• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.17-20
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• 2000

Structural genomics aims to provide a good experimental structure or computational model of every tractable protein in a complete genome. Underlying this goal is the immense value of protein structure, especially in permitting recognition of distant evolutionary relationships for proteins whose sequence analysis has failed to find any significant homolog. A considerable fraction of the genes in all sequenced genomes have no known function, and structure determination provides a direct means of revealing homology that may be used to infer their putative molecular function. The solved structures will be similarly useful for elucidating the biochemical or biophysical role of proteins that have been previously ascribed only phenotypic functions. More generally, knowledge of an increasingly complete repertoire of protein structures will aid structure prediction methods, improve understanding of protein structure, and ultimately lend insight into molecular interactions and pathways. We use computational methods to select families whose structures cannot be predicted and which are likely to be amenable to experimental characterization. Methods to be employed included modern sequence analysis and clustering algorithms. A critical component is consultation of the presage database for structural genomics, which records the community's experimental work underway and computational predictions. The protein families are ranked according to several criteria including taxonomic diversity and known functional information. Individual proteins, often homologs from hyperthermophiles, are selected from these families as targets for structure determination. The solved structures are examined for structural similarity to other proteins of known structure. Homologous proteins in sequence databases are computationally modeled, to provide a resource of protein structure models complementing the experimentally solved protein structures.

• Journal of Dairy Science and Biotechnology
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• v.26 no.2
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• pp.39-43
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• 2008

EMC have a similar enzymatic reaction to cheese, but the EMC produce the stronger flavors than cheese by much more enzymatic reaction. It is important to find appropriate enzyme in order to develop these kind of superior EMC. Calf PGE is more suitable than that of kid and lamb to develop the mild cheese flavors. Especially, it was known that animal esterase and peptidase were more benefit than microbial enzyme for Cheddar cheese flavors. On the Cheddar and Swiss cheese, EMC flavors were much more 3 times than the cheese flavors. In the ratio of each component, butyric acid, myristic acid, palmitic acid and oleic acid were high in free fatty acid, and glutamic acid, valine, leucine and lysine were high in free amino acid of the Cheddar EMC.

• Smart Structures and Systems
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• v.7 no.3
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• pp.213-222
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• 2011

The native extracellular matrix (ECM) consists of an integrated fibrous protein network and proteoglycan-based ground (hydrogel) substance. We designed a novel electrospinning technique to engineer a three dimensional fiber-hydrogel composite that mimics the native ECM structure, is injectable, and has practical macroscale dimensions for clinically relevant tissue defects. In a model system of articular cartilage tissue engineering, the fiber-hydrogel composites enhanced the biological response of adult stem cells, with dynamic mechanical stimulation resulting in near native levels of extracellular matrix. This technology platform was expanded through structural and biochemical modification of the fibers including hydrophilic fibers containing chondroitin sulfate, a significant component of endogenous tissues, and hydrophobic fibers containing ECM microparticles.

• The Korean Journal of Zoology
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• v.34 no.1
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• pp.44-53
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• 1991

Distribution of the antigens during the cell cycle of amoebae was followed by immunof-luorescence microscopy using a monoclonal antibody against the nucleus as a probe. While the cells were in the interphase, the antigen was localized on the nucleus membrane. But it was dispersed all over the cytoplasm during mitosis and cytokinesis. The molecular weights of the immunoreacted antigens were 210 KD and 190 KD as determined by SDS PAGE and western blotting of the purified nuclei. The antigens were not soluble in non-ionic detergent, but were released from the nucleus by incubation with 0.05 M sodium carbonate, pH 10.6 or with 8 M urea at serial chemical extraction. Thus the antigens appeared to be peripheral proteins of the nurBeus envelope. The isoelectic point of both antigens was 7.64 as determined by 2 D PAGE and transfer blotting. Considering the peiipherd association with the nucleus membrane and the dispersed distribution during mitosis, the antigens could be lamin like proteins. Hourever, it appears also possible that they are the component molecules of the unusually structured aurous lamina of amoeba nucleus since they have the large molecular weight and the basic pl.

