• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.325-330
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• 2005

We are generally interested in the analysis, detection and prediction of structural motifs in proteins, in order to infer compatibility of amino acid sequence to structure in proteins of known three-dimensional structure available in the Protein Data Bank. In this context, we are analyzing some of the well-characterized structural motifs in proteins. We have analyzed simple structural motifs, such as, ${\beta}$-turns and ${\gamma}$-turns by evaluating the statistically significant type-dependent amino acid positional preferences in enlarged representative protein datasets and revised the amino acid preferences. In doing so, we identified a number of ‘unexpected’ isolated ${\beta}$-turns with a proline amino acid residue at the (i+2) position. We extended our study to the identification of multiple turns, continuous turns and to peptides that correspond to the combinations of individual ${\beta}$ and ${\gamma}$-turns in proteins and examined the hydrogen-bond interactions likely to stabilize these peptides. This led us to develop a database of structural motifs in proteins (DSMP) that would primarily allow us to make queries based on the various fields in the database for some well-characterized structural motifs, such as, helices, ${\beta}$-strands, turns, ${\beta}$-hairpins, ${\beta}$-${\alpha}$-${\beta}$, ${\psi}$-loops, ${\beta}$-sheets, disulphide bridges. We have recently implemented this information for all entries in the current PDB in a relational database called ODSMP using Oracle9i that is easy to update and maintain and added few additional structural motifs. We have also developed another relational database corresponding to amino acid sequences and their associated secondary structure for representative proteins in the PDB called PSSARD. This database allows flexible queries to be made on the compatibility of amino acid sequences in the PDB to ‘user-defined’ super-secondary structure conformation and vice-versa. Currently, we have extended this database to include nearly 23,000 protein crystal structures available in the PDB. Further, we have analyzed the ‘structural plasticity’ associated with the ${\beta}$-propeller structural motif We have developed a method to automatically detect ${\beta}$-propellers from the PDB codes. We evaluated the accuracy and consistency of predicting ${\beta}$ and ${\gamma}$-turns in proteins using the residue-coupled model. I will discuss results of our work and describe databases and software applications that have been developed.

• Asian Pacific Journal of Cancer Prevention
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• 제15권23호
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• pp.10413-10420
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• 2015

Side effects are an unavoidable consequence of chemotherapy drugs, during which liver injury often takes place. The current study was designed to investigate the protective effect of Astragalus polysaccharides (APS) against the hepatotoxicity induced by frequently-used chemical therapy agents, cyclophosphamide (CTX), docetaxel (DTX) and epirubicin (EPI)) in mice. Mice were divided into five groups, controls, low or high dose groups ($DTX_L$, $CTX_L$, $EPI_L$ or $DTX_H$, $CTX_H$, $EPI_H$), and low or high dose chemotherapeutics+APS groups ($DTX_L$+APS, $CTX_L$+APS, $EPI_L$+APS or $DTX_H$+APS, $CTX_H$+APS, $EPI_H$+APS). Controls were treated with equivalent normal saline for 28 days every other day; low or high dose group were intraperitoneal (i.p) injected with low or high doses of CTX, DTX and EPI for 28 days every other day; low or high dose chemotherapeutics+APS group were separately intraperitoneal (i.p) injected with chemotherapeutics for 28 days every other day and i.p with APS (100 mg/kg) for 7 days continually from the 22th to the 28th days. The body weight, serum levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST), histopathological features, and ultrastructure morphological change of liver tissues, protein expression level of caspase-3 were estimated at different time points. With high dose treatment of DTX, CTX and EPI, weight gain was inhibited and serum levels of ALT and AST were significantly increased. Sections of liver tissue showed massive hepatotoxicity in $CTX_H$ group compared to the control group, including hepatic lobule disorder, granular and vacuolar degeneration and necrosis in hepatic cells. These changes were confirmed at ultrastructural level, including obvious pyknosis, heterochromatin aggregation, nuclear membrane resolution, and chondrosome crystal decrease. Western blotting revealed that the protein levels of caspase-3 increased in $CTX_H$ group. The low dose groups exhibited trivial hepatotoxicity. More interestingly, after 100 mg/kg APS, liver injury was redecued not only regarding serum transaminase activities (low or high dose chemotherapeutics+APS group), but also from pathological and ultrastructural changes and the protein levels of caspase-3 ($CTX_H$+APS group). In conclusion, DTX, CTX and EPI induce liver damage in a dose dependent manner, whereas APS exerted protective effects.

