• Bulletin of the Korean Chemical Society
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• v.34 no.8
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• pp.2419-2424
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• 2013

Guanosine-5'-diphosphate 3'-diphosphate (ppGpp) serves as alarmone in bacterial stringent responses. In this study, an affinity column was constructed by immobilizing ppGpp to NHS-Sepharose for isolating ppGpp-binding proteins. A novel ppGpp-binding protein, YjgA, was isolated and characterized by MALDI-TOF MS (matrix-assisted laser desorption ionization-time-of-flight mass spectrometry) coupled with two-dimensional gel electrophoresis. YjgA and truncated forms of YjgA were cloned and over-expressed in BL21 (DE3). The binding affinity of YjgA to ppGpp was determined by equilibrium dialysis. The interaction of YjgA with ppGpp was very specific, considering that the dissociation constant of YjgA with ppGpp was measured as $5.2{\pm}2.0{\mu}M$, while the affinities to GTP and GDP were about 60 and 30 times weaker than ppGpp. Expression of yjgA gene in Escherichia coli K-12 MG1655 was examined by reverse transcription polymerase chain reaction (RT-PCR). RT-PCR results revealed that yjgA was expressed from early to late stationary phase. The yjgA deletion mutant exhibited decreased cell number at stationary phase compared to parent strain and the over-expression of YjgA increased the cell number. These results suggested that YjgA might stimulate cell division under stationary phase. In most prokaryotic genome, about half of the protein candidates are hypothetical, that are expected to be expressed but there is no experimental report on their functions. The approach utilized in this study may serve as an effective mean to probe the functions of hypothetical proteins.

• Animal Bioscience
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• v.34 no.5
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• pp.867-879
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• 2021

Objective: Fibronectin 3 (FN3) and immunoglobulin like modules (Ig) are usually collocated beside modular cellulase catalytic domains. However, very few researches have investigated the role of these modules. In a previous study, we have sequenced and analyzed bacterial metagenomic DNA in Vietnamese goats' rumen and found that cellulase-producing bacteria and cellulase families were dominant. In this study, the properties of modular cellulases and the role of a FN3 in unique endoglucanase belonging to glycosyl hydorlase (GH) family 5 were determined. Methods: Based on Pfam analysis, the cellulases sequences containing FN3, Ig modules were extracted from 297 complete open reading frames (ORFs). The alkaline, thermostability, tertiary structure of deduced enzymes were predicted by AcalPred, TBI software, Phyre2 and Swiss models. Then, whole and truncated forms of a selected gene were expressed in Escherichia coli and purified by His-tag affinity column for assessment of FN3 ability to enhance enzyme activity, solubility and conformation. Results: From 297 complete ORFs coding for cellulases, 148 sequences containing FN3, Ig were identified. Mostly FN3 appeared in 90.9% beta-glucosidases belonging to glycosyl hydrolase family 3 (GH3) and situated downstream of catalytic domains. The Ig was found upstream of 100% endoglucanase GH9. Rarely FN3 was seen to be situated downstream of X domain and upstream of catalytic domain endoglucanase GH5. Whole enzyme (called XFN3GH5 based on modular structure) and truncate forms FN3, XFN3, FN3GH5, GH5 were cloned in pET22b (+) and pET22SUMO to be expressed in single and fusion forms with a small ubiquitin-related modifier partner (S). The FN3, SFN3 increased GH5 solubility in FN3GH5, SFN3GH5. The SFN3 partly served for GH5 conformation in SFN3GH5, increased modules interaction and enzyme-soluble substrate affinity to enhance SXFN3GH5, SFN3GH5 activities in mixtures. Both SFN3 and SXFN3 did not anchor enzyme on filter paper but exfoliate and separate cellulose chains on filter paper for enzyme hydrolysis. Conclusion: Based on these findings, the presence of FN3 module in certain cellulases was confirmed and it assisted for enzyme conformation and activity in both soluble and insoluble substrate.

• Journal of Ginseng Research
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• v.47 no.5
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• pp.662-671
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• 2023

Background: 20(S)-protopanaxadiol (PPD), a ginsenoside metabolite, has prominent benefits for the central nervous system, especially in improving learning and memory. However, its transcriptional targets in brain tissue remain unknown. Methods: In this study, we first used mass spectrometry-based drug affinity responsive target stability (DARTS) to identify the potential proteins of ginsenosides and intersected them with the transcription factor library. Second, the transcription factor PURA was confirmed as a target of PPD by biolayer interferometry (BLI) and molecular docking. Next, the effect of PPD on the transcriptional levels of target genes of PURA in brain tissues was determined by qRT-PCR. Finally, bioinformatics analysis was used to analyze the potential biological features of these target proteins. Results: The results showed three overlapping transcription factors between the proteomics of DARTS and transcription factor library. BLI analysis further showed that PPD had a higher direct interaction with PURA than parent ginsenosides. Subsequently, BLI kinetic analysis, molecular docking, and mutations in key amino acids of PURA indicated that PPD specifically bound to PURA. The results of qRT-PCR showed that PPD could increase the transcription levels of PURA target genes in brain. Finally, bioinformatics analysis showed that these target proteins were involved in learning and memory function. Conclusion: The above-mentioned findings indicate that PURA is a transcription target of PPD in brain, and PPD upregulate the transcription levels of target genes related to cognitive dysfunction by binding PURA, which could provide a chemical and biological basis for the study of treating cognitive impairment by targeting PURA.

