• BMB Reports
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• 제42권2호
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• pp.113-118
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• 2009

Despite the growing body of evidence suggesting a role for MsrA in antioxidant defense, little is currently known regarding the function of MsrB in cellular protection against oxidative stress. In this study, we overexpressed the mammalian MsrB and MsrA genes in Saccharomyces cerevisiae and assessed their subcellular localization and antioxidant functions. We found that the mitochondrial MsrB3 protein (MsrB3B) was localized to the cytosol, but not to the mitochondria, of the yeast cells. The mitochondrial MsrB2 protein was detected in the mitochondria and, to a lesser extent, the cytosol of the yeast cells. In this study, we report the first evidence that MsrB3 overexpression in yeast cells protected them against $H_2O_2$-mediated cell death. Additionally, MsrB2 overexpression also provided yeast cells with resistance to oxidative stress, as did MsrA overexpression. Our results show that mammalian MsrB and MsrA proteins perform crucial functions in protection against oxidative stress in lower eukaryotic yeast cells.

• 한국정보과학회논문지:소프트웨어및응용
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• 제37권1호
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• pp.74-79
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• 2010

단백질의 아미노산 조성은 생물정보학의 여러 문제를 해결하기 위한 기초적인 정보로 자주 활용된다. 본 논문에서는 아미노산간의 진화적인 연관성을 정의한 BLOSUM 행렬에서 유도한 유사도 함수를 사용하여 아미노산 조성을 결정한다. 이러한 방법은 생물학적인 연관성이 있는 단백질 서열일수록 비슷한 아미노산 조성을 갖도록 한다. 또한 단백질의 구조와 기능에 중요한 역할을 하는 위치-특이적인 아미노산의 분포를 추정하기 위해서 레이더나 음성 신호의 스펙트럼 분석에 사용되는 개념인 시간-종속 분석, 시간 해상도와 주파수 해상도의 개념을 적용하였다. 제안한 방법을 단백질의 세포내 위치예측에 적용하여 기존의 아미노산 조성 추정 방법을 사용하는 것보다 크게 향상된 성능을 보임을 확인하였다.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2004년도 The 3rd Annual Conference for The Korean Society for Bioinformatics Association of Asian Societies for Bioinformatics 2004 Symposium
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• pp.158-166
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• 2004

Predicting the destination of a protein in a cell gives valuable information for annotating the function of the protein. Recent technological breakthroughs have led us to develop more accurate methods for predicting the subcellular localization of proteins. The most important factor in determining the accuracy of these methods, is a way of extracting useful features from protein sequences. We propose a new method for extracting appropriate features only from the sequence data by computing pairwise sequence alignment scores. As a classifier, support vector machine (SVM) is used. The overall prediction accuracy evaluated by the jackknife validation technique reach 94.70% for the eukaryotic non-plant data set and 92.10% for the eukaryotic plant data set, which show the highest prediction accuracy among methods reported so far with such data sets. Our numerical experimental results confirm that our feature extraction method based on pairwise sequence alignment, is useful for this classification problem.

• 대한의생명과학회지
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• 제12권3호
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• pp.201-208
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• 2006

PI3-kinase activity through p85, the regulatory subunit of class IA PI3-kinase, is indispensable for the growth, differentiation, and survival of skeletal muscle cells, but little is known about the function of other regulatory subunits such as p55 and p50. We examined the subcellular localization and the expression of the regulatory subunits of class IA PI3-kinase in L6 myoblasts. Both p55 and p50 as well as p85 were expressed in L6 myoblasts. Whereas p85 was localized at both cytosolic and nuclear tractions, p55 and p50 were localized at only the nuclear traction. During the differentiation of L6 myoblasts, the protein concentrations of both p55 and p50 were decreased but that of p85 was not significantly changed. Menadione-induced oxidative stress induced the translocation of p85 from cytosol to nucleus and the increase of p55 expression. These results suggest that the regulatory subunits of class IA PI3-kinase play an important role in L6 myoblasts.

• 동의생리병리학회지
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• 제22권2호
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• pp.315-320
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• 2008

This study investigated the signaling mechanisms contributed to the vasodilatory effects of HMC05, a herbal prescription. HMC05 acted in an endothelium-independent manner. To elucidate the fundamental mechanisms of its vascular actions, we focused on the signaling molecules involved in actin-myosin filament regulation including 20 kDa myosin light chains (LC20), Rho-associated kinase (ROCK), PKC, JNK and extracellular signal-regulated protein kinase (ERK) in the endothelium-denuded thoracic aorta or isolated smooth muscle cells (SMCs). It lowered the phosphorylation level of LC20 and showed that ROCK, ERK, JNK and $PKC{\alpha}$ pathways played important roles in the effects, as confirmed by the observations with a specific inhibition or activation, and with the activity and the subcellular localization of these molecules. In particular, HMC05 dramatically inhibited the activity of ERK and the downstream signaling of ROCK. It also changed the subcellular localization of the phophorylated $PKC{\alpha}$ as well as the amount of phosphorylation. Taken together, these data indicate that the vascular relaxation effects of HMC05 are attributed to the regulation of these signaling mechanisms.

