• Molecules and Cells
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• v.39 no.4
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• pp.316-321
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• 2016

The receptor activator of nuclear factor ${\kappa}B$ (RANK) and its ligand RANKL are key regulators of osteoclastogenesis and well-recognized targets in developing treatments for bone disorders associated with excessive bone resorption, such as osteoporosis. Our previous work on the structure of the RANK-RANKL complex revealed that Loop3 of RANK, specifically the non-canonical disulfide bond at the tip, performs a crucial role in specific recognition of RANKL. It also demonstrated that peptide mimics of Loop3 were capable of interfering with the function of RANKL in osteoclastogenesis. Here, we reported the structure-based design of a smaller peptide with enhanced inhibitory efficiency. The kinetic analysis and osteoclast differentiation assay showed that in addition to the sharp turn induced by the disulfide bond, two consecutive arginine residues were also important for binding to RANKL and inhibiting osteoclastogenesis. Docking and molecular dynamics simulations proposed the binding mode of the peptide to the RANKL trimer, showing that the arginine residues provide electrostatic interactions with RANKL and contribute to stabilizing the complex. These findings provided useful information for the rational design of therapeutics for bone diseases associated with RANK/RANKL function.

• Journal of Ginseng Research
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• v.48 no.2
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• pp.171-180
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• 2024

Background: Epimers of ginsenoside Rg3 (Rg3) have a low bioavailability and are prone to deglycosylation, which produces epimers of ginsenoside Rh2 (S-Rh2 and R-Rh2) and protopanaxadiol (S-PPD and R-PPD). The aim of this study was to compare the efficacy and potency of these molecules as anti-cancer agents. Methods: Crystal violet staining was used to study the anti-proliferatory action of the molecules on a human epithelial breast cancer cell line, MDA-MB-231, and human umbilical vein endothelial cells (HUVEC) and compare their potency. Cell death and cell cycle were studied using flow cytometry and mode of cell death was studied using live cell imaging. Anti-angiogenic effects of the drug were studied using loop formation assay. Molecular docking showed the interaction of these molecules with vascular endothelial growth factor receptor-2 (VEGFR2) and aquaporin (AQP) water channels. VEGF bioassay was used to study the interaction of Rh2 with VEGFR2, in vitro. Results: HUVEC was the more sensitive cell line to the anti-proliferative effects of S-Rh2, S-PPD and R-PPD. The molecules induced necroptosis/necrosis in MDA-MB-231 and apoptosis in HUVEC. S-Rh2 was the most potent inhibitor of loop formation. In silico molecular docking predicted a good binding score between Rh2 or PPD and the ATP-binding pocket of VEGFR2. VEGF bioassay showed that Rh2 was an allosteric modulator of VEGFR2. In addition, SRh2 and PPD had good binding scores with AQP1 and AQP5, both of which play roles in cell migration and proliferation. Conclusion: The combination of these molecules might be responsible for the anti-cancer effects observed by Rg3.

• Journal of Life Science
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• v.20 no.6
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• pp.831-837
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• 2010

KR-31125 (2-butyl-5-dimethoxymethyl-6-phenyl-7-methyl-3-[[2'-(1H-tetrazol-5-yl)biphenyl-4-yl]methyl]-3H-imidazo[4,5-b]pyridine) is a potent inhibitor of angiotensin II type 1 ($AT_1$) receptors in human recombinant $AT_1$ receptors and rabbit aorta. These in vitro studies revealed that KR-31125 inhibited specific [$^{125}I$] [$Sar^1$, $Ile^8$]-angiotensin II binding to human recombinant $AT_1$ receptors in a concentration dependent manner with an $IC_{50}$ value of $19.72{\pm}2.65$ nM. However, no interaction with $AT_2$ receptors was detected as displayed by the competition binding of [$^{125}I$] CGP 42112A to human recombinant $AT_2$ receptor. The binding action was also confirmed as a competitive mode that was identical to the previously studied compound, losartan. In addition, KR-31125 caused a nonparallel shift to the right in the concentration response curves to angiotensin II with a 30-80% decrease in the maximum contractile responses ($pK_B$: 7.63). Compared to the previous studies with losartan that showed a parallel right shift in the maximum contractile responses to AII ($pA_2$: 7.59), KR-31125 presented a different mode of action with a similar potency to losartan. These results demonstrate that KR-31125 is a highly potent and $AT_1$ selective angiotensin II receptor antagonist that can be applied to the fields of new diagnostic and research tools with upcoming in vivo study results.

