• Bulletin of the Korean Chemical Society
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• v.35 no.3
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• pp.709-714
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• 2014

Protein tyrosine nitration is considered as an important indicator of nitrosative stresses and as one of the main factors for pathogenesis of inflammation and neuronal degeneration. In this study, we investigated various nitrosative modifications of bovine carbonic anhydrase II (CAII) through qualitative and semi-quantitative analysis using the combined strategy of Fourier transformation ion cyclotron resonance mass spectrometry (FT-ICR MS) and ion-trap tandem mass spectrometry (IT-MS/MS). FT-ICR MS and its spectra were used for the search of the pattern of nitrosative modifications. Identification of nitrosatively modified tyrosine sites were executed through IT-MS/MS. In addition, we also tried to infer the reason for the site-specific nitrosative modifications in CAII. In view of the above purpose, we have explored- i) the side chain accessibility, ii) the electrostatic environment originated from the acidic/basic amino acid residues neighboring to the nitrosatively modified site and iii) the existence of competing amino acid residues for nitration.

• BMB Reports
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• v.31 no.5
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• pp.459-467
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• 1998

A new set of functional group interaction energy descriptors relevant to the ACE (Angiotensin-Converting Enzyme) inhibitory peptide, QSAR (Quantitative Structure Activity Relationships), is presented. The functional group interaction energies approximate the charged interactions and distances between functional groups in molecules. The effective energies of the computationally derived geometries are useful parameters for deriving 3D-QSAR models, especially in the absence of experimentally known active site conformation. ACE is a regulatory zinc protease in the renin-angiotensin system. Therapeutic inhibition of this enzyme has proven to be a very effective treatment for the management of hypertension. The non bond interaction energy values among functional groups of six-feature of ACE inhibitory peptides were used as descriptor terms and analyzed for multivariate correlation with ACE inhibition activity. The functional group interaction energy descriptors used in the regression analysis were obtained by a series of inhibitor structures derived from molecular mechanics and semi-empirical calculations. The descriptors calculated using electrostatic and steric fields from the precisely defined functional group were sufficient to explain the biological activity of inhibitor. Application of the descriptors to the inhibition of ACE indicates that the derived QSAR has good predicting ability and provides insight into the mechanism of enzyme inhibition. The method, functional group interaction energy analysis, is expected to be applicable to predict enzyme inhibitory activity of the rationally designed inhibitors.

• Bulletin of the Korean Chemical Society
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• v.35 no.12
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• pp.3495-3501
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• 2014

A novel crystal, the mono-protonated metformin acetate (1), was obtained and characterized by elemental analysis, IR spectroscopy and X-ray crystallography. It was found that one of the imino group in the metformin cation was protonated along with the proton transfer from the secondary amino group to the other imino group. Its crystal structure was then compared with the previously reported diprotonated metformin oxalate (2). The difference between them is that the mono-protonated metformin cations can be linked by hydrogen bonding to form dimers while the diprotonated metformin cations cannot. Both of them are stabilized by intermolecular hydrogen bonds to assemble a 3-D supermolecular structure. The four potential tautomer of the mono-protonated metformin cation (tautomers 1a, 1b, 1c and 1d) were optimized and their single point energies were calculated by Density Functional Theory (DFT) B3LYP method based on the Polarized Continuum Model (PCM) in water, which shows that the most likely existed tautomer in human cells is the same in the crystal structure. Based on the optimized structure, their Wiberg bond orders, Natural Population Analysis (NPA) atomic charges, molecular electrostatic potential (MEP) maps were calculated to analyze their electronic structures, which were then compared with the corresponding values of the diprotonated metformin cation (cation 2) and the neutral metformin (compound 3). Finally, the possible tautomeric mechanism of the mono-protonated metformin cation was discussed based on the observed phenomena.

