• Bulletin of the Korean Chemical Society
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• 제17권1호
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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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• 제16권1호
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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.

• 한국막학회:학술대회논문집
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• 한국막학회 1998년도 춘계 총회 및 학술발표회
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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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• 제33권11호
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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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• 제35권2호
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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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• 제38권7호
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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.

• 한국콘텐츠학회논문지
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• 제15권9호
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• pp.418-424
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• 2015

본 연구에서는 비방사능 값에 따른 소동물 in vivo실험에서 어느 정도의 비방사능에서부터 수용체-리간드의 결합능력의 변화와 선조체에서의 방사능 집적에 변화가 있는지를 규명하고자 실험을 진행하다. 18F-Fallypride을 3가지 값 ; 높은 비방사능 : 43.29~74 GBq/umol, 중간 비방사능 : 20.72~29.23 GBq/umol, 낮은 비방사능 : 6.29~8.51 GBq/umol)으로 나누어 순차적으로 혈관주사 후 Micro PET을 이용하여 90분 동적 스캔 하였다. 스캔 후 양쪽 선조체에서 Binding Potential(BP)을 구한 후 비교 분석하였다. 높은 비방사능과 낮은 비방사능, 중간 비방사능과 낮은 비방사능에서 유의한 차이가 나타났다. 또한 18F-Fallypride을 이용한 PET 영상비교에서는 높은 비방사능과 중간 비방사능에서는 선조체 에서 높은 방사능집적을 보여주었지만, 낮은 비방사능에서는 다른 두 비방사능에 비해 낮은 방사능 집적을 볼 수 있었다. 이는 18F-Fallypride의 약동학적 특성상 D2/D3에 대한 친화성이 좋기 때문에 비방사능 값이 어느 정도 떨어진 상태에서도 BP의 차이가 크지 않았다. 하지만 높은 비방사능에 비해 6.5배 낮은 비방사능 값 부터는 이미지 및 BP의 차이가 유의하게 나왔으므로 앞으로 18F-Fallyprdie을 이용한 선조체 PET연구에서는 이를 고려하여 실험 할 필요가 있을 것이다.

• Transactions on Electrical and Electronic Materials
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• 제3권1호
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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.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2003년도 제2차 연례학술대회 발표논문집
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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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• 제35권1호
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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.