• International Journal of Computer Science & Network Security
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• 제21권3호
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• pp.41-47
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• 2021

Detection of protein-protein interactions (PPIs) remains essential for the development of therapies against diseases. Experimental studies to detect PPI are longer and more expensive. Today, with the availability of PPI data, several computer models for predicting PPIs have been proposed. One of the big challenges in this task is feature extraction. The relevance of the information extracted by some extraction techniques remains limited. In this work, we first propose an extraction method based on correlation relationships between the physicochemical properties of amino acids. The proposed method uses a correlation matrix obtained from the hydrophobicity and hydrophilicity properties that it then integrates in the calculation of the bigram. Then, we use the SVM algorithm to detect the presence of an interaction between 2 given proteins. Experimental results show that the proposed method obtains better performances compared to the approaches in the literature. It obtains performances of 94.75% in accuracy, 95.12% in precision and 96% in sensitivity on human HPRD protein data.

• 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.

• 한국식물병리학회:학술대회논문집
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• 한국식물병리학회 2003년도 정기총회 및 추계학술발표회
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• pp.29-29
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• 2003

Incompatible plant-pathogen interactions result in the rapid cell death response known as hypersensitive response (HR) and activation of host defense-related genes. To understand the molecular and cellular mechanism controlling defense response better, several approaches including isolation and characterization of novel genes, promoter analysis of those genes, protein-protein interaction analysis and reverse genetic approach etc. By using the yeast two-hybrid system a clone named Tsipl, Tsil -interacting protein 1, was isolated whose translation product apparently interacted with Tsil, an EREBP/AP2 type DNA binding protein. RNA gel blot analysis showed that the expression of Tsipl was increased by treatment with NaCl, ethylene, salicylic acid, or gibberellic acid. Transient expression analysis using a Tsipl::smGFP fusion gene in Arabidopsis protoplasts indicated that the Tsipl protein was targeted to the outer surface of chloroplasts. The targeted Tsipl::smGFP proteins were diffused to the cytoplasm of protoplasts in the presence of salicylic acid (SA) The PEG-mediated co-transfection analysis showed that Tsipl could interact with Tsil in the nucleus. These results suggest that Tsipl-Tsil interaction might serve to regulate defense-related gene expression. Basically the useful promoters are valuable tools for effective control of gene expression related to various developmental and environmental condition.(중략)

• 한국콘텐츠학회:학술대회논문집
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• 한국콘텐츠학회 2008년도 춘계 종합학술대회 논문집
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• pp.842-845
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• 2008

단백질 상호작용 네트워크는 허브(Hub)라 할 수 있는 상호작용 수가 많은 소수의 단백질과 상호작용 수가 적은 다수의 단백질들로 구성된다. 최근 들어 여러 연구들에서 허브 단백질이 비 허브(Non-hub) 단백질보다 상호작용 네트워크에 필수적인 단백질일 가능성이 높다고 설명하고 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 데이터베이스들(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 비교해보았다.

• BMB Reports
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• 제54권9호
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• pp.464-469
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• 2021

Cardiomyocyte differentiation occurs through complex and finely regulated processes including cardiac lineage commitment and maturation from pluripotent stem cells (PSCs). To gain some insight into the genome-wide characteristics of cardiac lineage commitment, we performed transcriptome analysis on both mouse embryonic stem cells (mESCs) and human induced PSCs (hiPSCs) at specific stages of cardiomyocyte differentiation. Specifically, the gene expression profiles and the protein-protein interaction networks of the mESC-derived platelet-derived growth factor receptor-alpha (PDGFRα)⁺ cardiac lineage-committed cells (CLCs) and hiPSC-derived kinase insert domain receptor (KDR)⁺ and PDGFRα⁺ cardiac progenitor cells (CPCs) at cardiac lineage commitment were compared with those of mesodermal cells and differentiated cardiomyocytes. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that the genes significantly upregulated at cardiac lineage commitment were associated with responses to organic substances and external stimuli, extracellular and myocardial contractile components, receptor binding, gated channel activity, PI3K-AKT signaling, and cardiac hypertrophy and dilation pathways. Protein-protein interaction network analysis revealed that the expression levels of genes that regulate cardiac maturation, heart contraction, and calcium handling showed a consistent increase during cardiac differentiation; however, the expression levels of genes that regulate cell differentiation and multicellular organism development decreased at the cardiac maturation stage following lineage commitment. Additionally, we identified for the first time the protein-protein interaction network connecting cardiac development, the immune system, and metabolism during cardiac lineage commitment in both mESC-derived PDGFRα⁺ CLCs and hiPSC-derived KDR⁺PDGFRα⁺ CPCs. These findings shed light on the regulation of cardiac lineage commitment and the pathogenesis of cardiometabolic diseases.

