• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.103-113
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• 2014

Hydrophobicity is the key concept to understand the role of water in protein folding, protein self-assembly, and protein-ligand interaction. Conventionally, hydrophobicity of amino acids in a protein has been argued based on hydrophobicity scales determined for individual free amino acids, assuming that those scales are unaltered when amino acids are embedded in a protein. Here, we investigate how the hydrophobicity of constituent amino acids depends on the protein context, in particular, on the total charge and secondary structures of a protein. To this end, we compute and analyze the hydration free energy - free energy change upon hydration quantifying the hydrophobicity - of three short proteins based on the integral-equation theory of liquids. We find that the hydration free energy of charged amino acids is significantly affected by the protein total charge and exhibits contrasting behavior depending on the protein net charge being positive or negative. We also observe that amino acids in the central ${\beta}$-strand sandwiched by ${\beta}$-sheets display more enhanced hydrophobicity than free amino acids, whereas those in the ${\alpha}$-helix do not clearly show such a tendency. Our results provide novel insights into the hydrophobicity of amino acids, and will be valuable for rationalizing and predicting the strength of water-mediated interaction involved in the biological activity of proteins.

• The Journal of Korean Medicine
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• v.26 no.3 s.63
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• pp.204-214
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• 2005

Objectives : The verity extract of the Gagam-Hyungbang-Gihwang-tang (GHG) was assessed to determine the mechanisms of its antioxidant activity. Methods : The fellowing effects were measured : GHG exhibited a concentration-treatment; scavenging ${\alpha},\;{\alpha}-diphenyl-\beta-picrylhydrazyl$ (DPPH) radical, linoleic acid oxidation in a thiocyanate assay system, and superoxide anion, hydroxyl radical-induced DNA nicking. We investigated mRNA levels such as superoxide-dismutase. Results : The GHG extract showed dose-dependent free radical scavenging activity, including DPPH radicals, hydroxyl radicals, and superoxide anion, using different systems. The GHG was also found to be effective in protecting plasmid DNA against the strand breakage induced by hydroxyl radicals in Fenton's reaction mixture. Furthermore, SOD-1 mRNA expression levels increased in tat hepatoma H4IIE cells Conclusions : We expect that GHG will to helpful to the development of antioxidant activity treatments.

• Journal of Microbiology
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• v.34 no.3
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• pp.236-240
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• 1996

Rifampin is the most powerful drug for treating leprosy and tuberculosis today. It inhibits initiation and elongation of RNA transcription by binding to $\beta$-subunit of RNA polymerase, leading to kill mycobacteria. We isolated one variant strain of Mycobacterium leprae from 24 Korean leprosy patients who are less susceptible to rifampin or have suffered from relapse by polymerase chain reaction and single strand conformation polymorphism (PCR-SSCP) of the rpoB gene. Direct sequencing of the rpoB region of M. leprae variant revealed missense mutations which altered the amino acids sequenceof RpoB to Ser-464, Arg-465, Arg-467 and Ala-468. This is the first finding on rpoB gene mutation of M. leprae from Korean patients ; moreover the mutant type was found to be different from the previously reported cases in other countries.

• Journal of the Korean Geotechnical Society
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• v.28 no.5
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• pp.13-25
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• 2012

Ground anchor method is one of the most popular reinforcing technology for slope in Korea. For the health monitoring of slope which is reinforced by permanent anchor for a long period, monitoring of the tension force of ground anchor is very important. However, since electromechanical sensors such as strain gauge and V/W type load cell are also subject to long-term risk as well as suffering from noise during long distance transmission and immunity to electromagnetic interference (EMI), optical FBG sensors embedded tendon was developed to measure strain of 7-wire strand by embedding FBG sensor into the center king cable of 7-wire strand. This FBG sensors embedded tendon has been successfully applied to measuring the short-term anchor force. But to adopt this tendon to long-term monitoring, temperature compensation of the FBG sensors embedded tendon should be done. In this paper, we described how to compensate the effect in compliance with the change of underground temperature during long-term tension force monitoring of ground anchors by using optical fiber sensors (FBG: Fiber Bragg Grating). The model test was carried out to determine the temperature sensitivity coefficient (${\beta}^{\prime}$) of FBG sensors embedded tendon. The determined temperature sensitivity coefficient ${\beta}^{\prime}=2.0{\times}10^{-5}/^{\circ}C$ was verified by comparing the ground temperatures predicted from the proposed sensor using ${\beta}^{\prime}$ with ground temperatures measured from ground thermometer. Finally, temperature compensations were carried out based on ${\beta}^{\prime}$ value and ground temperature measurement from KMA for the tension force monitoring results of tension type and compression type anchors, which had been installed more than 1 year before at the test site. Temperature compensated tension forces are compared with those measured from conventional load cell during the same measuring time. Test results show that determined temperature sensitivity coefficient (${\beta}^{\prime}$) of FBG sensors embedded tendon is valid and proposed temperature compensation method is also appropriate from the fact that the temperature compensated tension forces are not dependent on the change of ground temperature and are consistent with the tension forces measured from the conventional load cell.

