• Bulletin of the Korean Chemical Society
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• v.30 no.7
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• pp.1505-1515
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• 2009

A new method to semicontinuously determine $PM_{2.5}$ ionic species with a short time resolution is described in detail. In this system, a particle collection section (mixing part, particle collection chamber, and air/liquid separator) was developed. A Y-type connector was used to mix steam and an air sample. The particle collection chamber was constructed in the form of a helix coil and was cooled by a water circulation system. Particle size growth occurred due to the high relative humidity and water absorbed particles were efficiently collected in it. Liquid samples were drained out with a short residence time (0.08-0.1 s). The air/liquid separator was also newly designed to operate efficiently when the flow rate of the air sample was 16.7 L $min^{-1}$. For better performance, the system was optimized for particle collection efficiency with various types of test aerosols such as ($NH_4)_2SO_4,\;NaCl,\;NH_4HSO_4,\;and\;NH_4NO_3$. The particle collection efficiencies were almost 100% at different concentration levels in the range over 500 nm in diameter but 50-90% in the range of 50-500 nm under the following experimental conditions: 15 coil turns, a water flow rate for steam generation of 0.65 mL $min^{-1}$, and an air sample flow rate of 16.7 L $min^{-1}$. Finally, for atmospheric applications, chemical compositions of $PM_{2.5}$ were determined with a time resolution of 20 min on January 11-24, 2006 in Seoul, Korea, and the chemical characteristics of $PM_{2.5}$ ions were investigated.

• Molecules and Cells
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• v.46 no.8
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• pp.513-525
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• 2023

Orange carotenoid protein (OCP) of photosynthetic cyanobacteria binds to ketocarotenoids noncovalently and absorbs excess light to protect the host organism from light-induced oxidative damage. Herein, we found that mutating valine 40 in the α3 helix of Gloeocapsa sp. PCC 7513 (GlOCP1) resulted in blue- or red-shifts of 6-20 nm in the absorption maxima of the lit forms. We analyzed the origins of absorption maxima shifts by integrating X-ray crystallography, homology modeling, molecular dynamics simulations, and hybrid quantum mechanics/molecular mechanics calculations. Our analysis suggested that the single residue mutations alter the polar environment surrounding the bound canthaxanthin, thereby modulating the degree of charge transfer in the photoexcited state of the chromophore. Our integrated investigations reveal the mechanism of color adaptation specific to OCPs and suggest a design principle for color-specific photoswitches.

• Journal of Gastric Cancer
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• v.20 no.2
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• pp.190-201
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• 2020

Purpose: This study sought to investigate the prognostic significance of tumor-infiltrating lymphocytes (TILs) in relation to tumor location within the stomach. Materials and Methods: The densities and prognostic significance of TIL subsets were evaluated in 542 gastric cancer patients who underwent gastrectomy. Immunohistochemical staining for CD3, CD4, CD8, forkhead/winged helix transcription factor (Foxp3), and granzyme B was performed. Results: Cardia cancer was associated with significantly lower densities of CD8 T-cells and higher densities of Foxp3 and granzyme B T-cells than non-cardia tumors. Multivariate analysis showed that advanced age (hazard ratio [HR], 1.023; 95% confidence interval [CI], 1.006-1.040), advanced T classification (HR, 2.029; 95% CI, 1.106-3.721), lymph node metastasis (HR, 3.319; 95% CI, 1.947-5.658), low CD3 expression (HR, 0.997; 95% CI, 0.994-0.999), and a high Foxp3/CD4 ratio (HR, 1.007; 95% CI, 1.001-1.012) were independent predictors of poor overall survival in cardia cancer patients. In non-cardia cancer patients, total gastrectomy (HR, 2.147; 95% CI, 1.507-3.059), advanced T classification (HR, 2.158; 95% CI, 1.425-3.266), lymph node metastasis (HR, 1.854; 95% CI, 1.250-2.750), and a low Foxp3/CD4 ratio (HR, 0.978; 95% CI, 0.959-0.997) were poor prognostic factors for survival. Conclusions: The densities and prognostic effects of TILs differed in relation to the location of tumors within the stomach. The contrasting prognostic effects of Foxp3/CD4 ratio in cardia and non-cardia gastric cancer patients suggests that clinicians ought to consider tumor location when determining treatment strategies.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.13 no.11
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• pp.5350-5355
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• 2012

