• Mass Spectrometry Letters
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• 제12권4호
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• pp.131-136
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• 2021

Collision-induced dissociation of peptides involves a series of proton-transfer reactions in the activated peptide. To describe the kinetics of energy-variable dissociation, we considered the heat capacity of the peptide and the Marcus-theory-type proton-transfer rate. The peptide ion was activated to the high internal energy states by collision with a target gas in the collision cell. The mobile proton in the activated peptide then migrated from the most stable site to the amide oxygen and subsequently to the amide nitrogen (N-protonated) of the peptide bond to be broken. The N-protonated intermediate proceeded to the product-like complex that dissociated to products. Previous studies have suggested that the proton-transfer equilibria in the activated peptide affect the dissociation kinetics. To take the extent of collisional activation into account, we assumed a soft-sphere collision model, where the relative collision energy was fully available to the internal excitation of a collision complex. In addition, we employed a Marcus-theory-type rate equation to account for the proton-transfer equilibria. Herein, we present results from the integrated thermochemical approach using a tryptic peptide of ubiquitin.

• Bulletin of the Korean Chemical Society
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• 제34권5호
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• pp.1401-1406
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• 2013

This study tested the feasibility of observing H/D exchange of intact protein by top-down electron capture dissociation (ECD) mass spectrometry for the investigation of protein structure. Ubiquitin is selected as a model system. Local structural information was obtained from the deuteration levels of c and $z^{\cdot}$ ions generated from ECD. Our results showed that ${\alpha}$-helix region has the lowest deuteration level and the C-terminal fraction containing a highly mobile tail has the highest deuteration level, which correlates well with previous X-Ray and HDX/NMR analyses. We studied site-specific H/D exchange kinetics by monitoring H/D exchange rate of several structural motives of ubiquitin. Two hydrogen bonded ${\beta}$-strands showed similar HDX rates. However, the outer ${\beta}$-strand always has higher deuteration level than the inner ${\beta}$-strand. The HDX rate of the turn structure (residues 8-11) is lower than that of ${\beta}$-strands (residues 1-7 and residues 12-17) it connects. Although isotopic distribution gets broader after H/D exchange which results in a limited number of backbone cleavage sites detected, our results demonstrate that this method can provide valuable detailed structural information of proteins. This approach should also be suitable for the structural investigation of other unknown proteins, protein conformational changes, as well as protein-protein interactions and dynamics.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2000년도 제18회 학술발표회 논문개요집
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• pp.147-147
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• 2000

Chemisorption of oxygen molecules on the Si(111)-(7x7) surface has been studied extensively as a model for the initial-stage oxidation of the surface. The basic step to the surface oxidation is the dissociation of the adsorbed O2 molecules, but the dissociation procedure and the atomic structure of the reaction products still remains as a subject of debates. We present here density-functional theory calculations on the initial-stage oxidation states of the Si adatom site for all possible dissociation configurations that can be generated by multiple O2 reactions. We determine the equilibrium structures and analyze their electronic and vibrational properties in comparison with measured UPS, XPS, and EELS spectra. The O(ad) atom bonded on top of the Si adatom is always less stable than the O(ins) atom inserted into one of the adatom backbonds. Our electronic and vibrational analysis demonstrates further that the O(ad) and O(ins) atoms account well for the metastable and stable features in previous experiments, respectively. Moreover, the calculated decay pathways of the metastable structures and the comparison of the calculated O ls core-level shifts with XPS data provides a convincing argument in unambiguously identifying the experimental metastable and stable structures, thereby making it possible to build a correct atomic-scale picture of the initial-stage oxidation process on this surface.

• BMB Reports
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• 제30권3호
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• pp.211-215
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• 1997

A photoactive analog of ATP, 3'(2')-O-(p-azidobenzoyl)-adenosine 5-triphosphate (AB-ATP) was synthesized by chemically coupling N-hydroxysuccinimidyl-4-azidobenzoate (NHS-AB) and ATP. The utility of AB-ATP as an effective active-site-directed photoprobe was demonstrated using catalytic subunit of protein kinase A as a model enzyme. Photoincorporation of AB-ATP was saturated with apparent dissociation constant of $30{\mu}m$ and protected completely by $100{\mu}m$ of ATP. When the enzyme was covalently modified by photolysis in the presence of saturating amounts of photoprobe, about 60% inhibition of enzyme activity was observed. These results demonstrate that AB-ATP has potential application as a probe to characterize ATP-binding proteins including protein kinases.