• Journal of Microbiology and Biotechnology
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• v.16 no.9
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• pp.1434-1440
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• 2006

The stable anchorage of pyridoxal 5'-phosphate (PLP) in the active site of D-amino acid transaminase (D-AT) is crucial for the enzyme catalysis. The three-dimensional structure of D-AT revealed that Glu32 is one of the active site groups that may playa role in PLP binding. To prove the role of Glu32 in PLP stability, we firstly checked the rate of the potential rate-limiting step. The kinetic analysis showed that the rate of the ${\alpha}$-deprotonation step reduced to 26-folds in E32A mutant enzyme. Spectral analyses of the reaction of D-AT with D-serine revealed that the E32A mutant enzyme failed to stabilize the key enzyme-substrate intermediate, namely a quinonoid intermediate (E-Q). Finally, analysis of circular dichroism (CD) on the wild-type and E32A mutant enzymes showed that the optical activity of PLP in the enzyme active site was lost by the removal of the carboxylic group, proving that Glu32 is indeed involved in the cofactor anchorage. The results suggested that the electrostatic interaction network through the groups from PLP, Glu32, His47, and Arg50, which was observed from the three-dimensional structure of the enzyme, plays a crucial role in the stable anchorage of the cofactor to give necessary torsion to the plane of the cofactor-substrate complex.

• Bulletin of the Korean Chemical Society
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• v.32 no.1
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• pp.251-262
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• 2011

Human ether-a-go-go related gene (hERG) potassium channel blockade, an undesirable side effect which might cause sudden cardiac death, is one of the major concerns facing the pharmaceutical industry. The purpose of this study is to develop an in silico QSAR model which uncovers the structural parameters of T-type calcium channel blockers to reduce hERG blockade. Comparative molecular similarity indices analysis (CoMSIA) was conducted on a series of piperazine and benzimidazole derivatives bearing methyl 5-(ethyl(methyl)amino)-2-isopropyl-2-phenylpentanoate moieties, which was synthesized by our group. Three different alignment methods were applied to obtain a reliable model: ligand based alignment, pharmacophore based alignment, and receptor guided alignment. The CoMSIA model with receptor guided alignment yielded the best results : $r^2$ = 0.955, $q^2$ = 0.781, $r^2_{pred}$ = 0.758. The generated CoMSIA contour maps using electrostatic, hydrophobic, H-bond donor, and acceptor fields explain well the structural requirements for hERG nonblockers and also correlate with the lipophilic potential map of the hERG channel pore.

• Journal of the Institute of Electronics Engineers of Korea SD
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• v.47 no.2
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• pp.40-50
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• 2010

The studies of PMOS transistors in CMOS technologies are reviewed- focusing on the snapback and breakdown behavior of the parasitic PNP BJTs in high current regime. A new failure mechanism of PMOSFET devices under ESD conditions is also analyzed by investigating various I/O structures in a $0.13\;{\mu}m$ CMOS technology. Localized turn-on of the parasitic PNP transistor can be caused by localized charge injection from the adjacent diodes into the body of the PMOSFET, significantly degrading the ESD robustness of PMOSFETs. Based on 2-D device simulations the critical layout parameters affecting this problem are identified. Design guidelines for avoiding this new PMOSFET failure mode are also suggested.

• Particle and aerosol research
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• v.19 no.2
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• pp.31-42
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• 2023

The charge and magnetic characteristics of LM (Low-metallic) and NAO (Non-asbestos-organic) brake wear particles were analyzed. The ratio of charged particles from total particles is about 86% of the LM pad and about 92% of the NAO pad. Number of charge per particle from the NAO pad is also higher than that of the LM pad. The ratio of magnetic particles from total particles increases with the particle size. The ratio of magnetic particles from the LM pad is about 15% for the particles with the size of 1 ㎛, and about 74% for ones with 5 ㎛. The ratio from the NAO pad is about 5% for the particles with the size from 0.5 ㎛ to 2 ㎛, and about 80% for the particles with 5 ㎛. Through the analysis of the components of the two pads with SEM-EDS (Scanning Electron Microscopy - Energy Dispersive X-ray Spectroscopy), it was found that the LM pad was occupied with more iron fraction than the NAO pad and that PM_2.5-10 was occupied with more iron fraction than PM_2.5. The particles smaller than 10 ㎛ (i.e. PM₁₀) from the LM pad contained about 83% of charged particles, about 43% of magnetic particles, and about 93% of charged or magnetic particles. PM₁₀ from the NAO pad contained about 88% of charged particles, about 15% of magnetic particles, and about 89% of charged or magnetic particles.

