• Proceedings of the Korea Information Processing Society Conference
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• 2014.04a
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• pp.677-679
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• 2014

생명현상은 기능적 요소인 단백질의 활성에 의해 유지되고 조절된다. 최근 단백질의 복잡한 네트워크 정보가 생명현상을 조절하는 기능적 단위로 인식되면서 단백질 네트워크의 최소 단위인 단백질-단백질 상호작용 정보의 중요성이 강조되고 있다. 특히 단백질의약품의 경우 단백질 네트워크 상에서 리셉터 단백질과 리간드 단백질 사이의 상호작용에 의해서 약효가 나타나도록 설계되기 때문에 상호작용에 관여하는 인터페이스 정보의 확보가 필수적이다. 단백질-단백질 상호작용 인터페이스 확인을 위한 연구들이 활발히 이루어지고 있으나 인터페이스 정보의 가시화에 대한 연구는 극히 제한적이다. 본 논문에서는 리셉터 단백질과 리간드 단백질에 대한 3차구조 분석을 통해 단백질-단백질 상호작용에 관여하는 인터페이스 정보를 가시화하였다. 기존의 단백질 3차구조 정보 서비스 사이트인 PDB에서 확인할 수 없는 인터페이스 정보를 3차원으로 시각화하여 인터페이스 상에 위치하는 아미노산 정보를 새롭게 제공함으로써 의약품 연구자들이 단백질 구조와 인터페이스 구조를 쉽게 파악할 수 있도록 하였다. 이는 의약품 등 단백질-단백질 상호작용 정보를 활용하는 바이오 산업 분야에 필요한 정보를 제공함으로써 산업 활성화에 기여할 것으로 기대된다.

• Proceedings of the Korea Information Processing Society Conference
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• 2015.04a
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• pp.873-874
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• 2015

단백질 의약품 개발 시 단백질 구조는 단백질 기능을 규명하기 위한 필수적인 정보이다. 따라서 단백질 구조를 효과적으로 전달할 수 있는 단백질 가시화 서비스가 증가하고 있으며, 대표적으로 Cn3D, Jmol, Chimera 등이 있다. 각 서비스는 단백질 가시화 서비스와 함께 단백질 분석을 위한 부가 기능을 제공하고 있다. 본 논문에서는 단백질 의약품의 효율적 정보전달 서버스를 위한 사전 연구로 업계종사 기간이 5년 이상인 피험자를 대상으로 단백질 가시화 이용현황을 설문하였다. 설문 분석 결과 자주 이용하는 단백질 가시화 서비스로 피험자 모두 PDB를 사용한다고 응답하였으며, 단백질 1, 2차구조 혼합 가시화 서비스를 일주일에 4회 이상 사용하는 응답자가 58.3%였다. 특히 단백질 의약품 개발 시 반드시 필요한 단백질 정보로는 91.6%가 단백질 1차구조, 단백질 2차구조, 단백질 2차구조 비율이라고 응답하였다.

• Journal of Integrative Natural Science
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• v.5 no.3
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• pp.190-194
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• 2012

Human P-gp is one of the protein responsible for the multidrug resistance (MDR) develpment. MDR is a major cause of the cancer chemotherapy. In this paper, we performed homology modeling, docking study of papayriferic acid into the P-gp nucleotide binding domain (NBD2). For human P-gp, X-ray crystal structure is not known yet. We developed homology model for human NBD2 using HlyB ABC transporter structure (PDB code: 1XEF, resolution 2.5 ${\AA}$). Docking study was performed using Autodock. Docking result was analyzed, which shows that ligand docks into steroid binding site and interacts through hydrophobic and hydrophilic interactions.

• The Korean Journal of Pharmacology
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• v.30 no.3
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• pp.263-272
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• 1994

