• 한국생물공학회:학술대회논문집
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• 2005.10a
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• pp.1006-1006
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• 2005

• Bulletin of the Korean Chemical Society
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• v.34 no.1
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• pp.299-302
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• 2013

• Bulletin of the Korean Chemical Society
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• v.25 no.10
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• pp.1571-1574
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• 2004

• Analytical Science and Technology
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• v.11 no.1
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• pp.8-12
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• 1998

The 2,2'-Biimidazole was synthesized by the reaction between glycol and ammonium solution. The correct solid structure of 2,2'-biimidazole in this method reported either trans ($C_{2h}$) or cis ($C_{2v}$) form. In this study, the correct structure of 2,2'-biimidazole was analysed by both FTIR and Raman spectroscopy using mutual exclusion properties of them. Also, it was analysed by $^1H$ and $^{13}C$ NMR and computer molecular modeling. The structure of 2,2'-biimidazole found to be trans ($C_{2h}$) than cis ($C_{2v}$) by comparison between FTIR and Raman Spectra. This results agree with computer molecular modeling and x-ray crystallography. This study provide good evidence for identifying structural orientation of the 2,2'-biimidazole containing pyridyl nitrogen.

• Bulletin of the Korean Chemical Society
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• v.35 no.6
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• pp.1769-1776
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• 2014

Binding modes of a series of catechol derivatives such as protein tyrosine phosphatase 1B (PTP1B) inhibitors were identified by molecular modeling techniques. Docking, molecular dynamics simulations and free energy calculations were employed to determine the modes of these new inhibitors. Binding free energies were calculated by involving different energy components using the Molecular Mechanics-Poisson-Boltzmann Surface Area and Generalized Born Surface Area methods. Relatively larger binding energies were obtained for the catechol derivatives compared to one of the PTP1B inhibitors already in use. The Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) free energy decomposition analysis indicated that the hydroxyl functional groups and biphenyl ring system had favorable interactions with Met258, Tyr46, Gln262 and Phe182 residues of PTP1B. The results of hydrogen bound analysis indicated that catechol derivatives, in addition to hydrogen bonding interactions, Val49, Ile219, Gln266, Asp181 and amino acid residues of PTP1B are responsible for governing the inhibitor potency of the compounds. The information generated from the present study should be useful for the design of more potent PTP1B inhibitors as anti-diabetic agents.

• BMB Reports
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• v.35 no.5
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• pp.498-507
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• 2002

A gene that encodes a thermostable protease, coined thermicin, has been isolated from Thermoanaerobacter yonseiensis that is expressed and characterized in E. coli.. In order to elucidate the molecular characteristics on thermostability of the enzyme, molecular modeling and mutagenesis technology were applied. In the modeling structure, the structural core, including the active site, was well conserved; whereas, the two loop regions were unique when compared to thermitase. The mutant enzyme with the small loop deleted (D190-I196), based on modeling structural information, showed identical enzyme activity. However, when the large loop was deleted (P233-P244), a little lower $K_m$ and even a lower kcat was found. This indicates that the large loop could influence catalytic activity. However, the unfolding temperature ($T_m$), which was determined by a differential-scanning calorimetry for the mutant enzyme deleted the small loop, was $96^{\circ}C$. This is $14^{\circ}C$ lower than that for the parent thermicin. These results suggest that the small loop may play a role in maintaining the proper folding of the enzyme at high temperatures, whereas the large loop might be related to catalysis.

• Bulletin of the Korean Chemical Society
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• v.28 no.6
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• pp.941-946
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• 2007

Bacillus halodurans O-methyltransferase (BhOMT) is a S-adenosylmethionine (SAM or AdoMet) dependent methyltransferase. Three dimensional structure of the BhOMT bound to S-adenosyl-L-homocysteine (SAH or AdoHcy) has been determined by comparative homology modeling. BhOMT has 40% sequence identity with caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) from alfalfa. Based on x-ray structure of CCoAOMT, three dimensional structure of BhOMT was determined using MODELLER. The substrate binding sites of these two proteins showed slight differences, but these differences were important to characterize the substrate of BhOMT. Automated docking study showed that four flavonoids, quercetin, fisetin, myricetin, and luteolin which have two hydroxyl groups simultaneously at 3'- and 4'-position in the B-ring and structural rigidity of Cring resulting from the double bond characters between C2 and C3, were well docked as ligands of BhOMT. These flavonoids form stable hydrogen bondings with K211, R170, and hydroxyl group at 3'-position in the Bring has stable electrostatic interaction with Ca2+ ion in BhOMT. This study will be helpful to understand the biochemical function of BhOMT as an O-methyltransferase for flavonoids.

• Journal of the Semiconductor & Display Technology
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• v.11 no.2
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• pp.81-84
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• 2012

Cantilevered carbon-nanotube-resonator was investigated via classical molecular dynamics simulations. The resonator system is including the attached nanocluster. A nanocluster with a finite length was modeling by some atomic rings. The mass of the nanocluster was equally distributed on the carbon atoms, composed of the atomic rings. The effective density factor, which could be considered as the single parameter affecting the resonance frequency shift, was significantly influenced by the mass, the position, and the linear density of the attached nanocluster. The linear density of the attached nanocluster was an important parameter to analyze the vibrational behavior of the CNT-resonator, including the attached nanocluster.

• The Korea Genome Conference
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• 2003.09a
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• pp.50.2-50.2
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• 2003

• Polymer Science and Technology
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• v.9 no.4
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• pp.274-282
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• 1998