protein drug were prepared by double emulsification method, and various conditions such as mixing rate, volume of outer phase and isopropyl alcohol concentration in outer phase during secondary emulsification were observed to control the size of microspheres. In addition, entrapment efficiency of OVA and protein denaturation were also evaluated. As the rate of stirring was increased, the size of particles was decreased. But excessive stirring increased the particle size of microspheres. In a preparation condition of small volume of outer phase, the particle size was decreased but the entrapment efficiency was increased. Adding isopropyl alcohol to outer phase decreased the size of particles, but increased the entrapment efficiency. Microparticles should have smaller size than $10\;{\mu}m$ to be uptaked by Peyer's patch in small intestine. High speed of mixing and relatively small volume of outer phase are needed to reduce the size. In addition, appropriate amount of isopropyl alcohol in outer phase also plays an important role in size reduction of PLGA microspheres.

• Journal of Integrative Natural Science
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• v.3 no.1
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• pp.49-53
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• 2010

Molecular docking is a critical event which mostly forms Van der waals complex in molecular recognition. Since the majority of developed drugs are small molecules, docking them into proteins has been a prime concern in drug discovery community. Since the binding pose space is too vast to cover completely, many search algorithms such as genetic algorithm, Monte Carlo, simulated annealing, distance geometry have been developed. Proper evaluation of the quality of binding is an essential problem. Scoring functions derived from force fields handle the ligand binding prediction with the use of potential energies and sometimes in combination with solvation and entropy contributions. Knowledge-based scoring functions are based on atom pair potentials derived from structural databases. Forces and potentials are collected from known protein-ligand complexes to get a score for their binding affinities (e.g. PME). Empirical scoring functions are derived from training sets of protein-ligand complexes with determined affinity data. Because non of any single scoring function performs generally better than others, some other approaches have been tried. Although numerous scoring functions have been developed to locate the correct binding poses, it still remains a major hurdle to derive an accurate scoring function for general targets. Recently, consensus scoring functions and target specific scoring functions have been studied to overcome the current limitations.

• Korean Journal of Microbiology
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• v.16 no.3
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• pp.93-102
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• 1978

Saccharomyces cerevisiae strain M was cultured in a molasses-containing media with repeated transplantations of the yeasts from one culture to another to adapt to molasses. After that only different amounts of phosphorous and nitrogen sources were added to the media. And then some variations during the culture time and the effects of consituents of cell mass on the functional activity and sensitivity of the cell were investigated. The results obtained were summarized as follows : 1. In the same culture condition of yeasts, the carbohydrates and trehaloses contents were more remarkably increased when small amounts of phosphate and nitrogen sources were added, then when alrge amounts were added, but yield percentage on assimilated sugars was lower. 2. The content of trehalose in yeast cells was reduced remarkably at the early stage in the culture, but this increased remarkably at later stage. When small amounts of nitrogen and phosphate were added to the culture medium, the amount of thehalose in the cells increased greasly. 3. The more protein content was present in the yeast cells, the smaller the carbohydrate and trehalose content, but more amino-N, RNA and moisture content were present in the cells. And in this case fermentability of the cells was stronger, but sugar tolerance was lower. 4. During the preservation period of compressed yeast cells at different temperature, the higher the temperature was, the more rapidly the amount of trehalose in the cells decreased. And in the cell where the amount of trehalose in the cells decreased. And in the cell where the amount of trehalose(carbohydrate) was large and the amount of protein was small, the amount of trehalose decreased at a slower rate during the preservation period.

• Journal of Microbiology
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• v.45 no.3
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• pp.193-198
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• 2007

A marine bacterium was isolated from Mai Po Nature Reserve of Hong Kong and identified as Vibrio cholerae MP-1. It contains a small plasmid designated as pVC of 3.8 kb. Four open reading frames (ORFs) are identified on the plasmid, but none of them shows homology to any known protein. Database search indicated that a 440 bp fragment is 96% identical to a fragment found in a small plasmid of another V. cholerae. Further experiments demonstrated that a 2.3 kb EcoRI fragment containing the complete ORF1, partial ORF4 and their intergenic region could self-replicate. Additional analyses revealed that sequence upstream of ORF1 showed the features characteristic of theta type replicons. Protein encoded by ORF1 has two characteristic motifs existed in most replication initiator proteins (Rep): the leucine zipper (LZ) motif located at the N-terminal region and the alpha helix-turn-alpha helix motif (HTH) located at the C-terminal end. The results suggest that pVC replicates via the theta type mechanism and is likely a novel type of theta replicon.

• Nutrition Research and Practice
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• v.17 no.5
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• pp.844-854
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• 2023

BACKGROUND/OBJECTIVES: Fucoidan, a polysaccharide content in brown algae, has been reported to inhibit the growth of cancer cells. The present study aimed to investigate the suppression effects of fucoidan on A549 non-small cell lung cancer cells migration. MATERIALS/METHODS: The anti-migratory activity of fucoidan in A549 cells was examined by wound healing assay and phalloidin-rhodamine staining in response to fucoidan (0-100 ㎍/mL) treatment for 48 h. Western blot analysis was performed to clarify the protein expressions relevant to migratory activity. RESULTS: Fucoidan (25-100 ㎍/mL) significantly suppressed A549 cells migration together with reduced the intensity of phalloidin-rhodamine which detect filopodia and lamellipodia protrusions at 48 h of treatment. The protein expression indicated that fucoidan significantly suppressed the phosphorylation of focal adhesion kinase (FAK), Src, and extracellular signal-related kinase (ERK). In addition, the phosphorylation of p38 in A549 cells was found to be increased. CONCLUSIONS: Our data conclude that fucoidan exhibits anti-migratory activities against lung cancer A549 cells mediated by inhibiting ERK1/2 and FAK-Src pathway.

• Preventive Nutrition and Food Science
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• v.3 no.2
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• pp.143-151
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• 1998

Protein -surfactant interactions have been investigate by measuring ζ-potential of $\beta$-lactoglobulin-coated emulsion droplets and $\beta$-lactoglobulin in solution in the rpesenceof surfactant, with particular emphasis on the effect of protein heat treatment(7$0^{\circ}C$, 30min). When ionic surfactant (SDS or DATEM) is added to the protein solution, the ζ-potential of the mixture is found to increase with increasing surfactant concentration, indicating surfactant binding to the protein molecules. For heat-denatured protein,it has been observed that the ζ-potential tends to be lower than that of the native protein. The effect of surfactant on emulsions is rather complicated .With SDS, small amounts of surfactant addition induce a sharp increase in zeta potential arising from the specific interaction of surfactant with protein. With further surfacant addition, there is a gradual reductio in the ζ-potential, presumably caused by the displacement of adsorped protein (and protein-surfactant complex) from the emulsion droplet surfac by the excess of SDS molecules. At even higher surfactant concentrations, the measured zeta potential appears to increase slightly, possibly due to the formation of a surfactant measured zeta potential appears to increase slightly, possibly due to the formation of surfactant micellar structure at the oil droplet surface. This behaviour contrastswith the results of the corresponding systems containing the anionic emulsifier DATEM, in which the ζ-potential of the system is found to increase continuously with R, particularly at very low surfactant concentration. Overall, such behaviour is consisten with a combination of complexation and competitive displacement between surfactant and protein occurring at the oil-water interface. In addition, it has also been found that above the CMC, there is a time-dependent increase in the negative ζ-potential of emulsion droplets in solutions of SDS, possibly due to the solublization of oil droplets into surfactant micelles in the aqueous bulk phase.

• Proceedings of the Korea Crystallographic Association Conference
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• 2000.11a
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• pp.7-7
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• 2000