• Genomics & Informatics
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• v.21 no.2
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• pp.25.1-25.12
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• 2023

Adaptation of infections and hosts has resulted in several metabolic mechanisms adopted by intracellular pathogens to combat the defense responses and the lack of fuel during infection. Human tuberculosis caused by Mycobacterium tuberculosis (MTB) is the world's first cause of mortality tied to a single disease. This study aims to characterize and anticipate potential antigen characteristics for promising vaccine candidates for the hypothetical protein of MTB through computational strategies. The protein is associated with the catalyzation of dithiol oxidation and/or disulfide reduction because of the protein's anticipated disulfide oxidoreductase properties. This investigation analyzed the protein's physicochemical characteristics, protein-protein interactions, subcellular locations, anticipated active sites, secondary and tertiary structures, allergenicity, antigenicity, and toxicity properties. The protein has significant active amino acid residues with no allergenicity, elevated antigenicity, and no toxicity.

• Journal of the Semiconductor & Display Technology
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• v.6 no.4
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• pp.1-4
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• 2007

Carbon nanotube oscillators encapsulating copper nanowire were investigated by molecular dynamics simulations. The excess forces due to the carbon-carbon van der Waals interactions are higher than the excess force due to carbon-copper interactions. And the masses of copper atoms are higher than those of carbon atoms. So, the carbon atoms are easier accelerated than the copper atoms. When the encapsulated copper nanowire deforms the encapsulating nanotube, the frequency can not be estimated by the mass-frequency dependence in classical oscillation theory.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2004.10a
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• pp.69-71
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• 2004

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• Proceedings of the Korean Magnetic Resonance Society Conference
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• 2002.01a
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• pp.16-16
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• 2002

• Bulletin of the Korean Chemical Society
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• v.31 no.8
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• pp.2147-2150
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• 2010

c-Jun N-terminal kinase 1 (JNK1) is involved in apoptosis, cell differentiation and proliferation. It has been reported that a flavonol, quercetin, induces cell apoptosis and JNK inhibition. In order to understand the interactions of quercetin and JNK1, we performed receptor-oriented pharmacophore based in silico screening and determined a binding model of human JNK1 and quercetin at the ATP binding site of JNK1. 5-OH of A-ring and carbonyl oxygen of C-ring of quercetin participated in hydrogen bonding interactions with backbone of E109 and M111. Additionally, 3'-OH of quercetin formed a hydrogen bond with backbone of I32. One hydrophobic interaction is related on the binding of quercetin to JNK1 with I32, N114, and V158. Based on this model, we conducted a docking study with other 8 flavonols to find possible flavonoids inhibitors of JNK1. We proposed that one flavonols, rhamnetin, can be a potent inhibitor of JNK and 5-OH of A-ring and 3'-OH of B-ring of flavonols are the essential features for JNK1 inhibition.

• Journal of the Korean Society of Manufacturing Technology Engineers
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• v.24 no.4
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• pp.421-427
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• 2015

In this paper, a description is given of finite element method (FEM) simulations of the elastic bending modulus of multi-layered graphene sheets that were carried out to investigate the mechanical behavior of graphene sheets with different gap thicknesses through molecular mechanics theory. The interaction forces between layers with various gap thicknesses were considered based on the van der Waals interaction. A finite element (FE) model of a multi-layered rectangular graphene sheet was proposed with beam elements representing bonded interactions and spring elements representing non-bonded interactions between layers and between diagonally adjacent atoms. As a result, the average elastic bending modulus was predicted to be 1.13 TPa in the armchair direction and 1.18 TPa in the zigzag direction. The simulation results from this work are comparable to both experimental tests and numerical studies from the literature.

• Journal of the Korean Chemical Society
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• v.37 no.8
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• pp.753-756
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• 1993

Studies on the molecular interactions of dimethylsulfoxide (DMSO) with water and/or some alkanols were carried out by vapor pressure osmometry at 40$^{\circ}C$. Negative deviation from Raoult's law was observed for the DMSO-water, methanol, ethanol, 1-propanol, 2-propanol, and 2-methyl-1-propanol systems, whereas positive deviation from Raoult's law was observed for the DMSO-1-butanol and 1-pentanol systems. The results were interpreted in terms of molecular interactions between unlike molecules, and of self-association of DMSO molecules, respectively. Measured chemical shift of hydroxyl proton of the solvents also supported the results.

• Bulletin of the Korean Chemical Society
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• v.30 no.8
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• pp.1835-1838
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• 2009

Inhibition of human phenylethanolamine N-methyltransferase (hPNMT) has been proposed as a method for the treatment of several mental processes which related on adrenaline metabolism. We performed in silico screening to identify flavonoid inhibitors of hPNMT using automated docking method and selected 9 inhibitor candidates based on ligand score (LigScore) and binding free energy (${\Delta}G_{bind}$) estimation. Among 9 flavonoid candidates, 7 flavonoids belong to flavones while the rest of them belong to flavanone. All candidates have common chemical features; two hydrogen bond interactions with side chain of Lys75 and backbone carbonyl oxygen of Asn39, and two hydrophobic interactions. One hydrophobic site is formed by Val53, Leu262, and Met258 and the other is made up of Phe182, Ala186, Tyr222, and Val269. This study can be helpful to understand the structural features for inhibition of PNMT and showed flavonoids as promising inhibitor candidates for hPNMT.

• Genomics & Informatics
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• v.12 no.2
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• pp.64-70
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• 2014

Human papillomavirus (HPV) infection is the leading cause of cancer mortality among women worldwide. The life-threatening infection caused by HPV demands the need for designing anticancerous drugs. In the recent years, different compounds from natural origins, such as carrageenan, curcumin, epigallocatechin gallate, indole-3-carbinol, jaceosidin, and withaferin, have been used as a hopeful source of anticancer therapy. These compounds have been shown to suppress HPV infection by different researchers. In the present study, we explored these natural inhibitors against E6 oncoprotein of high-risk HPV-16, which is known to inactivate the p53 tumor suppressor protein. A robust homology model of HPV-16 E6 was built to anticipate the interaction mechanism of E6 oncoprotein with natural inhibitory molecules using a structure-based drug designing approach. Docking analysis showed the interaction of these natural compounds with the p53-binding site of E6 protein residues 113-122 (CQKPLCPEEK) and helped the restoration of p53 functioning. Docking analysis, besides helping in silico validation of natural compounds, also helps understand molecular mechanisms of protein-ligand interactions.

• Polymer(Korea)
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• v.32 no.3
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• pp.290-294
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• 2008

Induction mechanism of molecular orientations for a rubbed polymer film as an alignment layer was investigated using polarized UV/Vis spectroscopic experiments for polyimide and polyvinylcinnamate whose conjugated electrons are located along main chain and side chain, respectively. By determining anisotropy formed in the rubbed film, LC director formed in the LC cell, and orientation direction of deposited pentacene molecules, it was found that LC orientation was induced mainly by molecular interactions whereas surface microgrooves formed by the rubbing process affect the orientation direction of deposited pentacene molecules.