• IMMUNE NETWORK
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• v.1 no.1
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• pp.77-86
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• 2001

Background: Hepatitis C virus(HCV), a family of Flaviviridae, has a host cell-derived envelope containing a positive-stranded RNA genome, and has been known as the maj or etiological agent for chronic hepatitis, hepatic cirrhosis, and hepatocellular carcinoma. There remains a need to dissect a molecular mechanism of pathogenesis for the development of therapeutic and effective preventive measure for HCV. Identification of cellular receptor is of central importance not only to understand the viral pathogenesis, but also to exploit strategies for prevention of HCV. This study was aimed at identifying peptide mimotopes inhibiting the binding of E2 protein of HCV to MOLT-4 cell. Methods: In this study, phage peptide library displaying a random peptides consisting of 7 or 12 random peptides was employed in order to pan against E2 protein. Free HCV particles were separated from the immune complex forms by immunoprecipitation using anti-human IgG antibody, and used for HCV-capture ELISA. To identify the peptides inhibiting E2-binding to MOLT-4 cells, E2 protein was subj ect to bind to MOLT-4 cells under the competition with phage peptides. Results: Several phage peptides were selected for their specific binding to E2 protein, which showed the conserved sequence of SHFWRAP from 3 different peptide sequences. They were also able to recognize the HCV particles in the sera of HCV patients captured by monoclonal antibody against E2 protein. Two of them, showing peptide sequence of HLGPWMSHWFQR and WAPPLERSSLFY respectively, were revealed to inhibit the binding of E2 protein to MOLT-4 cell efficiently in dose dependent mode. However, few membrane-associated receptor candidates were seen using Fasta3 programe for homology search with these peptides. Conclusion: Phage peptides containing HLGPWMSHWFQR and WAPPLERSSLFY respectively, showed the inhibition of E2-binding to MOLT-4 cells. However, they did not reveal any homologues to cellular receptors from GenBank database. In further study, cellular receptor could be identified through the screening of cDNA library from MOLT-4 or hepatocytes using antibodies against these peptide mimotopes.

• Journal of the Korean Chemical Society
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• v.55 no.1
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• pp.70-80
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• 2011

Two new palladium (II) complexes, [Pd (phen)(pip-dtc)]$NO_3$ and [Pd(phen)(mor-dtc)]$NO_3$, (where phen is 1,10-Phenantroline, pip-dtc is piperidinedithiocarbamate anion and mor-dtc is morpholinedithiocarbamate anion) have been synthesized and characterized by elemental analysis, spectroscopic studies (FT-IR, $^1H$ NMR, UV-Vis) and conductance measurement. In these complexes, the dithiocarbamate ligands coordinate with Pd (II) center as bidentate with two sulfur atoms. These two complexes have been tested against chronic myelogenous leukemia cell line, K562. They show $IC_{50}$ values less than cisplatin and thus the mode of binding of the complexes to calf thymus DNA (CT-DNA) were investigated by ultraviolet difference and fluorescence spectroscopy. They can denature DNA, exhibit cooperative binding and intercalate into DNA. Several binding and thermodynamic parameters are also described.

• Journal of the Institute of Electronics Engineers of Korea TC
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• v.46 no.9
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• pp.39-45
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• 2009

When Mobile IPv6 is deployed in commercial network, a mobile node needs AAA services for an authentication, authorization and accounting. AAA and Mobile IPv6 are protocols which are operated independently. Then schemes which merge these protocols have been emerged. These schemes can enable a mobile node to establish a security association between the mobile node and a home agent and to perform a binding update for the home agent using AAA authentication request. But these schemes introduce many signal messages and long handover latency during the handover, since Route Optimization mode for Mobile Ipv6 is performed using Return Routability procedure. To solve this problem, we propose a scheme for Route Optimization mode that the home agent performs the binding update for a correspondent node via the AAA infrastructure between the home agent and the correspondent node instead of Return Routability procedure. For performance evaluation, we analyze signal message transmission costs and handover latencies during handover. We show performance improvement of the proposed scheme which reduces handover latency as 61% compared with the existing scheme.

• Journal of the Institute of Electronics and Information Engineers
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• v.51 no.9
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• pp.11-20
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• 2014

For Web-based applications in IoT environment, IETF CoRE WG has standardizing the CoAP. One of limitations of CoAP is that CoAP standard does not consider the mobility management of the CoAP sensor node. In this paper, we propose the mobility management protocol of CoAP sensor node by considering the characteristics of the constrained network. The proposed mobility management protocol supports for Web client to be transmitted the sensing data from CoAP node reliably while the CoAP sensor moves into different wireless networks. To do this, we designed the architecture with the separate IP address management of CoAP sensor node and presented the mobility management protocol, which includes the holding and binding mode, in order to provide the reliable transmission. Finally, the numerical analysis and simulation with NS2 tool have been done for the performance evaluation in terms of the handover latency and packet loss with comparing the proposed mobility management protocol with other the existing mobility management protocols. The performance result shows that the proposed mobility management can provide the transmission of sensing data without the packet loss comparing with the existing mobility management protocol reliably.

