• Journal of Ginseng Research
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• v.39 no.4
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• pp.406-413
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• 2015

Background: Pathogenesis-related 10 (PR-10) proteins are small, cytosolic proteins with a similar three-dimensional structure. Crystal structures for several PR-10 homologs have similar overall folding patterns, with an unusually large internal cavity that is a binding site for biologically important molecules. Although structural information on PR-10 proteins is substantial, understanding of their biological function remains limited. Here, we showed that one of the PgPR-10 homologs, PgPR-10.3, shares binding properties with flavonoids, kinetin, emodin, deoxycholic acid, and ginsenoside Re (1 of the steroid glycosides). Methods: Gene expression patterns of PgPR-10.3 were analyzed by quantitative real-time PCR. The three-dimensional structure of PgPR-10 proteins was visualized by homology modeling, and docking to retrieve biologically active molecules was performed using AutoDock4 program. Results: Transcript levels of PgPR-10.3 expressed in leaves, stems, and roots of 3-wk-old ginseng plantlets were on average 86-fold lower than those of PgPR-10.2. In mature 2-yr-old ginseng plants, the mRNA of PgPR-10.3 is restricted to leaves. Ginsenoside Re production is especially prominent in leaves of Panax ginseng Meyer, and the binding property of PgPR-10.3 with ginsenoside Re suggests that this protein has an important role in the control of secondary metabolism. Conclusion: Although ginseng PR-10.3 gene is expressed in all organs of 3-wk-old plantlets, its expression is restricted to leaves in mature 2-yr-old ginseng plants. The putative binding property of PgPR-10.3 with Re is intriguing. Further verification of binding affinity with other biologically important molecules in the large hydrophobic cavity of PgPR-10.3 may provide an insight into the biological features of PR-10 proteins.

• Journal of Periodontal and Implant Science
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• v.28 no.3
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• pp.475-489
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• 1998

The main goal for the treatment of periodontal diseases is the regeneration of lost cementum, bone and connective tissue. Clinical and histological research suggests that it is possible to restore periodontal structures. Seeds of Carthamus tinctorius L. has been used for the treatment of bone fracture and osteoporosis in traditional Korean medicine. The purpose of this study is to examine the effect of extract of seeds of Carthamus tinctorius L. on mineralization in periodontal ligament cells and osteoblastic cells. Periodontal ligament cells were primarily obtained from a extracted premolars with non-periodontal diseases, Osteoblastic cells were obtained from calvariae of a fetal rat, Cells were cultured with DMEM at $37^{\circ}C$ with 5% $CO_2$ in 100% humidity incubator. Alkaline phosphatase(ALP) level and the number of calcification nodules were examined and western blot analysis using osteonectin was performed, Measurements of ALP levels and calcification nodules showed that extract of seeds of Carthamus tinctorius L. had significantly higher activity than control in all of both cells. In western blot analysis, protein expression of osteonectin indicated that extract of seeds of Carthamus tinctorius L. showed an increased pattern than control in all of both cells. From the above results, it seems that extract of seeds of Carthamus tinctorius L. has excellent effect on mineralization in periodontal ligament cells and osteoblastic cells.

• Journal of Korean Medicine Rehabilitation
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• v.20 no.2
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• pp.51-61
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• 2010

Objectives : The purpose of this study was to investigate antioxidant effects of curcumin from Curcumae Longae Radix. Methods : Using HepG2 Iiver-like cells, the antioxidant effects of curcumin, one of main components from Curcumae Longae Radix, and its analogues have been evaluated by measuring their effects on cytotoxicity induced by $H_2O_2$. Results : The pre-incubation for 6 hours with curcumin, bis-demethoxycurcumin, or dimethoxycurcumin protected HepG2 cells from $H_2O_2$-induced toxicity in a dose-dependent manner. However, tetrahydrocurcumin, one of curcumin metabolites, did not protect HepG2 cells from $H_2O_2$-induced toxicity. Interestingly, curcumin, bis-demethoxycurcumin, and dimethoxycurcumin were increased in the protein levels of heme oxygenase-1(HO-1) at concentrations that were also effective in cellular protection. In contrast, tetrahydrocurcumin did not induce HO-1 expression. Tin protoporphyrin-IX, an inhibitor of HO-1 activity, significantly abolished cytoprotection afforded by curcumin, bis-demethoxycurcumin and dimethoxycurcumin. Conclusions : These results demonstrate that curcumin, bis-demethoxycurcumin, and dimethoxycurcumin with two conjugated doble bonds on their structures may reduce $H_2O_2$-induced oxidative stress through HO-1 expression. HO-1 induction may be one of antioxidant pathways by which curcumin protects from oxidative stress-induced cytotoxicity.

