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The interactions between proteins are important for many biological functions. For example, signals from the exterior of a cell are mediated to the inside of that cell by protein-protein interactions of the signaling molecules. This process, called signal transduction, plays a fundamental role in many biological processes and in many diseases (e.g. cancer). Proteins might interact for a long time to form part of a protein complex, a protein may be carrying another protein (for example, from cytoplasm to nucleus or vice versa in the case of the nuclear pore importins), or a protein may interact briefly with another protein just to modify it (for example, a protein kinase will add a phosphate to a target protein). This modification of proteins can itself change protein-protein interactions. For example, some proteins with SH2 domains only bind to other proteins when they are phosphorylated on the amino acid tyrosine. In conclusion, protein-protein interactions are of central importance for virtually every process in a living cell. Information about these interactions improves our understanding of diseases and can provide the basis for new therapeutic approaches.
Methods to investigate protein-protein interactions
As protein-protein interactions are so important there are a multitude of methods to detect them. Each of the approaches has its own strengths and weaknesses, especially with regard to the sensitivity and specificity of the method. A high sensitivity means that many of the interactions that occur in reality are detected by the screen. A high specificity indicates that most of the interactions detected by the screen are also occurring in reality.
Protein-protein interaction network visualization
Visualization of protein-protein interaction networks is a popular application of scientific visualization techniques. Although protein interaction diagrams are common in textbooks, diagrams of whole cell protein interaction networks were not as common since the level of complexity made them difficult to generate. One example of a manually produced molecular interaction map is Kurt Kohn's 1999 map of cell cycle control. Drawing on Kohn's map, in 2000 Schwikowski, Uetz, and Fields published a paper on protein-protein interactions in yeast, linking together 1,548 interacting proteins determined by two-hybrid testing. They used a force-directed (Sugiyama) graph drawing algorithm to automatically generate an image of their network.
Protein-protein interaction databases
- HPRD Human Protein Reference Database a (manually) curated database of human protein information with visualization tools.
- IntAct Interaction Database is a public repository for manually curated molecular interaction data from literature.
- Database of Interacting Proteins, a manual and automatic catalog of experimentally determined interactions between proteins.
- MINT Molecular INTeraction Database focuses on experimentally verified protein interactions mined from the scientific literature by expert curators.
- The MIPS Mammalian Protein-Protein Interaction Database
Interaction network software
- Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.
- yEd, graph editor.
- APID Agile Protein Interaction DataAnalyzer is an interactive bioinformatics web tool to explore and analyze in a unified and comparative platform main currently known information about protein–protein interactions.
- NetPro Is a comprehensive fully hand-curated knowledgebase of Protein-Protein, Protein-Small molecules DNA and RNA interactions.
- PA 800 Protein Characterization System uses Capillary Electrophoreses technology to determine a protein's molecular weight, resolve differences in iso electric point, generate high-resolution peptide maps and carbohydrate profiles, and provide front-end separation and introduction of these proteins to mass spectrometry.
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