• Proceedings of the Plant Resources Society of Korea Conference
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• 2022.09a
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• pp.70-70
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• 2022

Corchoropsis Siebold & Zucc. was traditionally included in Tiliaceae, however, several morphological characters and molecular phylogenetic studies supported that it was the member of Dombeyoideae (Malvaceae). It is used as compost, medicinal, and ornamental herbs. Out of total three species, two species and one variety, grow in Korea. Although it is an East Asian endemic genus, plastome data has not been defined. Here, we characterize the plastome sequences of C. tomentosa (160,093 bp) and C. tomentosa var. psilocarpa (160,724 bp). Corchoropsis encodes 78 protein-coding genes, 30 tRNAs, and four rRNAs with a pseudogene inf A. Phylogenetic study revealed that Tilioideae is sister of Dombeyoideae. This study will contribute to define the genome structures, phylogenetic, and evolutionary studies of the genus Corchoropsis.

• Mass Spectrometry Letters
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• v.15 no.3
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• pp.121-140
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• 2024

Proteoform diversity is greatly increased by glycosylation, the primary post-translational modification of proteins. Glycans, also known as oligosaccharides, are molecules that are essential to almost all living things. They can affect protein folding and functionality, modulate cell-cell interactions, and support the proliferation of numerous diseases when they are found on cell surfaces or bound to proteins. A thorough understanding of their fundamental structure is necessary to gain insight into their characteristics and functions. But a major obstacle is the structural intricacy of glycans by design. The stereochemistry and regiochemistry of carbohydrates vary and are frequently branched. Because of its superior sensitivity and the abundance of fragmentation information it can provide, mass spectrometry is now the method of choice for glycan and glycopeptide analysis. Differentiating between the structures of isomeric and isobaric glycopeptides, however, presents a difficulty for MS-based characterization. Ion mobility plus mass spectrometry (IM-MS) has become a very promising new method for glycan research in recent years. Recent developments in the growing discipline of glycosylation analysis utilizing IM-MS are outlined in this review, with a focus on the MS methodology and its ability to resolve isomeric glycans.

• Bulletin of the Korean Chemical Society
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• v.31 no.3
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• pp.606-610
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• 2010

Aminoacyl-tRNA synthetases (aaRSs) play vital roles in protein biosynthesis of living organisms and are interesting antibacterial drug targets. In order to find out new inhibitor candidate molecules as antibacterial agent, the binding modes of the candidate molecules were investigated at the active sites of aaRSs by molecular docking study. The docking simulations were performed with 48 compounds from four different scaffolds into the eight different aaRSs. The results show that scaffolds 3 and 4 compounds have consistently better binding capabilities, specifically for HisRS (E. coli) and IleRS (S. aureus). The binding modes of the best compounds with the proteins were well compatible with those of two ligands in crystal structures. Therefore, we expect that the final compounds we present may have reasonable aaRS inhibitory activity.

• Journal of the Korean Institute of Intelligent Systems
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• v.25 no.6
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• pp.529-535
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• 2015

Biological networks have been handled with the static concept. However, life phenomena in cells occur depending on the cellular state and the external environment, and only a few proteins and their interactions are selectively activated. Therefore, we should adopt the dynamic network concept that the structure of a biological network varies along the flow of time. This concept is effective to analyze the progressive transition of the disease. In this paper, we applied the proposed method to Alzheimer's disease to analyze the structural and functional characteristics of the disease network. Using gene expression data and protein-protein interaction data, we constructed the sub-networks in accordance with the progress of disease (normal, early, middle and late). Based on this, we analyzed structural properties of the network. Furthermore, we found module structures in the network to analyze the functional properties of the sub-networks using the gene ontology analysis (GO). As a result, it was shown that the functional characteristics of the dynamics network is well compatible with the stage of the disease which shows that it can be used to describe important biological events of the disease. Via the proposed approach, it is possible to observe the molecular network change involved in the disease progression which is not generally investigated, and to understand the pathogenesis and progression mechanism of the disease at a molecular level.

