• BMB Reports
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• v.39 no.5
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• pp.530-536
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• 2006

Thermal conformational changes of human serum albumin (HSA) in phosphate buffer, 10 mM at pH = 7 are investigated using differential scanning calorimetric (DSC), circular dichroism (CD) and UV spectroscopic methods. The results indicate that temperature increment from $25^{\circ}C$ to $55^{\circ}C$ induces reversible conformational changes in the structure of HSA. Conformational change of HSA are shown to be a three-step process. Interestingly, melting temperature of the last domain is equal to the maximum value of fever in pathological conditions, i.e. $42^{\circ}C$. These conformational alterations are accompanied by a mild alteration of secondary structures. Study of HSA-SDS (sodium dodecyl sulphate) interaction at $45^{\circ}C$ and $35^{\circ}C$ reveals that SDS affects the HSA structure at least in three steps: the first two steps result in more stabilization and compactness of HSA structure, while the last one induces the unfolding of HSA. Since HSA has a more affinity for SDS at $45^{\circ}C$ compared to $35^{\circ}C$, It is suggested that the net negative charge of HSA is decreased in fever, which results in the decrease of HSA-associated cations and plasma osmolarity, and consequently, heat removal via the increase in urine volume.

• Bulletin of the Korean Chemical Society
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• v.35 no.8
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• pp.2494-2504
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• 2014

P38 mitogen activated protein (MAP) kinase is an important anti-inflammatory drug target, which can be activated by responding to various stimuli such as stress and immune response. Based on the conformation of the conserved DFG loop (in or out), binding inhibitors are termed as type-I and II. Type-I inhibitors are ATP competitive, whereas type-II inhibitors bind in DFG-out conformation of allosteric pocket. It remains unclear that how these allosteric inhibitors stabilize the DFG-out conformation and interact. Organosilicon compounds provide unusual opportunity to enhance potency and diversity of drug molecules due to their low toxicity. However, very few examples have been reported to utilize this property. In this regard, we performed docking of an inhibitor (BIRB) and its silicon analog (Si-BIRB) in an allosteric binding pocket of p38. Further, molecular dynamics (MD) simulations were performed to study the dynamic behavior of the simulated complexes. The difference in the biological activity and mechanism of action of the simulated inhibitors could be explained based on the molecular mechanics/generalized Born surface area (MM/GBSA) binding free energy per residue decomposition. MM/GBSA showed that biological activities were related with calculated binding free energy of inhibitors. Analyses of the per-residue decomposed energy indicated that van der Waals and non-polar interactions were predominant in the ligand-protein interactions. Further, crucial residues identified for hydrogen bond, salt bridge and hydrophobic interactions were Tyr35, Lys53, Glu71, Leu74, Leu75, Ile84, Met109, Leu167, Asp168 and Phe169. Our results indicate that stronger hydrophobic interaction of Si-BIRB with the binding site residues could be responsible for its greater binding affinity compared with BIRB.

• Archives of Pharmacal Research
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• v.14 no.3
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• pp.271-278
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• 1991

To investigate further whether the effects of the dihydropyridine (DHP) drugs on calcium channels are related to those of these drugs on muscarinic receptors, the binding characteristics of the DHP calcium channel agonist, Bay K 8644, on muscarinic receptors and calcium channels were compared to those of the DHP calcium channel antagonists, nicardipine and nimodipine in the dog cardiac sarcolemma. Bay K 8644, nicardipine and nimodipine inhibited the specific $[^3H]$QNB binding with $K_i$ values of 16.7\mu{M}$, 3.5\mu{M}$ and 15.5\mu{M}$ respectively. Saturation data of $[^3H]$QNB binding with $K_i$ VALUES OF 16.7\mu{M}$ 3.5\mu{M}$ and 15.5\mu{M}$ respectively. Saturation data of $[^3H]$QNB binding in the presence of these DHP drugs showed this inhibition to be competitive. Bay K 8644, like nicardipine and nimodipine, blocked the binding of $[^3H]$nitrendipine to the high affinity DHP binding sites, but atropine did not, indicating that the muscarinic receptors and the DHP binding sites m but atropine did not, indicating that the muscarinic receptors and the DHP bindings sites on calcium channels are distinct. The $K_i$ value of Bay K 8644 for the DHP binding sites was 4nM. Nicardipine and nimodipine $(K_i:0.1-0.2\;nM)$ were at least 20 times more potent than Bay K 8644 in inhibiting $[^3H]$ nitrendipine binding. Thus, the muscarinic receptors were about 4000 times less sensitive than thes high afinity DHP binding sites to Bay K 8644. These results suggest that the DHP calcium agonist Bay K 8644 binds directly to the muscarinic receptors but its interaction with the muscarinic receptors is not related to its binding to the DHP binding sites on calcium channels.

