• Bulletin of the Korean Chemical Society
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• v.32 no.8
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• pp.2628-2632
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• 2011

The nucleophilic substitution reactions of Y-O-aryl phenyl phosphonochloridothioates with substituted anilines ($XC_6H_4NH_2$) and deuterated anilines ($XC_6H_4ND_2$) are kinetically investigated in acetonitrile at $55.0^{\circ}C$. The deuterium kinetic isotope effects (DKIEs) invariably increase from an extremely large secondary inverse ($k_H/k_D$ = 0.439; min) to a primary normal ($k_H/k_D$ = 1.34; max) as both substituents of nucleophile (X) and substrate (Y) change from electron-donating to electron-withdrawing. These results are opposite to the DKIEs on Y-O-aryl methyl phosphonochloridothioates, and can be rationalized by the gradual transition state (TS) variation from backside to frontside attack. The trigonal bipyramidal pentacoordinate TS is proposed for a backside attack, while the hydrogen-bonded, four-center-type TS is proposed for a frontside attack. The negative values of the cross-interaction constants (${\rho}_{XY(H)}$ = -0.38 for $XC_6H_4NH_2$ and ${\rho}_{XY(D)}$ = -0.29 for $XC_6H_4ND_2$) indicate that the reactions proceed by a concerted $S_N2$ mechanism.

• Bulletin of the Korean Chemical Society
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• v.31 no.8
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• pp.2247-2254
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• 2010

The surface structures of copper phthalocyanine (CuPc) thin films deposited on sulphur-passivated and plane perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA)-covered InAs(100) surfaces have been studied by low energy electron diffraction (LEED) and van der Waals (vdW) intermolecular interaction energy calculations. The annealing to $300^{\circ}C$ and $450^{\circ}C$ of $(NH_4)_2S_x$-treated InAs(100) substrates produces a ($1{\times}1$) and ($2{\times}1$) S-passivated surface respectively. The CuPc deposition onto the PTCDA-covered InAs(100) surface leads to a ring-like diffraction pattern, indicating that the 2D ordered overlayer exists and the structure is dominantly determined by the intermolecular interactions rather than substrate-molecule interactions. However, no ordered LEED patterns were observed for the CuPc on S-passivated InAs(100) surface. The intermolecular interaction energy calculations have been carried out to rationalise this structural difference. In the case of CuPc unit cells on PTCDA layer, the planar layered CuPc structure is more stable than the $\alpha$-herringbone structure, consistent with the experimental LEED results. For CuPc unit cells on a S-($1{\times}1$) layer, however, the $\alpha$-herringbone structure is more stable than the planar layered structure, consistent with the absence of diffraction pattern. The results show that the lattice structure during the initial stages of thin film growth is influenced strongly by the intermolecular interactions at the interface.

• Korean Journal of Environmental Agriculture
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• v.25 no.3
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• pp.262-267
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• 2006

Increased application of glyphosate (Gly) in glyphosate-resistant (GR) soybean cropping systems may affect rhizospheric microorganisms including IAA-producing rhizobacteria (IPR) and their effect on the growth of soybean. This field experiment was conducted to assess IPR populations in the rhizosphere of GR soybean ('Roundup-Ready' DeKalb DKB38-52) treated with glyphosate and foliar amendment treatments such as $PT21^{(R)}$ (urea solution with N 21 %) and $Grozyme^{(R)}$ (Biostimulant: mixtures of micro nutrients and enzymes). Effects of herbicide, sampling date, and their interaction on total bacterial numbers were significant (P < 0.001, 0.001, 0.013, respectively). Total bacteria (TB) numbers were increased with glyphosate treatment at 20 d after application and highest TB populations were associated with $Grozyme^{(R)}$ application, possibly due to the additional substrate from this product. The IPR of the soybean rhizosphere was significantly affected by herbicide, sampling date, and the herbicide*foliar amendment interaction. The ratios of numbers of IPR to TB ranged from 0.79 to 0.99 across the sampling dates irrespective of treatments. IPR numbers were slightly hindered by glyphosate application regardless of foliar amendment.

