• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.250-261
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• 2004

A novel method for ab initio prediction of protein tertiary structures, PROFESY (PROFile Enumerating SYstem), is introduced. This method utilizes secondary structure prediction information and fragment assembly. The secondary structure prediction of proteins is performed with the PREDICT method which uses PSI-BLAST to generate profiles and a distance measure in the pattern space. In order to predict the tertiary structure of a protein sequence, we assemble fragments in the fragment library constructed as a byproduct of PREDICT. The tertiary structure is obtained by minimizing the potential energy using the conformational space annealing method which enables one to sample diverse low lying minima of the energy function. We apply PROFESY for prediction of some proteins with known structures, which shows good performances. We also participated in CASP5 and applied PROFESY to new fold targets for blind predictions. The results were quite promising, despite the fact that PROFESY was in its early stage of development. In particular, the PROFESY result is the best for the hardest target T0161.

• Bulletin of the Korean Chemical Society
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• v.26 no.2
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• pp.233-237
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• 2005

Cyclopentadiene compounds, 2-[CR'R(OMe)]-1,3-Me$_2C_5H_3$ (R, R' = 2,2'-biphenyl, 2) and 2-[CR'R(OSiMe$_3$)]-1,3-Me$_2C_5H_3$ (R, R' = 2,2'-biphenyl, 3; R = ph, R' = ph, 4; R = 2-naphthyl, R' = H, 5) are readily synthesized from 2-bromo-3-methoxy-1,3-dimethylcyclopentene (1). Reaction of the cyclopentadienes with Ti(NMe$_2$)$_4$ in toluene results in clean formation of the cyclopentadienyl tris(dimethylamido)titanium complexes, which are transformed to the trichloride complexes, 2-[CR'R(OMe)]-1,3-Me$_2C_5H_2$}TiCl$_3$ (R, R' = 2,2'-biphenyl, 6) and {2-[CR'R(OSiMe$_3$)]-1,3-Me$_2C_5H_2$}TiCl$_3$ (R, R' = 2,2'-biphenyl, 7; R = ph, R' = ph, 8; R = 2-naphthyl, R' = H, 9). Attempts to form C1-bridged Cp/oxido complexes by elimination of MeCl or Me$_3$SiCl were not successful. X-ray structures of 6, 7 and an intermediate complex {2-[Ph$_2$C(OSiMe$_3$)]-1,3-Me$_2C_5H_2$}TiCl$_2$(NMe$_2$) (10) were determined.

• BMB Reports
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• v.39 no.6
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• pp.774-781
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• 2006

Human nucleolar phosphoprotein p140 (hNopp140) is a nucleolar phosphoprotein that can bind to doxorubicin, an anti-cancer agent. We have examined the interaction between hNopp140 and doxorubicin as well as the folding property of hNopp140. Also, the effects of ATP and phosphorylation on the affinity of hNopp140 to doxorubicin are investigated by affinity dependent co-precipitation and surface plasmon resonance methods. Doxorubicin preferentially binds to un-phosphorylated form of hNopp140 with a $K_D$ value of $3.3\;{\times}\;10^{-7}$ M. Furthermore, doxorubicin reduces the protein kinase CK2-dependent phosphorylation of hNopp140, indicating that doxorubicin may perturb the cellular function of hNopp140 by reducing the protein kinase CK2-dependent phosphorylation of hNopp140. Low contents of the secondary structures of hNopp140 and the fast rate of proteolysis imply that hNopp140 has a high percentage of flexible regions or extended loop structures.

