• 한국대기환경학회지
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• 제31권2호
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• pp.105-117
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• 2015

Sources related to road dust is one of the biggest sources, which is responsible for a large portion of emission. In particular, PM2.5 is a potential cause for respiratory diseases, thus it should be managed and a mitigation plan using results of statistical apportionment modeling such as chemical mass balance needs to be established. Recently, identifying sources of PM2.5 and analyzing the contribution of the road dust through a contribution assessment is required. Therefore, this study provides the chemical source profiles of PM2.5 using IC, GC/MS, OCEC, and XRF for both paved sidewalk and paved roadway collected at seven different sampling sites. As a result, for paved sidewalk, $NH{_4}^+$ (70%), $NO{_3}^-$ (12%), $PO{_4}^-$ (9%), and $SO{_4}^{2-}$ (9%) have been analyzed in PM2.5 mass. Major molecular marker such as Si has been indicated as $12.0{\pm}3.4%$ and $13.6{\pm}6.9%$ for paved sidewalk and roadway, respectively. PAHs such as Fluoranthene, Pyrene, Chrysene, and 1,3,5-Triphenylbenzene are suggested as molecular markers for road dust.

• BMB Reports
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• 제45권5호
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• pp.275-280
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• 2012

Nicotinic acetylcholine receptors (nAChRs) are a diverse family of homo- or heteropentameric ligand-gated ion channels. Understanding the physiological role of each nAChR subtype and the key residues responsible for normal and pathological states is important. ${\alpha}$-Conotoxin neuropeptides are highly selective probes capable of discriminating different subtypes of nAChRs. In this study, we performed homology modeling to generate the neuronal ${\alpha}3$, ${\beta}2$ and ${\beta}4$ subunits using the x-ray structure of the ${\alpha}1$ subunit as a template. The structures of the extracellular domains containing ligand binding sites in the ${\alpha}3{\beta}2$ and ${\alpha}3{\beta}4$ nAChR subtypes were constructed using MD simulations and ligand docking processes in their free and ligand-bound states using ${\alpha}$-conotoxin GIC, which exhibited the highest ${\alpha}3{\beta}2$ vs. ${\alpha}3{\beta}4$ discrimination ratio. The results provide a reasonable structural basis for such a discriminatory ability, supporting the idea that the present strategy can be used for future investigations on nAChR-ligand complexes.

• Bulletin of the Korean Chemical Society
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• 제28권8호
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• pp.1335-1340
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• 2007

β-Ketoacyl acyl carrier protein synthase (KAS) III is a particularly attractive target in the type II fatty acid synthetic pathway, since it is central to the initiation of fatty acid synthesis. Enterococcus faecalis, a Grampositive bacterium, is one of the major causes of hospital acquired infections. The rise of multidrug-resistant of most bacteria requires the development of new antibiotics, such as inhibition of the KAS III. In order to block the fatty acid synthesis by inhibition of KAS III, at first, three dimensional structure of Enterococcus faecalis KAS III (efKAS III) was determined by comparative homology modeling using MODELLER based on x-ray structure of Staphylococcus aureus KAS III (saKAS III) which is a gram-positive bacteria and is 36.1% identical in amino acid sequences with efKAS III. Since His-Asn-Cys catalytic triad is conserved in efKAS III and saKAS III, substrate specificity of efKAS III and saKAS III and the size of primer binding pocket of these two proteins are expected to be similar. Ligand docking study of efKAS III with naringenin and apigenin showed that naringenin docked more strongly with efKAS III than apigenin, resulting in the intensive hydrogen bond network between naringenin and efKAS III. Also, only naringenin showed antibacterial activity against E. faecalis at 256 μg/mL. This study may give practical implications of flavonoids for antimicrobial effects against E. faecalis.

• Bulletin of the Korean Chemical Society
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• 제29권3호
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• pp.647-655
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• 2008

Microsomal prostaglandin E2 synthase (mPGES-1) is a potent target for pain and inflammation. Various QSAR (quantitative structure activity relationship) analyses used to understand the factors affecting inhibitory potency for a series of MK886 analogues. We derived four QSAR models utilizing various quantum mechanical (QM) descriptors. These QM models indicate that steric, electrostatic and hydrophobic interaction can be important factors. Common pharmacophore hypotheses (CPHs) also have studied. The QSAR model derived by best-fitted CPHs considering hydrophobic, negative group and ring effect gave a reasonable result (q2 = 0.77, r2 = 0.97 and Rtestset = 0.90). The pharmacophore-derived molecular alignment subsequently used for 3D-QSAR. The CoMFA (Comparative Molecular Field Analysis) and CoMSIA (Comparative Molecular Similarity Indices Analysis) techniques employed on same series of mPGES-1 inhibitors which gives a statistically reasonable result (CoMFA; q2 = 0.90, r2 = 0.99. CoMSIA; q2 = 0.93, r2 = 1.00). All modeling results (QM-based QSAR, pharmacophore modeling and 3D-QSAR) imply steric, electrostatic and hydrophobic contribution to the inhibitory activity. CoMFA and CoMSIA models suggest the introduction of bulky group around ring B may enhance the inhibitory activity.

