• Journal of Microbiology and Biotechnology
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• v.16 no.3
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• pp.457-464
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• 2006

Three extracellular proteases (Vpr, peptidase T, and subtilisin) were identified from the culture supernatant of Bacillus subtilis KCTC 3014. All the proteins were partially purified as a mature form by using a DEAE-cellulose ion-exchange column chromatography. Their activities were determined by using zymography and densitometry. The relative molecular masses of Vpr and peptidase T (PepT) were determined to be 68 and 48 kDa by SDS-PAGE and zymography, respectively. However, subtilisin formed a 'binding mode' at the top of the separating gel. After denaturation by boiling at $100^{\circ}C$ for 5 min, its molecular mass was determined to be 29 kDa, whereas its activity was lost. The optimal pH of Vpr, PepT, and subtilisin were 9.0, 6.0-7.0, and 7.0-8.0, respectively. The optimal temperature of Vpr, PepT, and subtilisin was 40, 50, and $40^{\circ}C$, respectively. Inhibitor test revealed that Vpr and subtilisin were serine proteases and that PepT was a metalloprotease. Interestingly, we found that Vpr showed no enzyme activity on a 2DE zymogram gel. Three genes, vpr, pepT, and apr (encoding subtilisin protein), were cloned and their nucleotide and deduced amino acid sequences were determined.

• Journal of Microbiology and Biotechnology
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• v.30 no.2
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• pp.187-195
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• 2020

To understand the molecular mechanism involved in the survivability of cold-tolerant lactic acid bacteria was of great significance in food processing, since these bacteria play a key role in a variety of low-temperature fermented foods. In this study, the cold-stress response of probiotic Lactobacillus plantarum K25 isolated from Tibetan kefir grains was analyzed by iTRAQ proteomic method. By comparing differentially expressed (DE) protein profiles of the strain incubated at 10℃ and 37℃, 506 DE proteins were identified. The DE proteins involved in carbohydrate, amino acid and fatty acid biosynthesis and metabolism were significantly down-regulated, leading to a specific energy conservation survival mode. The DE proteins related to DNA repair, transcription and translation were up-regulated, implicating change of gene expression and more protein biosynthesis needed in response to cold stress. In addition, two-component system, quorum sensing and ABC (ATP-binding cassette) transporters also participated in cell cold-adaptation process. These findings provide novel insight into the cold-resistance mechanism in L. plantarum with potential application in low temperature fermented or preserved foods.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.13 no.4
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• pp.691-699
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• 2009

Recently, the ERO protocol has been adopted as a standard to protect the routing optimization mode introduced by MIPv6. This protocol uses the public key cryptography and the early binding update method to improve the Return Routeability protocol while optimizing both security and performance. On the other hand, though various security approaches including the ERO protocol have been proposed for MIPv6, they lack formal verification. Especially, to our best knowledge, there is no formal analysis on the ERO protocol. In order to provide a good example for formal analysis on MIPv6 security protocols, this paper verifies the correctness of the ERO protocol through BAN-logic. For this goal, BAN-logic is extended to consider the address tests on the mobile nodes's CoA and HoA. It is expected that the analysis presented in this paper will be useful for the formal verifications on the security protocols related to MIPv6.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.181-190
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• 2004

The docking and in silico ligand screening procedures can select small sets of lead -like candidates from large libraries of either commercially or synthetically available compounds; however, the vast number of such molecules make the potential size of this task enormous. To accelerate the discovery of drugs to inhibit several targets, we have exploited massively distributed computing to screen compound libraries virtually. The Korea@HOME project was launched in Feb. 2002, and one year later, more than 1200 PC's have been recruited. This has created a 31 -gigaflop machine that has already provided more than 1400 hours of CPU time. It has all owed databases of millions of compounds to be screened against protein targets in a matter of days. Now, the virtual screening software suitable for distributed environments is developed by BMD. It has been evaluated in terms of the accuracy of the scoring function and the search algorithm for the correct binding mode.

