• 한국콘텐츠학회논문지
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• 제8권6호
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• pp.74-81
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• 2008

단백질 상호작용 네트워크는 허브(hub)라 할 수 있는 상호작용 수가 많은 소수의 단백질과 상호작용수가 적은 다수의 단백질들로 구성된다. 최근 들어 여러 연구들에서 허브 단백질이 비 허브(non-hub) 단백질보다 상호작용 네트워크에 필수적인 단백질일 가능성이 높다고 보고되고 있다. 이러한 현상을 중심-치명 룰(centrality-lethality rule)이라 하는데, 이는 복잡계 네트워크에서 허브단백질의 중요성 및 네트워크 구조의 중요성을 설명하기 위한 방법으로 폭넓게 신뢰받고 있다. 이에 본 논문에서는 중심-치명 룰이 항상 옳게 적용되는지를 확인하기 위해 Uetz, Ito, MIPS, DIP, SGD, BioGRID와 같은 효모에 관한 공개된 모든 단백질 상호작용 데이터베이스들을 분석하였다. 흥미롭게도, 상호작용 데이터가 적은 데이터베이스들(Uetz, Ito, DIP)에서는 중심-치명 룰을 잘 나타냈지만 상호작용 데이터가 대용량인 데이터 베이스들(SGD, BioGRID)에서는 중심-치명 룰이 잘 맞지 않음을 확인하였다. 이에 따라 SGD와 BioGRID 데이터베이스로 부터 얻은 상호작용 네트워크의 특징을 분석하고 DIP 데이터베이스의 상호작용 네트워크와 비교하였다.

• BMB Reports
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• 제38권1호
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• pp.97-103
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• 2005

Under the condition of expression of $\lambda$ P protein at lethal level, the oriC DNA-binding activity is significantly affected in wild-type E. coli but not in the rpl mutant. In purified system, the $\lambda$ P protein inhibits the binding of both oriC DNA and ATP to the wild-type DnaA protein but not to the rpl DnaA protein. We conclude that the $\lambda$ P protein inhibits the binding of oriC DNA and ATP to the wild-type DnaA protein, which causes the inhibition of host DNA synthesis initiation that ultimately leads to bacterial death. A possible beneficial effect of this interaction of $\lambda$ P protein with E. coli DNA initiator protein DnaA for phage DNA replication has been proposed.

• 정보처리학회논문지D
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• 제19D권1호
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• pp.21-28
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• 2012

모노머 단백질의 상호작용 사이트 예측은 기능을 알지 못하는 단백질에 대해서 이것과 상호작용하는 단백질로부터 기능을 예측하거나 단백질 도킹을 위한 검색 공간의 감소에 중요한 역할을 한다. 그러나 상호작용사이트 예측은 대부분 단백질 상호작용이 세포 내에서 순간적 반응에 일어나는 약한 상호작용으로 실험에 의한 3차원 결정 구조 식별의 어려움이 따르며 이로 인해 3차원의 복합체 데이터가 제한적으로 양산된다. 이 논문에서는 모노머 단백질의 3차원 패치 계산을 통하여 구조가 알려진 복합체의 상호작용사이트와 비상호작용사이트에 대한 패치 속성을 추출하고 이를 기반으로 Support Vector Machine (SVM) 분류기법을 이용한 예측 모델 개발을 제시한다. 타겟 클래스의 데이터 불균형 문제 해결을 위해 under-sampling 기법을 이용한다. 사용된 패치속성은 2차 구조 요소와 아미노산 구성으로부터 총 9개가 추출된다. 147개의 단백질 복합체에 대해서 10 fold cross validation을 통해서 다양한 분류모델의 성능 평가를 하였다. 평가한 분류 모델 중 SVM은 92.7%의 높은 정확성을 보이고 이를 이용하여 분류 모델을 개발하였다.

• 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.

• 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.