• Computers and Concrete
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• 제27권2호
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• pp.111-130
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• 2021

In the present work, an extensive study for predicting efficiency parameters (��i) of various simulated nanocomposites including Polymethyl methacrylate (PMMA) as matrix and different structures including various sizes of graphene platelets (GPLs), single, double, and multi-walled carbon nanotubes (SWCNTs-DWCNTs-MWCNTs), and single and double-walled boron nitride nanotubes (SWBNNTs-DWBNNTs) are investigated. It should be stated that GPLs, carbon and boron nitride nanotubes (CNTs, BNNT) with different chiralities (5, 0), (5, 5), (10, 0), and (10, 10) as reinforcements are considered. In this research, molecular dynamics (MDs) method with Materials studio software is applied to examine the mechanical properties (Young's modulus) of simulated nanocomposite boxes and calculate η1 of each nanocomposite boxes. Then, it is noteworthy that by changing length (6.252, 10.584, and 21.173 nm) and width (7.137, 10.515, and 19.936) of GPLs, ��1, ��2, and ��3 approximately becomes (0.101, 0.114, and 0.124), (1.15, 1.22, and 1.26), (1.04, 1.05, and 1.07) respectively. After that efficiency parameters of SWCNTs, DWCNTs, and MWCNTs are calculated and discussed separately. Finally efficiency parameters of SWBNNTs and DWBNNTs with different chiralities by PMMA as matrix are determined by MD and discussed separately. It is known that the accurate efficiency parameters helps a lot to calculate the properties of nanocomposite analytically. In particular, the obtained results from this research can be used for analytical work based on the extended rule of mixture (ERM) in bending, buckling and vibration analysis of structure in future study.

• Smart Structures and Systems
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• 제8권1호
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• pp.17-37
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• 2011

The microcantilever (MCL) sensor is one of the most promising platforms for next-generation label-free biosensing applications. It outperforms conventional label-free detection methods in terms of portability and parallelization. In this paper, an overview of recent advances in our understanding of the coupling between biomolecular interactions and MCL responses is given. A dual compact optical MCL sensing platform was built to enable biosensing experiments both in gas-phase environments and in solutions. The thermal bimorph effect was found to be an effective nanomanipulator for the MCL platform calibration. The study of the alkanethiol self-assembly monolayer (SAM) chain length effect revealed that 1-octanethiol ($C_8H_{17}SH$) induced a larger deflection than that from 1-dodecanethiol ($C_{12}H_{25}SH$) in solutions. Using the clinically relevant biomarker C-reactive protein (CRP), we revealed that the analytical sensitivity of the MCL reached a diagnostic level of $1{\sim}500{\mu}g/ml$ within a 7% coefficient of variation. Using grazing incident x-ray diffractometer (GIXRD) analysis, we found that the gold surface was dominated by the (111) crystalline plane. Moreover, using X-ray photoelectron spectroscopy (XPS) analysis, we confirmed that the Au-S covalent bonds occurred in SAM adsorption whereas CRP molecular bindings occurred in protein analysis. First principles density functional theory (DFT) simulations were also used to examine biomolecular adsorption mechanisms. Multiscale modeling was then developed to connect the interactions at the molecular level with the MCL mechanical response. The alkanethiol SAM chain length effect in air was successfully predicted using the multiscale scheme.