• Korean Journal of Pharmacognosy
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• v.51 no.4
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• pp.244-254
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• 2020

Atractylodes macrocephala is a perennial herb and is a member of the Compositae family. This plant is known to contain various bioactive constituents indicating anti-inflammatory, neuroprotective, anti-oxidant, immunological enhancement, and gastroprotective effects. In this investigation, we isolated four compounds with similar chemical structures from A. macrocephala, and evaluated their anti-inflammatory effects. Among the four compounds, compound 2(atractylenolide II) showed the second-best inhibitory effect on the lipopolysaccharide(LPS)-induced production of nitric oxide in RAW264.7 macrophages and BV2 microglial cells. Compound 2 also inhibited the LPS-induced the production of prostaglandin E2(PGE2), and the expression of inducible nitric oxide synthase(iNOS) and cyclooxygenase(COX)-2 proteins in both cells. In addition, compound 2 suppressed the production of pro-inflammatory cytokines including interleukin(IL)-1β, IL-6, and tumor necrosis factor(TNF)-α. These inhibitory effects were contributed by inactivation of nuclear factor kappa B(NF-κB) and mitogen-activated protein kinases(MAPKs) pathways by treatment with compound 2. This compound did not induce the expression of heme oxygenase(HO)-1 protein indicating that the anti-inflammatory effect of compound 2 was independent with HO-1 protein. Taken together, these results suggested that atractylenolide II can be a candidate material to treat inflammatory diseases.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.2
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• pp.184-193
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• 2007

In mammalian ovary, steroidogenic acute regulatory (StAR) protein mediates the true rate-limiting step of transport of cholesterol from outer to inner mitochondrial membrane. Appropriate expression of StAR gene represents an indispensable component of steroidogenesis and its regulation has been found to be species specific. However, limited information is available regarding StAR gene expression during estrous cycle in buffalo ovary. In the present study, expression, localization and hormonal regulation of StAR mRNA were analyzed by semi-quantitative RT-PCR in buffalo ovary and partial cDNA was cloned. Total RNA was isolated from whole follicles of different sizes, granulosa cells from different size follicles and postovulatory structures like corpus luteum and Corpus albicans. Semi-quantitative RT-PCR analyses showed StAR mRNA expression in the postovulatory structure, corpus luteum. No StAR mRNA was detected in total RNA isolated from whole follicles of different size including the preovulatory follicle (>9 mm in diameter). However, granulosa cells isolated from preovulatory follicles showed the moderate expression of StAR mRNA. To assess the hormonal regulation of StAR mRNA, primary culture of buffalo granulosa cells were treated with FSH (100 ng/ml) alone or along with IGF-I (100 ng/ml) for 12 to 18 h. The abundance of StAR mRNA increased in cells treated with FSH alone or FSH with IGF-I. However, effect of FSH with IGF-I on mRNA expression was found highly significant (p<0.01). In conclusion, differential expression of StAR messages was observed during estrous cycle in buffalo ovary. Also, there was a synergistic action of IGF-I on FSH stimulation of StAR gene.

• Molecules and Cells
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• v.20 no.1
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• pp.1-16
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• 2005

The peptidyl transferase center (PTC) is located in a protein free environment, thus confirming that the ribosome is a ribozyme. This arched void has dimensions suitable for accommodating the 3'ends of the A-and the P-site tRNAs, and is situated within a universal sizable symmetry-related region that connects all ribosomal functional centers involved in amino-acid polymerization. The linkage between the elaborate PTC architecture and the A-site tRNA position revealed that the A-to P-site passage of the tRNA 3'end is performed by a rotatory motion, which leads to stereochemistry suitable for peptide bond formation and for substrate mediated catalysis, thus suggesting that the PTC evolved by genefusion. Adjacent to the PTC is the entrance of the protein exit tunnel, shown to play active roles in sequence-specific gating of nascent chains and in responding to cellular signals. This tunnel also provides a site that may be exploited for local co-translational folding and seems to assist in nascent chain trafficking into the hydrophobic space formed by the first bacterial chaperone, the trigger factor. Many antibiotics target ribosomes. Although the ribosome is highly conserved, subtle sequence and/or conformational variations enable drug selectivity, thus facilitating clinical usage. Comparisons of high-resolution structures of complexes of antibiotics bound to ribosomes from eubacteria resembling pathogens, to an archaeon that shares properties with eukaryotes and to its mutant that allows antibiotics binding, demonstrated the unambiguous difference between mere binding and therapeutical effectiveness. The observed variability in antibiotics inhibitory modes, accompanied by the elucidation of the structural basis to antibiotics mechanism justifies expectations for structural based improved properties of existing compounds as well as for the development of novel drugs.

