• 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.

• Journal of Microbiology and Biotechnology
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• v.25 no.11
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• pp.1827-1834
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• 2015

The SMG1 lipase from Malassezia globosa is a newly found mono- and diacylglycerol (DAG) lipase that has a unique lid in the loop conformation that differs from the common alpha-helix lid. In the present study, we characterized the contribution of three residues, L103 and F104 in the lid and F278 in the rim of the binding site groove, on the function of SMG1 lipase. Site-directed mutagenesis was conducted at these sites, and each of the mutants was expressed in the yeast Pichia pastoris, purified, and characterized for their activity toward DAG and p-nitrophenol (pNP) ester. Compared with wild-type SMG1, F278A retained approximately 78% of its activity toward DAG, but only 11% activity toward pNP octanoate (pNP-C8). L103G increased its activity on pNP-C8 by approximately 2-fold, whereas F104G showed an approximate 40% decrease in pNP-C8 activity, and they both showed decreased activity on the DAG emulsion. The deletion of 103-104 retained approximately 30% of its activity toward the DAG emulsion, with an almost complete loss of pNP-C8 activity. The deletion of 103-104 showed a weaker penetration ability to a soybean phosphocholine monolayer than wild-type SMG1. Based on the modulation of the specificity and activity observed, a pNP-C8 binding model for the ester (pNP-C8, N102, and F278 form a flexible bridge) and a specific lipid-anchoring mechanism for DAG (L103 and F104 serve as "anchors" to the lipid interface) were proposed.

• Proceedings of the Korea Crystallographic Association Conference
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• 2002.11a
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• pp.4-4
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• 2002

PDZ domains bind to short segments within target proteins in a sequence-specific fashion. GRIP/ABP family proteins contain six to seven PDZ domains and interact via its sixth PDZ domain (class Ⅱ) with the C-termini of various proteins, including liprin-α. In addition the PDZ456 domain mediates the formation of homo- and heteromultimers of GRIP proteins. To better understand the structural basis of peptide recognition by a class Ⅱ PDZ domain and DZ-mediated multimerization, we determined the crystal structures of the GRIPI PDZ6 domain, alone and in complex with a synthetic C-terminal octapeptide of human liprin-α, at resolutions of 1.5 Å and 1.8 Å, respectively. Remarkably, unlike other class Ⅱ PDZ domains, Ile736 at αB5 rather than conserved Leu732 at αB1 makes a direct hydrophobic contact with the side chain of the Tyr at the -2 position of the ligand. Moreover, the peptide-bound structure of PDZ6 shows a slight reorientation of helix αB, indicating that the second hydrophobic pocket undergoes a conformational adaptation to accommodate the bulkiness of the Tyr's side chain, and forms an antiparallel dimer through an interface located at a site distal to the peptide-binding groove. This configuration may enable formation of GRIP multimers and efficient clustering of GRIP-binding proteins.

• Journal of Microbiology and Biotechnology
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• v.22 no.12
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• pp.1724-1730
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• 2012

An ${\alpha}$-L-arabinofuranosidase (TmAFase) from Thermotoga maritima MSB8 is a highly thermostable exo-acting hemicellulase that exhibits a relatively higher activity towards arabinan and arabinoxylan, compared with other glycoside hydrolase 51 family enzymes. In the present study, we carried out the enzymatic characterization and structural analysis of TmAFase. Tight domain associations found in TmAFase, such as an inter-domain disulfide bond (Cys306 and Cys476) in each monomer, a novel extended arm (amino acids 374-385) at the dimer interface, and total 12 salt bridges in the hexamer, may account for the thermostability of the enzyme. One of the xylan binding determinants (Trp96) was identified in the active site, and a region of amino acids (374-385) protrudes out forming an obvious wall at the substrate-binding groove to generate a cavity. The altered cavity shape with a strong negative electrostatic distribution is likely related to the unique substrate preference of TmAFase towards branched polymeric substrates.

