• The Journal of the Korea Contents Association
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• v.19 no.11
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• pp.632-643
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• 2019

In recent years, large scale damages from arbovirus infections by mosquitoes have been reported worldwide due to factors such as change in global climate, increased overseas travel, and increased logistics movement between countries. Among them, Zika virus and dengue virus belonging to genus Flavivirus are representative. In this study, we performed in-depth analyses of the envelope (E) protein that perform essential functions for host infection of Zika virus and dengue virus based on bioinformatics databases. The domain analysis of E protein was performed to determine the type, location, and function, and homology analysis for each domain. From these results, EDIII showing low homology was identified. The homology and immunogenicity of each peptide constituting EDIII were analyzed and three-dimensional structures were modeled. Furthermore, we discussed their biological meaning and how they could be used.

• KSBB Journal
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• v.22 no.4
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• pp.179-184
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• 2007

This study introduces the characteristics and some applications of repetitive polypeptides, especially to the biomaterial, tissue engineering scaffolds, drug delivery system, and DNA separation systems. Since some fibrous proteins, which consist of repeating peptide monomers, have been reported that their physical properties are changed dramatically by means of temperature alteration or pH shifting. For that reason, fibrous protein-mimetic polypeptides, which are produced by the recombinant technology, can be applied to the diverse biological fields. Repetitive polypeptides can also be used in the bioseparation area such as DNA sequencing, because they make DNA separation possible in free-solution electrophoresis by conjugating DNA fragments to them. Moreover, artificial synthesis of repetitive polypeptides helps to demonstrate the correlations between mechanical properties and structures of natural protein polymer, which have been proven that repetitive domains are affected by the sequence of the repeating domains and the number of repeating subunits. Repetitive polypeptides can be biologically synthesized using some special cloning methods, which are represented here. Recursive directional ligation (RDL) and controlled cloning method (CCM) have been proposed as excellent cloning methods in that we can control the number of repetition in the multimerization of polypeptides and the components of repetitive polypeptides by either method.

• 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.

• International Journal of Oral Biology
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• v.47 no.1
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• pp.1-8
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• 2022

Inflammation is a protective mechanism against pathogens, but if maintained continuously, it destroys tissue structures. Aggregatibacter actinomycetemcomitans is a gram-negative, facultative anaerobic bacterium often found in severe periodontitis. A. actinomycetemcomitans invades epithelial cells and triggers inflammatory response in the immune cells. In this study, we investigated the effect of water-soluble rosehip extract on A. actinomycetemcomitans-induced inflammatory responses. A human monocytic cell line (THP-1) was differentiated to macrophages by phorbol 12-mystristate 13-acetate treatment. The cytotoxic effect of extract was determined using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. The effects of extract on bacterial growth were examined by measuring the optical densities using a spectrophotometer. THP-1-derived macrophages were infected A. actinomycetemcomitans after extract treatment, and culture supernatants were analyzed for cytokine production using enzyme-linked immunosorbent assay. Protein expression was measured by western blotting. Extract was not toxic to THP-1-derived macrophages. A. actinomycetemcomitans growth was inhibited by 1% extract. The extract suppressed A. actinomycetemcomitans-induced tumor necrosis factor-α, interleukin (IL)-1β, and IL-8 production. It also decreased mitogen-activated protein kinase (MAP kinase) and nuclear factor-κB (NF-κB) phosphorylation. Moreover, the extract inhibited the expression of inflammasome components, including nucleotide-binding oligomerization domain-like receptor pyrin domain-containing protein 3, Absent in Melanoma 2, and apoptosis associated speck-like protein containing a CARD. And cysteine-aspartic proteases-1 and IL-1β expression were decreased by the extract. In summary, extract suppressed A. actinomycetemcomitans growth and decreased inflammatory cytokine production by inhibiting activation of MAP kinase, NF-κB, and inflammasome signaling. Rosehip extract could be effective in the treatment of periodontal inflammation induced by A. actinomycetemcomitans infection.

