• Bulletin of the Korean Chemical Society
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• v.32 no.7
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• pp.2325-2331
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• 2011

Human CDX1 and CDX2 genes play important roles in the regulation of cell proliferation and differentiation in the intestine. Hox genes clustered on four chromosomal regions (A-D) specify positional signaling along the anterior-posterior body axis, including intestinal development. Using glutathione S-transferase (GST) pulldown assays, molecular interaction measurements, and fluorescence measurements, we found that the homeodomains (HDs) of CDX1 and CDX2 directly interact with that of HOXD8 in vitro. CDX1 showed significant affinity for HOXD8, but CDX2 showed weak affinity for HOXD8. Thus far, three-dimensional structures of CDX1/2 and HOXD8 have not been determined. In this study, we developed a molecular docking model by homology modeling based on the structures of other HD members. Proteins with mutations in the HD of CDX1 (S185A, N190A, T194A, and V212A) also bound to the HD of HOXD8. Our study suggests that the HDs of CDX1/2 resemble those of HOXD8, and we provide the first insight into the interaction between the HDs of CDX1/2 proteins and those of HOXD8.

• Bulletin of the Korean Chemical Society
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• v.28 no.3
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• pp.379-385
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• 2007

Receptor-oriented pharmacophore-based in silico screening is a powerful tool for rapidly screening large number of compounds for interactions with a given protein. Inhibition of the enzyme catechol-Omethyltransferase (COMT) offers a novel possibility for treating Parkinson's disease. Bisubstrate inhibitors of COMT containing the adenine of S-adenosylmethionine (SAM) and a catechol moiety are a new class of potent and selective inhibitor. In the present study, we used receptor-oriented pharmacophore-based in silico screening to examine the interactions between the active site of human COMT and bisubstrate inhibitors. We generated 20 pharmacophore maps, of which 4 maps reproduced the docking model of hCOMT and a bisubstrate inhibitor. Only one of these four, pharmacophore map I, effectively described the common features of a series of bisubstrate inhibitors. Pharmacophore map I consisted of one hydrogen bond acceptor (to Mg2+), three hydrogen bond donors (to Glu199, Glu90, and Gln120), and one hydrophobic feature (an active site region surrounded by several aromatic and hydrophobic residues). This map represented the most essential pharmacophore for explaining interactions between hCOMT and a bisubstrate inhibitor. These results revealed a pharmacophore that should help in the development of new drugs for treating Parkinson's disease.

• Journal of Sensor Science and Technology
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• v.14 no.4
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• pp.278-285
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• 2005

This paper describes techniques of camera calibration and artificial landmarks detection for the automatic charging of a mobile robot, equipped with a fish-eye camera in the direction of its operation for movement or surveillance purposes. For its identification from the surrounding environments, three landmarks employed with infrared LEDs, were installed at the charging station. When the robot reaches a certain point, a signal is sent to the LEDs for activation, which allows the robot to easily detect the landmarks using its vision camera. To eliminate the effects of the outside light interference during the process, a difference image was generated by comparing the two images taken when the LEDs are on and off respectively. A fish-eye lens was used for the vision camera of the robot but the wide-angle lens resulted in a significant image distortion. The radial lens distortion was corrected after linear perspective projection transformation based on the pin-hole model. In the experiment, the designed system showed sensing accuracy of ${\pm}10$ mm in position and ${\pm}1^{\circ}$ in orientation at the distance of 550 mm.

• Bulletin of the Korean Chemical Society
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• v.29 no.3
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• pp.590-594
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• 2008

The inclusion complexes of cyclodextrins (CDs) with flavones in aqueous solution were investigated by phase solubility measurements. The effect of b -cyclodextrin (b -CD), heptakis (2,6-di-O-methyl) b -cyclodextrin (DM-b -CD) and 2-hydroxypropyl-b -cyclodextrin (HP-b -CD) on the aqueous solubility of three flavones, namely, chrysin, apigenin and luteolin was investigated, respectively. Solubility enhancements of all flavones obtained with three CDs followed the rank order: HP-b -CD > DM-b -CD > b -CD, and besides, CDs show higher stability constant on luteolin than that on others flavones. 1H-nuclear magnetic resonance (NMR) spectroscopy and molecular modeling was used to help establish the model of interaction of the CDs with luteolin. NMR spectroscopic analysis suggested that A-C ring, and part of the B ring of luteolin display favorable interaction with the CDs, which was also confirmed by docking studies based on the molecular simulation. The observed augmentation of solubility of luteolin by three CDs was explained by the difference of electrostatic interaction of each complex, especially hydrogen bonding.

• Proceedings of the Korean Biophysical Society Conference
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• 2003.06a
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• pp.70-70
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• 2003

Active sites and substrate bindings of 1-aminoxyclopropane-1-carboxylate oxidase (MD-ACO1) catalyzing the oxidative conversion of ACC to ethylene have been determined based on site-directed mutagenesis and comparative modeling methods. Molecular modeling based on the crystal structure of Isopenicillin N synthase (IPNS) provided MD-ACO1 structure. MD-ACO1 protein folds into a compact jelly roll shape, consisting of 9 ${\alpha}$-helices, 10 ${\beta}$-strands and several long loops. The MD-ACO1/ACC/Fe(II)/Ascorbate complex conformation was determined from automated docking program, AUTODOCK. The MD-ACO1/Fell complex model was consistent with well known binding motif information (HIS177-ASP179-HIS234). The cosubstrate, ascorbate is placed between iron binding pocket and Arg244 of MD-ACO1 enzyme, supporting the critical role of Arg244 for generating reaction product. These findings are strongly supported by previous biochemical data as well as site-directed mutagenesis data. The structure of enzyme/substrate suggests the structural mechanism for the biochemical role as well as substrate specificity of MD-ACO1 enzyme.

