• Bulletin of the Korean Chemical Society
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• v.32 no.8
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• pp.2695-2699
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• 2011

${\beta}$ Ketoacyl acyl carrier protein synthase III (KAS III) initiates fatty acid synthesis in bacteria and is a key target enzyme to overcome the antibiotic resistance problem. In our previous study, we found flavonoid inhibitors of Enterococcus faecalis KAS III and proposed three potent antimicrobial flavonoids against Enterococcus faecalis and Vancomycin-resistant Enterococcus faecalis with MIC values in the range of 128-512 ${\mu}g/mL$ as well as high binding affinities on the order from $10^6$ to $10^7\;M^{-1}$. Using these series of flavonoids, we conducted biological assays as well as docking study to find potent flavonoids inhibitors of Staphylococcus aureus KAS III with specificities against Staphylococcus aureus and Methicillin-resistant Staphylococcus aureus. Here, we propose that naringenin (5,7,4'-trihydroxyflavanone) and eriodictyol (5,7,3',4'-tetrahydroxyflavanone) are potent antimicrobial inhibitors of Staphylococcus aureus KAS III with binding affinity of $3.35{\times}10^5$ and $2.01{\times}10^5\;M^{-1}$, respectively. Since Arg38 in efKAS III is replaced with Met36 in saKAS III, this key difference caused one hydrogen bond missing in saKAS III compared with efKAS III, resulting in slight discrepancy in their binding interactions as well as decrease in binding affinities. 4'-OH and 7-OH of these flavonoids participated in hydrogen bonding interactions with backbone carbonyl of Phe298 and Ser152, respectively. In particular, these flavonoids display potent antimicrobial activities against various MRSA strains in the range of 64 to 128 ${\mu}M$ with good binding affinities.

• Bulletin of the Korean Chemical Society
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• v.29 no.7
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• pp.1311-1314
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• 2008

Bacillus halodurans O-methyltransferase (BhOMT) is an S-adenosylmethionine dependent methyltransferase. In our previous study, three dimensional structure of the BhOMT has been determined by comparative homology modeling and automated docking study showed that two hydroxyl groups at 3'- and 4'-position in Bring and structural rigidity of C-ring resulting from the double bond characters between C2 and C3 of flavonoid, were key factors for interaction with BhOMT. In the present study, BhOMT was cloned and expressed. Binding assay was performed on purified BhOMT using fluorescence experiments and binding affinity of luteolin, quercetin, fisetin, and myricetin were measured in the range of $10^7$. Fluorescence quenching experiments indicated that divalent cation plays a critical role on the metal-mediated electrostatic interactions between flavonoid and substrate binding site of BhOMT. Fluorescence study confirmed successfully the data obtained from the docking study and these results imply that hydroxyl group at 7-position of luteolin, quercetin, fisetin, and myricetin forms a stable hydrogen bonding with K211 and carboxyl oxygen of C-ring forms a stable hydrogen bonding with R170. Hydroxyl group at 3'-and 4'-position in the B-ring also has strong $Ca^{2+}$ mediated electrostatic interactions with BhOMT.

• Bulletin of the Korean Chemical Society
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• v.24 no.6
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• pp.757-762
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• 2003

Since theoretical investigations of gas phase clusters enable the evaluation of intrinsic molecular properties and intermolecular interactions, one can predict the macroscopic properties of bulk matter, from a microscopic determination of the properties of individual atoms, molecules, or clusters. Based on the insights obtained from theoretical investigations of the properties of a large number of cluster systems (ranging from simple water clusters to large π-systems), we have investigated the properties of various novel molecular systems including endo/exohedral fullerenes, nanotori, nonlinear optical materials, ionophores/receptors, polypeptides, enzymes, organic nanotubes, nanowires, and electronic and nano-mechanical molecular devices. The present minireview highlights some of the interesting results obtained in the course of our extensive theoretical investigations of clusters and nanomaterials.

• The Bulletin of The Korean Astronomical Society
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• v.36 no.1
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• pp.62.2-62.2
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• 2011

It is well known that the cluster environment can change the atomic gas properties of galaxies through tidal interactions and/or by the hot cluster medium. Meanwhile, the molecular gas is expected to be less vulnerable to its surroundings due to its higher density, and no obvious influence of the environment on the molecular gas properties had been found among cluster spirals until recently. However, in a recent study by Fumagalli et al. (2009) of a sub-sample of Virgo spirals, it has been suggested that HI deficient galaxies can be also CO deficient. In order to further investigate if the HI deficiency indeed can result in the deficiency in molecular gas content, we compare the global CO and HI gas properties of Virgo spirals with those of galaxies in the Ursa Major cluster and the Pisces cluster, much lower density environments than Virgo. We discuss possible consequences of molecular gas deficiency in star formation activity of spiral galaxies in high density environment.