• Proceedings of the Korean Vacuum Society Conference
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• 2014.02a
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• pp.335-335
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• 2014

Over the past several years, transparent conducting oxides have been extensively studied in order to replace indium tin oxide (ITO). Here we report on fluorine doped zinc tin oxide (FZTO) films deposited on glass substrates by radio-frequency (RF) magnetron sputtering using a 30 wt% ZnO with 70 wt% SnO2 ceramic targets. The F-doping was carried out by introducing a mixed gas of pure Ar, CF4, and O2 forming gas into the sputtering chamber while sputtering ZTO target. Annealing temperature affects the structural, electrical and optical properties of FZTO thin films. All the as-deposited FZTO films grown at room temperature are found to be amorphous because of the immiscibility of SnO2 and ZnO. Even after the as-deposited FZTO films were annealed from $300{\sim}500^{\circ}C$, there were no significant changes. However, when the sample is annealed temperature up to $600^{\circ}C$, two distinct diffraction peaks appear in XRD spectra at $2{\Theta}=34.0^{\circ}$ and $52.02^{\circ}$, respectively, which correspond to the (101) and (211) planes of rutile phase SnO2. FZTO thin film annealed at $600^{\circ}C$ resulted in decrease of resistivity $5.47{\times}10^{-3}{\Omega}cm$, carrier concentration ~1019 cm-3, mobility~20 cm2 V-1s-1 and increase of optical band gap from 3.41 to 3.60 eV with increasing the annealing temperatures and well explained by Burstein-Moss effect. Change of work function with the annealing temperature was obtained by ultraviolet photoemission spectroscopy. The increase of annealing temperature leads to increase of work function from ${\phi}=3.80eV$ (as-deposited FZTO) to ${\phi}=4.10eV$ ($600^{\circ}C$ annealed FZTO) which are quite smaller than 4.62 eV for Al-ZnO and 4.74 eV for SnO2. Through X-ray photoelectron spectroscopy, incorporation of F atoms was found at around the binding energy of 684.28 eV in the as-deposited and annealed FZTO up to 400oC, but can't be observed in the annealed FZTO at 500oC. This result indicates that F atoms in FZTO films are loosely bound or probably located in the interstitial sites instead of substitutional sites and thus easily diffused into the vacuum from the films by thermal annealing. The optical transmittance of FZTO films was higher than 80% in all specimens and 2-3% higher than ZTO films. FZTO is a possible potential transparent conducting oxide (TCO) alternative for application in optoelectronics.

• Bulletin of the Korean Chemical Society
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• v.34 no.7
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• pp.1972-1984
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• 2013

Microtubules play an important role in intracellular transport, mobility, and particularly mitosis. Paclitaxel (Taxol$^{TM}$) and paclitaxel-like compounds have been shown to be anti-tumor agents useful for various human tumors. Paclitaxel-like compounds operate by stabilizing microtubules through interface binding at the interface between two ${\beta}$-tubulin monomers in adjacent protofilaments. In this paper we present the elucidation of the structural features of paclitaxel and paclitaxel-like compounds (e.g., epothilones) with microtubule stabilizing activities, and relate their activities to spatial and chemical features of the molecules. CATALYST program was used to generate three-dimensional quantitative structure activity relationships (3D-QSARs) resulting in 3D pharmacophore models of epothilone- and paclitaxel-derivatives. Pharmacophore models were generated from diverse conformers of these compounds resulting in a high correlation between experimental and predicted biological activities (r = 0.83 and 0.91 for epothilone and paclitaxel derivatives, respectively). On the basis of biological activities of the training sets, five- and four-feature pharmacophore hypotheses were generated in the epothilone and paclitaxel series. The validation of generated hypotheses was achieved by using twelve epothilones and ten paclitaxels, respectively, which are not in the training sets. The clustering (grouping) and merging techniques were used in order to supplement spatial restrictions of each of hypothesis and to develop more comprehensive models. This approach may be of use in developing novel inhibitor candidates as well as contributing a better understanding of structural characters of many compounds useful as anticancer agents targeting microtubules.

• Journal of Adhesion and Interface
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• v.17 no.4
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• pp.149-154
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• 2016

In this study, natural polymer-based virus neutralizing agent was developed in an attempt to replace the conventional sterilization method for mammalian cell culture. A catechol conjugated heparin was synthesized by using EDC chemistry, and it show unique binding ability to virus which has heparin affinity (adenovirus, adeno-associated virus). To evaluate neutralization ability of catechol conjugated heparin, adeno-associated virus was used for test model, instead of using a pathogenic virus. The catechol conjugated heparin exhibited resistance to high concentration of salt and complete inactivation of adeno-associated virus. The result suggests that the catechol conjugated heparin, which is biocompatible and efficiency, may replace conventional sterilization method for mammalian cell culture.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.9
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• pp.1355-1362
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• 2019

