• Bulletin of the Korean Chemical Society
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• v.17 no.1
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• pp.19-24
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• 1996

The potential energies of HIV-1 protease, inhibitor, and their complex have been calculated by molecular mechanics and the "binding energy", defined as the difference between the potential energy of complex and the sum of potential energies of HIV-1 protease and its inhibitor, has been compared to the free energy in inhibition reaction. The trend in these binding energies seems to agree with that in free energies.

• Journal of Microbiology and Biotechnology
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• v.16 no.1
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• pp.109-117
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• 2006

The Rev binding to Rev Responsive Element (RRE) of HIV-1 mRNA plays an important role in the HIV-I viral replication cycle. The disruption of the Rev-RRE interaction has been studied extensively in order to develop a potential antiviral drug. In order to provide the basis for a more promising approach to develop a Rev-RRE binding inhibitor against HIV-I infection, it is necessary to understand the binding modes of the aminoglycoside antibiotics to RRE. In the present study, the binding mode of a modified antibiotic, a neamine conjugated with pyrene and arginine (NCPA), to RRE has been studied by the methods of $T_m$ measurement and spectroscopic analysis of RRE with or without antibiotics. The results confirmed that NCPA competes with Rev in binding to RRE.

• Proceedings of the Membrane Society of Korea Conference
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• 1998.04a
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• pp.31-35
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• 1998

1. INTRODUCTION : Recognition and binding of organic substrates by biological molecules are of vital importance in biophysics and biophysical chemistry. Most studies of the application focused on the development of biosensors, which detected reaction products generated by the binding between enzymes and substrates. Other types of biosensors in which membrane proteins (e.g., nicotinic acetylcholine receptor, auxin receptor ATPase, maltose bining protein, and glutmate receptor) were utilized as a receptor function were also developed. In the previous study[1], the shifts in membrane potential, caused by the injection of substrates into a permeation cell, were measured using immobilized glucose oxidase membranes. It was suggested that the reaction product was not the origin of the potential shifts, but the changes in the charge density in the membrane due to the binding between the enzyme and the substrates generated the potential shifts. In this study, $\gamma$-globulin was immobilized (entrapped) in a poly($\gamma$-amino acid) network, and the shifts in the membrane potential caused by the injection of some amino acids were investigated.

• Bulletin of the Korean Chemical Society
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• v.33 no.11
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• pp.3597-3600
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• 2012

Thrombin binding aptamter (TBA-15) is a 15-mer guanine-rich oligonucleotide. This DNA apamer specifically binds to the thrombin protein involved in blood coagulation. Using extensive umbrella sampling molecular dynamics simulation method at all atom level, we investigated the potential of mean force (PMF) upon pulling the DNA aptamer from the binding mode of aptamer/thrombin complex. From this calculation, the free energy cost for a full dissociation of this aptamer/protein complex is 17 kcal/mol, indicating a substantial binding affinity of TBA-15. Interestingly, this PMF reveals noticeable plateau regions along the pulling coordinate. Possible structural changes of this complex in the plateau were investigated in details.

• BMB Reports
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• v.35 no.2
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• pp.194-198
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• 2002

Eukaryotic replication protein A (RPA) is a single-stranded(ss) DNA binding protein with multiple functions in DNA replication, repair, and genetic recombination. The 70-kDa subunit of eukaryotic RPA contains a conserved four cysteine-type zinc-finger motif that has been implicated in the regulation of DNA replication and repair. Recently, we described a novel function for the zinc-finger motif in the regulation of human RPA's ssDNA binding activity through reduction-oxidation (redox). Here, we show that yeast RPA's ssDNA binding activity is regulated by redox potential through its RPA32 and/or RPA14 subunits. Yeast RPA requires a reducing agent, such as dithiothreitol (DTT), for its ssDNA binding activity. Also, under non-reducing conditions, its DNA binding activity decreases 20 fold. In contrast, the RPA 70 subunit does not require DTT for its DNA binding activity and is not affected by the redox condition. These results suggest that all three subunits are required for the regulation of RPA's DNA binding activity through redox potential.

