• Bulletin of the Korean Chemical Society
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• 제6권5호
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• pp.287-291
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• 1985

The addition of poly(styrenesulfonate) (PSS) to $Ru(bpy)_3^{2+}$ solutions shifted the emission peak by 3 nm to red, and increased emission intensity by 1.8 times. By contrast, poly(vinylsulfonate) (PVS) had little effect on the fluorescence spectrum. The effects of PSS on the spectral properties of $Ru(bpy)_3^{2+}$, were attributed to the presence of a hydrophobic phenyl group in PSS, which interact with $Ru(bpy)_3^{2+}$ by, at least in part, hydrophobic effect. The binding constant of $Ru(bpy)_3^{2+}$ to PSS in 0.1 M NaCl was $6{\times}10^4\;M^{-1}$, and this value was about $10^3$ times higher than those of methyl viologen ($MV^{2+}$) and $Cu^{2+}$. The Stern-Volmer constants of emission quenching of $Ru(bpy)_3^{2+}$ by $MV^{2+}$ and $Cu^{2+}$ in 0.1 M NaCl solutions were 426 and 40 $M^{-1}$, which correspond to second order rate constants($k_q$) of $1.1{\times}10^9\;and\; 1.0{\times}10^8\;M^{-1}s^{-1}$, respectively. The presence of PSS enhanced $K_{SV's}\;by\;{\sim}50$ times, whereas PVS increased the values only 1-4 times. The large enhancing effect of PSS, despite of lower charge density than PVS, was explained in terms of longer life-time of photoexcited $Ru(bpy)_3^{2+}$ bound to PSS and strong association of $Ru(bpy)_3^{2+}$ to PSS due to a specific interaction involving hydrophobic effect. The variation of $K_{SV's}$ on the concentrations of PVS and PSS were also investigated for $Ru(bpy)_3^{2+}-MV^{2+}\;and \;Ru(bpy)_3^{2+}-Cu^{2+}$ photoredox systems.

• 한국환경보건학회지
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• 제28권5호
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• pp.65-70
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• 2002

Recently, surfactants were frequently used in order to desorb the hydrophobic organic compounds (HOCs) from soil and to enhance the bioavailability. Among them, -cyclodextrin ($\beta$-CD) is one of those. This study was performed to investigate the binding characteristics between benzene and $\beta$-CD and to examine the bioavailability of benzene. First, we investigated binding characteristics between benzene and $\beta$-CD in water and water/soil system. Then, we examined the effect of $\beta$-CD on the biodegradation of benzene in water and water/soil system. Experimental results on the binding characteristics showed that $\beta$-CD resulted in an efficient complex formation with benzene. As -CD concentration increased, the benzene concentration complexed with $\beta$-CD rapidly increased to 30-40% initial benzene added, and reached the equilibrium. We also investigated the effect of $\beta$-CD on the desorption of benzene from soil in the water/soil system. As $\beta$-CD concentration increased, benzene concentration desorbed into water increased up to 90%. How-ever, in its application to biodegradation of benzene in water and water/soil system, the biodegradation rate of benzene did not improved in the presence of $\beta$-CD compared with in the absense of $\beta$-CD. This result indicated that $\beta$-CD was more preferentially used as a carbon source than benzene. Therefore, for remediation of benzene contaminated soils, $\beta$-CD can be used as a surfactant to desert benzene from soil, and then ex-situ chemical treatment can be applied for the remediation.

• Journal of Pharmaceutical Investigation
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• 제21권3호
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• pp.133-141
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• 1991

The fluorescence characteristics of l-anilinonaphthalene-8-sulfonate (ANS) and 2-p-toluidinylnaphthalene-6-sulfonate (TNS) made the dyes useful probes for the determination of the polarity at the binding sites of several water-soluble polyparacyclophanes. Polyparacyclophanes used were 1,6,20,25-tetraaza[ 6.1.6.1]paracyclophane (CPM 44), 1,7,21,27 -tetraaza[7.1.7.1]paracyclophane (CPM 55). 1,7,21,27 -tetraaza-14,34-dioxa[7.1.7.1]paracyclophane (CPE 55) and 1,8,22,29-tetraaza-15,36-dioxa[8.1.8.1] paracyclophane (CPE 66). The fluorescence quantum yield, emission maximum, and half bandwidth of ANS or TNS obtained in a variety of solvent systems were plotted as a function of four kinds of empirical solvent polarity scales such as dielectric constant (D), (D-l)/(2D+1). Y and Z values. It was found that the Z-value-emission maximum $(\overline}V_F,\;cm^{-1})$ profile showed the most reliable linearity. ANS and TNS interacted with CPM 44, CPM 55, CPE 55. CPE 66. ${\alpha}-cyclodextrin$ (CyD) and ${\beta}-CyD$ in the aqueous solution, and from the emission maxima the polarities (Z-value) of their binding sites were calculated to be 92.65, 87.50, 93.35, 84.52, 94.36, and 90.48 for ANS, respectively. and 91.07, 89.68, 85.44, 86.74 and 87.6 for TNS except for ${\alpha}-CyD$, respectively.

