• Proceedings of the PSK Conference
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• 2002.10a
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• pp.330.2-330.2
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• 2002

The conformational study on cyclic Ac-Cys-Pro-Xaa-Cys-NHMe (Ac-CPXC-NHMe: X = Ala, Val. Leu. Aib. Gly. His. Phe, Tyr. Asn. and Ser) peptides has been carried out using the ECEPP/3 force field and the hydration shell model in the unhydrated and hydrated states. This work has been undertaken to investigate structural implications of the CPXC sequence as the chain reversal for the initiation of protein folding and as the motif for active site of disulfide oxidoreductases. The backbone conformation DAAA is in common the most feasible for cyclic CPXC peptides in the hydrated state. which has a type 1${\beta}$-turn at the Pro-Xaa sequence. The proline residue and the hydrogen bond between backbones of two cystines appear to play a role in stabilizing this preferred conformation of cycilc CPXC peptides. However. the distributions of backbone conformations and ${\beta}$-turns may indicate that the cyclic CPXC peptide seems to exist as an ensemble of ${\beta}$-turns and coiled conformations. The intirnsic stability of the cyclic CPXC motif itself the active conformation appears to play a role in determining electrochemical properties of disulfide oxidoreductases.

• Journal of Marine Bioscience and Biotechnology
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• v.2 no.3
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• pp.174-186
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• 2007

Amphora coffeaeformis and Achnanthes longipes are commonly found as dominant benthic microalgae in Jeju coastal water throughout the year. In order to investigate pharmaceutical uses of these diatoms, each single species was isolated with micropipette under phase contrast microscope and subcultured with synthetic seawater media which was enriched with F/2 media, trace metal solution and $Na_2SiO_3$). Growth characteristics of these species were also determined with different combination of salinity, nutrients concentration and temperature. Thereafter, mass culture of each species was done based on the maximum growth condition. Biomass was collected after two weeks of mass culture and freeze dried for antioxidant study. The antioxidant properties of different fractions (n-hexane, chloroform and ethylacetate) obtained by solvent fractionation of 80% methanolic extract of two microalgae were investigated for free radical, reactive oxygen species scavenging (Super oxide, Hydrogen peroxide, Hydroxyl radical and Nitric oxide), metal chelating and lipid peroxidation inhibition activities. All fractions of A. longipes showed higher $DPPH^{\cdot}$ (free radical) scavenging activities (n-hexane: 89.0%, Chloroform: 76.0%, Ethylacetate: 66.0%, Methanol: 90.6% and aqueous residue: 63.0%). N-hexane fraction of A. longipes showed significantly higher activity (49.0%) on nitric-oxide. Ethylacetate fraction of A. longipes and aqueous residue of A. coffeaeformis exhibited 64.0% and 75.6% metal chelating activity which was higher than commercial antioxidants (${\alpha}$-tocopherol: 18.0% and BHT: 16.0%). The n-hexane fraction of A. coffeaeformis had 67.5% activity on $DPPH^{\cdot}$. Chloroform and n-hexane fractions of A. coffeaeformis exhibited 46.2% and 47.6% $H_2O_2$ scavenging effects which were closely similar to commercial antioxidants (${\alpha}$-tocopherol: 49.2% and BHT: 58.6%). Chloroform and ethylacetate fractions of A. longipes and fraction of n-hexane and chloroform of A. coffeaeformis showed better lipid peroxidation activities than ${\alpha}$-tocopherol. These data suggest that both organic and aqueous fractions have good antioxidative compounds with different antioxidant properties.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.325-330
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• 2005