• 유체기계공업학회:학술대회논문집
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• 유체기계공업학회 2006년 제4회 한국유체공학학술대회 논문집
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• pp.497-500
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• 2006

An theoretical analysis on the electro-osmotic flow in a 2-dimensional slit, that is induced by an external electric field acting on the electrical double layers near the slit wall, was performed. Especially, although there were many studies on the interacting electrical double layers, it was found in this study that they have several physical or mathematical fallacies. To resolve these, the general solution on the charge-regulating slit with the height as a parameter was obtained. The results of this work can provide the electrokinetic solution of nanoscale slit with the electrical double layer interaction as well as that of microscale slit without the interaction and can be used as the benchmark of a numerical analysis and the reference of electrokinetic flow path design.

• 에너지공학
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• 제23권3호
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• pp.102-115
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• 2014

국내 동해 울릉분지에는 막대한 부존량과 청정 에너지원으로 높은 잠재력을 지닌 가스하이드레이트가 부존되어 있으며, 2010년 울릉분지 2차 시추지역(UBGH2)에서 현장 생산 시험 후보지 선정을 위한 목적으로 시추작업이 수행되었다. 이 연구에서는 동해 울릉분지 현장 생산 시험 후보지역의 지질학적 모델을 바탕으로 전산 수치 해석을 이용하여 가스하이드레이트 퇴적층 내 해리 유동 및 산출성을 분석하였으며, 주요 생산 조건별 감압 생산 거동에 대한 민감도 분석을 수행하였다. 이를 통해 가스하이드레이트 현장 생산 시험 계획 수립 시 요구되는 예비 분석 자료를 도출하였다.

• 한국재료학회지
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• 제4권1호
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• pp.9-23
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• 1994

Multitarget bias cosputter deposition(MBCD)에 의해 저온($200^{\circ}C$)에서 NaCI(100)상에 정합$CoSi_2$를 성장시켰다. X-선회절과 투과전자현미경에 의해 증착온도와 기판 bias전압에 따른 각각 silicide의 상전이와 결정성을 관찰하였다. Metal induced crystallization(MIC) 과 self bias 효과에 의해 $200^{\circ}C$에서 기판전압을 인가하지 않은 경우에도 결정질 Si이 성장하였다. MIC현상을 이론 및 실험적으로 고찰하였다. 관찰된 상전이는 $Co_2Si \to CoSi \to Cosi_2$로서 유효생성열법칙에 의해 예측된 상전이와 일치하였다. 기판 bias전압 인가시 발생한 이온충돌에 의한 충돌연쇄혼합(collisional cascade mixing), 성장박막 표면의 in situ cleaning, 핵생성처(nucleation site)이 증가로 인하여 상전이, CoSi(111)우선방위, 결정성은 증착온도에 비해 기판bias전압에 더 큰 영향을 받았다. $200^{\circ}C$에서 기판 bias전압을 증가시킴에 따라 이온충돌에 의한 결정입성장이 관찰되었으며, 이를 이온충독파괴(ion bombardment dissociation)모델에 의해 해석하였다. $200^{\circ}C$에서의 기판 bias전압증가에 따른 결정성변화를 정량적으로 고찰하기 위해 Langmuir탐침을 이용하여 $E_{Ar},\; \alpha(V_s)$를 계산하였다.

• Bulletin of the Korean Chemical Society
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• 제35권7호
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• pp.2013-2018
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• 2014

The adsorption and decomposition of trimethylene oxide ($C_3H_6O$) molecule on the Al(111) surface were investigated by the generalized gradient approximation (GGA) of density functional theory (DFT). The calculations employed a supercell ($6{\times}6{\times}3$) slab model and three-dimensional periodic boundary conditions. The strong attractive forces between $C_3H_6O$ molecule and Al atoms induce the C-O bond breaking of the ring $C_3H_6O$ molecule. Subsequently, the dissociated radical fragments of $C_3H_6O$ molecule oxidize the Al surface. The largest adsorption energy is about -260.0 kJ/mol in V3, V4 and P2, resulting a ring break at the C-O bond. We also investigated the decomposition mechanism of $C_3H_6O$ molecules on the Al(111) surface. The activation energies ($E_a$) for the dissociations V3, V4 and P2 are 133.3, 166.8 and 174.0 kJ/mol, respectively. The hcp site is the most reactive position for $C_3H_6O$ decomposing.

