• Reproductive and Developmental Biology
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• v.34 no.1
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• pp.7-13
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• 2010

The binding affinity constants ($p(Od)_{50}$) and molecular docking scores (OS) between porcine odorant binding proteins pOBP (1HQP) and pPBP (1GM6) as receptor and a series of tetrahydrofuran-2-yl (A & B) analogues as substrate, and their interactions were discussed quantitatively using three-dimensional quantitative structure-activity relationship (30-QSAR) models. The statistical qualities of the optimized CoMF A models for pOBP were better than those of the CoMSIA models. The binding affinity constants and OS between substrate and receptor molecules were dependent upon steric and hydrophobic interaction. The DS constants of the substrates into the binding site of OBP (1HQP) were bigger than those of PBP (1GM6). The resulting contour maps produced by the optimized CoMFA model were used to identify the structural features relevant to the binding affinity in binding site of pOBP.

• Reproductive and Developmental Biology
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• v.33 no.3
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• pp.119-123
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• 2009

The two dimensional quantitative structure-activity relationships (2D-QSARs) models concerning the binding affinity constants ($p[Od.]_{50}$) between 2-cyclohexyltetrahydropyrane and 2-cyclohexyltetrahydrofurane analogues as substrates, and bovine odorant binding protein (bOBP) as receptor were derived by multiple regression analyses method and discussed. The statistical quality of the optimized 2D-QSAR model (5) was good (r=0.907). From the model, the binding affinity constants ($p[Od.]_{50}$) were dependent upon the optimal value ($(TL)_{opt.}$=2.737) of total lipole (TL) of substrate molecules. Based on these findings, the high active compounds predicted by optimized 2D-QSAR model (5) were 2-(dimethylcyclohexyl)tetrahydropyrane molecule and their isomer molecules. The binding affinity constants regarding bOBP of the tetrahydrofuryl-2-yl family compounds were dependent upon the hydrophobicity (logP) of whole substrate molecules. In any case of porcine odorant-binding proteins (pOBP), the constants were dependent upon the hydrophobicity (${\pi}x={\log}P_X-{\log}P_H$) of substituents (R) in substrate molecules. Also, from the optimal values of hydrophobic constant, the hydrophobicity for bOBP influenced ca. twice time bigger (bOBP>pOBP) than that for pOBP.

• Bulletin of the Korean Chemical Society
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• v.25 no.7
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• pp.1031-1035
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• 2004

The adsorption kinetics of ${\beta}$-casein on a hydrophobic surface has been studied by means of the quartz crystal microbalance (QCM). The self assembled monolayer of 1-octadecanethiol on a gold coated quartz crystal was used as a hydrophobic surface for adsorption. The adsorption kinetics was monitored in different solution conditions. Formation of monolayer is observed in most cases. At high concentration of protein, micelle formation which is interrupted by high ionic strength of solution is observed. Casein binding cations such as $Ca^{2+},\;Ba^{2+}\;and\;Al^{3+}$ increase the hydrophobicity of the protein and the multiple layer adsorption occurs. The strong and weak points of the QCM method in the study of protein adsorption are discussed.

• Textile Coloration and Finishing
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• v.14 no.2
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• pp.85-85
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• 2002

The interaction between berberine and tannin in aqueous solution was investigated spectrophotometerically. The dyeing mechanism of silk fabrics (control and tannin treated silk fabrics) with berberine was based on thermodynamic parameters obtained from equilibrium adsorption experiments. In adsorption spectra of aqueous solution of berberine and tannin mixture two isosbestic points (328nm, 357nm) were found and the mole fraction of reaction of components was 1:1. Initial dyeing rates were increased and the diffusion of dye was more effective by tannin treatment. Without regard to tannin treatment the adsorption isotherm of berberine was the langmuir type except high temperature, 80℃. By tannin treatment the saturation dye uptake was increased, the increase of dye uptake appeared to be a result of entropy change rather than enthalpy change. All these results can be interpreted by the hydrophobic interaction between berberine and silk treated with tannin and it is reasonable to conclude that not only the ionic force, but also the hydrophobic interaction contributes to the binding of berberine and tannin treated silk treated with tannin.

• Textile Coloration and Finishing
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• v.14 no.2
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• pp.9-17
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• 2002

The interaction between berberine and tannin in aqueous solution was investigated spectrophotometerically. The dyeing mechanism of silk fabrics (control and tannin treated silk fabrics) with berberine was based on thermodynamic parameters obtained from equilibrium adsorption experiments. In adsorption spectra of aqueous solution of berberine and tannin mixture two isosbestic points (328nm, 357nm) were found and the mole fraction of reaction of components was 1:1. Initial dyeing rates were increased and the diffusion of dye was more effective by tannin treatment. Without regard to tannin treatment the adsorption isotherm of berberine was the langmuir type except high temperature, $80^\circ{C}$. By tannin treatment the saturation dye uptake was increased, the increase of dye uptake appeared to be a result of entropy change rather than enthalpy change. All these results can be interpreted by the hydrophobic interaction between berberine and silk treated with tannin and it is reasonable to conclude that not only the ionic force, but also the hydrophobic interaction contributes to the binding of berberine and tannin treated silk treated with tannin.

