• Bulletin of the Korean Chemical Society
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• 제31권6호
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• pp.1519-1526
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• 2010

The behavior of peptide or protein solutes in saline aqueous solution is a fundamental topic in physical chemistry. Addition of ions can strongly alter the thermodynamic and physical properties of peptide molecules in solution. In order to study the effects of added ionic salts on protein conformation and dynamics, we have used the molecular dynamics (MD) simulations to investigate the behavior of Staphylococcus aureus Hfq protein under two different ionic concentrations: 0.1 M NaCl and 1.0 M NaCl in presence and absence of RNA (a hepta-oligoribonucleotide AU5G). Hfq, a global regulator of gene expression is highly conserved and abundant RNA-binding protein. It is already reported that in vivo the increase of ionic strength results in a drastic reduction of Hfq affinity for $Q{\beta}$ RNA and reduces the tendency of aggregation of Escherichia coli host factor hexamers. Our results revealed the crucial role of 0.1 M NaCl Hfq system on the bases with strong hydrogen bonding interactions and by stabilizing the aromatic stacking of Tyr42 residue of the adjacent subunits/monomers with the adenine and uridine nucleobases. An increase in RNA pore diameter and weakened compactness of the Hfq-RNA complex was clearly observed in 1.0 M NaCl Hfq system with bound RNA. Aggregation of monomers in Hfq and the interaction of Hfq with RNA are greatly affected due to the presence of high ionic strength. Higher the ionic concentration, weaker is the aggregation and interaction. Our results were compatible with the experimental data and this is the first theoretical report for the experimental study done in 1980 by Uhlenbeck group for the present system.

• Journal of Ginseng Research
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• 제44권2호
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• pp.247-257
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• 2020

Background: Multidrug resistance (MDR) to chemotherapy drugs remains a major challenge in clinical cancer treatment. Here we investigated whether and how ginsenoside Rg5 overcomes the MDR mediated by ABCB1 transporter in vitro and in vivo. Methods: Cytotoxicity and colon formation as well as the intracellular accumulation of ABCB1 substrates were carried out in MDR cancer cells A2780/T and A549/T for evaluating the reversal effects of Rg5. The expressions of ABCB1 and Nrf2/AKT pathway were determined by Western blotting. An A549/T cell xenograft model was established to investigate the MDR reversal activity of Rg5 in vivo. Results: Rg5 significantly reversed ABCB1-mediated MDR by increasing the intracellular accumulation of ABCB1 substrates without altering protein expression of ABCB1. Moreover, Rg5 activated ABCB1 ATPase and reduced verapamil-stimulated ATPase activity, suggesting a high affinity of Rg5 to ABCB1 binding site which was further demonstrated by molecular docking analysis. In addition, co-treatment of Rg5 and docetaxel (TXT) suppressed the expression of Nrf2 and phosphorylation of AKT, indicating that sensitizing effect of Rg5 associated with AKT/Nrf2 pathway. In nude mice bearing A549/T tumor, Rg5 and TXT treatment significantly suppressed the growth of drug-resistant tumors without increase in toxicity when compared to TXT given alone at same dose. Conclusion: Therefore, combination therapy of Rg5 and chemotherapy drugs is a strategy for the adjuvant chemotherapy, which encourages further pharmacokinetic and clinical studies.

• 대한약침학회지
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• 제18권2호
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• pp.7-18
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• 2015

