• YAKHAK HOEJI
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• v.47 no.2
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• pp.110-119
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• 2003

The purpose of the present study was to kinetically investigate the carrier-mediated uptake in the hepatic transport of organic anions, and to simulate the ″in vivo counter-transport″ phenomena, using kinetic model which was developed in this study. The condition that the mobility of carrier-ligand complex is greater than that of free carrier is not essential for the occurrence of ″counter-transport″ phenomenon. To examine the inhibitory effects on the initial uptake of a ligand by the liver, it is necessary to judge whether the true counter-transport mechanism (trans-stimulation) is working or not. The initial plasma disappearance curves of a organic anion were then kinetically analyzed based on a flow model, in which the ligand is eliminated only from the peripheral compartment (liver compartment). Moreover, ″in vive counter-transport″ phenomena were simulated based on the perfusion model which incorporated the carrier-mediated transport and the saturable intracellular binding. The ″in vivo counter-transport″ phenomena in the hepatic transport of a organic anion were well demonstrated by incorporating the carrier-mediated process. However, the ″in vivo counter-transport″ phenomena may be also explained by the enhancement of back diffusion due to the displacement of intracellular binding. In conclusion, one should be more cautious in interpreting data obtained from so-called ″in vivo counter-transport″ experiments.

• Archives of Pharmacal Research
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• v.19 no.4
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• pp.269-274
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• 1996

The binding interactions between human serum albumin (HSA) and the edible food dyes amaranth, tartrazine and sunset yellow have been studied. Intrinsic association constants and the free energy changes associated with dye-protein binding at physiological pH for amaranth and tartrazine, and at two different pH values for sunset yellow have been calculated from ultrafiltration data. The temperature dependence $(20-40^{\circ}C)$ of the intrinsic association constants at pH 7.4 for amaranth-HSA and tartrazine-HSA mixtures have been measured, from which a plot of the van't Hoff isochore exhibits a marked change in slope around $30^{\circ}C$ indicating a possible change in protein conformation. The number of dye binding sites on HSA is reported for all the above conditions. HSA-ligand binding enthalpies have been used in conjunction with the N-B transitional binding enthalpy for HSA, to calculate the enthalpy for the N-B transition when ligands are bound with the protein.

• Journal of the Korean Society of Food Science and Nutrition
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• v.23 no.3
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• pp.414-419
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• 1994

This study was trying to find what physical changes occurred to albumin when it reacted with estrogen and other ligands. Each concentration of human serum albumin with 100$\mu$l estradiol reacted at the highest binding capacity of 280nm. In addition, 1 hr of reaction time showed the highest binding rate. Conformational changes in human serum albumin with dietylstillbesterol and N-ethyl-maleimide produced strong binding capacities. The changes were immediate and they did not increase or decrease over time. Effects of human serum albumin with estriol induced no interaction each other. The binding capacity of human serum albumin with vitamin D$_2$was lower than estradiol. and the highest binding rate showed 1 hr of reaction time. Vitamin D$_2$ was very similar to the binding capacity of estradiol.

• Bulletin of the Korean Chemical Society
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• v.32 no.4
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• pp.1133-1137
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• 2011

Ordered array of gold nanoparticles (Au NPs) over ITO glass was investigated in terms of ITO pretreatment, particle size, and diamines with different chain length. Owing to the indium-tin-oxide (ITO) layer coated on the glass, the substrate surface has a limited number of hydroxyl groups which can produce functionalized amine groups for Au binding, which resulted in the loosely-packed array of Au NPs on the ITO surface. Diamine ligand as a molecular linker was introduced to enhance the lateral binding of adjacent Au NPs immobilized on the amine-functionalized ITO glass, consequently leading to the densely-packed array of Au NPs over the ITO substrate. The molecular bridging effect was strengthened with the increase of chain length of diamines: C-12 > C-8. The packing density of small Au NPs (< 40 nm) was significantly increased with the increase of C-8 diamine, but large Au NPs (> 60 nm) did not produce densely-packed array on the ITO glass even for the dosage of C-12 diamine.

• Bulletin of the Korean Chemical Society
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• v.26 no.1
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• pp.151-156
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• 2005

The conformational dynamics of heme pocket, a small vacant site near the binding site of heme proteins -myoglobin (Mb) and hemoglobin (Hb), was investigated after photolysis of carbon monoxide from MbCO and HbCO in D$_2$O solution at 283 K by probing time-resolved vibrational spectra of photolyzed CO. Two absorption bands, arising from CO in the heme pocket, evolve nonexponentially in time. The band at higher energy side blue shifts and broadens with time and the one at lower energy side narrows significantly with a negligible shift. These spectral evolutions are induced by protein conformational changes following photolysis that modify structure and electric field of heme pocket, and ligand dynamics in it. The conformational changes affecting the spectrum of photolyzed CO in heme pocket likely modulates ligand-binding activity.

• Bulletin of the Korean Chemical Society
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• v.21 no.10
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• pp.1052-1054
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• 2000

Binding geometries of $[Ru(II)(110-phenanthroline)_2L]^2+$, complexes (where L = dipyrido [3,2-a:2',3'-c]phena-zine (DPPZ) or benzodipyrido[3,2-a:2',3'-c] phenazine (BDPPZ)) to poly(dG)${\cdot}$poly(dC)${\cdot}$poly(dC) + triplex DNA (CGC + triplex) has been investigated by linear dichroism and normal absorption spectroscopy. Analysis of the linear dichroism for the CGC+ triplex and $[Ru(II)(phen)_2BDPPZ]^2+$ complex indicates that the extended ligand of the metal complex lie perpendicular to the polynucleotide helix axis. Together with strong hypochromism and red shift in the interligand absorption region, we concluded that the extended BDPPZ or DPPZ ligand in-tercalated between the bases of polynucleotide. The spectral properties of the metal complexes bound to CGC+ triplex are similar to those bound to $poly(dA)[poly(dT)]^2$ triplex (Choi et al., Biochemistry 1997, 36, 214), sug-gesting that the metal complex is located in the minor groove of the CGC+ triplex.