• Maxillofacial Plastic and Reconstructive Surgery
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• v.36 no.5
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• pp.192-200
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• 2014

Purpose: The objective of this study was to evaluate the interaction between 4-hexylresorcinol (4HR) and antibody as that affects the performance of a silk-4HR combination graft for soft tissue augmentation in an animal model. Methods: The silk graft materials consisted of four types: silk+10% tricalcium phosphate (TCP) (ST0), silk+10% TCP+1% 4HR (ST1), silk+10% TCP+3% 4HR (ST3), and silk+10% TCP+6% 4-HR (ST6). The antibody binding assay tested the 4HR effect and scanning electron microscopic (SEM) exam was done for silk grafts. The animal experiment used a subcutaneous pocket mouse model. The graft - SH0 or SH1 or SH3 or SH6 - was placed in a subcutaneous pocket. The animals were killed at one, two, and four weeks, postoperatively. The specimens were subjected to histological analysis and lysozyme assay. Results: Groups with 4HR applied showed lower antibody binding affinity to antigen compared to groups without 4HR. In the SEM examination, there was no significant difference among groups. Histological examinations revealed many foreign body giant cells in ST0 and ST1 group at four weeks postoperatively. Both ST3 and ST6 groups developed significantly lower levels of giant cell values compared to ST0 and ST1 groups (P < 0.001) at four weeks postoperatively. In the lysozyme assay, the ST1 and ST3 groups showed denser signals than the other groups. Conclusion: 4HR combined silk implants resulted in high levels of vascular and connective tissue regeneration.

• Journal of Korean Society of Coastal and Ocean Engineers
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• v.21 no.1
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• pp.30-38
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• 2009

In recent years, there's been strong demand for coastal structures that have a permeability that serves water affinity and disaster prevention from wave attack. The aim of this study is to examine the wave transformation, including wave run-up that propagates over the coastal structures with a steep slope. A numerical model based on the nonlinear shallow water equation, together with the unsteady nonlinear Darcy law for fluid motion in permeable underlayer and laboratory measurements was carried out in terms of the free surface elevations and fluid particle velocities for the cases of regular and irregular waves over 1:5 impermeable and permeable slopes. The numerical results were used to evaluate the application and limitations of the PBREAK numerical model. The numerical model could predict the cross-shore variation of the wave profile reasonably, but showed less accurate results in the breaking zone that the mass and momentum influx is exchanged the most. Except near the wave crest, the computed depth averaged velocities could represent the measured profile below the trough level fairly well.

• Journal of The Korean Digital Architecture Interior Association
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• v.1 no.1
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• pp.59-66
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• 2001

The purpose of this study is to improve productivity of architectural space planning(A.S.P,) by computer system and to optimize ASP. A searching algorithm is the best way to slave optimized A.S.P. Because architectural design is too many various site situations and client's demands to specify the general solving methods. This method seek the best design case in all possibility and to be modeled as this; Seongbukgu's case that is city structure former times negative by in facilities utilization of the near street limit. But, case of Gangnamgu and Songpagu is thought that environment and utilization etc. of area life of old people are affinity with quality of life environment of old people when see that is using various area facilities using electric railway and a bus etc. actively. It is looked by the other that individual's special quality uses area facilities according to life partner's existence and nonexistence and family composition and existence and nonexistence of profession and distinction of sex. Show difference of external behavior according to public garden and market and supermarket and welfare facilities etc.'s location in dwelling environment of area and relation about facilities of area has been formed and old people and dwelling environment of area can know that is that do interaction. Environment that access about facilities may have to be easy, and can live that communicating closely with area's inhabitantses may have to consist so that old people may can run various external life.. Notions of the evaluated value is an profit(+) and expense(-) that decide design intention. To adapt real planning, 1. A raster type space cell has logical site informations. 2. To be evaluate various factor. 3. To reflect operator's design mind, they should add an extra weight on evaluated value.