• Bulletin of the Korean Chemical Society
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• v.23 no.8
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• pp.1106-1109
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• 2002

Studies on subtle spacer ligand effects of AgCF3SO3 with 3,3'-Py2X (X = O vs S) have been carried out. The reaction of AgCF3SO3 with 3,3'-Py2O and 3,3'-Py2S produces [Ag(CF3SO3)(3,3'-Py2O)] and [Ag(3,3'-Py2S)] (CF3SO3), respectively. Crystallographic characterization of [Ag(CF3SO3)(3,3'-Py2O)] (monoclinic P1, a =8.405(2) $\AA$, b = 10.714(2) $\AA$, c = 18.031(2) $\AA$, $\alpha=$ 77.36(2), $\beta=107.83(2)^{\circ}$, $\gamma=$ 66.92(2), V = 1438.0(5) $\AA3$ , Z =2,R = 0.0486) reveals that the skeletal structure is an anion-bridged double-strand. The double-strands are packed like a plywood. The framework of [Ag(3,3'-Py2S)](CF3SO3) (orthorhombic Pcab, a = 17.330(2) $\AA$, b = 8.640(1) $\AA$, c = 19.933(6) $\AA$, V = 2985(1) $\AA3$ , Z =8, R = 0.0437) is a sinusoidal single-strand. The formation of each coordination polymer appears to be primarily associated with the donating ability and the confor ma-tional energy barrier of the spacer ligands. Thermal analyses indicate that [Ag(CF3SO3)(3,3'-Py2O)] and [Ag(3,3'-Py2S)](CF3SO3) are stable up to 250 $^{\circ}C$ and 210 $^{\circ}C$, respectively. For the anion exchangeability, the nature of the spacer ligand is more significant factor than the distance of silver(Ⅰ)···triflate.

• Molecules and Cells
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• v.26 no.2
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• pp.206-211
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• 2008

HI0381 of Haemophilus influenzae was investigated by circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy. HI0381 is a 153-residue peptidoglycan-associated outer membrane lipoprotein, and a part of the larger Tol/Pal network. Here, we report its backbone $^1H$, $^{15}N$, and $^{13}C$ resonance assignments, and secondary structure predictions. About 97% of all of the $^1HN$, $^{15}N$, $^{13}CO$, $^{13}C{\alpha}$, and $^{13}C{\beta}$ resonances covering 131 non-proline residues of the 134 residue, mature protein, were clarified by sequential and specific assignments. CSI and TALOS analyses revealed that HI0381 contains five ${\alpha}$-helices and five ${\beta}$-strands. To characterize the structure of HI0381, the effects of pH and salt concentration were investigated by CD. In addition, the structural changes occurring when HI0381 was in a membranous environment were investigated by comparing its HSQC spectra and CD data in buffer and in DPC micelles; the results showed that helix ${\alpha}4$ and strand ${\beta}4$ became aligned with the membrane. We conclude that the conformation of HI0381 is affected by the membrane environment, implying that its folded state is directly related to its function.

• Environmental Analysis Health and Toxicology
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• v.22 no.4
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• pp.349-355
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• 2007

장수풍뎅이 유충(Allomyrina dichotoma larva, ADL)은 중국의 전통 약재로서, 특히 항산화 효과가 우수하여 항당료 제재로 사용되고 있다. 본 연구에서는 이러한 ADL의 추출물을 이용하여 헴스터 췌장의 ${\beta}$-세포(HIT-T15)에서 Streptozotocin에 의해 유발된 산화적 손상에 대한 보호효과 및 그 작용기전을 조사하였다. ADL추출물은 처리농도 의존적으로 Streptozotocin에 의해 유발된 지질과산화 및 세포 내 자유산 소종의 양을 억제함으로서 ${\beta}$-세포의 산화적 스트레스에 의한 손상을 보호하였다. 또한 DNA laddering 방법을 사용하여 Streptozotocin에 의해 유발된 DNA 손상을 조사한 결과, ADL추출물 처리농도에 비례하여 Streptozotocin에 의해 유발된 DNA 손상이 감소하였다. 이러한 산화적 손상의 억제능 관련 작용 기전을 조사하기 위해 DPPH free radical 소거능을 실시하였다. 그 결과 ADL추출물 자체가 DPPH 자유 레디컬 소거능이 있음을 확인하였으며, 또한 플라스미드를 이용한 Single-strand break 방법을 통한 DNA 손상 보호능을 측정한 결과도 $Fe^{3+}$ 및 $H_2O_2$에 의해 유발된 DNA 손상이 ADL추출물 처리농도에 비례하여 감소하였다. 이러한 결과들을 종합하여 볼 때, 장수풍뎅이 유충의 추출물들이 자체의 레디컬 소거능 및 산화적 손상에 의한 DNA손상을 억제함으로써, Streptozotocin에 의해 유발된 산화적 손상을 억제할 수 있을 것이라 사료된다.