• Genomics & Informatics
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• 제21권2호
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• pp.23.1-23.9
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• 2023

The mammalian sirtuin family, consisting of SIRT1-SIRT7, plays a vital role in various biological processes, including cancer, diabetes, neurodegeneration, cardiovascular disease, cellular metabolism, and cellular homeostasis maintenance. Due to their involvement in these biological processes, modulating sirtuin activity seems promising to impact immuneand aging-related diseases, as well as cancer pathways. However, more understanding is required regarding the safety and efficacy of sirtuin-targeted therapies due to the complex regulatory mechanisms that govern their activity, particularly in the context of multiple targets. In this study, the interaction landscape of the sirtuin family was analyzed using a systems biology approach. A sirtuin protein-protein interaction network was built using the Cytoscape platform and analyzed using the NetworkAnalyzer and stringApp plugins. The result revealed the sirtuin family's association with numerous proteins that play diverse roles, suggesting a complex interplay between sirtuins and other proteins. Based on network topological and functional analysis, SIRT1 was identified as the most prominent among sirtuin family members, demonstrating that 25 of its protein partners are involved in cancer, 22 in innate immune response, and 29 in aging, with some being linked to a combination of two or more pathways. This study lays the foundation for the development of novel therapies that can target sirtuins with precision and efficacy. By illustrating the various interactions among the proteins in the sirtuin family, we have revealed the multifaceted roles of SIRT1 and provided a framework for their possible roles to be precisely understood, manipulated, and translated into therapeutics in the future.

• 한국콘텐츠학회논문지
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• 제5권6호
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• pp.31-40
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• 2005

포스트 게놈 시대에는 단백질에 대한 연구의 필요성이 증대되고 있다. 특히 단백질-단백질 상호작용 및 단백질 네트워크에 대한 연구를 기반으로 전체 생물 체계를 분석하는 연구가 중요하게 대두되고 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. 다행히도 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 기타 정보 매체로부터 단백질 정보를 추출한 데이터베이스로부터 단백질 네트워크를 구성하고, 단백질 네트워크를 통해서 생물학적 의미를 가지는 여러가지 경로 분석 알고리즘을 설계하고 구현한다.

• 한국컴퓨터정보학회논문지
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• 제20권2호
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• pp.137-147
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• 2015

본 논문에서는 유전자 네트워크를 기반으로 유방암 환자의 예후를 예측하는 알고리듬을 제안한다. 유방암 환자의 마이크로어레이 데이터와 PPI(Protein-protein interaction)데이터를 이용하여 알고리듬의 분류자로 사용될 예후 특이 네트워크(Prognosis specific gene network)를 추출한다. PPI에 속한 모든 유전자 네트워크에 대하여 각각의 네트워크가 예후 좋음과 나쁨을 잘 구분하는지에 대한 점수를 피어슨 상관계수(Pearson's correlation coefficient)와 마이크로어레이 데이터를 이용하여 계산한다. 이들 중 가장 예후에 유의한 네트워크를 식별하고, 이 네트워크를 분류자로 사용하여 에스트로겐 수용체 음성 유방암 환자의 예후를 분류 분석 한다. 본 연구와 기존 연구의 알고리듬 정확도를 비교 분석 하기 위하여 독립 실험을 진행하고, 본 연구에서 제안된 알고리듬의 성능이 더 우수함을 보인다. 또한, Gene Ontology 데이터베이스를 활용하여 식별된 예후 특이 네트워크를 기능적으로 검증 한다.

• 한국정보과학회논문지:시스템및이론
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• 제36권2호
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• pp.60-67
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• 2009

단백질 상호작용 네트워크는 어떤 단백질들 간에 상호 작용 관계가 있는지를 네트워크 형태로 나타낸 것이며 단백질 상호작용을 발견하거나 분석하는 것은 생명 공학에서 중요한 연구분야이다. 본 논문에서는 방대한 단백질 상호작용 데이터를 유전자 온톨로지와 연계한 시각화를 통하여 효과적으로 직관을 얻을 수 있는 효율적인 단백질 상호작용 네트워크 분석시스템을 다룬다. 단백질 상호작용 네트워크는 데이터 양이 매우 방대하기 때문에 이를 효율적으로 분석하는 방법과 효과적인 시각화 기법이 요구된다. 본 연구에서는 이를 위하여 동적이고 상호작용 가능한 그래프와 관심 노드와 그 주변 노드를 표시하며 점진적으로 탐색할 수 있는 컨텍스트 기반 탐색 기법을 도입하였다. 이 밖에도 특화된 기능으로써 단백질 상호작용과 유전자 온톨로지 간의 빠르고 자유로운 상호참조 기능과 최소 공통 조상을 사용한 유전자 온톨로지 분석 기능 등을 지원한다. 인터페이스 측면에서는 상호참조 기능을 효과적으로 사용하게 하기 위하여 유전자 온톨로지 그래프와 단백질 상호작용의 시각화 결과를 2차원 윈도우로 나란히 보여주는 인터페이스를 디자인 하였다.

• The Journal of the Acoustical Society of Korea
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• 제21권3E호
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• pp.126-131
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• 2002

Ultrasonic measurements are made in egg white to study the properties of the solution of the natural protein. The high-Q ultrasonic resonator method is used to get the ultrasonic absorption spectra over the range 0.2-10 ㎒ at 20℃. It is proportional to the 1.25th power of the frequency. The gelation process caused by heat is studied from the change in the velocity and the absorption. at 3 ㎒ using the pulse echo overlap technique over the range of 10-80℃. The absorption decreases with increasing temperature up to 60℃ where it turns up sharply and rapidly increases thereafter. The strong absorption in the gel region is described by the interaction between the solution and the network structure made of protein. Very slow variation in time elapse is observed after the temperature is quickly raised. It would be a real-time observation of the network building process and the characteristic time for the process is shown to be 400 min. A hysteresis phenomenon with respect to the temperature is observed. This phenomenon is associated with the memorizing effect of the network structure of protein of the gel.