• Bulletin of the Korean Chemical Society
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• v.28 no.12
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• pp.2248-2252
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• 2007

SOMT-9 is an O-methyltransferase that utilizes quercetin to produce 3'-methoxy quercetin. In order to determine which amino acids of SOMT-9 are important for this reaction and its regioselectivity, molecular docking experiments followed by site directed mutagenesis were performed. Molecular modeling and molecular docking experiments identified several amino acid residues involved in metal binding, AdoMet binding, and substrate binding. Site-directed mutagenesis showed that Asp188 is critical for metal binding and that Lys165 assists other metal binding residues in maintaining quercetin in the proper position during the reaction. In addition, Tyr207 was shown to play an important role in the determination of the regioselectivity and Met60 was shown to be involved in formation of the hydrophobic pocket necessary for substrate binding. The molecular modeling and docking experiments discussed in this study could be applicable to future research including prediction of substrate binding and regioselectivity of an enzyme.

• Proceedings of the Korean Fiber Society Conference
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• 1987.06a
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• pp.47-48
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• 1987

• Archives of Pharmacal Research
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• v.28 no.7
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• pp.756-760
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• 2005

Polyene macrolide amphotericin B (AmB) is the drug of choice for the treatment of disseminated fungal infections. However, because of its pronounced side effects, the drug has limited applicability. There are few interesting reports, which state that co-administration of the drug with homo-peptide of polyaspartic acid reduces the side effects of the drug. In our present study, an approach has been made to systematically synthesize low molecular weight heteropeptides consisting of L-aspartic acid and its derivative. It was hypothesized that such heteropeptides will reduce the toxic side effects of the drug by facile hydrophobic binding between the polymer and the drug. We have employed the strategy of solid phase peptide synthesis (SPPS) to synthesize low molecular weight hetero-peptides by using L-aspartic acid and benzyl-L-aspartic acid to induce the hydrophobic binding between the peptide and the drug. In future, the proposed methodology can be employed to tailor other polypeptides substituted with benzyl groups to reduce the nephrotoxicity of AmB.

• Rapid Communication in Photoscience
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• v.4 no.2
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• pp.37-40
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• 2015

To examine the photosensitized biomolecules damaging activity, dimethoxyP(V)tetrakis(2-naphthyl)porphyrin (NP) and dimethoxyP(V)tetraphenylporphyrin (PP) were synthesized. The naphthyl moiety of NP hardly deactivated the photoexcited P(V)porphyrin ring in ethanol. In aqueous solution, the naphthyl moiety showed the quenching effect on the photoexcited porphyrin ring, possibly through electron transfer and self-quenching by a molecular association. Binding interaction between human serum albumin (HSA), a water soluble protein, and these porphyrins could be confirmed by the absorption spectral change. The apparent association constant of NP was larger than that of PP. It is explained by that more hydrophobic NP can easily bind into the hydrophobic pockets of HSA. The photoexcited PP effectively induced damage of the tryptophan residue of HSA, through electron transfer-mediated oxidation and singlet oxygen generation. NP also induced HSA damage during photo-irradiation and the contributions of the electron transfer and singlet oxygen mechanisms were speculated. The electron transfer-mediated mechanism to the photosensitized protein damage should be advantageous for photodynamic therapy in hypoxic condition. The quantum yield of the HSA photodamage by PP was significantly larger than that of NP. The quenching effect of the naphthyl moiety is considered to suppress the photosensitized protein damage. In conclusion, the naphthalene substitution to the P(V)porphyrins can enhance the binding interaction with hydrophobic biomacromolecules such as protein, however, this substitution may reduce the photodynamic effect of P(V)porphyrin ring in aqueous media.

• Journal of the Korean Chemical Society
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• v.67 no.4
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• pp.226-235
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• 2023

Chikungunya fever has a high morbidity rate in humans and is caused by chikungunya virus. There are no treatments available until now for this particular viral disease. The present study was carried out by selecting 19 flavonoids, which are available naturally in fruits, vegetables, tea, red wine and medicinal plants. The molecular docking of selected 19 flavonoids was carried out against the Chikungunya virus capsid protein using the Autodock4.2 software. Binding affinity analysis based on the Intermolecular interactions such as Hydrogen bonding and hydrophobic interactions and drug-likeness properties for all the 19 flavonoids have been carried out and it is found that the top four molecules are Chrysin, Fisetin, Naringenin and Biochanin A as they fit to the chikungunya protein and have binding energy of -8.09, -8.01, -7.6, and 7.3 kcal/mol respectively. This result opens up the possibility of applying these compounds in the inhibition of chikungunya viral protein.