• Journal of the Korean Chemical Society
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• v.22 no.2
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• pp.86-94
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• 1978

The crystal and molecular structure of theophylline hydrochloride has been determined from X-ray data by Patterson techniques. The structure has been refined by block-diagonal least-squares and Fourier synthesis on three dimensional data. The unit cell is orthorhombic, space group $P_{na21}$, with a = 14.01, b = 11.49, c = 6.77${\AA}$, and contains four molecules. The final R value based on 743 observed reflexions is 12.2%. The intramolecular distances are similar to those in other compounds containing a purine or pyrimidine group. The molecules are nearly planar and are stacked in layers parallel to the (001)plane. The chlorine atom is coordinated to N(1) atom at a distance of 3.06${\AA}$. The structure is stabilized mainly by van der Waals interactions; however, a short N${\cdot}{\cdot}{\cdot}$Cl contact of length $3.06\AA$, which is slightly less than the expected van der Waals separation, suggest that weak charge transfer interaction may be present. The relationship between this structure and the known structures of theophylline monohydrate and caffeine monohydrate are discussed.

• BMB Reports
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• v.44 no.11
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• pp.719-724
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• 2011

The $Sec61{\alpha}$ subunit is the core subunit of the protein conducting channel which is required for protein translocation in eukaryotes and prokaryotes. In this study, we cloned a $Sec61{\alpha}$ subunit from Penicillium ochrochloron ($PoSec61{\alpha}$). Sequence and 3D structural model analysis showed that $PoSec61{\alpha}$ conserved the typical characteristics of eukaryotic and prokaryotic $Sec61{\alpha}$ subunit homologues. The pore ring known as the constriction point of the channel is formed by seven hydrophobic amino acids. Two methionine residues from transmembrane ${\alpha}$-helice 7 (TM7) contribute to the pore ring formation and projected notably to the pore area and narrowed the pore compared with the superposed residues at the corresponding positions in the crystal structures or the 3D models of the $Sec61{\alpha}$ subunit homologues in archaea or other eukaryotes, respectively. Results reported herein indicate that the pore ring residues differ among $Sec61{\alpha}$ subunit homologues and two hydrophobic residues in the TM7 contribute to the pore ring formation.

• Journal of the Korean Society of Food Science and Nutrition
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• v.35 no.2
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• pp.177-181
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• 2006

In this study, phytochemicals from the wold and cultivated Lithospermum erythrorhizon (gromwell), which has been used for medicinal purpose or natural coloring material from the old days, were extracted by methanol and fractionated with hexane. The shikonin compounds in the fraction was isolated and their chemical structures were identified by $^1H$ and $^{13}C-NMR$. It was found that compound I was the shikonin substance with molecular weight of 288.3 and chemical formula of $C_{16}H_{16}O_5$, and compound II being deoxyshikonin substance with molecular weight of 272.3 and chemical formula of $C_{16}H_{16}O_4$. The Quantities of these compounds in the wild and cultivated gromwells was determined.

• Toxicological Research
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• v.31 no.2
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• pp.97-104
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• 2015

The skin exposure to solar irradiation and photoreactive xenobiotics may produce abnormal skin reaction, phototoxicity. Phototoxicity is an acute light-induced response, which occurs when photoreacive chemicals are activated by solar lights and transformed into products cytotoxic against the skin cells. Multifarious symptoms of phototoxicity are identified, skin irritation, erythema, pruritis, and edema that are similar to those of the exaggerated sunburn. Diverse organic chemicals, especially drugs, are known to induce phototoxicity, which is probably from the common possession of UV-absorbing benzene or heterocyclic rings in their molecular structures. Both UVB (290~320 nm) and UVA (320~400 nm) are responsible for the manifestation of phototoxicity. Absorption of photons and absorbed energy (hv) by photoactive chemicals results in molecular changes or generates reactive oxygen species and depending on the way how endogenous molecules are affected by phototoxicants, mechanisms of phototoxcity is categorized into two modes of action: Direct when unstable species from excited state directly react with the endogenous molecules, and indirect when endogeneous molecules react with secondary photoproducts. In order to identify phototoxic potential of a chemical, various test methods have been introduced. Focus is given to animal alternative test methods, i.e., in vitro, and in chemico assays as well as in vivo. 3T3 neutral red uptake assay, erythrocyte photohemolysis test, and phototoxicity test using human 3-dimensional (3D) epidermis model are examples of in vitro assays. In chemico methods evaluate the generation of reactive oxygen species or DNA strand break activity employing plasmid for chemicals, or drugs with phototoxic potential.

• Proceedings of the Korean Society of Applied Pharmacology
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• 1995.04a
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• pp.81-81
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• 1995

It is well known that Src Homology 2(SH2) domain in many intracellular signal transduction proteins is very important. The domain has about 100 amino acid residues and bind phosphotyrosine-containing peptide with high affinity and specificity. Lck SH2 domain is a Src-like, lymphocyte-specific tyrosine kinase. An 11-residue phosphopeptide derived from the hamster polvoma middle-T antigen, EPQp YEEIPIYL, binds with an 1 nM dissociation constant to Lck SH2 domain. And it is known that the phosphotyrosine and isoleucine residues of the peptide are tightly bound by two well-defined pockets on Lck SH2 domain's surface. To investigate the conformational changes during complexation of SH2 domain with phosphopeptide we have performed the molecular dynamics simulation for Lck SH2 domain with peptide and peptide-free form at look in aqueous solution. More than 3000 water molecules were incorporated to solvate Lck SH2 domain and peptide. Periodic boundary condition has been applied in molecular dynamics simulation. Data analysis with the results of that simulation shows that the phosphopeptide makes primary interaction with the Lck SH2 domain at six central residues, The comparison of the complexed and uncomplexed SH2 domain structures in solution has revealed only relatively small change. But the hydrophilic and hydrophobic pockets in the protein surface show the conformational changes in spite of the small structural difference between the complex and peptide-free forms.

