• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.13-16
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• 2000

Microorganisms have been widely employed for the production of useful bioproducts including primary metabolites such as ethanol, succinic acid, acetone and butanol, secondary metabolites represented by antibiotics, proteins, polysaccharides, lipids and many others. Since these products can be obtained in small quantities under natural condition, mutation and selection processes have been employed for the improvement of strains. Recently, metabolic engineering strategies have been employed for more efficient production of these bioproducts. Metabolic engineering can be defined as purposeful modification of cellular metabolic pathways by introducing new pathways, deleting or modifying the existing pathways for the enhanced production of a desired product or modified/new product, degradation of xenobiotics, and utilization of inexpensive raw materials. Metabolic flux analysis and metabolic control analysis along with recombinant DNA techniques are three important components in designing optimized metabolic pathways, This powerful technology is being further improved by the genomics, proteomics, metabolomics and bioinformatics. Complete genome sequences are providing us with the possibility of addressing complex biological questions including metabolic control, regulation and flux. In silico analysis of microbial metabolic pathways is possible from the completed genome sequences. Transcriptome analysis by employing ONA chip allows us to examine the global pattern of gene expression at mRNA level. Two dimensional gel electrophoresis of cellular proteins can be used to examine the global proteome content, which provides us with the information on gene expression at protein level. Bioinformatics can help us to understand the results obtained with these new techniques, and further provides us with a wide range of information contained in the genome sequences. The strategies taken in our lab for the production of pharmaceutical proteins, polyhydroxyalkanoate (a family of completely biodegradable polymer), succinic acid and me chemicals by employing metabolic engineering powered by genomics, proteomics, metabolomics and bioinformatics will be presented.

• Journal of Plant Biotechnology
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• v.30 no.3
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• pp.281-291
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• 2003

In this review, we described the catalogues of the rice proteome which were constructed in our program, and functional characterization of some of these proteins was discussed. Mass-spectrometry is the most prevalent technique to rapidly identify a large number of proteome analysis. However, the conventional Western blotting/sequencing technique has been used in many laboratories. As a first step to efficiently construct protein cata-file in proteome analysis of major cereals, we have analyzed the N-terminal sequences of 100 rice embryo proteins and 70 wheat spike proteins separated by two-dimensional electrophoresis. Edman degradation revealed the N-terminal peptide sequences of only 31 rice proteins and 47 wheat proteins, suggesting that the rest of separated protein sports are N-terminally blocked. To efficiently determine the internal sequence of blocked proteins, we have developed a modified Cleveland peptide mapping method. Using this above method, the internal sequences of all blocked rice proteins(i, e., 69 proteins) were determined. Among these 100 rice proteins, thirty were proteins for which homologous sequence in the rice genome database could be identified. However, the rest of the proteins lacked homologous proteins. This appears to be consistent with the fact that about 45% of total rice cDNA have been deposited in the EMBL database. Also, the major proteins involved in the growth and development of rice can be identified using the proteome approach. Some of these proteins, including a calcium-binding protein that tuned out to be calreticulin, gibberellin-binding protein, which is ribulose-1.5-bisphosphate carboxylase/oxygense active in rice, and leginsulin-binding protein in soybean have functions in the signal transduction pathway. Proteomics is well suited not only to determine interaction between pairs of proteins, but also to identify multisubunit complexes. Currently, a protein-protein interaction database for plant proteins(http://genome.c.kanazawa-u.ac.jp/Y2H)could be a very useful tool for the plant research community. Also, the information thus obtained from the plant proteome would be helpful in predicting the function of the unknown proteins and would be useful be in the plant molecular breeding.

• Bulletin of the Korean Chemical Society
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• v.35 no.4
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• pp.1144-1148
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• 2014

Here we report a facile synthesis of ruthenium (Ru) Nanoparticles (NPs) by chemical co-precipitation method. The calcination of ruthenium hydroxide samples at $500^{\circ}C$ under hydrogen atmosphere lead to the formation of $Ru^0$ NPs. The size and aggregation of Ru NPs depends on the pH of the medium, and type of surfactant and its concentration. The X-ray diffraction (XRD), scanning electron microscope (SEM) and transmission electron microscope image (TEM) analyses of particles indicated the formation of $Ru^0$ NPs, and have 10 to 20 nm sizes. As-synthesized $Ru^0$ NPs are characterized and investigated their catalytic ability in click chemistry (azidealkyne cycloaddition reactions), showing good results in terms of reactivity. Interestingly, small structural differences in triazines influence the catalytic activity of $Ru^0$ nanocatalysts. Click chemistry has recently emerged to become one of the most powerful tools in drug discovery, chemical biology, proteomics, medical sciences and nanotechnology/nanomedicine. In addition, preliminary tests of recycling showed good results with neither loss of activity or significant precipitation.

• Bulletin of the Korean Chemical Society
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• v.27 no.5
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• pp.793-796
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• 2006

• Journal of Microbiology and Biotechnology
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• v.18 no.8
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• pp.1439-1444
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• 2008

The recombinant E. coli $\Delta$6 mutant (galR, glpK, gldA, IdhA, lacI, tpiA) was used to produce 1,3-propanediol (PD) from glucose. The 1,3-PD production increased with feedback control of the glucose concentration using fed-batch fermentation. The maximum 1,3-PD concentration produced was 43 g/l after 60 h of fermentation. Glycerol production was minimized when controlling the glucose concentration at less than 1 g/l. The expression levels of seven enzymes related to the 1,3-PD production metabolism were compared during the cell growth phase and 1,3-PD production phase, and their expression levels all increased during 1,3-PD production, with the exception of alcohol dehydrogenase.

• Journal of the Korean Chemical Society
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• v.59 no.5
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• pp.466-470
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• 2015

• 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.

• Bulletin of the Korean Chemical Society
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• v.26 no.8
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• pp.1168-1169
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• 2005

• Bulletin of the Korean Chemical Society
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• v.33 no.12
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• pp.4041-4046
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• 2012

The recombinant expression of proteins has been the method of choice to meet the demands from proteomics and structural genomics studies. Despite its successful production of many heterologous proteins, Escherichia coli failed to produce many other proteins in their native forms. This may be related to the fact that the stresses resulting from the overproduction interfere with cellular processes. To better understand the physiological change during the overproduction phase, we profiled the metabolites along the time course of the recombinant protein expression. We identified 32 metabolites collected from different time points in the protein production phase. The stress induced by protein production can be characterized by (A) the increased usage of aspartic acid, choline, glycerol, and N-acetyllysine; and (B) the accumulation of adenosine, alanine, oxidized glutathione, glycine, N-acetylputrescine, and uracil. We envision that this work can be used to create a strategy for the production of usable proteins in large quantities.

• Proceedings of the KIEE Conference
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• 2003.10a
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• pp.45-48
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• 2003

In the research of proteomics, mass spectrometry analysis is the essential method for identification of the unknown proteins. Trypsin treatment for the sample preparation of mass spectrometry is the inevitable procedure[1]. However, sample preparation procedure is cumbersome and time consuming. To resolve these problems, Temperature controllable microreactor was designed and fabricated. It consists of metering chamber, micro channel, reaction chamber, platinum (Pt) thin film heater and a temperature sensor so that micro metering and mixture of reagent with temperature control can be done on the same chip. The total size of the fabricated microreactor was $37{\times}30{\times}1\;mm^3$ and the size of channel cross section was $200{\times}100{\mu}m^2$. PID temperature controller was realized using NI DAQ, PCI-MIO-l6E-1 board and LabVIEW program.