Since it was been reported that the depolarization-induced ACh release is inhibited by activation of presynaptic $A_1-adenosine$ heteroreceptor in hippocampus, a large body of experimental data on the post-receptor mechanism of this process has been accumulated. But, the post-receptor mechanism of presynaptic $A_1-adenosine$ receptor on the ACh release has not been clearly elucidated yet. Therefore, it was attempted to clarify the post-receptor mechanisms of the $A_1-adenosine$ receptor-mediated control of ACh release in this study. Slices from rat hippocampus were equilibrated with $^3H-choline$ and the release of the labelled products was evoked by electrical stimulation (3 Hz, 5 $VCm^{-1}$, 2ms, rectangular pulses), and the influence of various agents on the evoked tritium-outflow was investigated. Adenosine, in concentrations ranging from $0.3{\sim}300\;{\mu}M$, decreased the ACh release in a dose-dependent manner, without affecting the basal rate of release. The adenosine effects were significantly inhibited by $DPCPX\;(2\;{\mu}M)$, a selective $A_1-receptor$ antagonist. The responses to N-ethylmaleimide $(10&30{\mu}M)$, a SH-alkylating agent of G-protein, were characterized by increments of the evoked ACh-release and the basal release, and the adenosine effects were completely abolished by NEM pretreatment. PDB $(1{\sim}10\;{\mu}M)$, a specific protein kinase C (PKC) activator, increased, whereas PMB $(0.03{\sim}1\;mg)$, a PKC inhibitor, decreased the evoked ACh-release, and the adenosine effects were not affected by these agents. Nifedipine $(1\;{\mu}M)$, a $Ca^{2+}\;-channel$ blocker of dihydropyridine analogue, significantly inhibited the adenosine effect, but glibenclamide, a $K^+-channel$ blocker, did not. Finally, 8-bromo cyclic AMP $(100\;&\;300{\mu}M)$, a membrane-permeable analogue of cAMP, did not alter the ACh release, but adenosine effects were inhibited by pretreatment with large dose of 8-br-cAMP $(300\;{\mu}M)$. These results indicate that the decrement of the evoked ACh-release by $A_1-adenosine$ receptor is mediated by the G-protein, and nifedipine-sensitive $Ca^{2+}-channel$ and adenylate cyclase system are coupled partly to this effect, and that protein kinase C and glibenclamide-sensitive $K{^+}-channel$ are not involved in this process.

• The Korean Journal of Pharmacology
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• v.32 no.1
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• pp.1-11
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• 1996

Since it has been reported that the depolarization-induced norepinephrine (NE) release is inhibited by activation of presynaptic $A_1-adenosine$ heteroreceptor in hippocampus, a large body of experimental data on the post-receptor mechanism of this process has been accumulated. But, the post-receptor mechanism of presynaptic $A_1-adenosine$ receptor on the NE release has not been clearly elucidated yet. Therefore, it was attempted to clarify the post-receptor mechanisms of the $A_1-adenosine$ receptor-mediated control of NE release in this study. Slices from rat hippocampus were equilibrated with $^3H-norepinephrine$ and the release of the labelled products was evoked by electrical stimulation (3 Hz, 5 $Vcm^{-1}$, 2 ms, rectangular pulses), and the influence of various agents on the evoked tritium-outflow was investigated. Adenosine, in concentrations ranging from $1{\sim}30{\mu}M$, decreased the NE release in a dose-dependent manner, without affecting the basal rate of release. The adenosine effects were significantly inhibited by 8-cyclopentyl-1,3-dipropylxanthine (DPCPX, $2{\mu}M$), a selective $A_1-receptor$ antagonist. The responses to N-ethylmaleimide (NEM, 10 & $30{\mu}M$), a SH-alkylating agent of G-protein, were characterized by increments of the evoked NE-release and the basal release, and the adenosine effects were completely abolished by NEM pretreatment. $4{\beta}-Phorbol$ 12,13-dibutyrate (PDB, $1{\mu}M$), a specific protein kinase C (PKC) activator, increased the evoked NE release, whereas polymyxin B sulfate (PMB,0.1 mg), a PKC inhibitor, decreased the release, and the adenosine effects were inhibited by these agents. Nifedipine $(1{\mu}M)$, a $Ca^{2+}-channel$ blocker of dihydropyridine analogue, did not affect the adenosine effect. Tetraethylammonium (TEA, 3 mM) increased the evoked NE release, and inhibited the adenosine effects, but glibenclamide, a ATP dependent $K^+-channel$ blocker, did not. Finally, 8-bromo cyclic AMP (100 & $300{\mu}M$), a membrane-permeable analogue of cAMP, did not alter the NE release, but adenosine effects were inhibited by pretreatment with 8br-cAMP. These results suggest that the decrement of the evoked NE-release by $A_1-adenosine$ receptor is mediated by the C-protein, which is coupled to protein kinase C, adenylate cyclase system and TEA sensitive $K^+-channel$, and that nifedipine-sensitive $Ca^{2+}-channel$ and glibenclamide-sensitive $K^+-channel$ are not involved in this process.

• Food Science and Preservation
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• v.17 no.3
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• pp.365-369
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• 2010

This study was conducted to investigate the cultural characteristics of Paecilomyces tenuipes PJ-1 separated from the nature. We investigated the effect of media, pH and temperature in growth of Paecilomyces tenuipes PJ-1 on solid culture media and the effect of inoculum size, glass beads in liquid culture condition. Paecilomyces tenuipes showed the most favorable growth on PDA among 5 different media. The optimum growth pH and temperature were at pH 6.0 and $25^{\circ}C$ on solid culture. Mycelial growth of P. tenuipes decreased rapidly above $35^{\circ}C$ and under $15^{\circ}C$. In liquid culture, the optimum inoculum size was 10.0% and the SED and PMV value were increased with adding glass bead and glass bead size in the range of glass bead 0~50 ea and size 3, 5 mm.

