• Mass Spectrometry Letters
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• v.12 no.4
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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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• v.34 no.5
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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.

• Proceedings of the Korean Vacuum Society Conference
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• 2000.02a
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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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• v.30 no.3
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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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• 2006.08a
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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.

• Journal of Energy Engineering
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• v.23 no.3
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• pp.102-115
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• 2014

In the Ulleung basin in the East Sea of Korea, it is assumed that huge amounts of gas hydrate(GH) are buried. In 2010, drilling operation was performed at the 2nd Ulleung Basin Gas Hydrate Drilling Expedition(UBGH2) to designate a site for field production test. In this study, based on the field production test site model reflecting geological properties, GH dissociation flow interpretation is analyzed and sensitivity analysis is performed to gain understanding of production behavior properties following bottomhole pressure(BHP) variation by using the numerical simulation. The results of this study provide a basis for the preliminary analysis of field production test site.

• Korean Journal of Materials Research
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• v.4 no.1
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• pp.9-23
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• 1994

Epitaxial $CoSi_2$ layer has been grown on NaCl(100) substrate at low deposition temperature($200^{\circ}C$) by multitarget bias cosputter deposition(MBCD). The phase sequence and crystallinity of deposited silicide as a function of deposition temperature and substrate bias voltage were studied by X-ray diffraction(XRD) and transmission electron microscopy(TEM) analysis. Crystalline Si was grown at $200^{\circ}C$ by metal induced crystallization(M1C) and self bias effect. In addition to, the MIC was analyzed both theoretically and experimentally. The observed phase sequence was $Co_2Si \to CoSi \to Cosi_2$ and was in good agreement with that predicted by effective heat of formation rule. The phase sequence, the CoSi(l11) preferred orientation, and the crystallinity had stronger dependence on the substrate bias voltage than the deposition temperature due to the collisional cascade mixing, the in-situ cleaning, and the increase in the number of nucleation sites by ion bombardment of growing surface. Grain growth induced by ion bombardment was observed with increasing substrate bias voltage at $200^{\circ}C$ and was interpreted with ion bombardment dissociation model. The parameters of $E_{Ar}\;and \alpha(V_s)$ were chosen to properly quantify the ion bombardment effect on the variation in crystallinty at $200^{\circ}C$ with increasing substrate bias voltage using Langmuir probe.

• Bulletin of the Korean Chemical Society
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• v.35 no.7
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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.

• Proceedings of the Korean Society of Applied Pharmacology
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• 1995.04a
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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.

• The Korean Journal of Pharmacology
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• v.30 no.1
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• pp.49-57
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• 1994

The binding properties of oxomemazine to muscarinic receptors using the ability of oxomemazine to inhibit $[^3H]QNB$ binding in membrane fractions of rat cerebrum and guinea pig ventricle and ileum were investigated. $[^3H]QNB$ bound to a single class of muscarinic receptors with a dissociation constant of approximately 60 pM in three tissue preparations. Pirenzepine and oxomemazine inhibited $[^3H]QNB$ binding in cerebrum with a Hill coefficient lower than unity, and the inhibition data were best described by a two-site model. The relative densities of the high $(M_1)\;and\;low\;(M_2)$ affinity sites for pirenzepine were 60 and 40%, with corresponding Ki values of 16 and 431 nM, and those $(O_H\;and\;O_L)$ for oxomemazine 40 and 60%, with corresponding Ki values of 80 and 1350 nM. However, the inhibition data of both drugs vs $[^3H]QNB$ in ventricle and ileum appeared to obey the law of mass-action (Hill coefficient close to 1). The apparent Ki values of pirenzepine were 850 and 250 nM, and those of oxomemazine 1460 and 570 nM in ventricle and ileum, respectively. Thus, oxomemazine like pirenzepine has high affinity for cerebrum, moderate affinity for ileum and low affinity for ventricle. These results suggest that oxomemazine could recognize the muscarinic receptor subtypes with a high affinity for the $M_1$ sites.