• YAKHAK HOEJI
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• v.46 no.6
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• pp.416-425
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• 2002

A comparative study to validate the reliability of a fully automated docking program, FlexiDock, was carried out to predict the binding modes of DHFR-inhibitor complex. The inhibitors were extracted from the crystallographically determined DHFR-NADP$^{+}$(H)-inhibitor ternary complexes of human, Escherichia coli and Candida albicans and then docked back into the remaining DHFR-NADP$^{+}$(H) binary complexes using FlexiDock. The resulting conformations and orientations were compared to the original crystal complex structures for reproducibility. Then, folate, the substrate, and known inhibitors such as methotrexate, piritrexim and trimethoprim were docked into the wild-type human DHFR and their binding modes were compared with X-ray crystallographic or other modeling data. The root mean square deviations (RMSDs) for ligands ranged from 1.14 to 1.57$\AA$, and the protein backbone RMSDs from 0.94 to 1.26$\AA$. FlexiDock reproduced the orientations and binding modes of all seven ligands in good agreement with the crystal structures. It proved to be a reliable and efficient program in studying binding modes of DHFR-inhibitor complexes of different species, and the information obtained from this work may provide additional insight into the design of new agents with improved activity.ity.

• Journal of Microbiology
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• v.40 no.4
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• pp.319-326
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• 2002

Cellular DNA in prokaryotes is organized in nucleic acid-protein self-assemblies referred to as the nucleoid. The physical forces responsible for its stability inside the poor solvent properties of the cytoplasm and their functional implications are not understood. Studies on the organisation and functioning of the cytosol of cells largely rely on experimental protocols performed in highly dilute solutions using biochemically purified molecules, which is not a reliable substitute for the situation existing in vivo. Our current research interest is focused on the characterization of biological and physical forces determining the compaction and phase separation of DNA in Escherichia coli cytoplasm. We have emphasized the effect of excluded volume in solutions with high macromolecular concentrations (macromolecular crowding) upon self-association patterns of reactions. The prokaryotic cytosol was simulated by addition of inert polymer polyethylene glycol (PEG) (average molecular weight 20000), as an agent which afterwards facilitates the self-association of macromolecules. Fluorescence microscopy was used for direct visualization of nucleoids in intact cells, after staining with DAPI (4',6-diamidino-2-phenylindole dihydrochloride). Addition of the crowding agent PEG 20,000, in increasing concentrations generated progressively enhanced nucleoid compaction, the effect being stronger in the presence of 0.2 M NaCl and 5 mM MgCl$\_$2/. Under these conditions, the nucleoids were compacted to volumes of around 2 ㎛$\^$3/ or comparable sizes with that of living cells.

• Macromolecular Research
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• v.12 no.2
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• pp.178-188
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• 2004

We performed molecular dynamics (MD) simulations at 300 K on a series of poly(benzyl ether) (PBE) dendrimers having a different core functionalities. We used the rotational isomeric state Metropolis Monte Carlo (RMMC) method to construct the initial configuration in a periodic boundary cell (PBC) before the MD simulations were undertaken. To elucidate the effects that the structural features have on the chain dimension, the overall internal structure, and the morphology, we monitored the radii of gyration, R$\sub$g/ and the conformational changes during the simulations. The PBE dendrimers in a glassy state adopted less-extended structures when compared with the conformations obtained from the RMMC calculations. We found that R$\sub$g/ of the PBE dendrimer depends on the molecular weight, M, according to the relation, R$\sub$g/∼M$\^$0.22/. The radial distributions of the dendrimers were developed identically in the PBC, irrespective of the core functionality. A gradual decrease in radial density resulted from the fact that the terminal branch ends are distributed all over the molecule, except for the core region.

• Bulletin of the Korean Chemical Society
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• v.32 no.4
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• pp.1143-1145
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• 2011

The synthesis of novel iminecalix[4]arenes and further modification thereafter is described using a synthetic strategy. The reaction of the benzaldehyde derivatives with tetraamine functions on the calix[4]arene easily afforded the pure compounds in 92.4-95.7% yields, regardless of the effect of the substituents on the benzaldehyde derivatives. These compounds were stable under the conditions to obtain their analogue dialkylated in the narrow rim, with 83.2-89.9% yields. Characterization of the newly synthesized iminecalix[4]arene derivatives by spectroscopic methods revealed that all compounds are in the cone conformations.

• Journal of Photoscience
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• v.7 no.2
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• pp.67-71
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• 2000

A quantum-chemical investigation on the conformations and electronic properties of trans(diphenyl-diheterocyclic) ethenes(t-PHEs) as building block for fully $\pi$-conjuated polymer are performed in order to display the effects of heterocyclic ring substitution. Structures for the molecules, t-PHEs were fully optimized by using semiempirical AM1, PM3 methods, and ab initio HF methods, with 6-31G basic set. The potential energy curves with respect to the change of single are obtained by using ab initio HF/6-31G basic set. The curves are not similar shapes in the molecules with respect to heterocyclic rings. It is shown that the steric repulsion interactions between phenyl ring and heterocyclic ring are subjected to different type with the respect to each heterocyclic ring. Electronic properties of the molecules were molecules were obtained by applying the optimized structures and selected geometries to the extended Huckel method. To investigate the change of HOMO-LUMO gap with respedt to the torsion angle, we select the optimized structures. By using the results, the dependency of conjugation for the energy gaps is analyzed. For t-PHE the energy gap increase up to 0.52 eV compared with its planar structure. In the cases of t-PHE and t-PHE, the energy gap increase by 1.29 and 1.15 eV, respectively, compared with its planar structure.