• Interdisciplinary Bio Central
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• v.1 no.1
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• pp.3.1-3.6
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• 2009

Introduction: GTPases known as translation factor play a vital role as ribosomal subunit assembly chaperone. The bacterial Obg proteins ($Spo{\underline{0B}}$-associated ${\underline{G}}TP$-binding protein) belong to the subfamily of P-loop GTPase proteins and now it is considered as one of the new target for antibacterial drug. The majority of bacterial Obgs have been commonly found to be associated with ribosome, implying that these proteins may play a fundamental role in ribosome assembly or maturation. In addition, one of the experimental evidences suggested that Bacillus subtilis Obg (BsObg) protein binds to the L13 ribosomal protein (BsL13) which is known to be one of the early assembly proteins of the 50S ribosomal subunit in Escherichia coli. In order to investigate binding mode between the BsObg and the BsL13, protein-protein docking simulation was carried out after generating 3D structure of the BsL13 structure using homology modeling method. Materials and Methods: Homology model structure of BsL13 was generated using the EcL13 crystal structure as a template. Protein-protein docking of BsObg protein with ribosomal protein BsL13 was performed by DOT, a macro-molecular docking software, in order to predict a reasonable binding mode. The solvated energy minimization calculation of the docked conformation was carried out to refine the structure. Results and Discussion: The possible binding conformation of BsL13 along with activated Obg fold in BsObg was predicted by computational docking study. The final structure is obtained from the solvated energy minimization. From the analysis, three important H-bond interactions between the Obg fold and the L13 were detected: Obg:Tyr27-L13:Glu32, Obg:Asn76-L13:Glu139, and Obg:Ala136-L13:Glu142. The interaction between the BsObg and BsL13 structures were also analyzed by electrostatic potential calculations to examine the interface surfaces. From the results, the key residues for hydrogen bonding and hydrophobic interaction between the two proteins were predicted. Conclusion and Prospects: In this study, we have focused on the binding mode of the BsObg protein with the ribosomal BsL13 protein. The interaction between the activated Obg and target protein was investigated with protein-protein docking calculations. The binding pattern can be further used as a base for structure-based drug design to find a novel antibacterial drug.

• Journal of the Korean Magnetic Resonance Society
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• v.9 no.1
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• pp.38-47
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• 2005

Axin is a scaffold protein of the APC/axin/GSK complex, binding to all of the other signalling components. Axin interacts with Glycogen synthase kinase 3$\beta$ (GSK 3$\beta$) and functions as a negative regulator of Wnt signalling pathways. To determine the solution structure of the GSK3$\beta$ binding regions of the axin, we initiated NMR study of axin fragment comprising residues 3$Val^{388} - Arg^{401}$using circular dichroism (CD) and two-dimensional NMR spectroscopy. The CD spectra of 3$axin^{pep}$ in the presence of 30% TFE displayed a standard 3$\alpha$-helical conformation, exhibiting the bound structure of 3$axin^{pep}$ to GSK3$\bata$. On the basis of experimental restraints including $NOE_s$, and $^3J_{HN\alpha} $ coupling constants, the solution conformation of $axin^{pep}$ was determined with program CNS. The 20 lowest energy structures were selected out of 50 final simulated-annealing structures in both water and TFE environment, respectively. The $RMSD_s$ for the 20 structures in TFE solution were 0.086 nm for backbone atoms and 0.195 nm for all heavy atoms, respectively. The Ramachandran plot indicates that the $\varphi$, $\psi$ angles of the 20 final structures is properly distributed in energetically acceptable regions. $Axin^pep$ in aqueous solutions consists of a stable $\alpha$-helix spanning residues form $Glu^{391}$ to $Val^{391} $, which is an interacting motif with GSK3$\beta$.

• Journal of Microbiology and Biotechnology
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• v.9 no.6
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• pp.695-703
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• 1999