• Journal of Magnetics
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• v.3 no.4
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• pp.105-111
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• 1998

The low energy excitations of spin waves (SWR) in thin films can be used for determination of the surface anisotropy constant and the nonhomogeneities of magnetization in the close-to-surface layer. The dispersion relation in SWR is sensitive on the geometry of experiment. We report on temperature dependence of surface magnetic anisotropy energy constant in magnetic semiconductor thin films of$ CdCr_{2-2x}In_{2x}Se_4$ at spin glass state. Samples were deposited by rf sputtering technique on Corning glass substrate in controlled temperature conditions. Coexistence of the infinite ferromagnetic network (IFN) and finite spin slusters (FSC) in spin glass state (SG) is know phenomena. Some behavior typical for long range magnetic ordering is expected in samples at SG state. The spin wave resonance experiment (microwave spectrometer at X-band) with excited surface modes was applied to describe the energy state of surface spins. We determined the surface magnetic anisotropy energy constant versus temperature using the surface inhomogeneities model of magnetic thin films. It was found that two components contribute to the surface magnetic anisotropy energy. One originates from the exchange interaction term due to the lack of translation symmetry for surface spin as well as from the originates from the exchange interaction term due to the lack of translation symmetry for surface spin as well as from the stray field of the surface roughness. The second one comes from the demagnetizing field of close-to surface layer with grad M. Both term linearly decrease when temperature is increased from 5 to 123 K, but dominant contribution is from the first component.

• Bulletin of the Korean Chemical Society
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• v.25 no.1
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• pp.115-118
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• 2004

We have examined the feasibility of using the specific interaction between mistletoe lectin I (ML I) and ${\beta}$-Dgalactose instead of the anti-ML I antibody in developing a homogeneous type competitive binding assay for ML I. We also have examined the feasibility of adapting the biotin/avidin mediated homogeneous assay for this system. Alkaline phosphatase (AKP) was employed as a single substrate enzyme label. The dose-response curve shows a detection range of 1-25 ${\mu}$g/mL and a linear response with a correlation coefficient of 0.99. To demonstrate the analytical utility of this method, 10 ${\mu}$g/mL of ML I was spiked into distilled water. The results show that the mean recovery was 10.03 ${\mu}$g/mL with an SD of 0.18. The difference between the spiked value and the mean recovery was 0.03 ${\mu}$g/mL, with a relative error of 0.3 and 1.6 % of RSD.

• The Korean Journal of Physiology and Pharmacology
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• v.2 no.3
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• pp.385-393
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• 1998

Human neutrophil elastase (HNElastase, EC 3.4.21.37), a causative factor of inflammatory diseases, was purified by Ultrogel AcA54 gel filtration and CM-Sephadex ion exchange chromatography. HNElastase was inhibited by phenylbutazone in a concentration dependent manner up to 0.4 mM, but as the concentration increased, the inhibitory effect gradually diminished. Binding of phenylbutazone to the human neutrophil elastase caused strong Raman shifts at 200, 440, and 1194 $cm^{-1}$. The peak at 1194 $cm^{-1}$ might be evidence of the presence $of\;-N=N-{\Phi}$ radical. The core area of the elastase, according to the visual molecular model of human neutrophil elastase, was structurally stable. A deeply situated active center was at the core area surrounded by hydrophobic amino acids. Directly neighboring the active site was one positively charged atom and two atoms carrying a negative charge, which enabled the enzyme and the drug to form a strong interaction. Phenylbutazone may form a binding, similar to a key & lock system to the atoms carrying opposite charges near the active site of the enzyme molecule. Furthermore, the hydrophobicity of the surrounding amino acid near the active site seemed to enhance the binding strength of phenylbutazone. Binding of phenylbutazone near the active site may cause masking of the active site, preventing the substrate from approaching the active site and inhibiting elastase activity.

• Journal of Preventive Medicine and Public Health
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• v.42 no.6
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• pp.360-370
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• 2009

Genetic factors clearly play a role in carcinogenesis, but migrant studies provide unequivocal evidence that environmental factors are critical in defining cancer risk. Therefore, one may expect that the lower availability of substrate for biochemical reactions leads to more genetic changes in enzyme function; for example, most studies have indicated the variant MTHFR genotype 677TT is related to biomarkers, such as homocysteine concentrations or global DNA methylation particularly in a low folate diet. The modification of a phenotype related to a genotype, particularly by dietary habits, could support the notion that some of inconsistencies in findings from molecular epidemiologic studies could be due to differences in the populations studied and unaccounted underlying characteristics mediating the relationship between genetic polymorphisms and the actual phenotypes. Given the evidence that diet can modify cancer risk, gene-diet interactions in cancer etiology would be anticipated. However, much of the evidence in this area comes from observational epidemiology, which limits the causal inference. Thus, the investigation of these interactions is essential to gain a full understanding of the impact of genetic variation on health outcomes. This report reviews current approaches to gene-diet interactions in epidemiological studies. Characteristics of gene and dietary factors are divided into four categories: one carbon metabolism-related gene polymorphisms and dietary factors including folate, vitamin B group and methionines; oxidative stress-related gene polymorphisms and antioxidant nutrients including vegetable and fruit intake; carcinogen-metabolizing gene polymorphisms and meat intake including heterocyclic amins and polycyclic aromatic hydrocarbon; and other gene-diet interactive effect on cancer.