• Bulletin of the Korean Chemical Society
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• v.26 no.6
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• pp.952-958
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• 2005

Angiotensin-converting enzyme (ACE) is known to be primarily responsible for hypertension. Threedimensional quantitative structure-activity relationship (3D-QSAR) models have been constructed using the comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) for a series of 28 ACE inhibitors. The availability of ACE crystal structure (1UZF) provided the plausible biological orientation of inhibitors to ACE active site (C-domain). Alignment for CoMFA obtained by docking ligands to 1UZF protein using FlexX program showed better statistical model as compared to superposition of corresponding atoms. The statistical parameters indicate reasonable models for both CoMFA ($q^2$ = 0.530, $r^2$ = 0.998) and CoMSIA ($q^2$ = 0.518, $r^2$ = 0.990). The 3D-QSAR analyses provide valuable information for the design of ACE inhibitors with potent activity towards C-domain of ACE. The group substitutions involving the phenyl ring and carbon chain at the propionyl and sulfonyl moieties of captopril are essential for better activity against ACE.

• Journal of Microbiology and Biotechnology
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• v.29 no.2
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• pp.268-273
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• 2019

The specificity of a Bacillus licheniformis uridine diphosphate (UDP) glycosyltransferase, YjiC, was increased towards thymidine diphosphate (TDP)-sugar by site-directed mutagenesis. The Arg-282 of YjiC was identified and investigated by substituting with Trp. Conversion rate and kinetic parameters were compared between YjiC and its variants with several acceptor substrates such as 7-hydroxyflavone (7-HF), 4',7-dihydroxyisoflavone, 7,8-dihydroxyflavone and curcumin. Molecular docking of TDP-glucose and 7-HF with YjiC model showed pi-alkyl interaction with Arg-282 and His-14, and pi-pi interaction with $His^{14}$ and thymine ring. YjiC (H14A) variant lost its glucosylation activity with TDP-glucose validating significance of His-14 in binding of TDP-sugars.

• Natural Product Sciences
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• v.25 no.3
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• pp.215-221
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• 2019

Inflammation is the crucial biological process of immune system which acts as body's defense and protective response against the injuries or infection. However, the systemic inflammation devotes the adverse effects such as multiple inflammation associated diseases. One of the best ways to treat this entity is by blocking the tumor necrosis factor alpha ($TNF-{\alpha}$) and TNF-related apoptosis-inducing ligand (TRAIL) to avoid the proinflammation cytokines production. Thus, this study aims to evaluate the potency of Sambucus bioactive compounds as anti-inflammation through in silico approach. In order to assess that, molecular docking was performed to evaluate the interaction properties between the $TNF-{\alpha}$ or TRAIL with the ligands. The 2D structure of ligands were retrieved online via PubChem and the 3D protein modeling was done by using SWISS Model. The prediction results of the study showed that caffeic acid (-6.4 kcal/mol) and homovanillic acid (-6.6 kcal/mol) have the greatest binding affinity against the $TNF-{\alpha}$ and TRAIL respectively. This evidence suggests that caffeic acid and homovanillic acid may potent as anti-inflammatory agent against the inflammation associated diseases. Finally, this study needs further examination and evaluation to validate the potency of Sambucus bioactive compounds.

• International Journal of Naval Architecture and Ocean Engineering
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• v.12 no.1
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• pp.184-198
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• 2020

Decisions of the design speed, MCR, and engine capacity have been empirically made by assuming the value termed the sea margin. Due to ambiguity regarding the effect of some factors on the sea margin, the value has been commonly decided based on experience. To evaluate the value from a new viewpoint, it is necessary to construct an approach to estimate the sea margin through an objective procedure based on a physical and mathematical model. In this paper, a framework to estimate the actual sea margin of an LNGC based on the maneuvering equations of motion is suggested by considering the hull, propeller, rudder, and given sea route under wind and waves. The fouling effect is additionally quantified as the increase of total resistance by considering the re-docking period. The operation data is reviewed to amend the increase of the total resistance considering the speed loss of a ship. Finally, the factor of how much the resistance increases due to fouling is newly obtained for the vessel. Based on the comparison of the estimated sea margin with the empirical range of the sea margin, the constructed framework is regarded as feasible.

• Proceedings of the Korean Institute of Navigation and Port Research Conference
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• 2022.11a
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• pp.188-188
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• 2022

선박의 운용 효율을 높일 수 있는 방법인 무인 운용체계는 근래에 많은 관심을 받고 연구되어 왔다. 특히 무인수상선과 무인수중체의(USV-AUV)의 복합 운용 분야는 그 동안 어려움이 있었던 심해저 탐사 및 특수 임무 활용에 용이하여 많은 연구가 수행되고 있다. 본 연구에서는 쌍동선 형태인 무인수상선이 모선이 되고 무인수중체가 결합하여 충전하고 다시 진수하여 원거리 및 심해저 조건에서 무인수중체가 운용 가능하도록 하는 시스템의 일부인 USV-AUV의 docking을 위한 DP 시스템을 개발하고 선박해양플랜트연구소 해양공학수조에서 모형시험을 통해 이를 검증하였다. 또한, 실제 제작된 무인쌍동선과 추진 시스템을 활용하여 모형시험을 통해 검증한 DP 알고리즘을 적용하여 화성 제부도 앞바다에서 실선 DP 테스트를 수행하였다. 실 해역에서의 DP 시스템 테스트는 정확한 환경 조건의 계측 및 구현이 어려워 모형시험과 같은 정량적인 평가는 어렵지만, 정성적으로 DP 시스템이 작동하는 것을 확인할 수 있었다.