Objectives: Lawsone (1,4 naphthoquinone) is a non redox cycling compound that can be catalyzed by DT diaphorase (DTD) into 1,2,4-trihydroxynaphthalene (THN), which can generate reactive oxygen species by auto oxidation. The purpose of this study was to evaluate the toxicity of the phytomarker 1,4 naphthoquinone and its metabolite THN by using the molecular docking program AutoDock 4. Methods: The 3D structure of ligands such as hydrogen peroxide ($H_2O_2$), nitric oxide synthase (NOS), catalase (CAT), glutathione (GSH), glutathione reductase (GR), glucose 6-phosphate dehydrogenase (G6PDH) and nicotinamide adenine dinucleotide phosphate hydrogen (NADPH) were drawn using hyperchem drawing tools and minimizing the energy of all pdb files with the help of hyperchem by $MM^+$ followed by a semi-empirical (PM3) method. The docking process was studied with ligand molecules to identify suitable dockings at protein binding sites through annealing and genetic simulation algorithms. The program auto dock tools (ADT) was released as an extension suite to the python molecular viewer used to prepare proteins and ligands. Grids centered on active sites were obtained with spacings of $54{\times}55{\times}56$, and a grid spacing of 0.503 was calculated. Comparisons of Global and Local Search Methods in Drug Docking were adopted to determine parameters; a maximum number of 250,000 energy evaluations, a maximum number of generations of 27,000, and mutation and crossover rates of 0.02 and 0.8 were used. The number of docking runs was set to 10. Results: Lawsone and THN can be considered to efficiently bind with NOS, CAT, GSH, GR, G6PDH and NADPH, which has been confirmed through hydrogen bond affinity with the respective amino acids. Conclusion: Naphthoquinone derivatives of lawsone, which can be metabolized into THN by a catalyst DTD, were examined. Lawsone and THN were found to be identically potent molecules for their affinities for selected proteins.

• 미생물학회지
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• 제54권3호
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• pp.208-213
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• 2018

Nuclear factor kappa B ($NF{\kappa}B$)의 활성화는 염증을 일으킨다. 이 때, inducible nitric oxide synthase (iNOS)가 발현된다. 우리 선행 연구에 의하면 Bacillus licheniformis B1에 의해 제조된 발효대두에 있는 septapeptide (GVAWWMY)가 대식세포에서 iNOS mRNA 발현과 NO 생산을 억제하였다. 본 연구에서 septapeptide의 처리가 $I{\kappa}B{\alpha}$ ($NF{\kappa}B$ 억제 단백질)의 분해를 억제하여 LPS에 의해 유도되는 $NF{\kappa}B$의 활성화를 억제함을 확인했다. 분자 docking에 의해 septapeptide가 ${\kappa}B$ kinase ${\beta}$ ($IKK{\beta}$)에 부착하여 $I{\kappa}B{\alpha}$의 인산화를 방해할 가능성이 있다. Septapeptide는 높은 친화도로(-8.7 kcal/Mol) $IKK{\beta}$의 kinase domain에 부착해서 kinase 활성에 크게 영향을 미칠 수 있다.

• Archives of Pharmacal Research
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• 제27권1호
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• pp.77-82
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• 2004

DA-125, a novel derivative of adriamycin, is known for its anti-cancer activity. In this study, the inhibitory mechanism of DA-125 on topoisomerase was investigated in the simian virus 40 (SV40) replicating CV-1 cell by studying the SV40 DNA replication intermediates and DNA-topoisomerase complexes. DNA-protein complexes that were formed in the drug-treated cells were quantitated by using a glass filter assay. SV40 DNA replication intermediates that were accumulated in the drug-treated CV-1 cell were analyzed in a high resolution gel. DA-125 did not accumulate B-dimers of SV40 DNA replication intermediates which were found in the adriamycin-treated CV-1 cells. DA-125 induced a dose-dependent formation of the DNA-protein complexes, while adriamycin did not. When adriamycin and etoposide (VP16) were added to the SV40-infected cells at the same time, adriamycin blocked the formation of the DNA-protein complexes induced by VP16 in a dose-dependent manner. However, DA-125 blocked the formation of the DNA-protein complexes induced by VP16 up to the maximum level of the DNA-protein complexes that were induced by DA-125 alone. Adriamycin and DA-125 did not inhibit the formation of the DNA-protein complexes that were caused by camptothecin, a known topoisomerase I poison. DA-125 is bifunctional in inhibiting topoisomerase II because it simultaneously has the properties of the topoisomerase II poison and the DNA intercalator. As a topoisomerase II poison, DA-125 alone induced dose-dependent formation of the DNA-protein complexes. However, as a DNA intercalator, it quantitatively inhibited the formation of the DNA-protein complexes induced by a strong topoisomerase II poison VP16. Furthermore considering that the levels of the DNA-protein complex induced by VP16 were decreased by DA-125 in terms of the topoisomerase II poison, we suggest that DA-125 has a higher affinity to the drug-binding sites of DNA than VP16 has.