Human tyrosinase (hTyr) catalyzes the first and rate limiting step in the biosynthesis of a skin color determinant, melanin. Although a number of cosmetic companies have tried to develop hTyr inhibitors for several decades, absence of 3D structure of hTyr make it impossible to design or screen inhibitors by structure-based approach. Therefore, we built a 3D structure by comparative modeling technique based on the crystal structure of tyrosinase from Bacillus megaterium to provide structural information and to search new hit compounds from database. Our model revealed that two copper atoms of active site located deep inside and were coordinated with six strictly conserved histidine residues coming from four-helix-bundle. Substrate binding site had narrow funnel like shape and its entrance was wide and exposed to solvent. In addition, hTyr-tyrosine and hTyr-kojic acid, a well-known inhibitor, complexes were modeled with the guide of solvent accessible surface generated by in-house software. Our model demonstrated that only phenol group or its analogs could fill the binding site near the nuclear copper center, because inside of binding site had narrow shape relatively. In conclusion, the results of this study may provide helpful information for designing and screening new anti-melanogenic agents.

• Journal of the Korean Society of Food Science and Nutrition
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• v.33 no.10
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• pp.1668-1675
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• 2004

The effect of pH on surface hydrophobicity, sulfhydryl group, infrared spectrum, SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis) pattern and enthalpy was investigated in recovered protein from mackerel and frozen blackspotted croaker by alkaline processing. Hydrophobic residue in myofibrillar protein exposed to the surface of protein, and hydrophobic interaction were the highest around 6$0^{\circ}C$. The surface hydrophobicity was different between myofibrillar protein and myofibrillar protein including sarcoplasmic protein (recovered protein). The peak at 1636 c $m^{-l}$ was increased with pH, and the recovered protein was unfolded in alkali pH. Difference of surface and total sulfhydryl group at pH 7.0 and 10 was comparative high, and decrease of surface sulfhydryl group indicated formation of S-S bonds. Mackerel and frozen blackspotted croaker in alkaline pH showed bands of polymerized myosin heavy chain on SDS-PAGE pattern. The transition temperatures of recovered protein were 33.1, 44.3 and 65.5$^{\circ}C$. Gelation of recovered protein from alkali processing was estimated by increase of $\beta$-sheet structure by pH treatment, S-S bonds by oxidation of surface sulfhydryl group in heating, polymerization of myosin heavy chain in order.r.

• BMB Reports
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• v.37 no.3
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• pp.304-313
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• 2004

Three-dimensional (3D) models for the 65-kDa activated Cry4A and Cry4B $\delta$-endotoxins from Bacillus thuringiensis subsp. israelensis that are specifically toxic to mosquito-larvae were constructed by homology modeling, based on atomic coordinates of the Cry1Aa and Cry3Aa crystal structures. They were structurally similar to the known structures, both derived 3D models displayed a three-domain organization: the N-terminal domain (I) is a seven-helix bundle, while the middle and C-terminal domains are primarily comprise of anti-parallel $\beta$-sheets. Circular dichroism spectroscopy confirmed the secondary structural contents of the two homology-based Cry4 structures. A structural analysis of both Cry4 models revealed the following: (a) Residues Arg-235 and Arg-203 are located in the interhelical 5/6 loop within the domain I of Cry4A and Cry4B, respectively. Both are solvent exposed. This suggests that they are susceptible to tryptic cleavage. (b) The unique disulphide bond, together with a proline-rich region within the long loop connecting ${\alpha}4$ and ${\alpha}5$ of Cry4A, were identified. This implies their functional significance for membrane insertion. (c) Significant structural differences between both models were found within domain II that may reflect their different activity spectra. Structural insights from this molecular modeling study would therefore increase our understanding of the mechanic aspects of these two closely related mosquito-larvicidal proteins.

• Journal of Life Science
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• v.20 no.3
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• pp.365-373
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• 2010

To monitor newly emerged influenza virus variants and to investigate the prevalence pattern, our laboratory performed isolation of the viruses from surveillance sentinel hospitals. In the present study, we analysed influenza A/H1N1, A/H3N2, B viruses isolated in Busan during the 2006/07 and 2007/08 seasons by sequence analysis of the hemagglutinin (HA1 subunit) and neuraminidase (NA) genes. The isolates studied here were selected by the stratified random sample method from a total of 277 isolates, in which 15 were A/H1N1, 16 were A/H3N2 and 29 were B. Based on the phylogenetic tree, the HA1 gene showed that A/H1N1 isolates had a 96.7% to 97.7% homology with the A/Brisbane/59/2007, A/H3N2 isolates had a 98.4% to 99.7% homology with the A/Brisbane/10/2007, and B isolates had a 96.5% to 99.7% homology with the B/Florida/4/2006(Yamagata lineage), which are all the vaccine strains for the Northern Hemisphere in 2008~2009 season. In the case of the NA gene, A/H1N1 isolates had 97.8% to 98.5% homologies, A/H3N2 isolates had 98.9% to 99.4% homologies, and B isolates had 98.9% to 100% homologies with each vaccine strain in the 2008~2009 season, respectively. Characterization of the hemagglutinin gene revealed that amino acids at the receptor-binding site and N-linked glycosylation site were highly conserved. These results provide useful information for the control of influenza viruses in Busan and for a better understanding of vaccine strain selection.