• Applied Chemistry for Engineering
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• v.17 no.3
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• pp.260-266
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• 2006

For the synthesis of polyurethane memory foam stabilizer with fine cells, hydrosilylation reaction with various polyalkyleneoxides and hydrogen functional group of polymethylhydrogensiloxane (D = 75, D' = 15) was conducted. Polyalkyleneoxides (PAO) used in this research were ethylene oxides or ethylene-co-propylene oxides with terminal groups of hydroxides or methyl groups. To analyze the molecular structures and molecular weights as well as the reaction yields (98%), NMR and GPC analysis were executed. Synthesized siloxane surfactants modified with polyalkylene (EO = 12 units) were applied to producing flexible polyurethane fine memory foams from 0.6 pphp to 2.0 pphp. By controlling the amount of the surfactant, physical characteristics, the polyurethane memory foam with cell size (minimum $0.868{\mu}m$), air flows (-78 KPa), and recovery times (8 sec) were achieved.

• 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.

• Proceedings of the Korean Vacuum Society Conference
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• 2011.02a
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• pp.428-429
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• 2011

Recently, we performed ab initio total energy calculation and tight-binding molecular dynamics (TBMD) simulation to study structures and the reconstruction of native defects in graphene. In the previous study, we predicted by TBMD simulation that a double vacancy in graphene is reconstructed into a 555-777 composed of triple pentagons and triple heptagons [1]. The structural change from pentagon-octagon-pentagon (5-8-5) to 555-777 has been confirmed by recent experiments [2,3] and the detail of the reconstruction process is carefully studied by ab initio calculation. Pentagon-heptagon (5-7) pairs are also found to play an important role in the reconstruction of vacancy in graphene and single wall carbon nanotube [4]. In the TBMD simulation of graphene nanoribbon (GNR), we found the evaporation of carbon atoms from both the zigzag and armchair edges is preceded by the formation of heptagon rings, which serve as a gateway for carbon atoms to escape. In the simulation for a GNR armchair-zigzag-armchair junction, carbon atoms are evaporated row-by-row from the outermost row of the zigzag edge [5], which is in excellent agreement with recent experiments [2, 6]. We also present the recent results on the formation and development of dislocation in graphene. It is found that the coalescence of 5-7 pairs with vacancy defects develops dislocation in graphene and induces the separation of two 5-7 pairs. Our TBMD simulations also show that adatoms are ejected and evaporated from graphene surface due to large strain around 5-7 pairs. It is observed that an adatom wanders on the graphene surface and helps non-hexagonal rings change into stable hexagonal rings before its evaporation.

• Journal of the Korean Chemical Society
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• v.34 no.3
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• pp.232-238
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• 1990

To study the biological roles of Zn, we investigated simple model systems of $Zn^{++}, coordinated with OH_2 or NH_3,$ or with O=C- in peptide. The geometrical structures and net atomic charges were calculated by the ab initio HF-SCF theory using double zeta basis sets. The ligands of O-H, N-H, and O=C- are very polar due to $Zn^{++}$. Therefore, the carbon atom in peptide becomes so electrophilic that it can be easily attacked by other nucleophiles. In addition, to understand how $Zn^{++}$ is coordinated with ligands in enzyme, a molecular mechanics method is applied to the system of the enzyme of carboxypeptidase A (CPA) with the substrate of glycyltyrosine. From our results, it appears that the Zn ion is coordinated not only by four ligands in enzyme and substrate but also by one water molecule.

• Molecules and Cells
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• v.19 no.3
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• pp.356-364
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• 2005

Intramolecular excimer formation of 1,3-di(1-pyrenyl) propane(Py-3-Py) and fluorescence polarization of 1,6-diphenyl-1,3,5-hexatriene (DPH) were used to evaluate the effect of ethanol on the rate and range of lateral and rotational mobilities of bulk bilayer structures of synaptosomal plasma membrane vesicles (SPMVs) from the bovine cerebral cortex. Ethanol increased the excimer to monomer fluorescence intensity ratio (I'/I) of Py-3-Py in the SPMVs. Selective quenching of both DPH and Py-3-Py by trinitrophenyl groups was used to examine the range of transbilayer asymmetric rotational mobility and the rate and range of transbilayer asymmetric lateral mobility of SPMVs. Ethanol increased the rotational and lateral mobility of the outer monolayer more than of the inner one. Thus ethanol has a selective fluidizing effect within the transbilayer domains of the SPMVs. Radiationless energy transfer from the tryptophans of membrane proteins to Py-3-Py was used to examine both the effect of ethanol on annular lipid fluidity and protein distribution in the SPMVs. Ethanol increased annular lipid fluidity and also caused membrane proteins to cluster. These effects on neuronal membranes may be responsible for some, though not all, of the general anesthetic actions of ethanol.