• Proceedings of the Korea Crystallographic Association Conference
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• 2003.05a
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• pp.17-17
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• 2003

tRNA (m¹ G37) methyltransferase (TrmD) catalyze s the trans for of a methyl group from S-adenosyl-L-methionine (AdoMet) to G/sup 37/ within a subset of bacterial tRNA species, which have a residue G at 36th position. The modified guanosine is adjacent to and 3' of the anticodon and is essential for the maintenance of the correct reading frame during translation. We have determined the first crystal structure of TrmD from Haemophilus influenzae, as a binary complex with either AdoMet or S-adenosyl-L-homocysteine (AdoHcy), as a ternary complex with AdoHcy/phosphate, and as an apo form. The structure indicates that TrmD functions as a dimer (Figure 1). It also suggests the binding mode of G/sup 36/G/sup 37/ in the active site of TrmD and catalytic mechanism. The N-terminal domain has a trefoil knot, in which AdoMet or AdoHcy is bound in a novel, bent conformation. The C-terminal domain shows a structural similarity to DNA binding domain of trp or tot repressor. We propose a plausible model for the TrmD₂-tRNA₂ complex, which provides insights into recognition of the general tRNA structure by TrmD (Figure 2).

• YAKHAK HOEJI
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• v.53 no.4
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• pp.228-234
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• 2009

Topoisomerase I (Topo I) participates in the DNA replication, transcription, and repair. Binding of Topo I inhibitor to the Topo I-DNA cleavage complex forms stabilized ternary complex which blocks DNA religation and ultimately causes cell death. Camptothecin (CPT) and its derivatives have been among the most effective anticancer drugs by inhibition of topo I. However, efforts to synthesize non-CPT drugs have been actively going on because the CPT derivatives have several limitations such as poor solubility, short half-life, and side effects. As an indenoisoquinoline, NSC314622 is not as potent as CPT, but its chemical stability and slower reversibility of the cleavage complex made it a good lead compound. Recently, a series of indenoisoquinoline analogues were synthesized with substituted dimethoxy or methylenedioxy on the aromatic ring and alkylamino on the lactam nitrogen. Some of them showed quite good Topo I inhibitory activity. Using the computer docking program, Surflex-Dock, indenoisoquinoline analogues were docked into the human Topo I-DNA cleavable complex. The docking results showed that the compounds with activity better than NSC314622 intercalated between the -1 and +1 base pairs at the cleavage site, but those with little or no activities did not appear to intercalate. These results could be useful to design new Topo I inhibitors improved than CPT.

• 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.

• BMB Reports
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• v.50 no.2
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• pp.55-57
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• 2017

Toll-like receptor 4 (TLR4) together with MD2, one of the key pattern recognition receptors for a pathogen-associated molecular pattern, activates innate immunity by recognizing lipopolysaccharide (LPS) of Gram-negative bacteria. Although LBP and CD14 catalyze LPS transfer to the TLR4/MD2 complex, the detail mechanisms underlying this dynamic LPS transfer remain elusive. Using negative-stain electron microscopy, we visualized the dynamic intermediate complexes during LPS transfer-LBP/LPS micelles and ternary CD14/LBP/LPS micelle complexes. We also reconstituted the entire cascade of LPS transfer to TLR4/MD2 in a total internal reflection fluorescence (TIRF) microscope for a single molecule fluorescence analysis. These analyses reveal longitudinal LBP binding to the surface of LPS micelles and multi-round binding/unbinding of CD14 to single LBP/LPS micelles via key charged residues on LBP and CD14. Finally, we reveal that a single LPS molecule bound to CD14 is transferred to TLR4/MD2 in a TLR4-dependent manner. These discoveries, which clarify the molecular mechanism of dynamic LPS transfer to TLR4/MD2 via LBP and CD14, provide novel insights into the initiation of innate immune responses.

• Journal of the Korean Ceramic Society
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• v.53 no.2
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• pp.178-183
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• 2016

Ferroelectric relaxor ceramics with $BaTiO_3-NaNbO_3-Bi(Mg_{1/2}Ti_{1/2})O_3$ ternary compositions (BT-NN-BMT) have been prepared by sol-gel powder synthesis and consequent bulk ceramic processing. Through the modified chemical approach, fine and single-phase complex perovskite compositions were successfully obtained. Temperature and frequency dependent dielectric properties indicated typical relaxor characteristics of the BT-NN-BMT compositions. The ferroelectric-paraelectric phase transition became diffusive when NN and BMT were added to form BT based solid solutions. BMT additions to the BT-NN solid solutions affected the high temperature dielectric properties, which might be attributable to the compositional inhomogeneity of the complex perovskite and resulting weak dielectric coupling of the Bi-containing polar nanoregions (PNRs). The temperature stability of the dielectric properties was good enough to satisfy the X9R specification. The quasi-linear P-E response and the temperature- stable dielectric properties imply the high potential of this ceramic compound for use in high temperature capacitors.