• Molecules and Cells
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• v.28 no.6
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• pp.545-551
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• 2009

Mitogen-activated protein kinases (MAPK) affect the activation of activator protein-1 (AP-1), which plays an important role in regulating a range of cellular processes. However, the roles of these signaling factors on hydrogen peroxide ($H_2O_2$)-induced cell death are unclear. This study examined the effects of $H_2O_2$ on the activation of MAPK and AP-1 by exposing the cells to $H_2O_2$ generated by either glucose oxidase or a bolus addition. Exposing BJAB or Jurkat cells to $H_2O_2$ affected the activities of MAPK differently according to the method of $H_2O_2$ exposure. $H_2O_2$ increased the AP-1-DNA binding activity in these cells, where continuously generated $H_2O_2$ led to an increase in mainly the c-Fos, FosB and c-Jun proteins. The c-Jun-$NH_2$-terminal kinase (JNK)-mediated activation of c-Jun was shown to be related to the $H_2O_2$-induced cell death. However, the suppression of $H_2O_2$-induced oxidative stress by either JNK inhibitor or c-Jun specific antisense transfection was temporary in the cells exposed to glucose oxidase but not to a bolus $H_2O_2$. This was associated with the disruption of death signaling according to the severe and prolonged depletion of reduced glutathione. Overall, these results suggest that $H_2O_2$ may decide differently the mode of cell death by affecting the intracellular redox state of thiol-containing antioxidants, and this depends more closely on the duration exposed to $H_2O_2$ than the concentration of this agent.

• Food Science and Biotechnology
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• v.14 no.2
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• pp.200-206
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• 2005

Effect of quercetin on NO production and regulation mode of quercetin on oxidative stress, $NF{\kappa}B$ activation, and iNOS expression, possible mechanisms of NO suppression in LPS-stimulated macrophages were investigated. Treatment of RAW 264.7 cells with quercetin significantly reduced lipopolysaccharide (LPS)-stimulated nitric oxide (NO) production dose-dependently ($IC_{50}$, $9.2\;{\mu}M$). Expression of iNOS and specific DNA binding activities of nuclear factor kB ($NF{\kappa}B$) were significantly suppressed by quercetin pretreatment. Quercetin reduced thiobarbituric acid-reactive substances (TBARS) accumulation, enhancing GSH level and antioxidant activities of enzymes, such as superoxide dismutase (SOD) and catalase. These results demonstrate quercetin may ameliorate inflammatory diseases by suppressing NO production through inhibition of iNOS expression, $NF{\kappa}B$ transactivation, and oxidative stress, which may be mediated partially by antioxidative effect of quercetin. Thus, quercetin appears to be used as a potential therapeutic agent for treating LPS-induced inflammatory processes.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.17
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• pp.7419-7424
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• 2014

Gliomas are the most common type of primary brain tumors. The XRCC1 Arg194Trp variant affects the proliferating cell nuclear antigen(PCNA) binding region, which suggests that this mutation may contribute to gliomagenesis and a number of articles have examine the association between XRCC1 Arg194Trp and the susceptibility to glioma. However, the results were conflicting. Test of heterogeneity, sensitivity analysis, meta-analysis, and assessment of publication bias were all performed in our present meta-analysis, covering a total of 5,407 patients and 7,715 healthy persons. In the overall analysis the XRCC1 Arg194Trp polymorphism showed a significant association with glioma susceptibility in a recessive mode l(for TrpTrp vs ArgArg+ArgTrp: OR=1.918, 95%CI=1.575-2.336, $I^2$=2.3%). In addition, analysis of subgroups presented an increased risk in Asians and populations-based on hospitals. The results suggested that the XRCC1 Arg194Trp polymorphism is a genetic risk factor for glioma, especially in Asian population. To further evaluate gene-gene and gene-environment interactions on XRCC1 polymorphisms and glioma risk, thousands of subjects and tissue-specific biochemical characterizations are required.

• Bulletin of the Korean Chemical Society
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• v.26 no.2
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• pp.285-291
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• 2005