• Applied Biological Chemistry
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• 제22권2호
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• pp.123-134
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• 1979

Bacillus thuringiensis Berliner를 이용한 미생물 살충제의 개발을 위하여 연구를 행한바 다음과 같은 결과를 얻었다. (1) 제사공장에서 폐기되는 자견수의 냉동 건조물 중에는 조단백질 함량이 51.825%가 함유되어 있으며 기타 무기염류도 다량 함유되어 있어 자견수는 본 세균 배양의 좋은 영양원이 될 수 있다. (2) 현수성으로 보아 가장 양호한 제제는 F-5로서 그 조성은 Cell-Spore-Crystal 혼합을 0.2 g, 200-mesh Kaolin 25 g, New Kalgen NX-150, 2.59 그리고 glycerine 2.5 g을 증류수 8ml의 비율로 혼합하여 80 mesh 입제로 한 것이다. (3) F-5, F-6, 및 F-7의 조성중 다른 것은 전부 같고 다만 Cell-Spore-Crystal 혼합들의 함량이 F-5에서는 0.2 g, F-6에서는 0.4 g, F-7에서는 0.6 g인 점이 다르므로 이들 제제의 물리성은 거의 동일하다. (4) F-5, F-6 및 F-7은 5% 농도에서 무궁화잎 밤나방, 송충, 회양목 명나방 유충 등에 우수한 살충효과를 보였다. (5) 제제의 일 성분으로 $NaHCO_3$를 첨가한 F-8과 F-9는 무궁화잎 밤나방과 송충에 대한 독성 실험에서 $NaHCO_3$를 함유하지 않은 F-6 보다 현저한 독성의 감소를 보여주었다. (6) $(NH_4)_2SO_4$ 0.2%와 glucose 0.8%를 자견수에 용해하여 pH를 7.05로 조정한 배지인 M-3을 사용하여 aeration 시키면서 96시간 배양하였을때 포자수는 최고 $2.97{\times}10^9/ml$에 도달하였다. (7) F-6은 제제후 70일 동안 실온에서 저장시 무궁화잎 밤나방과 송충에 대한 독성이 약간 감소하는 경향이 있었으므로 냉암소에 저장함이 바람직하다. (8) F-6은 야외 살포로 대추나무의 노랑쐐기나방 회양목 명나방유충, 장미의 찔레수염 진딧물 등의 방제에 좋은 효과를 보였다.

• Journal of Applied Biological Chemistry
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• 제51권6호
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• pp.277-284
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• 2008

유과 품질에 큰 영향을 주는 수침 처리가 찹쌀, 찹쌀 가루 및 찹쌀 전분의 물리화학적 특성에 미치는 영향을 조사하였다. 수침처리는 세 가지 시료 모두의 등온흡습곡선에 큰 영향을 주었으나 특정한 경향을 나타내지는 않았다. 용해도는 세 가지 시료 모두 호화개시온도 이후 급격히 증가하였고 수침기간이 증가함에 따라 점차 증가하는 경향을 나타내었다. 팽윤력은 찹쌀 및 찹쌀가루의 경우 수침기간이 증가함에 따라 감소하였으나 찹쌀 전분의 경우 감소하였다가 증가하는 경향을 나타내었다. X-선 회절 분석 결과, 수침처리를 한 시료 모두 A형 결정형 형태를 유지하였고, 상대적 결정화도는 수침이 진행될수록 감소하였다. 이로 보아 수침 과정 동안 전분의 일부 결정형 영역이 분해된다는 것을 확인할 수 있었다. RVA 점도 특성을 분석한 결과, 찹쌀과 찹쌀 가루의 경우 유사한 경향을 나타내었고, 찹쌀 전분의 경우 이들과 다른 RVA 점도 특성을 나타내었다. 이처럼 Native 상태의 찹쌀, 찹쌀 가루와 찹쌀 전분의 RVA 점도 특성 차이는 수침 초기에 단백질과 지질 등이 용출되어 제거되는 것에 기인한 것으로 보이며, 점도가 감소하는 이유는 수침동안 일어나는 미생물의 생육작용에 의한 것으로 생각된다.

• 한국잠사곤충학회지
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• 제38권2호
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• pp.160-167
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• 1996

견단백질을 구성하는 액상견사막인 중부견사막을 추출한 후, 약3배로 급속히 연신하여 견 monofilament를 제작하였다. 이 시료를 연화시켜 분자간의 수소결합능을 저하시키기 위해 비등상태의 증류수에 팽윤시킨 다음 연신처리를 행한 결과는 다음과 같다. 1. 열분석과 X선회석의 결과로부터 견사막건조물시료은 Silk I형의 결정영역 및 random 무정형분자로 구성되어 있었으나 monofilament시료에서는 부분적으로 Silk II형결정이 발현하기 시작하여 더욱더 연신한 62.5% 연신시료에서는 거의 완전한 Silk II형결정으로 전이하는 것을 알 수 있다. 2. 복굴절율 및 밀도는 monofilament시료에 비해 연신율의 상승과 함께 증가하는 경향을 나타내어 견 fibroin분자의 배향은 초기에 급격히 증가하여 fibroin분자의 배향이 완성되었다. 3. 가수분해처리에 의한 복굴절율은 연신율의 상승에 따라서 증가하는 경향이었다. 또, 가수분해의 처리시간과의 관계에서는 연신율이 증가함에 따라 복굴절율도 거의 일정하게 나타나 배향결정화가 진행되어 배열이 좋게 되어진 무정형이 결정으로 전이하는 것이 시사되었다. 4. 62.5% 연신시료를 가수분해한 경우의 X선회절은 가수분해에 의해 배향의 흐트러짐은 생기나 결정풍괴는 일어나지 않았다. 열분석에서도 가수분해의 처리시간이 증가함에 따라 최대흡열 peak 온도는 저온측으로 이동하여 가수분해처리에 의해 고배향의 무정형부분이 유출로 인하여 결정부분의 배향이 흐트러진다는 것이 X선분석 결과로부터 추측되어진다.