• Molecular & Cellular Toxicology
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• 제4권4호
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• pp.307-310
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• 2008

AAD16034 is an alginate lyase from Pseudoalteromonas sp. IAM14594. A very close homologue with known 3D structure exists (marine bacterium Pseudoalteromonas sp. strain no. 272). A three-dimensional structure of AAD16034 was generated based on this template (PDB code: 1J1T) by comparative modeling. The modeled enzyme exhibited a jelly-roll like structure very similar to its template structure. Both enzymes possess the characteristic alginate sequence YFKhG+Y-Q. Since AAD16034 displays enzymatic activity for poly-M alginate, docking of a tri-mannuronate into the modeled structure was performed. Two separate and adjacent binding sites were found. The ligand was accommodated inside each binding site. By considering both binding sites, a plausible binding pose for the poly-M alginate polymer could be deduced. From the modeled docking pose (i.e., the most important factor that attracts alginate polymer into this lyase) the most likely interaction was electrostatic. In accordance with a previous report, the hydroxyl group of Y345 was positioned close to the ${\alpha}$-hydrogen of ${\beta}$-mannuronate, which was suitable to initiate a ${\beta}$-elimination reaction. K347 was also very near to the carboxylatemoiety of the ligand, which might stabilize the dianion intermediate during the ${\beta}$-elimination reaction. This implies that the characteristic alginate sequence is absolutely crucial for the catalysis. These results may be exploited in the design of novel enzymes with desired properties.

• 대한방사성의약품학회지
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• 제2권2호
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• pp.108-112
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• 2016

Molecular imaging with the radiolabeled RGD peptides for ${\alpha}_v{\beta}_3$ integrin has been an increasing interest for tumor diagnosis and the treatment monitoring. Recently, $^{64}Cu$-NODAGA-gluco-E[c(RGDfK)]$_2$ was developed for quantification of ${\alpha}_v{\beta}_3$ integrin and its biological properties was elucidated. To better understand the molecular process in vivo, we performed the kinetic analysis for the $^{64}Cu$-NODAGA-gluco-E[c(RGDfK)]$_2$. After preparation of a radiotracer, dynamic PET images were obtained in the U87MG xenograft mice for 60 min (n = 6). Binding potential values were estimated from the 3-tissue compartment model, reference Logan and simplified reference tissue model. In the early time frame (0-20 min), the liver, kidney, intestine, urinary bladder and tumor were visualized but these uptakes were diminished as time went by. The tumors showed a good contrast at 40 min after administration. $^{64}Cu$-NODAGA-gluco-E[c(RGDfK)]$_2$ showed the 2-fold uptake in the tumor compared with that in the muscle. The parametric maps for binding values also provide the higher tumor-to-background contrast than the static images. A binding value obtained from the 3-tissue compartment model was comparable to other modeling methods. From these results, we conclude that $^{64}Cu$-NODAGA-gluco-E[c(RGDfK)]$_2$ may be a promising PET radiotracer for the evaluation of angiogenesis.

• 청정기술
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• 제19권4호
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• pp.476-480
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• 2013

라만 분광학과 분자 모델링을 이용하여 메탄과 육불화황의 혼합 기체 가스 하이드레이트의 성장거동을 연구하였다. 라만 분광학 결과에 의하면 메탄을 객체 가스로 사용할 경우 메탄이 물 분자로 이루어지는 가스 하이드레이트 호스트 구조 내의 큰 동공을 채우고 차례로 작은 동공이 채워지게 되는데 반하여 육불화황을 혼합한 경우 육불화황과 메탄이 경쟁적으로 큰 동공을 채우고 이어 작은 동공에는 메탄만 채워지는 방식으로 전체 가스 하이드레이트 구조가 안정화됨을 관찰하였다. 분자 모델링에 의한 결합에너지 계산 결과 큰 동공의 경우 육불화황은 -26.9 kcal/mol, 메탄은 -24.2 kcal/mol의 결합에너지를 보여 육불화황이 채워지는 것이 약간 더 안정함을 알 수 있었고 작은 동공의 경우 육불화황은 1.2 kcal/mol, 메탄은 -22.0 kcal/mol로 큰 크기의 육불화황이 작은 동공에는 채워질 수 없음을 보여주었다. 이와 같은 접근법은 향후 다양한 객체 기체 가스 하이드레이트의 성장거동을 예측하는데 적용될 수 있을 것이다.

• Bulletin of the Korean Chemical Society
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• 제28권10호
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• pp.1705-1708
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• 2007

Geometric manipulation of molecules is an essential elementary component in computational modeling programs for molecular structure, stability, dynamics, and design. The computational complexity of transformation of internal coordinates to Cartesian coordinates was discussed before.1 The use of rotation matrices was found to be slightly more efficient than that of quaternion although quaternion operators have been widely advertised for rotational operations, especially in molecular dynamics simulations of liquids where the orientation is a dynamical variable.2 The discussion on computational efficiency is extended here to a more general case in which bond angles and sidechain torsion angles are allowed to vary. The algorithm of Thompson3 is derived again in terms of quaternions as well as rotation matrices, and an algorithm with optimal efficiency is described. The algorithm based on rotation matrices is again found to be slightly more efficient than that based on quaternions.