• Journal of the Korean Magnetic Resonance Society
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• v.21 no.2
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• pp.72-77
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• 2017

${\beta}-catenin$ is a key signaling protein which regulates cell signaling and gene transcription. Abnormal activation of ${\beta}-catenin$ is linked to many cancers, particularly with colorectal cancers. Although many genetic and biological studies on $Wnt/{\beta}-catenin$ have been reported and structures of the complex between ${\beta}-catenin$ and its diverse binding partners have been published, many of them have focused on armadillo repeat domain of ${\beta}-catenin$. Both N- and C-terminal domains have been suggested to regulate interactions of ${\beta}-catenin$ with other molecules, but still little is known about the C-terminal unstructured domain. To investigate the structure of this domain, construct of C-terminus was designed and structural studies were performed using size exclusion chromatography (SEC), circular dichroism (CD), fluorescence and nuclear magnetic resonance (NMR) spectroscopy. We observed that not only the purified full-length construct but the purified C-terminal construct also dimerizes in solution by SEC, suggesting that this domain involves in dimerization of ${\beta}-catenin$. CD and fluorescence data indicate its flexibility and structural formation in the presence of membrane environments.

• Journal of the Institute of Convergence Signal Processing
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• v.6 no.1
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• pp.27-32
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• 2005

As a large quantity of Genome sequencing has happened to be done a very much a surprising speed in short period, an automatic genome annotation process has become prerequisite. The most difficult process among with this kind of genome annotation works is to finding out the protein-coding genes within a genome. The main 2 subjects of gene prediction are Eukaryotes and Prokaryotes ; their genes have different structures, therefore, their gene prediction methods will also obviously varies. Until now, it is found that among of the 231 genome sequenced species, 200 have been found to be prokaryotes, therefore, for study of biotechnology studies, through comparative genomics, prokaryotes, rather than eukaryotes could may be more appropriate than eukaryotes. Even more, prokaryotes does not have the gene structure called an intron, so it makes the gene prediction easier. Former prokaryotes gene predictions have been shown to be 80%～ to 90% of accuracy. A recent study is aiming at 100% of gene prediction accuracy. In this paper, especially in the case of the E. coli K-12 and S. typhi genomes, gene prediction accuracy which showed 98.5% and 98.7% was more efficient than previous GLIMMER.

• Journal of Korean Society on Water Environment
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• v.23 no.4
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• pp.482-489
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• 2007

Fluorescence properties and carbohydrate content were investigated using ultrafiltrated size fractions of dissolved organic matters (DOM) originated from different sources. The materials included a treated sewage, an algal organic matter, and a soil leachate, all of which are major constituents of dissolved organic matter in a typical urban river. Four different size fractions were separated from the three sources of each DOM. The size distribution demonstrated that a higher molecular weight fraction was more present in soil leachate compared to two other source DOMs. A higher content of carbohydrates was observed in the following order - algal DOM > treated sewage > soil leachate. A wide range of specific UV absorbance was observed from size fractions of a single source DOM, indicating that aromatic carbon structures are heterogeneously distributed within one source of DOM. The structural heterogeneity was the most pronounced for the soil leachate. The fluorescence index ($F_{450}/F_{500}$) of the treated sewage was similar to that (2.0) typically obtained from autochthonous DOM, suggesting that the treated sewage exhibited autochthonous organic matter-like properties. No protein-like fluorescence intensities were observed for all of the soil leachate size fractions whereas they were observed with two other source DOMs. Based upon the fluorescence peak ratios from fluorescence excitation-emission matrix (EEM), two discrimination indices could be suggested to distinguish three different source DOMs. It is expected that the suggested discrimination indices will be useful to predict the sources of DOM in a typical urban river affected by treated sewage.

• Molecules and Cells
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• v.28 no.5
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• pp.447-453
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• 2009

The quorum sensing (QS) inhibitors that antagonize TraR, a receptor protein for N-3-oxo-octanoyl-L-homoserine lactones (3-oxo-C8-HSL), a QS signal of Agrobacterium tumefaciens were developed. The structural analogues of 3-oxo-C8-HSL were designed by in silico molecular modeling using SYBYL packages, and synthesized by the solid phase organic synthesis (SPOS) method, where the carboxamide bond of 3-oxo-C8-HSL was replaced with a nicotinamide or a sulfonamide bond to make derivatives of N-nicotinyl-L-homoserine lactones or N-sulfonyl-L-homoserine lactones. The in vivo inhibitory activities of these compounds against QS signaling were assayed using reporter systems and compared with the estimated binding energies from the modeling study. This comparison showed fairly good correlation, suggesting that the in silico interpretation of ligand-receptor structures can be a valuable tool for the pre-design of better competitive inhibitors. In addition, these inhibitors also showed anti-biofilm activities against Pseudomonas aeruginosa.

