• Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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• 2006.12a
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• pp.96-100
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• 2006

A pulsed laser ablation deposition (PLAD) technique is an excellent method for the fabrication of amorphous carbon (a-C) films. This paper was focused on the understanding and analysis of the motion of carbon atom (C) and carbon ion ($C^+$) particles in laser ablation assisted by Ar plasmas. The simulation has carried out under the pressure P=10~100 mTorr of Ar plasmas. Two-dimensional hybrid model consisting of fluid and Monte-Carlo models was developed and three kinds of the ablated particles which are C, $C^+$ and electron were considered in the calculation of particle method. The motions of energetic $C^+$ and C deposited upon the substrate were investigated and compared.

• Journal of Microbiology and Biotechnology
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• v.30 no.9
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• pp.1436-1442
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• 2020

Amylosucrase (ASase, E.C. 2.4.1.4) is capable of efficient glucose transfer from sucrose, acting as the sole donor molecule, to various functional acceptor compounds, such as polyphenols and flavonoids. An ASase variant from Deinococcus geothermalis, in which the 226^th alanine is replaced with asparagine (DgAS-A226N), shows increased polymerization activity due to changes in the flexibility of the loop near the active site. In this study, we further investigated how the mutation modulates the enzymatic activity of DgAS using molecular dynamics and docking simulations to evaluate interactions between the enzyme and phenolic compounds. The computational analysis revealed that the A226N mutation could induce and stabilize structural changes near the substrate-binding site to increase glucose transfer efficiency to phenolic compounds. Kinetic parameters of DgAS-A226N and WT DgAS were determined with sucrose and 4-methylumbelliferone (MU) as donor and acceptor molecules, respectively. The k_cat/K_m value of DgAS-A226N with MU (6.352 mM^-1min^-1) was significantly higher than that of DgAS (5.296 mM^-1min^-1). The enzymatic activity was tested with a small phenolic compound, hydroquinone, and there was a 1.4-fold increase in α-arbutin production. From the results of the study, it was concluded that DgAS-A226N has improved acceptor specificity toward small phenolic compounds by way of stabilizing the active conformation of these compounds.

• Journal of Microbiology and Biotechnology
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• v.29 no.2
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• pp.244-255
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• 2019

Xylose isomerase (XI; E.C. 5.3.1.5) catalyzes the isomerization of xylose to xylulose, which can be used to produce bioethanol through fermentation. Therefore, XI has recently gained attention as a key catalyst in the bioenergy industry. Here, we identified, purified, and characterized a XI (PbXI) from the psychrophilic soil microorganism, Paenibacillus sp. R4. Surprisingly, activity assay results showed that PbXI is not a cold-active enzyme, but displays optimal activity at $60^{\circ}C$. We solved the crystal structure of PbXI at $1.94-{\AA}$ resolution to investigate the origin of its thermostability. The PbXI structure shows a $({\beta}/{\alpha})_8$-barrel fold with tight tetrameric interactions and it has three divalent metal ions (CaI, CaII, and CaIII). Two metal ions (CaI and CaII) located in the active site are known to be involved in the enzymatic reaction. The third metal ion (CaIII), located near the ${\beta}4-{\alpha}6$ loop region, was newly identified and is thought to be important for the stability of PbXI. Compared with previously determined thermostable and mesophilic XI structures, the ${\beta}1-{\alpha}2$ loop structures near the substrate binding pocket of PbXI were remarkably different. Site-directed mutagenesis studies suggested that the flexible ${\beta}1-{\alpha}2$ loop region is essential for PbXI activity. Our findings provide valuable insights that can be applied in protein engineering to generate low-temperature purpose-specific XI enzymes.