• The Journal of the Convergence on Culture Technology
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• v.9 no.4
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• pp.503-508
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• 2023

Tryptane derivatives are substances that treat acute migraines, and many studies have been conducted on analysis methods such as chromatography, electrochemistry, spectroscopy, and capillary electrophysiology. Recently, analytical chemists have become more interested in drug analysis and solving fundamental problems of biological importance. Therefore, in this study, the chemical properties of each derivative were investigated by calculating the total energy, band gap, electrostatic potential, and charge of Sumatriptan, Lizatriptan, Naratriptan, and Eletriptan using HyperChem8.0's semi-empirical PM3 method. As a result of this study, in the case of Sumatriptan, Naratriptan, and Eletriptan, chemical reactions are expected to proceed centering on oxygen and nitrogen atoms bonded to sulfur atoms. In addition, in the case of Rizatriptan without a sulfur atom, it was shown that the chemical reaction proceeds at the 17th and 19th nitrogens of the 5-membered heterocyclic compound.

• Journal of electromagnetic engineering and science
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• v.6 no.2
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• pp.135-145
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• 2006

This paper presents the theory, design, fabrication and characterization of the novel low actuation voltage capacitive shunt RF-MEMS switch using a corrugated membrane with HRS MEMS packaging. Analytical analyses and experimental results have been carried out to derive algebraic expressions for the mechanical actuation mechanics of corrugated membrane for a low residual stress. It is shown that the residual stress of both types of corrugated and flat membranes can be modeled with the help of a mechanics theory. The residual stress in corrugated membranes is calculated using a geometrical model and is confirmed by finite element method(FEM) analysis and experimental results. The corrugated electrostatic actuated bridge is suspended over a concave structure of CPW, with sputtered nickel(Ni) as the structural material for the bridge and gold for CPW line, fabricated on high-resistivity silicon(HRS) substrate. The corrugated switch on concave structure requires lower actuation voltage than the flat switch on planar structure in various thickness bridges. The residual stress is very low by corrugating both ends of the bridge on concave structure. The residual stress of the bridge material and structure is critical to lower the actuation voltage. The Self-alignment HRS MEMS package of the RF-MEMS switch with a $15{\Omega}{\cdot}cm$ lightly-doped Si chip carrier also shows no parasitic leakage resonances and is verified as an effective packaging solution for the low cost and high performance coplanar MMICs.

• Bulletin of the Korean Chemical Society
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• v.31 no.5
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• pp.1314-1318
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• 2010

The $[Ru(tpy)_2]Cl_2$ (tpy:2,2':6',2"-terpyridine) complex was synthesized and its structure was confirmed by $^1H$-NMR and elemental analysis. Its binding mode toward DNA was compared with the well-known $[Ru(bpy)_3]Cl_2$ (bpy:2,2-bipyridyl), using isotropic absorption, linear dichroism(LD) spectroscopy, and an energy minimization study. Compared to $[Ru(bpy)_3]^{2+}$, the $[Ru(tpy)_2]^{2+}$ complex exhibited very little change in its absorption pattern, especially in the MLCT band, upon binding to DNA. Furthermore, upon DNA binding, both Ru(II) complexes induced a decrease in the LD magnitude in the DNA absorption region. The $[Ru(tpy)_2]^{2+}$ complex produced a strong positive LD signal in the ligand absorption region, which is in contrast with the $[Ru(bpy)_3]^{2+}$ complex. Observed spectral properties led to the conclusion that the interaction between the ligands and DNA bases is negligible for the $[Ru(tpy)_2]^{2+}$ complex, although it formed an adduct with DNA. This conclusion implies that both complexes bind to the surface of DNA, most likely to negatively charged phosphate groups via a simple electrostatic interaction, thereby orienting to exhibit the LD signal. The energy minimization calculation also supported this conclusion.