• Food Science and Preservation
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• v.24 no.4
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• pp.536-541
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• 2017

Hyperglycemia found in diabetes mellitus causes several physiological abnormalities including the formation of advanced glycation end products (AGEs) and oxidative stress. Accumulation of AGEs and elevation of oxidative stress plays major roles in the development of diabetic complications. Adiponectin secreted from adipocytes is known to improve insulin sensitivity and blood glucose level. Curcumin (CCM), a bioactive component of turmeric, has been reported as a potent antioxidant. Present work aimed to elucidate the roles of CCM in high glucose-induced protein glycation and intracellular events in mature adipocytes. The results demonstrated that CCM inhibited the formation of fluorescent AGEs by approximated 52% at 3 weeks of bovine serum albumin (BSA) glycation with glucose. Correspondingly, CCM decreased the levels of fructosamine and ${\alpha}-dicarbonyl$ compounds during BSA glycation with glucose. These data suggested that CCM might be a new promising anti-glycation agent. Also, CCM reduced high glucose-induced oxidative stress in a dose dependent manner, whereas CCM treatment time-dependently elevated the expression of adiponectin gene in 3T3-L1 adipocytes. The findings from this study suggested the possibility of therapeutic use of CCM for the prevention of diabetic complications and obesity-related diseases.

• BMB Reports
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• v.29 no.6
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• pp.507-512
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• 1996

The NADPH oxidase of phagocytes catalyzes the reduction of oxygen to $O_{2}^{-}$ at the expense of NADPH The enzyme is dormant in resting neutrophils and hecomes activated on stimulation. During activation. $p47^{phox}$ (phagocyte oxidase factor), a cytosolic oxidase subunit, becomes extensively phosphorylated on a number of serines located between S303-S379. Although the biochemical role of phosphorylation is speculative, it has been suggested that phosphorylation could neutralize the strongly cationic C-terminal which may result in the change of conformation of $p47^{phox}$ and subsequent translocation of this protein and other cytosolic components to the membrane. In order to mimic the effect of phosphorylation in terms of neutralizing the positive charges, recombinant $p47^{phox}$ was treated with phenylglyoxal, which removes positive charges of arginine residues. Modification of recombinant $p47^{phox}$ resulted in the activation of oxidase in a cell-free translocation system as well as a conformational change in recombinant $p47^{phox}$ which may be responsible for the activation of the enzyme.

• Journal of Ginseng Research
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• v.31 no.4
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• pp.210-216
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• 2007

The backbone structure of ginsenosides, active ingredients of Panax ginseng, is similar with that of sterol, especially cholesterol. Caenorhabditis elegans (c. elegans) is one of free living nematodes and is well-established animal model for biochemical and genetic studies. C. elegans cannot synthesize de novo cholesterol, although cholesterol is essential requirement for its growth and development. In the present study, we investigated the effects of Korean red ginseng total extract (KRGE), ginseng total saponins (GTS) on life span of C. elegans in cholesterol-deprived and -fed medium. Cholesterol deprivation caused damages on life span of worms throughout F1 to F3 generations. KRGE or GTS supplement to cholesterol-deprived medium restored the life span of worms as much as cholesterol alone-fed medium. In study to identify which ginsenosides are responsible for life span restoring effects of KRGE, we found that ginsenoside Rc supplement not only restored life span of worms grown in cholesterol-deprived medium but also prolonged life span of worms grown in cholesterol-fed medium. These results show a possibility that ginsenosides could be utilized by C. elegans as a sterol substitute and further indicate that ginsenoside Rc is the effective component of Korean red ginseng that prolongs the life span of C. elegans.