• 미생물학회지
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• 제54권4호
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• pp.420-427
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• 2018

효모균 타이로실-tRNA 합성효소(Sc YRS)와 엠버 멈춤코돈을 인식하는 대장균 시작tRNA 변이체(fMam $tRNA_{CUA}$)쌍은 대장균에서 단백질 생합성시 원하는 특정 위치에 비천연아미노산을 도입하는데 활용된다. Sc YRS/fMam $tRNA_{CUA}$쌍의 엠버써프레션 활성을 높이기 위해 fMam $tRNA_{CUA}$의 첫번째 안티코돈 염기를 인식하는 Sc YRS의 320번, 321번 아미노산 잔기를 암호화하는 염기서열을 무작위로 돌연변이시킨 라이브러리를 제작하였다. 엠버써프레션에 의한 클로람페니콜 저항성을 이용해 라이브러리를 탐색하여 활성이 향상된 2개의 돌연변이주를 선별하였다. 이들의 클로람페니콜 저항성 성장의 $IC_{50}$값은 야생형 YRS보다 1.7~2.3배 높았으며, in vivo 엠버써프레션 활성을 비교한 결과 3~6.5배의 활성 증가가 나타났다. 높은 활성을 보인 mYRS-3 (P320A/D321A) 단백질의 fMam $tRNA_{CUA}$에 대한 in vitro aminoacylation kinetics 분석은 야생형보다 약 7배 높은 효소활성을 보였으며, 이는 주로 기질인 fMam $tRNA_{CUA}$에 대한 결합 친화도가 증가하여 나타났다. 이런 접근법을 이용하여 다양한 종류의 비천연 아미노산 도입에 활용되는 aminoacyl-tRNA 합성효소의 엠버써프레션 활성을 높임으로써 엠버 멈춤코돈을 이용한 비천연 아미노산 도입 효율성을 높일 수 있을 것이다.

• 미생물학회지
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• 제47권3호
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• pp.200-208
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• 2011

임상에서 가장 문제가 되는 MLS (macrolide-lincosamidestreptogramin B) 항생제 내성은 Erm 단백질에 의하여 23S rRNA의 A2058에 dimethylation시킴으로써 MLS 항생제의 부착능을 저해함으로써 나타내는 내성이다. ErmSF는 다른 Erm 단백질과 달리 매우 긴 N-terminal end region (NTER)을 가지고 있으며 RNA에 잘 부착되는 것으로 알려진 arginine이 25%를 차지하고 있다. 특히 NTER의 점차적인 제거는 이에 따른 점차적인 활성의 감소 그리고 이의 완전한 제거는 98%의 활성소실을 가져다 주는 것으로 밝혀져서 단순 부착에 의한 활성에의 기여를 암시하고 있다. 뿐만 아니라 NTER 다음에 붙어 있는 아미노산은 제거되었을 때 활성이 소실되는 매우 중요한 아미노산임이 밝혀졌다. 이러한 사실에 근거, 서로 다른 복제원점을 가짐으로써 동일한 세포 내에 존재할 수 있으며 발현 체계가 동일하나 copy수가 차이가 있어서 단백질 발현 양에 차이를 가져다 주는 새로운 단백질 동시 발현체계를 개발하고 이를 적용하여 NTER 함유 펩타이드를 copy수가 많은 pET23b 체계의 담체에서, ErmSF는 copy수가 적은 pACYC184 담체 체계에서 발현 시킴으로써 펩타이드가 한 세포 내에서 ErmSF 보다 훨씬 더 많이 발현되도록 하여 이 펩타이드가 ErmSF의 활성을 저해할 수 있는지 확인하였다. 계획된 대로 IPTG에 의한 유도 없이도 펩타이드가 ErmSF보다 세포 내에서 훨씬 많이 발현되었다. 그러나 생체 내에서는 그 활성의 저해를 확인 할 수 없었다. 따라서 ErmSF의 활성은 NTER 펩타이드의 단순한 부착에 의해서 이루어지는 것이 아니라 conformational change 등의 역동적인 상호작용을 통하여 이루어지는 것으로 사료되었다. 따라서 ErmSF와 23S rRNA와의 복합체 구조의 규명 그리고 NTER과 ErmSF protein body의 부착양식에 대한 구체적인 생화학적 규명이 이루어지면 이러한 접근법은 이 단백질의 억제제를 창출하는데 기여를 할 수 있을 것으로 사료된다.