• Bulletin of the Korean Chemical Society
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• v.33 no.5
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• pp.1547-1550
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• 2012

Second-order rate constants ($k_N$) have been measured spectrophotometrically for the reactions of benzyl 2-pyridyl carbonate $\mathbf{3}$ and $t$-butyl 2-pyridyl carbonate $\mathbf{3}$ with a series of alicyclic secondary amines in MeCN at $25.0{\pm}0.1^{\circ}C$. Substrate $\mathbf{4}$ is much less reactive than $\mathbf{3}$ and the steric hindrance exerted by the bulky $t$-Bu group in $\mathbf{4}$ has been attributed to its decreased reactivity. The Br${\o}$nsted-type plots for the reactions of $\mathbf{3}$ and $\mathbf{4}$ are linear with ${\beta}_{nuc}=0.57$ and 0.45, respectively. Thus, the reactions have been concluded to proceed through a concerted mechanism, although the current reactions were expected to proceed through a stepwise mechanism with a zwitterionic tetrahedral intermediate $T^{\pm}$. It has been proposed that the rate of leaving-group expulsion is accelerated by the intramolecular H-bonding interaction in $T^{\pm}$ and the "push" provided by the RO group through the resonance interaction. Thus, the enhanced nucleofugality forces the reactions to proceed through a concerted mechanism. The reactivity-selectivity principle (RSP) is not applicable to the current reaction systems, since the reaction of the less reactive $\mathbf{4}$ results in a smaller ${\beta}_{nuc}$ than that of the more reactive $\mathbf{3}$. Steric hindrance exerted by the bulky $t$-Bu group in $\mathbf{4}$ has been suggested to be responsible for the failure of the RSP.

• Journal of the Korean Vacuum Society
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• v.16 no.1
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• pp.52-57
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• 2007

The interaction force between biomolecules(DNA-DNA, antigen-antibody, ligand-receptor, protein-protein) defines not only biomolecular function, but also their mechanical properties and hence bio-sensor. Atomic force microscopy(AFM) is nowadays frequently applied to determine interaction forces between biological molecules and biomolecular force measurements, obtained for example using AFM can provide valuable molecular-level information on the interactions between biomolecules. A proper modification of an AFM tip and/or a substrate with biomolecules permits the direct measurement of intermolecular interactions, such as DNA-DNA, protein-protein, and ligand-receptor, etc. and a microcantilever-based sensor appeared as a promising approach for ultra sensitive detection of biomolecular interactions.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.5
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• pp.2345-2351
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• 2014

Lysyl oxidase-like 2 (LOXL2), a member of the lysyl oxidase (LOX) family, is a copper-dependent enzyme that catalyzes oxidative deamination of lysine residues on protein substrates. LOXL2 was found to be overexpressed in esophageal squamous cell carcinoma (ESCC) in our previous research. We later identified a LOXL2 splicing variant LOXL2-delta72 and we overexpressed LOXL2-delta72 and its wild type counterpart in ESCC cells following microarray analyses. First, the differentially expressed genes (DEGs) of LOXL2 and LOXL2-delta72 compared to empty plasmid were applied to generate protein-protein interaction (PPI) sub-networks. Comparison of these two sub-networks showed hundreds of different proteins. To reveal the potential specific roles of LOXL2- delta72 compared to its wild type, the DEGs of LOXL2-delta72 vs LOXL2 were also applied to construct a PPI sub-network which was annotated by Gene Ontology. The functional annotation map indicated the third PPI sub-network involved hundreds of GO terms, such as "cell cycle arrest", "G1/S transition of mitotic cell cycle", "interphase", "cell-matrix adhesion" and "cell-substrate adhesion", as well as significant "immunity" related terms, such as "innate immune response", "regulation of defense response" and "Toll signaling pathway". These results provide important clues for experimental identification of the specific biological roles and molecular mechanisms of LOXL2-delta72. This study also provided a work flow to test the different roles of a splicing variant with high-throughput data.