• Bulletin of the Korean Chemical Society
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• v.31 no.6
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• pp.1561-1567
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• 2010

In this study, we have developed a new detection method using Si field effect transistor (FET)-type biosensors, which enables the direct monitoring of antigen-antibody binding within very high-ionic-strength solutions such as 1$\times$PBS and human serum. In the new method, as no additional dilution or desalting processes are required, the FET-type biosensors can be more suitable for ultrasensitive and real-time analysis of raw sample solutions. The new detection scheme is based on the observation that the strength of antigen-antibody-specific binding is significantly influenced by the ionic strength of the reaction solutions. For a prostate specific antigen (PSA), in some conditions, the binding reaction between PSA and anti-PSA in a low-ionic strength reaction solution such as 10 ${\mu}M$ phosphate buffer is weak (reversible), while that in high-ionic strength reaction solutions such as 1$\times$PBS or human serum is strong.

• Journal of the Korean Chemical Society
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• v.40 no.4
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• pp.264-272
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• 1996

Cluster models of the Υ-Al2O3(111) and the Pt(111) surfaces have been used in an atom superposition and electron delocalization molecular orbital study of interfacial bond strengths between them. The reduced extents for Al3+ are due to the ratio of oxygen to aluminum atoms. The greater the reduced extent for Al3+ is, the stronger the binding energy is to Pt atoms in a cluster. The oxygen-covered surfaces of Υ-Al2O3(111) are shown to bind more weakly to Pt atoms, while the binding to the oxygen-covered surface formed under oxidizing conditions of Pt atoms is strong. The interfacial bond of platinum-alumina may be possible by a charge-transfer mechanism from the platinum surface to the partially empty O-2p band and Al3+ dangling surface orbital.

• Bulletin of the Korean Chemical Society
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• v.33 no.9
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• pp.2907-2909
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• 2012

A disintegrin and metalloprotease with thrombospondin domains (ADAMTS) are a member of peptidase and involved in processing of von Willebrand factor as well as cleavage of aggrecan, versican, brevican and neurocan. Among 19 subfamilies of human ADAMTS, ADAMTS-4 is a zinc-binding metalloprotease and is a famous therapeutic target for arthritis. It has been reported that a flavonoid luteolin shows inhibitory activity against ADMATS-4. In this study, we verified that luteolin is a potent inhibitor of ADAMTS-4 and probed the molecular basis of its action. On the basis of a docking study, we proposed a binding model between luteolin and ADAMTS-4 in which 3',4'-dihydroxyl groups in luteolin formed hydrogen bonding with ADMATS-4 and these interactions are important for its inhibitory activity against ADAMTS-4.

• Bulletin of the Korean Chemical Society
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• v.31 no.2
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• pp.453-456
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• 2010

The structural and energetic preferences of thiacalix[4]biscrown-5 with and without alkali metal ions ($Na^+$, $K^+$, $Rb^+$, and $Cs^+$) have been theoretically investigated for the first time using molecular dynamic (MD) simulations and density functional theory (MPWB1K/6-31G(d)//B3LYP/6-31G(d)) methods. The formation of the metal ion complex by the host is mainly driven by the electrostatic attraction between crown-5 oxygens and a cation together with the minor contribution of the cation-$\pi$ interaction between two facing phenyl rings around the cation. The computed binding energies and the atomic charge distribution analysis for the metal binding complexes indicate the selectivity toward a potassium ion. The theoretical results herein explain the experimentally observed extractability order by this host towards various alkali metal ions. The physical nature and the driving forces for cation recognition by this host are discussed in detail.

• Bulletin of the Korean Chemical Society
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• v.31 no.7
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• pp.2019-2024
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• 2010

Insulin-like growth factor binding protein 5 (IGFBP-5) plays an important role in controlling cell survival, differentiation and apoptosis. Apoptosis can be induced by an extrinsic pathway involving the ligand-mediated activation of death receptors such as tumor necrosis factor receptor 1 (TNFR1). To determine whether IGFBP-5 and TNFR1 interact as members of the same apoptosis pathway, recombinant IGFBP-5 and TNFR1 were isolated. The expression and purification of the full-length TNFR1 and truncated IGFBP-5 proteins were successfully performed in E. coli. The binding of both IGFBP-5 and TNFR1 proteins was detected by surface plasmon resonance spectroscopy (BIAcore), fluorescence measurement, electron microscopy, and size-exclusion column (SEC) chromatography. IGFBP-5 indeed binds to TNFR1 with an apparent $K_D$ of 9 nM. After measuring the fluorescence emission spectra of purified IGFBP-5 and TNFR1, it was found that the tight interaction of these proteins is accompanied by significant conformational changes of one or both. These results indicate that IGFBP-5 acts potently as a novel ligand for TNFR1.

