• Proceedings of the Korean Information Science Society Conference
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• 2002.10c
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• pp.226-228
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• 2002

현재 유전자 서열 분석이 완료된 유전체들이 점점 늘어나고 있다. 따라서 이에 대한 방대한 정보가 생성됨에 따라 다양한 생물체들에 대하여 대사 네트웍을 통한 다차원적 분석이 가능하게 되었다. 대사 네트웍은 단백질 또는 효소들의 전체적인 상호작용을 표현하기 때문에 생물학적 메카니즘에 대하여 보다 풍부한 정보를 제공해 준다. 본 논문에서는 일차원적인 유전자 서열에 의한 종의 계통 분류가 아니라 메타 수준의 생리 구조적 비교를 통하여 계통분류학에 대하여 새로운 방법의 접근을 제안하고자 한다. 제안된 방법은 기존의 상동성 비교에 의한 계통 분류와 함께 좀 더 포괄적이고 거시적인 분석을 가능하게 한다.

• The Korean Journal of Zoology
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• v.38 no.3
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• pp.417-425
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• 1995

The present study was carried out to investigate the effect of microwave fixation in comparison with that of chemical fixation in preparing the microscopic samples. The microwave fixator was equipped with infrared-temperature sensor, and that was designed to compensate air temperature in the microwave fixator. In the microwave fixation, rat tongue was well preserved in terms of muscular fasciculus and pancreas stained by Feulgen reagents showed clear reaction products in the nucleus. Reaction products by PAS method in duodenal villi appeared specifically at the goblet cells. In electron microscopy, pancreatic cellular components such as secretory granules and collagen bundles were well preserved in both fixations. In aspect of histochemical reaction and electron microscopy, high quality was due to the protein content of microwave fixed specimen. The microwave fixation method saved total duration engaging microscopic preparation.

• Korean Journal of Food Science and Technology
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• v.31 no.3
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• pp.586-592
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• 1999

The objective of this study was to investigate the fundamental characteristics of proteins effecting on Korean wheat flour quality. Mixing properties and protein contents of Eunpa, Allgreu, and Woori showed soft wheat characteristics. Tapdong had strong dough stability and high protein content like hard wheat flour. However, even though Greu had a high protein content, the dough strength was very weak like soft wheat flour. No major difference was observed in protein solubility with water, 0.1N NaCl, 70% ethyl alcohol, 0.1 N acetic acid solution and in sulfur and disulfide contents between Korean wheat flours and imported flours. However, DNS (Dark Norther Spring) had more contents of acid insoluble and SDS insoluble proteins compared with Korean wheat varieties. PAGE pattern of Tapdong was very similar to imported wheat flours at the high molecular weight regions and characteristic high molecular weight glutenin subunits were observed over 116 kD protein molecular weight region from 4 Korean wheat flours such as Eunpa, Woori, Allgreu, and Greu.

• Proceedings of the Korea Contents Association Conference
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• 2008.05a
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• pp.842-845
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• 2008

The protein interaction network contains a small number of highly connected protein, denoted hub and many destitutely connected proteins. Recently, several studies described that a hub protein is more likely to be essential than a non-hub protein. This phenomenon called as the centrality-lethality rule. This rule is widely credited to exhibit the importance of hub proteins in the complex network and the significance of network architecture as well. To confirm whether the rule is accurate, we investigated all protein interaction DBs of yeast in the public sites such as Uetz, Ito, MIPS, DIP, SGD, and BioGRID. Interestingly, the protein network shows that the rule is correct in lower scale DBs (e.g., Uetz, Ito, and DIP) but is not correct in higher scale DBs (e.g., SGD and BioGRID). We are now analyzing the features of networks obtained from the SGD and BioGRD and comparing those of network from the DIP.

• Korean Journal of Plant Resources
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• v.16 no.1
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• pp.82-88
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• 2003

Genomic RNA sequence of a tobamovirus infecting Eutrema wasabi plant(TMV-W) was determined. The RNA is composed 6,298 nucleotide and contains four OREs encoding the protein of 180KD(OREI), 130KD(ORE2),30KD(ORF3) and 18KD(coat protein, ORF4). ORE4, ORF 3, ORF 2 and ORF 1 are overlaped by 130, 20 and 40 nucleotides, and the overapping region can be folded into a stable hairpin styucture. This includes the 3'non-coding region of 238 nucleotides, coat protein gene(537 nucleotides,179 amino acid), 30KD movement protein gene(825 nucleotides, 275 amino acid), 13(IKD protein gene(1,896 nucleotides, 632 amino acid) and 180KD protein gene(2,958 nucleotides, 986 amino acid). The genomic RNA sequence was compared with homologous regions of eleven other tobamoviruses. TMV-WTE was similar to TMV-WSF(98.6%) in nucleotide sequence.

• The KIPS Transactions:PartD
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• v.15D no.5
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• pp.681-690
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• 2008

In proteomics research, the identification of differentially expressed proteins observed under specific conditions is one of key issues. There are several ways to detect the change of a specific protein's expression level such as statistical analysis and graphical visualization. However, it is quiet difficult to handle the spot information of an individual protein manually by these methods, because there are a considerable number of proteins in a tissue sample. In this paper, using database and data mining techniques, the application plan of OLAP data cube and Discovery-driven exploration is proposed. By using data cubes, it is possible to analyze the relationship between proteins and relevant clinical information as well as analyzing the differentially expressed proteins by disease. We propose the measure and exception indicators which are suitable to analyzing protein expression level changes are proposed. In addition, we proposed the reducing method of calculating InExp in Discovery-driven exploration. We also evaluate the utility and effectiveness of the data cube and Discovery-driven exploration in the lung cancer 2-DE gel image.

