• Bulletin of the Korean Chemical Society
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• v.31 no.11
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• pp.3291-3296
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• 2010

A gelastatins (1), natural MMP inhibitors, and their hydroxamate analogues (2) in TACE enzyme evaluated for discovery of potent TACE inhibitors. We have employed molecular dynamics simulations to compute the relative free energy of hydration and binding to TACE for gelastatin (1) and its hydroxamate analogue (2). The relative free energy difference is directly described in this article using the free energy perturbation approach as a means to accurately predict the TACE inhibitor of gelastatin analogues. The results show that the good agreement between the experimental and theoretical relative free energies of binding, gelastatin hydroxamate (2) binds stronger to TACE by -3.37 kcal/mol. The desolvation energy costs significantly reduced binding affinity, hydroxamate group associated with high desolvation energy formed strong favorable interactions with TACE with more than compensated for the solvation costs and therefore led to an improvement in relative binding affinity.

• Bulletin of the Korean Chemical Society
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• v.31 no.6
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• pp.1568-1572
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• 2010

The selective isolation of specific proteins from complex protein mixtures by nanoparticles is reported. Glutathionemodified superparamagnetic nanoparticles were used to purify specific proteins fused with glutathione S-transferase via enzyme-substrate interactions. They demonstrated greatly improved selectivity and efficiency over micron sized capturing beads. The ultra-specific enrichment of target proteins was confirmed by both SDS-PAGE and LC/MS/MS experiments.

• Proceedings of the PSK Conference
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• 2002.10a
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• pp.359.3-359.3
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• 2002

Protein-tyrosine phosphatase 1 B(PTP-l B). which plays a key role in insulin signaling. is rising as a fascinating target for type 2 diabetes and obesity. Many scientists in structural biology solved the three dimensional X-ray Crystal structure of this type of enzyme, so we could easily get the active site structure of PTP-1 B or complex structure with ligand. Our virtual screening study for PTP-1B exactly based on these crystal strucutures from public database. (omitted)

• Journal of Microbiology
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• v.41 no.3
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• pp.212-218
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• 2003

Citrus phytoene synthase (CitPsy) and ${\beta}$-carotene hydroxylase (CitChx), which are involved in caroteinoid biosynthesis, are distantly related to the corresponding bacterial enzymes from the point of view of amino acid sequence similarity. We investigated these enzyme activities using Pantoea ananatis carotenoid biosynthetic genes and Escherichia coli as a host cell. The genes were cloned into two vector systems controlled by the T7 promoter. SDS-polyacrylamide gel electrophoresis showed that CitPsy and CitChx proteins are normally expressed in E. coli in both soluble and insoluble forms. In vivo complementation using the Pantoea ananatis enzymes and HPLC analysis showed that ${\beta}$-carotene and zeaxanthin were produced in recombinant E. coli, which indicated that the citrus enzymes were functionally expressed in E. coli and assembled into a functional multi-enzyme complex with Pantoea ananatis enzymes. These observed activities well matched the results of other researchers on tomato phytoene synthase and Arabidopsis and pepper ${\beta}$-carotene hydroxylases. Thus, our results suggest that plant carotenoid biosynthetic enzymes can generally complement the bacterial enzymes and could be a means of carotenoid production by molecular breeding and fermentation in bacterial and plant systems.

• Proceedings of the IEEK Conference
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• 2005.11a
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• pp.755-758
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• 2005

This paper describes the novel immunoassay sensing system for a portable clinical diagnosis system. It consists of a bead cage reactor and a CMOS integrated biosensor. It showed the simple and easy antibody coating method on beads by flow-through avidin biotin complex technology in a microfluidic device. It showed just 90 nL sample consumption and good result for the application of alpha feto protein. The bead cage reactor has the role of the antibody coating, antigen binding and enzyme linking for the electrochemical sensing method. The CMOS biosensor consists of ISFET (ion selective field effect transistor) biosensor and temperature sensor for detecting pH that is the byproduct of enzyme reaction. The sensitivity is 8 $kHz/^{\circ}C$ in a temperature sensor and 33 mV/pH in a pH sensor. After filling the 15 um polystyrene beads in bead cage, antibody flowed and reacted to beads. Subsequently, the biotinylated antigen flowed and bound to the antibody and GOD (glucose oxidase)-avidin conjugate flowed and reacted to the biotin of the biotinylated antigen. After this reaction process, glucose solution flowed and reacted to the GOD on beads. The hydrogen was generated by glucose-GOD reaction. And it was detected by the pH sensor.