• Journal of Ecology and Environment
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• v.42 no.4
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• pp.198-204
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• 2018

Background: The effective use of habitats is essential for the successful adaptation of a species to the local environment. Although habitats exhibit a hierarchical structure, including macro-, meso-, and microhabitats, the relationships among habitats of differing hierarchy have not been well studied. In this study, we studied the quantitative measures of microhabitat use of Gekko japonicus from three field populations in Japan: one at Tsushima Island, one at Nishi Park, Fukuoka, and one at Ohori Park, Fukuoka. We investigated whether land cover type, a higher hierarchical habitat component, was associated with quantitative microhabitat use, a lower hierarchical component, in these populations. Results: The substrate temperature where we located geckos (SubT) and the distance from the ground to the gecko (Height) were significantly different among the three populations. In particular, SubT on Tsushima Island was lower than it was in the other two populations. Irradiance at gecko location and Height were significantly different among the land cover types. In particular, Height in evergreen needleleaf forest was significantly lower than that in deciduous broadleaf forest. Furthermore, significant interactions between population and land cover type were observed for the SubT and Height variables. Conclusions: The quantitative measures of microhabitat use of G. japonicus varied with population and land cover type, which exhibited significant interaction effects on microhabitat use variables. These results suggest that higher hierarchical habitat components can affect the quantitative measures of lower hierarchical microhabitat use in nocturnal geckos.

• Proceedings of the Korean Vacuum Society Conference
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• 2016.02a
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• pp.77-77
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• 2016

Thin films synthesized by plasma processes have been widely applied in a variety of industrial sectors. The structure control of thin film is one of prime factor in most of these applications. It is well known that the structure of this film is closely associated with plasma parameters and species of plasma which are electrons, ions, radical and neutrals in plasma processes. However the precise control of structure by plasma process is still limited due to inherent complexity, reproducibility and control problems in practical implementation of plasma processing. Therefore the study on the fundamental physical properties that govern the plasmas becomes more crucial for molecular scale control of film structure and corresponding properties for new generation nano scale film materials development and application. The thin films are formed through nucleation and growth stages during thin film depostion. Such stages involve adsorption, surface diffusion, chemical binding and other atomic processes at surfaces. This requires identification, determination and quantification of the surface activity of the species in the plasma. Specifically, the ions and neutrals have kinetic energies ranging from ~ thermal up to tens of eV, which are generated by electron impact of the polyatomic precursor, gas phase reaction, and interactions with the substrate and reactor walls. The present work highlights these aspects for the controlled and low-temperature plasma enhanced chemical vapour disposition (PECVD) of Si-based films like crystalline Si (c-Si), Si-quantum dot, and sputtered crystalline C by the design and control of radicals, plasmas and the deposition energy. Additionally, there is growing demand on the low-temperature deposition process with low hydrogen content by PECVD. The deposition temperature can be reduced significantly by utilizing alternative plasma concepts to lower the reaction activation energy. Evolution in this area continues and has recently produced solutions by increasing the plasma excitation frequency from radio frequency to ultra high frequency (UHF) and in the range of microwave. In this sense, the necessity of dedicated experimental studies, diagnostics and computer modelling of process plasmas to quantify the effect of the unique chemistry and structure of the growing film by radical and plasma control is realized. Different low-temperature PECVD processes using RF, UHF, and RF/UHF hybrid plasmas along with magnetron sputtering plasmas are investigated using numerous diagnostics and film analysis tools. The broad outlook of this work also outlines some of the 'Grand Scientific Challenges' to which significant contributions from plasma nanoscience-related research can be foreseen.

• Development and Reproduction
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• v.2 no.2
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• pp.149-155
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• 1998

