• BMB Reports
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• v.42 no.11
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• pp.697-704
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• 2009

Membrane proteins play important roles in the biology of the cell, including intercellular communication and molecular transport. Their well-established importance notwithstanding, the high-resolution structures of membrane proteins remain elusive due to difficulties in protein expression, purification and crystallization. Thus, accurate prediction of membrane protein topology can increase the understanding of membrane protein function. Here, we provide a brief review of the diverse computational methods for predicting membrane protein structure and function, including recent progress and essential bioinformatics tools. Our hope is that this review will be instructive to users studying membrane protein biology in their choice of appropriate bioinformatics methods.

• Molecules and Cells
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• v.25 no.1
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• pp.70-77
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• 2008

Proteome analysis was performed to identify proteins differentially expressed in an Arabidopsis mutant, ntm1-D. In this mutant the NAC transcription factor NTM1 is constitutively expressed and the resultant phenotypic changes include dwarfism, serrated leaves, and altered floral structures, probably due to reduced cell division. Marked elevation of proteins mediating environmental stress responses, including annexin, vegetative storage proteins, beta-glucosidase homolog 1, and glutathione transferases was observed. Overexpression of annexin was confirmed by RT-PCR and Western blotting. These observations suggest that the reduced growth observed in the ntm1-D mutant is caused by enhancement of its stress responses, possibly resulting in a cost in fitness.

• Journal of Mechanical Science and Technology
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• v.18 no.11
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• pp.2042-2048
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• 2004

A molecular dynamics study has been conducted on an external-force-field-induced isothermal crystallization process of amorphous structures as a new low-temperature athermal crystallization process. An external cyclic-force field with a dc bias is imposed on molecules selected randomly in an amorphous-phase of argon. Multiple peaks smoothed out in the radial distribution functions for amorphous states appear very clearly during the crystallization process that cannot be achieved otherwise. When the amorphous material is locally exposed to an external force field, crystallization starts and propagates from the interfacial region and crystallization growth rates can be estimated.

• Journal of Microbiology and Biotechnology
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• v.19 no.5
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• pp.491-494
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• 2009

Within the secondary metabolite class of flavonoids, which consist of more than 10,000 known structures, flavones define one of the largest subgroups. The diverse function of flavones in plants as well as their various roles in the interaction with other organisms offers many potential applications including in human nutrition and pharmacology. We used two genes, flavone synthase (PFNS-l) that converts naringenin into apigenin and flavone 7-O-methyltransferase (POMT-7) that converts apigenin into 7-O-methyl apigenin, to synthesize 7-O-methyl apigenenin from naringenin. The PFNS-l gene was subcloned into the E. coli expression vector pGEX and POMT-7 was subcloned into the pRSF vector. Since both constructs contain different replication origins and selection markers, they were cotransformed into E. coli. Using E. coli transformants harboring both PFNS-l and POMT-7, naringenin could be converted into 7-O-methyl apigenin, genkwanin.

• Proceedings of the Polymer Society of Korea Conference
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• 2006.10a
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• pp.116-117
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• 2006

Increasing the solvent molecular size leads to shrinkage of the polymer chains and increase of the critical overlap concentrations. In addition, the dependency of $R_{g}$ on polymer concentration under normal solvent conditions and solvent molecular size is in good agreement with scaling laws. When the solvent molecular size approaches the ideal end-to-end distance of the polymer chain, an extra aggregation of polymer chains occurs, and the solvent becomes the so-called medium-sized solvent. When the size of solvent molecules is smaller than the medium size, the polymer chains are swollen or partially swollen. However, when the size of solvent molecules is larger than the medium size, the polymer coils shrink and segregate, enwrapped by the large solvent molecules.

• 한국정보디스플레이학회:학술대회논문집
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• 2003.07a
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• pp.486-488
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• 2003

Some important properties of the liquid crystal molecules containing fluoro-isothiocyanated molecules have been studied using quantum chemical calculations and the results were correlated with respect to the structure of the molecules. Dielectric anisotropy, birefringence have been predicted for several unknown structures. The Maier-Meier, Vuks equation were used for the dielectric anisotropy and birefringence calculation. The results obtained by empirical approximation showed a good agreement with experiment ones.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.203-209
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• 2004

Molecular docking using Lamarckian genetic algorithm of AutoDock 3.0 (AD3) was employed to understand in retrospect the selectivity of phenylaminopyrimidine (PAP) derivatives against the kinase domain c-Abl, implicated in chronic myelogenous leukemia (CML). The energetics of protein-ligand complex was scored using AD3 to identify active drug conformations while Ligplot and ligand protein contact (LPC) programs were used to probe schematic molecular recognition of the bound inhibitor to the protein. Results signify correlation between model and crystal structures of STI-571 compound or Imatinib (IM), a PAP derivative and now clinically proven for its efficacy in CML. A prospect active form Abl inhibitor scaffold from matlystatin class of compounds will be published elsewhere.

• Molecules and Cells
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• v.26 no.6
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• pp.517-529
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• 2008

Porosomes are supramolecular, lipoprotein structures at the cell plasma membrane, where membrane-bound secretory vesicles transiently dock and fuse to release inravesicular contents to the outside during cell secretion. The mouth of the porosome opening to the outside, range in size from 150 nm in diameter in acinar cells of the exocrine pancreas, to 12 nm in neurons, which dilates during cell secretion, returning to its resting size following completion of the process. In the past decade, the composition of the porosome, its structure and dynamics at nm resolution and in real time, and its functional reconstitution into artificial lipid membrane, have all been elucidated. In this mini review, the discovery of the porosome, its structure, function, isolation, chemistry, and reconstitution into lipid membrane, the molecular mechanism of secretory vesicle swelling and fusion at the base of porosomes, and how this new information provides a paradigm shift in our understanding of cell secretion, is discussed.

• Bulletin of the Korean Chemical Society
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• v.35 no.8
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• pp.2277-2280
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• 2014

The contact properties between gold and poly(3-hexylthiophene) (P3HT) films having either of two distinct molecular orientations and orderings were investigated. Thermal treatment increased the molecular ordering of P3HT and remarkably reduced the contact resistance at the electrode/semiconductor interface, which enhanced the electrical performance. This phenomenon was understood in terms of a small degree of metal penetration into the P3HT film as a result of the thermal treatment, which formed a sharp interface at the contact interface between the gold electrode and the organic semiconductor.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.32 no.12
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• pp.1047-1054
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• 2008

In this paper, the molecular dynamics (MD) simulations are performed with single-crystal copper blocks under simple shear and simple tension to investigate the effect of size and crystal orientation. There are many variances to give influences such as deformation path, temperature, specimen size and crystal orientation. Among them, the crystal orientation has a primary influence on the volume averaged stress. The numerical results show that the volume averaged shear stress decreases as the specimen size increases and as the crystal orientation changes from single to octal. Furthermore, the Schmid factor and yield stress for crystal orientation are evaluated by using the MD simulation on the standard triangle of stereographic projection.