• Analytical Science and Technology
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• v.10 no.6
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• pp.433-438
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• 1997

The enhancing effect of n-octanol on the fluorescence intensity of the $Eu^{3+}$-thenoyltrifluoroacetone(TTA) system in the presence of Triton X-100 was studied using spectrofluorometric method. This complex exhibited very intense $Eu^{3+}$ ion fluorescence at 619nm, when optically excited at 345nm. Optimum conditions for the determination of n-octanol have also been investigated. The calibration graph was linear over the range $1{\times}10^{-5}M{\sim}1{\times}10^{-7}M$ and the detection limit for n-octanol is $1{\times}10^{-9}M$. The result obtained in the analysis of the synthetic sample agreed with the known value in the error range and the relative standard deviation was ca. 3.5%.

• Journal of the Korean Chemical Society
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• v.34 no.1
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• pp.76-84
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• 1990

Optical isomers of dansyl amino acids were separated by a chiral mobile phase addition method. Two metha and para isomers of xylenyl-L-proline were prepared and used as the ligands of copper(Ⅱ) chelate to resolve the dansyl amino acids. Their elution behaviors were similar to those obtained from the addition of copper (Ⅱ) benzyl-L-proline chelate. The matrix effect of the mobile phase such as pH, concentration of buffer and compositions of organic solvent acetonitrile affected the optical resolution. The separation mechanism could be explained by a cis-trans effect of the ligand exchange reaction and hydrophobic interaction between the ternary complex and the stationary phase.

• Proceedings of the Korean Magnetic Resonance Society Conference
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• 2002.08a
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• pp.90-90
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• 2002

Syndecans, transmembrane heparan sulfate proteoglycans, are coreceptors with integrin in cell adhesion process. It forms a ternary signaling complex with protein kinase C and phosphatidylinositol 4,5 bisphosphate (PIP2) for integrin signaling. NMR data indicates that cytoplasmic domain of syndecan-4 (4L) undergoes a conformational transition in the presence of PIP2, forming oligomeric conformation. The structure based on NMR data demonstrated that syndecan-4L itself forms a compact intertwined symmetric dimer with an unusual clamp shape for residues Leu$^{186}$ -Ala$^{195}$ . The molecular surface of the syndecan-4L dimer is highly positively charged. In addition, no inter-subunit NOEs in membrane proximal amino acid resides (Cl region) has been observed, demonstrating that the Cl region is mostly unstructured in syndecan-4L dimmer. However, the complex structure in the presence of PIP2 induced a high order multimeric conformation in solution. In addition, phosphorylation of cytoplasmic domain induces conformational change of syndecan-4, resulting inhibition of PKC signaling. The NMR structural data strongly suggest that PIP2 promotes oligomerization of syndecan-4 cytoplasmic domain for PKC activation and further induces structural reorganization of syndecan for mediating signaling network in cell adhesion procedure.

• Bulletin of the Korean Chemical Society
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• v.10 no.1
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• pp.50-57
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• 1989

A pressure effect of the dehydrogenation of ethylalcohol catalyzed by alcoholdehydrogenase was observed in Tris-HCl buffer, pH 8.8 from $25^{\circ}C$ to $35^{\circ}C$ under high pressure system by using our new theory. The theory makes it possible for us to obtain all rate and equilibrium constants for each step of all enzymatic reaction with a single intermediate. We had enthalpy and volume profiles of the dehydrogenation to suggest a detail and reasonable mechanism of the reaction. In these profiles, both enthalpy and entropy of the reaction are positive and their values decrease with enhancing pressure. It means that the first step is endothermic reaction, and its strength decrease with elevating pressure. At the same time, all activation entropies have large negative values, which prove that not only a ternary complex has a more ordered structure at transition state, but also water molecules make a iceberg close by the activated complex. In addition to this fact, the first and second step equilibrium states are controlled by enthalpy. The first step kinetic state is controlled by enthalpy but the second step kinetic state is controlled by entropy.

• Journal of the Korean institute of surface engineering
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• v.55 no.6
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• pp.342-352
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• 2022

Purine catabolite screening enables reliable diagnosis of certain diseases. In this regard, the development of a facile detection strategy with high sensitivity and selectivity is demanded for point-of-care applications. In this work, the simultaneous detection of uric acid (UA), xanthine (XA), and hypoxanthine (HX) was carried out as model purine catabolites by surface-enhanced Raman Spectroscopy (SERS). The detection assay was conducted by employing high-aspect ratio Au nanopillar substrates coupled with in-situ Au electrodeposition on the substrates. The additional modification of the Au nanopillar substrates via electrodeposition was found to be an effective method to encapsulate molecules in solution into nanogaps of growing Au films that increase metal-molecule contact and improve substrate's sensitivity and selectivity. In complex solutions, the approach facilitated ternary identification of UA, XA, and HX down to concentration limits of 4.33 𝜇M, 0.71 𝜇M, and 0.22 𝜇M, respectively, which are comparable to their existing levels in normal human physiology. These results demonstrate that the proposed platform is reliable for practical point-of-care analysis of biofluids where solution matrix effects greatly reduce selectivity and sensitivity for rapid on-site disease diagnosis.