• Microbiology and Biotechnology Letters
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• v.48 no.1
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• pp.12-23
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• 2020

Edible films containing antimicrobial agents can be used as safe alternatives to preserve food products. Essential oils are well-recognized antimicrobials. However, their low water solubility, volatility and high sensitivity to oxygen and light limit their application in food preservation. These limitations could be overcome by embedding these essential oils in complexed product matrices exploiting the encapsulation efficiency of β-cyclodextrin. This study focused on the maximization of β-cyclodextrin production using cyclodextrin glucanotransferase (CGTase) and the evaluation of its encapsulation efficacy to fabricate edible antimicrobial films. Response surface methodology (RSM) was used to optimize CGTase production by Brevibacillus brevis AMI-2 isolated from mangrove sediments. This enzyme was partially purified using a starch adsorption method and entrapped in calcium alginate. Cyclodextrin produced by the immobilized enzyme was then confirmed using high performance thin layer chromatography, and its encapsulation efficiency was investigated. The clove oil/β-cyclodextrin inclusion complexes were prepared using the coprecipitation method, and incorporated into chitosan films, and subjected to antimicrobial testing. Results revealed that β-cyclodextrin was produced as a major product of the enzymatic reaction. In addition, the incorporation of clove oil/β-cyclodextrin inclusion complexes significantly increased the antimicrobial activity of chitosan films against Staphylococcus aureus, Staphylococcus epidermidis, Salmonella Typhimurium, Escherichia coli, and Candida albicans. In conclusion, B. brevis AMI-2 is a promising source for CGTase to synthesize β-cyclodextrin with considerable encapsulation efficiency. Further, the obtained results suggest that chitosan films containing clove oils encapsulated in β-cyclodextrin could serve as edible antimicrobial food-packaging materials to combat microbial contamination.

• Genomics & Informatics
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• v.13 no.1
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• pp.15-24
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• 2015

Fatty acid synthase (FASN, EC 2.3.1.85), is a multi-enzyme dimer complex that plays a critical role in lipogenesis. This lipogenic enzyme has gained importance beyond its physiological role due to its implications in several clinical conditions-cancers, obesity, and diabetes. This has made FASN an attractive pharmacological target. Here, we have attempted to predict the theoretical models for the human enoyl reductase (ER) and ${\beta}$-ketoacyl reductase (KR) domains based on the porcine FASN crystal structure, which was the structurally closest template available at the time of this study. Comparative modeling methods were used for studying the structure-function relationships. Different validation studies revealed the predicted structures to be highly plausible. The respective substrates of ER and KR domains-namely, trans-butenoyl and ${\beta}$-ketobutyryl-were computationally docked into active sites using Glide in order to understand the probable binding mode. The molecular dynamics simulations of the apo and holo states of ER and KR showed stable backbone root mean square deviation trajectories with minimal deviation. Ramachandran plot analysis showed 96.0% of residues in the most favorable region for ER and 90.3% for the KR domain, respectively. Thus, the predicted models yielded significant insights into the substrate binding modes of the ER and KR catalytic domains and will aid in identifying novel chemical inhibitors of human FASN that target these domains.