• Journal of Microbiology and Biotechnology
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• v.18 no.5
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• pp.845-851
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• 2008

TolC is an outer membrane porin protein and an essential component of drug efflux and type-I secretion systems in Gram-negative bacteria. TolC comprises a periplasmic $\alpha$-helical barrel domain and a membrane-embedded $\beta$-barrel domain. TdeA, a functional and structural homolog of TolC, is required for toxin and drug export in the pathogenic oral bacterium Actinobacillus actinomycetemcomitans. Here, we report the expression of the periplasmic domain of TdeA as a soluble protein by substitution of the membrane-embedded domain with short linkers, which enabled us to purify the protein in the absence of detergent. We confirmed the structural integrity of the TdeA periplasmic domain by size-exclusion chromatography, circular dichroism spectroscopy, and electron microscopy, which together showed that the periplasmic domain of the TolC protein family fold correctly on its own. We further demonstrated that the periplasmic domain of TdeA interacts with peptidoglycans of the bacterial cell wall, which supports the idea that completely folded TolC family proteins traverse the peptidoglycan layer to interact with inner membrane transporters.

• Molecules and Cells
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• v.26 no.4
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• pp.329-337
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• 2008

Src-family kinases are critically involved in the control of cytoskeleton organization and in the generation of integrin-dependent signaling responses, inducing tyrosine phosphorylation of many signaling and cytoskeletal proteins. Activity of the Src family of tyrosine kinases is tightly controlled by inhibitory phosphorylation of a carboxy-terminal tyrosine residue, inducing an inactive conformation through binding with its SH2 domain. Dephosphorylation of C-ter tyrosine, as well as its deletion of substitution with phenylalanine in oncogenic Src kinases, leads to autophosphorylation at a tyrosine in the activation loop, thereby leading to enhanced Src activity. Beside this phophorylation/dephosphorylation circuitry, cysteine oxidation has been recently reported as a further mechanism of enzyme activation. Mounting evidence describes Src activation via its redox regulation as a key outcome in several circumstances, including growth factor and cytokines signaling, integrin-mediated cell adhesion and motility, membrane receptor cross-talk as well in cell transformation and tumor progression. Among the plethora of data involving Src kinase in physiological and pathophysiological processes, this review will give emphasis to the redox component of the regulation of this master kinase.

• Journal of Microbiology and Biotechnology
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• v.28 no.12
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• pp.1971-1981
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• 2018

In this study, we investigated the altered enzymatic activities and metabolite profiles of koji fermented using varying permutations of Aspergillus oryzae and/or Bacillus amyloliquefaciens. Notably, the protease and ${\beta}$-glucosidase activities were manifold increased in co-inoculated (CO) koji samples (co-inoculation of A. oryzae and B. amyloliquefaciens). Furthermore, gas chromatography-mass spectrometry (GC-MS)-based metabolite profiling indicates that levels of amino acids, organic acids, sugars, sugar alcohols, fatty acids, nucleosides, and vitamins were distinctly higher in CO, SA (sequential inoculation of A. oryzae, followed by B. amyloliquefaciens), and SB (sequential inoculation of B. amyloliquefaciens, followed by A. oryzae). The multivariate principal component analysis (PCA) plot based on GC-MS datasets indicated a clustered pattern for MA and MB (koji samples inoculated either with A. oryzae or B. amyloliquefaciens) across PC2 (20.0%). In contrast, the CO, SA, and SB metabolite profiles displayed segregated patterns across PLS1 (22.2%) and PLS2 (21.1%) in the partial least-square discriminant analysis (PLS-DA) model. Intriguingly, the observed disparity in the levels of primary metabolites was engendered largely by higher relative levels of sugars and sugar alcohols in MA, SA, and CO koji samples, which was commensurate with the relative amylase activities in respective samples. Collectively, the present study emphasizes the utility of integrated biochemical and metabolomic approaches for achieving the optimal permutation of fermentative inocula for industrial koji preparation.