• Journal of the Korean Chemical Society
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• v.56 no.4
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• pp.424-430
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• 2012

Densities, viscosities, refractive indices and speed of sounds of the binary mixtures of Acetophenone with Ethylchloroacetate were measured over the entire mole fractions at (303.15, 313.15 and 323.15) K. From these experimental results, excess molar volume $V^E$, viscosity deviation ${\Delta}{\eta}$, refractive index deviation ${\Delta}n_D$, deviations in speed of sound ${\Delta}u$, deviations in isentropic compressibility ${\Delta}k_s$ and excess intermolecular free length ${\Delta}L_f$ were calculated. The viscosity data have been correlated with the equations of Grunberg and Nissan, Hind et al., Tamura and Kurata, Katti and Chaudri, Sedgwick, Krishnan-Laddha and McAllister. The thermo physical properties under study were fit to the Jouyban-Acree model. The excess values were correlated using Redlich-Kister polynomial equation to obtain their coefficients and standard deviations. It was found that in all cases, the data obtained fitted with the values correlated by the corresponding models very well. The results are interpreted in terms of molecular interactions occurring in the solution.

• Genomics & Informatics
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• v.5 no.3
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• pp.113-117
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• 2007

The development of microarray technology has facilitated the understanding of gene expression profiles. Despite its convenience, the cause of dye-bias that confounds data interpretation in dual-color DNA microarray experiments is not well known. In order to economize time and money, it is necessary to identify the cause of dye bias, since designing dye-swaps to reduce the dye-specific bias tends to be very expensive. Hence, we sought to determine the reliable cause of systematic dye bias after treating murine macrophage RAW 264.7 cells with 2-keto-3-deoxyoctonate (KDO), interferon-beta $(IFN-{\beta})$, and 8-bromoadenosine (8-BR). To find the cause of systematic dye bias from the point of view of fluorescence quenching, we examined the correlation between systematic dye bias and the proportion of each nucleotide in mRNA and oligonucleotide probe sequence. Cy3-dye bias was highly correlated with the proportion of adenines. Our results support the fact that systematic dye bias is affected by fluorescence quenching of each feature. In addition, we also found that the strength of fluorescence quenching is based on not only dye-dye interactions but also dye-nucleotide interactions as well.

• Molecules and Cells
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• v.25 no.3
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• pp.323-331
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• 2008

Plants are continually exposed to a variety of potentially pathogenic microbes, and the interactions between plants and pathogenic invaders determine the outcome, disease or disease resistance. To defend themselves, plants have developed a sophisticated immune system. Unlike animals, however, they do not have specialized immune cells and, thus all plant cells appear to have the innate ability to recognize pathogens and turn on an appropriate defense response. Using genetic, genomic and biochemical methods, tremendous advances have been made in understanding how plants recognize pathogens and mount effective defenses. The primary immune response is induced by microbe-associated molecular patterns (MAMPs). MAMP receptors recognize the presence of probable pathogens and evoke defense. In the co-evolution of plant-microbe interactions, pathogens gained the ability to make and deliver effector proteins to suppress MAMP-induced defense responses. In response to effector proteins, plants acquired R-proteins to directly or indirectly monitor the presence of effector proteins and activate an effective defense response. In this review we will describe and discuss the plant immune responses induced by two types of elicitors, PAMPs and effector proteins.

• Korean Chemical Engineering Research
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• v.56 no.5
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• pp.663-678
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• 2018

Refractive index and speeds of sound for the binary mixture of isomer of butanol (1) + cyclohexane, benzene and toluene (2) were measured at 308.15 K. The measured data were used to calculate deviation in refractive index ${\Delta}n$, ultrasonic speed ${\Delta}u$, isentropic compressibility $K_s^E$, available volume $V_a$, excess intermolecular free length $L_f$ and molecular association $M_A$. All the derived properties were correlated with polynomial equation. Ultrasonic speed data were predicted using various empirical correlations like Nomoto, van Dael, impedance dependence and theoretically with Schaaff's collision factor theory (CFT). Jacobson free length theory (FLT) was used to calculate $L_f$. The measured refractive index was also correlated with various mixing rules. The deviation in refractive index Δn and ultrasonic speed ${\Delta}u$ was used to determine the intermolecular interactions.

• Molecules and Cells
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• v.41 no.2
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• pp.150-159
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• 2018

Animals use their odorant receptors to receive chemical information from the environment. Insect odorant receptors differ from the G protein-coupled odorant receptors in vertebrates and nematodes, and very little is known about their protein-protein interactions. Here, we introduce a mass spectrometric platform designed for the large-scale analysis of insect odorant receptor protein-protein interactions. Using this platform, we obtained the first Orco interactome from Drosophila melanogaster. From a total of 1,186 identified proteins, we narrowed the interaction candidates to 226, of which only two-thirds have been named. These candidates include the known olfactory proteins Or92a and Obp51a. Around 90% of the proteins having published names likely function inside the cell, and nearly half of these intracellular proteins are associated with the endomembrane system. In a basic loss-of-function electrophysiological screen, we found that the disruption of eight (i.e., Rab5, CG32795, Mpcp, Tom70, Vir-1, CG30427, Eaat1, and CG2781) of 28 randomly selected candidates affects olfactory responses in vivo. Thus, because this Orco interactome includes physiologically meaningful candidates, we anticipate that our platform will help guide further research on the molecular mechanisms of the insect odorant receptor family.