• Archives of Pharmacal Research
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• v.23 no.5
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• pp.518-524
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• 2000

We examined the modulation of protein kinase C (PKC) subtypes during apoptosis induced by ginsenoside Rh2 (G-Rh2) in human neuroblastoma SK-N-Bl(2) and rat glioma C6Bu-1 cells. Apoptosis induced by C-Rh2 in both cell lines was confirmed, as indicated by DNA fragmentation and in situ strand breaks, and characteristic morphological changes. During apoptosis induced by G-Rh2 in SK-N-BE(2) cells, PKC subtypes $\alpha$, $\beta$ and $\gamma$ were progressively increased with prolonged treatment, whereas PKC $\delta$ increased transiently at 3 and 6 h and PKC $\varepsilon$ was gradually down-regulated after 6 h following the treatment. On the other hand, PKC subtype $\beta$ markedly increased at 24 h when maximal apoptosis was achieved. In C6Bu-l cells, no significant changes in PKC subtypes $\alpha$, $\gamma$, $\delta$, $\varepsilon$ and $\beta$ were observed during apoptosis induced by G-Rh2. These results suggest the evidence for a possible role of PKC subtype in apoptosis induced by G-Rh2 in SK-N-BE(2) cells but not in C6Bu-1 cells, and raise the possibility that G-Rh2 may induce apoptosis via different pathways interacting with or without PKC in different cell types.

• Molecules and Cells
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• v.39 no.6
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• pp.495-500
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• 2016

We have solved the crystal structure of a predicted fructose-specific enzyme $IIB^{fruc}$ from Escherichia coli ($EcEIIB^{fruc}$) involved in the phosphoenolpyruvate-carbohydrate phosphotransferase system transferring carbohydrates across the cytoplasmic membrane. $EcEIIB^{fruc}$ belongs to a sequence family with more than 5,000 sequence homologues with 25-99% amino-acid sequence identity. It reveals a conventional Rossmann-like ${\alpha}-{\beta}-{\alpha}$ sandwich fold with a unique ${\beta}$-sheet topology. Its C-terminus is longer than its closest relatives and forms an additional ${\beta}$-strand whereas the shorter C-terminus is random coil in the relatives. Interestingly, its core structure is similar to that of enzyme $IIB^{cellobiose}$ from E. coli ($EcIIB^{cel}$) transferring a phosphate moiety. In the active site of the closest $EcEIIB^{fruc}$ homologues, a unique motif CXXGXAHT comprising a P-loop like architecture including a histidine residue is found. The conserved cysteine on this loop may be deprotonated to act as a nucleophile similar to that of $EcIIB^{cel}$. The conserved histidine residue is presumed to bind the negatively charged phosphate. Therefore, we propose that the catalytic mechanism of $EcEIIB^{fruc}$ is similar to that of $EcIIB^{cel}$ transferring phosphoryl moiety to a specific carbohydrate.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.11
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• pp.5333-5338
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• 2012

Vitamin B6 functions as a coenzyme in >140 enzymatic reactions involved in the metabolism of amino acids, carbohydrates, neurotransmitters, and lipids. It comprises a group of three related 3-hydroxy-2-methyl-pyrimidine derivatives: pyridoxine (PN), pyridoxal (PL), pyridoxamine (PM) and their phosphorylated derivatives [pyridoxal 5'-phosphate (PLP) and pyridoxamine 5'-phosphate (PMP)], In the folate metabolism pathway, PLP is a cofactor for the mitochondrial and cytoplasmic isozymes of serine hydroxymethyltransferase (SHMT2 and SHMT1), the P-protein of the glycine cleavage system, cystathionine ${\beta}$-synthase (CBS) and ${\gamma}$-cystathionase, and betaine hydroxymethyltransferase (BHMT), all of which contribute to homocysteine metabolism either through folate-mediated one-carbon metabolism or the transsulfuration pathway. Folate cofactors carry and chemically activate single carbons for the synthesis of purines, thymidylate and methionine. So the evidence indicates that vitamin B6 plays an important role in maintenance of the genome, epigenetic stability and homocysteine metabolism. This article focuses on studies of strand breaks, micronuclei, or chromosomal aberrations regarding protective effects of vitamin B6, and probes whether it is folate-mediated one-carbon metabolism or the transsulfuration pathway for vitamin B6 which plays critical roles in prevention of cancer and cardiovascular disease.