• 생명과학회지
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• 제32권2호
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• pp.135-141
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• 2022

Mouse thymosin β-4 (TB4) 유전자를 Escherichia coli에서 intein-tag 융합 단백질로 발현시키고 정제하였다. 재조합 TB4-intein 융합 단백질의 분자량을 10% glycine SDS-PAGE로 확인한 결과, 세포내 soluble 분획에서 60 kDa의 단백질을 얻을 수 있었고, 유도발현 최적 조건은 0.1 mM IPTG, 25℃에서 3시간 동안 유도 발현할 때가 최적임을 확인하였다. TB4 만을 얻기 위해서 유도발현된 TB4-intein을 DTT를 이용해 self-cleavage를 일으킨 다음, chitin bead를 이용한 친화성 크로마토그라피로 정제 후 분자량을 확인 한 결과, 5 kDa으로 확인되었으며, 순도는 95%이상 이었다. 정제한 recombinant TB4가 생물학적 기능을 보유하고 있는지 확인을 하기 위하여, TB4를 농도 별(1~1,000 ng/ml)로 하여 HT1080 cell을 이용한 cell migration을 측정한 결과, 모든 농도에서 recombinant TB4가 화학합성한 TB4 보다 약 20% 이상 높은 활성을 보였으며, recombinant TB4 1 ng/ml의 농도에서 cell migration 활성이 가장 높게 나타났다. Recombinant TB4를 마우스 상처 부위에 5일 동안 매일 처리한 결과(최종 처리 농도 0.5 mg/ml), 화학합성 TB4 보다 recombinant TB4의 상처치유 활성이 약 35% 더 높음을 알 수 있었다. 이상의 결과는 recombinant TB4가 화학합성 TB4보다 cell migration과 상처치유에 훨씬 높은 활성을 나타냄을 보여주고 있다.

• Journal of Oral Medicine and Pain
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• 제33권3호
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• pp.229-240
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• 2008

동물성 mucin은 인체 타액 mucin과 유사한 구조적 특성을 가지고 있으므로 효과적인 타액대체제의 개발에 적합한 성분으로 여겨져 왔다. 구강건조증 환자가 동물성 mucin 함유 타액대체제를 사용할 경우, 동물성 mucin과 인체 타액에 존재하는 항균 단백질이 용액상태인 전타액과 구강표면에 형성된 pellicle에 동시에 존재할 수 있으므로 이들 물질사이에 상호작용이 일어 날 수 있을 것이다. 본 연구의 목적은 용액과 hydroxyapatite(HA) 표면에서 동물성 mucin이 peroxidase 활성에 미치는 영향을 평가하기 위하여 시행되었다. 동물성 mucin이 peroxidase 활성에 미치는 영향은 돼지의 위장 mucin(porcine gastric mucin, PGM) 이나 소의 악하선 mucin(bovine submaxillary mucin, BSM)을 소의 lactoperoxidase(bovine lactoperoxidase, bLPO)나 타액검체와 incubation하는 방법을 사용하여 분석하였고, 표면상태에서의 연구를 위해 HA beads, HA disc, 소의 치아와 같은 3가지 종류의 HA 표면을 활용하였다. Peroxidase 활성은 NbsSCN 법을 이용하여 분석하였다. 1. 돼지위장 mucin은 용액상태에서 bLPO 활성을 증가시켰으나 타액검체의 peroxidase(peroxidase in saliva sample, POS) 활성에는 영향을 미치지 않았다. 2. 소 악하선 mucin은 용액상태에서 bLPO와 POS 활성에 영향을 미치지 않았다. 3. HA 표면에 부착된 돼지위장 mucin은 peroxidase의 부착과 활성을 증가시켰고 이러한 효과는 세 종류의 HA 표면 모두에서 일어났으며, POS의 활성증가는 HA beads와 소 치아 표면에서만 나타났다. 4. bLPO와 돼지위장 mucin의 혼합물을 HA 표면에 부착시킬 경우, HA beads와 HA disc 표면에서의 peroxidase 활성은 증가하였다. 5. bLPO의 돼지위장 mucin에 대한 부착친화도는 소 악하선 mucin에 비해 컸다. 이상의 결과를 종합해 볼 때 동물성 mucin은 용액상태와 HA 표면에서 peroxidase 활성에 영향을 미침을 알 수 있으며, 동물성 mucin을 포함하고 있는 타액대체제는 인체타액 및 타액대체제에 있는 peroxidase 활성에 영향을 미칠 수 있을 것이다.

