• Bulletin of the Korean Chemical Society
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• v.30 no.5
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• pp.1139-1142
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• 2009

Refinement of NMR structures by molecular dynamics (MD) simulations with a solvent model has improved the structural quality. In this study, we applied MD refinement with the generalized Born (GB) implicit solvent model to protein structure determined under membrane-like environments. Despite popularity of the GB model, its applications to the refinement of NMR structures of hydrophobic proteins, in which detergents or organic solvents enclose proteins, are limited, and there is little information on the use of another GB parameter for these cases. We carried out MD refinement of crambin NMR structure in dodecylphosphocholine (DPC) micelles (Ahn et al., J. Am. Chem. Soc. 2006, 128, 4398-4404) with GB/Surface area model and two different surface tension coefficients, one for aquatic and the other for hydrophobic conditions. Our data show that, of two structures by MD refinement with GB model, the one refined with the parameter to consider hydrophobic condition had the better qualities in terms of precision and solvent accessibility.

• Molecules and Cells
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• v.27 no.6
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• pp.651-656
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• 2009

The formation of ${\beta}$-amyloid peptide ($A{\beta}$) is initiated from cleavage of amyloid precursor protein (APP) by a family of protease, ${\alpha}$-, ${\beta}$-, and ${\gamma}$-secretase. Sub W, a substrate peptide, consists of 10 amino acids, which are adjacent to the ${\beta}$-cleavage site of wild-type APP, and Sub M is Swedish mutant with double mutations on the left side of the ${\beta}$-cleavage site of APP. Sub W is a normal product of the metabolism of APP in the secretary pathway. Sub M is known to increase the efficiency of ${\beta}$-secretase activity, resulting in a more specific binding model compared to Sub W. Three-dimensional structures of Sub W and Sub M were studied by CD and NMR spectroscopy in water solution. On the basis of these structures, interaction models of ${\beta}$-secretase and substrate peptides were determined by molecular dynamics simulation. Four hydrogen bonds and one water-mediated interaction were formed in the docking models. In particular, the hydrogen bonding network of Sub M-BACE formed spread over the broad region of the active site of ${\beta}$-secretase (P5-P3'), and the side chain of P2- Asn formed a hydrogen bond specifically with the side chain of Arg235. These are more favorable to the cleavage of Sub M by ${\beta}$-secretase than Sub W. The two substrate peptides showed different tendency to bind to ${\beta}$-secretase and this information may useful for drug development to treat and prevent Alzheimer's disease.

• Proceedings of the Polymer Society of Korea Conference
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• 2006.10a
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• pp.173-173
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• 2006

We have explored a strategy to control the supramolecular nano-structures self-assembled from rigid segments through attachment of flexible chains through microphase separation and anisotropic arrangement. Supramolecular structures formed by self-assembly of rigid building blocks can be precisely controlled from 1-D layered, 3-D bicontinuous cubic to 2-D cylindrical structures by systematic variation of the type and relative length of the respective blocks. Furthermore, depending on the individual molecular architectures, rigid building blocks self-assemble into a wide range of supramolecular structures such as honeycomb, disk, cylinder, helix, tube, barrel stave, and nano-cage.

• 한국정보디스플레이학회:학술대회논문집
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• 2004.08a
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• pp.812-815
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• 2004

The molecular structure influences the thermal behavior of HTM. For OLED the glass transition temperature and evaporation temperature are critical. We report how changes in structure cause changes on both parameters. The results may be of interest for chemists when they design new molecule structures for OLED.

• Proceedings of the Korean Vacuum Society Conference
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• 2005.02a
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• pp.36-36
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• 2005

• Proceedings of the Korean Vacuum Society Conference
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• 2008.08a
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• pp.230-230
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• 2008

• Proceedings of the Polymer Society of Korea Conference
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• 2006.10a
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• pp.221-221
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• 2006

The stereochemical control in polypropylenes and styrene-ethylene copolymers based on homogeneous single-site polymerization catalysts has received great attention since the stereocpecificity is one of the key factors in tailoring the polymer properties. Thus, we have developed new tactics for isospecificity in propylene polymerization with the unbridged metallocenebased systems and syndiospecific styrene-styrene sequence in styrene-ethylene copolymerization with the group 4 metallocene system. Brief details of the synthesis, structures and the polymerization behavior of a set of new metallocene catalysts will be presented.

• 한국정보디스플레이학회:학술대회논문집
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• 2003.07a
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• pp.178-180
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• 2003

We performed semiempirical (AMl and ZINDO) and ab initio (HF and DFT) calculations, to investigate molecular structures and optical properties of DCM and its derivatives. DCM and its derivatives are used as a red fluorescent dopant of the organic electroluminescent host materials, $Alq_3$. We have studied the relationship between the molecular structure and the optical properties of these molecules for the improvement of EL efficiencies. Wavelength at the absorption maximum was found to be red-shifted when the molecule is substituted with both strong electron donating and withdrawing functional groups. A new red fluorescent dye was predicted by QSPR study based on calculations and experimental data.

• BMB Reports
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• v.40 no.6
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• pp.870-874
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• 2007

We cloned a uridine-diphosphate dependent glycosyl-transferase RUGT-10 from Oryza sativa. The recombinant enzyme was expressed by glutathione-S transferase gene fusion system in Escherichia coli. RUGT10 showed different regioselectivity depending on the structures of substrates (e.g. flavanone, flavonol, and flavone). Apparently, flavanone such as naringenin and eriodictyol gave one 7-O-glucoside while flavone and flavonol gave more than two products with preferential glucosylation position of hydroxyl group at C-3 position.

• Journal of Advanced Marine Engineering and Technology
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• v.31 no.8
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• pp.932-938
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• 2007

The interaction between adherent molecules and gas molecules was modeled in molecular scale and simulated by the molecular dynamics method in order to understand the evaporation and removal processes of adherent molecules on metallic surface using high temperature gas flow. Methanol molecules were chosen as adherent molecules to investigate effects of adhesion quantify and gas molecular collisions because the industrial oil has too complex structures of fatty acid. The effects of adherent quantify, gas temperature and surface temperature for the evaporation rate of adherent molecules and the molecular removal mechanism were investigated and discussed in the present study. Evaporation and removal rates of adherent molecules from metallic surface calculated by the molecular dynamics method showed the similar dependence on surface temperature shown in the experimental results.