• Bulletin of the Korean Chemical Society
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• v.29 no.8
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• pp.1499-1504
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• 2008

Pyrazine derivatives bind to b-RAF receptor which is important in cancer therapy. The ligand-receptor interactions have been studied by comparative molecular field analysis (CoMFA) and molecular docking methods. Applying conventional ligand-based alignment schemes for the whole set was not successful. However, QM and DFT results suggested that some ligands have electrostatic interaction while others have steric interactions. On the basis of these results, we divided the dataset into two subsets. Electrostatic effect was found to be important in one set while steric effect for the other. Best docking modes were obtained for each subset based on the available crystal structure. These receptor-guided CoMFA models propose an interesting possibility which is difficult to obtain otherwise. i.e., in one binding mode the electrostatic interaction plays a key role for one subset ($q^2$ = 0.46, $r^2$ = 0.98), while in another binding mode steric effect is important with another subset ($q^2$ = 0.43, $r^2$ = 0.74).

• Bulletin of the Korean Chemical Society
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• v.29 no.6
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• pp.1107-1114
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• 2008

It is important to identify selective ligands for the estrogen receptor subtypes ER$\alpha$ or ER$\beta$ to evaluate them as pharmaceutical targets in breast cancer. To develop ER$\beta$-selective ligands as PET imaging agents, a series of aryl indazole estrogen analogues substituted at the C3 position with fluoroethyl and fluoropropyl groups were synthesized and evaluated for their relative binding affinities and selectivities for ER$\alpha$ vs ER$\beta$. The fluoroethylated indazole estrogen (FEIE, 1i) and fluoropropylated indazole estrogen (FPIE, 1h) showed 41- fold and 17-fold ER$\beta$/ER$\alpha$ selectivity, respectively. However, their binding affinities to ER$\alpha$ and ER$\beta$ were very low.

• Bulletin of the Korean Chemical Society
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• v.34 no.7
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• pp.2063-2066
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• 2013

While many eukaryotic and some prokaryotic proteins show a phosphorylation-dependent mobility shift (PDMS) on SDS-PAGE, the molecular mechanism for this phenomenon had not been elucidated. We have recently shown that the distribution of negatively charged amino acids around the phosphorylation site is important for the PDMS of some proteins. Here, we show that replacement of the phosphorylation site with a negatively charged amino acid results in a similar degree of the mobility shift of a protein as phosphorylation, indicating that the PDMS is due to the introduction of a negative charge by phosphorylation. Compared with a protein showing no shift, one showing a retarded mobility on SDS-PAGE had a decreased capacity for SDS binding. The elucidation of the consensus sequence (${\Theta}X_{1-3}{\Theta}X_{1-3}{\Theta}$, where ${\Theta}$ corresponds to an acidic function) for a PDMS suggests a general strategy for mutagenizing a phosphorylatable protein resulting in a PDMS.

• Journal of the Korean Chemical Society
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• v.23 no.6
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• pp.374-384
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• 1979

Hydration scheme and hydration energy are determined in ${\alpha}$ cage of zeolite NaA. The selectivity between Na(1) and Na(2) is determined from energy calculation. The waters in ${\alpha}$ cage form a distorted dodecahedral cage. The average binding energies of water(1), water(2) and water(3) are -29.847, -25.344 and -15.888 kcal/mole respectively. The positions of oxygens of hydrated waters are in good agreement with the X-ray data. The heat of immersion curve is also obtained. This result is in good agreement with the differential heat of sorption curve obtained from differential thermal analysis. It is concluded that theoretical method provides considerable uses in the determination and understanding of the hydration and interaction energy of zeolites sorbate binding.

• Bulletin of the Korean Chemical Society
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• v.27 no.10
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• pp.1648-1650
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• 2006

The synthesis of a new C,N-bipyrazolic ligand with a functionalized donor-group is reported. The binding properties of the ligand and two other ligand of similar structures towards heavy metal ions ($Hg^{2+}$, $Cd^{2+}$, $Pb^{2+}$, $Zn^{2+}$, $Cu^{2+}$) and alkaline metal ions ($K^+$, $Na^{+}$, $Li^+$) were studied by a liquid-liquid extraction process and the extracted cation percentage was determined by atomic absorption measurements. The selectivity of the ligand to Hg(II) has been mentioned in the abstract.