• Applied Microscopy
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• v.47 no.4
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• pp.223-225
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• 2017

Cryo-electron microscopy (cryo-EM) is arguably the most powerful tool used in structural biology. It is an important analytical technique that is used for gaining insight into the functional and molecular mechanisms of biomolecules involved in several physiological processes. Cryo-EM can be separated into the following three groups according to the analytical purposes and the features of the biological samples: cryo-electron tomography (cryo-ET), cryo-single-particle reconstruction, and cryo-electron crystallography. Cryo-tomography is a unique EM technique that is used to study intact biomolecular complexes within their original environments; it can provide mechanistic insights that are challenging for other EM-methods. However, the resolution of reconstructed three-dimensional (3D) models generated by cryo-ET is relatively low, while single-particle reconstruction can reproduce biomolecular structures having near-atomic resolution without the need for crystallization unless the samples are large (>200 kDa) and highly symmetrical. Cryo-electron crystallography is subdivided into the following two categories according to the types of samples: one category that deals with two-dimensional (2D) crystalline arrays and the other category that uses 3D crystals. These two categories of electron-crystallographic techniques use different diffraction data obtained from still diffraction and continuous-rotation diffraction. In this paper, we review crystal-based cryo-EM techniques and focus on the recently developed 3D electron-crystallographic technique called microcrystal-electron diffraction.

• The Korean Journal of Cytopathology
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• v.18 no.1
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• pp.87-91
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• 2007

Langerhans cell histiocytosis (LCH) is a pleomorphic disease entity characterized by local or disseminated atypical Langerhans cells (LCs) found most commonly in bone, lungs, mucocutaneous structures and endocrine organs. Among different sites, unifocal disease confined to a lymph node (LN) is rare. We report a case of LCH confined to a LN in a 38-year-old male who presented with a 2 cm-sized cervical mass. The fine needle aspiration (FNA) smears of cervical LN showed high cellularity having isolated LCs with contorted nuclei and nuclear grooves mixed in multinucleated giant cells, small lymphocytes and eosinophils. Charcot-Leyden crystals were also seen, as were a few dendritic-like cells and intranuclear inclusions. Confirmation of LCH was made by histopathologic studies, positive reactions for S-100 protein and CD1a immunohistochemical staining and by the demonstration of Birbeck granules on electron microscopy. The differentials to be considered include dermatopathic lymphadenitis, sinus histiocytosis with massive lymphadenopathy, Hodgkin's lymphoma and malignant histiocytosis. The characteristic cytomorphologic pattern of LCH in a LN FNA smear plays an important role in suggesting the diagnosis of LCH.

• Proceedings of the Korean Institute of Surface Engineering Conference
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• 2012.11a
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• pp.4-4
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• 2012

Proteins enable biology to be viable through molecular interactions (such as in antigen-antibody, ligand-receptor, and drug-target) with

• Fisheries and Aquatic Sciences
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• v.11 no.2
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• pp.88-97
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• 2008

Lipoproteins are complexes of lipids and specific apolipoproteins that are involved in lipid transport and redistribution among various tissues. In this study, we isolated full-length apolipoprotein cDNA sequences encoding apolipoprotein A-I (apoA-I), apoE, apoC-II, and apo-14 kDa in barred knifejaw, Oplegnathus fasciatus. In addition, we reconstructed phylogenetic trees and investigated mRNA tissue distributions. Alignment analyses of amino acid sequences revealed that secondary structures of the polypeptides apoA-I, apoE, and apoC-II in barred knifejaw are well conserved with their teleostean and mammalian counterparts in terms of characteristic tandem repetitive units forming amphipathic ${\alpha}$-helices. Both the sequence alignment data and cleavage sites of apo-14 kDa indicated a clear differentiation between Percomorpha and Cypriniformes. Meanwhile, the phylogenetic trees of apolipoprotein sub-families suggested that the common ancestor prior to the split of the Actinopterygii (ray-finned fishes) and Sarcopterygii (tetrapods) would have possessed the primordial protein-encoding genes. Tissue distribution of each apolipoprotein transcript determined by semi-quantitative RTPCR showed that barred knifejaw apoA-I transcripts were more or less ubiquitously expressed in the liver, intestines, brain, muscle, spleen, and kidney. The most striking difference from previous observations on barred knifejaw was the ubiquitous expression of apoE across all somatic tissues. Barred knifejaw apoC-II showed tissue-specific expression in the liver and intestines, while the liver and brain were the major sites of apo-14kDa mRNA synthesis.