• Asian-Australasian Journal of Animal Sciences
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• 제18권5호
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• pp.747-754
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• 2005

Nutritional regulation of gene expression associated with growth and feeding behavior in avian species can become an important technique to improve poultry production according to the supply of nutrients in the diet. Insulin-like growth factor-I (IGF-I) found in chickens has been characterized to be a 70 amino acid polypeptide and plays an important role in growth and metabolism. Although it is been well known that IGF-I is highly associated with embryonic development and post-hatching growth, changes in the distribution of IGF-I gene expression throughout early- to late-embryogenesis have not been studied so far. We revealed that the developmental pattern of IGF-I gene expression during embryogenesis differed among various tissues. No bands of IGF-I mRNA were detected in embryonic liver at 7 days of incubation, and thereafter the amount of hepatic IGF-I mRNA was increased from 14 to 20 days of incubation. In eyes, a peak in IGF-I mRNA levels occurred at mid-embryogenesis, but by contrast, IGF-I mRNA was barely detectable in the heart throughout all incubation periods. In the muscle, no significant difference in IGF-I gene expression was observed during different stages of embryogenesis. After hatching, hepatic IGF-I gene expression as well as plasma IGF-I concentration increases rapidly with age, reaches a peak before sexual maturity, and then declines. The IGF-I gene expression is very sensitive to changes in nutritional conditions. Food-restriction and fasting decreased hepatic IGF-I gene expression and refeeding restored IGF-I gene expression to the level of fed chickens. Dietary protein is also a very strong factor in changing hepatic IGF-I gene expression. Refeeding with dietary protein alone successfully restored hepatic IGF-I gene expression of fasted chickens to the level of fed controls. In most circumstances, IGF-I makes a complex with specific high-affinity IGF-binding proteins (IGFBPs). So far, four different IGFBPs have been identified in avian species and the major IGFBP in chicken plasma has been reported to be IGFBP-2. We studied the relationship between nutritional status and IGFBP-2 gene expression in various tissues of young chickens. In the liver of fed chickens, almost no IGFBP-2 mRNA was detected. However, fasting markedly increased hepatic IGFBP-2 gene expression, and the level was reduced after refeeding. In the gizzard of well-fed young chickens, IGFBP-2 gene expression was detected and fasting significantly elevated gizzard IGFBP-2 mRNA levels to about double that of fed controls. After refeeding, gizzard IGFBP-2 gene expression decreased similar to hepatic IGFBP-2 gene expression. In the brain, IGFBP-2 mRNA was observed in fed chickens and had significantly decreased by fasting. In the kidney, IGFBP-2 gene expression was observed but not influenced by fasting and refeeding. Recently, we have demonstrated in vivo that gizzard and hepatic IGFBP-2 gene expression in fasted chickens was rapidly reduced by intravenous administration of insulin, as indicated that in young chickens the reduction in gizzard and hepatic IGFBP-2 gene expression in vivo stimulated by malnutrition may be, in part, regulated by means of the increase in plasma insulin concentration via an insulin-response element. The influence of dietary protein source (isolated soybean protein vs. casein) and the supplementation of essential amino acids on gizzard IGFBP-2 gene expression was examined. In both soybean protein and casein diet groups, the deficiency of essential amino acids stimulated chickens to increase gizzard IGFBP-2 gene expression. Although amino acid supplementation of a soybean protein diet significantly decreased gizzard IGFBP-2 mRNA levels, a similar reduction was not observed in chickens fed a casein diet supplemented with amino acids. This overview of nutritional regulation of IGF-I and IGFBP-2 gene expression in young chickens would serve for the establishment of the supply of nutrients to diets to improve poultry production.