• 한국전기전자재료학회:학술대회논문집
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• 한국전기전자재료학회 2006년도 추계학술대회 논문집 광주전남지부
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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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• 제30권9호
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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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• 제29권2호
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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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• 제42권4호
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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.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2016년도 제50회 동계 정기학술대회 초록집
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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.

• 한국발생생물학회지:발생과생식
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• 제2권2호
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• pp.149-155
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• 1998

폴리시알린산 (polysialic acid)은 미생물로부터 인간에 이르기까지 다양한 세포의 세포 표면 복합당사슬에 공유 결합하는 당사슬의 일종이다. 최근 성게 난자의 젤리층과 성게 난자의 표면에서 폴리시알린산이 연결된 당단백질이 발견됨으로써 폴리시알린산의 생합성과 그 기능에 대한 의문이 제기되었다. 둥근성게의 난자와 배에서 추출한 효소액과 CMP-[$^{14}$ C]Neu5Ac를 기질로 사용하여 Neu5Ac를 endogenous acceptor에 전달하는 CMP-Neu5Ac:poly-$\alpha$2, 8 sialosyl sialyltransferase (polyST)를 발견하였다. polyST는 20mM MOPS (pH 7.0), 2$0^{\circ}C$에서 최적 활성을 나타냈다. 10 mM $Mg^2$$^{+}$를 효소 반응액에 첨가하면 polyST의 황성은 2.7배 증가하였다. poiyST는 또한 포유류의 gang1ioside인 GD3에 폴리시알린산을 합성할 수 있었다. 이와 같은 폴리시알린산이 존재하는 ganglioside가 현재까지 자연계에서 알려진 바가 없다는 사실은 하나의 polyST가 endogenous acceptor와 ganglioside에 폴리시알린산을 합성했다고 결론지을 수 있다. 과량의 GD3를 exogenous acceptor로 사용하여 둥근성게에 존재하는 polyST의 활성을 조사한 결과 mesenchyme 포배기 때부터 그 활성이 급격히 증가하고 낭배기 때에 최고에 도달했다. 성게의 배발생 때에 polyST의 활성이 조절된다는 것은 낭배기 때에 일어나는 세포나 조직 사이에 일어나는 변화와 초기 단계 spicule 형성에 어떤 중요한 기능을 담당하고 있을 가능성이 있다.

• 생명과학회지
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• 제14권5호
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• pp.752-760
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• 2004

Nitrogenase 촉매에서 Fe-단백질을 포함하는 [4Fe-4S] 클라스터의 기능은 기질의 결합과 환원 자리를 포함하는 MoFe-단백질로 핵산 의존 전자 주개로 작용하는 것이다. 이러한 방법의 Fe-단백질의 기능은 Mofe-단백질과 상호작용을 위해 적합한 구조를 갖추며 전자 전달을 위한 추진력을 제공하기 위해 산화 환원 퍼텐셜을 변화시키는 능력에 의존한다. Nitrogenase Fe-단백질에 MgADP가 결합한 (혹은 떨어진) 구조적 정보는 핵산 결합 자리로부터 MoFe-단백질과의 결합력을 조절하기 위한 장거리 상호작용 메커니즘을 제시한다. 스위치 I과 II의 두 가지 경로가 뉴클레오티드의 신호전달 메커니즘을 담당한다. MgADP가 결합된 Fe-단백질의 구조는 Fe 단백질이 핵산과 결합할 때 관찰되는 [4Fe-4S] 클라스터의 생물리학적 특성 변화의 기초를 제공한다. 스위치, I과 II의 핵산 의존 신호전달 경로에서 특정 아미노산이 치환된 nitrogenase Fe-단백질의 구조들이 X-선 회절법에 의해서 결정되었다. 이들 경로는 아미노산 치환 연구, 구조 분석, 유사한 핵산 의존 신호전달 경로에 이용된 다른 단백질 등에 의해서도 분석되었다. 이들 경로가 거대분자 착물 형성과 분자간 전자 전달을 위한 MgADP 결합과 가수분해의 신호전달 경로로의 타당성이 조사되었다. 이러한 결과는 nitrogenase Fe 단백질과 MoFe-단백질 착물에서 Fe-단백질의 변이와 상호작용의 생물리학적 및 생화학적 특성을 위한 기초적 자료를 제공할 것이다.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2011년도 제40회 동계학술대회 초록집
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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.

• 한국재료학회지
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• 제6권7호
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• pp.733-741
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• 1996

본 연구에서는 MeV Si 자기 이온주업을 실시하여 주업원자와 모재 원자와의 화학적 영향이 배제된 결함 형성 거동을 관찰하였다. 자기 이온주업을 위하여 Tandem Accelerator가 사용되었고 1~3 MeV의 에너지 범위의 이온주입이 실시되었다. MeV 이온주입된 시편의 격자결함은 표면으로부터 고립된 $R_p$ 근처에 집중된 것이 관찰되었다. 주입에너지 변화에 따른 격자결함 생성 거동을 관찰하기 위하여 조사량을 $1{\times}10^{15}/cm^2$으로 고정하고 주입에너지를 1~3 MeV로 증가하였다. RBS 분석 결과 격자결함의 형성층 깊이는 에너지 증가에 따라 증가하였고 표면층에는 에너지 증가시 더욱 좋은 결정성을 유지하였다. 또한 주입에너지가 일정한 경우 조사량 증가시 $R_p$ 부근에 집중된 결함층의 농도는 증가하였으나 표면부근의 결함농도는 임계조사량 이상에서 포화되는 것이 관찰되었다. XTEM 분석 결과는 RBS의 결과와 잘 일치하였다. XTEM 관찰 결과 이온주업 상태의 결함층은 dark band의 형태로 관찰되었고 열처리시 이차결함은 이곳으로부터 생성되었다. 2MeV $Si^+$ 자기 이온주입시 이차결함이 형성되는 임계조사량은 $3{\times}10^{14}{\sim}5{\times}10^{14}/cm^2$ 사이로 관찰되었다. 열처리시 dark band의 하단부의 위치는 변화하지 않고 상단부만이 제거되었다. 실험을 통하여 얻은 결과들은 Monte-Carlo technique을 이용한 TRIM-code를 사용하여 해석하였다. SIMS 분석을 통하여 이차결함은 모재내에 존재하는 oxygen 불순물을 gettering함을 관찰하였다.

• 한국결정학회:학술대회논문집
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• 한국결정학회 2003년도 춘계학술연구발표회
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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.