• Journal of Microbiology and Biotechnology
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• v.8 no.6
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• pp.669-675
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• 1998

Taq DNA polymerase exhibits a sizable drawback compared to the other thermophilic DNA polymerases in that it demonstrates lower proof-reading activity due to the deficiency of 3'-5'exonuclease activity. A study was undertaken to improve the 3'-5' exonuclease activity in the PCR of Taq DNA polymerase. The three-dimensional structural alignment of the polymerase and 3'-5' exonuclease domains from the pol I family DNA polymerases explains why Taq DNA polymerase has just a background level of 3'-5'exonuclease activity. A comparison indicated that the two polymerase domains are very similar in primary and tertiary conformations, even though Taq DNA polymerase carries a much shorter 3'-5'exonuclease domain than that of E. coli DNA polymerase I. Those two polymerase domains were interchanged between Taq DNA polymerase and E. coli DNA polymerase I. The 3'-5' exonuclease domain from E. coli DNA polymerase I was separated and pasted into the polymerase domain of Taq DNA polymerase I, which resulted in a functional fusion-Stoffel fragment. The 3'-5'exonuclease activity of the fusion-Stoffel fragment increased up to 48% of the value of the Klenow fragment, while that of Taq DNA polymerase remained at 6.0% of the Klenow fragment.

• Journal of Microbiology and Biotechnology
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• v.15 no.6
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• pp.1229-1239
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• 2005

Human immunodeficiency virus-like particles (HIVVLPs) with native conformations similar to that of the wild-type virion could be valid candidates for vaccine development. To this end, we used a Semliki Forest Virus (SFV) expression system to produce HIV- VLPs containing high quantities of native envelope proteins. Here, we described a single SFV replicon containing the HIV gagpol and env genes under the control of separate subgenomic promoters. Mature VLPs incorporating the Gag and Env proteins were detected in the supernatant of replicon-expressing cells by Western blot analysis. The HIV-VLPs showed the expected molecular density (1.14-1.18 g/ml) on a $20-60\%$ sucrose gradient; the particles were 100-120 nm in diameter and Env proteins were observed on their surfaces by immunogold electron microscopy. RT-PCR analysis of VLP-associated RNAs in mature HIV-VLPs revealed two SF V-derived RNA species (full-length and subgenomic). Immunization studies in Balb/c mice showed that these HIV-VLPs were capable of inducing both HIV-specific antibodies and cell-mediated immune responses. Taken together, our results indicate that the SFV replicon system is useful for the production of HIV-VLPs, which may be valuable candidates for an HIV vaccine.

• Journal of the Korean Graphic Arts Communication Society
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• v.14 no.1
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• pp.47-54
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• 1996

Deuterium NMR studies have been carried out for two kinds of main- chain dimer liquid crystals $\alpha$.$\omega$-bis[(4,4`-cyanobipheny0oxy] alkane (CBA-n, n=9,100.The H-NMR spectra were recorded on a JEOP JNM-GSX-500 spectrometer by using deuterium labelled CBA-n at various temperatures. The RIS analysis of the NMR spectra was performed so as to elucidate the conformational characteristics of the spacer in the nematic phase. Following the previous treatment, the single-ordering-matrix model was adopted, in which the molecular axis was defined parallel to the line connecting the centers of the terminal mesogenic cores. Conformer fractions of the spacer were estimated by simulation so as to reproduce the observed NMR profile. The conformational entropy changes at both CN and NI interphases were estimated on the basis of the nematic conformations taken from the conformation map as well as those derived from the simulation. In these calculations the spacer was assumed th by in the all-trans conformation and in the random coil stats in the crystal and isotropic phases respectively. The esimated conformational entropy change values were then compared with the corresponding constant-volume entropies obtained from PVT measurements. The correspondence between both entropy values was found to be quite good in consideration of the uncertainties involved in both experiment and calculations.

• Korean Journal of Microbiology
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• v.42 no.1
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• pp.62-66
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• 2006

To study the packaging mechanism of the bacteriophage P2-P4 system which is a useful experimental tool for the study of viral capsid assembly, we analyzed the DNA contents of P4 sid- mutant, P4 ash8 sid71's phage particles. Two kind of particles having different density were separated by the CsCl buoyant equilibrium density gradient experiment with fresh made stock of P4 ash8 sid71. The DNA from each particles was prepared and its conformations was analyzed by electrophoresis. Unexpectedly, both particles contain not only dimeric and trimeric but also monomeric P4 DNA.

• Journal of the Korean Chemical Society
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• v.25 no.4
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• pp.207-213
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• 1981

Conformations of thioacetamide (TAA) and its protonated form were determined using the CNDO/2 method, and the intermolecular interaction energies between the protonated TAA and water were calculated. It was found that: (1) protonation occurs preferentially on the N rather than on the S atom, (2) the stabilization energy of intermolecular perturbation between the protonated TAA and water was also large for the N-protonated TAA. This causes preferential CS bond cleavage due to large antibonding nature of the CS bond in the LUMO, and leads to an orbital controlled reaction.