• KSBB Journal
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• 제21권4호
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• pp.279-285
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• 2006

본 연구에서는 trypsin을 모델 단백질로 하여 단백질 본연의 환성을 유지할 수 있는 고정화 방법을 찾기 위하여 공유결합방법과 친화력 결합방법을 이용하여 trypsin을 고정화 하였다. Streptavidin-biotin system을 이용한 고정화 방법은 bioactivity 유지측면에서 공유결합 방법보다 우수함을 확인하였다. 하지만 streptavidin-biotin system을 이용하였을 때 고정화 수율이 낮은 것은 해결해야 할 과제이다. 분자량이 다른 기질들(BAPNA, insulin, BSA)을 대상으로 고정화 trypsin의 부위 특이적 절단 특성을 분석한 결과 streptavidin-biotin에 의해 고정화된 trypsin이 절단효율도 높고 sequence coverage도 높은 것으로 확인되었다. 또한 공유결합된 trypsin은 견고한 분자구조를 나타낸 반면 streptavidin-biotin system으로 고정화된 trypsin은 유연성이 높은 것을 QCM-D를 이용하여 관찰할 수 있었다. 따라서 streptavidin-biotin system에 의한 고정화 방법에서 streptavidin-biotin 결합이 일종의 spacer arm 역할을 하면서 고정화된 trypsin의 분자유연성을 향상시켜 절단반응의 부위특이성과 절단수율을 향상시키는 것으로 판단되었다.

• BMB Reports
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• 제40권5호
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• pp.773-782
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• 2007

Different isolates of the soil bacterium Bacillus thuringiensis produce multiple crystal (Cry) proteins toxic to a variety of insects, nematodes and protozoans. These insecticidal Cry toxins are known to be active against specific insect orders, being harmless to mammals, birds, amphibians, and reptiles. Due to these characteristics, genes encoding several Cry toxins have been engineered in order to be expressed by a variety of crop plants to control insectpests. The cotton boll weevil, Anthonomus grandis, and the fall armyworm, Spodoptera frugiperda, are the major economically devastating pests of cotton crop in Brazil, causing severe losses, mainly due to their endophytic habit, which results in damages to the cotton boll and floral bud structures. A cry1Ia-type gene, designated cry1Ia12, was isolated and cloned from the Bt S811 strain. Nucleotide sequencing of the cry1Ia12 gene revealed an open reading frame of 2160 bp, encoding a protein of 719 amino acid residues in length, with a predicted molecular mass of 81 kDa. The amino acid sequence of Cry1Ia12 is 99% identical to the known Cry1Ia proteins and differs from them only in one or two amino acid residues positioned along the three domains involved in the insecticidal activity of the toxin. The recombinant Cry1Ia12 protein, corresponding to the cry1Ia12 gene expressed in Escherichia coli cells, showed moderate toxicity towards first instar larvae of both cotton boll weevil and fall armyworm. The highest concentration of the recombinant Cry1Ia12 tested to achieve the maximum toxicities against cotton boll weevil larvae and fall armyworm larvae were 230 ${\mu}g/mL$ and 5 ${\mu}g/mL$, respectively. The herein demonstrated insecticidal activity of the recombinant Cry1Ia12 toxin against cotton boll weevil and fall armyworm larvae opens promising perspectives for the genetic engineering of cotton crop resistant to both these devastating pests in Brazil.

