• BMB Reports
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• v.44 no.2
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• pp.118-122
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• 2011

Most widely used secondary structure assignment methods such as DSSP identify structural elements based on N-H and C=O hydrogen bonding patterns from X-ray or NMR-determined coordinates. Secondary structure assignment algorithms using limited $C{\alpha}$ information have been under development as well, but their accuracy is only ~80% compared to DSSP. We have hereby developed SABA (Secondary Structure Assignment Program Based on only Alpha Carbons) with ~90% accuracy. SABA defines a novel geometrical parameter, termed a pseudo center, which is the midpoint of two continuous $C{\alpha}s$. SABA is capable of identifying $\alpha$-helices, $3_{10}$-helices, and $\beta$-strands with high accuracy by using cut-off criteria on distances and dihedral angles between two or more pseudo centers. In addition to assigning secondary structures to $C{\alpha}$-only structures, algorithms using limited $C{\alpha}$ information with high accuracy have the potential to enhance the speed of calculations for high capacity structure comparison.

• BMB Reports
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• v.28 no.5
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• pp.458-463
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• 1995

Two apparent rho-independent transcription terminator structures within the coding sequence of aceK have been destroyed to access their roles in the differential expression between aceA and aceK in the glyoxylate bypass operon of E. coli. The effect of mutations on the expression of aceK was evaluated in two different ways: one by maxicell labeling and the other by lacZ fusion gene construction. The maxicell labeling experiment with the mutant operon clones has failed, like that of the wild type operon clone, to visibly show isocitrate dehrogenase (IDH) kinase/phosphatase, the product of aceK, on the autoradiogram of a protein gel. When the same mutations were introduced into an aceK::lacZ fusion gene to quantitatively evaluate the mutational effect, the activity of ${\beta}-galactosidase$ in neither of the mutant versions of the fusion gene was elevated significantly enough to explain the degree of polarity observed in this region. Thus, we conclude that neither of these intragenic, apparent rho-independent transcription terminator structures, which have long been suspected as a major determinant in the down regulation of aceK, really act as a premature transcriptional terminator.

• Journal of Microbiology and Biotechnology
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• v.18 no.2
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• pp.228-233
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• 2008

Effects of chaperones on mRNA stability and gene expression were studied in order to develop an efficient Escherichia coli expression system that can maximize gene expression. The stability of mRNA was modulated by introducing various secondary structures at the 5'-end of mRNA. Four vector systems providing different 5'-end structures were constructed, and genes encoding GFPuv and endoxylanase were cloned into the four vector systems. Primer extension assay revealed different mRNA half-lives depending on the 5'-end secondary structures of mRNA. In addition to the stem-loop structure at the 5'-end of mRNA, coexpression of dnaK-dnaJ-grpE or groEL-groES, representative heat-shock genes in E. coli, increased the mRNA stability and the level of gene expression further, even though the degree of stabilization was varied. Our work suggests that some of the heat-shock proteins can function as mRNA stabilizers as well s protein chaperones.

• Journal of the Korean Society of Food Culture
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• v.16 no.4
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• pp.316-322
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• 2001

This study was performed to investigate flavor modification effects of ${\beta}-cyclodextrin$ $({\beta}-CD)$ inclusion complex on the flavor of Doenjang (Korean traditional fermented soy paste) with various substitution levels of 10, 20, and 30%. Water and protein contents of the substituted samples showed significantly lower values compared to those of control(p<0.05). Results of DSC(Differential Scanning Calorimetry) showed that significantly higher ${\Delta}H$ values (386.03 and 304.23) in the 20 and 30% substituted samples represented the stabilized internal cell structures(p<0.05). Internal structures observed with the scanning electronic microscope tended to be less rough and organized making even and ordered internal cell structures as the substitution levels were increased. Results of sensory evaluation showed significantly higher savory flavor and significantly lower bitter and astringent flavors with the substituted samples compared to those of control(p<0.05). Results from this study showed the substitutions of ${\beta}-CD$ could possibly modify unfavored flavors of Doenjang while keeping the unique, nutritional and functional properties when ${\beta}-CD$ was used as a flavor modifier.

• Bulletin of the Korean Chemical Society
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• v.32 no.11
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• pp.4106-4108
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• 2011

• Proceedings of the Korean Information Science Society Conference
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• 2003.04a
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• pp.869-871
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• 2003

단백질 부분 구조는 일종의 단백질 패턴으로써 진화적인 성질을 띄고 있다. 본 논문에서는 단백질 간의 열 안정성과 이러한 단백질 부분 구조 간의 관련성에 대해서 알아보고자 한다. 또한 오류 허용 알고리즘 (FT-Apriori)의 성능을 향상시킬 수 있는 효과적인 기법을 제안한다. 이러한 기법을 단백질 부분 구조에 적용시킴으로써 실제 단백질 데이터에서 그 효용성을 일아본다.

• Proceedings of the PSK Conference
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• 2002.10a
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• pp.181-182
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• 2002

Recentadvancesin '-omics ' technologies enable us to discover more diverse disease- relevant target proteins, which encourages us to find out more target-specific novel lead compounds as new drug candidates. Therefore, high-throughput screening (HTS) becomes an essential tool in this area. Among many HTS tools, in silico HTS is a very fast and cost-effective tool to try to derive a new lead compound for any new targets, especially when the target protein structures are known or readily modeled. (omitted)

• Proceedings of the PSK Conference
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• 2001.04a
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• pp.77-77
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• 2001

• Polymer Science and Technology
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• v.24 no.6
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• pp.590-595
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• 2013

• Annals of Clinical Neurophysiology
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• v.20 no.1
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• pp.3-11
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• 2018

Skin biopsy and staining the specimens with immuno-reactive markers has been proven to be a useful method to demonstrate the pathologic status of small nerve fibers. Quantification of intraepidermal nerve fiber density using anti-protein gene product 9.5 antibody is a standard method to diagnose small fiber neuropathy. Skin biopsy also makes it possible to differentiate the nerve fibers according to their function by using different markers. Quantification of dermal structures with different types of nerve fibers could reveal the pathophysiologic mechanism of the disease state.