• BMB Reports
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• 제41권8호
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• pp.587-592
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• 2008

Cotesia vestalis is an endoparasitoid of Plutella xylostella larvae and injects a polydnavirus (CvBV) into its host during oviposition. In this report we characterize the gene, CvBV3307, and its products. CvBV3307 is located on segment S33 of the CvBV genome, is 517 bp, and encodes a putative protein of 122 amino acids, including a serine-rich region. The expression pattern of CvBV3307 in parasitized larvae and the subcellular localization of CvBV3307 only in granulocytes indicated that it might be involved in early protection of parasitoid eggs from host cellular encapsulation and in manipulating the hormone titer and developmental rhythm of host larvae. Western blot analysis showed that the size of the immunoreactive protein (about 55 kDa) in parasitized hosts at 48 hours post parasitization (h p.p.) is much larger than the predicted molecular weight of 13.6 kDa, which suggests that CvBV3307 undergoes extensive post-translational modification in hosts.

• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2005년도 한국컴퓨터종합학술대회 논문집 Vol.32 No.1 (B)
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• pp.226-228
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• 2005

Predicting the cellular location of an unknown protein gives valuable information for inferring the possible function of the protein. For more accurate Prediction system, we need a good feature extraction method that transforms the raw sequence data into the numerical feature vector, minimizing information loss. In this paper we propose new methods of extracting underlying features only from the sequence data by computing pairwise sequence alignment scores. In addition, we use composition based features to improve prediction accuracy. To construct an SVM ensemble from separately trained SVM classifiers, we propose specificity based weighted majority voting . The overall prediction accuracy evaluated by the 5-fold cross-validation reached $88.53\%$ for the eukaryotic animal data set. By comparing the prediction accuracy of various feature extraction methods, we could get the biological insight on the location of targeting information. Our numerical experiments confirm that our new feature extraction methods are very useful forpredicting subcellular localization of proteins.

• 미생물학회지
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• 제32권2호
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• pp.139-146
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• 1994

Photobacterium leiognathi CuZuSOD(PSOD)의 부세포성 분포에 따른 방어효과가 paraquat, 열 쇼크, 과산화수소 그리고 $CuSO_4$의 처리시 각각 조사되었다. 서로 달리 periplasm내에 분포하는 PSOD와 세포질에 분포하는 PSOD 사이의 생리적 특성은 본 연구에서는 조건에 따란 차이를 보였다. Paraquat나 $H_2O_2$ 처리시에는 periplasm에 SOD를 발현하는 세포에서 세포질내에 SOD를 분포하는 경우보다 약간 방호효과가 나았으며 SOD 발현 정도는 이와 일관되게 아주 중요한 변화를 보였다. 그러나 열 쇼크와 $CuSO_4$의 처리시는 각각 이런 현상이 역으로 나타났다.

• Journal of Microbiology and Biotechnology
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• 제31권4호
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• pp.621-629
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• 2021

Shigella flexneri is a facultative intracellular pathogen that causes bacillary dysentery in humans. Infection with S. flexneri can result in more than a million deaths yearly and most of the victims are children in developing countries. Therefore, identifying novel and unique drug targets against this pathogen is instrumental to overcome the problem of drug resistance to the antibiotics given to patients as the current therapy. In this study, a comparative analysis of the metabolic pathways of the host and pathogen was performed to identify this pathogen's essential enzymes for the survival and propose potential drug targets. First, we extracted the metabolic pathways of the host, Homo sapiens, and pathogen, S. flexneri, from the KEGG database. Next, we manually compared the pathways to categorize those that were exclusive to the pathogen. Further, all enzymes for the 26 unique pathways were extracted and submitted to the Geptop tool to identify essential enzymes for further screening in determining the feasibility of the therapeutic targets that were predicted and analyzed using PPI network analysis, subcellular localization, druggability testing, gene ontology and epitope mapping. Using these various criteria, we narrowed it down to prioritize 5 novel drug targets against S. flexneri and one vaccine drug targets against all strains of Shigella. Hence, we suggest the identified enzymes as the best putative drug targets for the effective treatment of S. flexneri.

• Toxicological Research
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• 제24권1호
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• pp.1-9
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• 2008

Ptdlns(4,5)$P_2$ is a key cellular phosphoinositide that localizes in separate and distinctive pools in subcellular membrane and vesicular compartments. In membranes, Ptdlns(4,5)$P_2$ acts as a precursor to second messengers and is itself a main signaling and targeting molecule. Specific subcellular localization of type I PIP kinases directed by interacting with specific targeting module differentiates Ptdlns(4,5)$P_2$ production in a spatial and temporal manner. Several lines of evidences support the idea that Ptdlns(4,5)$P_2$ is generated in very specific pools in a spatial and temporal manner or by feeding Ptdlns(4,5)$P_2$ directly to effectors. In this concept, the interaction of PIPKI isoforms with a specific targeting module to allow precise subcellular targeting modulates highly specific Ptdlns(4,5)$P_2$ synthesis and channeling overall effectors. For instance, localization of PIPKI${\gamma}$661 to focal adhesions by an interaction with talin results in spatial and temporal production of Ptdlns(4,5)$P_2$, which regulates EGF-stimulated directional cell migration. In addition, Type $I{\gamma}$ PIPK is targeted to E-cadherin in cell adherence junction and plays a role in controlling dynamics of cell adherence junction and endocytosis of E-cadherin. Characterizing how PIP kinase isoforms are regulated by interactions with their targeting modules, as well as the mechanisms by which their product, Ptdlns(4,5)$P_2$, exerts its effects on cellular signaling processes, is crucial to understand the harmonized control of numerous cellular signaling pathways. Thus, in this review the roles of the Ptdlns(4)P(5) kinases and Ptdlns(4,5)$P_2$ were described and critically reviewed in terms of regulation of the E-cadherin trafficking, cell migration, and formation of cell adherence junction which is indispensable and is tightly controlled in epithelial-to-mesenchymal transition process.