• Molecules and Cells
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• v.40 no.2
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• pp.151-161
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• 2017

Proper synaptic function in neural circuits requires precise pairings between correct pre- and post-synaptic partners. Errors in this process may underlie development of neuropsychiatric disorders, such as autism spectrum disorder (ASD). Development of ASD can be influenced by genetic factors, including copy number variations (CNVs). In this study, we focused on a CNV occurring at the 16p11.2 locus in the human genome and investigated potential defects in synaptic connectivity caused by reduced activities of genes located in this region at Drosophila larval neuromuscular junctions, a well-established model synapse with stereotypic synaptic structures. A mutation of rolled, a Drosophila homolog of human mitogen-activated protein kinase 3 (MAPK3) at the 16p11.2 locus, caused ectopic innervation of axonal branches and their abnormal defasciculation. The specificity of these phenotypes was confirmed by expression of wild-type rolled in the mutant background. Albeit to a lesser extent, we also observed ectopic innervation patterns in mutants defective in Cdk2, Gq, and Gp93, all of which were expected to interact with Rolled MAPK3. A further genetic analysis in double heterozygous combinations revealed a synergistic interaction between rolled and Gp93. In addition, results from RT-qPCR analyses indicated consistently reduced rolled mRNA levels in Cdk2, Gq, and Gp93 mutants. Taken together, these data suggest a central role of MAPK3 in regulating the precise targeting of presynaptic axons to proper postsynaptic targets, a critical step that may be altered significantly in ASD.

• Journal of the Korean Magnetic Resonance Society
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• v.20 no.3
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• pp.95-101
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• 2016

Apolipoprotein B-100 (Apo-B100) is a major component of low density lipoprotein (LDL). Apo B-100 protein has 4,536 amino acid sequence and these amino acids are classified into peptide groups A to G with subsequent 20 amino acids (P1-P302). The peptide groups were act as immunoglobulin (Ig) antigens which oxidized via malondialdehyde (MDA). The mimetic peptide P1 (EEEMLENVSLVCPKDAT RFK) out of D-group peptides carrying the highest value of IgG antigens were selected for structural studies that may provide antigen specificity. Circular Dichroism (CD) spectra were measured for peptide secondary structure in the range of 190-250 nm. Experimental results show that P1 exhibit partial of ${\beta}-sheet$ and random coil structure. Homonuclear (COSY, TOCSY, NOESY) 2D-NMR experiments were carried out for NMR signal assignments and structure determination for P1. On the basis of these completely assigned NMR spectra and distance data, distance geometry (DG) and Molecular dynamics (MD) were carried out to determine the structures of P1. The proposed structure was selected by comparisons between experimental NOE spectra and back calculated 2D NOE results from determined structure showing acceptable agreement. The total Root-Mean-Square-Deviation (RMSD) value of P1 obtained upon superposition of all atoms was in the range $0.33{\AA}$. The solution state P1 has mixed structure of ${\beta}-sheet$ (Glu[1] to Cys[12]) and random coil (Pro[13] to Lys[20]). These NMR results are well consistent with secondary structure from experimental results of circular dichroism. Structural studies based on NMR may contribute to the studies of atherosclerosis and observed conformational characteristics of apo B-100 in LDL using monoclonal antibodies.

• Journal of Korean Neurosurgical Society
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• v.64 no.6
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• pp.864-872
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• 2021

Objective : The aim of our study is to investigate the cytotoxic, antioxidant, and antimicrobial effects of newly synthesized boron compounds in U87MG glioblastoma cell treatment. Methods : We synthesized boron glycine monoester (BGM) and boron glycine diester (BGD) structures containing boron atoms and determined their cytotoxic activities on glioblastoma by the MTT method. The inhibitory concentration 50 (IC₅₀) value was calculated with GraphPad Prism 5.0 program. The IC₅₀ values were administered 48 hours on U87MG glioblastoma cell. Catalase (CAT), acid phosphatase (ACP) and alkaline phosphatase (ALP) enzyme activity, malondialdehyde (MDA), total glutathione (GSH), and total protein levels were detected using spectrophotometric methods. We determined the antimicrobial activities of BGM and BGD with the disc diffusion method. Results : After 48 hours of BGM and BGD application to U87MG glioblastoma cells, we found the IC₅₀ value as 6.6 mM and 26 mM, respectively. CAT and ACP enzyme activities were decreased in BGM and BGD groups. MDA which is a metabolite of lipid peroxidation was increased in both boron compounds groups. GSH level was reduced especially in BGD group. BGM and BGD have been found to be antimicrobial effects. Conclusion : Boron compounds, especially the BGM, can provide a new therapeutic approach for the treatment of glioblastoma with their anticancer, antioxidant, and antimicrobial effects.