• Textile Coloration and Finishing
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• v.12 no.1
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• pp.52-60
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• 2000

In the prior studies, we reported that the dye uptakes of C. I. Disperse Violet 1 on polyester fiber in hexane and cyclohexane were higher than those in the other solvents, as the number of carbon atoms of alkanes decreased, the dye uptake increased, and the logarithmic plot of the dye uptakes vs. the solubilities of the dye showed that the dye uptakes are inversely proportional to the solubilities. In this study, for Interpretation of dyeing behavior of C. I. Disperse Violet 1 on polyester in alkanes, the thremodynamic parameters of dyeing, such as standard affnity, heat of dyeing(enthalpy change), entropy change, diffusion coefficient, and activation energy of diffusion, were obtained from isotherms and dyeing rates at different temperature. As the number of carbon atoms of alkanes increased, the standard affinity decreased, but the heat of dyeing(enthalpy change) and the entropy change showed larger negative values. These results mean that as the number of carbon atoms of alkanes increases, the dye uptake decreases, but both the fraction of the dye molecules dyed at relatively highly aligned or compact region of polyester fiber and the regularity of dye aggregates in the fiber become increased. As the number of carbon atoms of alkanes increased, the diffusion coefficient decreased, but the activation energy of diffusion increased. In the alkane of larger number of carbon atoms, because the solubility of the dye is higher, the desorption rate of the dye is faster and the diffusion coefficient is smaller than those in the smaller alkanes. But the energy required to separate the dye molecules from the alkane molecules is much higher because the interaction between the alkane molecule and the dye molecule become strong with the number of carbon atoms.

• Environmental Sciences Bulletin of The Korean Environmental Sciences Society
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• v.10 no.S_2
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• pp.79-88
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• 2001

Humic acids react with chlorine to produce Trihalomethanes(THMs), known as carcinogens, during disinfection, the last stage in water purification. Currently, the removal of organic humic acids is considered the best approach to solve the problem of THM formation. Accordingly, the current study examined the adsorption of organic compounds of humic acids onto an inorganic carrier prepared from oyster shell waste. The adsorbent used was activated oyster shell powder(HAP) and silver ion-exchanged oyster shell powder(HAP-Ag), with CaCO$_3$ as the control. The adsorbates were phthalic acid, chelidamic acid, catechol, dodecylpyridinium chloride(DP), and 2-ethyl phenol(2-EP). The adsorption experiments were carried out in a batch shaker at $25^{\circ}C$ for 15 hours. The equilibrium concentration of the adsorbate solution was analyzed using a UV spectrophotometer and the data fitted to the Langmuir isotherm model. Since the solution pH values were found to be greater than the pKa values of the organic compounds used as adsorbates, the compounds apparently existed in ionic form. The adsorptive affinities of the organic acid and phenolic compounds varied depending on the interaction of electrostatic forces, ion exchange, and chelation. More carboxylic acids and catechol, rather than DP and 2-EP, were adsorbed onto HAP and HAP-Ag. HAP and HAP-Ag exhibited a greater adsorptive affinity for the organic compounds than CaCO$_3$, used as the control.

• BMB Reports
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• v.31 no.2
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• pp.149-155
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• 1998

The N199H variant of the EcoRI endonuclease has about twice the catalytic activity of the wild-type. A comparison of their biochemical characteristics, using synthetic oligonucleotides 5'-dAAAACTTAAGAAAAAAAAAAA-3' (KA) and 5'-dTTTTTGAATTCTTTTTTTTTT-3' (KT), helps to define the cleavage reaction pathway of these enzymes. Both EcoRI and EcoRI variant N199H were found to cleave singlestranded KA or KT about three times faster than the double-stranded forms, although the KT oligonucleotide was more susceptible. Using the ssDNA substrate in kinetic analyses, lower $K_m$ values were obtained for the N199H variant than for the wild-type at low (50 mM), as well as high (200 mM), sodium chloride concentrations. This difference between the endonucleases is attributed to a grealter accessibility for tbe substrate by the variant, and also a higher affinity for the DNA backbone. It also appears that the relative activities of the two enzymes, particularly at high ionic strength, are proportional to their populations in the monomeric enzyme form. That is, according to gel filtration data, half of the N199H molecules exist as monomers in 200 mM NaCl, whereas those of the wild-type are mainly dimeric. Consequently, the Asp199 residue of the EcoRI endonuclease may be implicated in the protein-protein interaction leading to dimerization, as well as in coupling to DNA substrates. In summary, it is proposed that active monomeric endonuclease molecules, derived from the dimeric enzyme, recognize and form a complex with a single stranded form of the DNA substrate, which then undergoes nucleophilic substitution and cleavage.