• Proceeding of EDISON Challenge
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• 2013.04a
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• pp.89-100
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• 2013

생물정보학의 다양한 이론적 내용과 계산적 방법들이 갈수록 전문화 되어짐에 따라 신약 개발, 신 물질 합성, 단백질의 구조 예측 등 다양한 분야에서 필요성이 커져가고 있다. 이 중 molecular docking 기술은 단백질과 특정 분자간의 결합 형태를 분자 모델링 기법을 통해 알아내는 방법이며 신약개발 연구에 큰 영향을 미치고 있다. Molecular docking을 통하여 분자간의 결합 형태를 예측하는 과정에서 Protein-ligand complex의 정확한 에너지 측정을 가능하게 하는 scoring function이 필요하다. 그런데 본 연구에서 사용한 B-Raf kinase protein 은 active site 부분에서 ligand와 receptor 간에 aromatic ring로 인한 ${\pi}-{\pi}$ interaction이 정확한 에너지 계산을 어렵게 한다. 이러한 ${\pi}-{\pi}$ interaction 부분의 에너지를 정확하게 계산하기 위해 양자역학 계산을 실시하였다. Active site 부분에서 ligand와 receptor에서 발생하는 각각 다른 5개의 ${\pi}-{\pi}$ interaction 구조를 준비하여 Gaussian을 통해 양자역학 에너지를 계산하였다. 그리고 이러한 결과 값들이 ligand의 활성 값과 어떤 상관관계를 갖는지 살펴보았다. 그 결과 ${\pi}-{\pi}$ interaction을 양자역학으로 계산한 값이 그렇지 않은 것보다 더 좋은 상관관계를 보여주었다. 이는 특별한 구조의 영향으로 ligand와 receptor 간의 결합에너지를 정확하게 계산하기 어려운 문제에서 양자역학을 적용할 경우 더욱 좋은 결과값을 얻을 수 있었다. 또한 이러한 데이터가 신 물질 개발이나 신약 개발 등의 다양한 분야에서 계산화학 방법이 신뢰성을 얻는데 도움 될 수 있다고 생각된다.

• Bulletin of the Korean Chemical Society
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• v.34 no.6
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• pp.1673-1678
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• 2013

Lumazine protein is a member of the riboflavin synthase superfamily and the intense fluorescence is caused by non-covalently bound to 6,7-dimethyl 8-ribityllumazine. To figure out the binding modes and the structure of the N-terminal domain of lumazine protein, the wild type of protein extending to amino acid 118 (N-LumP 118 Wt) and mutants of N-LumP 118 V41W, S48W, T50W, D64W, and A66W from Photobacterium leiognathi were purified. The biochemical properties of the wild type and mutants of N-LumP 118 proteins were analyzed by absorbance and fluorescence spectroscope. The peak of absorbance and fluorescence of lumazine ligand were shifted to longer wavelength on binding to N-LumPs. The observed absorbance value at 410 nm of lumazine bound to N-LumP 118 proteins indicate that one mole of N-LumP 118 proteins bind to one mole of ligand of lumazine. Fluorescence analysis show that the maximum peak of fluorescence of N-LumP S48W was shifted to the longest wavelength by binding with 6,7-dimethyl 8-ribityllumazine and was shown to the greatest quench effect by acrylamide among all tryptophan mutants.

• Journal of Biomedical Engineering Research
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• v.34 no.3
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• pp.123-128
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• 2013

The 'Dielectrophoretic Tweezers(DEP Tweezers)' can be used as a facile, economical toolkit for quantitative measurement of chemical and biological binding forces related to many biological interactions within a microfluidic device. Our experimental setup can probe the interaction between a single receptor molecule and its specific ligand. Immunoglobulin G(IgG) functionalized on polystyrene microspheres has been used to detect individual surface linked Staphylococcus protein A(SpA) molecules and to characterize the strength of the noncovalent IgG-SpA bond. It was measured and compared with the existing measurements. Measured single binding force of between Goat, Rabbit IgG and SpA were $17{\pm}7pN$, $74{\pm}16pN$. This work can be used to investigate several different ligand-receptor interactions and antigen-antibody interactions.

• Journal of Soil and Groundwater Environment
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• v.16 no.6
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• pp.122-132
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• 2011

Mercury accumulates in biota mainly as methylmercury. In nature, methylmercury shows high affinity to organic matter and $CH_3Hg^+$-organic matter complexation affects the mobility and bioavailabiity of methylmercury. In this study, we examined the methylmercury binding sites in an aquatic humic acid as affected by the pH condition using Hg $L_{III}$-edge extended X-ray absorption fine structure (EXAFS). We evaluated methylmercury binding humic ligands using methylmercury-thiol, methylmerury-carboxyl, and methylmercury-amine complexation models. When $CH_3Hg^+$-to-humic reduced sulfur ratio is 0.3, we found that most of $CH_3Hg^+$ binds to thiol ligands at pH 5 and 7. At pH 7, however, some carboxyl or amine ligand contribution is observed, unlike at pH 5 where $CH_3Hg^+$ almost exclusively binds to thiol ligands. The carboxyl or amine ligand contribution may indicate that some types of thiol ligands in the natural organic matter have relatively low complexation constants or acid dissociation constants compared to those of some carboxyl or amine ligands. Analysis results indicate that ~0.2 fraction of methylmercury binds to amine or carboxyl ligands and ~0.8 to thiol ligands at pH 7.