• BMB Reports
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• 제34권5호
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• pp.452-456
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• 2001

Surface plasmon resonance has been used for a biospecific interaction analysis between two macromolecules in real time. Determination of an antibody that is capable of specifically interacting with the native form of antigen is very useful for many biological and medical applications. Twenty monoclonal antibodies against the $\alpha$ subunit of E. coli DNA polymerase III were screened for specifically recognizing the native form of protein using surface plasmon resonance. Only four monoclonal antibodies among them specifically recognized the native $\alpha$ protein, although all of the antibodies were able to specifically interact with the denatured $\alpha$ subunit. These antibodies failed to interfere with the interaction between the $\tau$ and $\alpha$ subunits that were required for dimerization of the two polymerases at the DNA replication fork. This real-time analysis using surface plasmon resonance provides an easy method to screen antibodies that are capable of binding to the native form of the antigen molecule and determine the biological interaction between the two molecules.

• Genomics & Informatics
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• 제5권3호
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• pp.133-136
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• 2007

The Gene Set network viewer (GSnet) visualizes the functional enrichment of a given gene set with a protein interaction network and is implemented as a plug-in for the Cytoscape platform. The functional enrichment of a given gene set is calculated using a hypergeometric test based on the Gene Ontology annotation. The protein interaction network is estimated using public data. Set operations allow a complex protein interaction network to be decomposed into a functionally-enriched module of interest. GSnet provides a new framework for gene set analysis by integrating a priori knowledge of a biological network with functional enrichment analysis.

• 한국정보과학회논문지:컴퓨팅의 실제 및 레터
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• 제11권6호
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• pp.503-513
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• 2005

계산을 통한 단백질 상호작용 예측 기법의 중요성이 제기되면서 많은 단백질 상호 작용 예측 기법이 제안되고 있다. 하지만 이러한 기법들이 일반 사용자가 손쉽게 사용할 수 있는 서비스 형태로 제공되고 있는 경우는 드물다. 본 논문에서는 현재까지 알려진 단백질 상호작용 예측 기법 중 예측 기법의 완성도가 높고 상대적으로 예측 정확도가 높은 것으로 알려진 도메인 조합 기반 단백질 상호 작용 예측 기법을 이용하여 서비스 시스템으로 설계하고 구현하였다. 효모(Yeast)의 단백질 집합에 대하여 학습한 후, 학습된 단백질 집합과 공통된 도메인을 가지지만 학습 집합에 존재하지 않는 단백질 쌍들에 예측 기법을 적용하여 매우 높은 $77\%$의 민감도(sensitivity)와 $95\%$의 특이도(specificity)를 보였다. 더불어 DIP CORE, HMS-PCI, TAP 데이타의 테스트를 통해서 이 기법의 안정성을 확인하였다. 시스템의 기능들은 핵심 기능, 부가 기능 그리고 일반 서비스 기능으로 분류하였다. 시스템 설계의 주요 목표인 성능, 개방성 그리고 확장성에 따라, 개별 서비스들은 병렬화, 웹 서비스 표준 준수 및 계층화된 구조화를 지원하도록 구현하였다. 본 논문에서는 몇 가지 대표적인 사용자 인터페이스와 상세한 사용 지침도 소개한다.

• 한국산학기술학회:학술대회논문집
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• 한국산학기술학회 2010년도 춘계학술발표논문집 2부
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• pp.1197-1200
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• 2010

Post-genomic 시대에 접어들면서 단백질의 기능의 주석이 중요한 문제로 떠오르기 시작하였다. 이런 단백질 기능을 예측하기 위해 단백질 상호작용(Protein-Protein interaction) 데이터를 이용한 방법들이 지난 10여 년간 발표되어왔다. 단백질 상호작용(Protein-Protein interaction) 데이터는 단백질들 간의 서열 등의 특징을 이용해 상호간의 연결 관련성이 있는 단백질끼리의 관계를 네트워크로 나타낸 자료이다. 현재 이러한 단백질 상호작용(Protein-Protein interaction) 데이터들은 MIPS, DIP, BioGrid등 약 5~6군데에서 제공되고 있다. 각각의 데이터는 다른 형식을 가지고 있고, 중복되는 정보도 포함하고 있다. 여러 연구 방법에서 데이터를 사용할 때 한군데에서만 추출하기 보다는 여러 데이터에서 추출하는 경우가 많기 때문에 다른 형식의 데이터를 이용하는데 불필요한 수고가 들어가게 된다. 때문에 여러군데의 데이터를 한 가지 형식으로 맞추어 통합적으로 구축하여 연구 시 데이터 사용에 용이하도록 설계 하였다. 또한 발표된 단백질 기능 예측 방법에 대한 정리를 통해 앞으로의 연구를 하는데 있어서 필요한 자료를 얻고 열람할 수 있도록 설계하였다. 이를 통해 관련 연구를 하거나 관심이 있는 사람들의 데이터를 검색하는데 많은 도움이 될 것이다.