• Applied Microscopy
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• v.26 no.4
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• pp.431-446
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• 1996

This experiment was performed to study the ultrastructural changes of the juxtaglomerular cell of mice following subcutaneous injection of heavy metallic agents. Male mice were divided into normal and experimental groups. The mice were subcutaneouly injected with $HgCl_2$ (2mg, 5mg or 10 mg/Kg/BW) or with $K_{2}Cr_{2}O_7$(5 mg, 10 mg or 20 mg/Kg/BW). Mice were sacrificed on 6 hours, 3 days and 14 days after the injection. Kidneys were fixed in the 2.5% glutaraldehyde-1.5% paraformaldehyde solution, followed by refixation in the 1% osmium tetroxide solution. Dehydrated blocks were embedded in araldite mixture. The sections were cut on a LKB-V ultratome, and ultrathin sections stained with uranyl acetate and lead citrate were observed with JEM 100CX II electron microscope. The results were as follow: 1. Juxtaglomerular cell of the experimental groups showed some alterations, especially in the structures of protein synthesis including dilations and degradations of granular endoplasmic reticula, atrophy of Golgi complex, and numerous free ribosomes in the cytoplasm. 2. Juxtaglomerular cells treated groups showed a number of vacuoles, protogranules and some myelin figures in the cytoplasm, especially in the earlier groups. 3. Juxtaglomerular cells of treated groups, contained a large number of secretory granules showing variable electron densities and pleomorphism in later groups (2 weeks). From the above results, it was concluded that, the mercuric chloride or potassium bichromate induces acute renin release from juxtaglomerular cells of the mice, but many juxtaglomerular cells may secrete prematured secretory granules, or the synthetic system of the cell can not perform normal function.

• Journal of Integrative Natural Science
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• v.3 no.2
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• pp.72-77
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• 2010

Alginate lyases, also known as alginases or alginate depolymerases, catalyze the degradation of alginate by a ${\beta}$-elimination mechanism that has yet to be fully elucidated. Alginate is a copolymer of ${\alpha}$-L-guluronate (G) and its C5 epimer ${\beta}$-D-mannuronate (M), arranged as homopolymeric G blocks, M blocks, alternating GM or random heteropolymeric G/M stretches. Almost all alginate lyases depolymerize alginate in an endolytical fashion via a ${\beta}$-elimination reaction. The alginate lyase Atu3025 from Agrobacterium tumefaciens strain C58, consisting of 776 amino-acid residues, is a novel exotype alginate lyase classified into polysaccharide lyase family 15. Till now there is no crystal structure available for this class of proteins. Since there is no template with high sequence identity, three-dimensional coordinates for exotype alginate lyase (PL 15 family) were determined using modeling methods (Comparitive modeling and Fold recognition). The structures were modeled using the X-ray coordinates from Heparinase protein family (PDB code: 3E7J). This enzyme (Atu3025) displays enzymatic activity for both poly-M and poly-G alginate. Since poly-M is widespread; docking of a tri-mannuronate against the modeled structure was performed. We identified some of those residues which are crucial for lyase activity. The results from this study should guide future mutagenesis studies and also provides a starting point for further proceedings.

• Bulletin of the Korean Chemical Society
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• v.34 no.11
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• pp.3429-3443
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• 2013

