• Bulletin of the Korean Chemical Society
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• v.24 no.11
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• pp.1627-1631
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• 2003

Molecular modeling was performed to comprehend the chiral recognition of ${\alpha}$-methoxy-${\alpha}$-trifluoromethylphenylacetic acid (MTPA) enantiomers by cyclomaltoheptaose (${\beta}$-cyclodextrin,${\beta}$-CD) and 6-amino-6-deoxy-cyclomaltoheptaose (am-${\beta}$-CD). Monte Carlo (MC) docking coupled to constant temperature molecular dynamics (MD) simulations was applied to the investigation for the ${\alpha}$-methoxy-${\alpha}$-trifluoromethylphenylacetic acid complexation with two different CDs in terms of the relative distribution of the interaction energies. The calculated results are finely correlated with the experimental observations in chiral recognition thermodynamics. Am-${\beta}$-CD as a host showed the superior enantio-discrimination ability to the native ${\beta}$-CD where the amino group of am-${\beta}$-CD was critically involved in enhancing the ability of chiral discrimination via the Coulombic interaction with MTPA.

• 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.

• BMB Reports
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• v.50 no.5
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• pp.275-280
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• 2017

Herpes simplex virus type 1 ICP27 is a multifunctional protein responsible for viral replication, late gene expression, and reactivation from latency. ICP27 interacts with various cellular proteins, including Daxx. However, the role of interaction between ICP27 and Daxx is largely unknown. Since Daxx is known to repress $NF-{\kappa}B$ activity, there is a possibility that ICP27 may influence the inhibitory effect of Daxx on $NF-{\kappa}B$ activity. In this study, we tested whether ICP27 affects the $NF-{\kappa}B$ activity through its interaction with Daxx. Interestingly, ICP27 enhanced the Daxx-mediated repression of $NF-{\kappa}B$ activity. In addition, we found that sumoylation of Daxx regulates its interaction with p65. ICP27 binds to Daxx, inhibits Daxx sumoylation, and enhances p65 deacetylation induced by Daxx. Consequently, ICP27 represses the $NF-{\kappa}B$ activity, by elevating the inhibitory effect of Daxx on $NF-{\kappa}B$ activity through desumoylation of Daxx.

• Proceedings of the Zoological Society Korea Conference
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• 2001.04a
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• pp.90.1-90
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• 2001

No Abstract, See Full Text

• Journal of Ginseng Research
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• v.41 no.3
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• pp.330-338
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• 2017

Background: Ginsenoside Rh2 (G-Rh2) is a ginseng saponin that is widely investigated because of its remarkable antitumor activity. However, the molecular mechanism by which (20S) G-Rh2 triggers its functions and how target animals avoid its cytotoxic action remains largely unknown. Methods: Phage display was used to screen the human targets of (20S) G-Rh2. Fluorescence spectroscopy and UV-visible absorption spectroscopy were used to confirm the interaction of candidate target proteins and (20S) G-Rh2. Molecular docking was utilized to calculate the estimated free energy of binding and to structurally visualize their interactions. MTT assay and immunoblotting were used to assess whether human serum albumin (HSA), bovine serum albumin (BSA), and bovine serum can reduce the cytotoxic activity of (20S) G-Rh2 in HepG2 cells. Results: In phage display, (20S) G-Rh2-beads and (20R) G-Rh2-beads were combined with numerous kinds of phages, and a total of 111 different human complementary DNAs (cDNA) were identified, including HSA which had the highest rate. The binding constant and number of binding site in the interaction between (20S)-Rh2 and HSA were $3.5{\times}10^5M^{-1}$ and 1, and those in the interaction between (20S) G-Rh2 and BSA were $1.4{\times}10^5M^{-1}$ and 1. The quenching mechanism is static quenching. HSA, BSA and bovine serum significantly reduced the proapoptotic effect of (20S) G-Rh2. Conclusion: HSA and BSA interact with (20S) G-Rh2. Serum inhibited the activity of (20S) G-Rh2 mainly due to the interaction between (20S) G-Rh2 and serum albumin (SA). This study proposes that HSA may enhance (20S) G-Rh2 water solubility, and thus might be used as nanoparticles in the (20S) G-Rh2 delivery process.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.313-318
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• 2005

Estimating the reliability of protein-protein interaction data sets obtained by high-throughput technologies such as yeast two-hybrid assays and mass spectrometry is of great importance. We develop a maximum likelihood estimation method that uses both protein localization and gene expression data to estimate the reliability of protein interaction data sets. By integrating protein localization data and gene expression data, we can obtain more accurate estimates of the reliability of various interaction data sets. We apply the method to protein physical interaction data sets and protein complex data sets. The reliability of the yeast two-hybrid interactions by Ito et al. (2001) is 27%, and that by Uetz et at.(2000) is 68%. The reliability of the protein complex data sets using tandem affinity purification-mass spec-trometry (TAP) by Gavin et at. (2002) is 45%, and that using high-throughput mass spectrometric protein complex identification (HMS-PCI) by Ho et al. (2002) is 20%. The method is general and can be applied to analyze any protein interaction data sets.