• 한국응용약물학회:학술대회논문집
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• 한국응용약물학회 1995년도 춘계학술대회
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• pp.87-87
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• 1995

The muscarinic effects of carbachol were compared on the isolated ileums of guinea-pig, rat and rabbit to elucidate the underlying mechanism of species differences in sensitivity for carbachol. The ED$\_$50/ value estimated on the guinea-pig ileum was 4 to 6-fold lower than those obtained on the rat and rabbit ileums, but the K$\_$A/ values of carbachol determined by functional assays were almost identical with 12-l7 ${\mu}$M in all of three ileums. The competition data of carbachol for [$^3$H]QNB binding were best described by a two-site model yielding the Ki values of 0.4-0.6${\mu}$M and 12-16${\mu}$M for high(K$\_$H/) and low(K$\_$L/) affinity sites, respectively. The low affinity dissociation constants(K$\_$L/) of carbachol determined from receptor binding studies thus were not significantly different from the K$\_$A/ values estimated from functional studies. The percentage of receptor occupation that carbachol requires for half-maximal response was approximately 3 to 5-fold lower in guinea-pig compared to rat and rabbit whereas the density of muscarinic binding sites per gram of ileum measured by [$^3$H]QNB saturation isotherms was two-fold higher in guinea-pig than that in rat and rabbit. Therefore, the numbers of muscarinic receptors occupied at ED$\_$50/ values of carbachol were about two-fold lower in guinea-pig, suggesting two-fold greater intrinsic efficacy. These results indicate that the guinea-pig ileum has higher muscarinic receptor density and greater intrinsic efficacy for carbachol than the rat and rabbit ileums.

• 대한약리학회지
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• 제30권1호
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• pp.49-57
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• 1994

Oxomemazine이 muscarinic receptor subtypes에 대하여 선택성을 가지는지에 관한 지견을 얻고자, 대뇌, 심실 및 회장 muscarinic receptor에 대한 oxomemazine의 결합성질을 조사, 비교하였다. $[^3H]QNB$ 포화결합실험 결과 세 조직의 muscarinic receptor는 $[^3H]QNB$에 대해서는 affinity가 약 60pM인 단일 receptor인 것으로 추정되었다. 대뇌에서 pirenzepine과 oxomemazine의 $[^3H]QNB$ 결합억제에 대한 Hill coefficient는 각각 0.67 및 0.8로서 대뇌에는 이들 약물에 대하여 affinity가 서로 다른 두 종류의 muscarinic receptor subtypes가 존재하는 것으로 나타났으며, pirenzepine에 대한 high $affinity(M_1)$와 $low affinity(M_2)$ receptor 및 oxomemazine에 대한 high $affinity(O_H)$와 $low\;affinity (O_L)$ receptor의 분포비는 약 60:40 및 40:60이었고, $M_1$과 $M_2$ receptor에 대한 pirenzepine의 $K_i$치는 16nM 및 431 nM, $O_H$와 $O_L$, receptor에 대한 oxomemazine 의 $K_i$치는 80nM 및 1350nM이었다. 그러나 심실과 회장에서 이들 약물의 $[^3H]QNB$ 결합억제에 대한 Hill coefficient는 1에 가까웠다. 심실과 회장 muscarinic receptor에 대한 pirenzepine의 $K_i$치는 850nM 및 250nM, oxomemazine의 $K_i$치는 1460nM 및 670nM로서 대피에서 이들 약물의 low affinity receptor에 대한 $K_i$치에 가까웠다. 즉, muscarinic receptor에 대한 affinity면에서 oxomemazine은 pirenzepine과 같이 대뇌에서 가장 높았으며, 회장에 대해서는 중등도였고, 심실에서 가장 낮았다. 이로 보아 oxomemazine은 $M_1\;receptor$에 선택성이 있는 것으로 추정된다.