• Molecules and Cells
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• 제27권3호
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• pp.271-277
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• 2009

Proteins interact with each other within a cell, and those interactions give rise to the biological function and dynamical behavior of cellular systems. Generally, the protein interactions are temporal, spatial, or condition dependent in a specific cell, where only a small part of interactions usually take place under certain conditions. Recently, although a large amount of protein interaction data have been collected by high-throughput technologies, the interactions are recorded or summarized under various or different conditions and therefore cannot be directly used to identify signaling pathways or active networks, which are believed to work in specific cells under specific conditions. However, protein interactions activated under specific conditions may give hints to the biological process underlying corresponding phenotypes. In particular, responsive functional modules consist of protein interactions activated under specific conditions can provide insight into the mechanism underlying biological systems, e.g. protein interaction subnetworks found for certain diseases rather than normal conditions may help to discover potential biomarkers. From computational viewpoint, identifying responsive functional modules can be formulated as an optimization problem. Therefore, efficient computational methods for extracting responsive functional modules are strongly demanded due to the NP-hard nature of such a combinatorial problem. In this review, we first report recent advances in development of computational methods for extracting responsive functional modules or active pathways from protein interaction network and microarray data. Then from computational aspect, we discuss remaining obstacles and perspectives for this attractive and challenging topic in the area of systems biology.

• 한국식품과학회지
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• 제19권2호
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• pp.89-96
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• 1987

방어와 갈색띠 매물고둥에서 myosin과 paramyosin 을 추출하고, 이들 단백질의 가열중에 일어나는 변성기구를 아미노산 잔기와 SH기의 변화 및 단백질간의 상호작용 등을 측정하므로서 분석하였다. 각 단백질을 이루는 구성아미노산의 측쇄중 소수성 잔기의 유리정도는 가열온도 $65^{\circ}C$까지는 증가하였으나, 그 이상의 가열온도에서는 감소하는 경향을 보였다. 유리 소수성 잔기가 증가하여 감에 따라, 단백질간 상호작용도 활발하여 갔으며, 소수성 잔기의 유리정도가 감소하는 가열온도$65^{\circ}C$부터는 단백질의 응집이 일어나기 시작 하였다. 단백질간의 상호작용을 탁도로써 분석하여 Arrhenius식으로 해석한 결과, 방어 myosin은 3단계이상의 변성과정으로 구분할 수 있었으며, 갈색띠 매물고둥 paramyos은 2단계의 변성과정으로 구분할 수 있었다. 이들 두 단백질 소수성, 용해도, 유리 SH기의 수 및 단백질간의 상호작용 등은 온도함수와 밀접한 상관관계를 보였다.

• 한국자기공명학회논문지
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• 제15권1호
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• pp.80-89
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• 2011

3D structures of STAM1 UIM-ubiquitin complex were presented to predict and analyze the interaction between UIM and ubiquitin. To generate the protein-peptide complex structure, the RosettaDock method was used with and without NMR restraints. High resolution complex structure was acquired successfully and evaluated electrostatic interaction in the protein-peptide binding with several charged residues at the binding site. From docking results, the Rosettadock method could be useful to acquire essential information of protein-protein or protein-peptide interaction with minimal biological evidences.

• 통합자연과학논문집
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• 제11권1호
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• pp.9-13
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• 2018

KiSS1-derived peptide receptor, a GPCR protein, binds with the hormone Kisspeptin plays a major role in the neuroendocrine regulation of reproduction. It is important in the onset of puberty and triggers the release of gonadotrophin-releasing hormone. It is a potential drug target for the disorders related to GnRH, hence, analysing the structural features of the receptor becomes important. The three dimensional of the receptor modelled in a previous study was utilised. In this study, we have analysed the protein - protein interaction of the receptor with Kisspeptin 10 and 15. The study revealed the important residues which are involved in the interaction. The result of this study could be helpful in understanding the mechanism of Kiss1 receptor activation and the pathophysiology of the disorders related to the receptor.

• Animal cells and systems
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• 제6권3호
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• pp.277-282
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• 2002

Topoisomearse II is an essential enzyme in all organisms with several independent roles in DNA metabolism. Recently, it has been demonstrated that the C-terminal region of topoisomerases II is associated with hetero-logous protein-protein interactions in human and yeast. In this study, we identified that RTP1, a rat homologue of EIA binding protein BS69, is another topoisomerae II interacting protein by yeast two-hybrid screening. RTP1 has an E1A-binding domain and a MYND motif, which are known to be required for transcriptional regulation by binding to other proteins and interaction with the leucine zipper motif of topoisomerase II. The physical interaction between RTP1 and topoisomerase ll$\alpha$ was examined by GST pull-down assay in vitro. The expression level of RTP1 peaks in S phase as that of topoisomerase ll$\alpha$. These results suggest that the interaction between topoisomerase ll$\alpha$ and RTP1 might play an important role in regulating the transcription of genes involved in DNA metabolism in higher eukaryotes.

• 한국염색가공학회지
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• 제19권4호
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• pp.32-37
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• 2007

In this study, we have obtained the protein patterns using the membrane patterning of soft-lithography technique. The rapid detection of protein including bovine serum albumin (BSA) was resulted from the interaction with 1,3-bisdicyanovinylindane. For the proof of the interaction between BSA and dye, the UV-vis absorption spectra of BSA and dye were observed at 278 nm and 580 nm, respectively. As expected, the absorption spectrum of the interaction between BSA and dye was observed at 584nm. The absorption spectrum of the interaction was red-shifted. In addition, the optical images of the selectively reacted protein patterns showed the distinctive change of patterned color at different pH conditions. Because the dye has negative charges, the charge of BSA at different pH conditions could influence the interaction behavior between dye and BSA. Therefore, in the case of pH 7, the selectively patterned protein substrates obtained deep blue color pattern caused by electrostatic interaction between negative charges of the dye and positive charges of the BSA. However, in the case of pH 10, selectively patterned protein substrates obtained light blue color pattern because the electrostatic interaction was relatively lower than pH 7 due to the change of overall charge distribution of BSA.