• Journal of Life Science
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• v.26 no.2
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• pp.253-258
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• 2016

In this study, nano-micelled curcumin was produced with natural sea salt with a view to comparing the in silico molecular binding affinity of pure curcumin compound to the active site of transthyretin. Using an optical light microscope and an electron microscope, it was found that the structure of the surface and the cross-section of nano-micelled curcumin was significantly different from natural sea salt. In particular, the crystal structure and nano-components in the nano-micelled curcumin were united, and the layer was more strongly stabilized than untreated salts. In the virtual 3D structure, in silico molecular docking study, the ligand binding affinity of nano-micelled curcumin to the transthyretin active site was found to be higher than that of pure curcumin. In addition, a nano-micelled curcumin formula interacted with more amino acid residues of transthyretin domains. The pharmacophore feature of the nano-micelled curcumin also showed more condensed and constrained features than normal curcumin. These results suggest that nano-micelled curcumin may effectively bind to and stabilize transthyretin, thereby regulating transthyretin-related physiological diseases. Collectively, the nano-micelled curcumin process suggests that normal curcumin can be modified more efficiently into the novel bio-functional chemical formula to stabilize the transthyretin structure. Therefore, the nano-micelled curcumin process can be applied to the field of the regulation of Alzheimer's disease.

• Korean Journal of Microbiology
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• v.26 no.4
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• pp.283-290
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• 1988

A spontaneous revertant of mutation rbsB103 that is ribose taxis-positive was characterized. This revertant was found to be export-competent in the export of ribose-binding protein shown by the disappearance of accumulated mutant precursor protein and the export of mature ribose-binding protein to the periplasm. The reversional change was shown to be in the region of risB gene that codes for the amino terminal portion of ribose-binding protein. Analysis by high-performance liquid chromatography of peptide patterns of ribose-binding proteins confirmed the relationship between the wild-type and the revertant proteins as shown for the mutant previously (Iida et al., 1985). When the processing rate of presursor proteins from the wild type and the revertant strain in vivo was compared by pulse-chase experiment, it was found that processing is less efficient than normal in the revertant. Purified mature proteins from both wild-type and revertant were subjected to amino acid sequencing. The results confirmed the amino acid changes deduced from the DNA sequencing and showed that processing of the revertant precursor occured in the correct position even though there are two different amino acids present in the signal sequence.

• Journal of Life Science
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• v.28 no.2
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• pp.195-200
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• 2018

Beta-asarone is the well-known active ingredient of Rhizoma acori graminei. In this study, we investigated and compared the binding affinity of mosquito oviposition pheromone (MOP; (5R,6S)-6-acetoxy-5-hexadecanolide) and beta-asarone on the A domain of the mosquito odorant binding protein 1 (CquiOBP1) by in silico computational docking studies. The three-dimensional crystallographic structure of CquiOBP1 was obtained from the PDB database (PDB ID: 3OGN). In silico computational auto-docking analysis was performed using PyRx, Autodock Vina, Discovery Studio Version 4.5, and the NX-QuickPharm option based on scoring functions. The beta-asarone showed optimum binding affinity (docking energy) with CquiOBP1 as -6.40 kcal/mol as compared to the MOP (-6.00 kcal/mol). Among the interacting amino acids (LEU76, LEU80, ALA88, MET89, HIS111, TRP114, and TYR122), tryptophan 114 in the CquiOBP1 active site significantly interacted with both MOP and beta-asarone. Amino acids substitution (mutation) from non-polar groups to the polar (or charged) groups of the CquiOBP1 dramatically changed the X, Y, Z grid position and binding affinity of both ligands. These results significantly indicated that beta-asarone could be a more potent ligand to the CquiOBP1 than MOP. Therefore, the extract of Rhizoma acori graminei or beta-asarone can be applied to the fields of insecticidal and repellant biomaterial development.

• Journal of Life Science
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• v.28 no.4
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• pp.408-414
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• 2018

Actein is the well-known active ingredient of Cimicifugae rhizoma (Black cohosh). In this study, we investigated and compared the binding affinity of tubocurarine, actein, and actein derivatives on the B&C domain of the acetylcholine binding protein through in silico computational docking studies. The three-dimensional crystallographic structure of the acetylcholine binding protein B&C domain was obtained from the PDB database (PDB ID: 2XYT). An in silico computational autodocking analysis was performed using PyRx, Autodock Vina, Discovery Studio Version 4.5, and NX-QuickPharm based on scoring functions. The actein showed an optimum binding affinity (docking energy), with the acetylcholine binding protein at -10.50 kcal/mol as compared to the tubocurarine (-9.80 kcal/mol). The interacting amino acids tryptophan 84 and tryptophan 147, in the B domain of the acetylcholine binding protein active site, significantly interacted with the actein and 27-deoxyactein, and (26R)-actein. The centroid XYZ grid position of the tubocurarine was X=38.300689, Y=112.053467, and Z=51.991022, but the actein and its derivatives showed values around X=26.4, Y=127.3, Z=43.7. These results clearly indicated that actein and its derivatives could be a more potent antagonist to the acetylcholine binding protein than tubocurarine. Therefore, the extract of Cimicifugae rhizoma or actein containing biomaterials can substitute for the botulinum toxin-mediated acetylcholine receptor regulation, and be applied to the anti-wrinkle cosmetics industry.