• 한국임상수의학회지
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• 제21권3호
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• pp.253-258
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• 2004

DNA double-strand break (DSB) is a serious treat for the cells including mutations, chromosome rearrangements, and even cell death if not repaired or misrepaired. Ku heterodimer regulatory DNA binding subunits (Ku70/Ku80) bound to double strand DNA breaks are able to interact with 470-kDa DNA-dependent protein kinase catalytic subunit (DNA-PKcs), and the interaction is essential for DNA-dependent protein kinase (DNA-PK) activity. The Ku80 mutants were designed to bind Ku70 but not DNA end binding activity and the peptides were treated in breast cancer cells for co-therapy strategy to see whether the targeted inhibition of DNA-dependent protein kinase (DNA-PK) activity sensitized breast cancer cells to ionizing irradiation or chemotherapy drug to develop a treatment of breast tumors by targeting proteins involved in damage-signaling pathway and/or DNA repair. We designed domains of Ku80 mutants, 26 residues of amino acids (HN-26) as a control peptide or 38 (HNI-38) residues of amino acids which contain domains of the membrane-translocation hydrophobic signal sequence and the nuclear localization sequence, but HNI-38 has additional twelve residues of peptide inhibitor region. We observed that the synthesized peptide (HNI-38) prevented DNA-PKcs from binding to Ku70/Ku80, resulting in inactivation of DNA-PK complex activity in breast cancer cells (MDA-465 and MDA-468). Consequently, the peptide treated cells exhibited poor to no DNA repair, and became highly sensitive to irradiation or chemotherapy drugs. The growth of breast cancer cells was also inhibited. These results demonstrate the possibility of synthetic peptide to apply breast cancer therapy to induce apoptosis of cancer cells.

• Molecules and Cells
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• 제39권3호
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• pp.211-216
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• 2016

CYP107W1 from Streptomyces avermitilis is a cytochrome P450 enzyme involved in the biosynthesis of macrolide oligomycin A. A previous study reported that CYP107W1 regioselectively hydroxylated C12 of oligomycin C to produce oligomycin A, and the crystal structure of ligand free CYP107W1 was determined. Here, we analyzed the structural properties of the CYP107W1-oligomycin A complex and characterized the functional role of the Trp178 residue in CYP107W1. The crystal structure of the CYP107W1 complex with oligomycin A was determined at a resolution of $2.6{\AA}$. Oligomycin A is bound in the substrate access channel on the upper side of the prosthetic heme mainly by hydrophobic interactions. In particular, the Trp178 residue in the active site intercalates into the large macrolide ring, thereby guiding the substrate into the correct binding orientation for a productive P450 reaction. A Trp178 to Gly mutation resulted in the distortion of binding titration spectra with oligomycin A, whereas binding spectra with azoles were not affected. The Gly178 mutant's catalytic turnover number for the 12-hydroxylation reaction of oligomycin C was highly reduced. These results indicate that Trp178, located in the open pocket of the active site, may be a critical residue for the productive binding conformation of large macrolide substrates.

• Bulletin of the Korean Chemical Society
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• 제28권5호
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• pp.758-762
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• 2007

A new alkyldithiocarbonate (xanthate), as sodium salts, C2H5OCS2Na, was synthesized by the reaction between CS2 with ethyl alcohol in the presence of NaOH. The new xanthate was characterized by 1H NMR, IR and elemental analysis. Then, the new synthesized compound was examined for functional study of cresolase activity of Mushroom Tyrosinase (MT) from a commercial source of Agricus bisporus in 10 mM phosphate buffer pH 6.8, at three temperatures of 10, 20 and 33℃ using UV spectrophotemetry. 4-[(4-methylphenyl)- azo]-phenol (MePAPh) was used as a synthetic substrate for the enzyme for cresolase reaction. The results show that ethyl xanthate can activate or inhibit the cresolase activity of mushroom tyrosinase depending to the concentration of ethyl xanthate. It was concluded that the enzyme has two distinct sites for ethyl xanthate. The first one is a high-affinity activation site and the other is a low-affinity inhibition site. Activation of the enzyme in the low concentration of ethyl xanthate arises from increasing the affinity of binding for the substrate as well as increasing the enzyme catalytic constant. The affinity of ligand binding in the activation site is decreased by increasing of the temperature, which is the opposite result for the inhibition site. Hence, the nature of the interaction of ethyl xanthate is different in two distinct sites. The binding process for cresolase inhibition is only entropy driven, meanwhile the binding process for cresolase activation is not only entropy driven but also enthalpy driven means that hydrophobic interaction is more important in the inhibition site.

