• BMB Reports
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• v.40 no.4
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• pp.539-546
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• 2007

The lysozymes encoded by bacteriophage T7 and K11 are both bifunctional enzymes sharing an extensive sequence homology (75%). The constructions of chimeric lysozymes were carried out by swapping the N-terminal and C-terminal domains between phage T7 and K11 lysozymes. This technique generated two chimeras, T7K11-lysozyme (N-terminal T7 domain and C-terminal K11 domain) and K11T7-lysozyme (N-terminal K11 domain and C-terminal T7 domain), which are both enzymatically active. The amidase activity of T7K11-lysozyme is comparable with the parental enzymes while K11T7-lysozyme exhibits an activity that is approximately 45% greater than the wild-type lysozymes. Moreover, these chimeric constructs have optimum pH of 7.2-7.4 similar to the parental lysozymes but exhibit greater thermal stabilities. On the other hand, the chimeras inhibit transcription comparable with the parental lysozymes depending on the source of their N-terminals. Taken together, our results indicated that domain swapping technique localizes the N-terminal region as the domain responsible for the transcription inhibition specificity of the wild type T7 and K11 lysozymes. Furthermore, we were able to develop a simple and rapid purification scheme in purifying both the wild-type and chimeric lysozymes.

• Journal of the Korean Magnetic Resonance Society
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• v.11 no.1
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• pp.30-41
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• 2007

The backbone molecular dynamics of the C-terminal part of the mouse Cdt1 protein (tCdt1, residues 420-557) was studied by high field NMR spectroscopy. The Secondary structure of this protein was suggested by analyzing of chemical shift of backbone atoms with programs TALOS and PECAN, together with NOE connectivities from 3D $^{15}N-HSQC-NOESY$ data. Measurement of dynamic parameters $T_1,\;T_2$ and NOE and limited proteolysis experiment provided information for domain organization of tCdt1(420-557). Analysis of the experimental data showed that the C-terminal part of the tCdt1 has well folded domain for residues 455-553. The residues 420-453 including ${\alpha}-helix$ (432-441) are flexible and probably belong to other functional domain in intact full length Cdt1 protein.

• Journal of Korean Elementary Science Education
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• v.35 no.2
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• pp.166-180
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• 2016

This paper examines the effects on academic achievement, scientific process skills and affective domain for elementary students learning the 'Chicken life cycle' through traditional science class versus a smart media based STEAM approach. Students designed and built a hatching jar and created a smart media content for chickens using time-lapse technology. This STEAM program was developed to improve their scientific concepts of animals over nine periods of classes using integrated education methods. The experimental study took place in the third grade of public schools in a province, with the STEAM approach applied in 2 classes (44 students) and the traditional discipline approach implemented in 2 classes (46 students). The STEAM education significantly influenced the improvement of academic achievements, basic scientific process skills and affective domain. The results suggest that this STEAM approach for teaching scientific concepts of animal life cycles has the performance in terms of knowledge, skills and affect gain achievements in elementary school students' learning when compared to a traditional approach. Moreover, the smart media based STEAM program is helpful to lead students to engage in integrated problem-solving designs and learning science and technology.

• Journal of Korean Elementary Science Education
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• v.35 no.3
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• pp.377-387
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• 2016

Whether textbooks faithfully reflect the curriculum contents is an important educational issue. The previous studies on the textbooks did not analyze the relationship described in the textbooks or the structure. In this regard, this study aims to analyze how the concept of life science area in the elementary school science textbooks developed on the basis of the 2009 revised curriculum is linked. In addition, it seeks to analyze how the concept presented in the learning content achievement standards of the curriculum is connected to other concepts. Towards this end, the conceptual linkage of eight units in the life science domain of elementary school science textbooks based on the 2009 revised curriculum was analyzed. The contents of the life science domain in the science textbooks were analyzed through a semantic network analysis, and the semantic network on the concept linked to the one described in curriculum's learning objectives was also analyzed. The results are as follows: 1) It will be difficult for students to understand the concept due to the complexity of the semantic network resulting from a number of concepts. 2) The curriculum's learning objectives presented in the curriculum are not faithfully reflected in the textbooks. 3) The textbooks are described on the basis of specific curriculum's learning objectives. Based on the findings of this study, the number of concepts described in the elementary school science textbooks needs to be significantly reduced so that the concepts can be meaningfully linked to each other.

• Bioinformatics and Biosystems
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• v.1 no.2
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• pp.95-98
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• 2006

Recent proteomic studies of protein domains require high-throughput and systematic approaches. Since most experiments using protein domains, the modules of protein-protein interactions, require gene cloning, the first experimental step should be retrieving DNA sequences of domain encoding regions from databases. For a large scale proteomic research, however, it is a laborious task to extract a large number of domain sequences manually from several inter-linked databases. We present a new methodology to retrieve DNA sequences of domain encoding regions through automatic database cross-referencing. To extract protein domain encoding regions, it traverses several inter-connected database with validation process. And we applied this method to retrieve all the EGF domain encoding DNA sequences of homo sapiens. This new algorithm was implemented using Python library PAMIE, which enables to cross-reference across distinct databases automatically.