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 2001.06a
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• pp.149-153
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• 2001

To investigate the mode of bactericidal action for antimicrobial peptide, pediocin, synthetic and mutant pediocins were prepared by direct chemical synthesis. Native pediocin was purified from Pedio-coccus acidilactici M and its conformational structure and bactericidal functions were analyzed and compared to synthetic pediocin. Schematic mode of pediocin actions, how pediocin binds on the target cell membrane, penetrates and makes tunnel are proposed. For these purposes, primary and secondary structures of pediocin was analyzed and disulfide bond assignment was also done. The pediocin purified from P. acidilactici M had high effective bactericidal ability against gram positive bacteria, especially Listeria monocytogenes and was very stable at extreme pHs and even at high temperatures such as autoclaving temperature (121$^{\circ}C$). Pediocin was consisted of 44 amino acids with four cysteines. Novel synthetic peptides were achieved by solid phase peptide synthesis(SPPS) method. To explain the function of cysteine in C-terminal region, mutant pediocin, Ped[C24A＋C44A], was synthesized and their structural and biological functions were analyzed. Second mutant pediocin, Ped[KllE], was prepared to explain the function of lysine at 11 of N-terminal part of pediocin, especially loop of $\beta$-sheet, and to predict the initial binding site of pediocin. The native and synthetic pediocins was showed random coil conformation by spectropolarimetry in moderate conditions. This conformation was observed in extreme conditions such as high temperature and low and high pHs, also. Circular dichroism(CD) data also showed the existence of $\beta$-turn structure in N-terminal part both native and synthetic pediocins. A structural model for pediocin predicts that 18 amino acids in the N-terminal part of the peptide assume a three-strand $\beta$-sheet conformation. This random coil in C-terminal part of pediocin was converted to folding structure, helix structure, in nonpolar solvents such as alcohol and TFE. The disulfide bond between $^{9}$ Cys and $^{14}$ Cys was concrete and inevitable, however, evidences of disulfide bond between $^{24}$ Cys and $^{44}$ Cys was not. Data of Ped[C24A＋C44A], pediocin mutant showed that $^{44}$ Cys was required during killing the target cells but not inevitable, since Ped[C24A＋C44A] still have bactericidal activity but much less than native pediocin. Another pediocin mutant, Ped[KllE], had still bactericidal activity, was controversial to propose that positive charge like as $^{11}$ Lys in loop or hinge in bacteriocin bound or helped to binding to microorganism with electrostatic interaction between cell membrane especially teichoic acid and positive amino acid nonspecifically. The conformation of pediocin among native, synthetic and mutant pediocins did not show big difference. The conformations between oxidized and reduced pediocin were almost similar regardless of native or synthetic.

• Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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• 1995.05a
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• pp.73-76
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• 1995

In this study, the slab waveguide was fabricated using potassium-nitride(KNO$_3$) or silver-nitride (AgNO$_3$) molten sources by ion-exchange process. The effective refractive indices of waveguide were measured by Prism-Coupling method. and The characteristics of waveguide(mode dispersion, effective diffusion depth. surface refractive index, diffusion coefficient, and refractive index profile etc,) were investigated by WKB method, In the case of potassium ion-exchange, the computer calculation showed that the refractive index profile of waveguide followed Gaussian function, the surface refractive index increased with ion-exchange time and the effective diffusion depth increased a little as ion-exchange time increased, while the surface refractive index of silver ion-exchanged waveguide decreased with ion-exchange time because of the ion depletion on the surface of waveguide, and the effective diffusion depth seriously with ion-exchange tim. Double ion-exchanged waveguide was fabricated by performing silver ion-exchange after potassium ion-exchange. Double ion-exchanged waveguide had a tight mode binding force since the surface refractive index was larger than single step ion-exchanged waveguide.

• Bulletin of the Korean Chemical Society
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• v.29 no.7
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• pp.1374-1378
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• 2008

Using DFT B3LYP/6-31+G(d,p)//B3LYP/6-31G(d,p) calculation method, stable molecular structures were optimized for the p-tert-butylcalix[4]arene functionalized at lower rim by cage-annulated crown ether (1) in two different conformers and their potassium-ion complexes. Cone conformer of free host 1 was slightly more stable than partial-cone conformer. For two different kinds of complexation mode, the potassium ion in benzene-rings (bz) pocket showed comparable complexation efficiency with the cation in cage-annulated crown-ether (cr) for the cone and partial-cone conformers of 1. The complex (1${\bullet}K^+$) in the cr-binding mode for the partial-cone conformer was more stable than the cone conformer for B3LYP/6-31G(d,p) geometry optimization. However, $1_{(cone)}{\bullet}K^+$(cr) showed lower single-point energy than the $1_{(pc)}{\bullet}K^+$(cr) for B3LYP/6- 31+G(d,p) calculation method.