• Bulletin of the Korean Chemical Society
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• v.20 no.8
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• pp.948-952
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• 1999

Electrophilic substitutions on β-position of 2,5-dimethyl pyrrole have been investigated theoretically. The electron donating methyl groups enrich electron densities on C-3, C-4 positions and π* interactions with methyl groups substituted on C-2 and C-5 positions pushed up the HOMO level of the pyrroles consequently induce rapid substitutions on C-3, C-4 sites. Substitution of phenylsulfonyl group on nitrogen stabilized LUMO levels through weak π bonding interactions. Unexpected deoxidation reaction underwent on the sulfonyl group substituted at C-3 position. The structures were solved by X-ray crystallography. Meanwhile, gas phase HF/6-31G* and density functional method (B3LYP/6-31G*) calculations gave favorable energies for 1-phenylsulfinyl pyrrole (6) over 3-phenylsulfinyl pyrrole (5) by 3.6-4.7 kcal/mol which is contrary to the experimental result. However the methods involve the effects of molecular polarizability and solvent, molecular dynamics (MD) and ab-initio self consistent reaction field (SCRF) calculations showed same trend as experiments. According to MD calculations, compound 5 is more stable than compound 6 by 4.15 kcal/mol and the SCRF, HF/6-31G* calculations gave more stable energy value for structure 5 than 6 by 0.03 kcal/mol.

• Journal of Integrative Natural Science
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• v.3 no.4
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• pp.231-236
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• 2010

Partial charge is an important and fundamental concept which can explain many aspects of chemistry. Since a molecule can be regarded as neclei surrounded by electron cloud, there is no way to define a partial charge accurately. Nevertheless, there have been many attempts to define these seemingly impossible parameters, since they would facilitate the understanding of molecular properties such as molecular dipole moment, solvation, hydrogen bonding, molecular spectroscopy, chemical reaction, etc. Common methods are based on the charge equalization, orbital occupancy, charge density, and electric multipole moments, and electrostatic potential fitting. Methods based on the charge equalization using electronegativity are very fast, and therefore they have been used to study many compounds. Methods to subdivide orbital occupancy using basis set conversion, relies on the notion that molecular orbitals are composed of atomic orbitals. The main idea is to reduce overlap integral between two nuclei using converted orthogonal basis sets. Using some quantum mechanical observables like electrostatic potential or charge multipole moments. Using potential grids obtained from wavefunction, partial charges can be fitted. these charges are most useful to describe intermolecular electrostatic interactions. Methods to using dipole moment and its derivatives, seems to be sensitive the level of theory, Dividing electron density using density gradient being the most rigorous theoretically among various schemes, bears best potential to describe the charge the most adequately in the future.

• Molecules and Cells
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• v.44 no.9
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• pp.670-679
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• 2021

Vesicle-associated membrane proteins 721 and 722 (VAMP721/722) are secretory vesicle-localized arginine-conserved soluble N-ethylmaleimide-sensitive factor attachment protein receptors (R-SNAREs) to drive exocytosis in plants. They are involved in diverse physiological processes in plants by interacting with distinct plasma membrane (PM) syntaxins. Here, we show that synaptotagmin 5 (SYT5) is involved in plant defense against Pseudomonas syringae pv tomato (Pst) DC3000 by regulating SYP132-VAMP721/722 interactions. Calcium-dependent stimulation of in vitro SYP132-VAMP722 interaction by SYT5 and reduced in vivo SYP132-VAMP721/722 interaction in syt5 plants suggest that SYT5 regulates the interaction between SYP132 and VAMP721/722. We interestingly found that disease resistance to Pst DC3000 bacterium but not to Erysiphe pisi fungus is compromised in syt5 plants. Since SYP132 plays an immune function to bacteria, elevated growth of surface-inoculated Pst DC3000 in VAMP721/722-deficient plants suggests that SYT5 contributes to plant immunity to Pst DC3000 by promoting the SYP132-VAMP721/722 immune secretory pathway.

• 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.

• Molecules and Cells
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• v.28 no.4
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• pp.321-329
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• 2009

Rapid production of nitric oxide (NO) and reactive oxygen species (ROS) has been implicated in the regulation of innate immunity in plants. A potato calcium-dependent protein kinase (StCDPK5) activates an NADPH oxidase StRBOHA to D by direct phosphorylation of N-terminal regions, and heterologous expression of StCDPK5 and StRBOHs in Nicotiana benthamiana results in oxidative burst. The transgenic potato plants that carry a constitutively active StCDPK5 driven by a pathogen-inducible promoter of the potato showed high resistance to late blight pathogen Phytophthora infestans accompanied by HR-like cell death and $H_2O_2$ accumulation in the attacked cells. In contrast, these plants showed high susceptibility to early blight necrotrophic pathogen Alternaria solani, suggesting that oxidative burst confers high resistance to biotrophic pathogen, but high susceptibility to necrotrophic pathogen. NO and ROS synergistically function in defense responses. Two MAPK cascades, MEK2-SIPK and cytokinesis-related MEK1-NTF6, are involved in the induction of NbRBOHB gene in N. benthamiana. On the other hand, NO burst is regulated by the MEK2-SIPK cascade. Conditional activation of SIPK in potato plants induces oxidative and NO bursts, and confers resistance to both biotrophic and necrotrophic pathogens, indicating the plants may have obtained during evolution the signaling pathway which regulates both NO and ROS production to adapt to wide-spectrum pathogens.