• Journal of Microbiology and Biotechnology
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• 제19권10호
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• pp.1223-1229
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• 2009

To construct a new recombinant strain of Bacillus velezensis that has antifungal and insecticidal activity via the expression of the insecticidal Bacillus thuringiensis crystal protein, a B. thuringiensis expression vector (pHT1K-1Ac) was generated that contained the B. thuringiensis cry1Ac gene under the control of its endogenous promoter in a minimal E. coli-B. thuringiensis shuttle vector (pHT1K). This vector was introduced into a B. velezensis isolate that showed high antifungal activities against several plant diseases, including rice blast (Magnaporthe grisea), rice sheath blight (Rhizotonia solani), tomato gray mold (Botrytis cinerea), tomato late blight (Phytophthora infestans), and wheat leaf rust (Puccinia recondita), by electroporation. The recombinant B. velezensis strain was confirmed by PCR using cry1Ac-specific primers. Additionally, the recombinant strain produced a protein approximately 130 kDa in size and parasporal inclusion bodies similar to B. thuringiensis. The in vivo antifungal activity assay demonstrated that the activity of the recombinant B. velezensis strain was maintained at the same level as that of wild-type B. velezensis. Furthermore, it exhibited high insecticidal activity against a lepidopteran pest, Plutella xylostella, although its activity was lower than that of a recombinant B. thuringiensis strain, whereas wild-type B. velezensis strain did not show any insecticidal activity. These results suggest that this recombinant B. velezensis strain can be used to control harmful insect pests and fungal diseases simultaneously in one crop.

• Journal of Dairy Science and Biotechnology
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• 제27권1호
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• pp.1-12
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• 2009

In 2008, baby formula containing melamine was found to be responsible for a large outbreak of renal failure in infants in China. A total of 294,000 infants were hospitalized, and at least 6 babies died due to ingestion of the tainted formula. Melamine contains high levels of nitrogen (>60%), which is used as an indicator of protein content. Therefore, high levels of melamine in infant formula were thought to be the result of deliberate contamination m an attempt to increase its apparent protein content. Following inspections by China's national inspection agency, assorted products from at least 22 dairy manufacturers across China were found to have varied levels of melamine (range: 0.096196.61 mg/kg). Melamine co-exposure with cyanuric acid can induce acute melamine-cyanurate crystal nephropathy, which can lead to renal failure at much lower doses than if either compound were ingested alone. However, currently, there are very few data on melamine analogues other than cyanuric acid. At an expert meeting of the WHO and FAO held to review toxicological aspects of melamine and cyanuric acid on December 14, 2008, a new tolerable daily intake (TDI) of melamine was established that could be applied to the entire population, including infants. Therefore, a risk assessment of the various theoretical melamine contamination levels in infant formula and selected representative foods (other than infant formula and sole-source nutrition products) is urgently needed for Korean babies and children up to 7 years of age. Although the undetectable level regulation for infant formula may be low enough to guarantee the safety of babies under the age of 1 year (including premature babies), the melamine standard of 2.5 ppm for foods other than baby formula could be insufficient to protect the 95th percentile population aged 1~2 years because of this demographic's high consumption of milk, yogurt, and soy milk (hazard index = 1.79). Because TDIs are chronic values intended to protect an individual over his/her lifetime, occasional modest ingestion in excess of the TDI is not likely to be a health concern. However, children aged 1~2 years may have renal systems that are comparatively more sensitive to the crystallization of melamine and its analogues. Therefore, governmental jurisdictions may need to practice more prudent management of food items that could raise the melamine exposure for this population.

• The Korean Journal of Physiology and Pharmacology
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• 제19권4호
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• pp.365-372
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• 2015

Aripiprazole (ARI) is a commonly prescribed medication used to treat schizophrenia and bipolar disorder. To date, there have been no studies regarding the molecular pathological and immunotoxicological profiling of aripiprazole. Thus, in the present study, we prepared two different formulas of aripiprazole [Free base crystal of aripiprazole (ARPGCB) and cocrystal of aripiprazole (GCB3004)], and explored their effects on the patterns of survival and apoptosis-regulatory proteins under acute toxicity and cytotoxicity test conditions. Furthermore, we also evaluated the modulatory activity of the different formulations on the immunological responses in macrophages primed by various stimulators such as lipopolysaccharide (LPS), pam3CSK, and poly(I:C) via toll-like receptor 4 (TLR4), TLR2, and TLR3 pathways, respectively. In liver, both ARPGCB and GCB3004 produced similar toxicity profiles. In particular, these two formulas exhibited similar phospho-protein profiling of p65/nuclear factor $(NF)-{\kappa}B$, c-Jun/activator protein (AP)-1, ERK, JNK, p38, caspase 3, and bcl-2 in brain. In contrast, the patterns of these phospho-proteins were variable in other tissues. Moreover, these two formulas did not exhibit any cytotoxicity in C6 glioma cells. Finally, the two formulations at available in vivo concentrations did not block nitric oxide (NO) production from activated macrophage-like RAW264.7 cells stimulated with LPS, pam3CSK, or poly(I:C), nor did they alter the morphological changes of the activated macrophages. Taken together, our present work, as a comparative study of two different formulas of aripiprazole, suggests that these two formulas can be used to achieve similar functional activation of brain proteins related to cell survival and apoptosis and immunotoxicological activities of macrophages.