• Macromolecular Research
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• v.13 no.3
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• pp.257-264
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• 2005

Polyurethanes containing z-Iysine segments in the main chain (PULL) were synthesized from 4,4'-diphe-nylmethyl diisocyanate, poly(tetramethylene glycol), and z-Iysine oligomer as a chain extender. The PULL film was treated first with a $10\%$ HBr-acetic acid solution and subsequently with a saturated sodium bicarbonate aqueous solution to produce a primary amine group on the surface (PULL-N). Lactobionic acid (LA)-immobilized PULL (PULL-L) was prepared by the coupling reaction of the PULL surface amine groups and the LA carboxylic acid groups. The surface-modified PULLs were then characterized by attenuated total reflection-Fourier transform infra-red spectroscopy, electron spectroscopy for chemical analysis, atomic force microscopy, and contact angle goniometry. In the hepatocytes adhesion experiment, the cells poorly adhered to the PULL surface, although they adhered moderately well to the PULL-N surface. On the other hand, the cells adhered well to the PULL-L surface, suggesting the good affinity of the surface $\beta$-galactose moieties for hepatocytes. When hepatocytes were cultured in the presence of epidermal growth factor for 48 h, the cells rapidly aggregated on the PULL-L surface, whereas they aggregated only slowly on the other surfaces. The PULL prepared in this study has the potential to be used as a coating material for the enhancement of hepatocyte adhesion.

• Journal of Life Science
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• v.14 no.1
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• pp.26-31
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• 2004

Redox factor-1 (Ref-1), known as a redox regulator, controls the DNA binding of AP-1 and is activated in HT29 colon cancer cells by hypoxia in vitro. REF-1 also increases tile DNA binding affinity of Hypoxia-inducible Factor-lalpha$ (HIF-lalpha$), HIF-like Factor (HLF) and early growth response-1 (Egr-1) which induce expression of the genes involved in angiogenesis, so that we speculate that REF-1 may play a role in hypoxia-induced angiogenesis. In this research we tried to detect novel proteins interacting with REF-1 using Yeast two-hybrid system using full-length REF-1 cDNA as bait. As result of such screening we detected 3 positive clones. DNA sequencing and GeneBank search revealed that one of the clones contained the same sequences as M.musculus cDNA for tioredoxin.

• 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.

• Proceedings of the Korean Society of Applied Pharmacology
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• 1995.04a
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• pp.86-86
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• 1995

The analysis of membrane receptors for hormones and neurotransmitters has progressed considerably by pharmacological and biochemical means and more recently by the use of specific anti-receptor antibodies. A 14-mer peptide (from Phe102 to Leu115 of ${\beta}$2-adrenergic receptor) was synthesized and this peptide was coupled to carrier protein Keyhole Limpet Hemocyanin(KLH) by glutaraldehyde method. A 0.5mg of KLH-coupled peptide was emulsified with equal volume of complete Freund's adjuvant and injected via popliteal lymph node to each of the three Newzealnd White rabbits. Booster injections were repeated at 4 weeks interval for three times with incomplete Freund's adjuvants. One week after the final injection, serum was prepared from ear artery. Nonspecific immunoglobulins were removed by passing the serum through KLH-Sepharose 6B affinity matrix and further by incubation with bovine lung aceton powder. The titer of the antibody for synthetic peptide which was determined by enzyme linked immunosorbent assay(ELISA) was about l/l,000. The antibody produced in this study revealed 67kDa protein band in the western blot of partially purified guinea pig lung ${\beta}$-adrenergic receptor preparation. The antibody inhibited ${\beta}$-adrenergic antaginist [3H] Dihydroalprenolol binding to soluble ${\beta}$-adrenergic receptor by 25% while control sera did not show any inhibitory effects, The result of this study suggests that the peptide sequence selected in this study may play some important roles in adrenergic receptor-ligand interaction.