• Journal of the Computational Structural Engineering Institute of Korea
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• v.20 no.3
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• pp.365-370
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• 2007

Many engineering problems often require the large amount of computing resources for iterative simulations of problems treating many parameters and input files. In order to overcome the situation, this paper proposes an e-Science based computational system. The system exploits the Grid computing technology to establish an integrated web service environment which supports distributed high throughput computational simulations and remote executions. The proposed system provides an easy-to-use parametric study service where a computational service includes real time monitoring. To verify usability of the proposed system, two kinds of applications were introduced. The first application is an Aerospace Integrated Research System (e-AIRS). The e-AIRS adapts the proposed computational system to solve CFD problems. The second one is design and optimization of protein 3-dimensional structures in structural biology.

• BMB Reports
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• v.40 no.4
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• pp.595-603
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• 2007

To investigate whether phospholipase D (PLD, EC 3.1.4.4) plays a role in adaptive response of post-harvest fruit to environment, a PLD gene was firstly cloned from grape berry (Vitis Vinifera L. cv. Chardonnay) using RT-PCR and 3'- and 5'-RACE. The deduced amino acid sequence (809 residues) showed 84.7% identity with that of PLD from Ricinus communis. The secondary structures of this protein showed the characteristic C2 domain and two active sites of a phospholipid-metabolizing enzyme. The PLD activity and its expression in response to heat acclimation were then assayed. The results indicated PLD was significantly activated at enzyme activity, as well as accumulation of PLD mRNA and synthesis of new PLD protein during the early of heat acclimation, primary suggesting that the grape berry PLD may be involved in the heat response in post-harvest grape berry. This work offers an important basis for further investigating the mechanism of post-harvest fruit adaptation to environmental stresses.

• Molecules and Cells
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• v.19 no.2
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• pp.219-222
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• 2005

The a-subunit of Escherichia coli tryptophan synthase (${\alpha}TS$), a component of the tryptophan synthase ${\alpha}_2{\beta}_2$ complex, is a monomeric 268-residues protein (Mr = 28,600). ${\alpha}TS$ by itself catalyzes the cleavage of indole-3-glycerol phosphate to glyceraldehyde-3-phosphate and indole, which is converted to tryptophan in tryptophan biosynthesis. Wild-type and P28L/Y173F double mutant ${\alpha}$-subunits were overexpressed in E. coli and crystallized at 298 K by the hanging-drop vapor-diffusion method. X-ray diffraction data were collected to $2.5{\AA}$ resolution from the wild-type crystals and to $1.8{\AA}$ from the crystals of the double mutant, since the latter produced better quality diffraction data. The wild-type crystals belonged to the monoclinic space group C2 ($a=155.64{\AA}$, $b=44.54{\AA}$, $c=71.53{\AA}$ and ${\beta}=96.39^{\circ}$) and the P28L/Y173F crystals to the monoclinic space group $P2_1$ ($a=71.09{\AA}$, b=52.70, $c=71.52{\AA}$ and ${\beta}=91.49^{\circ}$). The asymmetric unit of both structures contained two molecules of ${\alpha}TS$. Crystal volume per protein mass ($V_m$) and solvent content were $2.15{\AA}^3\;Da^{-1}$ and 42.95% for the wild-type and $2.34{\AA}^3\;Da^{-1}$ and 47.52% for the double mutant.