Chemokine receptor (CCR2) is a G protein-coupled receptor that contains seven transmembrane helices. Recent pharmaceutical research has focused on the antagonism of CCR2 and candidate drugs are currently undergoing clinical studies for the treatment of diseases like arthritis, multiple sclerosis, and type 2 diabetes. In this study, we analyzed the time dependent behavior of CCR2 docked with a potent 4-azetidinyl-1-aryl-cyclohexane (4AAC) derivative using molecular dynamics simulations (MDS) for 20 nanoseconds (ns). Homology modeling of CCR2 was performed and the 4AAC derivative was docked into this binding site. The docked model of selected conformations was then utilized to study the dynamic behavior of the 4AAC enzyme complexes inside lipid membrane. MDS of CCR2-16b of 4AAC complexes allowed us to refine the system since binding of an inhibitor to a receptor is a dynamic process and identify stable structures and better binding modes. Structure activity relationships (SAR) for 4AAC derivatives were investigated and reasons for the activities were determined. Probable binding pose for some CCR2 antagonists were determined from the perspectives of binding site. Initial modeling showed that Tyr49, Trp98, Ser101, Glu291, and additional residues are crucial for 4AAC binding, but MDS analysis showed that Ser101 may not be vital. 4AAC moved away from Ser101 and the hydrogen bonding between 4AAC and Ser101 vanished. The results of this study provide useful information regarding the structure-based drug design of CCR2 antagonists and additionally suggest key residues for further study by mutagenesis.

• Journal of the Korean Chemical Society
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• v.38 no.8
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• pp.608-615
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• 1994

The isolation, purification and characterization of a carotenoprotein from the carapace of Pnaeus orientalis were investigated. The carotenoprotein was purple with broad λmax between 480, 409, 318 and 280 nm. Apparent structures were estimated by using X-ray diffractometry and scanning electron microscope, respectively. The molecular weight of the carotenoprotein complex had been determined by GPC and PAGE. The heavier complex, designated the $\alpha$-form (M.W = 170 KDa), was dissociated to a major subunit, $\beta$-form (M.W = 42 KDa). SDS-PAGE of $\alpha$-form showed apparently oligomeric pattern, and also $\beta$-form gave two polypeptides corresponding to 22 KDa and 19 KDa, respectively. The amino acid of the two proteins $({\alpha}-and\;{\beta})$-form, lipid and free fatty acid compositions were described. The prosthetic groups of the carotenoprotein were confirmed by TLC, IR, $^1H$-NMR, MS and various organic reactions as astaxanthin, astaxanthin monoester and astaxnathin diester.

• Molecules and Cells
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• v.25 no.3
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• pp.385-389
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• 2008

Septins are a family of filament-forming GTP-binding proteins involved in a variety of cellular process such as cytokinesis, exocytosis, and membrane dynamics. Here we report the biochemical and immunocytochemical characterization of a recently identified mammalian septin, SEPT12. SEPT12 binds GTP in vitro, and a mutation (Gly56 to Asn) in the GTP-binding motif abolished binding. Immunocytochemical analysis revealed that wild-type SEPT12 formed filamentous structures when transiently expressed in Hela cells whereas $SEPT12^{G56A}$ generated large aggregates. In addition, wild-type SEPT12 failed to form filaments when coexpressed with $SEPT12^{G56A}$. We also observed that GTP-binding by SEPT12 is required for interaction with SEPT11 but not with itself.

• Genomics & Informatics
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• v.3 no.4
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• pp.142-148
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• 2005

The immune response-related genes have been suggested to be the most favorable genes for positive selection during evolution. Comparing the entire DNA sequence of chimpanzee chromosome 22 (PTR22) with human chromosome 21 (HSA21), we have identified 15 orthologs having indel in their coding sequences. Among them, interferon-${\alpha}$ receptor-1 gene (IFNAR1), an immuneresponse-related gene, is subjected to comparative genomic analysis. Chimpanzee IFNAR1 showed the same genomic structure as human IFNAR1 (11 exons and 10 introns) except the 3 bp insertion in exon 4. The sequence alignment of IFNAR1 coding sequence indicated that 'ISPP' amino acid sequence motif is highly conserved in chimpanzee and other animals including mouse and chicken. However, the human IFNAR1 shows that one proline residue is missing in the sequence motif. The homology modeling of the IFNAR1 structures suggests that the proline deletion in human IFNAR1 leads to the formation of the following ${\alpha}$-helix, whereas two sequential prolines in chimpanzee IFNAR1 inhibit it. As a result, human IFNAR1 may adopt a characteristic structure distinct from chimpanzee IFNAR1. This human specific trait could contribute to specific immune response in the most optimized manner for humans. Further molecular biological studies on the IFNAR1 will help us to gain insights into the molecular implication of species-specific host-pathogen interaction in primate evolution.