We are generally interested in the analysis, detection and prediction of structural motifs in proteins, in order to infer compatibility of amino acid sequence to structure in proteins of known three-dimensional structure available in the Protein Data Bank. In this context, we are analyzing some of the well-characterized structural motifs in proteins. We have analyzed simple structural motifs, such as, ${\beta}$-turns and ${\gamma}$-turns by evaluating the statistically significant type-dependent amino acid positional preferences in enlarged representative protein datasets and revised the amino acid preferences. In doing so, we identified a number of ‘unexpected’ isolated ${\beta}$-turns with a proline amino acid residue at the (i+2) position. We extended our study to the identification of multiple turns, continuous turns and to peptides that correspond to the combinations of individual ${\beta}$ and ${\gamma}$-turns in proteins and examined the hydrogen-bond interactions likely to stabilize these peptides. This led us to develop a database of structural motifs in proteins (DSMP) that would primarily allow us to make queries based on the various fields in the database for some well-characterized structural motifs, such as, helices, ${\beta}$-strands, turns, ${\beta}$-hairpins, ${\beta}$-${\alpha}$-${\beta}$, ${\psi}$-loops, ${\beta}$-sheets, disulphide bridges. We have recently implemented this information for all entries in the current PDB in a relational database called ODSMP using Oracle9i that is easy to update and maintain and added few additional structural motifs. We have also developed another relational database corresponding to amino acid sequences and their associated secondary structure for representative proteins in the PDB called PSSARD. This database allows flexible queries to be made on the compatibility of amino acid sequences in the PDB to ‘user-defined’ super-secondary structure conformation and vice-versa. Currently, we have extended this database to include nearly 23,000 protein crystal structures available in the PDB. Further, we have analyzed the ‘structural plasticity’ associated with the ${\beta}$-propeller structural motif We have developed a method to automatically detect ${\beta}$-propellers from the PDB codes. We evaluated the accuracy and consistency of predicting ${\beta}$ and ${\gamma}$-turns in proteins using the residue-coupled model. I will discuss results of our work and describe databases and software applications that have been developed.

• Food Science of Animal Resources
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• v.30 no.1
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• pp.20-27
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• 2010

Deer velvet antler was subjected to the extraction process using boiling water at three different temperatures (100, 110 and $120^{\circ}C$) and 70% ethanol solution. Functional components such as uronic acid, sulfated-glycosaminoglycans (sulfated-GAGs) and sialic acid in the extracts were analyzed, and their antioxidant activities were investigated using several in vitro models. Uronic acid and sulfated-GAGs content of each extract significantly decreased with increasing extraction temperature (p<0.05), while the residues obtained from the upper and middle part of the antler had a higher uronic acid content than the residues obtained from the base section. Sialic acid contents were highest in compounds extracted at $110^{\circ}C$, followed by 120 and $100^{\circ}C$. The 70% ethanol extracts also had a high levels of uronic acid content, but not for sulfated-GAGs and sialic acid. All extracts showed good antioxidant ability in a dose-dependant manner, with the $100^{\circ}C$ residue exhibiting the strongest activity compared to the 110 and $120^{\circ}C$ extracts. In relation to the hydroxyl radical scavenging activity and reduction power, the 70% ethanol extract exhibited the strongest activity. Furthermore, the velvet antler extracts inhibited apoptosis in hydrogen peroxide-induced PC-12 cells.

• Journal of the Mineralogical Society of Korea
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• v.29 no.3
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• pp.113-122
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• 2016

This study aims to improve the recovery of gold and silver by removing hematite from gold ore of an oxidation zone with ammonia solution. Quartz, hematite and muscovite were present in the oxidation zone, while hematite was hydrogenous. As a result of performing an ammonia leaching test on variables, it is found that the maximum Fe leaching parameter was $-45{\mu}m$ particle size, 1.0 M sulfuric acid concentration, 5.0 g/l ammonium sulfate concentration and 2.0 M hydrogen peroxide concentration. It is also confirmed that goethite was precipitated and formed from that ammonia elution. As the amount of Fe-removal was increased in a solid-residue, the recovery of Au and Ag were increased, too.

• Microbiology and Biotechnology Letters
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• v.31 no.4
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• pp.311-321
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• 2003

Bacteria produce lipases, which can catalyze both the hydrolysis and the synthesis of long chain triglycerides. These reactions usually proceed with high regioselectivity and enantioselectivity, and, therefore, lipases have become very important biocatalysts used in organic chemistry. 3D lipase structures were solved from several bacterial lipases. They have an $\alpha/\beta$ hydrolase fold and a catalytic triad consisting of a nucleophilic serine, and an aspartate or glutamate residue that is hydrogen bonded to a histindine. Active sites are covered with $\alpha$-helical lid structure, of which movement is involved in the enzyme's activation at oil/water interface. Four substrate binding pockets were identified for triglycerides: an oxyanion hole and three pockets accommodating the fatty acids bound at positions sn-1, sn-2, and sn-3. These pockets determine the enantiopreference of a lipase. The understanding of structure-function relationships as well as the development of molecular evolution techniques will enable researchers to tailor new lipases for biotechnological applications.