• Ocean and Polar Research
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• v.33 no.2
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• pp.159-169
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• 2011

Antifreeze proteins (AFPs) have ice binding affinity, depress freezing temperature and inhibit ice recystallization which protect cellular membranes in polar organisms. Recent structural studies of antifreeze proteins have significantly expanded our understanding of the structure-function relationship and ice crystal growth inhibition. Although AFPs (Type I-IV AFP from fish, insect AFP and Plant AFP) have completely different fold and no sequence homology, they share a common feature of their surface area for ice binding property. The conserved ice-binding sites are relatively flat and hydrophobic. For example, Type I AFP has an amphipathic, single ${\alpha}$-helix and has regularly spaced Thr-Ala residues which make direct interaction with oxygen atoms of ice crystals. Unlike Type I AFP, Type II and III AFP are compact globular proteins that contain a flat ice-binding patch on the surface. Type II and Type III AFP show a remarkable structural similarity with the sugar binding lectin protein and C-terminal domain of sialic acid synthase, respectively. Type IV is assumed to form a four-helix bundle which has sequence similarity with apolipoprotein. The results of our modeling suggest an ice-binding induced structural change of Type IV AFP. Insect AFP has ${\beta}$-helical structure with a regular array of Thr-X-Thr motif. Threonine residues of each Thr-X-Thr motif fit well into the ice crystal lattice and provide a good surface-surface complementarity. This review focuses on the structural characteristics and details of the ice-binding mechanism of antifreeze proteins.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.277-287
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• 2003

Acetolactate synthase (ALS, EC 4.1.3.18; also referred to as acetohydroxy acid synthase) catalyzes the first common step in the biosynthesis of valine, leucine, and isoleucine in microorganisms and plants. Recently X-ray structure of yeast ALS was available. Pair-wise alignment of yeast and tobacco ALS sequences revealed 63% sequence similarity. Using Deep View and automatic modeling on Swiss model server, we have generated reliable models of tobacco ALS based on yeast ALS template with a calculated pair-wise RMSD of 0.86 Angstrom. Functional roles of four residues located on the subunit interface (H142, El43, M350, and R376) were examined by site-directed mutagenesis. Seven mutants were generated and purified, of which three mutants (H142T, M350V, and R376F) were found to be inactivated under various assay conditions. The H142k mutant showed moderately altered kinetic properties. The E143A mutant increased 10-fold in K$_m$ value while other parameters remained unchanged. The M350C mutant was strongly resistant to three tested herbicides, while the R376k mutant can bind with herbicide carder at similar affinity to that of wild type enzyme, as determined by tryptophan quenching study. Except M350V mutant, all other mutants were ate to bind with cofactor FAD. Taken together, it is likely that residues H142 and E143 are located at the active site, while residues M350 and R376 are possibly located at the overlapping region of active site and herbicide binding site of the enzyme. Our data also allows us to hypothesize that the interaction between side chains of residues M350 and R376 are probably essential for the correct conformation of the active site. It remains to be elucidated that, whether the herbicide, upon binding with enzyme, inactivates the enzyme by causing change in the active site allosterically, which is unfavorable for catalytic activity.

• BMB Reports
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• v.30 no.6
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• pp.397-402
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• 1997

A thiol-specific spin label was attached to cysteine-102 of yeast cytochrome c and electron paramagnetic resonance (EPR) spectra were measured as a function of added cytochrome c oxidase concentration. The intensity decreased due to line broadening as cytochrome c formed a complex with cytochrome c oxidase and reached a minimum when the ratio of cytochrome c to cytochrome c oxidase became one. Replacement of either Lys-72 or Lys-87 of cytochrome c by Glu did not result in a significant change in binding affinity. Interestingly the K72E mutant, unlike K87E, had a much lower rate of electron transfer than the wild type. These results indicate that many positively charged residues as a group participate in complex formation but Lys-72 might be important for cytochrome c to be locked in an orientation for an efficient electron transfer. A stoichiometry of 1 was also confirmed by optical absorption of the cytochrome c-cytochrome c oxidase complex which had been run through a gel chromatography cloumn to remove unbound cytochrome c. The EPR spectrum of this 1:1 complex, however, was a mixture of two components. This explains a biphasic kinetics for a single binding site on cytochrome c oxidase without invoking conformational transition.

• The Journal of the Korea Contents Association
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• v.7 no.4
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• pp.213-223
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• 2007

In this paper, we carry out a cyber group consultation by means of the video-based education system, and verify the effects. For the verification of this study, two assumptions were set up. These assumptions were inspected by selecting 45 students of D elementary school located in a big city, and coming up with a test utilizing one of video-based education systems. Following up, a self-respect test form and a questionnaire were made to verify of the group consultation to the video-based education system, and by analyzing the test form and the questionnaire, the conclusion of this study was finally drawn. The conclusion gained through the process adove is as follows: It turned out that real-time video-based cyber group consultation promoted self-respect and enthusiastic participation of consulters as well as formed emotinal stability and a close affinity between the consultant and the consulter through active interaction. The results of this video-based education system operation will be helpful to broaden the area of elementary school cyber group consultation. Further, it is thought that it will contribute to the basic investigation to verify the educational effects of Multi-point imaging system in the run-up to the operation of full-scale real-time video-based education systems.