• BMB Reports
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• v.34 no.2
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• pp.102-108
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• 2001

A time-dependent folding process was used to determine whether or not protein disulfide isomerase (PDI) plays an important role in the maturation of nascent lactoferrin polypeptides. Interaction between lactoferrin and PDI was analyzed according to the co-immunoprecipitation of the two proteins. The results indicate that lactoferrin folding requires a significant interaction with PDI and its binding is relatively brief compared to other nascent polypeptides. The amount of lactoferrin interacting with PDI increases up to half a minute and sharply decreases beyond this time point. During the refolding process that follows reduction by DTT, lactoferrin polypeptides heavily interact with PDI and the interaction period was extended compared to the normal folding process. In terms of the temperature effect on PDI-lactoferrin interaction, PDI binds to lactoferrin polypeptides longer at a lower temperature (here, $25^{\circ}C$) than $37^{\circ}C$. The lactoferrin-PDI interaction was also studied in vitro. According to the in vitro experiment data, PDI was still functional in cell lysates assisting lactoferrin folding into the mature form. PDI interacts with lactoferrin polypeptides for an extended period during the folding in vitro. During the refolding process in vitro, intermolecular aggregates and refolding oligomers matured into a functional form after PDI binds to the lactoferrin. These results suggest that PDI provides a prolonged chaperoning activity in the refolding processes and that there appears to be a greater requirement for PDI chaperone activity in the refolding of lactoferrin polypeptides.

• Bulletin of the Korean Chemical Society
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• v.28 no.6
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• pp.959-964
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• 2007

The benzene complexes with dimethyl sulfur (DMS) and fluorinated DMS (FDMS) have been investigated using ab initio calculations. The natural bond orbital (NBO) charge population on S atom varies remarkably for different conformations of DMS and FDMS, which determines the possible binding modes for their benzene complexes. The electronegative substituent at the methyl group of DMS causes a significant change in the molecular electrostatic potential around the sulfur atom and changes the interaction mode with aromatic ring. It was found that the sulfur…π interaction mode does not occur in the DMS-benzene complex, while it does in the FDMS-benzene complex. Both B3LYP and MP2 methods provide reliable structures, while the interaction energy obtained by B3LYP is unreliable.

• Journal of Information Display
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• v.4 no.2
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• pp.29-34
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• 2003

We have studied liquid crystal (LC) molecular alignment on rubbed and photoaligned surfaces. Particular attention was paid to the intermolecular liquid crystalline interaction. We will first show that uniform molecular orientation on a rubbed surface does not mean spatially uniform interaction between the surface and LC molecules. Rather LCs tend to align themselves through LC interaction. The existence of nonuniformity of rubbing was successfully visualized by double surface treatment. The importance of intermolecular LC interaction was also found in the orientation formation process in 5CB evaporated on rubbed and photoaligned surfaces. By simultaneously analyzing polarized UVNIS absorption and second-harmonic generation (SHG) using the maximum entropy method, we succeeded in obtaining the temporal variation of the orientational distribution functions in the film forming process. The distribution anisotropy and pretilt are found to be generated under the influence of intermolecular LC interaction.

• Tribology and Lubricants
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• v.31 no.6
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• pp.264-271
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• 2015

Adhesion force of nanomaterials such as nanoparticle, nanowire, and nanorods should be significantly considered for its mechanical applications. However, examination of the adhesion force is limited since it is technically challenging to carry out experiments with such small objects. Therefore, in this work, molecular dynamics simulation (MDS) was conducted to determine the adhesion force between a nanowire and a flat surface, which could not be readily assessed through experiments. The adhesion force of a cylindrical-shaped nanowire was assessed by performing MDS and applying an equation of Van der Waals interaction. Simulation was conducted in two steps: indentation of a spherical tip on the flat surface and indentation of a cylinder on the flat surface, because the purpose of the simulation was comparing the results of the simulation and calculation of the Van der Waals interaction equation. From the simulation, Hamaker constant used for the equation of Van der Waals interaction was determined to be 2.93 °ø 10?18 J. Using this constant, the adhesion force of the nanowire on the flat surface was readily estimated by calculating Van der Waals equation to be approximately 65~89 nN with respect to the diameter of the nanowire. Moreover, the adhesion force of the nanowire was determined to be 52~77 nN from the simulation It was observed that there was a slight discrepancy (approximately 15~25%) between the results of the simulation and the theoretical calculation. Thus, it was confirmed that the calculation of Van der Waals interaction could be utilized to assess the adhesion force of the nanowire.