We have studied the stereospecificities of various pyridoxal 5'-phosphate (PLP) dependent enzymes for the hydrogen transfer between the C-4' of a bound coenzyme and the C-2 of a substrate in the transamination catalyzed by the enzymes. Stereospecificities reflect the structures of enzyme active-sites, in particular the geometrical relationship between the coenzyme-substrate Schiff base and the active site base participating in an $\alpha$-hydrogen abstraction. The PLP enzymes studied so far catalyze only a si-face specific (pro-S) hydrogen transfer. This stereochemical finding suggests that the PLP enzymes have the same topological active-site structures, and that the PLP enzymes have evolved divergently from a common ancestral protein. However, we found that o-amino acid aminotransferase, branched chain L-amino acid aminotransferase, and 4-amino-4-deoxychorismate lyase, which have significant sequence homology with one another, catalyze a re-face specific (pro-R) hydrogen transfer. We also showed that PLP-dependent amino acid racemases, which have no sequence homology with any aminotransferases, catalyze a non-stereospecific hydrogen transfer: the hydrogen transfer occurs on both faces of the planar intermediate. Crystallographical studies have shown that the catalytic base is situated on the re-face of the C-4' of the bound coenzyme in o-amino acid aminotransferase and branched chain L-amino acid aminotransferase, whereas the catalytic base is situated on the si-face in other aminotransferases (such as L-aspartate aminotransferase) catalyzing the si-face hydrogen transfer. Thus, we have clarified the stereospecificities of PLP enzymes in relation with the primary structures and three-dimensional structures of the enzymes. The characteristic stereospecificities of these enzymes for the hydrogen transfer suggest the convergent evolution of PLP enzymes.

• Applied Microscopy
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• v.41 no.1
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• pp.61-67
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• 2011

The purpose of this study is to investigate the hemp (Cannabis sativa cv. Chungsam) seed structure and ultrastructure of food reserves by scanning and transmission electron microscopy. We examined the seed coat and embryo consisting of a hypocotyl-radicle axis and two cotyledons. The seed coat consisted of exotesta and endotesta. The exotesta was a mechanical layer with lignified and elongated cells, while endotesta of the underlying layers of the exotesta was consisted of two separated cell layers. The collapsed outer layer of endotesta showed the unique reticulate structures. In cotyledon cells, protein and lipid bodies occupied most of cytoplasm. Protein bodies varied in diameter from 1.8 to $5.0{\mu}m$ and possessed a protein matrix containing electron-dense globoid crystals. Numerous lipid bodies ranged from 0.8 to $3.0{\mu}m$ in diameter were distributed around the protein bodies. During the early stages of breakdown, protein bodies rapidly changed their shape into the granular feature, however, lipid bodies were gradually degradated and fused each other. The degeneration process of protein bodies and lipid bodies of cotyledon cells might be correlated with the reports which hemp seeds rapidly lose their ability to germinate.

• Biomedical Science Letters
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• v.18 no.3
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• pp.276-282
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• 2012

High-intensive endurance exercises induce cell changes in body, changes in structures and functions of the heart, the muscles, the cartilages, and the liver, as well as increase of inflammatory cytokine. The purpose of this study was to estimate the biochemical changes in the liver and muscles during ultra-marathon race (100 km) by sections. The blood of the subjects was collected before the marathon as a control in order to analyze serum creatine kinase (CK), lactic dehydrogenase (LDH), asprtate aminotransferase (AST), alanine aminotransferase (ALT), total(T)-bilirubin, direct(D)-bilirubin, total protein, albumin, uric acid, gamma-glutamyltranspeptidase (${\gamma}$-GTP), alkaline phosphatase (ALP), creatinine, blood urea nitrogen (BUN), and high sensitive C-reactive protein (hs-CRP) concentrations. The CK, LDH, D-bilirubin, AST and ALT concentrations at 50 km and 100 km were significantly increased compared to the control (P<0.05). The markers at 100 km were higher than those at 50 km (P<0.05). The T-bilirubin and hs-CRP concentrations showed no difference among the groups, whereas the markers at 100 km were higher than those of the control and at 50 km (P<0.05). In conclusion, this study shows that the ultra-marathon race (100 km) may induce the damage of the skeletal muscle, liver and kidney, intravascular hemolysis and inflammatory responses.

• Bulletin of the Korean Chemical Society
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• v.35 no.5
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• pp.1375-1378
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• 2014

In this study, maghemite (${\gamma}-Fe_2O_3$) nanoparticles were produced using gelatin protein as an effective mediator. Size, shape, surface morphology and magnetic properties of the prepared ${\gamma}-Fe_2O_3$ nanoparticles were characterized using XRD, FT-IR, TEM, SEM and VSM data. The effects of furnace temperature and time of heating together with the amount of gelatin on the produced gelatin-$Fe_3O_4$ nanocomposite were examined to prove the fundamental effect of gelatin; both as a capping agent in the nanoscale synthesis and as the director of the spinel ${\gamma}-Fe_2O_3$ synthesis among possible $Fe_2O_3$ crystalline structures.