• Molecules and Cells
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• v.38 no.7
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• pp.657-662
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• 2015

Rapid and efficient engulfment of apoptotic cells is an essential property of phagocytes for removal of the large number of apoptotic cells generated in multicellular organisms. To achieve this, phagocytes need to be able to continuously uptake apoptotic cells. It was recently reported that uncoupling protein 2 (Ucp2) promotes engulfment of apoptotic cells by increasing the phagocytic capacity, thereby allowing cells to continuously ingest apoptotic cells. However, the functions of Ucp2, beyond its possible role in dissipating the mitochondrial membrane potential, that contribute to elevation of the phagocytic capacity have not been determined. Here, we report that the anion transfer or nucleotide binding activity of Ucp2, as well as its dissipation of the mitochondrial membrane potential, is necessary for Ucp2-mediated engulfment of apoptotic cells. To study these properties, we generated Ucp2 mutations that affected three different functions of Ucp2, namely, dissipation of the mitochondrial membrane potential, transfer of anions, and binding of purine nucleotides. Mutations of Ucp2 that affected the proton leak did not enhance the engulfment of apoptotic cells. Although anion transfer and nucleotide binding mutations did not affect the mitochondrial membrane potential, they exerted a dominant-negative effect on Ucp2-mediated engulfment. Furthermore, none of our Ucp2 mutations increased the phagocytic capacity. We conclude that dissipation of the proton gradient by Ucp2 is not the only determinant of the phagocytic capacity and that anion transfer or nucleotide binding by Ucp2 is also essential for Ucp2-mediated engulfment of apoptotic cells.

• The Journal of the Korea Contents Association
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• v.15 no.9
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• pp.418-424
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• 2015

In this study, we proceed if there are any changes in binding ability of receptor-ligand in some degree of SA and in radioactive uptake from the corpus striatum based on small animal experiment in vivo based on the S.A values. By dividing 18F-Fallypride into 3 S.A values(high S.A : 43.29~74 GBq/umol, ordinary S.A : 20.72~29.23 GBq/umol, low S.A : 6.29~8.51 GBq/umol), we injected directly into the veins and performed 90 minutes of dynamic scan using Micro PET. After scanning, we compared and analyzed with Binding Potential (Binding Potential) from the bilateral striatum. high SA and low SA, ordinary SA and low SA showed significant differences. Also, in the image comparison using 18F-Fallypride show high radioactive uptake in the striatum at high SA and ordinary SA, but the radioactive uptake at low SA is lower than other two SA. Since 18F-Fallypride has affinity to dopamine D2/3 pharmacokinetic, the difference of Binding Potentials at decreased level of SA values was not that significant. However, further PET research of the corpus striatum using 18F-Fallypride is necessary because the differences in images and Binding Potentials at 6.5 times smaller SA values compared to high SA value showed were significant.

• Transactions on Electrical and Electronic Materials
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• v.3 no.1
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• pp.23-29
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• 2002

The electronic properties of Carbon Nanotube(CNT) are currently the focus of considerable interest. In this paper, the electronic properties of finite length effect in CNT for the carbon nano-scale device is presented. To Calculate the electronic properties of CNT, Empirical potential method (the extended Brenner potential for C-Si-H) for carbon and Tight Binding molecular dynamic (TBMD) simulation are used. As a result of study, we have known that the value of the band gap decreases with increasing the length of the tube. The energy band gap of (6,6) armchair CNT have the ranges between 0.3 eV and 2.5 eV. Also, our results are in agreements with the result of the other computational techniques.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.17-25
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• 2003

Determining the binding sites in protein-nucleic acid complexes is essential to the complete understanding of protein-nucleic acid interactions and to the development of new drugs. We have developed a set of algorithms for analyzing protein-nucleic acid interactions and for predicting potential binding sites in protein-nucleic acid complexes. The algorithms were used to analyze the hydrogen-bonding interactions in protein-RNA and protein-DNA complexes. The analysis was done both at the atomic and residue level, and discovered several interesting interaction patterns and differences between the two types of nucleic acids. The interaction patterns were used for predicting potential binding sites in new protein-RNA complexes.

• Bulletin of the Korean Chemical Society
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• v.35 no.1
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• pp.253-256
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• 2014

Functionalization of zigzag graphene nanoribbon (ZGNR) segment containing 120 C atoms with pyridine (3NV-ZGNR) defects was investigated on the basis of density-functional theory (DFT) calculations, results show that edge-modified ZGNRs by Sc can adsorb multiple hydrogen molecules in a quasi-molecular fashion, thereby can be a potential candidate for hydrogen storage. The stability of Sc functionalization is dictated by a strong binding energy, suggesting a reduction of clustering of metal atoms over the metal-decorated ZGNR.