The polysialic acid (polySia) glycotope covalently modifies cell surface glycoconjugates on cells as evolutionarily diverse as microbes and human. The recent chemical identification of polysialylated glycoproteins in the jelly coat and on the cell surface of the sea urchin egg raises important questions about their biosynthesis and possible function. Using CMP-[$^{14}$ C]Neu5Ac as substrate and cell free preparations from eggs and embryos of the sea urchin Stronglylcentrotus nudus, we have identified a membrane associated CMP-Neu5Ac:poly-$\alpha$2, 8 sialosyl sialyltransferase (polyST) that transfers Neu5Ac to an endogenous acceptor. Optimal conditions for the polyST activity were found to be 2$0^{\circ}C$ in 20 mM MOPS buffer (pH 7.0). The polyST activity was increased 2.7 times by the addition of 10 mM $Mg^2$$^{+}$. The membrane-associated polyST also catalyzed the polysialylation of mammalian ganglioside GD3. Given that no structurally similar natural polysialylated gangliosides have been described, nor were observed in the present study, we conclude that a single polyST activity catalyzes sialylation of the endogenous acceptor and the gangliosides. Using an excess of GD3 as an exogenous acceptor, it was established that the expression of the polyST in S. nudus embryos increased rapidly at the mesenchyme blastula stage and reached at maximum at the gastrula stage. The finding that this polyST in the sea urchin embryo is developmentally regulated raises the possibility that it may play a role in the changing cell and tissue interactions that occur during gastrulation and the early stages of spicule formation.n.

• Journal of Life Science
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• v.14 no.5
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• pp.752-760
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• 2004

The function of the [4Fe-4S] cluster containing iron (Fe-) protein in nitrogenase catalysis is to serve as the nucleotide-dependent electron donor to the MoFe protein which contains the sites for substrate binding and reduction. The ability of the Fe protein to function in this manner is dependent on its ability to adopt the appropriate conformation for productive interaction with the MoFe protein and on its ability to change redox potentials to provide the driving force required for electron transfer. The MgADP-bound (or off) conformational state of the nitrogenase Fe protein structure described reveals mechanisms for long-range communication from the nucleotide-binding sites to control affinity of association with the MoFe protein component. Two pathways, termed switches I and II, appear to be integral to this nucleotide signal transduction mechanism. In addition, the structure of the MgADP bound Fe protein provides the basis for the changes in the biophysical properties of the [4Fe-4S] observed when Fe protein binds nucleotides. The structures of the nitrogenase Fe protein with defined amino acid substitutions in the nucleotide dependent signal transduction pathways of the Switch I and Switch II have been determined by X-ray diffraction methods. These two pathways have been also implicated by site directed mutagenesis studies, structural analysis and analogies to other proteins that utilize similar nucleotide dependent signal transduction pathways. We have examined the validity of the assignment of these pathways in linking the signals generated by MgATP binding and hydrolysis to macromolecular complex formation and intermolecular electron transfer. The results provide a structural basis for the observed biophysical and biochemical properties of the Fe protein variants and interactions within the nitrogenase Fe protein-MoFe protein complex.

• Proceedings of the Korean Vacuum Society Conference
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• 2011.02a
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• pp.27-27
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• 2011

For the design of real applicable molecular devices, current-voltage properties through molecular nanostructures such as metal-molecule-metal junctions (molecular junctions) have been studied extensively. In thiolate monolayers on the gold electrode, the chemical bonding of sulfur to gold and the van der Waals interactions between the alkyl chains of neighboring molecules are important factors in the formation of well-defined monolayers and in the control of the electron transport rate. Charge transport through the molecular junctions depends significantly on the energy levels of molecules relative to the Fermi levels of the contacts and the electronic structure of the molecule. It is important to understand the interfacial electron transport in accordance with the increased film thickness of alkyl chains that are known as an insulating layer, but are required for molecular device fabrication. Thiol-tethered RuII terpyridine complexes were synthesized for a voltage-driven molecular switch and used to understand the switch-on mechanism of the molecular switches of single metal complexes in the solid-state molecular junction in a vacuum. Electrochemical voltammetry and current-voltage (I-V) characteristics are measured to elucidate electron transport processes in the bistable conducting states of single molecular junctions of a molecular switch, Ru(II) terpyridine complexes. (1) On the basis of the Ru-centered electrochemical reaction data, the electron transport rate increases in the mixed self-assembled monolayer (SAM) of Ru(II) terpyridine complexes, indicating strong electronic coupling between the redox center and the substrate, along the molecules. (2) In a low-conducting state before switch-on, I-V characteristics are fitted to a direct tunneling model, and the estimated tunneling decay constant across the Ru(II) terpyridine complex is found to be smaller than that of alkanethiol. (3) The threshold voltages for the switch-on from low- to high-conducting states are identical, corresponding to the electron affinity of the molecules. (4) A high-conducting state after switch-on remains in the reverse voltage sweep, and a linear relationship of the current to the voltage is obtained. These results reveal electron transport paths via the redox centers of the Ru(II) terpyridine complexes, a molecular switch.