• Journal of Ginseng Research
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• 제44권5호
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• pp.690-696
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• 2020

Background: As the main metabolites of ginsenosides, 20(S, R)-protopanaxadiol [PPD(S, R)] and 20(S, R)-protopanaxatriol [PPT(S, R)] are the structural basis response to a series of pharmacological effects of their parent components. Although the estrogenicity of several ginsenosides has been confirmed, however, the underlying mechanisms of their estrogenic effects are still largely unclear. In this work, PPD(S, R) and PPT(S, R) were assessed for their ability to bind and activate human estrogen receptor α (hERα) by a combination of in vitro and in silico analysis. Methods: The recombinant hERα ligand-binding domain (hERα-LBD) was expressed in E. coli strain. The direct binding interactions of ginsenosides with hERα-LBD and their ERα agonistic potency were investigated by fluorescence polarization and reporter gene assays, respectively. Then, molecular dynamics simulations were carried out to simulate the binding modes between ginsenosides and hERα-LBD to reveal the structural basis for their agonist activities toward receptor. Results: Fluorescence polarization assay revealed that PPD(S, R) and PPT(S, R) could bind to hERα-LBD with moderate affinities. In the dual luciferase reporter assay using transiently transfected MCF-7 cells, PPD(S, R) and PPT(S, R) acted as agonists of hERα. Molecular docking results showed that these ginsenosides adopted an agonist conformation in the flexible hydrophobic ligand-binding pocket. The stereostructure of C-20 hydroxyl group and the presence of C-6 hydroxyl group exerted significant influence on the hydrogen bond network and steric hindrance, respectively. Conclusion: This work may provide insight into the chemical and pharmacological screening of novel therapeutic agents from ginsenosides.

• Archives of Pharmacal Research
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• 제25권6호
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• pp.807-816
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• 2002

Dihydrofolate reductases (DHFR) of human, Candida albicans and E. coli were docked with their original ligands of X-ray crystal complex using QXP (Quick eXPlore), a docking program. Conditions to reproduce the crystal structures within the root mean square deviation (rmsd) of 2.00 $\AA$ were established. Applying these conditions, binding modes and species-specificities of a novel antibacterial compound, $N^4-(2-acetoxyethoxymethyl)-2-acetylpyridine$ thiosemicarbazone (MTSC), were studied. As the results, the docking program reproduced the crystal structures with average rmsd of six ligands as 0.91 $\AA$ ranging from 0.49 to 1.45 $\AA$. The interactions including the numbers of hydrogen bonds and hydrophobic interactions were the same as the crystal structures and superposition of the crystal and docked structures almost coincided with each other. For AATSC, the results demonstrated that it could bind to either the substrate or coenzyme sites of DHFR in all three species with different degrees of affinity. It confirms the experimentally determined kinetic behavior of uncompetitive inhibition against either the inhibitor or the coenzyme. The docked MTSC overlapped well with the original ligands and major interactions were consistent with the ones in the crystal complexes. The information generated from this work should be useful for future development of antibacterial and antifungal agents.

• BMB Reports
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• 제45권8호
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• pp.452-457
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• 2012

Diketoreductase (DKR) from Acinetobacter baylyi contains two tryptophan residues at positions 149 and 222. Trp-149 and Trp-222 are located along the entry path of substrate into active site and at the dimer interface of DKR, respectively. Single and double substitutions of these positions were generated to probe the roles of tryptophan residues. After replacing Trp with Ala and Phe, biochemical and biophysical characteristics of the mutants were thoroughly investigated. Enzyme activity and substrate binding affinity of W149A and W149F were remarkably decreased, suggesting that Trp-149 regulates the position of substrate at the binding site. Meanwhile, enzyme activity of W222F was increased by 1.7-fold while W222A was completely inactive. In addition to lower thermostability of Trp-222 mutants, molecular modeling of the mutants revealed that Trp-222 is vital to protein folding and dimerization of the enzyme.

• Journal of Microbiology and Biotechnology
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• 제26권4호
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• pp.637-647
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• 2016

Proliferating cell nuclear antigen (PCNA) is a critical eukaryotic replication accessory factor that supports DNA binding in DNA processing, such as DNA replication, repair, and recombination. PCNA consists of three toroidal-shaped monomers that encircle double-stranded DNA. The diverse functions of PCNA may be regulated by its interactions with partner proteins. Many of the PCNA partner proteins generally have a conserved PCNA-interacting peptide (PIP) motif, located at the N- or C- terminal region. The PIP motif forms a 3₁₀ helix that enters into the hydrophobic groove produced by an interdomain-connecting loop, a central loop, and a C-terminal tail in the PCNA. Post-translational modification of PCNA also plays a critical role in regulation of its function and binding partner proteins. Structural and biochemical studies of PCNA-protein will be useful in designing therapeutic agents, as well as estimating the outcome of anticancer drug development. This review summarizes the characterization of eukaryotic PCNA in relation to the protein structures, functions, and modifications, and interaction with proteins.