• Journal of the Korean Magnetic Resonance Society
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• v.21 no.2
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• pp.72-77
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• 2017

${\beta}-catenin$ is a key signaling protein which regulates cell signaling and gene transcription. Abnormal activation of ${\beta}-catenin$ is linked to many cancers, particularly with colorectal cancers. Although many genetic and biological studies on $Wnt/{\beta}-catenin$ have been reported and structures of the complex between ${\beta}-catenin$ and its diverse binding partners have been published, many of them have focused on armadillo repeat domain of ${\beta}-catenin$. Both N- and C-terminal domains have been suggested to regulate interactions of ${\beta}-catenin$ with other molecules, but still little is known about the C-terminal unstructured domain. To investigate the structure of this domain, construct of C-terminus was designed and structural studies were performed using size exclusion chromatography (SEC), circular dichroism (CD), fluorescence and nuclear magnetic resonance (NMR) spectroscopy. We observed that not only the purified full-length construct but the purified C-terminal construct also dimerizes in solution by SEC, suggesting that this domain involves in dimerization of ${\beta}-catenin$. CD and fluorescence data indicate its flexibility and structural formation in the presence of membrane environments.

• Molecules and Cells
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• v.43 no.8
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• pp.749-762
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• 2020

The migration, dedifferentiation, and proliferation of vascular smooth muscle cells (VSMCs) are responsible for intimal hyperplasia, but the mechanism of this process has not been elucidated. WD repeat domain 1 (WDR1) promotes actin-depolymerizing factor (ADF)/cofilin-mediated depolymerization of actin filaments (F-actin). The role of WDR1 in neointima formation and progression is still unknown. A model of intimal thickening was constructed by ligating the left common carotid artery in Wdr1 deletion mice, and H&E staining showed that Wdr1 deficiency significantly inhibits neointima formation. We also report that STAT3 promotes the proliferation and migration of VSMCs by directly promoting WDR1 transcription. Mechanistically, we clarified that WDR1 promotes the proliferation and migration of VSMCs and neointima formation is regulated by the activation of the JAK2/STAT3/WDR1 axis.

• Biodesign
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• v.5 no.3
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• pp.122-125
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• 2017

Receptor for advanced glycation end products (RAGE) is one of the single transmembrane domain containing receptors and causes various inflammatory diseases including diabetes and atherosclerosis. RAGE extracellular domain has three consecutive IgG-like domains (V-C₁-C₂ domain) which interact with various soluble ligands including heparan sulfate or HMGB1. Studies have shown that each ligand induces different oligomeric forms of RAGE which results in a ligand-specific signal transduction. The structure of mouse RAGE bound to heparan sulfate has been previously determined but the electron density map of heparan sulfate was too ambiguous that the exact position of heparin sulfate could not be defined. Furthermore, the complex structure of human RAGE and heparin sulfate still remains elusive. Therefore, to determine the structure, human RAGE was overexpressed using bacterial expression system and crystallized using the sitting drop method in the condition of 0.1 M sodium acetate trihydrate pH 4.6, 8 % (w/v) polyethylene glycol 4,000 at 290 K. The crystal diffracted to 3.6 Å resolution and the space group is C121 with unit cell parameters a= 206.04 Å, b= 68.64 Å, c= 98.73 Å, α= 90.00°, β= 90.62°, γ= 90.00°.

• Journal of Microbiology and Biotechnology
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• v.16 no.7
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• pp.1104-1110
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• 2006

Recombinant antibody-toxin is a bifunctional protein that binds and kills a target cell expressing a specific antigen on the surface of the cell, and its structure is chimeric, in which a toxin is fused to an antigen-binding domain such as scFv or Fab. Divalent antibody-toxin molecules showed higher cytotoxicities against cancer cell lines than monovalent molecules. However, the yields of the divalent molecules were very low. In this study, we introduced the CH2, CH3, or CH2-CH3 (=Fc) domain of antibody in the middle of the Fab-toxin between the hinge region of human IgG1 and the toxin domain to increase the yield. The covalently bonded dimer could be formed by three disulfide bridges from cysteine residues in the hinge region. The molecule with the CH3 domain showed about 3-fold higher dimerization yield than previously constructed Fab-toxin molecules, while maintaining the cytotoxic activity comparable to that of scFv-toxin. However, the introduction of CH2 or Fc domain to the same position showed little effect on the dimerization yield. We also observed that the introduction of the CH3 region made it possible to form noncovalently associated dimer molecules.

• Molecules and Cells
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• v.19 no.1
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• pp.39-45
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• 2005

RPK118 is a sphingosine kinase-1-binding protein that has been implicated in sphingosine 1 phosphate-mediated signaling. It contains a PX (phox homology) domain and two pseudo-kinase domains, and co-localizes with sphingosine kinase-1 on early endosomes. In this study we identified a novel RPK118-binding protein, PRDX3 (peroxiredoxin-3), by yeast two-hybrid screening. The interaction between these proteins was confirmed by pull-down assays and co-immunoprecipitation experiments. Deletion studies showed that RPK118 interacted with PRDX3 through its pseudokinase domains, and with early endosomes through its PX domain. Double immunofluorescence experiments demonstrated that PRDX3 co-localized with RPK118 on early endosomes in COS7 cells. PRDX3 is a member of the antioxidant family of proteins synthesized in the cytoplasm and functioning in mitochondria. Our findings indicate that RPK118 is a PRDX3-binding protein that may be involved in transporting PRDX3 from the cytoplasm to its mitochondrial site of function or to other membrane structures via endosome trafficking.