• BMB Reports
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• 제35권3호
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• pp.343-347
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• 2002

The human protein tyrosine kinase-6 (PTK6) polypeptide that is deduced from the cDNA sequence contains a Src homology (SH) 3 domain, SH2 domain, and catalytic domain of tyrosine kinase. We initiated biochemical and NMR characterization of PTK6 SH3 domain in order to correlate the structural role of the PTK6 using circular dichroism and heteronuclear NMR techniques. The circular dichroism data suggested that the secondary structural elements of the SH3 domain are mainly composed of $\beta$-sheet conformations. It is most stable when the pH is neutral based on the pH titration data. In addition, a number of cross peaks at the low-field area of the proton chemical shift of the NMR spectra indicated that the PTK6 SH3 domain retains a unique and folded conformation at the neutral pH condition. For other pH conditions, the SH3 domain became unstable and aggregated during NMR measurements, indicating that the structural stability is very sensitive to pH environments. Both the NMR and circular dichroism data indicate that the PTK6 SH3 domain experiences a conformational instability, even in an aqueous solution.

• 한국식품조리과학회지
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• 제20권4호
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• pp.396-402
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• 2004

증편의 sponge상의 망상구조에 쌀 단백질의 영향을 조사하기 위하여 증편제조시 주원료인 쌀 단백질을 분리하고 증편 발효시 그 변화를 살펴보았으며 protease 첨가가 증편의 점도 및 부피에 미치는 영향을 살펴보았다. 또한 쌀 전분에 단백질을 첨가하여 증편의 점도 및 부피에 미치는 영향을 살펴본 결과 쌀 단백질이 증편의 부피 팽창에 영향을 주는 것으로 생각되었다. 쌀 및 증편 반죽에서는 SDS 가용성 단백질 함량이 밀가루와 비교해 높게 나타났으며 발효시간에 따른 단백질 추출량은 큰 변화가 없었다. 그러나 증편반죽의 시간별 FPLC패턴은 발효시간에 따라 저분자 peak가 감소하여 고분자화함을 알 수 있었다. 단백질 분해효소 protease를 첨가하여 본 결과 증편의 점도 및 부피는 현저히 감소하였고 쌀 전분에 단백질을 첨가하여 증편을 재구성한 결과, 점도, 부피는 증가하는 것으로 나타나 증편내에서 쌀 단백질이 증편의 부피 내지는 조직감 형성에 크게 영향을 미치는 것으로 생각되어진다.

• Journal of Animal Science and Technology
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• 제60권6호
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• pp.11.1-11.7
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• 2018

After pubertal, cohort of small antral follicles enters to gonadotrophin-sensitive development, called recruited follicles. This study was aimed to identify candidate genes in follicular cyclic recruitment via analysis of protein-protein interaction (PPI) network. Differentially expressed genes (DEGs) in ovine granulosa cells of small antral follicles between follicular and luteal phases were accumulated among gene/protein symbols of the Ensembl annotation. Following directed graphs, PTPN6 and FYN have the highest indegree and outdegree, respectively. Since, these hubs being up-regulated in ovine granulosa cells of small antral follicles during the follicular phase, it represents an accumulation of blood immune cells in follicular phase in comparison with luteal phase. By contrast, the up-regulated hubs in the luteal phase including CDK1, INSRR and TOP2A which stimulated DNA replication and proliferation of granulosa cells, they known as candidate genes of the cyclic recruitment.

• 한국정보처리학회:학술대회논문집
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• 한국정보처리학회 2011년도 추계학술발표대회
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• pp.1115-1118
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• 2011

단백질 사이의 상호작용 네트워크(PPI network: Protein-Protein Interaction network)를 이용하여 단백질 기능을 예측 하는 것은 단백질 기능 예측 기법들 중에서 중요한 작용을 한다. 하지만 PPI를 이용한 단백질 기능 예측은 기능의 복잡도와 다양성으로 인해 제한적인 결과를 나타내 왔다. 따라서 본 논문에서는 기존의 연구들 보다 높은 정확도로 단백질 기능을 예측하기 위해 기능 예측을 하려는 단백질과 상호작용 하는 단백질들에 그래프 마이닝 기법을 적용하여 빈발 2-노드 상호작용 패턴을 찾고, 그 패턴을 이용하여 단백질 기능을 예측하는 접근법을 제안하였다. 실험데이터로 DIP(Database of Interacting Proteins)에서 제공하는 단백질 상호작용 데이터를 사용하였으며, 다른 기존의 단백질 기능 예측 기법들보다 높은 정확도를 보여주었다.