• Journal of Mushroom
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• v.7 no.1
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• pp.9-21
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• 2009

This study was executed in an attempt to investigate a artificial requisites of fruitbody occurrence. Environmental requirements on habitat for fruitbody occurrence of collected cultures resulted in leading to $13-16^{\circ}C$ and 75% relative humidity, and requiring silt loam of soil texture which had more nutritional substances than a dry field. Optimal temperature was $25^{\circ}C$, medium PDB, and pH 5.0 in cultural conditions. Mannose required of 5% in ASI 59002, 59003, 59004, but 3% in ASI 59001 was selected as optimum carbon source. The substrates stimulating sclerotium formation were cotton waste, or cotton waste + oak sawdust (mixture ratio of 8:2), which had 20% additive of wheat barn respectively. Sclerotium was formed well in the substrate adjusted chemical properties by applying 2% of calcium sulfate. Sclerotium formation was the most effective in the treatment of peat moss + oak sawdust (mixture ratio of 5:5) + 30% of wheat barn.

• Journal of Life Science
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• v.28 no.8
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• pp.969-976
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• 2018

In this study, transglucosidase (TG), an enzyme produced by Aspergillus niger, synthesized isomaltooligosaccharide from ${\alpha}-(1{\rightarrow}4)$ linked substrates. The highest TG-producing A. niger KCTC6913 was selected from six kinds of species, and optimized TG producing conditions were established. Five different carbon sources (potato starch, sweet potato starch, corn starch, wheat starch, and dextrin) and three different nitrogen sources (yeast extract, malt extract, and beef extract) were tested to establish the carbon and nitrogen sources favorable for TG production. Measurements of TG activity after an initial culture at pH 5.0 for 15 days revealed that potato starch and yeast extract, which are basic culture media, resulted in the highest TG activity. In addition, A. niger KCTC6913 increased TG production under aerobic conditions and a controlled carbon/nitrogen ratio. In conclusion, to evaluate TG activity in the established optimal medium, it is confirmed that the basal and potato dextrose broth medium were used as a control, and the highest TG production was measured, which was highlighted in the established optimal medium.

• Journal of Applied Biological Chemistry
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• v.53 no.4
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• pp.225-231
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• 2010

To understand the inhibitory activity with changing hydroxyl substituents ($R_l-R_9$) of polyhydroxy substituted 2-phenyl-l,4-benzopyrone analogues (1-25) against tyrosinase (PDB ID: oxy-form; 1WX2), molecular docking and the three dimensional quantitative structure-activity relationships (3D-QSARs: Comparative molecular field analysis (CoMFA) & Comparative molecular similarity indices analysis (CoMSIA)) were studied quantitatively. The statistically best models were CoMFA 1 and CoMSIA 1 model from the results. The optimized CoMSIA 1 model with the sensitivity of the perturbation and the prediction produced ($dq^2'/dr_{yy'}^2$=1.009 & $q^2$=0.51l) by a progressive scrambling analysis were not dependent on chance correlation. The inhibitory activities with optimized CoMSIA 1 model were dependent upon electrostatic factor (51.4%) of substrate molecules. Contour mapping the 3D-QSAR models to the active site of tyrosinase provides new insight into the interaction between tyrosinase as receptor and 2-phenyl-l,4-benzopyrone analogues as inhibitor. Therefore, the results will he able to apply to the optimization of a new potent tyrosinase inhibitors.

• The Korean Journal of Pesticide Science
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• v.14 no.3
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• pp.183-190
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• 2010

To search the new potent herbicidal agents by receptor-based approach, the interactions between receptor and substrate molecules from molecular docking to acetyl-CoA carboxylase(PDB code: 3K8X) of 2-(4-(6-chloro-2-benzoxazolyl)oxy)phenoxy-N-phenylpropionamide analogues (1-38) as substrate molecules were performed and discussed quantitatively. The most of the substrate molecules were formated 2 H-bonds between carbonyl oxygen atom of the substrate molecules and the amino acid residues (Ala1627 and Ile1735) in binding site of acetyl-CoA carboxylase (ACCase). But, the substrate molecules such as $R_l$=Acetyl substituents (6 & P9) were formated 3 H-bonds between H-bond acceptors in the substrate molecules and the H-bond donors in three amino acid residues including the rest residue (Gly 1998). Therefore, the inhibitory activity factors of the substrate molecules against ACCase are due to the H-bonding characters that will be able to apply to the optimization of herbicidal agents.