• Genomics & Informatics
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• 제2권2호
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• pp.99-106
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• 2004

In this paper we introduce PubMiner, an intelligent machine learning based text mining system for mining biological information from the literature. PubMiner employs natural language processing techniques and machine learning based data mining techniques for mining useful biological information such as protein­protein interaction from the massive literature. The system recognizes biological terms such as gene, protein, and enzymes and extracts their interactions described in the document through natural language processing. The extracted interactions are further analyzed with a set of features of each entity that were collected from the related public databases to infer more interactions from the original interactions. An inferred interaction from the interaction analysis and native interaction are provided to the user with the link of literature sources. The performance of entity and interaction extraction was tested with selected MEDLINE abstracts. The evaluation of inference proceeded using the protein interaction data of S. cerevisiae (bakers yeast) from MIPS and SGD.

• 셀메드
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• 제4권1호
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• pp.6.1-6.12
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• 2014

Anthrax is the deadly disease for human being caused by Bacillus anthracis. Instantaneous research work on the mode of infection of the organism revealed that different proteases are involved in different steps of pathogenesis. Present study reports the in silico characterization and the detection of pathogenic proteases involved in anthrax infection through protein-protein interaction. A total of 13 acid, 9 neutral, and 1 alkaline protease of Bacillus anthracis were selected for analysing the physicochemical parameter, the protein superfamily and family search, multiple sequence alignment, phylogenetic tree construction, protein-protein interactions and motif finding. Among the 13 acid proteases, 10 were found as extracellular enzymes that interact with immune inhibitor A (InhA) and help the organism to cross the blood brain barrier during the process of infection. Multiple sequence alignment of above acid proteases revealed the position 368, 489, and 498-contained 100% conserved amino acids which could be used to deactivate the protease. Among the groups analyzed, only acid protease were found to interact with InhA, which indicated that metalloproteases of acid protease group have the capability to develop pathogenesis during B. anthracis infection. Deactivation of conserved amino acid position of germination protease can stop the sporulation and germination of B anthracis cell. The detailed interaction study of neutral and alkaline proteases could also be helpful to design the interaction network for the better understanding of anthrax disease.

• Asian-Australasian Journal of Animal Sciences
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• 제7권2호
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• pp.207-212
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• 1994

Effects of dietary cellulose and protein levels on nutrient utilization in chickens were investigated. Four experimental diets containing 5% (low cellulose) or 20% (high cellulose) cellulose in combination with 10% (low protein) or 20% (high protein) protein of 70 g/day were alternatively forced-fed to eight colostomized White Leghorn cockerels once a day to make $4{\times}4$ Latin-square design. The digestibilities of DM and energy decreased with the increase in cellulose level, but not affected by dietary protein level. Ether extract digestibility was higher in the high cellulose diets than in the low cellulose protein level. Ether extract digestibility was higher in the high cellulose diets than in the low cellulose diets. The digestibility of nitrogen free extract had the same trend with the digestibility of DM and energy. The digestibility of acid detergent fiber was not so much different among the diets, but the NDF digestibility was lower in the high cellulose diets than in the low cellulose diets, due to the low hemicellulose digestibility. The true digestibility of protein was influenced by both of the dietary protein and cellulose levels, and their interaction was found. The dietary protein level affected the biological value of protein but the dietary cellulose level did not, and consequently the biological value of protein in the low protein diets was lower than in the high protein diets.

• 한국동물위생학회지
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• 제25권4호
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• pp.333-346
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• 2002

We previously reported that the equine herpesvirus type 1(EHV-1) immediate-early protein(IE protein) physically interacts with the general transcription factor human TFIIB(Jang et al, J Virol 75：10219-10230, 2001). The interaction between the IE protein and TFIIB is necessary for the IE protein to efficiently transactivate the early TK and late IR5 EHV-1 promoters. A panel of deletion and truncation mutants of the TFIIB gene was constructed and employed in protein-binding assays to map the IE protein-binding domain within TFIIB. Evidence is presented that the first direct repeat of TFIIB interacts specifically with the EHV-1 IE protein.