• 한국자기공명학회:학술대회논문집
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• 한국자기공명학회 1999년도 하계총회 및 제15회 자기공명 학술발표회
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• pp.36-36
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• 1999

• 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.

• 한국당과학회:학술대회논문집
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• 한국당과학회 2006년도 제1회 연례학술대회
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• pp.45-45
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• 2006

• 한국콘텐츠학회:학술대회논문집
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• 한국콘텐츠학회 2004년도 추계 종합학술대회 논문집
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• pp.511-515
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• 2004

Post-genome 시대에는 유전체뿐만 아니라 단백질에 대한 연구의 필요성이 증대되고 있다. 특히 단백질-단백질 상호작용 및 단백질 네트워크에 대한 연구를 기반으로 전체 생물 시스템을 분석하는 연구가 중요한 이슈로 떠오르고 있다. 기존에 생물학자들이 실험을 통해서 증명한 사실들을 논문이나 기타 매체를 통해서 공개를 하고 있다. 하지만 공개된 정보의 양이 방대하므로 생물학자들이 정보를 효율적으로 이용하지 못하는 경우가 많다. 인터넷의 발달로 하루에도 수 없이 쏟아져 나오는 연구 성과들에 쉽게 접근이 가능해졌다. 이러한 매체로부터 생물학적 의미를 가지는 정보를 효과적으로 추출하는 일이 중요하게 대두되었다. 따라서 본 연구에서는 인터넷상에 공개된 다량의 논문 및 기타정보 매체로부터 단백질-단백질 상호작용 정보를 추출한 데이터베이스로부터 단백질의 네트워크를 구성하고 단백질 네트워크를 통해서 생물학적 의미를 가지는 여러 가지 경로 분석 알고리즘을 설계하고 구현한다.

• Asian Pacific Journal of Cancer Prevention
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• 제15권16호
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• pp.6899-6904
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• 2014

NGAL (neutrophil gelatinase-associated lipocalin) is a novel cancer-related protein involves multiple functions in many cancers and other diseases. We previously overexpressed NGAL to analyze its role in esophageal squamous cell carcinoma (ESCC). In this study, a protein-protein interaction (PPI) was constructed and the shortest paths from NGAL to transcription factors in the network were analyzed. We found 28 shortest paths from NGAL to RELA, most of them obeying the principle of extracellular to cytoplasm, then nucleus. These shortest paths were also prioritized according to their normalized intensity from the microarray by the order of interaction cascades. A systems approach was developed in this study by linking differentially expressed genes with publicly available PPI data, Gene Ontology and subcellular localizaton for the integrated analyses. These shortest paths from NGAL to DEG transcription factors or other transcription factors in the PPI network provide important clues for future experimental identification of new pathways.

• Asian Pacific Journal of Cancer Prevention
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• 제15권5호
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• pp.2345-2351
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• 2014

Lysyl oxidase-like 2 (LOXL2), a member of the lysyl oxidase (LOX) family, is a copper-dependent enzyme that catalyzes oxidative deamination of lysine residues on protein substrates. LOXL2 was found to be overexpressed in esophageal squamous cell carcinoma (ESCC) in our previous research. We later identified a LOXL2 splicing variant LOXL2-delta72 and we overexpressed LOXL2-delta72 and its wild type counterpart in ESCC cells following microarray analyses. First, the differentially expressed genes (DEGs) of LOXL2 and LOXL2-delta72 compared to empty plasmid were applied to generate protein-protein interaction (PPI) sub-networks. Comparison of these two sub-networks showed hundreds of different proteins. To reveal the potential specific roles of LOXL2- delta72 compared to its wild type, the DEGs of LOXL2-delta72 vs LOXL2 were also applied to construct a PPI sub-network which was annotated by Gene Ontology. The functional annotation map indicated the third PPI sub-network involved hundreds of GO terms, such as "cell cycle arrest", "G1/S transition of mitotic cell cycle", "interphase", "cell-matrix adhesion" and "cell-substrate adhesion", as well as significant "immunity" related terms, such as "innate immune response", "regulation of defense response" and "Toll signaling pathway". These results provide important clues for experimental identification of the specific biological roles and molecular mechanisms of LOXL2-delta72. This study also provided a work flow to test the different roles of a splicing variant with high-throughput data.