• Journal of Life Science
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• v.21 no.12
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• pp.1778-1783
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• 2011

Hematopoietic cytokines regulate production of blood cells by stimulating proliferation and differentiation of bone marrow cells. Among these hematopoietic cytokines, called hematopoitic growth factors, glranulocyte-colony stimulating Factor (G-CSF), which regulates growth of neutrophils, is one of important therapeutic factors because cancer patients suffer with neutropenia which is severe reduction of neutrophils after chemotherapy. Two groups of recombinant G-CSF have approved and used for therapeutic purposes and many researches are still on-going to produce recombinant G-CSF by different techniques. We engineered human G-CSF with Bombyx specific endoplasmic reticulum (ER) signal sequence, therefore, secretion of human G-CSF protein was improved in Bombyx mori-origined cell line, Bm5. The Bombyx ER signal sequence and human G-CSF matured protein region chimera was further remodeled at the N-terminus of matured G-CSF protein to understand roles of N-terminus on outer cellular secretion and/or production. Three different mutants were generated deleting three amino acids in non alpha-helical region in N-terminus in order to scan important amino acids for G-CSF secretion. One of 3 different N-terminal deletion mutants showed dramatically reduction of secreted amount of G-CSF indicating its important role on secretion. The data suggest that remodeling in non alpha-helical region of N-terminus is also important for recombinant G-CSF production.

• BMB Reports
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• v.54 no.2
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• pp.118-123
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• 2021

The bacterial effector protein RavZ from a pathogen can impair autophagy in the host by delipidating the mammalian autophagy-related gene 8 (mATG8)-phosphatidylethanolamine (PE) on autophagic membranes. In RavZ, the membrane-targeting (MT) domain is an essential function. However, the molecular mechanism of this domain in regulating the intracellular localization of RavZ in cells is unclear. In this study, we found that the fusion of the green fluorescent protein (GFP) to the MT domain of RavZ (GFP-MT) resulted in localization primarily to the cytosol and nucleus, whereas the GFP-fused duplicated-MT domain (GFP-2xMT) localized to Rab5- or Rab7-positive endosomes. Similarly, GFP fusion to the catalytic domain (CA) of RavZ (GFP-CA) resulted in localization primarily to the cytosol and nucleus, even in autophagy-induced cells. However, by adding the MT domain to GFP-CA (GFP-CA-MT), the cooperation of MT and CA led to localization on the Rab5-positive endosomal membranes in a wortmannin-sensitive manner under nutrient-rich conditions, and to autophagic membranes in autophagy-induced cells. In autophagic membranes, GFP-CA-MT delipidated overexpressed or endogenous mATG8-PE. Furthermore, GFP-CA△α3-MT, an α3 helix deletion within the CA domain, failed to localize to the endosomal or autophagic membranes and could not delipidate overexpressed mATG8-PE. Thus, the CA or MT domain alone is insufficient for stable membrane localization in cells, but the cooperation of MT and CA leads to localization to the endosomal and autophagic membranes. In autophagic membranes, the CA domain can delipidate mATG8-PE without requiring substrate recognition mediated by LC3-interacting region (LIR) motifs.

• Journal of Life Science
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• v.31 no.7
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• pp.671-676
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• 2021

A cDNA encoding the protein lethal (2) essential for life [l(2)efl] was cloned from Gryllus bimaculatus and named GBl(2)efl. This protein is composed of 189 amino acids, including an N-glycosylation site and 15 phosphorylation sites. Its predicted molecular mass is 21.19 kDa, with a theoretical isoelectric point of 6.2. The secondary structure of GBl(2)efl was predicted from the identification of random coils (56.08%), alpha helices (22.22%), extended strands (17.99%), and beta turns (3.7%) through sequence analyses. A homology analysis revealed that GBl(2)efl exhibited a high similarity with other species at the amino acid level, ranging from 52% to 69%. While GBl(2)efl mRNA expression was higher in the dorsal longitudinal flight muscle following a three-day starvation and in the Malpighian tubules following a one-day starvation, no changes in expression were detected in other tissues. Furthermore, tunicamycin-induced endoplasmic reticulum (ER) stress resulted in an approximately 1.8-fold higher expression in the fat body compared with the wild type.