• Proceedings of the Korean Vacuum Society Conference
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• 2014.02a
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• pp.103.1-103.1
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• 2014

Due to their excellent optical and electrochemical properties, conjugated polymers have attracted much attention over the last two decades and employed to opto-electrical devices. In particular, conjugated polymers possess many attractive features that make them suitable for a variety of sensing task. For example, their delocalized electronic structures can be strongly modified by varying the surrounding environment, which significantly affected molecular energy level. In other word, conjugated polymers can detect and transduce the environmental information into a fluorescence signal. Conjugated polymers also display amplified quenching compared to small molecule counterparts. This amplified fluorescence quenching is attributed to the delocalization and migration of the excitons along the conjugated polymer backbones. Long backbones of conjugated polymer provide the transporting path for electron as a conduit, allowing that excitons migrate rapidly into quencher site along the backbone. This is often referred to as the molecular wire effect or antenna effect. Moreover, structures of conjugated polymers can be easily tailored to adjust solubility, absorption/emission properties, and regulation of electron/energy transfer. Based on this versatility, conjugated polymers have been utilized to many novel sensory platforms as a promising material. In this tutorial, I will highlight a variety of fluorescence sensors base on conjugated polymer and explain their sensory mechanism together with selected examples from reference literatures.

• Journal of Periodontal and Implant Science
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• v.28 no.2
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• pp.281-291
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• 1998

Chitosan is a biodegradable and non-toxic material with a molecular weight of 800-1,500Kd which can be obtained in various forms with extraordinary chemical structures and biological characteristics of which enables it to be used in many fields as a biomaterial. Ion irradiation is a useful tool to modify chemical structures and physical properties of high molecular weight polymers. The basic hypothesis of this study is that when surface properties of chitosan in a sponge form are modified with ion beam-irradiation and cell adhesion properties of chitosan would improve and thereby increase the regenerative ability of the damaged bone. The purpose of this study was to illuminate the changes in the cytocompatibility of chitosan sponges after ion beam-irradiation as a preliminary research. Argon($Ar^+$) ions were irradiated at doses of $5{\times}10^{13}$, $5{\times}10^{15}$ at 35 keV on surfaces of each sponges. Cell adhesion and activity of alkaline phosphatases were studied using rat fetal osteoblasts. The results of this study show hat ion beam-irradiation at optimal doses($5{\times}10^^{13}\;Ar^+\;ion/cm^2$) is a useful method to improve cytocompatibility without sacrificing cell viability and any changing cell phenotypes. These results show that ion beam-irradiated chitosan sponges can be further applied as carriers in tissue engineering and as bone filling materials.

• Journal of Microbiology and Biotechnology
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• v.7 no.2
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• pp.132-137
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• 1997

A novel protein (HEAAE, High Essential Amino Acid Encoding Protein), rich in essential amino acids ($75{\%}$ of total), was designed and constructed in our laboratory. The designed peptides were analyzed by SYBLE and stable secondary and tertiary structures were predicted. The monomeric form (HEAAE-1) of the protein consists of 20 amino acid residues with four additional amino acids comprising a potential ${\beta}$-turn (HEAAE-4). Size exclusion analysis demonstrated that the monomer is self-aggregates in aqueous solution to form higher ordered multimeric structures, which are very reminiscent of natural plant storage proteins. The DNA encoding this amino acid sequence was synthesized, and from this monomeric gene fragment (heaae-1), the stable tetrameric form of the gene (heaae-4) was generated by subcloning into the E. coli expression vector pKK223-3. A clear 6 kDa polypeptide band corresponding to the molecular weight of the dimeric form (HEAAE-2) was detected. The smeared band which appeared around the molecular weight corresponding to HEAAE-4 of 11 kDa suggested that the tetramer form of this protein might be processed into smaller size products.

• Proceedings of the Korean Vacuum Society Conference
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• 2010.02a
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• pp.340-340
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• 2010

Various structures of vacancy defects in graphene layers and carbon nanotubes have been reported by high resolution transmission electron microscope (HR-TEM) and those arouse an interest of reconstruction processes of vacancy defects. In this talk, we present reconstruction processes of vacancy defects in a graphene and a carbon nanotube by tight-binding molecular dynamics (TBMD) simulations and by first principles total energy calculations. We found that a structure of a dislocation defect with two pentagon-heptagon (5-7) pairs in graphene becomes more stable than other structures when the number of vacancy units is ten and over. The simulation study of scanning tunneling microscopy reveals that the pentagon-heptagon pair defects perturb the wavefunction of electrons near Fermi level to produce the $\sqrt{3}\;{\times}\;\sqrt{3}$ superlattice pattern, which is in excellent agreement with experiment. It is also observed in our tight-binding molecular dynamics simulation that 5-7 pair defects play a very important role in vacancy reconstruction in a graphene layer and carbon nanotubes.