• The Korean Journal of Physiology and Pharmacology
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• v.16 no.3
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• pp.199-204
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• 2012

We evaluated the role of Tat-mediated p66shc transduction on the activation of endothelial nitric oxide synthase in cultured mouse endothelial cells. To construct the Tat-p66shc fusion protein, human full length p66shc cDNA was fused with the Tat-protein transduction domain. Transduction of TAT-p66shc showed a concentration- and time-dependent manner in endothelial cells. Tat-mediated p66shc transduction showed increased hydrogen peroxide and superoxide production, compared with Tat-p66shc (S/A), serine 36 residue mutant of p66shc. Tat-mediated p66shc transduction decreased endothelial nitric oxide synthase phosphorylation in endothelial cells. Furthermore, Tat-mediated p66shc transduction augmented TNF-${\alpha}$-induced p38 MAPK phosphorylation in endothelial cells. These results suggest that Tat-mediated p66shc transduction efficiently inhibited endothelial nitric oxide synthase phosphorylation in endothelial cells.

• Journal of the Korean Chemical Society
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• v.36 no.4
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• pp.523-535
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• 1992

The conformations of hexapeptides, their complexation with alkali cations and the inhibition of the cation transport by 5,5-diphenylhydantoin(DPH) were studied theoretically using ECEPP/2 and MM2 force field. Several low energy conformations of uncomplexed cyclic hexapepides are obtained, and they adopt compact conformations in which most amide hydrogens form intramolecular hydrogen bond to amide carbonyl oxygens. The complexation energy of the peptide with $Na^+$ ion and DPH is -60 kcaal/mol and -18 kcal/mol, respectively. However, no suitable cavity to bind metal cation exists for the local minima of the peptide, and the internal energy of the uncomplexed hexapeptide having cavity is higher than that of the uncomplexed global minimum of this work by 10 kcal/mol. Also, one of the most important amino acid residue to bind DPH is Glycine, and this can explain experimental observation that the replacement of Gly by Sarcosine (N-methyl Glycine) reduce the inhibition ability of the cation transport.

• Journal of Korean Society of Environmental Engineers
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• v.31 no.1
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• pp.1-8
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• 2009

This research was performed to assess a Fenton-like oxidation using naturally present iron in the field to treat remained oils throughout silty clay residues which finally resided even after a series of soil washing process. Biodegradability was thus tested for reaction products to investigate a possible treatment of the Fenton-like oxidation coupled with a biological treatment process. For those purposes, two types of field soil samples (e.g., dewatered cake after conditioning with a polymer and not-dewatered residue) were tested to remove TPH by adding the various concentration of hydrogen peroxide ($H_2O_2$). Moreover the biodegradability of treated samples was observed based on the ratio of $BOD_5/COD_{Cr}$ after Fenton-like oxidation. The Highest removal of TPH was at 1% of hydrogen peroxide ($H_2O_2$) when hydrogen peroxide ($H_2O_2$) was continuously injected for a period of time rather than that of spot introduction with the same amount of it. For the dewatered cake, TPH was effectively treated when the ratio of solid and water was mixed at 1 : 2. Employing cooking oil could increase solubility of TPH due to enhanced surface-active escalating TPH desorption from silty clay. Nonetheless, the biodegradability was decreased as long as the oxidation duration being extended regardless of operational conditions. It was therefore proved that Fenton-like oxidation using $H_2O_2$ and natural iron minerals was able to remove adsorbed oils in silty clay but the removal efficiency of TPH was low. And if a biological treatment process followed after Fenton-like oxidation, microorganisms would need enough time for acclimation.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.26 no.3
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• pp.214-220
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• 1993

Browning of ascidian, Halocynthia roretzi, meat occurres very rapidly when skinned off or cut during processing and it resulted the quality loss of fresh frozen, dehydrated or fermented products. In this study, the causes of color development and prevention of browning were experimented. The browning of ascidian meat may be occurred enzymatically by a tyrosinase contained in meat and viscera which acted specifically on L-tyrosine as a substrate rather than on catechol. Activity of the enzyme in viscera was three times higher than in meat. The optimum pH and temperature on the tyrosinase activity of crude enzyme obtained from ascidian was 6.0 and $30{\sim}35^{\circ}C$, respectively. The enzyme was inactivated heating at $80^{\circ}C$ for 3 minutes or $90{\sim}100^{\circ}C$ for 1 minute and it was inhibited by $0.1{\sim}0.5mM$ solutions at ascorbic acid, sodium hydrogen sulfite, cystein, citric acid, cyanide but only sodium hydrogen sulfite treatment was effective to retard such a high content of enzyme as in case of viscera. In practical use for processing of ascidian meat browning was retarded by dipping the viscera removed ascidian meat in 0.2M citric acid for 5 minutes or $0.2\%$ sodium hydrogen sulfite solution for 1 minute resulting in sulfur dioxide residue less than 100 ppm.