Objective: S100A7A, a member of the S100 protein family, is involved in various biological processes, including innate immunity, antimicrobial function, and epithelial tumorigenesis. However, the expression and function of S100A7A in the endometrium during the estrous cycle and pregnancy are not well understood in pigs. Therefore, this study determined the expression and regulation of S100A7A at the maternal-conceptus interface in pigs. Methods: We obtained endometrial tissues from pigs throughout the estrous cycle and pregnancy, conceptus tissues during early pregnancy, and chorioallantoic tissues during midto late pregnancy and analyzed the expression of S100A7A in these tissues. We also determined the effects of steroid hormones, estradiol-$17{\beta}$ ($E_2$) and progesterone, and interleukin-$1{\beta}$ (IL1B) on S100A7A expression in endometrial tissues. Results: We found that S100A7A was expressed in the endometrium during the estrous cycle and pregnancy in a pregnancy status- and stage-dependent manner and was localized to endometrial luminal epithelial (LE) and superficial glandular epithelial cells with strong intensity in LE cells on day 12 of pregnancy. Early stage conceptuses and chorioallantoic tissues from day 30 to term pregnancy also expressed S100A7A. The expression of S100A7A was increased by $E_2$ and IL1B in endometrial tissues. Conclusion: S100A7A was expressed at the maternal-conceptus interface at the initiation of implantation in response to conceptus-derived estrogen and IL1B and could be a unique endometrial epithelial marker for conceptus implantation in pigs. These findings provide an important insight into the understanding of conceptus-endometrial interactions for the successful establishment of pregnancy in pigs.

• BMB Reports
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• v.40 no.3
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• pp.315-324
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• 2007

The novel $\alpha$-amylase purified from locally isolated strain, Bacillus sp. KR-8104, (KRA) (Enzyme Microb Technol; 2005; 36: 666-671) is active in a wide range of pH. The enzyme maximum activity is at pH 4.0 and it retains 90% of activity at pH 3.5. The irreversible thermoinactivation patterns of KRA and the enzyme activity are not changed in the presence and absence of $Ca^{2+}$ and EDTA. Therefore, KRA acts as a $Ca^{2+}$-independent enzyme. Based on circular dichroism (CD) data from thermal unfolding of the enzyme recorded at 222 nm, addition of $Ca^{2+}$ and EDTA similar to its irreversible thermoinactivation, does not influence the thermal denaturation of the enzyme and its Tm. The amino acid sequence of KRA was obtained from the nucleotide sequencing of PCR products of encoding gene. The deduced amino acid sequence of the enzyme revealed a very high sequence homology to Bacillus amyloliquefaciens (BAA) (85% identity, 90% similarity) and Bacillus licheniformis $\alpha$-amylases (BLA) (81% identity, 88% similarity). To elucidate and understand these characteristics of the $\alpha$-amylase, a model of 3D structure of KRA was constructed using the crystal structure of the mutant of BLA as the platform and refined with a molecular dynamics (MD) simulation program. Interestingly enough, there is only one amino acid substitution for KRA in comparison with BLA and BAA in the region involved in the calcium-binding sites. On the other hand, there are many amino acid differences between BLA and KRA at the interface of A and B domains and around the metal triad and active site area. These alterations could have a role in stabilizing the native structure of the loop in the active site cleft and maintenance and stabilization of the putative metal triad-binding site. The amino acid differences at the active site cleft and around the catalytic residues might affect their pKa values and consequently shift its pH profile. In addition, the intrinsic fluorescence intensity of the enzyme at 350 nm does not show considerable change at pH 3.5-7.0.

• Journal of Powder Materials
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• v.16 no.6
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• pp.416-423
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• 2009

Diamond/SiC composites are appropriate candidate materials for heat conduction as well as high temperature abrasive materials because they do not form liquid phase at high temperature. Diamond/SiC composite consists of diamond particles embedded in a SiC binding matrix. SiC is a hard material with strong covalent bonds having similar structure and thermal expansion with diamond. Interfacial reaction plays an important role in diamond/SiC composites. Diamond/SiC composites were fabricated by high temperature and high pressure (HPHT) sintering with different diamond content, single diamond particle size and bi-modal diamond particle size, and also the effects of composition of diamond and silicon on microstructure, mechanical properties and thermal properties of diamond/SiC composite were investigated. The critical factors influencing the dynamics of reaction between diamond and silicon, such as graphitization process and phase composition, were characterized. Key factor to enhance mechanical and thermal properties of diamond/SiC composites is to keep strong interfacial bonding at diamond/SiC composites and homogeneous dispersion of diamond particles in SiC matrix.