• Bulletin of the Korean Chemical Society
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• v.20 no.3
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• pp.285-290
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• 1999

In the present paper, we report a molecular dynamics (MD) simulation study for the structure and dynamics of H+ ions in non-rigid dehydrated H12-A zeolite framework at 298.15 K, using the same method we used in our previous studies of rigid and non-rigid zeolite-A frameworks. It is found that two different structures appear, depending on the choice of the Lennard-Jones parameter (σ) for the H+ ion, as is also observed in the study of rigid dehydrated H12-A zeolite framework, but the ranges of σ are different for the two structures. It is also found that some of the H+ ions exchanged their sites without changing the number of H+ ions at each site. The agreement between experimental and calculated structural parameters for non-rigid dehydrated H12-A zeolite is generally quite good. The calculated IR spectrum by Fourier transform of the total dipole moment auto-correlation function shows two major peaks, one around 2700 cm-1 and the other around 7000 cm-1. The former appears in the calculated IR spectra of non-rigid zeolite-A framework only system and the latter remains unexplained except, perhaps, as an indication of a new formation of a vibrational mode of the framework due to the adsorption of the H+ ions.

• Korean Journal of Mineralogy and Petrology
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• v.33 no.3
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• pp.143-152
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• 2020

Birnessite is a layered manganese oxide mineral with ~7 Å of d-spacing. Because of its high cation exchange capacity, birnessite greatly impacts the chemical compositions of ground water and fluids in sediment pores. Understanding the cation exchange mechanisms requires atomistic investigations of the crystal structures and coordination environments of hydrated cations in the interlayer. In this study, we conducted classical molecular dynamics (MD) simulations, an atomistic simulation method of computational mineralogy, for triclinic Na-birnessite and K-birnessite whose chemical formula are from previous experiments. We report our MD simulation results of the crystal structures, coordination environments of Na⁺ and K⁺, and the polytypes of birnessite and compare them with available experimental results. The simulation results well reproduced experimental lattice parameters and provided atomic level information for the interlayer cation and water molecule sites that are difficult to distinguish in X-ray experiments. We also report that the polytype of the Mn octahedral sheets is identical between Na- and K-birnessite, but the cation positions differ from each other, demonstrating a correlation between the coordination environment of the interlayer cations and the crystal lattice parameters. This study shows that MD simulations are very promising in elucidating ion exchange reactions of birnessite.

• Proceedings of the Korean Vacuum Society Conference
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• 2015.08a
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• pp.63.2-63.2
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• 2015

Controlling and sensing spin states of magnetic molecules such as metallo-porphyrins at the single molecule level is essential for spintronic molecular device applications. Axial coordinations of diatomic molecules to metallo-porphyrins also play key roles in dynamic processes of biological functions such as blood pressure control and immune response. However, probing such reactions at the single molecule level to understand their physical mechanisms has been rarely performed. Here we present on our single molecule association and dissociation experiments between diatomic and metallo-porphyrin molecules on Au(111) describing its adsorption structures, spin states, and dissociation mechanisms. We observed bright ring shapes in NO adsorbed metallo-porphyrin compelxes and explained them by considering tilted binding and precession motion of NO. Before NO exposure, Co-porphryin showed a clear zero-bias peak in scanning tunneling spectroscopy, a signature of Kondo effect in STS, whereas after NO exposures it formed a molecular complex, NO-Co-porphyrin, that did not show any zero-bias feature implying that the Kondo effect was switched off by binding of NO. Under tunneling junctions of scanning tunneling microscope, both positive and negative energy pulses. From the observed power law relations between dissociation rate and tunneling current, we argue that the dissociations were inelastically induced with molecular orbital resonances. Our study shows that single molecule association and dissociation can be used to probe spin states and reaction mechanisms in a variety of axial coordination between small molecules and metallo-porphyrins.