• Advances in nano research
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• v.15 no.2
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• pp.105-111
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• 2023

Integrin αvβ3 is one of the receptors expressed in cancer cells. RGD peptides have the potential to target integrin αvβ3 (receptor), which can increase drug delivery efficiency. In this study, 55 different RGD dimer motifs were investigated. At first, the binding energy between RGD peptides and the receptor was calculated using molecular docking. Then, three RGD peptides with the strongest binding energy with the receptor were selected, and their dynamic adsorption on the receptor was simulated by molecular dynamics (MD). The obtained results showed that a sequence that has RGD at the beginning and end with tryptophan (TRP) has strong Lennard-Jones (LJ) and electrostatic interactions with Integrin αvβ3 and has changed the conformation of receptor significantly, which analyzed by root mean square deviation (RMSD) and radius of gyration.

• BMB Reports
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• v.50 no.11
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• pp.535-536
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• 2017

A novel approach has been used to identify functional interactions relevant to human disease. Using high-throughput human-yeast genetic interaction screens, a first draft of disease interactome was obtained. This was achieved by first searching for candidate human disease genes that confer toxicity in yeast, and second, identifying modulators of toxicity. This study found potentially disease-relevant interactions by analyzing the network of functional interactions and focusing on genes implicated in amyotrophic lateral sclerosis (ALS), for example. In the subsequent proof-of-concept study focused on ALS, similar functional relationships between a specific kinase and ALS-associated genes were observed in mammalian cells and zebrafish, supporting findings in human-yeast genetic interaction screens. Results of combined analyses highlighted MAP2K5 kinase as a potential therapeutic target in ALS.

• Korean Journal Plant Pathology
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• v.14 no.5
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• pp.507-512
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• 1998

Molecular analysis has been done for characterization of the interactions between three beet curly top virus (BCTV) strains and two Arabidopsis ecotypes in terms of virus inducible disease symptoms and infectivities. The total DNA was isolated from three tissues (shoot tips, infection origins and roots) of virus infected plants and this DNA was analyzed by quantitatively and qualitatively to elucidate virus movement and symptom development. CTV-Worland infected Col-O and Sei-O showed only symptom shown in hypersusceptible ecotype Sei-O by BCTV-worland was shoot tip stunting. Kinetics of virus DNA accumulation of three different viruses indicated that roots contained more virus DNA than shoot tips or infection origins, and that disease symptom severity was strongly correlated with virus DNA accumulation. These results suggest that the mild and Worland-specific symptoms shown in Sei-O by BCTV-worland are caused by the interactions of host factors provided by hypersusceptible ecotype and viral factors of mild strain.

• The Plant Pathology Journal
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• v.36 no.3
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• pp.193-203
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• 2020

Volatile compounds (VOCs) are not only media for communication within a species but also effective tools for sender to manipulate behavior and physiology of receiver species. Although the influence of VOCs on the interactions among organisms is evident, types of VOCs and specific mechanisms through which VOCs work during such interactions are only beginning to become clear. Here, we review the fungal volatile compounds (FVOCs) and their impacts on different recipient organisms from perspective of distinct lifestyles of the filamentous fungi. Particularly, we discuss the possibility that different lifestyles are intimately associated with an ability to produce a repertoire of FVOCs in fungi. The FVOCs discussed here have been identified and analyzed as relevant signals under a range of experimental settings. However, mechanistic insight into how specific interactions are mediated by such FVOCs at the molecular levels, amidst complex community of microbes and plants, requires further testing. Experimental designs and advanced technologies that attempt to address this question will facilitate our understanding and applications of FVOCs to agriculture and ecosystem management.

• Advances in nano research
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• v.6 no.4
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• pp.357-375
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• 2018

Two dimensional (2D) atomic layered nanomaterials exhibit some of the most striking phenomena in modern materials research and hold promise for a wide range of applications including energy and biomedical technologies. Graphene has received much attention for having extremely high surface area to mass ratio and excellent electric conductivity. Graphene has also been shown to maximize the activity of surface-assembled metal nanoparticle catalysts due to its unique characteristics of enhancing mass transport of reactants to catalysts. This paper specifically investigates the strategy of pre-formed nanoparticle self-assembly used for the formation of various metal nanoparticles supported on graphene families such as graphene, graphene oxide, and reduced graphene oxide and aims at understanding the interactions between ligand-capped metal nanoparticles and 2D nanomaterials. By varying the functional groups on the ligands between alkyl, aromatic, amine, and alcohol groups, different interactions such as van der Waals, ${\pi}-{\pi}$ stacking, dipole-dipole, and hydrogen bonding are formed as the 2D hybrids produced.

• Bulletin of the Korean Chemical Society
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• v.32 no.12
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• pp.4415-4418
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• 2011