• BMB Reports
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• v.34 no.1
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• pp.80-84
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• 2001

The human papillomavirus E7 protein can form a specific complex with a retinoblastoma tumor suppressor gene product (p105-Rb) that results in the release of the E2F transcription factor, which is critical for the growth-deregulation and transforming properties of the viral E7 oncoprotein. In an attempt to apply interaction between the E7 oncoprotein and a target cellular protein Rb for an in vitro screening system for drugs against human papillomavirus infection, we primarily investigated the E7Rb binding through a pull down assay and enzyme-linked immunosorbent assay. The pull down assay showed that both glutathione S-transferase-tagged E7 and His-tagged E7 immobilized on resins specifically produced complexes with bacterially expressed Rb in a dose-dependent manner, as determined by immunoblot analyses. This result coincided with that of an enzyme-linked immunosorbent assay, which is a useful system for the mass screening of potential drugs. Taken together, this screening system (based on the interaction between E7 and Rb) can be a promising system in the development of drugs against cervical cancers caused by human papillomavirus infection.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.30 no.1
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• pp.79-87
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• 1997

A study on the processing method of anchovy hydrolysate paste (AHP) was carried out to improve the sensory quality of salted and fermented fish. Homogenized whole anchovy was hydrolyzed using commercial pretenses, Complex enzyme-2000 (CE, Pacific Chem. Co.) and Alcalase (AL, Novo), in a cylindrical vessel with 4 baffle plates and 6-bladed turbine impeller. Optimal pH, temperature, and enzyme concentration for the hydrolysis with CE and AL were $7.0,\;52^{\circ}C,\;7\%$, and $8.0,\;60^{\circ}C,\;6\%$, respectively. The rational amount of water for homogenization, agitation speed, and hydrolyzing time were $100\%\;(w/w)$, 100 rpm, and 210 min, respectively. To make the hydrolysate to paste type, it was effective to mix the additives, such as starch, soybean protein, agar, and carrageenan gum to the hydrolysate 5 min before the end of boiling at $100^{\circ}C$ for 30 min. Minimal NaCl concentration for long-term preservation was $15\%$, and this could be reduced to $12\%$ by adding $5\%$ of KCl. yield of the AHP based on the total nitrogen content was $94.6\~97.0\%,\;and\;86.0\~89.2\%$, of the nitrogen was amino nitrogen. Salinity, pH and histamine content of the AHP prepared with $12\%$ NaCl and $5\%$ KCl were $9.3\~9.9\%,\;6.1\~6.2$, and below 13 mg/100 g, respectively. The AHP was stable at $26{\pm}3^{\circ}C$ for 60 days on bacterial growth, and addition of $0.05\%$ of rosemary (Herbalox) extract was effective to inhibit the lipid oxidation of the AHP during storage.

• Journal of Ecology and Environment
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• v.33 no.4
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• pp.333-341
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• 2010

The objective of our study was to investigate the major reasons for the different growth and visible injury on the needles of black pine growing in Ulsan and Yeocheon industrial complex areas, South Korea. After 12 years of growth, we collected climatic and air pollutant data, and analyzed soil properties and the physiological characteristics of black pine needles. Annual and minimum temperatures in Ulsan were higher than those in Yeocheon from 1996 to 2008. Ozone ($O_3$) was the pollutant in greatest concentration in Yeocheon, and whereas the $SO_2$ concentration in most areas decreased gradually during the whole period of growth, $SO_2$ concentration in Yeocheon has increased continuously since 1999, where it was the highest out of four areas since 2005. Total nitrogen and cation exchange capacity in Yeocheon soil were significantly lower than those of Ulsan. The average growth of black pine in Yeocheon was significantly smaller than that in Ulsan, and the growth of damaged trees represented a significant difference between the two sites. Photosynthetic pigment and malondialdehyde content and antioxidative enzyme activity in the current needles of black pine in Yeocheon were not significantly different between damaged and healthy trees, but in 1-year-old needles, there were significant differences between damaged and healthy trees. In conclusion, needle damage in Yeocheon black pine can be considered the result of long-term exposure to oxidative stress by such as $O_3$ or $SO_2$, rather than a difference in climatic condition or soil properties, and the additional expense of photosynthate needed to overcome damage or alleviate oxidative stress may cause growth retardation.