The nonstructural protein 5B (NS5B) of hepatitis C virus (HCV) is the viral RNA-dependent RNA polymerase (RdRp), which is the essential catalytic enzyme for the viral replication and is an appealing target for the development of new therapeutic agents against HCV infection. A small amount of serum from a single patient with hepatitis C was used to get the genome of a Korean HCV isolate. Sequence analysis of NS5B 1701 nucleotides showed the genotype of a Korean isolate to be subtype 1b. The soluble recombinant HCV NS5B polymerase lacking the C-terminal 24 amino acids was expressed and purified to homogeneity. With the highly purified NS5B protein, we established in vitro systems for RdRp activity to identify potential polymerase inhibitors. The rhodanine family compounds were found to be potent and specific inhibitors of NS5B from high throughput screening (HTS) assay utilizing the scintillation proximity assay (SPA) system. The binding mode of an inhibitor was analyzed by measuring various kinetic parameters. Lineweaver-Burk plots of the inhibitor suggested it binds not to the active site of NS5B polymerase, but to an allosteric site of the enzyme. The activity of NS5B in in vitro polymerase reactions with homopolymeric RNA requires interaction with multiple substrates that include a template/primer and ribonucleotide triphosphate. Steady-state kinetic parameter, such as Km, was determined for the ribonucleotide triphosphate. One of compounds found interacts directly with the viral polymerase and inhibits RNA synthesis in a manner noncompetitively with respect to UTP. Furthermore, we also investigated the ability of the compound to inhibit NS5B-directed viral RNA replication using the Huh7 cell-based HCV replicon system. The investigation is potentially very useful for the utility of such compounds as anti-hepatitic agents.

• The Korean Journal of Physiology and Pharmacology
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• v.22 no.5
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• pp.585-595
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• 2018

Amitriptyline, a tricyclic antidepressant, is commonly used to treat depression and neuropathic pain, but its mechanism is still unclear. We tested the effect of amitriptyline on 5-hydroxytryptamine 3 ($5-HT_3$) receptor currents and studied its blocking mechanism because the clinical applications of amitriptyline overlapped with $5-HT_3$ receptor therapeutic potentials. Using a whole-cell voltage clamp method, we recorded the currents of the $5-HT_3$ receptor when 5-HT was applied alone or co-applied with amitriptyline in cultured NCB-20 neuroblastoma cells known to express $5-HT_3$ receptors. To elucidate the mechanism of amitriptyline, we simulated the $5-HT_3$ receptor currents using Berkeley $Madonna^{(R)}$ software and calculated the rate constants of the agonist binding and receptor transition steps. The $5-HT_3$ receptor currents were inhibited by amitriptyline in a concentration-dependent, voltage-independent manner, and a competitive mode. Amitriptyline accelerated the desensitization of the $5-HT_3$ receptor. When amitriptyline was applied before 5-HT treatment, the currents rose slowly until the end of 5-HT treatment. When amitriptyline was co-applied with 5-HT, currents rose and decayed rapidly. Peak current amplitudes were decreased in both applications. All macroscopic currents recorded in whole cell voltage clamping experiments were reproduced by simulation and the changes of rate constants by amitriptyline were correlated with macroscopic current recording data. These results suggest that amitriptyline blocks the $5-HT_3$ receptor by close and open state blocking mechanisms, in a competitive manner. We could expand an understanding of pharmacological mechanisms of amitriptyline related to the modulation of a $5-HT_3$ receptor, a potential target of neurologic and psychiatric diseases through this study.

• Proceedings of the Korean Vacuum Society Conference
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• 1998.02a
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• pp.133-133
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• 1998

In the thin film alloy formation of the transition metals ion-beam-mixing technique forms a metastable structure which cannot be found in the arc-melted metal alloys. Sppecifically it is well known that the studies about the electronic structure of ion-beam-mixed alloys pprovide the useful information in understanding the metastable structures in the metal alloy. We studied the electronic change in the ion-beam-mixed ppt-Ct alloys by XppS and XANES. These analysis tools pprovide us information about the charge transfer in the valence band of intermetallic bonding. The multi-layered films were depposited on the SiO2 substrate by the sequential electron beam evapporation at a ppressure of less than 5$\times$10-7 Torr. These compprise of 4 ppairs of ppt and Cu layers where thicknesses of each layer were varied in order to change the alloy compposition. Ion-beam-mixing pprocess was carried out with 80 keV Ae+ ions with a dose of $1.5\times$ 1016 Ar+/cm2 at room tempperature. The core and valence level energy shift in these system were investigated by x-ray pphotoelectron sppectroscoppy(XppS) pphotoelectrons were excited by monochromatized Al K ａ(1486.6 eV) The ppass energy of the hemisppherical analyzer was 23.5 eV. Core-level binding energies were calibrated with the Fermi level edge. ppt L3-edge and Cu K-edge XANES sppectra were measured with the flourescence mode detector at the 3C1 beam line of the ppLS (ppohang light source). By using the change of White line(WL) area of the each metal sites and the core level shift we can obtain the information about the electrons pparticippating in the intermetallic bonding of the ion-beam-mixed alloys.