• Korean Journal of Materials Research
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• v.6 no.7
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• pp.733-741
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• 1996

In this study MeV Si self ion implantations were done to reveal the intrinsic behavior of defect formation by excluding the possibility of chemical interactions between substrate atoms and dopant ones. Self implantations were conducted using Tandem Accelerator with energy ranges from 1 to 3 MeV. Defect formation by high energy ion implantation has a significant characteristics in that the lattice damage is concentrated near Rp and isolated from the surface. In order to investigate the energy dependence on defect formation, implantation energies were varied from 1 to 3 MeV under a constant dose of $1{\times}10^{15}/cm^2$. RBS channe!ed spectra showed that the depth at which as-implanted damaged layer formed increases as energy increases and that near surface region maintains better crystallinity as energy increases. Cross sectional TEM results agree well with RBS ones. In a TEM image as-implanted damaged layer appears as a dark band, where secondary defects are formed upon annealing. In the case of 2 MeV $Si^+$ self implantation a critical dose for the secondary defect formation was found to be between $3{\times}10^{14}/cm^24$ and $5{\times}10^{14}/cm^2$. Upon annealing the upper layer of the dark band was removed while the bottom part of the dark band did not move. The observed defect behavior by TEM was interpreted by Monte Carlo computer simulations using TRIM-code. SIMS analyses indicated that the secondary defect formed after annealing gettered oxygen impurities existed in silicon.

• Proceedings of the Korea Crystallographic Association Conference
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• 2003.05a
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• pp.18-18
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• 2003

Thioredoxin (Trx) is a small redox protein that is ubiquitously distributed from achaes to human. In diverse organisms, the protein is involved in various physiological roles by acting as electron donor and regulators of transcription and apoptosis as well as antioxidants. Sequences of Trx within various species are 27～69% identical to that of E. coli and all Trx proteins have the same overall fold, which consists of central five β strands surrounded by four α helices. The N-terminal cysteine in WCGPC motif of Trx is redox sensitive and the motif is highly conserved. Compared with general cysteine, the N-terminal cysteine has low pKa value. The result leads to increased reduction activity of protein. Recently, novel thio.edoxin-related protein (TRP14) was found from rat brain. TRP14 acts as disulfide reductase like Trx1, and its redox potential and pKa are similar to those of Trx1. However, TRP14 takes up electrons from cytosolic thioredoxin reductase (TrxR1), not from the mitochondrial thioredoxin reductase (TrxR2). Biological roles of TES14 were reported to be involved in regulating TNF-α induced signaling pathways in different manner with Trx1. In depletion experiments, depletion of TRP14 increased TNF-α induced phosphorylation and degradation of IκBα more than the depletion Trx1 did. It also facilitated activation of JNK and p38 MAP kinase induced by TNF-α. Unlike Trx1, TRP14 shows neither interaction nor interference with ASK1. Here, we determined three-dimensional crystal structure of TRP14 by MAD method at 1.8Å. The structure reveals that the conserved cis-Pro (Pro90) and active site-W-C-X-X-C motif, which may be involved in substrate recognition similar to Trx1 , are located at the beginning position of strand β4 and helix α2, respectively. The TRP14 structure also shows that surface of TRP14 in the vicinity of the active site, which is surrounded by an extended flexible loop and an additional short a helix, is different from that of Trx1. In addition, the structure exhibits that TRP14 interact with a distinct target proteins compared with Trx1 and the binding may depend mainly on hydrophobic and charge interactions. Consequently, the structure supports biological data that the TRP14 is involved in regulating TNF-α induced signaling pathways in different manner with Trx1.